2024-03-29T10:19:45Z
http://ir.lib.uwo.ca/do/oai/
oai:ir.lib.uwo.ca:biochempub-1001
2009-05-06T03:24:55Z
publication:biochempub
publication:pmid
publication:biochem
publication:faculties
18616809
Systematic Genetic Array Analysis Links the Saccharomyces Cerevisiae SAGA/SLIK and NuA4 Component Tra1 to Multiple Cellular Processes
Hoke, Stephen MT
Guzzo, Julie
Andrews, Brenda
Brandl, Christopher J.
Article
2008-07-10T07:00:00Z
Systematic genetic array analysis
Saccharomyces cerevisiae
Biochemistry
Background: Tra1 is an essential 437-kDa component of the Saccharomyces cerevisiae SAGA/SLIK and NuA4 histone acetyltransferase complexes. It is a member of a group of key signaling molecules that share a carboxyl-terminal domain related to phosphatidylinositol-3-kinase but unlike many family members, it lacks kinase activity. To identify genetic interactions for TRA1 and provide insight into its function we have performed a systematic genetic array analysis (SGA) on tra1SRR3413, an allele that is defective in transcriptional regulation.
Results: The SGA analysis revealed 114 synthetic slow growth/lethal (SSL) interactions for tra1SRR3413. The interacting genes are involved in a range of cellular processes including gene expression, mitochondrial function, and membrane sorting/protein trafficking. In addition many of the genes have roles in the cellular response to stress. A hierarchal cluster analysis revealed that the pattern of SSL interactions for tra1SRR3413 most closely resembles deletions of a group of regulatory GTPases required for membrane sorting/protein trafficking. Consistent with a role for Tra1 in cellular stress, the tra1SRR3413 strain was sensitive to rapamycin. In addition, calcofluor white sensitivity of the strain was enhanced by the protein kinase inhibitor staurosporine, a phenotype shared with the Ada components of the SAGA/SLIK complex. Through analysis of a GFP-Tra1 fusion we show that Tra1 is principally localized to the nucleus.
Conclusion: We have demonstrated a genetic association of Tra1 with nuclear, mitochondrial and membrane processes. The identity of the SSL genes also connects Tra1 with cellular stress, a result confirmed by the sensitivity of the tra1SRR3413 strain to a variety of stress conditions. Based upon the nuclear localization of GFP-Tra1 and the finding that deletion of the Ada components of the SAGA complex result in similar phenotypes as tra1SRR3413, we suggest that the effects of tra1SRR3413 are mediated, at least in part, through its role in the SAGA complex.
Published in: BMC Genetics 2008, 9:46 (doi:10.1186/1471-2156-9-46). This article is available from: http://www.biomedcentral.com/1471-2156/9/46
https://ir.lib.uwo.ca/biochempub/2
oai:ir.lib.uwo.ca:biochempub-1000
2009-05-06T03:25:34Z
publication:biochempub
publication:apmaths
publication:paed
publication:pmid
publication:biochem
publication:faculties
publication:apmathspub
publication:paedpub
18842153
The SWI/SNF Protein ATRX Co-regulates Pseudoautosomal Genes that Have Translocated to Autosomes in the Mouse Genome
Levy, Michael A.
Fernandes, Andrew D.
Tremblay, Deanna C.
Seah, Claudia
Bérubé, Nathalie G.
Article
2008-10-08T07:00:00Z
Pseudoautosomal genes
Autosomes
Mouse genome
Applied Mathematics
Biochemistry
Pediatrics
Background: Pseudoautosomal regions (PAR1 and PAR2) in eutherians retain homologous regions between the X and Y chromosomes that play a critical role in the obligatory X-Y crossover during male meiosis. Genes that reside in the PAR1 are exceptional in that they are rich in repetitive sequences and undergo a very high rate of recombination. Remarkably, murine PAR1 homologs have translocated to various autosomes, reflecting the complex recombination history during the evolution of the mammalian X chromosome.
Results: We now report that the SNF2-type chromatin remodeling protein ATRX controls the expression of eutherian ancestral PAR1 genes that have translocated to autosomes in the mouse. In addition, we have identified two potentially novel mouse PAR1 orthologs.
Conclusion: We propose that the ancestral PAR1 genes share a common epigenetic environment that allows ATRX to control their expression.
Published in: BMC Genomics 2008, 9:468 (doi:10.1186/1471-2164-9-468). This article is available from: http://www.biomedcentral.com/1471-2164/9/468
https://ir.lib.uwo.ca/biochempub/1
oai:ir.lib.uwo.ca:biochempub-1002
2009-12-27T16:23:19Z
publication:pathol
publication:patholpub
publication:biochempub
publication:oncpub
publication:biochem
publication:faculties
publication:onc
Epigenetic Mapping and Functional Analysis in a Breast Cancer Metastasis Model Using Whole-genome Promoter Tiling Microarrays
Rodenhiser, David I.
Andrews, Joseph
Kennette, Wendy
Sadikovic, Bekim
Mendlowitz, Ariel
Tuck, Alan B.
Chambers, Ann F.
Article
2008-07-18T07:00:00Z
Breast cancer
Breast cancer metastasis
Epigenetic mapping
Breast Cancer Research
10
R62
http://dx.doi.org/10.1186/bcr2121
Biochemistry
Oncology
Pathology
Introduction Breast cancer metastasis is a complex, multi-step biological process. Genetic mutations along with epigenetic alterations in the form of DNA methylation patterns and histone modifications contribute to metastasis-related gene expression changes and genomic instability. So far, these epigenetic contributions to breast cancer metastasis have not been well characterized, and there is only a limited understanding of the functional mechanisms affected by such epigenetic alterations. Furthermore, no genome-wide assessments have been undertaken to identify altered DNA methylation patterns in the context of metastasis and their effects on specific functional pathways or gene networks.
Methods We have used a human gene promoter tiling microarray platform to analyze a cell line model of metastasis to lymph nodes composed of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified, and target genes associated with epithelial–mesenchymal transition were validated with respect to DNA methylation effects on gene expression.
Results We integrated data from the tiling microarrays with targets identified by Ingenuity Pathways Analysis software and observed epigenetic variations in genes implicated in epithelial–mesenchymal transition and with tumor cell migration. We identified widespread genomic hypermethylation and hypomethylation events in these cells and we confirmed functional associations between methylation status and expression of the CDH1, CST6, EGFR, SNAI2 and ZEB2 genes by quantitative real-time PCR. Our data also suggest that the complex genomic reorganization present in cancer cells may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes.
Conclusion This is the first whole-genome approach to identify genome-wide and gene-specific epigenetic alterations, and the functional consequences of these changes, in the context of breast cancer metastasis to lymph nodes. This approach allows the development of epigenetic signatures of metastasis to be used concurrently with genomic signatures to improve mapping of the evolving molecular landscape of metastasis and to permit translational approaches to target epigenetically regulated molecular pathways related to metastatic progression.
https://ir.lib.uwo.ca/biochempub/3
oai:ir.lib.uwo.ca:biochempub-1003
2009-05-06T03:23:11Z
publication:med
publication:biochempub
publication:pmid
publication:biochem
publication:faculties
publication:medpub
18611256
Abetalipoproteinemia: Two Case Reports and Literature Review
Zamel, Rola
Khan, Razi
Pollex, Rebecca L.
Hegele, Robert A.
Article
2008-07-08T07:00:00Z
Abetalipoproteinemia
Biochemistry
Medical Biochemistry
Abetalipoproteinemia (ABL, OMIM 200100) is a rare, autosomal recessive disorder, characterized
by fat malabsorption, acanthocytosis and hypocholesterolemia in infancy. Later in life, deficiency of
fat-soluble vitamins is associated with development of atypical retinitis pigmentosa, coagulopathy,
posterior column neuropathy and myopathy. ABL results from mutations in the gene encoding the
large subunit of microsomal triglyceride transfer protein (MTP; OMIM 157147). To date at least 33
MTP mutations have been identified in 43 ABL patients. We describe the clinical progress of two
patients, both currently in the fifth decade of life, who were diagnosed with ABL as children and
were treated with high oral doses of fat soluble vitamins, including vitamin E over the last three
decades. Treatment appears to have been associated with arrest of the neuropathy and other
complications in both patients. Because pharmacologic inhibition of MTP is being developed as a
novel approach to reduce plasma cholesterol for prevention of cardiovascular disease, defining the
long-term clinical features of patients with a natural deficiency in MTP might provide some insight
into the possible effects of such treatments. We review the range of clinical, biochemical and
molecular perturbations in ABL.
Published in: Orphanet Journal of Rare Diseases 2008, 3:19 (doi:10.1186/1750-1172-3-19). This article is available from: http://www.ojrd.com/content/3/1/19
https://ir.lib.uwo.ca/biochempub/4
oai:ir.lib.uwo.ca:biochempub-1004
2009-05-06T03:22:32Z
publication:biochempub
publication:biochem
publication:faculties
The Structural Basis of Gas-Responsive Transcription by the Human Nuclear Hormone Receptor REV-ERBβ
Pardee, Keith I.
Xu, Xiaohui
Reinking, Jeff
Schuetz, Anja
Dong, Aiping
Liu, Suya
Zhang, Rongguang
Tiefenbach, Jens
Lajoie, Gilles
Plotnikov, Alexander N.
Botchkarev, Alexey
Krause, Henry M.
Edwards, Aled
Article
2009-02-24T08:00:00Z
Gas-responsive transcription
Nuclear hormone receptor
REV-ERB
Biochemistry
Heme is a ligand for the human nuclear receptors (NR) REV-ERBa and REV-ERBb, which are transcriptional repressors
that play important roles in circadian rhythm, lipid and glucose metabolism, and diseases such as diabetes,
atherosclerosis, inflammation, and cancer. Here we show that transcription repression mediated by heme-bound REVERBs
is reversed by the addition of nitric oxide (NO), and that the heme and NO effects are mediated by the C-terminal
ligand-binding domain (LBD). A 1.9A°
crystal structure of the REV-ERBb LBD, in complex with the oxidized Fe(III) form of
heme, shows that heme binds in a prototypical NR ligand-binding pocket, where the heme iron is coordinately bound
by histidine 568 and cysteine 384. Under reducing conditions, spectroscopic studies of the heme-REV-ERBb complex
reveal that the Fe(II) form of the LBD transitions between penta-coordinated and hexa-coordinated structural states,
neither of which possess the Cys384 bond observed in the oxidized state. In addition, the Fe(II) LBD is also able to bind
either NO or CO, revealing a total of at least six structural states of the protein. The binding of known co-repressors is
shown to be highly dependent upon these various liganded states. REV-ERBs are thus highly dynamic receptors that
are responsive not only to heme, but also to redox and gas. Taken together, these findings suggest new mechanisms
for the systemic coordination of molecular clocks and metabolism. They also raise the possibility for gas-based
therapies for the many disorders associated with REV-ERB biological functions.
Published in: Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, et al. (2009) The Structural Basis of Gas-Responsive Transcription by the Human Nuclear Hormone Receptor REV-ERBβ. PLoS Biol 7(2): e1000043 doi:10.1371/journal.pbio.1000043
https://ir.lib.uwo.ca/biochempub/5
oai:ir.lib.uwo.ca:robartspub-1000
2018-02-16T17:05:01Z
publication:physics
publication:anatomy
publication:robartspub
publication:biophysicspub
publication:pmid
publication:faculties
publication:physicspub
publication:electricalpub
publication:medpub
publication:anatomypub
publication:med
publication:biophysics
publication:biochempub
publication:electrical
publication:robarts
publication:biochem
publication:institutes
19293239
Clinical Field-strength MRI of Amyloid Plaques Induced by Low-level Cholesterol Feeding in Rabbits
Ronald, John A.
Chen, Yuanxin
Bernas, Lisa
Kitzler, Hagen H.
Rogers, Kem A.
Hegele, Robert A.
Rutt, Brian K.
Article
2009-05-01T07:00:00Z
Alzheimer’s disease
Cholesterol
Rabbit model
Magnetic resonance imaging
b-amyloid plaques
Brain
132
5
1346
1354
Other Medical Sciences
Other Medical Specialties
<p>Two significant barriers have limited the development of effective treatment of Alzheimer’s disease. First, for many cases the aetiology is unknown and likely multi-factorial. Among these factors, hypercholesterolemia is a known risk predictor and has been linked to the formation of b-amyloid plaques, a pathological hallmark this disease. Second, standardized diagnostic tools are unable to definitively diagnose this disease prior to death; hence new diagnostic tools are urgently needed. Magnetic resonance imaging (MRI) using high field-strength scanners has shown promise for direct visualization of b-amyloid plaques, allowing in vivo longitudinal tracking of disease progression in mouse models. Here, we present a new rabbit model for studying the relationship between cholesterol and Alzheimer’s disease development and new tools for direct visualization of b-amyloid plaques using clinical field-strength MRI. New Zealand white rabbits were fed either a low-level (0.125–0.25% w/w) cholesterol diet (n = 5) or normal chow (n = 4) for 27 months. High-resolution (66x66x100 mm3; scan time = 96 min) ex vivo MRI of brains was performed using a 3-Tesla (T) MR scanner interfaced with customized gradient and radiofrequency coils. b-Amyloid-42 immunostaining and Prussian blue iron staining were performed on brain sections and MR and histological images were manually registered. MRI revealed distinct signal voids throughout the brains of cholesterol-fed rabbits, whereas minimal voids were seen in control rabbit brains. These voids corresponded directly to small clusters of extracellular b-amyloid-positive plaques, which were consistently identified as iron-loaded (the presumed source of MR contrast). Plaques were typically located in the hippocampus, parahippocampal gyrus, striatum, hypothalamus and thalamus. Quantitative analysis of the number of histologically positive b-amyloid plaques (P50.0001) and MR-positive signal voids (P50.05) found in cholesterol-fed and control rabbit brains corroborated our qualitative observations. In conclusion, long-term, low-level cholesterol feeding was sufficient to promote the formation of extracellular b-amyloid plaque formation in rabbits, supporting the integral role of cholesterol in the aetiology of Alzheimer’s disease. We also present the first evidence that MRI is capable of detecting iron-associated b-amyloid plaques in a rabbit model of Alzheimer’s disease and have advanced the sensitivity of MRI for plaque detection to a new level, allowing clinical field-strength scanners to be employed. We believe extension of these technologies to an in vivo setting in rabbits is feasible and that our results support future work exploring the role of MRI as a leading imaging tool for this debilitating and life-threatening disease.</p>
<p>doi:10.1093/brain/awp031</p>
<p>PMID 19293239</p>
<p>PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677794/">PMC2677794</a></p>
https://ir.lib.uwo.ca/robartspub/1
oai:ir.lib.uwo.ca:biochempub-1006
2009-05-16T01:17:52Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19042975
The Global Bacterial Regulator H-NS Promotes Transpososome Formation and Transposition in the Tn5 System
Whitfield, Crystal R.
Wardle, Simon J.
Haniford, David B.
Article
2009-02-01T08:00:00Z
Histone-like nucleoid structuring protein
Transposition
Transpososome formation
Biochemistry
Medical Molecular Biology
The histone-like nucleoid structuring protein (H-NS) is an important regulator of stress response and virulence genes in gram-negative bacteria. In addition to binding regulatory regions of genes in a structure-specific manner, H-NS also binds in a structure-specific manner to sites in the Tn10 transpososome, allowing it to act as a positive regulator of Tn10 transposition. This is the only example to date of H-NS regulating a transposition system by interacting directly with the transposition machinery. In general, transposition complexes tend to include segments of deformed DNA and given the capacity of H-NS to bind such structures, and the results from the Tn10 system, we asked if H-NS might regulate another transposition system (Tn5) by directly binding the transposition machinery. We show in the current work that H-NS does bind Tn5 transposition complexes and use hydroxyl radical footprinting to characterize the H-NS interaction with the Tn5 transpososome. We also show that H-NS can promote Tn5 transpososome formation in vitro, which correlates with the Tn5 system showing a dependence on H-NS for transposition in vivo. Taken together the results suggest that H-NS might play an important role in the regulation of many different bacterial transposition systems and thereby contribute directly to lateral gene transfer.
Published in: Nucleic Acids Research 2009 37(2):309-321; doi:10.1093/nar/gkn935
https://ir.lib.uwo.ca/biochempub/7
oai:ir.lib.uwo.ca:oncpub-1000
2009-05-16T01:07:13Z
publication:mnipub
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:mni
publication:biochem
publication:onc
19129215
Transcriptional Control by Adenovirus E1A Conserved Region 3 via p300/CBP
Pelka, Peter
Ablack, Jailal N. G.
Torchia, Joseph
Turnell, Andrew S.
Grand, Roger J. A.
Mymryk, Joe S.
Article
2009-03-01T08:00:00Z
Human adenovirus type 5
HAdV-5
Transcriptional activation
Gene regulation
Chromatin
Epigenetics
Medical Biochemistry
Medical Genetics
Medical Microbiology
Oncology
The human adenovirus type 5 (HAdV-5) E1A 13S oncoprotein is a potent regulator of gene expression and is used extensively as a model for transcriptional activation. It possesses two independent transcriptional activation domains located in the N-terminus/conserved region (CR) 1 and CR3. The protein acetyltransferase p300 was previously identified by its association with the N-terminus/CR1 portion of E1A and this association is required for oncogenic transformation by E1A. We report here that transcriptional activation by 13S E1A is inhibited by co-expression of sub-stoichiometric amounts of the smaller 12S E1A isoform, which lacks CR3. Transcriptional inhibition by E1A 12S maps to the N-terminus and correlates with the ability to bind p300/CBP, suggesting that E1A 12S is sequestering this limiting factor from 13S E1A. This is supported by the observation that the repressive effect of E1A 12S is reversed by expression of exogenous p300 or CBP, but not by a CBP mutant lacking actyltransferase activity. Furthermore, we show that transcriptional activation by 13S E1A is greatly reduced by siRNA knockdown of p300 and that CR3 binds p300 independently of the well-characterized N-terminal/CR1-binding site. Importantly, CR3 is also required to recruit p300 to the adenovirus E4 promoter during infection. These results identify a new functionally significant interaction between E1A CR3 and the p300/CBP acetyltransferases, expanding our understanding of the mechanism by which this potent transcriptional activator functions.
Published in: Nucleic Acids Research 2009 37(4):1095-1106; doi:10.1093/nar/gkn1057
https://ir.lib.uwo.ca/oncpub/1
oai:ir.lib.uwo.ca:biochempub-1007
2009-05-20T21:34:30Z
publication:csd
publication:pmid
publication:faculties
publication:csdpub
publication:biochempub
publication:biochem
18424801
Prediction of Phosphotyrosine Signaling Networks Using a Scoring Matrix-assisted Ligand Identification Approach
Li, Lei
Wu, Chenggang
Huang, Haiming
Zhang, Kaizhong
Gan, Jacob
Li, Shawn S.-C.
Article
2008-06-01T07:00:00Z
Src homology 2
Scoring matrix-assisted ligand identification
SMALI
Biochemistry
Systematic identification of binding partners for
modular domains such as Src homology 2 (SH2) is
important for understanding the biological function
of the corresponding SH2 proteins. We have developed
a worldwide web-accessible computer program
dubbed SMALI for scoring matrix-assisted
ligand identification for SH2 domains and other
signaling modules. The current version of SMALI
harbors 76 unique scoring matrices for SH2 domains
derived from screening oriented peptide array
libraries. These scoring matrices are used to
search a protein database for short peptides preferred
by an SH2 domain. An experimentally determined
cut-off value is used to normalize an SMALI
score, therefore allowing for direct comparison in
peptide-binding potential for different SH2 domains.
SMALI employs distinct scoring matrices from
Scansite, a popular motif-scanning program.
Moreover, SMALI contains built-in filters for phosphoproteins,
Gene Ontology (GO) correlation and
colocalization of subject and query proteins.
Compared to Scansite, SMALI exhibited improved
accuracy in identifying binding peptides for SH2
domains. Applying SMALI to a group of SH2
domains identified hundreds of interactions that
overlap significantly with known networks mediated
by the corresponding SH2 proteins, suggesting
SMALI is a useful tool for facile identification of
signaling networks mediated by modular domains
that recognize short linear peptide motifs.
Published in: Nucleic Acids Research 2008 36(10):3263-3273; doi:10.1093/nar/gkn161
https://ir.lib.uwo.ca/biochempub/8
oai:ir.lib.uwo.ca:biochempub-1008
2009-05-20T21:49:01Z
publication:faculties
publication:biochempub
publication:biochem
Distance Determination by GIY-YIG Intron Endonucleases: Discrimination between Repression and Cleavage Functions
Liu, Qingqing
Derbyshire, Victoria
Belfort, Marlene
Edgell, David R.
Article
2006-03-01T08:00:00Z
GIY-YIG homing endonuclease
Zinc finger
Biochemistry
GIY-YIG homing endonucleases are modular
proteins, with conserved N-terminal catalytic
domains connected by linkers to C-terminal DNAbinding
domains. I-TevI, the T4 phage GIY-YIG intron
endonuclease, functions both in promoting td intron
homing, and in acting as a transcriptional autorepressor.
Repression is achieved by binding to an operator,
which is cleaved at 100-fold reduced efficiency relative
to the intronless homing site. The linker includes
a zinc finger, which functions in distance determination,
to constrain the catalytic domain to cleave
the homing site at a fixed position. Here we show
that I-BmoI, a related GIY-YIG endonuclease lacking
a zinc finger, also possesses some cleavage distance
discrimination. Furthermore, hybrid endonucleases
constructed by swapping the domains of I-BmoI
and I-TevI are active, precise and demonstrate that
features other than the zinc finger facilitate distance
determination. Most importantly, I-TevI zinc finger
mutants cleave the operator more efficiently than
the homing site, the converse of wild-type protein.
These results are consistent with the zinc finger
acting as a measuring device, directing efficient
cleavage of the homing site to promote intron
mobility, while reducing cleavage at the operator to
ensure transcriptional autorepression and phage
viability.
Published in: Nucleic Acids Research 2006 34(6):1755-1764; doi:10.1093/nar/gkl079
https://ir.lib.uwo.ca/biochempub/9
oai:ir.lib.uwo.ca:biochempub-1009
2009-06-11T00:24:31Z
publication:faculties
publication:biochempub
publication:biochem
Distortion of Quantitative Genomic and Expression Hybridization by Cot-1 DNA: Mitigation of This Effect
Newkirk, Heather L.
Knoll, Joan H. M.
Rogan, Peter K.
Article
2005-12-14T08:00:00Z
Cot-1 DNA
hybridization
Nucleic Acids Research
33
22
e191
Medical Biochemistry
Medical Genetics
Medical Molecular Biology
Cross-hybridization of repetitive sequences in genomic and expression arrays is reported to be suppressed with repeat-blocking nucleic acids (Cot-1 DNA). Contrary to expectation, we demonstrated that Cot-1 also enhanced non-specific hybridization between probes and genomic targets. When added to target DNA, Cot-1 enhanced hybridization (2.2- to 3-fold) to genomic probes containing conserved repetitive elements. In addition to repetitive sequences, Cot-1 was found to be enriched for linked single copy (sc) sequences. Adventitious association between these sequences and probes distort quantitative measurements of the probes hybridized to desired genomic targets. Quantitative microarray hybridization studies using Cot-1 DNA are also susceptible to these effects, especially for probes that map to genomic regions containing conserved repetitive sequences. Hybridization measurements with such probes are less reproducible in the presence of Cot-1 than for probes derived from sc regions or regions containing divergent repeat elements, a finding with significant ramifications for genomic and expression microarray studies. We mitigated the requirement for Cot-1 either by hybridizing with computationally defined sc probes lacking repeats or by substituting synthetic repetitive elements complementary to sequences in genomic probes.
Published in: Nucleic Acids Research 2005 33(22):e191; doi:10.1093/nar/gni190. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/11
oai:ir.lib.uwo.ca:surgerypub-1004
2009-05-30T01:00:50Z
publication:physpharmpub
publication:surgerypub
publication:faculties
publication:physpharm
publication:biochempub
publication:biochem
publication:surgery
Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture
Satish, Latha
LaFramboise, William A.
O'Gorman, David B.
Johnson, Sandra
Janto, Benjamin
Gan, Bing Siang
Baratz, Mark E.
Hu, Fen Z.
Post, J. Christopher
Ehrlich, Garth D.
Kathju, Sandeep
Article
2008-04-23T07:00:00Z
Dupuytren's contracture
Significance Analysis of Microarrays
BMC Medical Genomics
1
Medical Genetics
Medical Physiology
Surgery
Dupuytren's contracture (DC) is the most common inherited connective tissue disease of humans and is hypothesized to be associated with aberrant wound healing of the palmar fascia. Fibroblasts and myofibroblasts are believed to play an important role in the genesis of DC and the fibroproliferation and contraction that are hallmarks of this disease. This study compares the gene expression profiles of fibroblasts isolated from DC patients and controls in an attempt to identify key genes whose regulation might be significantly altered in fibroblasts found within the palmar fascia of Dupuytren's patients. Total RNA isolated from diseased palmar fascia (DC) and normal palmar fascia (obtained during carpal tunnel release; 6 samples per group) was subjected to quantitative analyses using two different microarray platforms (GE Code Link™ and Illumina™) to identify and validate differentially expressed genes. The data obtained was analyzed using The Significance Analysis of Microarrays (SAM) software through which we identified 69 and 40 differentially regulated gene transcripts using the CodeLink™ and Illumina™ platforms, respectively. The CodeLink™ platform identified 18 upregulated and 51 downregulated genes. Using the Illumina™ platform, 40 genes were identified as downregulated, eleven of which were identified by both platforms. Quantitative RT-PCR confirmed the downregulation of three high-interest candidate genes which are all components of the extracellular matrix: proteoglycan 4 (PRG4), fibulin-1 (FBLN-1) transcript variant D, and type XV collagen alpha 1 chain. Overall, our study has identified a variety of candidate genes that may be involved in the pathophysiology of Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies.
Published in: BMC Medical Genomics 2008, 1:10 (doi:10.1186/1755-8794-1-10). The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1755-8794/1/10
https://ir.lib.uwo.ca/surgerypub/5
oai:ir.lib.uwo.ca:biochempub-1010
2009-06-12T00:29:14Z
publication:faculties
publication:biochempub
publication:biochem
Ab Initio Exon Definition Using an Information Theory-based Approach
Rogan, Peter K.
Conference Proceeding
2009-03-01T08:00:00Z
Biological System Modeling
Genetics
Information Theory
Monte Carlo Methods
Biochemistry
Computational Biology
Transcribed exons in genes are joined together at donor and acceptor splice sites precisely and efficiently to generate mRNAs capa ble of being translated into proteins. The sequence variability in individual splice sites can be modeled using Shannon information theory. In the laboratory, the degree of individual splice site use is inferred from the structures of mRNAs and their relative abundance. These structures can be predicted using a bipartite information theory framework that is guided by current knowledge of biological mechanisms for exon recognition. We present the results of this analysis for the complete dataset of all expressed human exons.
