News & Announcements
- Coming this winter: Analysis of -omics data
- Dr. Alain Stintzi's Research Group
- Dr. Ilona S. Skerjanc's Research Group
- Dr. Couture's Research Group
- Dr. Ilya Ioshikhes's Research Group
- Dr. Zemin Yao guest speaker at the National Yang Ming University, Taipei, September 2011
- The high impact factor journal, Proteomics, just published a key article by ‘Europe’s MIT’
- Srf1 Is a Novel Regulator of Phospholipase D Activity and is Essential to Buffer the Toxic Effects of C16:0 Platelet Activating Factor
- The University of Ottawa Emerging Pathogens Research Centre (EPRC) held a Symposium on World AIDS Day entitled, "The Rising Tide Of Emerging Infectious Diseases In An Immunocompromised World."
- The Office of International Research in collaboration with the department of BMI, received the visit of a delegation of the CIHR and the National Foundation of Natural Sciences of China (NSFC) at the University.
- A new interplay between two families of transcription factors controlling skeletal muscle differentiation
- Two novel cell techniques for human stem cell research developed by OISB/BMI scientists
- BMI offers new course on the analysis of -omics data
- BMI researchers have found the mystery of fragile human ES cells
- Nobel Prize Laureate in Chemistry, Dr. Aaron Ciechanover, visits the Faculty of Medicine, April 27, 2010
Dr. Alain Stintzi' Research Group
The research group led by Dr. Alain Stintzi, a scientist at the Ottawa Institute of Systems Biology and Department of BMI, has discovered a group of genes that control the bacterial virulence of Campylobacter jejuni (C. jejuni). Campylobacter jejuni is a common gastrointestinal pathogen in humans and a common commensal colonizer of poultry. C. jejuni lacks several common metabolic pathways and was therefore thought not to use fructose as a carbon source for growth. However, Dr. Stintzi’s group has recently identified a group of genes (cj0480c-cj0490) that allow C. jejuni to use fucose as a substrate for growth, thereby linking a new metabolic pathway in C. jejuni with its virulent lifestyle. Their work is published in the Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7194-9, and highlighted by the Consortium for Functional Glycomics (CFG) and Nature Publishing Group at http://www.functionalglycomics.org/fg/update/2011/110512/full/fg.2011.17.shtml.
Dr. Ilona S. Skerjanc' Research Group
The research group led by Dr. Ilona S. Skerjanc, a professor at the Department of BMI, has identified the first kinase that regulates the expression of two important muscle factors (namely MyoD and Myf5) in embryonic stem cells and muscle progenitor stem cells. In a recent publication at EMBO Journal (http://www.ncbi.nlm.nih.gov/pubmed/21556048), Dr. Al-Madhoun and his colleagues delineated the importance of MEF2C phosphorylation and the recruitment of histone acetyltransferases in the lineage specification of skeletal muscle. They further found a non-myosin phosphorylation substrate for the skeletal muscle myosin light chain kinase (skMLCK), which may control the replenishment of muscle stem cells.Their findings provide new insights into skeletal muscle development and have important impact on the clinical treatment.
Dr. Couture' Research Group
One of the long-standing questions in the field of chromatin biology is how histone-modifying enzymes are tethered to a specific promoter region. Dr. Couture laboratory at OISB and BMI has recently found that Ash2L, a protein interacting with the histone H3 lysine 4 methyltransferase MLL1, harbors a novel helix-wing-helix DNA binding domain that is needed for targeting and H3K4 trimethylation in vivo. Given that MLL1 is linked to acute forms of leukemia, these findings will eventually guide structure-based drug discoveries for the treatment of leukemia and other MLL-linked disorders. Their work is published in Nature Structural and Molecular Biology (Sarvan, et al. 2011 http://www.nature.com/nsmb/journal/v18/n7/full/nsmb.2093.html)
Click to enlarge the image!
Dr. Ilya Ioshikhes' Research Group
Precise positioning of nucleosomes along DNA is important for a variety of gene regulatory processes. Among the factors directing nucleosome positioning, the DNA sequence is highly important. Two main classes of nucleosome positioning sequence (NPS) patterns have previously been described.
