Scientific Release 6 December 2013 A*Star Scientists
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Daniel Bernstein, MD Associate Dean for Curriculum and Scholarship Stanford University School of Medicine Alfred Woodley Salter and Mabel G
RESEARCHER PROFILES Daniel Bernstein, MD Associate Dean for Curriculum and Scholarship Stanford University School of Medicine Alfred Woodley Salter and Mabel G. Salter Endowed Professor of Pediatrics (Cardiology) Stanford University Former Division Chief, Pediatric Cardiology Former Director, Children’s Heart Center, Lucile Packard Children’s Hospital at Stanford EMAIL [email protected] PROFILE med.stanford.edu/profiles/Daniel-Bernstein LAB murinecvcore.stanford.edu CURRENT RESEARCH EDUCATION/TRAINING Our recent work has focused on the mechanism by which mutations in sarcomeric proteins such MD New York University as myosin lead to the clinical phenotypes of hypertrophic cardiomyopathy (HCM). Utilizing human induced pluripotent stem cell-derived cardiomyocytes, with mutations induced by CRISPR/Cas9 PEDIATRICS RESIDENCY Montefiore Medical Center gene editing, we are undertaking a multi-scale approach ranging from structural and function studies on the single myosin molecule, to the individual myofibril, to whole cells and to microengineered MEDICAL EDUCATION FELLOWSHIP Albert Einstein College of Medicine tissues. To better understand cardiomyocyte mechano-transduction, we are applying FRET sensors in critical sarcomeric and junctional proteins. We are also studying a large biobank of myocardial PEDIATRIC CARDIOLOGY FELLOWSHIP UCSF samples from patients with HCM, combining transcriptomics and metabolomics with measurements of mitochondrial function to determine the degree to which HCM is a disease of altered cardiac BOARD CERTIFICATION Pediatrics, ABP energetics. These studies will allow us to correlate findings from hiPSC-CMs with actual patient samples. Another focus of our lab has been on the molecular mechanisms of RV hypertrophy Pediatric Cardiology, ABP and its transition to RV failure, and how this differs from LV failure. -
ELABELA, a Peptide Hormone for Heart Development
RESEARCH HIGHLIGHTS parasites and confirmed its role in OXA resistance by showing that RNA The cancer epigenome of mice and men interference knockdown of Smp_089320 in drug-sensitive parasites Genetically engineered mouse models (GEMMs) of human resulted in an increase in resistance. They found that the Smp_089320 disease rarely take into account epigenetic alterations, which protein in sensitive but not resistant strains showed sulfonation activity, contribute to many human cancers. Now, Stephen Tapscott and identifying a mechanism for the drug in which it acts as a sulfotrans- colleagues compare genome-wide patterns of cancer-specific ferase that activates OXA. Finally, the authors determined the crystal DNA methylation in human patients and three GEMMs of structure of Smp_089320 protein from sensitive parasites with OXA medulloblastoma (Epigenetics 8, 1254–1260, 2013). Using two bound and suggest that the mechanism of resistance involves disruption independent methods to measure CpG methylation, they find, of the drug-protein interaction in resistant strains. Comparative and in contrast to the hypermethylation patterns previously observed phylogenetic analysis with other schistosomes also suggests the basis in patients with medulloblastoma, that GEMMs had only modest for the species specificity in OXA drug action. OB increase in CpG methylation of gene promoters relative to wild- type controls. Whereas a human medulloblastoma tumor sample showed >60% increase in methylation at 121 loci, consistent ELABELA, a peptide hormone for heart with the authors’ previous work, there were only 0–16 such loci development in the GEMMs. They further extend these findings to mouse models of Burkitt lymphoma and breast cancer, which showed Bruno Reversade and colleagues identify a highly conserved gene encod- similar results. -
DPP9 Is an Endogenous and Direct Inhibitor of the NLRP1 Inflammasome That Guards Against Human Auto-Inflammatory Diseases