This paper was presented at the 43rd Annual IEEE Conference on Information Sciences and Systems in March 2009.
https://ir.lib.uwo.ca/biochempub/10
oai:ir.lib.uwo.ca:biochempub-1011
2011-07-10T21:42:16Z
publication:faculties
publication:biochempub
publication:biochem
Development and Refinement of Pregnane X Receptor (PXR) DNA Binding Site Model Using Information Theory
Vyhlidal, Carrie A.
Rogan, Peter K.
Leeder, J. Steven
Article
2004-09-05T07:00:00Z
Pregnane X receptor
PXR
Retinoic acid receptor
RXR
Information theory
The Journal of Biological Chemistry
279
45
46779
46786
http://dx.doi.org/10.1074/jbc.M408395200
Computational Biology
Medical Biochemistry
Medical Genetics
<p>The pregnane X receptor (PXR) acts as a receptor to induce gene expression in response to structurally diverse xenobiotics through binding as a heterodimer with the 9-cis retinoic acid receptor (RXR) to enhancers in target gene promoters. We identified and estimated the affinities of novel PXR/RXR binding sites in regulated genes and additional genomic targets of PXR with an information theory-based model of the PXR/RXR binding site. Our initial PXR/RXR model, the result of the alignment of 15 previously characterized binding sites, was used to scan the promoters of known PXR target genes. Sites from these genes, with information contents of >8 bits bound by PXR/RXR in vitro, were used to revise the information weight matrix; this procedure was repeated by screening for progressively weaker binding sites. After three iterations of refinement, the model was based on 48 validated PXR/RXR binding sites and has an average information content (Rsequence) of 14.43 ± 3.21 bits. A scan of the human genome predicted novel PXR/RXR binding sites in the promoters of UGT1A3 (19.78 bits at –8040 and 16.37 bits at –6930) and UGT1A6 (12.74 bits at –9216), both of which were identified previously as targets for PXR. These sites were subsequently demonstrated to specifically bind PXR/RXR in competition electrophoretic mobility shift assays. A strong PXR site was also predicted upstream of the CASP10 gene (18.69 bits at –7872) and was validated by binding studies and reporter assays as a PXR responsive element. This suggests that the PXR-mediated response extends beyond genes involved in drug biotransformation and transport.</p>
<p>Dr. Peter Rogan was not affiliated with The University of Western Ontario at the time of publication. </p>
https://ir.lib.uwo.ca/biochempub/12
oai:ir.lib.uwo.ca:biochempub-1012
2009-06-13T00:16:25Z
publication:faculties
publication:biochempub
publication:biochem
Bipartite Pattern Discovery by Entropy Minimization-based Multiple Local Alignment
Bi, Chengpeng
Rogan, Peter K.
Article
2004-01-01T08:00:00Z
Bipartite pattern discovery
Bipad
Nucleic Acids Research
32
17
4979
4991
Computational Biology
Medical Genetics
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximization or Shannon's entropy minimization principle, for discovery of bipartite sequence patterns. Bipad is a C++ program that applies greedy methods to search the bipartite alignment space and examines the upstream or downstream regions of co-regulated genes, looking for cis-regulatory bipartite patterns. An input sequence file with zero or one site per locus is required, and the left and right motif widths and a range of possible gap lengths must be specified. Bipad can run in either single-block or bipartite pattern search modes, and it is capable of comprehensively searching all four orientations of half-site patterns. Simulation studies showed that the accuracy of this motif discovery algorithm depends on sample size and motif conservation level, but results were independent of background composition. Bipad performed equivalent with or better than other pattern search algorithms in correctly identifying Escherichia coli cyclic AMP receptor protein and Bacillus subtilis sigma factor binding site sequences based on experimentally defined benchmarks. Finally, a new bipartite information weight matrix for vitamin D3 receptor/retinoid X receptor {alpha} (VDR/RXR{alpha}) binding sites was derived that comprehensively models the natural variability inherent in these sequence elements.
Published in: Nucleic Acids Research 2004 32(17):4979-4991; doi:10.1093/nar/gkh825. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario. Bipad can be accessed through a webserver at
http://bipad.cmh.edu.
https://ir.lib.uwo.ca/biochempub/13
oai:ir.lib.uwo.ca:biochempub-1013
2010-01-06T02:46:46Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19440206
Structural Basis of Error-prone Replication and Stalling at a Thymine Base by Human DNA Polymerase iota
Kirouac, Kevin N.
Ling, Hong
Article
2009-06-03T07:00:00Z
incorporation specificity
mutagenesis
pol i
translesion synthesis
Y family DNA polymerase
The EMBO Journal
28
11
1644
1654
http://dx.doi.org/10.1038/emboj.2009.122
Biochemistry
Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.
Figures in the article are listed at the end of this record and are available for download.
https://ir.lib.uwo.ca/biochempub/66
oai:ir.lib.uwo.ca:biochempub-1014
2009-06-13T00:15:31Z
publication:faculties
publication:biochempub
publication:biochem
BIPAD: A Web Server for Modeling Bipartite Sequence Elements
Bi, Chengpeng
Rogan, Peter K.
Article
2006-02-16T08:00:00Z
bipartite nucleic acid
Bipad
position weight matrix
BMC Bioinformatics
7
76
Computational Biology
Medical Biochemistry
Medical Genetics
Background: Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences separated by intervening distances that vary among individual sites.
Results: We introduce the Bipad Server [1], a web interface to predict sequence elements embedded within unaligned sequences. Either a bipartite model, consisting of a pair of one-block position weight matrices (PWM's) with a gap distribution, or a single PWM matrix for contiguous single block motifs may be produced. The Bipad program performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy. The best models are refined by maximizing incremental information contents among a set of potential models with varying half site and gap lengths.
Conclusion: The web service generates information positional weight matrices, identifies binding site motifs, graphically represents the set of discovered elements as a sequence logo, and depicts the gap distribution as a histogram. Server performance was evaluated by generating a collection of bipartite models for distinct DNA binding proteins.
Published in: BMC Bioinformatics 2006, 7:76doi:10.1186/1471-2105-7-76. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/7/76. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/14
oai:ir.lib.uwo.ca:vascularpub-1000
2009-06-09T23:40:01Z
publication:vascularpub
publication:robartspub
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
Obstructive Sleep Apnea in 2 Women with Familial Partial Lipodystrophy due to a Heterozygous LMNA R482Q Mutation
Hegele, Robert A.
Al-Attar, Salam A.
Rutt, Brian K.
Article
2007-09-25T07:00:00Z
Obstructive sleep apnea
Familial partial lipodystrophy
Canadian Medical Association Journal
177
7
743
745
Bioimaging and Biomedical Optics
Medical Microbiology
Published in: CMAJ • September 25, 2007; 177 (7). doi:10.1503/cmaj.070135.
https://ir.lib.uwo.ca/vascularpub/1
oai:ir.lib.uwo.ca:biochempub-1015
2009-06-11T00:18:53Z
publication:faculties
publication:biochempub
publication:biochem
Genome-wide Prediction, Display and Refinement of Binding Sites with Information Theory-based Models
Gadiraju, Sashidhar
Vyhlidal, Carrie A.
Leeder, J. Steven
Rogan, Peter K.
Article
2003-09-08T07:00:00Z
Delila-genome
information theory
protein binding sites
BMC Bioinformatics
4
38
Biochemistry
Computational Biology
Medical Genetics
Background: We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices.
Results: Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths.
Conclusions: Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXRα, AHR and NF-κB p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. Comparisons of genome scans with the original and refined PXR/RXRα information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites.
Published in: BMC Bioinformatics 2003, 4:38doi:10.1186/1471-2105-4-38. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/4/38. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/15
oai:ir.lib.uwo.ca:biochempub-1016
2009-06-12T00:16:19Z
publication:faculties
publication:biochempub
publication:biochem
Tandem Machine Learning for the Identification of Genes Regulated by Transcription Factors
Dinakarpandian, Deendayal
Raheja, Venetia
Mehta, Saumil
Schuetz, Erin G.
Rogan, Peter K.
Article
2005-08-22T07:00:00Z
Tandem machine learning
transcription factor
target gene
BMC Bioinformatics
6
204
Biochemistry
Computational Biology
Genetics and Genomics
Background: The identification of promoter regions that are regulated by a given transcription factor has traditionally relied upon the identification and distributions of binding sites recognized by the factor. In this study, we have developed a tandem machine learning approach for the identification of regulatory target genes based on these parameters and on the corresponding binding site information contents that measure the affinities of the factor for these cognate elements.
Results: This method has been validated using models of DNA binding sites recognized by the xenobiotic-sensitive nuclear receptor, PXR/RXRα, for target genes within the human genome. An information theory-based weight matrix was first derived and refined from known PXR/RXRα binding sites. The promoter region of candidate genes was scanned with the weight matrix. A novel information density-based clustering algorithm was then used to identify clusters of information rich sites. Finally, transformed data representing metrics of location, strength and clustering of binding sites were used for classification of promoter regions using an ensemble approach involving neural networks, decision trees and Naïve Bayesian classification. The method was evaluated on a set of 24 known target genes and 288 genes known not to be regulated by PXR/RXRα. We report an average accuracy (proportion of correctly classified promoter regions) of 71%, sensitivity of 73%, and specificity of 70%, based on multiple cross-validation and the leave-one-out strategy. The performance on a test set of 13 genes showed that 10 were correctly classified.
Conclusion: We have developed a machine learning approach for the successful detection of gene targets for transcription factors with high accuracy. The method has been validated for the transcription factor PXR/RXRα and has the potential to be extended to other transcription factors.
Published in: BMC Bioinformatics 2005, 6:204doi:10.1186/1471-2105-6-204. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/6/204. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/16
oai:ir.lib.uwo.ca:biochempub-1017
2019-04-22T15:03:07Z
publication:pmid
publication:faculties
publication:biochempub
publication:apmaths
publication:biochem
publication:apmathspub
16545116
Development of an Unbiased Statistical Method for the Analysis of Unigenic Evolution
Behrsin, Colleen D.
Brandl, Chris J.
Litchfield, David W.
Shilton, Brian H.
Wahl, Lindi M.
Article
2006-03-17T08:00:00Z
unigenic evolution
statistical analysis
BMC Bioinformatics
7
150
https://doi.org/10.1186/1471-2105-7-150
Applied Mathematics
Biochemistry
<p>Background: Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of the protein which retain function, followed by statistical analysis comparing expected and observed mutation frequencies of each residue. Resultant mutability indices for each residue are averaged across a specified window of codons to identify hypomutable regions of the protein. As originally described, the effect of changes to the length of this averaging window was not fully eludicated. In addition, it was unclear when sufficient functional variants had been examined to conclude that residues conserved in all variants have important functional roles. Results: We demonstrate that the length of averaging window dramatically affects identification of individual hypomutable regions and delineation of region boundaries. Accordingly, we devised a region-independent chi-square analysis that eliminates loss of information incurred during window averaging and removes the arbitrary assignment of window length. We also present a method to estimate the probability that conserved residues have not been mutated simply by chance. In addition, we describe an improved estimation of the expected mutation frequency. Conclusion: Overall, these methods significantly extend the analysis of unigenic evolution data over existing methods to allow comprehensive, unbiased identification of domains and possibly even individual residues that are essential for protein function.</p>
<p>Published in: BMC Bioinformatics 2006, 7:150. doi:10.1186/1471-2105-7-150</p>
https://ir.lib.uwo.ca/biochempub/17
oai:ir.lib.uwo.ca:biochempub-1018
2009-07-25T20:37:01Z
publication:biophysicspub
publication:physpharmpub
publication:surgerypub
publication:faculties
publication:physpharm
publication:biophysics
publication:biochempub
publication:surgery
publication:biochem
A Novel Mass Spectrometry-based Assay for GSK-3β Activity
Bowley, Erin
Mulvihill, Erin
Howard, Jeffrey C.
Pak, Brian J.
Gan, Bing Siang
O'Gorman, David B.
Article
2005-12-16T08:00:00Z
kinase assay
Glycogen Synthase Kinase-3beta activity
BMC Biochemistry
6
29
Biochemistry
Medical Physiology
Surgery
Background: As a component of the progression from genomic to proteomic analysis, there is a need for accurate assessment of protein post-translational modifications such as phosphorylation. Traditional kinase assays rely heavily on the incorporation of γ-P32 radiolabeled isotopes, monoclonal anti-phospho-protein antibodies, or gel shift analysis of substrate proteins. In addition to the expensive and time consuming nature of these methods, the use of radio-ligands imposes restrictions based on the half-life of the radionucleotides and pose potential health risks to researchers. With the shortcomings of traditional assays in mind, the aim of this study was to develop a high throughput, non-radioactive kinase assay for screening Glycogen Synthase Kinase-3beta (GSK-3β) activity.
Results: Synthetic peptide substrates designed with a GSK-3β phosphorylation site were assayed with both recombinant enzyme and GSK-3β immunoprecipitated from NIH 3T3 fibroblasts. A molecular weight shift equal to that of a single phosphate group (80 Da.) was detected by surface enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) in a GSK-3β target peptide (2B-Sp). Not only was there a dose-dependent response in molecular weight shift to the amount of recombinant GSK-3β used in this assay, this shift was also inhibited by lithium chloride (LiCl), in a dose-dependent manner.
Conclusion: We present here a novel method to sensitively measure peptide phosphorylation by GSK-3β that, due to the incorporation of substrate controls, is applicable to either purified enzyme or cell extracts. Future studies using this method have the potential to elucidate the activity of GSK-3β in vivo, and to screen enzyme activity in relation to a variety of GSK-3β related disorders.
Published in: BMC Biochemistry 2005, 6:29. doi:10.1186/1471-2091-6-29
https://ir.lib.uwo.ca/biochempub/18
oai:ir.lib.uwo.ca:vascularpub-1001
2009-07-29T21:16:48Z
publication:vascularpub
publication:robartspub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
17352814
Quantitative and Qualitative Differences in Subcutaneous Adipose Tissue Stores across Lipodystrophy Types Shown by Magnetic Resonance Imaging
Al-Attar, Salam A.
Pollex, Rebecca L.
Robinson, John F.
Miskie, Brooke A.
Walcarius, Rhonda
Harper Little, Cynthia
Rutt, Brian K.
Hegele, Robert A.
Article
2007-03-12T07:00:00Z
Adipose Tissue
Adult
Female
Humans
Image Interpretation
Computer-Assisted
Lipodystrophy
Magnetic Resonance Imaging
Male
Middle Aged
Reproducibility of Results
Sensitivity and Specificity
BMC Medical Imaging
7
3
Bioimaging and Biomedical Optics
Medical Genetics
Medical Microbiology
Background: Lipodystrophies are characterized by redistributed subcutaneous fat stores. We previously quantified subcutaneous fat by magnetic resonance imaging (MRI) in the legs of two patients with familial partial lipodystrophy subtypes 2 and 3 (FPLD2 and FPLD3, respectively). We now extend the MRI analysis across the whole body of patients with different forms of lipodystrophy.
Methods: We studied five subcutaneous fat stores (supraclavicular, abdominal, gluteal, thigh and calf) and the abdominal visceral fat stores in 10, 2, 1, 1 and 2 female subjects with, respectively, FPLD2, FPLD3, HIV-related partial lipodystrophy (HIVPL), acquired partial lipodystrophy (APL), congenital generalized lipodystrophy (CGL) and in six normal control subjects.
Results: Compared with normal controls, FPLD2 subjects had significantly increased supraclavicular fat, with decreased abdominal, gluteal, thigh and calf subcutaneous fat. FPLD3 subjects had increased supraclavicular and abdominal subcutaneous fat, with less severe reductions in gluteal, thigh and calf fat compared to FPLD2 subjects. The repartitioning of fat in the HIVPL subject closely resembled that of FPLD3 subjects. APL and CGL subjects had reduced upper body, gluteal and thigh subcutaneous fat; the APL subject had increased, while CGL subjects had decreased subcutaneous calf fat. Visceral fat was markedly increased in FPLD2 and APL subjects.
Conclusion: Semi-automated MRI-based adipose tissue quantification indicates differences between various lipodystrophy types in these studied clinical cases and is a potentially useful tool for extended quantitative phenomic analysis of genetic metabolic disorders. Further studies with a larger sample size are essential for confirming these preliminary findings.
Published in: BMC Medical Imaging, 2007, 7:3. doi:10.1186/1471-2342-7-3
https://ir.lib.uwo.ca/vascularpub/2
oai:ir.lib.uwo.ca:vascularpub-1002
2009-07-29T21:20:10Z
publication:vascularpub
publication:robartspub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
16945131
Semi-automated Segmentation and Quantification of Adipose Tissue in Calf and Thigh by MRI: A Preliminary Study in Patients with Monogenic Metabolic Syndrome
Al-Attar, Salam A.
Pollex, Rebecca L.
Robinson, John F.
Miskie, Brooke A.
Walcarius, Rhonda
Rutt, Brian K.
Hegele, Robert A.
Article
2006-08-31T07:00:00Z
BMC Medical Imaging
6
11
Bioimaging and Biomedical Optics
Medical Microbiology
Background: With the growing prevalence of obesity and metabolic syndrome, reliable quantitative imaging methods for adipose tissue are required. Monogenic forms of the metabolic syndrome include Dunnigan-variety familial partial lipodystrophy subtypes 2 and 3 (FPLD2 and FPLD3), which are characterized by the loss of subcutaneous fat in the extremities. Through magnetic resonance imaging (MRI) of FPLD patients, we have developed a method of quantifying the core FPLD anthropometric phenotype, namely adipose tissue in the mid-calf and mid-thigh regions.
Methods: Four female subjects, including an FPLD2 subject (LMNA R482Q), an FPLD3 subject (PPARG F388L), and two control subjects were selected for MRI and analysis. MRI scans of subjects were performed on a 1.5T GE MR Medical system, with 17 transaxial slices comprising a 51 mm section obtained in both the mid-calf and mid-thigh regions. Using ImageJ 1.34 n software, analysis of raw MR images involved the creation of a connectedness map of the subcutaneous adipose tissue contours within the lower limb segment from a user-defined seed point. Quantification of the adipose tissue was then obtained after thresholding the connected map and counting the voxels (volumetric pixels) present within the specified region.
Results: MR images revealed significant differences in the amounts of subcutaneous adipose tissue in lower limb segments of FPLD3 and FPLD2 subjects: respectively, mid-calf, 15.5% and 0%, and mid-thigh, 25.0% and 13.3%. In comparison, old and young healthy controls had values, respectively, of mid-calf, 32.5% and 26.2%, and mid-thigh, 52.2% and 36.1%. The FPLD2 patient had significantly reduced subcutaneous adipose tissue compared to FPLD3 patient.
Conclusion: Thus, semi-automated quantification of adipose tissue of the lower extremity can detect differences between individuals of various lipodystrophy genotypes and represents a potentially useful tool for extended quantitative phenotypic analysis of other genetic metabolic disorders.
Published in: BMC Medical Imaging, 2006, 6:11. doi:10.1186/1471-2342-6-11
https://ir.lib.uwo.ca/vascularpub/3
oai:ir.lib.uwo.ca:vascularpub-1003
2009-07-31T19:29:34Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
18339204
Association between the FTO rs9939609 Polymorphism and the Metabolic Syndrome in a Non-Caucasian Multi-ethnic Sample
Al-Attar, Salam A.
Pollex, Rebecca L.
Ban, Matthew R.
Young, T Kue
Bjerregaard, Peter
Anand, Sonia S.
Yusuf, Salim
Zinman, Bernard
Harris, Stewart B.
Hanley, Anthony J. G.
Connelly, Philip W.
Huff, Murray W.
Hegele, Robert A.
Article
2008-03-13T07:00:00Z
Adult
Asian Continental Ancestry Group
Body Size
Canada
Cholesterol
HDL
Female
Gene Frequency
Genetic Predisposition to Disease
Humans
Indians
North American
Inuits
Male
Metabolic Syndrome X
Middle Aged
Odds Ratio
Phenotype
Polymorphism
Single Nucleotide
Proteins
Risk Assessment
Risk Factors
Sex Factors
Cardiovascular Diabetology
7
5
Cardiology
Medical Genetics
Medical Microbiology
Background: The rs9939609 T>A single-nucleotide polymorphism (SNP) in the FTO gene has previously been found to be associated with obesity in European Caucasian samples. The objective of this study is to examine whether this association extends to metabolic syndrome (MetS) and applies in non-Caucasian samples.
Methods: The FTO rs9939609 SNP was genotyped in 2121 subjects from four different non-Caucasian geographical ancestries. Subjects were classified for the presence or absence of MetS according to the International Diabetes Federation (IDF) and National Cholesterol Education Program Adult Treatment Panel (NCEP ATP) III definitions.
Results: Carriers of > or = 1 copy of the rs9939609 A allele were significantly more likely to have IDF-defined MetS (35.8%) than non-carriers (31.2%), corresponding to a carrier odds ratio (OR) of 1.23 (95% confidence interval [CI] 1.01 to 1.50), with a similar trend for the NCEP ATP III-defined MetS. Subgroup analysis showed that the association was particularly strong in men. The association was related to a higher proportion of rs9939609 A allele carriers meeting the waist circumference criterion; a higher proportion also met the HDL cholesterol criterion compared with wild-type homozygotes.
Conclusion: Thus, the FTO rs9939609 SNP was associated with an increased risk for MetS in this multi-ethnic sample, confirming that the association extends to non-Caucasian population samples.
Published in: Cardiovascular Diabetology, 2008, 7:5. doi:10.1186/1475-2840-7-5
https://ir.lib.uwo.ca/vascularpub/4
oai:ir.lib.uwo.ca:vascularpub-1004
2009-08-04T23:09:44Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
16098225
NPC1L1 Haplotype is Associated with Inter-individual Variation in Plasma Low-density Lipoprotein Response to Ezetimibe
Hegele, Robert A.
Guy, Justin
Ban, Matthew R.
Wang, Jian
Article
2005-08-12T07:00:00Z
Adult
Aged
Azetidines
Cholesterol
LDL
Female
Gene Frequency
Genetic Variation
Haplotypes
Humans
Hypercholesterolemia
Male
Membrane Proteins
Middle Aged
Polymorphism
Single Nucleotide
Proteins
Lipids in Health and Disease
4
16
Endocrinology, Diabetes, and Metabolism
Medical Microbiology
Background: NPC1L1 encodes a putative intestinal sterol transporter which is the likely target for ezetimibe, a new type of lipid-lowering medication. We previously reported rare non-synonymous mutations in NPC1L1 in an individual who had no plasma lipoprotein response to ezetimibe. We next hypothesized that common variants in NPC1L1 would underlie less extreme inter-individual variations in the plasma LDL cholesterol response to ezetimibe.
Results: In 101 dyslipidemic subjects, we found that NPC1L1 haplotype was significantly associated with inter-individual variation in the response of plasma LDL cholesterol to treatment with ezetimibe for 12 weeks. Specifically, about one subject in eight lacked the common NPC1L1 haplotype 1735C-25342A-27677T and these subjects had a significantly greater reduction in plasma LDL cholesterol with ezetimibe than subjects with at least one copy of this haplotype (-35.9+4.0 versus -23.6+1.6 percent reduction, P = 0.0054). This was paralleled by a similar non-significant trend of between-haplotype difference in reduction of total cholesterol.
Conclusion: These preliminary pharmacogenetic results suggest that NPC1L1 variation is associated with inter-individual variation in response to ezetimibe treatment.
Published in: Lipids in Health and Disease, 2005, 4:16. doi: 10.1186/1476-511X-4-16
https://ir.lib.uwo.ca/vascularpub/5
oai:ir.lib.uwo.ca:vascularpub-1005
2009-08-04T23:19:17Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
16412238
Peroxisomal Proliferator Activated Receptor-γ Deficiency in a Canadian Kindred with Familial Partial Lipodystrophy Type 3 (FPLD3)
Francis, Gordon A.
Li, Gang
Casey, Robin
Wang, Jian
Cao, Henian
Leff, Todd
Hegele, Robert A.
Article
2006-01-14T08:00:00Z
Canada
Cloning
Molecular
Codon
Nonsense
DNA Mutational Analysis
Diabetes Mellitus
Lipoatrophic
Family Health
Female
Heterozygote
Humans
Middle Aged
PPAR gamma
Pedigree
Transcription
Genetic
BMC Medical Genetics
7
3
Medical Genetics
Background: Familial partial lipodystrophy (Dunnigan) type 3 (FPLD3, Mendelian Inheritance in Man [MIM] 604367) results from heterozygous mutations in PPARG encoding peroxisomal proliferator-activated receptor-γ. Both dominant-negative and haploinsufficiency mechanisms have been suggested for this condition.
Methods: We present a Canadian FPLD3 kindred with an affected mother who had loss of fat on arms and legs, but no increase in facial, neck, suprascapular or abdominal fat. She had profound insulin resistance, diabetes, severe hypertriglyceridemia and relapsing pancreatitis, while her pre-pubescent daughter had normal fat distribution but elevated plasma triglycerides and C-peptide and depressed high-density lipoprotein cholesterol.
Results: The mother and daughter were each heterozygous for PPARG nonsense mutation Y355X, whose protein product in vitro was transcriptionally inactive with no dominant-negative activity against the wild-type receptor. In addition the mutant protein appeared to be markedly unstable.
Conclusion: Taken together with previous studies of human PPARG mutations, these findings suggest that PPAR-γ deficiency due either to haploinsufficiency or to substantial activity loss due to dominant negative interference of the normal allele product's function can each contribute to the FPLD3 phenotype.
Published in: BMC Medical Genetics, 2006, 7:3. doi: 10.1186/1471-2350-7-3
https://ir.lib.uwo.ca/vascularpub/6
oai:ir.lib.uwo.ca:biochempub-1020
2009-08-05T23:47:07Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
12036941
Splice Variants But Not Mmutations of DNA Polymerase ß Are Common in Bladder Cancer
Thompson, Tracy E.
Rogan, Peter K.
Risinger, John I.
Taylor, Jack A.
Article
2002-06-01T07:00:00Z
Alternative Splicing
Carcinoma
Transitional Cell
DNA Polymerase beta
DNA
Complementary
DNA
Neoplasm
Exons
Gene Deletion
Humans
Point Mutation
Polymorphism
Genetic
Tumor Cells
Cultured
Urinary Bladder Neoplasms
Cancer Research
62
11
3251
3256
Biochemistry, Biophysics, and Structural Biology
Genetics and Genomics
DNA polymerase ß (POLß) is a highly conserved protein that functions in base excision repair. Loss of the POLß locus on chromosome 8p is a frequent event in bladder cancer, and loss of POLß function could hinder DNA repair leading to a mutator phenotype. Both point mutations and large intragenic deletions of POLß have been reported from analysis of various tumor cDNAs but not from genomic DNA. We noticed that the breakpoints of the presumed rearrangements were delineated by exon-exon junctions, which could instead be consistent with alternative splicing of POLß mRNA. We tested the hypothesis that the reported intragenic deletion were splice variants by screening genomic DNA of human bladder tumors, bladder cancer cell lines, and normal bladder tissues for mutations or deletions in exons 1-14, exon alpha, and the promoter region of POLß. We found no evidence of somatic mutations or deletions in our sample set, although two polymorphisms were identified. Examination of cDNA from a subset of the original sample set revealed that truncated forms of POLß were surprisingly common. Forty-eight of 89 (54%) sequenced cDNA clones had large deletions, each beginning and/or ending exactly at exon-exon junctions. Because these deletions occur at exon-exon junctions and are seen in cDNA but not genomic DNA, they are consistent with alternative mRNA splicing. We describe 12 different splicing events occurring in 18 different combinations. Loss of exon 2 was the most frequent, being found in 42 of 49 (86%) of the variant sequenced clones. The splice variants appear to be somewhat more common and variable in bladder cancer cell lines and tumor tissues but occur at a high frequency in normal bladder tissues as well. We examine alternative splicing in terms of the information content of splice donor and acceptor site sequences, and discuss possible explanations for the predominant splicing event, the loss of exon 2.
Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/19
oai:ir.lib.uwo.ca:biochempub-1021
2009-08-07T00:07:53Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
17686179
C-terminal Processing of Yeast Spt7 Occurs in the Absence of Functional SAGA Complex
Hoke, Stephen M. T.
Liang, Gaoyang
Mutiu, A. Irina
Genereaux, Julie
Brandl, Christopher J.
Article
2007-08-08T07:00:00Z
Amino Acids
Epitopes
Gene Deletion
Molecular Weight
Protein Binding
Protein Processing
Post-Translational
Recombinant Proteins
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Trans-Activators
Transcription Factors
BMC Biochemistry
8
16
Biochemistry
Background: Spt7 is an integral component of the multi-subunit SAGA complex that is required for the expression of approximately 10% of yeast genes. Two forms of Spt7 have been identified, the second of which is truncated at its C-terminus and found in the SAGA-like (SLIK) complex.
Results: We have found that C-terminal processing of Spt7 to its SLIK form (Spt7SLIK) and to a distinct third form (Spt7Form3) occurs in the absence of the SAGA complex components Gcn5, Spt8, Ada1 and Spt20, the latter two of which are required for the integrity of the complex. In addition, N-terminally truncated derivatives of Spt7, including a derivative lacking the histone fold, are processed, indicating that the C-terminus of Spt7 is sufficient for processing and that processing does not require functional Spt7. Using galactose inducible Spt7 expression, we show that the three forms of Spt7 appear and disappear at approximately the same rate with full-length Spt7 not being chased into Spt7SLIK or Spt7Form3. Interestingly, reduced levels of Spt7SLIK and Spt7Form3 were observed in a strain lacking the SAGA component Ubp8, suggesting a regulatory role for Ubp8 in the truncation of Spt7.
Conclusion: We conclude that truncation of Spt7 occurs early in the biosynthesis of distinct Spt7 containing complexes rather than being a dynamic process linked to the action of the SAGA complex in transcriptional regulation.
Published in: BMC Biochemistry, 2007, 8:16. doi:10.1186/1471-2091-8-16
https://ir.lib.uwo.ca/biochempub/20
oai:ir.lib.uwo.ca:vascularpub-1006
2009-08-13T00:19:27Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
18154657
Alstrom Syndrome (OMIM 203800): A Case Report and Literature Review
Joy, Tisha
Cao, Henian
Black, Graeme
Malik, Rayaz
Charlton-Menys, Valentine
Hegele, Robert A.
Durrington, Paul N.
Article
2007-12-21T08:00:00Z
Adult
Blindness
Databases
Genetic
Diabetes Mellitus
Type 2
Female
Heterozygote
Humans
Hyperlipoproteinemia Type IV
Hypertension
Mutation
Obesity
Pedigree
Polymorphism
Single Nucleotide
Proteins
Sequence Analysis
DNA
Syndrome
Orphanet Journal of Rare Diseases
2
49
Medical Genetics
Background: Alstrom syndrome (AS) is a rare autosomal recessive disease characterized by multiorgan dysfunction. The key features are childhood obesity, blindness due to congenital retinal dystrophy, and sensorineural hearing loss. Associated endocrinologic features include hyperinsulinemia, early-onset type 2 diabetes, and hypertriglyceridemia. Thus, AS shares several features with the common metabolic syndrome, namely obesity, hyperinsulinemia, and hypertriglyceridemia. Mutations in the ALMS1 gene have been found to be causative for AS with a total of 79 disease-causing mutations having been described.
Case Presentation: We describe the case of a 27-year old female from an English (Caucasian) kindred. She had been initially referred for hypertriglyceridemia, but demonstrated other features suggestive of AS, including blindness, obesity, type 2 diabetes, renal dysfunction, and hypertension. DNA analysis revealed that she is a compound heterozygote with two novel mutations in the ALMS1 gene - H3882Y and V424I. Examination of her family revealed that her phenotypically unaffected mother and younger sister also had heterozygous mutations in the ALMS1 gene. In addition to presenting these novel molecular findings for AS, we review the clinical and genetic features of AS in the context of our case.
Conclusion: Two novel mutations in the ALMS1 gene causative for AS have been reported here, thereby increasing the number of reported mutations to 81 and providing a wider basis for mutational screening among affected individuals.
Published in: Orphanet Journal of Rare Diseases, 2007, 2:49. doi: 10.1186/1750-1172-2-49
https://ir.lib.uwo.ca/vascularpub/7
oai:ir.lib.uwo.ca:biochempub-1022
2009-08-15T00:50:12Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
17848527
A Structural Gap in Dpo4 Supports Mutagenic Bypass of a Major Bbenzo[a]pyrene dG Adduct in DNA through Template Misalignment
Bauer, Jacob
Xing, Guangxin
Yagi, Haruhiko
Sayer, Jane M.
Jerina, Donald M.
Ling, Hong
Article
2007-09-18T07:00:00Z
Base Pair Mismatch
Base Pairing
Base Sequence
Benzo(a)pyrene
Benzopyrenes
Binding Sites
Carcinogens
Environmental
Crystallography
X-Ray
DNA Adducts
DNA Polymerase beta
DNA Primers
Deoxyguanosine
Frameshift Mutation
Models
Molecular
Molecular Sequence Data
Mutagenesis
Structure-Activity Relationship
Templates
Genetic
PNAS: Proceedings of the National Academy of Sciences
104
38
14905
14910
Biochemistry
Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-N(2)-deoxyguanosine (BP-dG), was placed at a template-primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a -1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5' to the adduct to serve as the template, resulting in a -1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and -1 frameshift mutations.
Published in: PNAS, 2007, 104:14905-14910. doi: 10.1073/pnas.0700717104
https://ir.lib.uwo.ca/biochempub/22
oai:ir.lib.uwo.ca:biochempub-1023
2009-08-07T00:17:38Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
15998472
Rapid and Simultaneous Detection of Human Hepatitis B Virus and Hepatitis C Virus Antibodies Based on a Protein Chip Assay Using Nano-gold Immunological Amplification and Silver Staining Method
Duan, Lianlian
Wang, Yefu
Li, Shawn Shun-cheng
Wan, Zhixiang
Zhai, Jianxin
Article
2005-07-06T07:00:00Z
Hepacivirus
Hepatitis B Antibodies
Hepatitis B Core Antigens
Hepatitis B Surface Antigens
Hepatitis B e Antigens
Hepatitis B virus
Hepatitis C Antibodies
Hepatitis C Antigens
Humans
Nanotechnology
Protein Array Analysis
Silver Staining
BMC Infectious Diseases
5
53
Biochemistry
Background: Viral hepatitis due to hepatitis B virus and hepatitis C virus are major public health problems all over the world. Traditional detection methods including polymerase chain reaction (PCR)-based assays and enzyme-linked immunosorbent assays (ELISA) are expensive and time-consuming. In our assay, a protein chip assay using Nano-gold Immunological Amplification and Silver Staining (NIASS) method was applied to detect HBV and HCV antibodies rapidly and simultaneously.
Methods: Chemically modified glass slides were used as solid supports (named chip), on which several antigens, including HBsAg, HBeAg, HBcAg and HCVAg (a mixture of NS3, NS5 and core antigens) were immobilized respectively. Colloidal nano-gold labelled staphylococcal protein A (SPA) was used as an indicator and immunogold silver staining enhancement technique was applied to amplify the detection signals, producing black image on array spots, which were visible with naked eyes. To determine the detection limit of the protein chip assay, a set of model arrays in which human IgG was spotted were structured and the model arrays were incubated with different concentrations of anti-IgG. A total of 305 serum samples previously characterized with commercial ELISA were divided into 4 groups and tested in this assay.
Results: We prepared mono-dispersed, spherical nano-gold particles with an average diameter of 15 +/- 2 nm. Colloidal nano-gold-SPA particles observed by TEM were well-distributed, maintaining uniform and stable. The optimum silver enhancement time ranged from 8 to 12 minutes. In our assay, the protein chips could detect serum antibodies against HBsAg, HBeAg, HBcAg and HCVAg with the absence of the cross reaction. In the model arrays, the anti-IgG as low as 3 ng/ml could be detected. The data for comparing the protein chip assay with ELISA indicated that no distinct difference (P > 0.05) existed between the results determined by our assay and ELISA respectively.
Conclusion: Results showed that our assay can be applied with serology for the detection of HBV and HCV antibodies rapidly and simultaneously in clinical detection.
Published in: BMC Infectious Diseases, 2005, 5:53. doi: 10.1186/1471-2334-5-53
https://ir.lib.uwo.ca/biochempub/21
oai:ir.lib.uwo.ca:vascularpub-1007
2011-01-20T22:52:02Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
18237401
Heterozygous CAV1 Frameshift Mutations (MIM 601047) in Patients with Atypical Partial Lipodystrophy and Hypertriglyceridemia
Cao, Henian
Alston, Lindsay
Ruschman, Jennifer
Hegele, Robert A.
Article
2008-01-31T08:00:00Z
Adult
Base Sequence
Caveolin 1
DNA Mutational Analysis
Demography
Female
Frameshift Mutation
Heterozygote
Humans
Hypertriglyceridemia
Lipodystrophy
Male
Middle Aged
Molecular Sequence Data
Lipids in Health and Disease
7
3
http://dx.doi.org/10.1186/1476-511X-7-3
Medical Genetics
Background: Mice with a deleted Cav1 gene encoding caveolin-1 develop adipocyte abnormalities and insulin resistance. From genomic DNA of patients with atypical lipodystrophy and hypertriglyceridemia who had no mutations in any known lipodystrophy gene, we used DNA sequence analysis to screen the coding regions of human CAV1 (MIM 601047).
Results: We found a heterozygous frameshift mutation in CAV1, designated I134fsdelA-X137, in a female patient who had atypical partial lipodystrophy, with subcutaneous fat loss affecting the upper part of her body and face, but sparing her legs, gluteal region and visceral fat stores. She had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis. In addition, she had some atypical features, including congenital cataracts and neurological findings. Her father was also heterozygous for this mutation, and had a similar pattern of fat redistribution, hypertriglyceridemia and congenital cataracts, with milder neurological involvement. An unrelated patient had a different heterozygous frameshift mutation in the CAV1 gene, designated -88delC. He also had a partial lipodystrophy phenotype, with subcutaneous fat loss affecting the arms, legs and gluteal region, but sparing his face, neck and visceral fat stores. He also had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis; however he had no clinically apparent neurological manifestations. The mutations were absent from the genomes of 1063 healthy individuals.
Conclusion: Thus, very rare CAV1 frameshift mutations appear to be associated with atypical lipodystrophy and hypertriglyceridemia.
https://ir.lib.uwo.ca/vascularpub/8
oai:ir.lib.uwo.ca:biochempub-1024
2009-08-21T22:04:54Z
publication:fammedpub
publication:fammed
publication:robartspub
publication:physpharmpub
publication:brescia
publication:pmid
publication:affiliates
publication:faculties
publication:physpharm
publication:bresciafoodnutritionalsciences
publication:biochempub
publication:foodpub
publication:robarts
publication:biochem
publication:institutes
11063434
HDL-cholesterol-raising Effect of Orange Juice in Subjects with Hypercholesterolemia
Kurowska, Elzbieta M.
Spence, J. David
Jordan, John
Wetmore, Stephen
Freeman, David J.
Piché, Leonard A.
Serratore, Paula
Article
2000-11-01T08:00:00Z
Adult
Aged
Ascorbic Acid
Beverages
Body Mass Index
Cholesterol
HDL
Cholesterol
LDL
Citrus
Energy Intake
Female
Folic Acid
Homocysteine
Humans
Hypercholesterolemia
Male
Middle Aged
Nutritional Physiological Phenomena
Triglycerides
American Journal of Clinical Nutrition
72
5
1095
1100
Biochemistry
Food Science
Medicine and Health Sciences
Nutrition
Background: Orange juice-a rich source of vitamin C, folate, and flavonoids such as hesperidin-induces hypocholesterolemic responses in animals.
Objective: We determined whether orange juice beneficially altered blood lipids in subjects with moderate hypercholesterolemia.
Design: The sample consisted of 16 healthy men and 9 healthy women with elevated plasma total and LDL-cholesterol and normal plasma triacylglycerol concentrations. Participants incorporated 1, 2, or 3 cups (250 mL each) of orange juice sequentially into their diets, each dose over a period of 4 wk. This was followed by a 5-wk washout period. Plasma lipid, folate, homocyst(e)ine, and vitamin C (a compliance marker) concentrations were measured at baseline, after each treatment, and after the washout period.
Results: Consumption of 750 mL but not of 250 or 500 mL orange juice daily increased HDL-cholesterol concentrations by 21% (P: < 0.001), triacylglycerol concentrations by 30% (from 1.56 +/- 0.72 to 2.03 +/- 0.91 mmol/L; P: < 0.02), and folate concentrations by 18% (P: < 0.01); decreased the LDL-HDL cholesterol ratio by 16% (P: < 0.005); and did not affect homocyst(e)ine concentrations. Plasma vitamin C concentrations increased significantly during each dietary period (2.1, 3.1, and 3.8 times, respectively).
Conclusions: Orange juice (750 mL/d) improved blood lipid profiles in hypercholesterolemic subjects, confirming recommendations to consume >/=5-10 servings of fruit and vegetables daily.
https://ir.lib.uwo.ca/biochempub/23
oai:ir.lib.uwo.ca:surgerypub-1006
2009-09-16T00:32:03Z
publication:mnipub
publication:biophysicspub
publication:physpharmpub
publication:surgerypub
publication:pmid
publication:faculties
publication:physpharm
publication:biophysics
publication:biochempub
publication:mni
publication:biochem
publication:surgery
12866952
Elevated Levels of β-catenin and Fibronectin in Three-dimensional Collagen Cultures of Dupuytren's Disease Cells are Regulated by Tension in Vitro
Howard, Jeffrey C.
Varallo, Vincenzo M.
Ross, Douglas C.
Roth, James H.
Faber, Kenneth J.
Alman, Benjamin
Gan, Bing Siang
Article
2003-07-16T07:00:00Z
Biomechanics
Cells
Cultured
Collagen
Cytoskeletal Proteins
Dupuytren's Contracture
Fibroblasts
Fibronectins
Humans
Trans-Activators
beta Catenin
BMC Musculoskeletal Disorders
4
16
Surgery
Background: Dupuytren's contracture or disease (DD) is a fibro-proliferative disease of the hand that results in the development of scar-like, collagen-rich disease cords within specific palmar fascia bands. Although the molecular pathology of DD is unknown, recent evidence suggests that beta-catenin may play a role. In this study, collagen matrix cultures of primary disease fibroblasts show enhanced contraction and isometric tension-dependent changes in beta-catenin and fibronectin levels.
Methods: Western blots of beta-catenin and fibronectin levels were determined for control and disease primary cell cultures grown within stressed- and attached-collagen matrices. Collagen contraction was quantified, and immunocytochemistry analysis of filamentous actin performed.
Results: Disease cells exhibited enhanced collagen contraction activity compared to control cells. Alterations in isometric tension of collagen matrices triggered dramatic changes in beta-catenin and fibronectin levels, including a transient increase in beta-catenin levels within disease cells, while fibronectin levels steadily decreased to levels below those seen in normal cell cultures. In contrast, both fibronectin and beta-catenin levels increased in attached collagen-matrix cultures of disease cells, while control cultures showed only increases in fibronectin levels. Immunocytochemistry analysis also revealed extensive filamentous actin networks in disease cells, and enhanced attachment and spreading of disease cell in collagen matrices.
Conclusion: Three-dimensional collagen matrix cultures of primary disease cell lines are more contractile and express a more extensive filamentous actin network than patient-matched control cultures. The elevated levels of beta-catenin and Fn seen in collagen matrix cultures of disease fibroblasts can be regulated by changes in isometric tension.
Published in: BMC Musculoskeletal Disorders, 2003, 4:16. doi: 10.1186/1471-2474-4-16
https://ir.lib.uwo.ca/surgerypub/7
oai:ir.lib.uwo.ca:medpub-1012
2010-08-31T00:19:25Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19341499
Gene-gene and Gene-environment Interactions: New Insights into the Prevention, Detection and Management of Coronary Artery Disease
Lanktree, Matthew B.
Hegele, Robert A.
Article
2009-02-26T08:00:00Z
Coronary artery disease
Gene-gene interaction
Gene-environment interaction
Genome Medicine
Genome Medicine
1
28
http://dx.doi.org/10.1186/gm28
Cardiology
Medical Genetics
Despite the recent success of genome-wide association studies (GWASs) in identifying loci consistently associated with coronary artery disease (CAD), a large proportion of the genetic components of CAD and its metabolic risk factors, including plasma lipids, type 2 diabetes and body mass index, remain unattributed. Gene-gene and gene-environment interactions might produce a meaningful improvement in quantification of the genetic determinants of CAD. Testing for gene-gene and gene-environment interactions is thus a new frontier for large-scale GWASs of CAD. There are several anecdotal examples of monogenic susceptibility to CAD in which the phenotype was worsened by an adverse environment. In addition, small-scale candidate gene association studies with functional hypotheses have identified gene-environment interactions. For future evaluation of gene-gene and gene-environment interactions to achieve the same success as the single gene associations reported in recent GWASs, it will be important to pre-specify agreed standards of study design and statistical power, environmental exposure measurement, phenomic characterization and analytical strategies. Here we discuss these issues, particularly in relation to the investigation and potential clinical utility of gene-gene and gene-environment interactions in CAD.
https://ir.lib.uwo.ca/medpub/8
oai:ir.lib.uwo.ca:biochempub-1025
2009-09-17T05:03:20Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
15450123
A Comprehensive Evaluation of Food Fortification with Folic Acid for the Primary Prevention of Neural Tube Defects
Liu, Shiliang
West, Roy
Randell, Edward
Longerich, Linda
O'Connor, Kathleen Steel
Scott, Helen
Crowley, Marian
Lam, Angeline
Prabhakaran, Victor
McCourt, Catherine
Article
2004-09-27T07:00:00Z
food fortification
folic acid
neural tube defects
pregnancy
BMC Pregnancy and Childbirth
4
20
Biochemistry
Background: Periconceptional use of vitamin supplements containing folic acid reduces the risk of a neural tube defect (NTD). In November 1998, food fortification with folic acid was mandated in Canada, as a public health strategy to increase the folic acid intake of all women of childbearing age. We undertook a comprehensive population based study in Newfoundland to assess the benefits and possible adverse effects of this intervention.
Methods: This study was carried out in women aged 19-44 years and in seniors from November 1997 to March 1998, and from November 2000 to March 2001. The evaluation was comprised of four components: I) Determination of rates of NTDs; II) Dietary assessment; III) Blood analysis; IV) Assessment of knowledge and use of folic acid supplements.
Results: The annual rates of NTDs in Newfoundland varied greatly between 1976 and 1997, with a mean rate of 3.40 per 1,000 births. There was no significant change in the average rates between 1991-93 and 1994-97 (relative risk [RR] 1.01, 95% confidence interval [CI] 0.76-1.34). The rates of NTDs fell by 78% (95% CI 65%-86%) after the implementation of folic acid fortification, from an average of 4.36 per 1,000 births during 1991-1997 to 0.96 per 1,000 births during 1998-2001 (RR 0.22, 95% CI 0.14-0.35). The average dietary intake of folic acid due to fortification was 70 μg/day in women aged 19-44 years and 74 μg/day in seniors. There were significant increases in serum and RBC folate levels for women and seniors after mandatory fortification. Among seniors, there were no significant changes in indices typical of vitamin B12 deficiencies, and no evidence of improved folate status masking haematological manifestations of vitamin B12 deficiency. The proportion of women aged 19-44 years taking a vitamin supplement containing folic acid increased from 17% to 28%.
Conclusions: Based on these findings, mandatory food fortification in Canada should continue at the current levels. Public education regarding folic acid supplement use by women of childbearing age should also continue.
Published in: BMC Pregnancy and Childbirth, 2004, 4:20. doi: 10.1186/1471-2393-4-20
https://ir.lib.uwo.ca/biochempub/24
oai:ir.lib.uwo.ca:vascularpub-1008
2009-09-23T22:29:49Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
17376224
Genetic Determinants of Statin Intolerance
Oh, Jisun
Ban, Matthew R.
Miskie, Brooke A.
Pollex, Rebecca L.
Hegele, Robert A.
Article
2007-03-21T07:00:00Z
Adult
Aged
Alkyl and Aryl Transferases
Female
Genetic Predisposition to Disease
Haplotypes
Homozygote
Humans
Hydroxymethylglutaryl-CoA Reductase Inhibitors
Male
Middle Aged
Muscular Diseases
Myoglobinuria
Myositis
Polymorphism
Single Nucleotide
Rhabdomyolysis
Risk Factors
Lipids in Health and Disease
6
7
Medical Genetics
Medical Microbiology
Background: Statin-related skeletal muscle disorders range from benign myalgias--such as non-specific muscle aches or joint pains without elevated serum creatinine kinase (CK) concentration--to true myositis with >10-fold elevation of serum CK, to rhabdomyolysis and myoglobinuria. The genetic basis of statin-related muscle disorders is largely unknown. Because mutations in the COQ2 gene are associated with severe inherited myopathy, we hypothesized that common, mild genetic variation in COQ2 would be associated with inter-individual variation in statin intolerance. We studied 133 subjects who developed myopathy on statin monotherapy and 158 matched controls who tolerated statins without incident or complaint.
Results: COQ2 genotypes, based on two single nucleotide polymorphisms (SNP1 and SNP2) and a 2-SNP haplotype, all showed significant associations with statin intolerance. Specifically, the odds ratios (with 95% confidence intervals) for increased risk of statin intolerance among homozygotes for the rare alleles were 2.42 (0.99 to 5.89), 2.33 (1.13 to 4.81) and 2.58 (1.26 to 5.28) for SNP1 and SNP2 genotypes, and the 2-SNP haplotype, respectively.
Conclusion: These preliminary pharmacogenetic results, if confirmed, are consistent with the idea that statin intolerance which is manifested primarily through muscle symptoms is associated with genomic variation in COQ2 and thus perhaps with the CoQ10 pathway.
Published in: Lipids in Health and Disease, 2007, 6:7. doi: 10.1186/1476-511X-6-7
https://ir.lib.uwo.ca/vascularpub/9
oai:ir.lib.uwo.ca:vascularpub-1009
2023-03-16T14:08:08Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
16827932
Relationship of the Metabolic Syndrome to Carotid Ultrasound Traits
Pollex, Rebecca L.
Al-Shali, Khalid Z.
House, Andrew A.
Spence, J. David
Fenster, Aaron
Mamakeesick, Mary
Zinman, Bernard
Harris, Stewart B.
Hanley, Anthony J. G.
Hegele, Robert A.
Article
2006-07-07T07:00:00Z
Adult
Canada
Comorbidity
Coronary Artery Disease
Female
Humans
Incidence
Male
Metabolic Syndrome X
Prognosis
Risk Assessment
Risk Factors
Sensitivity and Specificity
Tunica Intima
Cardiovascular Ultrasound
4
28
http://dx.doi.org/10.1186/1476-7120-4-28
Cardiology
Medical Microbiology
<p>Background: The metabolic syndrome is associated with increased vascular disease risk. We evaluated two carotid ultrasound measurements, namely intima media thickness and total plaque volume, in a Canadian Oji-Cree population with a high metabolic syndrome prevalence rate. Methods: As part of the Sandy Lake Complications Prevalence and Risk Factor Study, 166 Oji-Cree subjects (baseline metabolic syndrome prevalence, 44.0%, according to the National Cholesterol Education Program Adult Treatment Panel III guidelines) were examined using a high-resolution duplex ultrasound scanner. Results: Image analysis showed that mean intima media thickness was elevated in subjects with the metabolic syndrome (818 +/- 18 vs 746 +/- 20 microm), as was total plaque volume (125 +/- 26 vs 77.3 +/- 17.0 mm3). However, after adjustment for age and sex, the differences were significant only for intima media thickness (P = 0.039). Furthermore, a significant trend towards increased intima media thickness was observed with increasing numbers of metabolic syndrome components: mean intima media thickness was highest among individuals with all five metabolic syndrome components compared to those with none (866 +/- 55 vs 619 +/- 23 microm, P = 0.0014). A similar, but non-significant trend was observed for total plaque volume. Conclusion: This is the first study of the relationship between the metabolic syndrome and two distinct carotid ultrasound traits measured in the same individuals. The results suggest that standard intima media thickness measurement shows a more consistent and stronger association with the metabolic syndrome than does total plaque volume.</p>
https://ir.lib.uwo.ca/vascularpub/10
oai:ir.lib.uwo.ca:vascularpub-1010
2009-09-25T00:29:45Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
18096054
Association Between the -455T>C Promoter Polymorphism of the APOC3 Gene and the Metabolic Syndrome in a Multi-ethnic Sample
Pollex, Rebecca L.
Ban, Matthew R.
Young, T. Kue
Bjerregaard, Peter
Anand, Sonia S.
Yusuf, Salim
Zinman, Bernard
Harris, Stewart B.
Hanley, Anthony J. G.
Connelly, Philip W.
Huff, Murray W.
Hegele, Robert A.
Article
2007-11-20T08:00:00Z
Adult
Apolipoprotein C-III
Canada
Ethnic Groups
Female
Genetic Predisposition to Disease
Humans
Male
Metabolic Syndrome X
Polymorphism
Genetic
Promoter Regions
Genetic
BMC Medical Genetics
8
80
Medical Genetics
Background: Common polymorphisms in the promoter of the APOC3 gene have been associated with hypertriglyceridemia and may impact on phenotypic expression of the metabolic syndrome (MetS). The rs7566605 marker, located near the INSIG2 gene, has been found to be associated with obesity, making it also a potential genetic determinant for MetS. The objective of this study is to examine the APOC3 -455T>C and the INSIG2 rs7566605 polymorphisms as potential genetic determinants for MetS in a multi-ethnic sample.
Methods: Subjects were genotyped for both the APOC3 -455T>C and INSIG2 rs7566605 polymorphisms, and classified for the presence or absence of MetS (NCEP ATP III and IDF definitions). The total study population included 2675 subjects (> or =18 years of age) from six different geographical ancestries.