In the present paper published in a high profile journal (GENOME RESERCH http://genome.cshlp.org/content/early/2011/06/30/gr.116228.110.full.pdf+html?sid=7f9706be-c931-441c-a524-9cea0ac564f0), a research group led by Dr. ILYA IOSHIKHES at OISB and BMI describe anti-NPS patterns. Anti-NPS patterns are inverse to the conventional NPS patterns by positioning of their key sequence elements (specific dinucleotides). Evidence for the biological relevance of anti-NPS patterns is presented. The new patterns are related to significant amount of nucleosomes, comparable to those described by the conventional patterns. These nucleosomes are relatively unstable and positioned predominantly in gene promoters, particularly at stress-induced genes. Involvement of the anti-NPS patterns in the computational nucleosome mapping leads to dramatic improvement of efficiency of such mapping comparing to those by the conventional NPS patterns alone. This finding will have significant impact on the genomic research.
Dr. Zemin Yao guest speaker at the National Yang Ming University, Taipei, September 2011
The high impact factor journal, Proteomics, just published a key article by ‘Europe’s MIT’
The high impact factor journal, Proteomics, just published a key article by ‘Europe’s MIT’ – the ETH university in Zurich, a review article that focuses heavily on the landmark article published by our Systems Biology collaboration between the Altosaar and Figeys laboratories: Wall ML, Wheeler HL, Smith JC, Figeys D, Altosaar I. 2010. Mass spectrometric analysis reveals remnants of host-pathogen molecular interactions at the starch granule surface in wheat endosperm. Phytopathology 100(9): 848-854, doi: 10.1094/PHYTO-100-9-0848. It was cited in: Bacterial adaptation to life in association with plants – A proteomic perspective from culture to in situ conditions. Claudia Knief, Nathanaël Delmotte and Julia A. Vorholt of the Institute of Microbiology, ETH Zurich, Switzerland, article first published online: 5 May 2011 | doi: 10.1002/pmic.201000818. Both articles are available by clicking here
Srf1 Is a Novel Regulator of Phospholipase D Activity and is Essential to Buffer the Toxic Effects of C16:0 Platelet Activating Factor
Development of Alzheimer disease is associated with accumulation of toxic lipids in patients’ brain. One of these lipids is C16:0 PAF. The research group led by Dr. Baetz at OISB and BMI has exploited yeast chemical genomics and proteomics to identify two proteins, the yeast phospholipase D (PLD) Spo14 and the novel protein Srf1, are essential for reducing the toxic effects of C16:0 PAF. They discovered that Srf1 is a novel regulator of PLD and that PLD activity is required to buffer the neurotoxic effect of C16:0 PAF in both yeast and human neuronal cells. Their findings will lead to the new therapeutic strategies in the treatment of Alzheimer disease (Kennedy, et al. PloS Genetics 2011)
Emerging Pathogens Research Centre (EPRC) - Symposium on World AIDS Day
The University of Ottawa Emerging Pathogens Research Centre (EPRC) held a Symposium on World AIDS Day entitled, "The Rising Tide Of Emerging Infectious Diseases In An Immunocompromised World." The event was attended by close to 100 people including 60 Ph.D. and M.Sc. students, members of EPRC and representatives from CIHR's Institute for Infection and Immunity, governmental departments, parliamentarians and the Honourable Dr. Keith Martin, Member of Parliament for the riding of Esquimault - Juan de Fuca, who presented a talk entitled "Translating Knowledge Into Action: Improving the health of the bottom 2 billion."
The photo shows (from right to left) Mr. Jason Tetro (co-coordinator of EPRC/CREM), Dr. Jun Wu (Public Health Agency of Canada), Dr. Earl Brown (Executive Director of EPRC), Dr. Susan Logan (NRC), Dr. Wangxue Chen (NRC) and Dr. Brent Dixon (Health Canada).
China - CIHR
The Office of International Research in collaboration with the department of BMI, received the visit of a delegation of the CIHR and the National Foundation of Natural Sciences of China (NSFC) at the University. During the presentations, it was highlighted the numerous research collaborations that uOttawa researchers have with Chinese institutions.