bioRxiv preprint doi: https://doi.org/10.1101/260919; this version posted February 7, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. DPP9 is an endogenous and direct inhibitor of the NLRP1 inflammasome that guards against human auto-inflammatory diseases Franklin L. Zhong1,2,3,*, Kim Robinson2,3, Chrissie Lim1, Cassandra R. Harapas4, Chien- Hsiung Yu4, William Xie2, Radoslaw M. Sobota1, Veonice Bijin Au1, Richard Hopkins1, John E. Connolly1,6,7, Seth Masters4,5 , Bruno Reversade1,2,8,9,10 *, # 1. Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore 138673 2. Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, Singapore 138648 3. Skin Research Institute of Singapore (SRIS), 8A Biomedical Grove, Immunos, Singapore 138648 4. Inflammation division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. 5. Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010 Australia 6. Institute of Biomedical Studies, Baylor University, Waco, Texas 76712, USA 7. Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545 8. Reproductive Biology Laboratory, Obstetrics and Gynaecology, Academic Medical Center (AMC), Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, Netherlands 9. Department of Paediatrics, National University of Singapore, 1E Kent Ridge Road, Singapore 119228 10. Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey * Corresponding authors. F.L.Z., [email protected]; B.R., [email protected] # Lead contact 1 bioRxiv preprint doi: https://doi.org/10.1101/260919; this version posted February 7, 2018. -
Computational Analysis Predicts Hundreds of Coding Lncrnas in Zebrafish
biology Communication Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish Shital Kumar Mishra 1,2 and Han Wang 1,2,* 1 Center for Circadian Clocks, Soochow University, Suzhou 215123, China; [email protected] 2 School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China * Correspondence: [email protected] or [email protected]; Tel.: +86-512-6588-2115 Simple Summary: Noncoding RNAs (ncRNAs) regulate a variety of fundamental life processes such as development, physiology, metabolism and circadian rhythmicity. RNA-sequencing (RNA- seq) technology has facilitated the sequencing of the whole transcriptome, thereby capturing and quantifying the dynamism of transcriptome-wide RNA expression profiles. However, much remains unrevealed in the huge noncoding RNA datasets that require further bioinformatic analysis. In this study, we applied six bioinformatic tools to investigate coding potentials of approximately 21,000 lncRNAs. A total of 313 lncRNAs are predicted to be coded by all the six tools. Our findings provide insights into the regulatory roles of lncRNAs and set the stage for the functional investigation of these lncRNAs and their encoded micropeptides. Abstract: Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Citation: Mishra, S.K.; Wang, H. Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool Computational Analysis Predicts (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify Hundreds of Coding lncRNAs in 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted Zebrafish. -
Novel Mutations in the Ciliopathy-Associated Gene CPLANE1 (C5orf42) Cause OFD Syndrome Type VI Rather Than Joubert Syndrome
Accepted Manuscript Novel mutations in the ciliopathy-associated gene CPLANE1 (C5orf42) cause OFD syndrome type VI rather than Joubert syndrome Carine Bonnard, Mohammad Shboul, Seyed Hassan Tonekaboni, Alvin Yu Jin Ng, Sumanty Tohari, Kakaly Ghosh, Angeline Lai, Jiin Ying Lim, Ene Choo Tan, Louise Devisme, Morgane Stichelbout, Adila Alkindi, Nazreen Banu, Zafer Yüksel, Jamal Ghoumid, Nadia Elkhartoufi, Lucile Boutaud, Alessia Micalizzi, Maggie Siewyan Brett, Byrappa Venkatesh, Enza Maria Valente, Tania Attié-Bitach, Bruno Reversade, Ariana Kariminejad PII: S1769-7212(17)30410-X DOI: 10.1016/j.ejmg.2018.03.012 Reference: EJMG 3440 To appear in: European Journal of Medical Genetics Received Date: 30 June 2017 Revised Date: 28 March 2018 Accepted Date: 28 March 2018 Please cite this article as: C. Bonnard, M. Shboul, S.H. Tonekaboni, A.Y.J. Ng, S. Tohari, K. Ghosh, A. Lai, J.Y. Lim, E.C. Tan, L. Devisme, M. Stichelbout, A. Alkindi, N. Banu, Z. Yüksel, J. Ghoumid, N. Elkhartoufi, L. Boutaud, A. Micalizzi, M.S. Brett, B. Venkatesh, E.M. Valente, T. Attié-Bitach, B. Reversade, A. Kariminejad, Novel mutations in the ciliopathy-associated gene CPLANE1 (C5orf42) cause OFD syndrome type VI rather than Joubert syndrome, European Journal of Medical Genetics (2018), doi: 10.1016/j.ejmg.2018.03.012. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. -