Results: For the overall study population, the prevalence of MetS was 22.6% (NCEP ATP III definition). Carriers of > or =1 copy of APOC3 -455C were more likely to have MetS (NCEP ATP III definition) than noncarriers (carrier odds ratio 1.73, 95% CI 1.40 to 2.14, adjusting for age and study group). The basis of the association was related not only to a higher proportion of -455C carriers meeting the triglyceride and high-density lipoprotein cholesterol criteria, but also the blood pressure criteria compared with wild-type homozygotes. Plasma apo C-III concentrations were not associated with APOC3 -455T>C genotype. The INSIG2 rs7566605 polymorphism was not associated with MetS or measures of obesity.
Conclusion: Meta-analysis of the sample of multiple geographic ancestries indicated that the functional -455T>C promoter polymorphism in APOC3 was associated with an approximately 2-fold increased risk of MetS, whereas the INSIG2 rs7566605 polymorphism was not associated with MetS.
Published in: BMC Medical Genetics, 2007, 8:80. doi: 10.1186/1471-2350-8-80
https://ir.lib.uwo.ca/vascularpub/11
oai:ir.lib.uwo.ca:vascularpub-1012
2023-03-16T14:09:27Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:robartspub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
15958169
A Comparison of Ultrasound Measurements to Assess Carotid Atherosclerosis Development in Subjects with and without Type 2 Diabetes
Pollex, Rebecca L.
Spence, J. David
House, Andrew A.
Fenster, Aaron
Hanley, Anthony J. G.
Zinman, Bernard
Harris, Stewart B.
Hegele, Robert A.
Article
2005-06-15T07:00:00Z
Adult
Aged
Anatomy
Cross-Sectional
Canada
Carotid Artery Diseases
Diabetes Mellitus
Type 2
Echocardiography
Female
Humans
Image Interpretation
Computer-Assisted
Imaging
Three-Dimensional
Incidence
Male
Middle Aged
Prognosis
Reproducibility of Results
Risk Assessment
Risk Factors
Sensitivity and Specificity
Single-Blind Method
Cardiovascular Ultrasound
3
15
http://dx.doi.org/10.1186/1476-7120-3-15
Cardiology
Medical Microbiology
<p>Background: Subjects with type 2 diabetes are at an increased risk of vascular complications. The use of carotid ultrasound remains an attractive, non-invasive method to monitor atherosclerotic disease progression and/or response to treatment in patients with type 2 diabetes, with intima-media thickness routinely used as the gold standard to detect pathology. However, alternative measurements, such as plaque area or volume, may represent a potentially more powerful approach. Thus, the objective of this study was to compare the traditional intima-media thickness measurement against the novel total plaque volume measurement in analyzing carotid atherosclerosis development in individuals with type 2 diabetes. Methods: The case-control study included 49 Oji-Cree adults with diabetes or impaired glucose tolerance, aged 21-69, and 49 sex- and age-matched normoglycemic subjects. At baseline, metabolic variables were measured, including body mass index, waist circumference, total cholesterol: high density lipoprotein ratio, plasma triglycerides, plasma glucose, and serum insulin. Carotid ultrasound measurements, 7 years later, assessed carotid arterial intima-media thickness and total plaque volume. Results: At baseline, the two groups were well matched for smoking habits, hypertension, body mass index, and waist circumference. Differences were noted in baseline measurements of total cholesterol:high density lipoprotein (P = 0.0006), plasma triglycerides (P < 0.0001) and fasting glucose (P < 0.0001). After seven years, carotid ultrasound scans revealed that total plaque volume measurements (P = 0.037), but not intima-media thickness measurements, were higher in subjects with diabetes/impaired glucose tolerance compared to the normoglycemic controls. Correlation between intima-media thickness and total plaque volume was moderate. Based on our study findings, to achieve power levels > 0.70 when comparing intima-media thickness measurements for diabetics versus non-diabetics, thousands of study subjects are required. For comparing total plaque volume measurements, only hundreds of study subjects are required. Conclusion: The development of atherosclerotic plaque is greater in subjects with diabetes/impaired glucose tolerance. Total plaque volume appears to capture the atherosclerotic disease burden more effectively in subjects with type 2 diabetes, and would be an appropriate outcome measure for studies aimed at changing the diabetic milieu.</p>
https://ir.lib.uwo.ca/vascularpub/13
oai:ir.lib.uwo.ca:vascularpub-1011
2009-09-26T00:00:46Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
16274479
Methylenetetrahydrofolate Reductase Polymorphism 677C>T is Associated with Peripheral Arterial Disease in Type 2 Diabetes
Pollex, Rebecca L.
Mamakeesick, Mary
Zinman, Bernard
Harris, Stewart B.
Hanley, Anthony J. G.
Hegele, Robert A.
Article
2005-11-07T08:00:00Z
Brachial Artery
Canada
Diabetes Mellitus
Type 2
Diabetic Angiopathies
Genotype
Humans
Indians
North American
Intermittent Claudication
Methylenetetrahydrofolate Reductase (NADPH2)
Odds Ratio
Polymorphism
Genetic
Risk Factors
Cardiovascular Diabetology
4
17
Cardiology
Medical Microbiology
Background: Individuals with diabetes are twice as likely to develop peripheral arterial disease (PAD), the manifestation of extensive atherosclerosis throughout the lower extremities. One putative determinant of PAD is the 677C>T polymorphism in the gene encoding methylenetetrahydrofolate reductase (MTHFR), which has previously been found to associate with various diabetic complications including retinopathy, nephropathy, atherosclerosis and coronary heart disease. The objective of this study was to investigate a possible role for the MTHFR 677C>T gene polymorphism with PAD in subjects with type 2 diabetes from an isolated aboriginal Canadian population.
Methods: The 677C>T MTHFR gene polymorphism was genotyped in 138 subjects of Oji-Cree descent. Participants were selected from a community-wide survey that included PAD assessment by ankle-brachial index (ABI) measurement, and also intermittent claudication assessment by the Rose questionnaire.
Results: MTHFR 677T allele carriers had an increased risk of PAD with an odds ratio of 3.54 (95% CI 1.01, 12.4), P = 0.049, after adjustment for age, sex, duration of diabetes, hypertension, current smoking habits, and use of insulin or oral treatment for diabetes. None of these additional co-variables was significantly associated with PAD. No association was found between MTHFR genotype and intermittent claudication.
Conclusion: The genetic influence of the MTHFR 677C>T genotype on diabetic PAD is modest, yet for the Oji-Cree it is a major risk factor in comparison to other traditional risk factors.
Published in: Cardiovascular Diabetology, 2005, 4:17. doi: 10.1186/1475-2840-4-17
https://ir.lib.uwo.ca/vascularpub/12
oai:ir.lib.uwo.ca:biochempub-1027
2011-07-10T21:35:10Z
publication:oncpub
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
publication:paedpub
15217500
Chemically Induced DNA Hypomethylation in Breast Carcinoma Cells Detected by the Amplification of Intermethylated Sites
Sadikovic, Bekim
Haines, Thomas R.
Butcher, Darci T.
Rodenhiser, David I.
Article
2004-04-30T07:00:00Z
Azacitidine
Breast Neoplasms
Carcinoma
Cell Line
Tumor
DNA (Cytosine-5-)-Methyltransferase
DNA Methylation
DNA
Neoplasm
Humans
Nucleic Acid Amplification Techniques
Promoter Regions
Genetic
Breast Cancer Research
6
4
R329
R337
http://dx.doi.org/10.1186/bcr799
Biochemistry
Oncology
Pediatrics
<p>Introduction: Compromised patterns of gene expression result in genomic instability, altered patterns of gene expression and tumour formation. Specifically, aberrant DNA hypermethylation in gene promoter regions leads to gene silencing, whereas global hypomethylation events can result in chromosomal instability and oncogene activation. Potential links exist between environmental agents and DNA methylation, but the destabilizing effects of environmental exposures on the DNA methylation machinery are not understood within the context of breast cancer aetiology. Methods: We assessed genome-wide changes in methylation patterns using a unique methylation profiling technique called amplification of intermethylated sites (AIMS). This method generates easily readable fingerprints that represent the investigated cell line's methylation profile, based on the differential cleavage of DNA with methylation-specific isoschisomeric restriction endonucleases. Results: We validated this approach by demonstrating both unique and reoccurring sites of genomic hypomethylation in four breast carcinoma cell lines treated with the cytosine analogue 5-azacytidine. Comparison of treated with control samples revealed individual bands that exhibited methylation changes, and these bands were excized and cloned, and the precise genomic location individually identified. In most cases, these regions of hypomethylation coincided with susceptible target regions previously associated with chromosome breakage, rearrangement and gene amplification. Similarly, we observed that acute benzopyrene exposure is associated with altered methylation patterns in these cell lines. Conclusion: These results reinforce the link between environmental exposures, DNA methylation and breast cancer, and support a role for AIMS as a rapid, affordable screening method to identify environmentally induced DNA methylation changes that occur in tumourigenesis.</p>
https://ir.lib.uwo.ca/biochempub/27
oai:ir.lib.uwo.ca:medpub-1013
2009-10-02T00:51:40Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
16255772
Treatment of Dyslipidemia with Lovastatin and Ezetimibe in an Adolescent with Cholesterol Ester Storage Disease
Tadiboyina, Venu T.
Liu, Dora M.
Miskie, Brooke A.
Wang, Jian
Hegele, Robert A.
Article
2005-10-28T07:00:00Z
Adolescent
Amino Acid Sequence
Azetidines
Base Sequence
Child
Child
Preschool
Cholesterol Ester Storage Disease
Drug Therapy
Combination
Dyslipidemias
Humans
Lipoproteins
Lovastatin
Male
Molecular Sequence Data
Sterol Esterase
Lipids in Health and Disease
Lipids in Health and Disease
4
26
Medical Sciences
Background: Cholesterol ester storage disease (CESD) is an autosomal recessive illness that results from mutations in the LIPA gene encoding lysosomal acid lipase. CESD patients present in childhood with hepatomegaly and dyslipidemia characterized by elevated total and low-density lipoprotein cholesterol (LDL-C), with elevated triglycerides and depressed high-density lipoprotein cholesterol (HDL-C). Usual treatment includes a low fat diet and a statin drug.
Results: In an 18-year old with CESD, we documented compound heterozygosity for two LIPA mutations: a novel frameshift nonsense mutation and a deletion of exon 8. The patient had been treated with escalating doses of lovastatin for approximately 80 months, with approximately 15% decline in mean LDL-C. The addition of ezetimibe 10 mg to lovastatin 40 mg resulted in an additional approximately 16% decline in mean LDL-C.
Conclusion: These preliminary anecdotal findings in a CESD patient with novel LIPA mutations support the longer term safety of statins in an adolescent patient and provide new data about the potential efficacy and tolerability of ezetimibe in this patient group.
Published in: Lipids in Health and Disease, 2005, 4:26. doi: 10.1186/1476-511X-4-26
https://ir.lib.uwo.ca/medpub/9
oai:ir.lib.uwo.ca:surgerypub-1013
2009-10-08T01:16:30Z
publication:physpharmpub
publication:surgerypub
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:biochem
publication:surgery
15541177
Enhanced Dupuytren's Disease Fibroblast Populated Collagen Lattice Contraction is Independent of Endogenous Active TGF-beta2
Tse, Raymond
Howard, Jeffrey
Wu, Yan
Gan, Bing Siang
Article
2004-11-12T08:00:00Z
Antibodies
Anti-Idiotypic
Cells
Cultured
Collagen
Dose-Response Relationship
Drug
Dupuytren's Contracture
Fibroblasts
Humans
Transforming Growth Factor beta
Transforming Growth Factor beta2
BMC Musculoskeletal Disorders
5
41
Medical Biochemistry
Musculoskeletal, Neural, and Ocular Physiology
Surgery
Background: Dupuytren's disease (DD) is a debilitating fibro-proliferative disorder of the hand characterized by the appearance of fibrotic lesions (nodules and cords) leading to flexion contractures of the fingers and loss of hand function. Although the molecular mechanism of DD is unknown, it has been suggested that transforming growth factor-beta2 (TGF-beta2) may play an important role in the underlying patho-physiology of the disease. The purpose of this study was to further explore this hypothesis by examining the effects of TGF-beta2 on primary cell cultures derived from patient-matched disease and normal palmar fascia tissue using a three-dimensional collagen contraction assay.
Methods: Fibroblast-populated collagen lattice (FPCL) contraction assays using primary cell cultures derived from diseased and control fascia of the same DD patients were studied in response to exogenous TGF-beta2 and neutralizing anti-TGF-beta2 antibodies.
Results: Contraction of the FPCLs occurred significantly faster and to a greater extent in disease cells compared to control cells. The addition of TGF-beta2 enhanced the rate and degree of collagen contraction in a dose-dependent fashion for both control and diseased cells. Neutralizing anti-TGF-beta2 antibodies abolished exogenous TGF-beta2 stimulated collagen contraction, but did not inhibit the enhanced basal collagen contraction activity of disease FPCL cultures.
Conclusions: Although exogenous TGF-beta2 stimulated both disease and control FPCL contraction, neutralizing anti-TGF-beta2 antibodies did not affect the elevated basal collagen contraction activity of disease FPCLs, suggesting that the differences in the collagen contraction activity of control and disease FPCL cultures are not due to differences in the levels of endogenous TGF-beta2 activity.
Published in: BMC Musculoskeletal Disorders, 2004, 5:41. doi: 10.1186/1471-2474-5-41
https://ir.lib.uwo.ca/surgerypub/15
oai:ir.lib.uwo.ca:vascularpub-1013
2009-10-12T02:54:16Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
17883852
Homozygous Missense Mutation (G56R) in Glycosylphosphatidylinositol-anchored High-density Lipoprotein-binding Protein 1 (GPI-HBP1) in Two Siblings with Fasting Chylomicronemia (MIM 144650)
Wang, Jian
Hegele, Robert A.
Article
2007-09-20T07:00:00Z
Amino Acid Substitution
Animals
Carrier Proteins
Chylomicrons
Conserved Sequence
Evolution
Molecular
Female
Genetic Variation
Homozygote
Humans
Lipid Metabolism
Inborn Errors
Male
Mice
Mutation
Missense
Pedigree
Receptors
Lipoprotein
Siblings
Lipids in Health and Disease
6
23
Medical Microbiology
Background: Mice with a deleted Gpihbp1 gene encoding glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPI-HBP1) develop severe chylomicronemia. We screened the coding regions of the human homologue--GPIHBP1--from the genomic DNA of 160 unrelated adults with fasting chylomicronemia and plasma triglycerides >10 mmol/L, each of whom had normal sequence of the LPL and APOC2 genes.
Results: One patient with severe type 5 hyperlipoproteinemia (MIM 144650), fasting chylomicronemia and relapsing pancreatitis resistant to standard therapy was found to be homozygous for a novel GPIHBP1 missense variant, namely G56R. This mutation was absent from the genomes of 600 control subjects and 610 patients with hyperlipidemia. The GPIHBP1 G56 residue has been conserved throughout evolution and the G56R mutation was predicted to have compromised function. Her homozygous brother also had refractory chylomicronemia and relapsing pancreatitis together with early coronary heart disease. G56R heterozygotes in the family had fasting mild hypertriglyceridemia.
Conclusion: Thus, a very rare GPIHBP1 missense mutation appears to be associated with severe hypertriglyceridemia and chylomicronemia.
Published in: Lipids in Health and Disease, 2007, 6:23. doi: 10.1186/1476-511X-6-23
https://ir.lib.uwo.ca/vascularpub/14
oai:ir.lib.uwo.ca:mnipub-1004
2009-10-12T04:28:24Z
publication:mnipub
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:mni
publication:biochem
publication:onc
19374760
Requirements for E1A Dependent Transcription in the Yeast Saccharomyces Cerevisiae
Yousef, Ahmed F.
Brandl, Christopher J.
Mymryk, Joe S.
Article
2009-04-17T07:00:00Z
Adenovirus E1A Proteins
Gene Expression Regulation
Gene Expression Regulation
Fungal
Protein Structure
Tertiary
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Transcription Factors
BMC Molecular Biology
BMC Molecular Biology
10
32
Immunology and Infectious Disease
Microbiology
Background: The human adenovirus type 5 early region 1A (E1A) gene encodes proteins that are potent regulators of transcription. E1A does not bind DNA directly, but is recruited to target promoters by the interaction with sequence specific DNA binding proteins. In mammalian systems, E1A has been shown to contain two regions that can independently induce transcription when fused to a heterologous DNA binding domain. When expressed in Saccharomyces cerevisiae, each of these regions of E1A also acts as a strong transcriptional activator. This allows yeast to be used as a model system to study mechanisms by which E1A stimulates transcription.
Results: Using 81 mutant yeast strains, we have evaluated the effect of deleting components of the ADA, COMPASS, CSR, INO80, ISW1, NuA3, NuA4, Mediator, PAF, RSC, SAGA, SAS, SLIK, SWI/SNF and SWR1 transcriptional regulatory complexes on E1A dependent transcription. In addition, we examined the role of histone H2B ubiquitylation by Rad6/Bre1 on transcriptional activation.
Conclusion: Our analysis indicates that the two activation domains of E1A function via distinct mechanisms, identify new factors regulating E1A dependent transcription and suggest that yeast can serve as a valid model system for at least some aspects of E1A function.
Published in: BMC Molecular Biology, 2009, 10:32. doi: 10.1186/1471-2199-10-32
https://ir.lib.uwo.ca/mnipub/11
oai:ir.lib.uwo.ca:biochempub-1028
2009-09-23T16:39:06Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19636915
1H, 13C and 15N Resonance Assignments for the Human E2 Conjugating Enzyme, UbcH7
Serniwka, Stephanie A.
Shaw, Gary S.
Article
2008-06-01T07:00:00Z
Amino Acid Sequence
Carbon Isotopes
Humans
Magnetic Resonance Spectroscopy
Molecular Sequence Data
Molecular Weight
Nitrogen Isotopes
Protons
Ubiquitin-Conjugating Enzymes
Biomolecular NMR Assignments
2
1
21
23
Biochemistry
Structural Biology
UbcH7 is a human E2 conjugating enzyme in the ubiquitin-dependent protein degradation pathway. The resonance assignments of UbcH7 will assist in elucidating the structural basis of interactions that occur within ubiquitination.
Published in: Biomolecular NMR Assignments, Volume 2, Number 1 / June, 2008, 21-23. DOI: 10.1007/s12104-007-9074-4
https://ir.lib.uwo.ca/biochempub/25
oai:ir.lib.uwo.ca:biochempub-1029
2009-09-23T16:51:23Z
publication:physpharmpub
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:mbrainpub
publication:robarts
publication:biochem
publication:institutes
19339245
Identification of a Novel Zn2+-binding Domain in the Autosomal Recessive Juvenile Parkinson-related E3 Ligase Parkin
Hristova, Ventzislava A.
Beasley, Steven A.
Rylett, Jane
Shaw, Gary S.
Article
2009-05-29T07:00:00Z
Amino Acid Sequence
Animals
Conserved Sequence
Humans
Models
Biological
Molecular Sequence Data
Parkinsonian Disorders
Protein Folding
Protein Processing
Post-Translational
Protein Stability
Protein Structure
Tertiary
Rats
Recombinant Fusion Proteins
Sequence Alignment
Serine Endopeptidases
Trypsin
Ubiquitin-Protein Ligases
Ubiquitination
Zinc
Journal of Biological Chemistry
284
22
14978
14986
Biochemistry
Neurosciences
Structural Biology
Missense mutations in park2, encoding the parkin protein, account for approximately 50% of autosomal recessive juvenile Parkinson disease (ARJP) cases. Parkin belongs to the family of RBR (RING-between-RING) E3 ligases involved in the ubiquitin-mediated degradation and trafficking of proteins such as Pael-R and synphillin-1. The proposed architecture of parkin, based largely on sequence similarity studies, consists of N-terminal ubiquitin-like and C-terminal RBR domains. These domains are separated by a approximately 160-residue unique parkin sequence having no recognizable domain structure. We used limited proteolysis experiments on bacterially expressed and purified parkin to identify a new domain (RING0) within the unique parkin domain sequence. RING0 comprises two distinct, conserved cysteine-rich clusters between Cys(150)-Cys(169) and Cys(196)-His(215) consisting of CX(2)-(3)CX(11)CX(2)C and CX(4-6)CX(10-16)-CX(2)(H/C) motifs. The positions of the cysteine/histidine residues in this region bear similarity to parkin RING1 and RING2 domains, as well as other E3 ligase RING domains. However, in parkin a 26-residue linker region separates the motifs, which is not typical of other RING domain structures. Further, the RING0 domain includes all but one of the known ARJP mutation sites between the ubiquitin-like and RBR regions of parkin. Using electrospray ionization mass spectrometry and inductively coupled plasma-atomic emission spectrometry analysis, we determined that the RING0, RING1, IBR, and RING2 domains each bind two Zn(2+) ions, the first observation of an E3 ligase with the ability to bind eight metal ions. Removal of the zinc from parkin causes near complete unfolding of the protein, an observation that rationalizes cysteine-based ARJP mutations found throughout parkin, including RING0 (C212Y) that form cellular inclusions and/or are defective for ubiquitination likely because of poor zinc binding and misfolding. The identification of the RING0 domain in parkin provides a new overall domain structure for the protein that will be important in assessing the roles of ARJP mutations and designing experiments aimed at understanding the disease.
Published in: J. Biol. Chem. 2009, 284: 14978-14986. doi: 10.1074/jbc.M808700200
https://ir.lib.uwo.ca/biochempub/26
oai:ir.lib.uwo.ca:surgerypub-1016
2009-10-10T03:22:14Z
publication:biophysicspub
publication:physpharmpub
publication:surgerypub
publication:pmid
publication:faculties
publication:physpharm
publication:biophysics
publication:biochempub
publication:biochem
publication:surgery
19545383
Type-1 Collagen Differentially Alters Beta-catenin Accumulation in Primary Dupuytren's Disease Cord and Adjacent Palmar Fascia Cells
Vi, Linda
Njarlangattil, Anna
Wu, Yan
Gan, Bing Siang
O'Gorman, David B.
Article
2009-06-19T07:00:00Z
Actins
Case-Control Studies
Cells
Cultured
Collagen Type I
Dupuytren's Contracture
Fascia
Humans
Recombinant Proteins
Time Factors
Transforming Growth Factor beta1
beta Catenin
BMC Musculoskeletal Disorders
10
72
Medical Biochemistry
Medical Biophysics
Medical Physiology
Surgery
Background: Dupuytren's Disease (DD) is a debilitating contractile fibrosis of the palmar fascia characterised by excess collagen deposition, contractile myofibroblast development, increased transforming growth factor-beta levels and beta-catenin accumulation. The aim of this study was to determine if a collagen-enriched environment, similar to in vivo conditions, altered beta-catenin accumulation by primary DD cells in the presence or absence of transforming growth factor-beta.
Methods: Primary DD and patient matched, phenotypically normal palmar fascia (PF) cells were cultured in the presence or absence of type-1 collagen and transforming growth factor-beta1. beta-catenin and alpha-smooth muscle actin levels were assessed by western immunoblotting and immunofluorescence microscopy.
Results: DD cells display a rapid depletion of cellular beta-catenin not evident in patient-matched PF cells. This effect was not evident in either cell type when cultured in the absence of type-1 collagen. Exogenous addition of transforming growth factor-beta1 to DD cells in collagen culture negates the loss of beta-catenin accumulation. Transforming growth factor-beta1-induced alpha-smooth muscle actin, a marker of myofibroblast differentiation, is attenuated by the inclusion of type-1 collagen in cultures of DD and PF cells.
Conclusion: Our findings implicate type-1 collagen as a previously unrecognized regulator of beta-catenin accumulation and a modifier of TGF-beta1 signaling specifically in primary DD cells. These data have implications for current treatment modalities as well as the design of in vitro models for research into the molecular mechanisms of DD.
Published in: BMC Musculoskeletal Disorders, 2009, 10:72. doi: 10.1186/1471-2474-10-72
https://ir.lib.uwo.ca/surgerypub/16
oai:ir.lib.uwo.ca:immunologypub-1015
2009-10-12T23:32:06Z
publication:mnipub
publication:anatomy
publication:biophysicspub
publication:pmid
publication:immunologypub
publication:faculties
publication:medpub
publication:anatomypub
publication:med
publication:biophysics
publication:biochempub
publication:mni
publication:robarts
publication:biochem
publication:institutes
17095724
Wilms’ Tumor 1–Associating Protein Regulates the Proliferation of Vascular Smooth Muscle Cells
Small, Theodore W.
Bolender, Zuzana
Bueno, Clara
O'Neil, Caroline
Nong, Zengxuan
Rushlow, Walter
Rajakumar, Nagalingham
Kandel, Christopher
Strong, Jennifer
Madrenas, Joaquin
Pickering, J. Geoffrey
Article
2006-12-08T08:00:00Z
Angioplasty
Balloon
Animals
Aorta
Thoracic
Apoptosis
Carotid Artery Injuries
Carrier Proteins
Cell Division
Cell Line
DNA-Binding Proteins
Gene Silencing
Glycoproteins
Humans
Intercellular Signaling Peptides and Proteins
Male
Muscle
Smooth
Vascular
Nuclear Proteins
Rats
Rats
Inbred WKY
Rats
Sprague-Dawley
Transcription
Genetic
Up-Regulation
WT1 Proteins
Circulation Research
Circulation Research
99
12
1338
1346
Immunology and Infectious Disease
Medical Anatomy
Medical Biochemistry
Medical Biophysics
Smooth muscle cells (SMCs) are called on to proliferate during vascular restructuring but must return to a nonproliferative state if remodeling is to appropriately terminate. To identify mediators of the reacquisition of replicative quiescence, we undertook gene expression screening in a uniquely plastic human SMC line. As proliferating SMCs shifted to a contractile and nonproliferative state, expression of TIMP-3, Axl, and KIAA0098 decreased whereas expression of complement C1s, cathepsin B, cellular repressor of E1A-activated genes increased. Wilms' tumor 1-associating protein (WTAP), a nuclear constituent of unknown function, was also upregulated as SMCs became nonproliferative. Furthermore, WTAP in the intima of injured arteries was substantially upregulated in the late stages of repair. Introduction of WTAP complementary DNA into human SMCs inhibited their proliferation, with a corresponding decrease in DNA synthesis and an increase in apoptosis. Knocking down endogenous WTAP increased SMC proliferation, because of increased DNA synthesis and G(1)/S phase transition, together with reduced apoptosis. WTAP was found to associate with the Wilms' tumor-1 protein in human SMCs and WTAP overexpression inhibited the binding of WT1 to an oligonucleotide containing a consensus WT1 binding site, whereas WTAP knockdown accentuated this interaction. Expression of the WT1 target genes, amphiregulin and Bcl-2, was suppressed in WTAP-overexpressing SMCs and increased in WTAP-deficient SMCs. Moreover, exogenous amphiregulin rescued the antiproliferative effect of WTAP. These findings identify WTAP as a novel regulator of the cell cycle and cell survival and implicate a WTAP-WT1 axis as a novel pathway for controlling vascular SMC phenotype.