From Left
to right:
Mr. WEI Qin, Program Manager, Division of American, Oceanian and East European Affairs, Bureau of International Cooperation, NSFC
Dr. DONG Erdan, Executive Deputy Director-General, Department of Health Sciences, NSFC
Juan Sarmiento, Coordinator, Strategic Initiatives, Vice-President Research
Dr. Zemin Yao, professor and Chair, BMI
Dr. SHEN Yan, Vice-President, NSFC
A new interplay between two families of transcription factors controlling skeletal muscle differentiation
The research group led by Dr. Alexandre Blais, a scientist at the Ottawa Institute of Systems Biology and Department of BMI, has discovered a new interplay between two families of transcription factors. One group is called “Myogenic Regulatory Factors family” and a second group called “Six family of proteins”. The research team found that a crosstalk exists between the two families. Indeed, members of each family can work in synergy to activate the expression of common target genes. The authors show that this phenomenon is involved in controlling skeletal muscle differentiation. In addition, the scientists uncovered several new gene targets of Six factors. These new findings help understand the complex interplay of regulatory mechanisms that control gene expression during myogenesis. The work is published in the journal Nucleic Acids Research, 2010 Jul 2 (online) http://nar.oxfordjournals.org/cgi/content/full/gkq585
Two novel cell techniques for human stem cell research developed by OISB/BMI scientists
A fully-integrated proteomics platform, termed rare cell proteomic reactor, was developed by Dr. Daniel Figeys and Dr. Lisheng Wang, at Ottawa Institute of Systems Biology and Department of BMI, to study differentiation of human stem cells. The platform allows large-scale quantitative proteomic analysis with small number of cells. They also developed a cell culture medium that is specifically designed for cell differentiation and proteomics studies. Their work is published in Molecular & Cellular Proteomics (MCP) (online) on June 8, 2010.
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BMI offers new course on the analysis of -omics data
In the post-genomic era, sophisticated computational and statistical methods of analyzing transcriptomics and proteomics data are increasingly used to generate hypotheses and to draw scientific conclusions. Consequently, students need familiarity with such methods in order to critically read much of the literature and often in order to interpret their own data in graduate studies and in future research careers. The Biochemistry Graduate Program is now offering the following course to meet this growing need, starting Winter 2011.
BCH5101, Analysis of –omics data (3 credits)
Coordinator: David Bickel
Course description
Theoretical and practical aspects of various methods currently used to analyze the mountain of –omics data. Methods: sequence alignment and database searches, sequence analysis and bioinformatics of gene regulation, DNA microarray and sequencing technologies to identify transcription factor binding sites, analysis of proteomics data, statistical analysis of preprocessed gene expression and protein/metabolite abundance data, epidemiology applications. Improve students’ ability to critically read the literature and to make informed choices of methods for the analysis of their own data.
PrerequisitesBCH2333 and BCH3170 or approval of coordinator
Instructors
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BMI researchers have found the mystery of fragile human ES cells
Dr. Lisheng Wang a Scientist with the department of BMI has found the decade-old mystery of why human embryonic stem cells are so difficult to culture in the laboratory. The research is published in the Stem Cells journal (http://www.stemcells.com/view/0/index.html) and was one of the most downloaded papers in February 2010.
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Human embryonic stem cells (hESCs) can give rise to almost any type of cell present in the adult body. They represent an important tool in the field of regenerative medicine with the prospect of providing cures for various diseases. However, the mechanisms underlying hESC self-renewal (unlimited dividing) remain incompletely understood. Questions such as why single hESCs exhibit ~100-fold lower self-renewal capacity/cloning efficiency than single mouse embryonic stem cells remain unanswered. Recently, Dr. Wang’s laboratory at BMI provides the first demonstration that adhesion molecule E-cadherin is an important player in hESC self-renewal. A unique interplay between small G-protein Rap1 and E-cadherin along the endocytic recycling pathway serves as a timely and efficient mechanism to regulate hESC self-renewal (Stem Cells 2010. 28: 247-257).
Nobel Prize Laureate in Chemistry, Dr. Aaron Ciechanover, visits the Faculty of Medicine, April 27, 2010
On April 27th 2010, students and Postdoctoral fellows from the Department of Biochemistry, Microbiology and Immunology took part in an informal gathering/open forum discussion with Professor Aaron Ciechanover winner of the 2004 Nobel Prize in chemistry.
Professor Ciechanover, a Professor/Researcher with the Janet and David Polak Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology in Haifa Israel, was in Ottawa as a speaker for the New Horizons Lecture Series on: Intracellular proteolysis and the ubiquitin system: From the backyard of biomedical research to the forefront of the patient bed.