Published in: Circulation Research, 2006, 99:1338-1346. doi: 10.1161/01.RES.0000252289.79841.d3
https://ir.lib.uwo.ca/immunologypub/14
oai:ir.lib.uwo.ca:biochempub-1030
2009-11-10T17:38:45Z
publication:physpharmpub
publication:paed
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:biochem
publication:paedpub
19814781
Retinoic Acid Enhances Skeletal Muscle Progenitor Formation and Bypasses Inhibition by Bone Morphogenetic Protein 4 but not Dominant Negative β-catenin
Kennedy, Karen A. M.
Porter, Tammy
Mehta, Virja
Ryan, Scott D.
Price, Feodor
Peshdary, Vian
Karamboulas, Christina
Savage, Josée
Drysdale, Thomas A.
Li, Shun-Cheng
Bennett, Steffany A. L.
Skerjanc, Ilona S.
Article
2009-10-08T07:00:00Z
retinoic acid
skeletal myogenesis
?-catenin
bone morphogenetic protein
BMC Biology
7
67
Biochemistry
Physiology
Background: Understanding stem cell differentiation is essential for the future design of cell therapies. While retinoic acid (RA) is the most potent small molecule enhancer of skeletal myogenesis in stem cells, the stage and mechanism of its function has not yet been elucidated. Further, the intersection of RA with other signalling pathways that stimulate or inhibit myogenesis (such as Wnt and BMP4, respectively) is unknown. Thus, the purpose of this study is to examine the molecular mechanisms by which RA enhances skeletal myogenesis and interacts with Wnt and BMP4 signalling during P19 or mouse embryonic stem (ES) cell differentiation.
Results: Treatment of P19 or mouse ES cells with low levels of RA led to an enhancement of skeletal myogenesis by upregulating the expression of the mesodermal marker, Wnt3a, the skeletal muscle progenitor factors Pax3 and Meox1, and the myogenic regulatory factors (MRFs) MyoD and myogenin. By chromatin immunoprecipitation, RA receptors (RARs) bound directly to regulatory regions in the Wnt3a, Pax3, and Meox1 genes and RA activated a β-catenin-responsive promoter in aggregated P19 cells. In the presence of a dominant negative β-catenin/engrailed repressor fusion protein, RA could not bypass the inhibition of skeletal myogenesis nor upregulate Meox1 or MyoD. Thus, RA functions both upstream and downstream of Wnt signalling. In contrast, it functions downstream of BMP4, as it abrogates BMP4 inhibition of myogenesis and Meox1, Pax3, and MyoD expression. Furthermore, RA downregulated BMP4 expression and upregulated the BMP4 inhibitor, Tob1. Finally, RA inhibited cardiomyogenesis but not in the presence of BMP4.
Conclusion: RA can enhance skeletal myogenesis in stem cells at the muscle specification/progenitor stage by activating RARs bound directly to mesoderm and skeletal muscle progenitor genes, activating β-catenin function and inhibiting bone morphogenetic protein (BMP) signalling. Thus, a signalling pathway can function at multiple levels to positively regulate a developmental program and can function by abrogating inhibitory pathways. Finally, since RA enhances skeletal muscle progenitor formation, it will be a valuable tool for designing future stem cell therapies.
Published in: BMC Biology, 2009, 7:67. doi: 10.1186/1741-7007-7-67
https://ir.lib.uwo.ca/biochempub/28
oai:ir.lib.uwo.ca:immunologypub-1033
2009-11-29T11:01:03Z
publication:mnipub
publication:pmid
publication:immunologypub
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:mni
publication:robarts
publication:biochem
publication:institutes
14585965
Regulation of T-cell Activation by Phosphodiesterase 4B2 Requires its Dynamic Redistribution during Immunological Synapse Formation
Arp, Jacqueline
Kirchhof, Mark G.
Baroja, Miren L.
Nazarian, Steven H.
Chau, Thu A.
Strathdee, Craig A.
Ball, Eric H.
Madrenas, Joaquín
Article
2003-11-01T08:00:00Z
3'
5'-Cyclic-AMP Phosphodiesterases
Cell Compartmentation
Cyclic Nucleotide Phosphodiesterases
Type 4
Enzyme Activation
Humans
Interleukin-2
Jurkat Cells
Lymphocyte Activation
Membrane Microdomains
Protein Structure
Tertiary
Receptors
Antigen
T-Cell
Recombinant Fusion Proteins
Sequence Deletion
Signal Transduction
T-Lymphocytes
Molecular and Cellular Biology
Molecular and Cellular Biology
23
22
8042
8057
10.1128/MCB.23.22.8042-8057.2003
Immunology and Infectious Disease
Medical Biochemistry
Stimulation of T cells through their antigen receptors (TCRs) causes a transient increase in the intracellular concentration of cyclic AMP (cAMP). However, sustained high levels of cAMP inhibit T-cell responses, suggesting that TCR signaling is coordinated with the activation of cyclic nucleotide phosphodiesterases (PDEs). The molecular basis of such a pathway is unknown. Here we show that TCR-dependent signaling activates PDE4B2 and that this enhances interleukin-2 production. Such an effect requires the regulatory N terminus of PDE4B2 and correlates with partitioning within lipid rafts, early targeting of this PDE to the immunological synapse, and subsequent accumulation in the antipodal pole of the T cell as activation proceeds.
https://ir.lib.uwo.ca/immunologypub/31
oai:ir.lib.uwo.ca:vascularpub-1014
2009-12-21T02:09:01Z
publication:vascularpub
publication:mnipub
publication:pmid
publication:immunologypub
publication:faculties
publication:biochempub
publication:mni
publication:robarts
publication:biochem
publication:institutes
12551893
Genomic Organization and Evolution of the CX3CR1/CCR8 Chemokine Receptor Locus
DeVries, Mark E.
Cao, Henian
Wang, Jian
Xu, Luoling
Kelvin, Alyson A.
Ran, Longsi
Chau, Luan A.
Madrenas, Joaquin
Hegele, Robert A.
Kelvin, David J.
Article
2003-04-04T08:00:00Z
Animals
Base Sequence
Chromosomes
Human
Pair 3
Conserved Sequence
Evolution
Molecular
Gene Duplication
Genome
Humans
Membrane Proteins
Mice
Molecular Sequence Data
Multigene Family
Phylogeny
Polymorphism
Single Nucleotide
Promoter Regions
Genetic
Receptors
CCR5
Receptors
CCR8
Receptors
Chemokine
Takifugu
Journal of Biological Chemistry
278
14
11985
11994
10.1074/jbc.M211422200
Biochemistry
Medical Immunology
Medical Microbiology
The chemokine receptors CCR8 and CX3CR1 are key players in adaptive immunity and are co-receptors for human immunodeficiency virus. We describe here the genomic organization and evolutionary history of both of these genes. CX3CR1 has three promoters that transcribe three separate exons that are spliced with a fourth exon containing the coding region. CCR8 has two promoters. One promoter produces a transcript of two spliced exons, and the other promoter transcribes an exon containing the coding region and lacks introns. We analyzed these promoters in the context of a luciferase reporter and identified several positive and negative regulatory elements. Identification of the genomic organization of these genes in mouse demonstrates a similar organization for CCR8, but mouse CX3CR1 lacks two of the human promoters and has an additional mouse-specific promoter that transcribes only the exon containing the coding region and therefore resembles the organization of the human and mouse CCR8 genes. We also identify two nontranscribed regions that are highly conserved between human and mouse CX3CR1 containing possible regulatory elements. Examination of the CX3CR1 and CCR8 genes and surrounding genomic regions indicates that these genes are the result of the duplication of an ancestral gene prior to the divergence of teleost fish. We characterize single nucleotide polymorphisms in the promoters of human CCR8 and CX3CR1 and establish linkage relationships between CX3CR1 promoter polymorphisms and two previously described CX3CR1 coding polymorphisms associated with human immunodeficiency virus disease progression and arteriosclerosis susceptibility.
https://ir.lib.uwo.ca/vascularpub/25
oai:ir.lib.uwo.ca:biochempub-1031
2009-12-07T02:49:50Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
18728350
Selfish DNA: Homing Endonucleases Find a Home
Edgell, David R.
Article
2009-02-10T08:00:00Z
Endonucleases
Evolution
Molecular
Introns
Repetitive Sequences
Nucleic Acid
Current Biology
189
3
115
117
http://dx.doi.org/10.1016/j.cub.2008.12.019
Biochemistry
Self-splicing group I introns come in two flavours - those with a homing endonuclease to promote mobility of the intron, and those without an endonuclease. How homing endonucleases and self-splicing introns associate to form a composite selfish genetic element is a question of long-standing interest. Recent work has revealed that a shared characteristic of both introns and endonucleases, the targeting of conserved sequences, may provide the impetus for the evolution of composite mobile genetic elements.
https://ir.lib.uwo.ca/biochempub/30
oai:ir.lib.uwo.ca:biochempub-1033
2009-12-07T02:58:49Z
publication:dentistrypub
publication:pmid
publication:faculties
publication:dentistry
publication:biochempub
publication:biochem
18728350
Activation of the Mitogen-Activated Protein Kinase Pathway by Bone Sialoprotein Regulates Osteoblast Differentiation
Gordon, Jonathan A. R.
Hunter, Graeme K.
Goldberg, Harvey A.
Article
2009-01-01T08:00:00Z
Animals
Bone Matrix
Calcification
Physiologic
Cell Differentiation
Cell Line
Enzyme Activation
Extracellular Signal-Regulated MAP Kinases
Focal Adhesion Protein-Tyrosine Kinases
Humans
MAP Kinase Signaling System
Mice
Mitogen-Activated Protein Kinases
Osteoblasts
Osteogenesis
Phosphorylation
Proto-Oncogene Proteins c-fos
Rats
Ribosomal Protein S6 Kinases
90-kDa
Sialoglycoproteins
Substrate Specificity
Cells Tissues Organs
189
1-4
138
143
http://dx.doi.org/10.1159/000151728
Biochemistry
Bone sialoprotein (BSP) is an abundant protein in the extracellular matrix of bone that has been suggested to have several different physiological functions, including the nucleation of hydroxyapatite (HA), promotion of cell attachment and binding of collagen. Studies in our lab have demonstrated that increased expression of BSP in osteoblast cells can increase expression of the osteoblast-related genes Runx2 and Osx as well as alkaline phosphatase and osteocalcin and increase matrix mineralization. To determine the molecular mechanisms responsible for the BSP-mediated increase in osteoblastic differentiation, several functional domain mutants of BSP were expressed in primary rat bone osteoblastic cells, including the contiguous glutamic acid sequences (polyGlu) and the arginine-glycine-aspartic acid (RGD) motif. Markers of osteoblast differentiation, including matrix mineralization and alkaline phosphatase staining, were increased in cells expressing BSP mutants of the polyGlu sequences but not in cells expressing RGD-mutated BSP. We also determined the dependence on integrin-associated pathways in promoting BSP-mediated differentiation responses in osteoblasts by demonstrating the activation of focal adhesion kinase, MAP kinase-associated proteins ERK1/2, ribosomal s6 kinase 2 and the AP-1 protein cFos. Thus, the mechanism regulating osteoblast differentiation by BSP was determined to be dependent on integrin-mediated intracellular signaling pathways.
https://ir.lib.uwo.ca/biochempub/31
oai:ir.lib.uwo.ca:biochempub-1032
2009-12-07T02:40:25Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
18728346
Hypertriglyceridemia: Phenomics and Genomics
Hegele, Robert A.
Pollex, Rebecca L.
Article
2009-06-01T07:00:00Z
Alleles
Atherosclerosis
Cluster Analysis
Genome-Wide Association Study
Genomics
Genotype
Humans
Hypertriglyceridemia
Pancreatitis
Phenotype
Molecular and Cellular Biochemistry
189
1-2
35
43
http://dx.doi.org/10.1007/s11010-008-0005-1
Biochemistry
Hypertriglyceridemia is a common complex metabolic trait that is associated with increased atherosclerosis risk, presence of the metabolic syndrome and, with extreme elevation, increased risk of pancreatitis. Hierarchical cluster analysis using clinical and biochemical features of the Frederickson hyperlipoproteinemia types can generate hypotheses for molecular genetic studies. High throughput resequencing of individuals at the extremes of plasma triglyceride concentration has shown that both rare genetic variants with large effects and common genetic variants with moderate effects explain a relatively large proportion of variation. Very recent progress using high-density sets of genome-wide markers have identified additional genetic determinants of plasma triglyceride concentrations, albeit within largely normolipidemic subjects and with small effect sizes. Phenomic evaluation of patients with hypertriglyceridemia might help to clarify genotype-phenotype correlations and responses to interventions.
https://ir.lib.uwo.ca/biochempub/29
oai:ir.lib.uwo.ca:dentistrypub-1003
2009-12-07T03:12:14Z
publication:dentistrypub
publication:pmid
publication:faculties
publication:dentistry
publication:biochempub
publication:biochem
18703867
Role of Phosphate Groups in Inhibition of Calcium Oxalate Crystal Growth by Osteopontin
Hunter, Graeme K.
Grohe, Bernd
Jeffrey, Sara
O'Young, Jason
Sørensen, Esben S.
Goldberg, Harvey A.
Article
2009-01-01T08:00:00Z
Adsorption
Animals
Calcium Oxalate
Cattle
Crystallization
Microscopy
Fluorescence
Osteopontin
Phosphates
Protein Isoforms
Rats
Cells Tissues Organs
Cells Tissues Organs
189
1-4
44
50
10.1159/000151430
Dentistry
Osteopontin (OPN) inhibits the growth of calcium oxalate monohydrate (COM) and other crystal phases in a phosphorylation-dependent manner. In the present study, the role of OPN phosphate groups in adsorption to, incorporation into and inhibition of COM crystals was studied by comparing OPN isoforms differing in phosphorylation. OPN isoforms purified from rat bone (bOPN), which contains 10 phosphates, and cow milk (mOPN), which contains 25 phosphates, were compared with rat recombinant OPN (rOPN), which is not phosphorylated. Using fluorescence-labeled proteins and confocal microscopy, we show that mOPN and rOPN, like bOPN, adsorb preferentially to the edges between {100} and {121} faces of preformed COM crystals, and to a lesser extent to the {100} and {121} faces. Using scanning electron microscopy, we show that growth of COM in the presence of bOPN or mOPN results in a 'dumbbell' morphology, whereas crystals grown with rOPN are only slightly affected. COM crystals grown in the presence of low concentrations of fluorescence-labeled bOPN incorporate the protein into the crystal lattice. In crystals imaged in the {010} plane, incorporation of bOPN results in a cross-shaped pattern of fluorescence, consistent with preferential adsorption to {100}/{121} edges throughout the growth process.
https://ir.lib.uwo.ca/dentistrypub/3
oai:ir.lib.uwo.ca:dentistrypub-1002
2009-12-07T03:04:31Z
publication:dentistrypub
publication:pmid
publication:faculties
publication:dentistry
publication:biochempub
publication:apmaths
publication:biochem
publication:apmathspub
18728346
Phosphorylation of Osteopontin Peptides Mediates Adsorption to and Incorporation into Calcium Oxalate Crystals
O'Young, Jason
Chirico, Sara
Al Tarhuni, Nehal
Grohe, Bernd
Karttunen, Mikko
Goldberg, Harvey A.
Hunter, Graeme K.
Article
2009-01-01T08:00:00Z
Adsorption
Amino Acid Sequence
Animals
Calcium Oxalate
Computer Simulation
Crystallization
Microscopy
Fluorescence
Models
Molecular
Molecular Sequence Data
Osteopontin
Peptides
Phosphorylation
Rats
Surface Properties
Cells Tissues Organs
Cells Tissues Organs
189
1-4
51
55
10.1159/000151724
Dentistry
Phosphorylated peptides of osteopontin (OPN) have been shown to inhibit the growth of the {100} face of calcium oxalate monohydrate (COM). The inhibitory potency has been shown to be dependent on the phosphate content of the peptide. The purpose of this study is to better understand the means by which phosphate groups promote crystal growth inhibition by OPN peptides. Peptides of rat bone OPN 220-235 peptides have been synthesized with zero (P0), 1 (P1) or 3 (P3) phosphate modifications. COM crystals were grown in the presence of 0.1-10 microg of P0, P1 or P3. P0 incorporation into COM crystals was evident at 10 microg/ml of peptide, whereas the phosphorylated peptides P1 and P3 were incorporated at all tested concentrations. At 5 microg/ml of P3, COM crystals exhibited a 'dumbbell' morphology. To study the peptide-mineral interaction, surface frequency plots were constructed from molecular dynamics simulations of OPN peptide adsorption. Carboxylate and phosphate groups were found to adsorb in specific orientations to the COM {100} surface. In conclusion, it appears that the phosphate groups on OPN peptides are capable of interacting with the COM {100} surface. This interaction appears to increase the adsorption energy of the peptide to the surface, thus enhancing its inhibitory potency.
https://ir.lib.uwo.ca/dentistrypub/2
oai:ir.lib.uwo.ca:vascularpub-1015
2009-12-07T03:22:44Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19181627
Carnitine Palmitoyltransferase IA Polymorphism P479L Is Common in Greenland Inuit and Is Associated with Elevated Plasma Apolipoprotein A-I
Rajakumar, Chandheeb
Ban, Matthew R.
Cao, Henian
Young, T Kue
Bjerregaard, Peter
Hegele, Robert A.
Article
2009-06-01T07:00:00Z
Adult
Alleles
Amino Acid Substitution
Apolipoprotein A-I
Atherosclerosis
Base Sequence
Carnitine O-Palmitoyltransferase
Cholesterol
HDL
DNA Primers
Female
Gene Frequency
Genotype
Greenland
Humans
Inuits
Lipoproteins
Male
Middle Aged
Mutation
Missense
Journal of Lipid Research
50
6
1223
1228
10.1194/jlr.P900001-JLR200
Epidemiology
Carnitine palmitoyltransferase IA, encoded by CPT1A, is a key regulator of fatty acid metabolism. Previously, a loss-of-function mutation, namely, c.1436 C-->T (p.P479L), was reported in CPT1A in the homozygous state in Canadian aboriginal male with presumed CPT1A deficiency. To determine the population frequency of this variant, we determined CPT1A p.P479L genotypes in 1111 Greenland Inuit. Associations between genotype and variation in plasma total cholesterol, triglycerides, LDL, HDL, apolipoprotein (apo) B, and apoA-I was also investigated. We found the L479 allele occurs at a high frequency in this sample (0.73), while it was completely absent in 285 nonaboriginal samples. This suggests that the original proband's symptoms were not likely due to the CPT1A p.P479L mutation because it is very common in Inuit and because symptoms suggesting CPT1A deficiency have not been reported in any carrier subsequently studied. However, CPT1A p.P479L was associated with elevated plasma HDL and apoA-I levels. The association with increased levels of HDL and apoA-I suggest that the polymorphism might protect against atherosclerosis.
https://ir.lib.uwo.ca/vascularpub/15
oai:ir.lib.uwo.ca:fammedpub-1002
2009-12-07T03:31:25Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:pmid
publication:faculties
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
19151417
Association of the Novel Cardiovascular Risk Factors Paraoxonase 1 and Cystatin C in Type 2 Diabetes
Connelly, Philip W.
Zinman, Bernard
Maguire, Graham F.
Mamakeesick, Mary
Harris, Stewart B.
Hegele, Robert A.
Retnakaran, Ravi
Hanley, Anthony J. G.
Article
2009-06-01T07:00:00Z
Adult
Aryldialkylphosphatase
Canada
Cardiovascular Diseases
Cystatin C
Diabetes Complications
Diabetes Mellitus
Type 2
Female
Genetic Predisposition to Disease
Genotype
Glomerular Filtration Rate
Humans
Indians
North American
Male
Middle Aged
Models
Biological
Polymorphism
Genetic
Regression Analysis
Risk Factors
Journal of Lipid Research
Journal of Lipid Research
50
6
1216
1222
10.1194/jlr.P800070-JLR200
Medicine and Health Sciences
Paraoxonase 1 (PON1) has been reported to be associated with proteinuria in subjects with type 2 diabetes mellitus (T2DM). Plasma cystatin C is more accurate than creatinine for identifying stage 3 kidney disease in T2DM. We tested the hypothesis that PON1 and cystatin C would be associated in T2DM subjects from an Aboriginal Canadian community, who are at high risk for the development of nephropathy. PON1 A(-162)G and PON2 Ala148Gly genotypes, cystatin C, HbA1c, high density lipoprotein cholesterol (HDLC), waist circumference (waist), and duration of diabetes were included in the regression analysis with log(e) (ln) of PON1 mass as the dependent variable. A regression model including PON2 Ala148Gly genotype, HDLC, and ln cystatin C explained 25.8% of the variance in PON1 mass. Conversely, waist, age, ln HbA1c, ln duration of diabetes, and ln PON1 mass, but not PON2 genotype, explained 38% of the variance in cystatin C. Subjects with cystatin C estimated glomerular filtration rate (eGFR) <60 ml>/min per 1.73 m(2) (stage 3 kidney disease) had significantly lower PON1 mass compared with subjects with cystatin C-eGFR >60 ml/min per 1.73 m(2). The lower mass of PON1, an anti-inflammatory HDL-associated enzyme, in T2DM with cystatin C-eGFR <60 ml>/min per 1.73 m(2) may contribute to their increased risk for cardiovascular disease.
https://ir.lib.uwo.ca/fammedpub/3
oai:ir.lib.uwo.ca:biochempub-1034
2009-12-07T03:37:37Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19055350
Structural Characterization of Short-Lived Protein Unfolding Intermediates by Laser-Induced Oxidative Labeling and Mass Spectrometry
Stocks, Bradley B.
Konermann, Lars
Article
2009-01-01T08:00:00Z
Amino Acid Sequence
Animals
Chromatography
Liquid
Horses
Hydrogen-Ion Concentration
Kinetics
Lasers
Models
Molecular
Molecular Sequence Data
Myoglobin
Osmolar Concentration
Oxidation-Reduction
Peptide Mapping
Protein Folding
Spectrometry
Mass
Electrospray Ionization
Analytical Chemistry
81
1
20
27
http://dx.doi.org/10.1021/ac801888h
Biochemistry
The structural characterization of short-lived intermediates provides insights into the mechanisms of protein folding and unfolding. Using holo-myoglobin as a model system, this work reports the application of oxidative pulse labeling for experiments of this kind. Protein unfolding is triggered by a pH jump from 6.5 to 3.2 in 150 mM NaCl. Subsequent (.-)OH exposure at various time points using laser photolysis of H2O2 leads to covalent modifications of solvent-exposed side chains within approximately 1 mus (Hambly, D. M.; Gross, M. L. J. Am. Soc. Mass Spectrom. 2005, 16, 2057-2063). Most of these modifications appear as 16 Da adducts in the mass spectrum of the intact protein. The overall extent of labeling increases with time, reflecting the exposure of reactive side chains that had previously been buried. Unfolding and disruption of heme-protein interactions go to completion within approximately 10 s. Spatially resolved information is obtained by monitoring the signal intensities of unmodified tryptic peptides. After 50 ms, many regions have lost most of their protection, whereas structure is retained in the B, E, F, and G helices. The BEF core remains partially folded, even after 500 ms, at which point helix G is fully unprotected. The observation of an "early" (BEFG) and a "late" (BEF) intermediate is in accord with optical stopped-flow measurements. Formation of these transient species is attributed to the persistence of heme-protein interactions during the early stages of the reaction. Overall, this work demonstrates the feasibility of laser-induced oxidative labeling as a tool for characterizing the structure of short-lived protein conformers. The combination of this approach with ultrarapid mixing or photochemical triggering should allow folding experiments in the submillisecond range.
https://ir.lib.uwo.ca/biochempub/32
oai:ir.lib.uwo.ca:vascularpub-1017
2009-12-08T07:54:05Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19185282
A Multiplex Human Syndrome Implicates a Key Role for Intestinal Cell Kinase in Development of Central Nervous, Skeletal, and Endocrine Systems
Lahiry, Piya
Wang, Jian
Robinson, John F.
Turowec, Jacob P.
Litchfield, David W.
Lanktree, Matthew B.
Gloor, Gregory B.
Puffenberger, Erik G.
Strauss, Kevin A.
Martens, Mildred B.
Ramsay, David A.
Rupar, C. Anthony
Siu, Victoria
Hegele, Robert A.
Article
2009-01-29T08:00:00Z
Animals
Autopsy
Bone Diseases
Brain
Central Nervous System Diseases
Conserved Sequence
Endocrine System Diseases
Ethnic Groups
Exons
Female
Genes
Recessive
Humans
Kidney
Liver
Male
Mutation
Pedigree
Protein-Serine-Threonine Kinases
Siblings
Species Specificity
Syndrome
American Journal of Human Genetics
84
2
134
147
10.1016/j.ajhg.2008.12.017
Cardiology
Medical Biochemistry
Six infants in an Old Order Amish pedigree were observed to be affected with endocrine-cerebro-osteodysplasia (ECO). ECO is a previously unidentified neonatal lethal recessive disorder with multiple anomalies involving the endocrine, cerebral, and skeletal systems. Autozygosity mapping and sequencing identified a previously unknown missense mutation, R272Q, in ICK, encoding intestinal cell kinase (ICK). Our results established that R272 is conserved across species and among ethnicities, and three-dimensional analysis of the protein structure suggests protein instability due to the R272Q mutation. We also demonstrate that the R272Q mutant fails to localize at the nucleus and has diminished kinase activity. These findings suggest that ICK plays a key role in the development of multiple organ systems.
https://ir.lib.uwo.ca/vascularpub/17
oai:ir.lib.uwo.ca:biochempub-1035
2009-12-08T07:25:13Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
18951976
The XLP Syndrome Protein SAP Interacts with SH3 Proteins to Regulate T Cell Signaling and Proliferation
Li, Chengjun
Schibli, David
Li, Shawn Shun-Cheng
Article
2009-01-01T08:00:00Z
Adaptor Proteins
Signal Transducing
Amino Acid Sequence
Cell Line
Extracellular Signal-Regulated MAP Kinases
Fluorescent Antibody Technique
Direct
Gene Knockdown Techniques
Humans
Intracellular Signaling Peptides and Proteins
Jurkat Cells
Large Neutral Amino Acid-Transporter 1
Lymphoproliferative Disorders
Magnetic Resonance Spectroscopy
Molecular Sequence Data
Mutagenesis
Site-Directed
Oncogene Proteins
Phosphoproteins
Phosphorylation
Proto-Oncogene Proteins c-fyn
RNA
Small Interfering
Signal Transduction
T-Lymphocytes
src Homology Domains
Cellular Signalling
21
1
111
119
http://dx.doi.org/10.1016/j.cellsig.2008.09.014
Biochemistry
The gene sap/shd1a, which encodes a 128-residue SH2 domain protein, is frequently deleted or mutated in the X-linked lymphoproliferative syndrome (XLP). The SAP SH2 domain differs from others in the same class in that it is not only capable of binding to a phosphotyrosine-containing peptide, it can also associate with an SH3 domain using a distinct surface. This novel mode of ligand-binding is initially discovered in the SLAM-SAP-Fyn complex that plays a critical role in T cell and natural killer cell activation. To identify additional binding partners for SAP, we screened a panel of 12 SH3 domains derived from regulatory proteins and identified NCK1 as a novel target of SAP in T cells. NMR analysis demonstrated that the NCK1 and Fyn SH3 domains possessed comparable affinities for SAP and engaged the same set of residues on the surface of the SAP SH2 domain. Depletion of SAP by siRNA caused a significant decrease in NCK1 tyrosine phosphorylation as well as the phosphorylation of other T cell receptor (TCR) downstream proteins such as LAT and SLP-76. Moreover, SAP was shown to regulate T cell proliferation through the MAP-kinase Erk. Taken together, our work identifies NCK1 as a novel physiological partner for SAP and a direct regulator of TCR signaling and T cell proliferation.
https://ir.lib.uwo.ca/biochempub/33
oai:ir.lib.uwo.ca:vascularpub-1016
2009-12-08T07:34:25Z
publication:vascularpub
publication:biophysicspub
publication:physpharmpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:physpharm
publication:biophysics
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19149606
NAD+, Sirtuins, and Cardiovascular Disease
Borradaile, Nica M.
Pickering, J. Geoffrey
Article
2009-01-01T08:00:00Z
Cardiovascular Diseases
Gene Expression Regulation
Enzymologic
Humans
Myocardium
NAD
Sirtuins
Current Pharmaceutical Design
15
1
110
117
Cardiology
Cardiovascular disease (CVD) is the most prevalent disease worldwide and there is intense interest in pharmaceutical approaches to reduce the burden of this chronic, aging-related condition. The sirtuin (SIRT) family of NAD(+)-dependent protein deacetylases and ADP-ribosyltransferases have emerged as exciting targets for CVD management that can impact the cardiovascular system both directly and indirectly, the latter by modulating whole body metabolism. SIRT1-4 regulate the activities of a variety of transcription factors, coregulators, and enzymes that improve metabolic control in adipose tissue, liver, skeletal muscle, and pancreas, particularly during obesity and aging. SIRT1 and 7 can control myocardial development and resist stress- and aging-associated myocardial dysfunction through the deacetylation of p53 and forkhead box O1 (FoxO1). By modulating the activity of endothelial nitric oxide synthase (eNOS), FoxO1, and p53, and the expression of angiotensin II type 1 receptor (AT1R), SIRT1 also promotes vasodilatory and regenerative functions in endothelial and smooth muscle cells of the vascular wall. Given the array of potentially beneficial effects of SIRT activation on cardiovascular health, interest in developing specific SIRT agonists is well-substantiated. Because SIRT activity depends on cellular NAD+ availability, enzymes involved in NAD+ biosynthesis, including nicotinamide phosphoribosyltransferase (Nampt), may also be valuable pharmaceutical targets for managing CVD. Herein we review the actions of the SIRT proteins on the cardiovascular system and consider the potential of modulating SIRT activity and NAD+ availability to control CVD.
https://ir.lib.uwo.ca/vascularpub/16
oai:ir.lib.uwo.ca:vascularpub-1018
2009-12-09T03:06:30Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19244606
Hoofbeats, Zebras, and Insights into Insulin Resistance
Hegele, Robert A.
Reue, Karen
Article
2009-02-02T08:00:00Z
Humans
Insulin Resistance
Mutation
Proto-Oncogene Proteins c-akt
Receptor
Insulin
Signal Transduction
Journal of Clinical Investigation
119
2
249
251
10.1172/JCI38420
Medical Genetics
In this issue of the JCI, Semple and colleagues report phenotypic evaluation of patients with a germline mutation in the gene encoding serine/threonine kinase AKT2 (see the related article beginning on page 315). Their findings support the idea that the postreceptor actions of insulin in the liver--suppression of gluconeogenesis and stimulation of lipogenesis--are mediated through divergent pathways that can be uncoupled. The results appear to refine the arrangement of crucial steps along these pathways and show how comprehensive study of the phenotype, "deep phenotyping," of patients who carry rare mutations might complement other types of experiments to elucidate complex pathways and mechanisms.
https://ir.lib.uwo.ca/vascularpub/18
oai:ir.lib.uwo.ca:chempub-1000
2009-12-16T08:07:27Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19055344
Structural Characterization of an Integral Membrane Protein in Its Natural Lipid Environment by Oxidative Methionine Labeling and Mass Spectrometry
Pan, Yan
Stocks, Bradley B.
Brown, Leonid
Konermann, Lars
Article
2009-01-01T08:00:00Z
Amino Acid Sequence
Bacteriorhodopsins
Halobacterium salinarum
Hydrogen Peroxide
Lasers
Lipid Bilayers
Membrane Proteins
Methionine
Models
Molecular
Molecular Sequence Data
Oxidation-Reduction
Photolysis
Tandem Mass Spectrometry
Analytical Chemistry
Analytical Chemistry
81
1
28
35
10.1021/ac8020449
Chemistry
Membrane proteins represent formidable challenges for many analytical techniques. Studies on these systems are often carried out after surfactant solubilization. Unfortunately, such a non-natural protein environment can affect conformation and stability, and it offers only partial protection against aggregation. This work employs bacteriorhodopsin (BR) as a model system for in situ structural studies on a membrane protein in its natural lipid bilayer. BR-containing purple membrane suspensions were exposed to hydroxyl radicals, generated by nanosecond laser photolysis of dilute aqueous H(2)O(2). The experiments rely on the premise that oxidative labeling occurs mainly at solvent-exposed side chains, whereas sites that are sterically protected will react to a much lesser extent. Following .OH exposure, the protein was analyzed by tryptic peptide mapping and electrospray tandem mass spectrometry. Oxidative labeling of BR was found to occur only at its nine Met residues. This is in contrast to the behavior of previously studied water-soluble proteins, which generally undergo modifications at many different types of residues. In those earlier experiments the high reactivity of Met has hampered its use as a structural probe. In contrast, the Met oxidation pattern observed here is in excellent agreement with the native BR structure. Extensive labeling is seen for Met32, 68, and 163, all of which are located in solvent-exposed loops. The remaining six Met residues are deeply buried and show severalfold less oxidation. Our results demonstrate the usefulness of Met oxidative labeling for structural studies on membrane proteins, especially when considering that many of these species are methionine-rich. The introduction of additional Met residues as conformational probes, as well as in vivo structural investigations, represents exciting future extensions of the methodology described here.
https://ir.lib.uwo.ca/chempub/1
oai:ir.lib.uwo.ca:biochempub-1037
2009-12-17T04:45:38Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19216510
Formation of Monomeric S100B and S100A11 Proteins at Low Ionic Strength
Marlatt, Nicole M.
Boys, Brian L.
Konermann, Lars
Shaw, Gary S.
Article
2009-03-10T07:00:00Z
Acetates
Animals
Dose-Response Relationship
Drug
Humans
Kinetics
Magnetic Resonance Spectroscopy
Models
Molecular
Nerve Growth Factors
Osmolar Concentration
Protein Folding
Protein Multimerization
Protein Structure
Quaternary
Protein Structure
Secondary
Protein Structure
Tertiary
Rabbits
S100 Proteins
Spectrometry
Mass
Electrospray Ionization
Biochemistry
48
9
1954
1963
http://dx.doi.org/10.1021/bi802086a
Biochemistry
Chemistry
The S100 proteins comprise a group of EF-hand proteins that undergo a calcium-induced conformational change allowing them to interact with other proteins and produce a biological response. A unique feature of these proteins is the fact that they can form both homo- and heterodimers independent of calcium binding. The reported dissociation constants for several S100 proteins span a very large range, from 1-4 microM to <<1 nM, suggesting that differing interface surface areas could govern the strength of the binding affinity. In this work, we examine the dimerization mechanism of S100B and S100A11 in the absence of calcium. Using electrospray mass spectrometry, we demonstrate that the monomer-dimer equilibrium in these S100 proteins is strongly dependent on the ionic strength of the solution. At higher ionic strengths (>or=22 mM), both S100A11 and S100B exist predominantly as homodimers. For apo-S100A11, a K(dimer) near 0.01 microM is estimated, while concentration-dependent experiments under these conditions show the K(dimer) for apo-S100B must be even lower. In contrast, lowering the ionic strength results in the formation of monomeric proteins with poorer dimer propensity. For example, the estimated K(dimer) for apo-S100A11 is more than 400 microM at 0.1 mM NH(4)Ac. (1)H-(15)N HSQC NMR experiments in combination with circular dichroism studies show that monomeric S100B and S100A11 proteins are alpha-helical and retain a significant amount of tertiary structure. Our results indicate that apo-S100B has at least a 10-fold stronger propensity to form dimers than does apo-S100A11 in line with a 400 A(2) greater buried surface area for apo-S100B at its dimer interface. These experiments are the first to show that folded monomeric S100 proteins can be isolated, thus paving the way for future experiments aimed at examining the possible role of these monomers in folding and calcium signaling.
https://ir.lib.uwo.ca/biochempub/35
oai:ir.lib.uwo.ca:vascularpub-1019
2009-12-17T04:37:43Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19139765
Plasma Lipoproteins: Genetic Influences and Clinical Implications
Hegele, Robert A.
Article
2009-02-01T08:00:00Z
Animals
Cholesterol
Dyslipidemias
Genomics
Humans
Hyperlipoproteinemias
Lipoproteins
Models
Biological
Triglycerides
Nature Reviews Genetics
10
2
109
121
10.1038/nrg2481
Medical Genetics
Susceptibility to the growing global public health problem of cardiovascular disease is associated with levels of plasma lipids and lipoproteins. Several experimental strategies have helped us to clarify the genetic architecture of these complex traits, including classical studies of monogenic dyslipidaemias, resequencing, phenomic analysis and, more recently, genome-wide association studies and analysis of metabolic networks. The genetic basis of plasma lipoprotein levels can now be modelled as a mosaic of contributions from multiple DNA sequence variants, both rare and common, with varying effect sizes. In addition to filling gaps in our understanding of plasma lipoprotein metabolism, the recent genetic advances will improve our ability to classify, diagnose and treat dyslipidaemias.
https://ir.lib.uwo.ca/vascularpub/19
oai:ir.lib.uwo.ca:paedpub-1007
2009-12-28T01:14:15Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
19185281
Mutations in SPINT2 Cause a Syndromic Form of Congenital Sodium Diarrhea
Heinz-Erian, Peter
Müller, Thomas
Krabichler, Birgit
Schranz, Melanie
Becker, Christian
Rüschendorf, Franz
Nürnberg, Peter
Rossier, Bernard
Vujic, Mihailo
Booth, Ian W.
Holmberg, Christer
Wijmenga, Cisca
Grigelioniene, Giedre
Kneepkens, C. M. Frank
Rosipal, Stefan
Mistrik, Martin
Kappler, Matthias
Michaud, Laurent
Dóczy, Ludwig-Christoph
Siu, Victoria Mok
Krantz, Marie
Zoller, Heinz
Utermann, Gerd
Janecke, Andreas R.
Article
2009-01-29T08:00:00Z
Amino Acid Sequence
Anus
Imperforate
Base Sequence
Chromosome Mapping
Cohort Studies
DNA Mutational Analysis
Diarrhea
Feces
Female
Genes
Recessive
Humans
Infant
Infant
Newborn
Malabsorption Syndromes
Male
Membrane Glycoproteins
Molecular Sequence Data
Mutation
Pedigree
RNA
Messenger
Sodium
Survival Analysis
American Journal of Human Genetics
American Journal of Human Genetics
84
2
188
196
10.1016/j.ajhg.2009.01.004
Medical Biochemistry
Pediatrics
Autosomal-recessive congenital sodium diarrhea (CSD) is characterized by perinatal onset of a persistent watery diarrhea with nonproportionally high fecal sodium excretion. Defective jejunal brush-border Na(+)/H(+) exchange has been reported in three sporadic patients, but the molecular basis of the disease has not been elucidated. We reviewed data from a large cohort of CSD patients (n = 24) and distinguished CSD associated with choanal or anal atresia, hypertelorism, and corneal erosions--i.e., a syndromic form of CSD--occurring in ten families from an isolated form--i.e., classic CSD--presenting in seven families. Patients from both groups have a high risk of mortality due to immediate electrolyte imbalances and complications from long-term parenteral nutrition in the first years of life, but survivors can eventually adapt to partial or complete enteral nutrition. A genome-wide SNP scan was applied and identified a homozygous c.593-1G-->A splicing mutation in SPINT2, encoding a Kunitz-type serine-protease inhibitor, in one extended kindred with syndromic CSD. The same mutation and four distinct, homozygous or compound heterozygous mutations (p.Y163C, c.1A-->T, c.337+2T-->C, c.553+2T-->A) were identified in all syndromic patients. No SPINT2 mutations were found in classic-CSD patients. SPINT2 mutations were associated with loss of protein synthesis or failure to inhibit the serine protease trypsin in vitro. We delineate syndromic CSD as a distinct disease entity caused by SPINT2 loss-of-function mutations. SPINT2 mutations might lead to an excess of yet unknown serine protease activity in affected tissues.
https://ir.lib.uwo.ca/paedpub/7
oai:ir.lib.uwo.ca:paedpub-1006
2009-12-17T04:16:09Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
19193607
Functional and Complementary Phosphorylation State Attributes of Human Insulin-like Growth Factor-Binding Protein-1 (IGFBP-1) Isoforms Resolved by Free Flow Electrophoresis
Nissum, Mikkel
Abu Shehab, Majida
Sukop, Ute
Khosravi, Javad M.
Wildgruber, Robert
Eckerskorn, Christoph
Han, Victor K. M.
Gupta, Madhulika B.
Article
2009-06-01T07:00:00Z
Biosensing Techniques
Blotting
Western
Electrophoresis
Polyacrylamide Gel
Humans
Insulin-Like Growth Factor Binding Protein 1
Isoelectric Focusing
Phosphorylation
Protein Isoforms
Molecular & Cellular Proteomics
Molecular & Cellular Proteomics
8
6
1424
1435
10.1074/mcp.M800571-MCP200
Medical Biochemistry
Pediatrics
Fetal growth restriction (FGR) is a common disorder in which a fetus is unable to achieve its genetically determined potential size. High concentrations of insulin-like growth factor-binding protein-1 (IGFBP-1) have been associated with FGR. Phosphorylation of IGFBP-1 is a mechanism by which insulin-like growth factor-I (IGF-I) bioavailability can be modulated in FGR. In this study a novel strategy was designed to determine a link between IGF-I affinity and the concomitant phosphorylation state characteristics of IGFBP-1 phosphoisoforms. Using free flow electrophoresis (FFE), multiple IGFBP-1 phosphoisoforms in amniotic fluid were resolved within pH 4.43-5.09. The binding of IGFBP-1 for IGF-I in each FFE fraction was determined with BIAcore biosensor analysis. The IGF-I affinity (K(D)) for different IGFBP-1 isoforms ranged between 1.12e-08 and 4.59e-07. LC-MS/MS characterization revealed four phosphorylation sites, Ser(P)(98), Ser(P)(101), Ser(P)(119), and Ser(P)(169), of which Ser(P)(98) was new. Although the IGF-I binding affinity for IGFBP-1 phosphoisoforms across the FFE fractions did not correlate with phosphopeptide intensities for Ser(P)(101), Ser(P)(98), and Ser(P)(169) sites, a clear association was recorded with Ser(P)(119). Our data demonstrate that phosphorylation at Ser(119) plays a significant role in modulating affinity of IGFBP-1 for IGF-I. In addition, an altered profile of IGFBP-1 phosphoisoforms was revealed between FGR and healthy pregnancies that may result from potential site-specific phosphorylation. This study provides a strong basis for use of this novel approach in establishing the linkage between phosphorylation of IGFBP-1 and FGR. This overall strategy will also be broadly applicable to other phosphoproteins with clinical and functional significance.
https://ir.lib.uwo.ca/paedpub/6
oai:ir.lib.uwo.ca:paedpub-1008
2009-12-17T05:16:32Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
19041960
Unusual 8p Inverted Duplication Deletion with Telomere Capture from 8q
Buysse, Karen
Antonacci, Francesca
Callewaert, Bert
Loeys, Bart
Fränkel, Ulrike
Siu, Victoria
Mortier, Geert
Speleman, Frank
Menten, Björn
Article
2009-01-01T08:00:00Z
Chromosome Aberrations
Chromosome Deletion
Chromosome Inversion
Chromosomes
Human
Pair 8
Cytogenetic Analysis
Gene Duplication
Humans
Infant
Telomere
European Journal of Medical Genetics
European Journal of Medical Genetics
52
1
31
36
10.1016/j.ejmg.2008.10.007
Medical Biochemistry
Pediatrics
Inverted 8p duplication deletions are recurrent chromosomal rearrangements that are mediated through non-allelic homologous recombination (NAHR) between olfactory receptor (OR) gene clusters at 8p23.1. These rearrangements result in a proximal inverted duplication of various extent, a single copy region between the OR gene clusters and a terminal 8p deletion. The terminal deletions are stabilized by direct addition of telomeric repeats, so called telomere healing. Here, we report a patient with an unusual inverted duplication deletion of 8p. Stabilization of the broken chromosome end was achieved by telomere capture instead of telomere healing, resulting in an additional duplication of 8q24.13-->qter on the short arm of chromosome 8. Moreover, the inverted duplication was only 3.4 Mb in size (restricted to band 8p22) and thus cytogenetically undetectable. To the best of our knowledge this is the smallest inverted duplication reported hitherto. We describe the molecular characterization by FISH and array CGH of this unusual inv dup del (8p) and a previously reported patient with a similar 8q duplication and review the literature on cases associated with telomere capture.
https://ir.lib.uwo.ca/paedpub/8
oai:ir.lib.uwo.ca:biochempub-1036
2010-06-18T06:54:12Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
19187398
FXYD1, a Modulator of Na+,K+-ATPase Activity, Facilitates Female Sexual Development by Maintaining Gonadotrophin-Releasing Hormone Neuronal Excitability
Garcia-Rudaz, C.
Deng, V.
Matagne, V.
Ronnekleiv, O. K.
Bosch, M.
Han, V.
Percy, A. K.
Ojeda, S. R.
Article
2009-02-01T08:00:00Z
Action Potentials
Adolescent
Animals
Child
Child
Preschool
Female
Gonadotropin-Releasing Hormone
Humans
Hypothalamus
Male
Membrane Glycoproteins
Membrane Proteins
Mice
Mice
Inbred C57BL
Mice
Knockout
Mice
Transgenic
Nerve Tissue Proteins
Neurons
Patch-Clamp Techniques
Phosphoproteins
Puberty
Rats
Sexual Development
Sodium-Potassium-Exchanging ATPase
Journal of Neuroendocrinology
21
2
108
122
http://dx.doi.org/10.1111/j.1365-2826.2008.01812.x
Biochemistry
Neurosciences
Pediatrics
The excitatory tone to gonadotrophin-releasing hormone (GnRH) neurones is a critical component underlying the pubertal increase in GnRH secretion. However, the homeostatic mechanisms modulating the response of GnRH neurones to excitatory inputs remain poorly understood. A basic mechanism of neuronal homeostasis is the Na(+),K(+)-ATPase-dependent restoration of Na(+) and K(+) transmembrane gradients after neuronal excitation. This activity is reduced in a mouse model of Rett syndrome (RTT), a neurodevelopmental disorder in which expression of FXYD1, a modulator of Na(+),K(+)-ATPase activity, is increased. We now report that the initiation, but not the completion of puberty, is advanced in girls with RTT, and that, in rodents, FXYD1 may contribute to the neuroendocrine regulation of female puberty by modulating GnRH neuronal excitability. Fxyd1 mRNA abundance reaches maximal levels in the female rat hypothalamus by the fourth postnatal week of life (i.e., around the time when the mode of GnRH secretion acquires an adult pattern of release). Although Fxyd1 mRNA expression is low in the hypothalamus, approximately 50% of GnRH neurones contain Fxyd1 transcripts. Whole-cell patch recording of GnRH-EGFP neurones revealed that the neurones of Fxyd1-null female mice respond to somatic current injections with a lower number of action potentials than wild-type cells. Both the age at vaginal opening and at first oestrous were delayed in Fxyd1(-/-) mice, but adult reproductive capacity was normal. These results suggest that FXYD1 contributes to facilitating the advent of puberty by maintaining GnRH neuronal excitability to incoming transsynaptic stimulatory inputs.
https://ir.lib.uwo.ca/biochempub/34
oai:ir.lib.uwo.ca:biochempub-1038
2009-12-17T04:51:50Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19054331
Structural Insight into Recruitment of Translesion DNA Polymerase Dpo4 to Sliding Clamp PCNA
Xing, Guangxin
Kirouac, Kevin
Shin, Yoon Jung
Bell, Stephen D.
Ling, Hong
Article
2009-02-01T08:00:00Z
Archaeal Proteins
DNA Polymerase beta
DNA Replication
Electrophoresis
Polyacrylamide Gel
Electrophoretic Mobility Shift Assay
Models
Molecular
Proliferating Cell Nuclear Antigen
Protein Binding
Protein Interaction Mapping
Protein Structure
Tertiary
Sulfolobus solfataricus
Molecular Microbiology
71
3
678
691
http://dx.doi.org/10.1111/j.1365-2958.2008.06553.x
Biochemistry
DNA polymerases are co-ordinated by sliding clamps (PCNA/beta-clamp) in translesion synthesis. It is unclear how these enzymes assemble on PCNA with geometric and functional compatibility. We report the crystal structure of a full-length Y-family polymerase, Dpo4, in complex with heterodimeric PCNA1-PCNA2 at 2.05 A resolution. Dpo4 exhibits an extended conformation that differs from the Dpo4 structures in apo- or DNA-bound form. Two hinges have been identified in Dpo4, which render the multidomain polymerase flexible conformations and orientations relative to PCNA. Dpo4 binds specifically to PCNA1 on the conserved ligand binding site. The C-terminal peptide of Dpo4 becomes structured with a 3(10) helix and dominates the specific binding. The Y-family polymerase also contacts PCNA1 with its finger, thumb and little finger domains, which are conformation-dependent protein-protein interactions that diversify the binding mode of Dpo4 on PCNA. The structure reveals a molecular model in which substrate/partner binding-coupled multiple conformations of a Y-family polymerase facilitate its recruitment and co-ordination on the sliding clamp. The conformational flexibility would turn the error-prone Y-family polymerase off when more efficient high-fidelity DNA polymerases work on undamaged DNA and turn it onto DNA templates to perform translesion synthesis when replication forks are stalled by DNA lesions.
https://ir.lib.uwo.ca/biochempub/36
oai:ir.lib.uwo.ca:biochempub-1040
2009-12-18T07:47:44Z
publication:anatomy
publication:surgerypub
publication:pmid
publication:faculties
publication:anatomypub
publication:biochempub
publication:surgery
publication:biochem
19189038
Kinetics of Calcium Oxalate Crystal Growth in the Presence of Osteopontin Isoforms: An Analysis by Scanning Confocal Interference Microcopy
Langdon, Aaron
Wignall, Geoffrey R.
Rogers, Kem
Sørensen, Esben S.
Denstedt, John
Grohe, Bernd
Goldberg, Harvey A.
Hunter, Graeme K.
Article
2009-03-01T08:00:00Z
Animals
Calcium Oxalate
Cattle
Crystallization
Kinetics
Microscopy
Confocal
Osteopontin
Protein Isoforms
Rats
Recombinant Proteins
Calcified Tissue International
84
3
240
248
http://dx.doi.org/10.1007/s00223-008-9215-5
Biochemistry
Medical Anatomy
Surgery
Proteins that inhibit the growth and aggregation of calcium oxalate crystals play important roles in the prevention of kidney stone disease. One such protein is osteopontin (OPN), which inhibits the formation of calcium oxalate monohydrate (COM) in a phosphorylation-dependent manner. To determine the role of phosphate groups in the inhibition of COM growth by OPN, we used scanning confocal interference microscopy to compare the effects of highly phosphorylated OPN from cow milk, less phosphorylated OPN from rat bone, and nonphosphorylated recombinant OPN. COM growth was measured in the principal crystallographic directions <001>, <010>, and <100>, representing lattice-ion addition to {121}, {010}, and {100} faces, respectively. While the shapes of growth curves were very consistent from crystal to crystal, absolute growth rates varied widely. To control for this, results were expressed as changes in the aspect ratios <010>/<001> and <100>/<001>. Compared to control, bone OPN increased <010>/<001> and had no effect on <100>/<001>; milk OPN had no effect on <010>/<001>and decreased <100>/<001>; recombinant OPN had no significant effect on either aspect ratio. These findings indicate that milk OPN interacts with COM crystal faces in order of preference {100} > {121} approximately {010}, whereas bone OPN interacts in order of preference {100} approximately {121} > {010}. As {100} is the most Ca(2+)-rich face of COM, while {010} is the least Ca(2+)-rich, it appears that the OPN-mediated inhibition of COM growth occurs through a nonspecific electrostatic interaction between Ca(2+) ions of the crystal and phosphate groups of the protein.
https://ir.lib.uwo.ca/biochempub/38
oai:ir.lib.uwo.ca:biochempub-1039
2009-12-18T07:22:33Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
19088125
Altered Visual Function and Interneuron Survival in Atrx Knockout Mice: inference for the Human Syndrome
Medina, Chantal F.
Mazerolle, Chantal
Wang, Yaping
Bérubé, Nathalie G.
Coupland, Stuart
Gibbons, Richard J.
Wallace, Valerie A.
Picketts, David J.
Article
2009-03-01T08:00:00Z
Adult
Amacrine Cells
Animals
Cell Survival
DNA Helicases
Female
Gene Expression
Humans
Interneurons
Male
Mental Retardation
X-Linked
Mice
Mice
Inbred C57BL
Mice
Knockout
Mice
Transgenic
Nuclear Proteins
Vision
Ocular
Human Molecular Genetics
18
5
966
977
http://dx.doi.org/10.1093/hmg/ddn424
Biochemistry
Pediatrics
ATRX is an SWI/SNF-like chromatin remodeling protein that is mutated in several X-linked mental retardation syndromes, including the ATR-X syndrome. In mice, Atrx expression is widespread and attempts to understand its function in brain development are hampered by the lethality associated with ubiquitous or forebrain-restricted ablation of this gene. One way to circumvent this problem is to study its function in a region of the brain that is dispensable for long-term survival of the organism. The retina is a well-characterized tractable model of CNS development and in our review of 202 ATR-X syndrome patients, we found ocular defects present in approximately 25% of the cases, suggesting that studying Atrx in this tissue will provide insight into function. We report that Atrx is expressed in the neuroprogenitor pool in embryonic retina and in all cell types of the mature retina with the exception of rod photoreceptors. Conditional inactivation of Atrx in the retina during embryogenesis ultimately results in a loss of only two types of neurons, amacrine and horizontal cells. We show that this defect does not arise from a failure to specify these cells but rather a defect in interneuron differentiation and survival post-natally. The timing of cell loss is concomitant with light-dependent changes in synaptic organization in the retina and with a change in Atrx subnuclear localization within these interneurons. Moreover, these interneuron defects are associated with functional deficits as demonstrated by reduced b-wave amplitudes upon electroretinogram analysis. These results implicate a role for Atrx in interneuron survival and differentiation.
Dr. Nathalie Bérubé is currently a faculty member at The University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/37
oai:ir.lib.uwo.ca:chempub-1001
2009-12-18T07:35:51Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19110444
A Simple Model for the Disintegration of Highly Charged Solvent Droplets during Electrospray Ionization
Konermann, Lars
Article
2009-03-01T08:00:00Z
Journal of the American Society for Mass Spectrometry
Journal of the American Society for Mass Spectrometry
20
3
496
506
10.1016/j.jasms.2008.11.007
Chemistry
Medical Biochemistry
This work uses a minimalist model for deciphering the opposing effects of Coulomb repulsion and surface tension on the stability of electrosprayed droplets. Guided by previous observations, it is assumed that progeny droplets are ejected from the tip of liquid filaments that are formed as protrusions of an initially spherical parent. Nonspherical shapes are approximated as assemblies of multiple closely spaced beads. This strategy greatly facilitates the calculation of electrostatic and surface energies. For a droplet at the Rayleigh limit the model predicts that growth of a very thin filament is a spontaneous process with a negligible activation barrier. In contrast, significant barriers are encountered for the formation of larger diameter filaments. These different barrier heights favor highly asymmetric droplet fission because the dimensions of the filament determine those of the ejected droplet(s). Substantial charge accumulation occurs at the filament termini. This allows each progeny droplet to carry a significant fraction of charge, despite its very small volume. In the absence of a long connecting filament, relieving electrostatic stress through progeny droplet emission would be ineffective. The model predicts the prevalence of fission events leading to the formation of several progeny droplets, instead of just a single one. Ejection bursts are followed by collapse back to a spherical shape. The resulting charge depleted system is incapable of producing additional progeny droplets until solvent evaporation returns it to the Rayleigh limit. Despite the very simple nature of the model used here, all of these predictions agree with experimental data.
https://ir.lib.uwo.ca/chempub/2
oai:ir.lib.uwo.ca:biochempub-1041
2009-12-19T01:52:14Z
publication:oncpub
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
publication:paedpub
18483851
Smoking and the Risk of Breast Cancer in BRCA1 and BRCA2 Carriers: An Update
Ginsburg, Ophira
Ghadirian, Parviz
Lubinski, Jan
Cybulski, Cezary
Lynch, Henry
Neuhausen, Susan
Kim-Sing, Charmaine
Robson, Mark
Domchek, Susan
Isaacs, Claudine
Klijn, Jan
Armel, Susan
Foulkes, William D.
Tung, Nadine
Moller, Pal
Sun, Ping
Narod, Steven A.
Hereditary Breast Cancer Clinical Study Group, Toronto, ON
Article
2009-03-01T08:00:00Z
Adolescent
Adult
Aged
Aged
80 and over
Breast Neoplasms
Case-Control Studies
Female
Genes
BRCA1
Genes
BRCA2
Heterozygote
Humans
Middle Aged
Mutation
Risk Factors
Smoking
Young Adult
Breast Cancer Research and Treatment
114
1
127
135
http://dx.doi.org/10.1007/s10549-008-9977-5
Biochemistry
Epidemiology
Oncology
Among women with a mutation in BRCA1 or BRCA2, the risk of breast cancer is high, but it may be modified by exogenous and endogenous factors. There is concern that exposure to carcinogens in cigarette smoke may increase the risk of cancer in mutation carriers. We conducted a matched case-control study of 2,538 cases of breast cancer among women with a BRCA1 (n = 1,920) or a BRCA2 (n = 618) mutation. One non-affected mutation carrier control was selected for each case, matched on mutation, country of birth, and year of birth. Odds ratios were calculated using conditional logistic regression, adjusted for oral contraceptive use and parity. Ever-smoking was not associated with an increased breast cancer risk among BRCA1 carriers (OR = 1.09; 95% CI 0.95-1.24) or among BRCA2 carriers (OR = 0.81; 95% CI 0.63-1.05). The result did not differ when cases were restricted to women who completed the questionnaire within two years of diagnosis. A modest, but significant increase in risk was seen among BRCA1 carriers with a past history of smoking (OR = 1.27; 95% CI 1.06-1.50), but not among current smokers (OR = 0.95; 0.81-1.12). There appears to be no increase in the risk of breast cancer associated with current smoking in BRCA1 or BRCA2 carriers. There is a possibility of an increased risk of breast cancer among BRCA1 carriers associated with past smoking. There may be different effects of carcinogens in BRCA mutation carriers, depending upon the timing of exposure.
Dr. Peter Ainsworth at The University of Western Ontario was one of the collaborators of this research project.
https://ir.lib.uwo.ca/biochempub/39
oai:ir.lib.uwo.ca:biochempub-1042
2010-09-21T06:49:25Z
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
19324971
Estrogen Receptor β Is Required for Optimal cAMP Production in Mouse Granulosa Cells
Deroo, Bonnie J.
Rodriguez, Karina F.
Couse, John F.
Hamilton, Katherine J.
Collins, Jennifer B.
Grissom, Sherry F.
Korach, Kenneth S.
Article
2009-07-01T07:00:00Z
Animals
Cells
Cultured
Cyclic AMP
Down-Regulation
Estrogen Receptor beta
Female
Fertility
Forskolin
Granulosa Cells
Luteinizing Hormone
Mice
Mice
Knockout
Ovulation
Receptors
LH
Molecular Endocrinology
23
7
955
965
http://dx.doi.org/10.1210/me.2008-0213
Biochemistry
Granulosa cells of preovulatory follicles differentiate in response to FSH, and this differentiation is augmented by estradiol. We have previously shown that FSH-mediated granulosa cell differentiation requires functional estrogen receptor-β (ERβ) by demonstrating that the granulosa cells of ERβ–/– FSH-treated mice are unable to maximally induce expression of the LH receptor (an indicator of granulosa cell differentiation) compared with ERβ+/+ controls. As a result, FSH-primed ERβ–/– granulosa cells exhibit a reduced response to a subsequent ovulatory dose of LH. In this study, we further characterized the attenuated response of ERβ–/– granulosa cells to stimulation by LH and FSH using isolated mouse granulosa cells and primary granulosa cell cultures. We observed a 50% reduction in cAMP levels in cultured ERβ–/– granulosa cells exposed to LH compared with ERβ+/+ controls. We also observed an attenuated genomic response in granulosa cells isolated from FSH-primed ERβ–/– mice compared with ERβ+/+ controls. Our data indicate that this attenuated response may result from inadequate levels of cAMP, because cAMP levels in cultured ERβ–/– granulosa cells exposed to forskolin were approximately 50% lower than in ERβ+/+ granulosa cells. Phosphorylation of cAMP regulatory element binding protein, an indicator of protein kinase A activity, was also reduced in FSH-treated ERβ–/– granulosa cells compared with ERβ+/+ controls. These are the first data to indicate that ERβ plays a role in the induction of the cAMP pathway in mouse granulosa cells and that disruption of proper ERβ signaling associated with this pathway may cause negative effects on ovulation and fertility.
Dr. Bonnie Deroo is currently a faculty member at The University of Western Ontario.
https://ir.lib.uwo.ca/biochempub/40
oai:ir.lib.uwo.ca:vascularpub-1020
2009-12-19T06:42:05Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19299407
Replication of Genetic Associations with Plasma Lipoprotein Traits in a Multiethnic Sample
Lanktree, Matthew B.
Anand, Sonia S.
Yusuf, Salim
Hegele, Robert A.
SHARE Investigators
Article
2009-07-01T07:00:00Z
Adult
Alleles
Asian Continental Ancestry Group
Cholesterol
HDL
Cholesterol
LDL
European Continental Ancestry Group
Genetic Predisposition to Disease
Genetic Variation
Genome-Wide Association Study
Genotype
Humans
Male
Microarray Analysis
Middle Aged
Polymorphism
Single Nucleotide
Triglycerides
Journal of Lipid Research
50
7
1487
1496
10.1194/jlr.P900008-JLR200
Medical Genetics
Recent genome-wide association studies (GWAS) have reproducibly identified loci associated with plasma triglycerides (TG), HDL cholesterol, and LDL cholesterol. We sought to replicate these findings in a multiethnic population-based cohort using the curated single nucleotide polymorphism (SNP) set found on the new Illumina cardiovascular disease (CVD) beadchip, which contains approximately 50,000 SNPs densely mapping approximately 2,100 genes, selected based on their potential role in CVD. The sample consisted of individuals with European (n = 272), South Asian (n = 330), and Chinese (n = 304) ancestry. Identity by state clustering successfully classified individuals according to self-reported ethnicities. Associations between TG and APOA5, TG and LPL, HDL and CETP, and LDL and APOE were all identified (P < 2 x 10(-6)). In 13 loci, associations with the same SNP or a proxy SNP were identified in the same direction as previously reported (P < 0.05). Assessing the cumulative number of risk-associated alleles at multiple replicated SNPs increased the proportion of explained lipoprotein variance over and above traditional variables such as age, sex, body mass index, and ethnicity. The findings indicate the potential utility of the Illumina CVD beadchip, but they underscore the need to consider meta-analysis of results from commonly studied clinical or epidemiological samples.
https://ir.lib.uwo.ca/vascularpub/20
oai:ir.lib.uwo.ca:paedpub-1009
2009-12-19T01:07:16Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:paedpub
18772238
Hypoxia and Leucine Deprivation Induce Human Insulin-Like Growth Factor Binding Protein-1 Hyperphosphorylation and Increase Its Biological Activity
Seferovic, Maxim D.
Ali, Rashad
Kamei, Hiroyasu
Liu, Suya
Khosravi, Javad M.
Nazarian, Steven
Han, Victor K. M.
Duan, Cunming
Gupta, Madhulika B.
Article
2009-01-01T08:00:00Z
Carcinoma
Hepatocellular
Cell Hypoxia
Cell Line
Tumor
Enzyme-Linked Immunosorbent Assay
Genetic Variation
Humans
Insulin-Like Growth Factor Binding Protein 1
Kinetics
Leucine
Liver Neoplasms
Mass Spectrometry
Phosphopeptides
Phosphorylation
Endocrinology
Endocrinology
150
1
220
231
10.1210/en.2008-0657
Medical Biochemistry
Pediatrics
Fetal growth restriction is often caused by uteroplacental insufficiency that leads to fetal hypoxia and nutrient deprivation. Elevated IGF binding protein (IGFBP)-1 expression associated with fetal growth restriction has been documented. In this study we tested the hypothesis that hypoxia and nutrient deprivation induce IGFBP-1 phosphorylation and increase its biological potency in inhibiting IGF actions. HepG2 cells were subjected to hypoxia and leucine deprivation to mimic the deprivation of metabolic substrates. The total IGFBP-1 levels measured by ELISA were approximately 2- to 2.5-fold higher in hypoxia and leucine deprivation-treated cells compared with the controls. Two-dimensional immunoblotting showed that whereas the nonphosphorylated isoform is the predominant IGFBP-1 in the controls, the highly phosphorylated isoforms were dominant in hypoxia and leucine deprivation-treated cells. Liquid chromatography-tandem mass spectrometry analysis revealed four serine phosphorylation sites: three known sites (pSer 101, pSer 119, and pSer 169); and a novel site (pSer 98). Liquid chromatography-mass spectrometry was used to estimate the changes of phosphorylation upon treatment. Biacore analysis indicated that the highly phosphorylated IGFBP-1 isoforms found in hypoxia and leucine deprivation-treated cells had greater affinity for IGF-I [dissociation constant 5.83E (times 10 to the power)--0 m and 6.40E-09 m] relative to the IGFBP-1 from the controls (dissociation constant approximately 1.54E-07 m). Furthermore, the highly phosphorylated IGFBP-1 had a stronger effect in inhibiting IGF-I-stimulated cell proliferation. These findings suggest that IGFBP-1 phosphorylation may be a novel mechanism of fetal adaptive response to hypoxia and nutrient restriction.
https://ir.lib.uwo.ca/paedpub/9
oai:ir.lib.uwo.ca:oncpub-1065
2009-12-19T06:34:31Z
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
19267325
Multipotent Stromal Cells Are Activated to Reduce Apoptosis in Part by Upregulation and Secretion of Stanniocalcin-1
Block, Gregory J.
Ohkouchi, Shinya
Fung, France
Frenkel, Joshua
Gregory, Carl
Pochampally, Radhika
DiMattia, Gabriel
Sullivan, Deborah E.
Prockop, Darwin J.
Article
2009-03-01T08:00:00Z
Animals
Apoptosis
Blotting
Western
Cell Line
Cell Survival
Cells
Cultured
Culture Media
Conditioned
Fibroblasts
Glycoproteins
Humans
Hydrogen-Ion Concentration
Mice
Microscopy
Fluorescence
Oligonucleotide Array Sequence Analysis
Reverse Transcriptase Polymerase Chain Reaction
Stromal Cells
Transfection
Ultraviolet Rays
Up-Regulation
Stem Cells
Stem Cells
27
3
670
681
10.1634/stemcells.2008-0742
Medical Biochemistry
Oncology
Multipotent stromal cells (MSCs) have been shown to reduce apoptosis in injured cells by secretion of paracrine factors, but these factors were not fully defined. We observed that coculture of MSCs with previously UV-irradiated fibroblasts reduced apoptosis of the irradiated cells, but fresh MSC conditioned medium was unable reproduce the effect. Comparative microarray analysis of MSCs grown in the presence or absence of UV-irradiated fibroblasts demonstrated that the MSCs were activated by the apoptotic cells to increase synthesis and secretion of stanniocalcin-1 (STC-1), a peptide hormone that modulates mineral metabolism and has pleiotrophic effects that have not been fully characterized. We showed that STC-1 was required but not sufficient for reduction of apoptosis of UV-irradiated fibroblasts. In contrast, we demonstrated that MSC-derived STC-1 was both required and sufficient for reduction of apoptosis of lung cancer epithelial cells made apoptotic by incubation at low pH in hypoxia. Our data demonstrate that STC-1 mediates the antiapoptotic effects of MSCs in two distinct models of apoptosis in vitro.
https://ir.lib.uwo.ca/oncpub/65
oai:ir.lib.uwo.ca:chempub-1002
2009-12-19T01:15:02Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19082176
In-capillary Enrichment, Proteolysis and Separation Using Capillary Electrophoresis with Discontinuous Buffers: Application on Proteins with Moderately Acidic and Basic Isoelectric Points
Nesbitt, Chandra A.
Yeung, Ken K.-C.
Article
2009-01-01T08:00:00Z
Animals
Buffers
Caseins
Electrophoresis
Capillary
Humans
Hydrogen-Ion Concentration
Isoelectric Point
Lectins
Metalloendopeptidases
Miniaturization
Proteins
Spectrometry
Mass
Matrix-Assisted Laser Desorption-Ionization
Trypsin
Analyst
Analyst
134
1
65
71
10.1039/b821547m
Chemistry
Medical Biochemistry
Advances in mass spectrometry and capillary-format separation continue to improve the sensitivity of protein analysis. Of equal importance is the miniaturization of sample pretreatment such as enrichment and proteolysis. In a previous report (Nesbitt et al., Electrophoresis, 2008, 29, 466-474), nanoliter-volume protein enrichment, tryptic digestion, and partial separation was demonstrated in capillary electrophoresis followed by MALDI mass spectral analysis. A discontinuous buffer system, consisting of ammonium (pH 10) and acetate (pH 4), was used to create a pH junction inside the capillary, trapping a protein with a neutral isoelectric point, myoglobin (pI 7.2). Moreover, co-enrichment of myoglobin with trypsin led to an in-capillary digestion. In this paper, the ability of this discontinuous buffer system to perform similar in-capillary sample pretreatment on proteins with moderately acidic and basic pI was studied and reported. Lentil lectin (pI 8.6) and a multi-phosphorylated protein, beta-casein (pI 5.1), were selected as model proteins. In addition to the previously shown tryptic digestion, proteolysis with endoproteinase Asp-N was also performed. Digestion of these acidic and basic pI proteins produced a few peptides with extreme pI values lying outside the trapping range of the discontinuous buffer. An alteration in the peptide trapping procedure was made to accommodate these analytes. Offline MALDI mass spectral analysis confirmed the presence of the expected peptides. The presented miniaturized sample pretreatment methodology was proven to be applicable on proteins with a moderately wide range of pI. Flexibility in the choice of protease was also evident.
https://ir.lib.uwo.ca/chempub/3
oai:ir.lib.uwo.ca:physpharmpub-1026
2009-12-21T00:44:30Z
publication:physpharmpub
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:biochem
19381935
Biochemical Analysis of Arginine Methylation in Transcription
Tini, Marc
Naeem, Hina
Torchia, Joseph
Book Chapter
2008-12-01T08:00:00Z
Animals
Antibody Specificity
Arginine
Baculoviridae
Biochemistry
Biological Assay
Biotinylation
Cell Extracts
Chromatin Immunoprecipitation
Histone Acetyltransferases
Humans
Mass Spectrometry
Methylation
Methyltransferases
Nuclear Receptor Coactivator 3
Peptides
Protein-Arginine N-Methyltransferases
Recombinant Fusion Proteins
Staining and Labeling
Trans-Activators
Transcription
Genetic
Methods in Molecular Biology Series
Methods in Molecular Biology Series
523
235
247
10.1007/978-1-59745-190-1_16
Medical Biochemistry
Medical Physiology
Protein arginine methylation has emerged as an important mechanism for regulating the functions of proteins involved in diverse aspects of gene regulation such as transcriptional activation and repression, mRNA processing and nuclear-cytoplasmic shuttling. This modification is catalyzed by the PRMT family of enzymes which utilize intracellular S-adenosyl methionine as a cofactor to dimethylate-specific arginines found within many target proteins.The establishment of in vitro biochemical assays as well as the development of modification-specific antibodies, and more recently mass spectrometry, have increased our understanding of the mechanism of catalysis of the PRMT family of enzymes. In the following discussion, we present some of the more commonly used in vivo and in vitro techniques which can be utilized to study the mechanism of arginine methylation and its role in transcription.
Published as a book chapter in: <em>Chromatin Protocols</em>. (2nd ed.). Srikumar P. Chellappan. (Ed.).
https://ir.lib.uwo.ca/physpharmpub/24
oai:ir.lib.uwo.ca:fammedpub-1003
2009-12-19T06:54:29Z
publication:vascularpub
publication:fammedpub
publication:fammed
publication:pmid
publication:faculties
publication:epidem
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
publication:epidempub
19289805
Metabolic Syndrome and Its Components as Predictors of Incident Type 2 Diabetes Mellitus in an Aboriginal Community
Ley, Sylvia H.
Harris, Stewart B.
Mamakeesick, Mary
Noon, Tina
Fiddler, Edith
Gittelsohn, Joel
Wolever, Thomas M. S.
Connelly, Philip W.
Hegele, Robert A.
Zinman, Bernard
Hanley, Anthony J. G.
Article
2009-03-17T07:00:00Z
Adolescent
Adult
Age Distribution
Blood Glucose
Body Fat Distribution
Body Height
Body Mass Index
Canada
Child
Diabetes Mellitus
Type 2
Dyslipidemias
Fasting
Female
Follow-Up Studies
Humans
Hyperglycemia
Hypertension
Incidence
Logistic Models
Male
Metabolic Syndrome X
Middle Aged
Predictive Value of Tests
Prospective Studies
Risk Factors
Sensitivity and Specificity
Sex Factors
Waist Circumference
Young Adult
CMAJ
CMAJ
180
6
617
624
10.1503/cmaj.080972
Endocrinology, Diabetes, and Metabolism
BACKGROUND: Risk factors for type 2 diabetes remain poorly characterized among Aboriginal Canadians. We aimed to determine the incidence of type 2 diabetes in an Aboriginal community and to evaluate prospective associations with metabolic syndrome and its components.
METHODS: Of 606 participants in the Sandy Lake Health and Diabetes Project from 1993 to 1995 who were free of diabetes at baseline, 540 (89.1%) participated in 10-year follow-up assessments. Baseline anthropometry, blood pressure, fasting insulin and serum lipid levels were measured. Fasting and 2-hour postload glucose levels were obtained at follow-up to determine incident cases of type 2 diabetes.
RESULTS: The 10-year cumulative incidence of diabetes was 17.5%. High adiposity, dyslipidemia, hyperglycemia, hyperinsulinemia and hypertension at baseline were associated with an increased risk of diabetes after adjustment for age and sex (all p < or = 0.03). Metabolic syndrome had high specificity (75%-88%) and high negative predictive value (85%-87%) to correctly detect diabetes-free individuals at follow-up. It had low sensitivity (26%-48%) and low positive predictive value (29%-32%) to detect future diabetes. Metabolic syndrome at baseline was associated with incident diabetes after adjustment for age and sex, regardless of whether the syndrome was defined using the National Cholesterol Education Program criteria (odds ratio [OR] 2.03, 95% confidence interval [CI] 1.10-3.75) or the International Diabetes Federation criteria (OR 2.14, 95% CI 1.29-3.55). The association was to the same degree as that for impaired glucose tolerance assessed using the oral glucose tolerance test (OR 2.87, 95% CI 1.52-5.40; p > 0.05 for comparison of C statistics).
INTERPRETATION: Metabolic syndrome and its components can be identified with readily available clinical measures. As such, the syndrome may be useful for identifying individuals at risk of type 2 diabetes in remote Aboriginal communities.
https://ir.lib.uwo.ca/fammedpub/4
oai:ir.lib.uwo.ca:vascularpub-1021
2009-12-19T07:03:56Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
18656198
Relationship of the ApoE Polymorphism to Plasma Lipid Traits among South Asians, Chinese, and Europeans Living in Canada
Burman, Debika
Mente, Andrew
Hegele, Robert A.
Islam, Shofiqul
Yusuf, Salim
Anand, Sonia S.
Article
2009-03-01T08:00:00Z
Adult
Apolipoproteins E
Asian Continental Ancestry Group
Canada
Carotid Artery Diseases
Diet
Ethnic Groups
European Continental Ancestry Group
Female
Humans
Life Style
Lipids
Lipoproteins
HDL
Male
Middle Aged
Polymorphism
Genetic
Atherosclerosis
203
1
192
200
10.1016/j.atherosclerosis.2008.06.007
Medical Genetics
BACKGROUND: The prevalence of cardiovascular risk factors and atherosclerosis vary between ethnic groups. We examined the apolipoprotein E (ApoE) polymorphism, its association with lipid traits and atherosclerosis, and its influence on ethnic variations on lipid traits.
METHODS: In a randomly sampled cross-sectional study of 985 South Asian, Chinese, and European Canadians, three common isoforms of ApoE (E2, E3 and E4), plasma lipid concentrations and atherosclerosis of the carotid artery were measured.
RESULTS: The E2, E3 and E4 allele frequencies were 5.7%, 84.0%, and 10.2%, respectively, and differed significantly between ethnic groups. There was a strong, stepwise association between ApoE and each plasma lipid trait, except triglycerides. The E4 genotype was associated with higher low-density lipoprotein cholesterol (p for trend<0.001), ApoB (p<0.001), ApoB/ApoA ratio (p<0.001) and lipoprotein (a) (p<0.001), and lower ApoA (p<0.001) and high-density lipoprotein cholesterol (HDL-C) (p=0.005). A similar pattern of effects was observed across all ethnic groups. Ethnicity accounted for modest variation in ApoA, ApoB/ApoA ratio and HDL-C (4.2-5.0%), whereas ApoE isoforms explained only a small proportion of variability (0.3-1.4%). Dietary and lifestyle factors accounted for modest variation in several traits including HDL-C (5.6% and 5.0%, respectively). Carotid atherosclerosis was lower among individuals with E2 isoform in keeping with the effect of E2 on lipid levels.
CONCLUSIONS: The ApoE isoform is associated with plasma lipoproteins in all ethnic groups, yet explains only a small proportion of the inter-ethnic variation for most plasma lipoproteins. Additional genetic variants and/or health behaviors likely contribute to ethnic variations in plasma lipid traits.
https://ir.lib.uwo.ca/vascularpub/21
oai:ir.lib.uwo.ca:biochempub-1044
2011-05-27T00:24:41Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
18936058
An Enhanced Mass Spectrometry Approach Reveals Human Embryonic Stem Cell Growth Factors in Culture
Bendall, Sean C.
Hughes, Chris
Campbell, J. Larry
Stewart, Morag H.
Pittock, Paula
Liu, Suya
Bonneil, Eric
Thibault, Pierre
Bhatia, Mickie
Lajoie, Gilles A.
Article
2009-03-01T08:00:00Z
Animals
Cell Fractionation
Cells
Cultured
Chromatography
Liquid
Complex Mixtures
Culture Media
Conditioned
Culture Media
Serum-Free
Embryonic Stem Cells
Extracellular Space
Humans
Intercellular Signaling Peptides and Proteins
Mass Spectrometry
Mice
Peptides
Proteins
Molecular & Cellular Proteomics
8
3
421
432
http://dx.doi.org/10.1074/mcp.M800190-MCP200
Biochemistry
<p>The derivation and long-term maintenance of human embryonic stem cells (hESCs) has been established in culture formats that are both dependent and independent of support (feeder) cells. However, the factors responsible for preserving the viability of hESCs in a nascent state remain unknown. We describe a mass spectrometry-based method for probing the secretome of the hESC culture microenvironment to identify potential regulating protein factors that are in low abundance. Individual samples were analyzed several times, using successive mass (m/z) and retention time-directed exclusion, without sampling the same peptide ion twice. This iterative exclusion -mass spectrometry (IE-MS) approach more than doubled protein and peptide metrics in comparison to a simple repeat analysis method on the same instrument, even after extensive sample pre-fractionation. Furthermore, implementation of the IE-MS approach was shown to enhance the performance of an older quadrupole time of flight (Q-ToF) MS. The resulting number of identified peptides approached that of a parallel repeat analysis on a newer LTQ-Orbitrap MS. The combination of the results of both instruments proved to be superior to that achieved by a single instrument in the identification of additional proteins. Using the IE-MS strategy, combined with complementary gel- and solution-based fractionation methods, the hESC culture microenvironment was extensively probed. Over 10 to 12 times more extracellular proteins were observed compared with previously published surveys. The detection of previously undetectable growth factors, present at concentrations ranging from 10(-9) to 10(-11) g/ml, highlights the depth of our profiling. The IE-MS approach provides a simple and reliable technique that greatly enhances instrument performance by increasing the effective depth of MS-based proteomic profiling. This approach should be widely applicable to any LC-MS/MS instrument platform or biological system.</p>
https://ir.lib.uwo.ca/biochempub/42
oai:ir.lib.uwo.ca:biochempub-1043
2009-12-21T01:30:07Z
publication:paed
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
publication:paedpub
19274631
De Novo Interpretation of Tandem Mass Spectra
Ma, Bin
Lajoie, Gilles
Article
2009-03-01T08:00:00Z
Automatic Data Processing
Computational Biology
Databases
Protein
Peptides
Sequence Analysis
Protein
Software
Tandem Mass Spectrometry
Curr Protoc Bioinformatics
Chapter 13
http://dx.doi.org/10.1002/0471250953.bi1310s25
Biochemistry
De novo sequencing is an effective method for identifying unknown peptide sequences from their tandem mass spectra. This unit briefly introduces how this can be done manually. A protocol for using the PEAKS online software for automated de novo sequencing is described. Finally, we show how to use the PEAKS scores to validate the de novo sequencing results.
Published as part of Chapter 13 (Unit 13.10) of <em>Current Protocols in Bioinformatics</em>.
https://ir.lib.uwo.ca/biochempub/41
oai:ir.lib.uwo.ca:vascularpub-1023
2010-07-18T23:59:27Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19287092
Loss-of-function Variants in Endothelial Lipase Are a Cause of Elevated HDL Cholesterol in Humans
Edmondson, Andrew C.
Brown, Robert J.
Kathiresan, Sekar
Cupples, L. Adrienne
Demissie, Serkalem
Manning, Alisa Knodle
Jensen, Majken K.
Rimm, Eric B.
Wang, Jian
Rodrigues, Amrith
Bamba, Vaneeta
Khetarpal, Sumeet A.
Wolfe, Megan L.
Derohannessian, Stephanie
Li, Mingyao
Reilly, Muredach P.
Aberle, Jens
Evans, David
Hegele, Robert A.
Rader, Daniel J.
Article
2009-04-01T07:00:00Z
Adult
Aged
Amino Acid Substitution
Animals
Atherosclerosis
Cholesterol
HDL
Cohort Studies
Cross-Sectional Studies
Exons
Female
Genetic Variation
Humans
Lipase
Male
Mice
Mice
Inbred C57BL
Mice
Knockout
Middle Aged
Mutation
Polymorphism
Single Nucleotide
Sequence Deletion
Journal of Clinical Investigation
119
4
1042
1050
http://dx.doi.org/10.1172/JCI37176
Endocrinology, Diabetes, and Metabolism
Elevated plasma concentrations of HDL cholesterol (HDL-C) are associated with protection from atherosclerotic cardiovascular disease. Animal models indicate that decreased expression of endothelial lipase (LIPG) is inversely associated with HDL-C levels, and genome-wide association studies have identified LIPG variants as being associated with HDL-C levels in humans. We hypothesized that loss-of-function mutations in LIPG may result in elevated HDL-C and therefore performed deep resequencing of LIPG exons in cases with elevated HDL-C levels and controls with decreased HDL-C levels. We identified a significant excess of nonsynonymous LIPG variants unique to cases with elevated HDL-C. In vitro lipase activity assays demonstrated that these variants significantly decreased endothelial lipase activity. In addition, a meta-analysis across 5 cohorts demonstrated that the low-frequency Asn396Ser variant is significantly associated with increased HDL-C, while the common Thr111Ile variant is not. Functional analysis confirmed that the Asn396Ser variant has significantly decreased lipase activity both in vitro and in vivo, while the Thr111Ile variant has normal lipase activity. Our results establish that loss-of-function mutations in LIPG lead to increased HDL-C levels and support the idea that inhibition of endothelial lipase may be an effective mechanism to raise HDL-C.
https://ir.lib.uwo.ca/vascularpub/23
oai:ir.lib.uwo.ca:vascularpub-1022
2009-12-21T01:20:43Z
publication:vascularpub
publication:pmid
publication:faculties
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19295657
Novel LPL Mutations Associated with Lipoprotein Lipase Deficiency: Two Case Reports and a Literature Review
Rahalkar, Amit R.
Giffen, Fiona
Har, Bryan
Ho, Josephine
Morrison, Katherine M.
Hill, John
Wang, Jian
Hegele, Robert A.
Joy, Tisha
Article
2009-03-01T08:00:00Z
Amino Acid Sequence
Child
Diagnosis
Differential
Exons
Gene Therapy
Humans
Infant
Lipoprotein Lipase
Male
Molecular Sequence Data
Mutation
Canadian Journal of Physiology and Pharmacology
87
3
151
160
10.1139/Y09-005
Medical Physiology
Lipoprotein lipase (LPL) is a key enzyme involved with hydrolysis and removal of triglycerides from plasma. LPL deficiency is a rare condition with an estimated prevalence of 1 in 106. It is characterized biochemically by elevated triglycerides and lowered HDL in the plasma and clinically by a constellation of signs and symptoms during childhood including failure to thrive, lipemia retinalis, eruptive xanthomas, hepatosplenomegaly, and acute pancreatitis. Nearly 100 mutations in the LPL gene have been associated with LPL deficiency. Here we report 2 unrelated pedigrees with LPL deficiency from 2 novel disease-causing LPL mutations: a Gly159Glu missense mutation in exon 5 and a 4-bp ACGG deletion at the 3' boundary of exon 2. We present molecular findings of these 2 cases and review the biochemical, clinical, and genetic features of LPL deficiency.
https://ir.lib.uwo.ca/vascularpub/22
oai:ir.lib.uwo.ca:vascularpub-1025
2009-12-21T02:22:44Z
publication:vascularpub
publication:mnipub
publication:biophysicspub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biophysics
publication:biochempub
publication:mni
publication:robarts
publication:biochem
publication:institutes
19229059
Lipid Incorporation Inhibits Src-Dependent Assembly of Fibronectin and Type I Collagen by Vascular Smooth Muscle Cells
Frontini, Matthew J.
O'Neil, Caroline
Sawyez, Cynthia
Chan, Bosco M. C.
Huff, Murray W.
Pickering, J. Geoffrey
Article
2009-04-10T07:00:00Z
Atherosclerosis
Cell Line
Collagen Type I
Fibronectins
Foam Cells
Focal Adhesion Kinase 1
Focal Adhesions
Humans
Lipoproteins
LDL
Lipoproteins
VLDL
Microfilament Proteins
Muscle
Smooth
Vascular
Myocytes
Smooth Muscle
Particle Size
Phenotype
Phosphorylation
Receptors
Vitronectin
Signal Transduction
Time Factors
Transduction
Genetic
Vinculin
src-Family Kinases
Circulation Research
104
7
832
841
10.1161/CIRCRESAHA.108.187302
Medical Biochemistry
Medical Biophysics
Medical Immunology
A vital role of vascular smooth muscle cells (SMCs) is to stabilize the artery wall by elaborating fibrils of type I collagen. This is especially important in atherosclerotic lesions. However, SMCs in these lesions can be laden with lipids and the impact of this modification on collagen fibril formation is unknown. To address this, we converted human vascular SMCs to a foam cell state by incubating them with either LDL or VLDL. Biochemical markers of a SMC phenotype were preserved. However, microscopic tracking revealed a profound perturbation in the ability of the cells to assemble collagen fibrils, reducing assembly by up to 79%. This dysfunction was mirrored by an inability of smooth muscle foam cells to assemble fibronectin. Lipid-loaded SMCs did not display a generalized defect in the actin cytoskeleton and the formation of vinculin-containing focal adhesion complexes was preserved. However, lipid-loaded SMCs were unable to assemble fibrillar adhesion complexes and clustering of tensin and alpha5beta1 integrin was disordered. Moreover, phosphorylation of tensin, required for fibrillar adhesion complex formation, was suppressed by up to 57%, with a concomitant decrease in activation of Src and FAK and restriction of activated Src to the cell edges. Forced activation of Src-FAK signaling in lipid-engorged SMCs rescued both fibrillar adhesion formation and fibrillogenesis. We conclude that lipid accumulation by SMCs disables the machinery for collagen and fibronectin assembly. This previously unknown relationship between atherogenic lipids and integrin-based signaling could underlie plaque vulnerability.
https://ir.lib.uwo.ca/vascularpub/26
oai:ir.lib.uwo.ca:vascularpub-1024
2009-12-21T02:01:34Z
publication:vascularpub
publication:pmid
publication:faculties
publication:medpub
publication:med
publication:biochempub
publication:robarts
publication:biochem
publication:institutes
19060253
Determination of Lipoprotein(a) Kringle Repeat Number from Genomic DNA: Copy Number Variation Genotyping Using qPCR
Lanktree, Matthew B.
Rajakumar, Chandheeb
Brunt, J. Howard
Koschinsky, Marlys L.
Connelly, Philip W.
Hegele, Robert A.
Article
2009-04-01T07:00:00Z
Alleles
Base Sequence
DNA
DNA Primers
Genetic Variation
Genotype
Humans
Kringles
Linkage Disequilibrium
Lipoprotein(a)
Minisatellite Repeats
Polymerase Chain Reaction
Journal of Lipid Research
50
4
768
772
10.1194/jlr.D800050-JLR200
Biochemistry
Molecular Biology
Plasma lipoprotein(a) [Lp(a)] concentration is related to risk of cardiovascular disease. The defining protein component of Lp(a) particles, apolipoprotein(a) [apo(a)], is encoded by the LPA gene. Apo(a) is extremely heterogeneous in size due to a common copy number variation, leading to a variable number of kringle-IV type 2 (KIV2)-like domains. Alleles with fewer KIV2 repeats, encoding smaller apo(a) isoforms, are associated with higher plasma Lp(a) concentrations. Two principal methods to detect variation in KIV2 repeat number are electrophoresis with immunoblotting to detect apo(a) protein isoforms or pulse-field electrophoresis of unamplified genomic DNA to detect the variation of the LPA gene. Both methods are technically challenging, laborious, and time consuming. Here, we report a rapid method to determine the number of KIV2 repeats in LPA from genomic DNA using quantitative real-time polymerase chain reaction (qPCR). With qPCR, we found KIV2 repeat number was correlated with both apo(a) isoform size as determined by immunoblotting (r(s) = 0.50, P < 1 x 10(-6)) and with plasma Lp(a) concentration (r(s) = 0.30, P < 1 x 10(-6)). The qPCR technique permits rapid evaluation of apo(a) size from genomic DNA, and thus would provide an adjunctive genomic variable, in addition to LPA single nucleotide polymorphisms, for evaluating the genetic determinants of plasma Lp(a) concentration in genetic epidemiology studies of cardiovascular disease outcomes.
https://ir.lib.uwo.ca/vascularpub/24
oai:ir.lib.uwo.ca:biochempub-1046
2009-12-22T00:05:23Z
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
19188443
Evidence for Regulation of Mitotic Progression through Temporal Phosphorylation and Dephosphorylation of CK2{alpha}
St-Denis, Nicole A.
Derksen, D. Richard
Litchfield, David W.
Article
2009-04-01T07:00:00Z
Animals
Binding Sites
Casein Kinase II
Cell Line
Cell Nucleus Division
Centrosome
Chromosome Segregation
Cytokinesis
Mice
Mitosis
Mitotic Spindle Apparatus
Phosphorylation
Molecular and Cellular Biology
29
8
2068
2081
http://dx.doi.org/10.1128/MCB.01563-08
Biochemistry
Proper mitotic progression is crucial for maintenance of genomic integrity in proliferating cells and is regulated through an intricate series of events, including protein phosphorylation governed by a complex network of protein kinases. One kinase family implicated in the regulation of mitotic progression is protein kinase CK2, a small family of enzymes that is overexpressed in cancer and induces transformation in mice and cultured fibroblasts. CK2alpha, one isoform of the catalytic subunits of CK2, is maximally phosphorylated at four sites in nocodazole-treated cells. To investigate the effects of CK2alpha phosphorylation on mitotic progression, we generated phosphospecific antibodies against its mitotic phosphorylation sites. In U2OS cells released from S-phase arrest, these antibodies reveal that CK2alpha is most highly phosphorylated in prophase and metaphase. Phosphorylation gradually decreases during anaphase and becomes undetectable during telophase and cytokinesis. Stable expression of phosphomimetic CK2alpha (CK2alpha-4D, CK2alpha-4E) results in aberrant centrosome amplification and chromosomal segregation defects and loss of mitotic cells through mitotic catastrophe. Conversely, cells expressing nonphosphorylatable CK2alpha (CK2alpha-4A) show a decreased ability to arrest in mitosis following nocodazole treatment, suggesting involvement in the spindle assembly checkpoint. Collectively, these studies indicate that reversible phosphorylation of CK2alpha requires precise regulation to allow proper mitotic progression.
https://ir.lib.uwo.ca/biochempub/44
oai:ir.lib.uwo.ca:biochempub-1045
2009-12-21T23:58:48Z
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
19150402
SAP Binds to CD22 and Regulates B Cell Inhibitory Signaling and Calcium Flux
Ostrakhovitch, Elena A.
Wang, Yefu
Li, Shawn S.-C.
Article
2009-04-01T07:00:00Z
Amino Acid Motifs
Animals
Antigens
CD22
B-Lymphocytes
Burkitt Lymphoma
Calcium Signaling
Cisplatin
Gene Expression Regulation
Herpesvirus 4
Human
Humans
Immunoglobulin M
Intracellular Signaling Peptides and Proteins
Mice
Mice
Inbred C57BL
Phosphorylation
Protein Binding
Protein Processing
Post-Translational
Protein-Tyrosine Kinases
Specific Pathogen-Free Organisms
T-Lymphocytes
Cellular Signalling
21
4
540
550
http://dx.doi.org/10.1016/j.cellsig.2008.12.006
Biochemistry
The signaling lymphocyte activation molecule (SLAM)-associated protein (SAP or SH2D1A) is an important regulator of immune function which, when mutated or deleted, causes the X-linked lymphoproliferative syndrome (XLP). Because B cell lymphoma is a major phenotype of XLP, it is important to understand the function of SAP in B cells. Here we report that SAP is expressed endogenously in mouse splenic B cells, is inducibly expressed in the human BJAB cells, and co-localizes and interacts with CD22. We also show that SAP binding to the inhibitory immunoreceptor CD22 regulates calcium mobilization in B cells. Moreover, forced expression of SAP leads to constitutive CD22 tyrosine phosphorylation and decreased Ca(2+) response in B cells. Biochemical analysis reveals that, in response to IgM cross-linking, the phosphorylation of Syk, Blnk, or PLCgamma2 and their interactions with one another were either diminished or completely abolished in SAP-expressing cells compared to cells that lack SAP. Collectively our work identifies a novel role for SAP in B cells and extends its function to inhibitory immunoreceptor signaling and calcium mobilization.
https://ir.lib.uwo.ca/biochempub/43
oai:ir.lib.uwo.ca:chempub-1004
2009-12-21T23:52:59Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19388688
Molecular Dynamics Simulations of Electrosprayed Water Nanodroplets: Internal Potential Gradients, Location of Excess Charge Centers, and “Hopping” Protons
Ahadi, Elias
Konermann, Lars
Article
2009-05-21T07:00:00Z
Diffusion
Models
Molecular
Molecular Conformation
Nanoparticles
Protons
Reproducibility of Results
Solvents
Spectrometry
Mass
Electrospray Ionization
Static Electricity
Water
Journal of Physical Chemistry B
Journal of Physical Chemistry B
113
20
7071
7080
10.1021/jp810599f
Biochemistry
Chemistry
Water nanodroplets charged with excess protons play a central role during electrospray ionization (ESI). In the current study molecular dynamics (MD) simulations were used for gaining insights into the nanodroplet behavior based on classical mechanics. The SPC/E water model was modified to permit the inclusion of protons as highly mobile point charges at minimum computational cost. A spherical trapping potential was assigned to every SPC/E oxygen, thereby allowing the formation of protonated water molecules. Within a tightly packed nanodroplet the individual potential wells merge to form a three-dimensional energy landscape that facilitates rapid proton hopping between water molecules. This approach requires short-range modifications to the standard Coulomb potential for modeling electrostatic proton-water interactions. Simulations on nanodroplets consisting of 1248 water molecules and 10 protons (radius, ca. 21 A) result in a proton diffusion coefficient that is in agreement with the value measured in bulk solution. Radial proton distributions extracted from 1 ns MD runs exhibit a large peak around 14 A, in addition to substantial population density closer to the droplet center. Similar radial distributions were found for nanodroplets charged with Na+ ions. This behavior is dramatically different from that expected on the basis of continuum electrostatic theory, which predicts that excess charge should be confined to a thin layer on the droplet surface. One important contributor to this effect seems to be the ordering of water molecules at the liquid/vacuum interface. This ordering results in an electrical double layer, generating a potential gradient that tends to pull positive charge carriers (such as protons, but also others such as Na+ ions) toward the droplet interior. This deviation from the widely assumed surface charge paradigm could have implications for the mechanism by which protonated analyte ions are formed during ESI.
https://ir.lib.uwo.ca/chempub/5
oai:ir.lib.uwo.ca:biochempub-1047
2011-09-06T02:14:05Z
publication:physpharmpub
publication:paed
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:biochem
publication:paedpub
19774083
Loss of ATRX in Chondrocytes Has Minimal Effects on Skeletal Development
Solomon, Lauren A.
Li, Jennifer R.
Bérubé, Nathalie G.
Beier, Frank
Article
2009-09-23T07:00:00Z
Genetics
Genomics
Developmental Biology
PLoS ONE
4
9
7106
7106
http://dx.doi.org/10.1371/journal.pone.0007106
Biochemistry
Medical Physiology
Pediatrics
<p>BACKGROUND: Mutations in the human ATRX gene cause developmental defects, including skeletal deformities and dwarfism. ATRX encodes a chromatin remodeling protein, however the role of ATRX in skeletal development is currently unknown. METHODOLOGY/PRINCIPAL FINDINGS: We induced Atrx deletion in mouse cartilage using the Cre-loxP system, with Cre expression driven by the collagen II (Col2a1) promoter. Growth rate, body size and weight, and long bone length did not differ in Atrx(Col2cre) mice compared to control littermates. Histological analyses of the growth plate did not reveal any differences between control and mutant mice. Expression patterns of Sox9, a transcription factor required for cartilage morphogenesis, and p57, a marker of cell cycle arrest and hypertrophic chondrocyte differentiation, was unaffected. However, loss of ATRX in cartilage led to a delay in the ossification of the hips in some mice. We also observed hindlimb polydactily in one out of 61 mutants. CONCLUSIONS/SIGNIFICANCE: These findings indicate that ATRX is not directly required for development or growth of cartilage in the mouse, suggesting that the short stature in ATR-X patients is caused by defects in cartilage-extrinsic mechanisms.</p>
https://ir.lib.uwo.ca/biochempub/45
oai:ir.lib.uwo.ca:chempub-1003
2009-12-21T23:47:28Z
publication:pmid
publication:faculties
publication:biochempub
publication:chempub
publication:biochem
publication:chem
19374432
Protein Oxidative Modifications During Electrospray Ionization: Solution Phase Electrochemistry or Corona Discharge-Induced Radical Attack?
Boys, Brian L.
Kuprowski, Mark C.
Noël, James J.
Konermann, Lars
Article
2009-05-15T07:00:00Z
Electrochemistry
Electrolysis
Hemoglobins
Hydroxyl Radical
Oxidation-Reduction
Proteins
Reactive Oxygen Species
Spectrometry
Mass
Electrospray Ionization
Analytical Chemistry
Analytical Chemistry
81
10
4027
4034
10.1021/ac900243p
Biochemistry
Chemistry
The exposure of solution-phase proteins to reactive oxygen species (ROS) causes oxidative modifications, giving rise to the formation of covalent +16 Da adducts. Electrospray ionization (ESI) mass spectrometry (MS) is the most widely used method for monitoring the extent of these modifications. Unfortunately, protein oxidation can also take place as an experimental artifact during ESI, such that it may be difficult to assess the actual level of oxidation in bulk solution. Previous work has demonstrated that ESI-induced oxidation is highly prevalent when operating at strongly elevated capillary voltage V(0) (e.g., +8 kV) and with oxygen nebulizer gas in the presence of a clearly visible corona discharge. Protein oxidation under these conditions is commonly attributed to OH radicals generated in the plasma of the discharge. On the other hand, charge balancing oxidation reactions are known to take place at the metal/liquid interface of the emitter. Previous studies have not systematically explored whether such electrochemical processes could be responsible for the formation of oxidative +16 Da adducts instead of (or in combination with) plasma-generated ROS. Using hemoglobin as a model system, this work illustrates the occurrence of extensive protein oxidation even under typical operating conditions (e.g., V(0) = 3.5 kV, N(2) nebulizer gas). Surprisingly, measurements of the current flowing in the ESI circuit demonstrate that a weak corona discharge persists for these relatively gentle settings. On the basis of comparative experiments with nebulizer gases of different dielectric strength, it is concluded that ROS generated under discharge conditions are solely responsible for ESI-induced protein oxidation. This result is corroborated through off-line electrolysis experiments designed to mimic the electrochemical processes taking place during ESI. Our findings highlight the necessity of using easily oxidizable internal standards in biophysical or biomedical ESI-MS studies where knowledge of protein oxidation in bulk solution is desired. Strategies for eliminating ESI-induced oxidation artifacts are discussed.
https://ir.lib.uwo.ca/chempub/4
oai:ir.lib.uwo.ca:biochempub-1048
2009-12-23T20:23:47Z
publication:oncpub
publication:pmid
publication:faculties
publication:biochempub
publication:biochem
publication:onc
19387552
Protein Kinase CK2 in Health and Disease: From Birth to Death: The Role of Protein Kinase CK2 in the Regulation of Cell Proliferation and Survival
St-Denis, N. A.
Litchfield, D. W.
Article
2009-06-01T07:00:00Z
Animals
Apoptosis
Casein Kinase II
Cell Cycle
Cell Proliferation
Cell Survival
Humans
Phosphorylation
Signal Transduction
Virus Diseases
Virus Replication
Cellular and Molecular Life Sciences
66
11-12
1817
1829
http://dx.doi.org/10.1007/s00018-009-9150-2
Biochemistry
Oncology
Protein kinase CK2 is a serine/threonine kinase with a multitude of protein substrates. The enzyme is ubiquitously expressed in mammalian cells, where it functions in a variety of cellular processes, including cell cycle progression, apoptosis, transcription, and viral infection. While the importance of CK2 in the mammalian life cycle is undisputed, the regulatory mechanisms coordinating its numerous functions remain elusive. In this review, we focus on the various roles of CK2 in the mammalian cell, with particular attention on its functions through the stages of the cell cycle and during the decision to undergo cell death. We highlight how these roles are controlled in part through direct transcriptional regulation by CK2, and how the constitutive activity of CK2 can be hijacked in the case of viral infection. Finally, we discuss possible ways in which these functions are integrated to allow the cell to respond appropriately in the presence of multiple signals.
https://ir.lib.uwo.ca/biochempub/46
oai:ir.lib.uwo.ca:biochempub-1049
2023-03-16T14:02:16Z
publication:physpharmpub
publication:surgerypub
publication:pmid
publication:faculties
publication:physpharm
publication:biochempub
publication:surgery
publication:biochem
19331810
Keloid Scarring, but Not Dupuytren's Contracture, Is Associated with Unexplained Carotid Atherosclerosis
Bhavsar, Sankalp
Nimigan, Andre
Hackam, Daniel G.
O'Gorman, David B.
Gan, Bing Siang
Spence, J. David
Article
2009-01-01T08:00:00Z
Aged
Carotid Artery Diseases
Dupuytren Contracture
Female
Humans
Keloid
Male
Middle Aged
Multivariate Analysis
Regression Analysis
Risk Factors
Clinical & Investigative Medicine
32
2
95
102
Biochemistry
Surgery
<p>BACKGROUND: Atherosclerosis, a response to injury, may be thought of as scarring in the artery wall. TGF-beta and associated signaling molecules have been implicated in the pathophysiology of keloid scarring, Dupuytren's Contracture and atherosclerotic plaques in independent studies. PURPOSE: To test the hypothesis that excess cutaneous scarring and Dupuytren's contractures predispose independently to carotid atherosclerosis . METHODS: Among 1,747 patients with plaque measurements and complete data for multivariable regression analysis, 57 Caucasian patients had Dupuytren's contractures and 12 had keloid scars. Carotid total plaque area (TPA) was measured by 2-Dimensional ultrasound. RESULTS: In linear multivariable regression analysis with coronary risk factors, keloid scars were associated with TPA (P= 0.018), but Dupuytren's contractures were not. Patients with keloid scarring were younger (P < 0.0001), and more likely to be diabetic (P < 0.0001) CONCLUSIONS: Keloid scarring is a clinical clue to excess atherosclerosis not explained by traditional risk factors. Such patients may benefit from therapy directed at targets related to signalling molecules common to both the process of keloid scarring and atherosclerosis. These findings suggest previously unexplored possibilities for the prevention and treatment of atherosclerosis. The differences between Dupuytren's and keloid scars that may identify such targets are discussed.</p>
https://ir.lib.uwo.ca/biochempub/47
oai:ir.lib.uwo.ca:physpharmpub-1027
2009-12-23T21:07:48Z
publication:biophysicspub
publication:physpharmpub
publication:surgerypub
publication:pmid
publication:faculties
publication:physpharm
publication:biophysics
publication:biochempub
publication:biochem
publication:surgery
19331809
An Alternative Kinase Activity Assay for Primary Cultures Derived from Clinical Isolates
McLean, Kristopher
Wu, Yan
Gan, Bing Siang
O'Gorman, David B.
Article
2009-01-01T08:00:00Z
Biological Assay
Biotinylation
Cells
Cultured
Humans
Peptides
Phosphorylation
Proto-Oncogene Proteins c-akt
Reproducibility of Results
Spectrometry
Mass
Matrix-Assisted Laser Desorption-Ionization
Clinical & Investigative Medicine
Clinical & Investigative Medicine
32
2
84
94
Medical Biochemistry
Medical Biophysics
Medical Physiology
Surgery
PURPOSE: The measurement of protein kinase activity is central to understanding the signaling pathways that regulate cellular proliferation and apoptosis in virtually all disease processes. These measurements typically involve either indirect, time consuming assessment methods that require large amounts of sample, such as western immunoblotting, or the use of high maintenance, specialized equipment not typically available to a small clinical research facility. The purpose of this project was to determine if a benchtop Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) unit could be used to detect and directly assess kinase activity of the serine/threonine kinase Akt.
METHOD: Biotinylated substrate peptides, predicted to be recognized and phosphorylated by Akt to varying extents, were incubated in crude lysates of primary cells derived directly from clinical isolates. Streptavidin-coated chips were then used to isolate the substrate peptides from the lysates after incubation. Finally SELDI-TOF-MS was used to detect the peptide substrates and identify any changes in mass resulting from phosphorylation.
RESULTS: The biotinylated peptide substrates were readily detected and a simple, rapid procedure that allows direct measurement of Akt activity in less than 1 microg of cell lysate in a 2microL volume was developed. Further, a linear correlation between native to phospho-peptide ratios and SELDI-TOF-MS output demonstrated that this approach is semi-quantitative.
CONCLUSION: This assay avoids many of the pitfalls associated with the currently available kinase protocols as well as labour-intensive mass-spectrometry analysis by specialist laboratories. We propose that this approach may be a viable alternative for clinical research laboratories aiming to measure the activity of kinases in clinical isolates.
https://ir.lib.uwo.ca/physpharmpub/25
813709/qualified-dublin-core/100//