Endothelial Cell Dynamics in Vascular Development: Insights from Live-Imaging in Zebrafish
fphys-11-00842 July 20, 2020 Time: 12:10 # 1 REVIEW published: 22 July 2020 doi: 10.3389/fphys.2020.00842 Endothelial Cell Dynamics in Vascular Development: Insights From Live-Imaging in Zebrafish Kazuhide S. Okuda1,2 and Benjamin M. Hogan1,2,3* 1 Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia, 2 Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia, 3 Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, VIC, Australia The formation of the vertebrate vasculature involves the acquisition of endothelial cell identities, sprouting, migration, remodeling and maturation of functional vessel networks. To understand the cellular and molecular processes that drive vascular development, live-imaging of dynamic cellular events in the zebrafish embryo have proven highly informative. This review focusses on recent advances, new tools and new insights from imaging studies in vascular cell biology using zebrafish as a model system. Keywords: vasculogenesis, angiogenesis, lymphangiogenesis, anastomosis, endothelial cell, zebrafish Edited by: INTRODUCTION Elizabeth Anne Vincent Jones, KU Leuven, Belgium Vascular development is an early and essential process in the formation of a viable vertebrate Reviewed by: embryo. Blood and lymphatic vascular networks are composed of a complex mix of cell types: for Anna Rita Cantelmo, example smooth muscle cells, fibroblasts, pericytes and immune cells are intimately associated and Université Lille Nord de France, even integrated within mature vessel walls (Rouget, 1873; Horstmann, 1952; Nicosia and Madri, France 1987; Fantin et al., 2010; Gordon et al., 2010). The inner lining of the vasculature, made up of Jingjing Zhang, endothelial cells (ECs), is the earliest part of the vasculature to develop in the embryo and is Affiliated Hospital of Guangdong Medical University, China instructive in recruiting other lineages and cell types as the vascular system matures. -
ELABELA and an ELABELA Fragment Protect Against AKI
BASIC RESEARCH www.jasn.org ELABELA and an ELABELA Fragment Protect against AKI † † ‡ Hong Chen,* Lin Wang, Wenjun Wang, Cheng Cheng,* Yu Zhang,* Yu Zhou, | † † Congyi Wang,§ Xiaoping Miao, Jiao Wang,* Chao Wang,* Jianshuang Li, Ling Zheng, and Kun Huang* *Tongji School of Pharmacy, §The Center for Biomedical Research, Tongji Hospital, and |School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; †Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China; and ‡Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri ABSTRACT Renal ischemia-reperfusion (I/R) injury is the most common cause of AKI, which associates with high mortality and has no effective therapy. ELABELA (ELA) is a newly identified 32-residue hormone pep- tide highly expressed in adult kidney. To investigate whether ELA has protective effects on renal I/R injury, we administered the mature peptide (ELA32) or the 11-residue furin-cleaved fragment (ELA11) to hypoxia-reperfusion (H/R)–injured or adriamycin-treated renal tubular cells in vitro.ELA32and ELA11 significantly inhibited the elevation of the DNA damage response, apoptosis, and inflammation in H/R-injured renal tubular cells and suppressed adriamycin-induced DNA damage response. Similarly, overexpression of ELA32 or ELA11 significantly inhibited H/R-induced cell death, DNA damage re- sponse, and inflammation. Notably, treatment of mice with ELA32 or ELA11 but not an ELA11 mutant with a cysteine to alanine substitution at the N terminus (AE11C) inhibited I/R injury-induced renal fibrosis, inflammation, apoptosis, and the DNA damage response and markedly reduced the renal tubular lesions and renal dysfunction. -
Media Release for Immediate Release
MEDIA RELEASE FOR IMMEDIATE RELEASE 22 May 2018 New genetic findings explain how embryos form arms and legs New discovery revises biologists’ understanding of how limbs and lungs develop in humans. The current understanding of limb and lung development in humans does not capture the full picture of the process, according to research published in Nature last week. This paper describes the importance of novel genes for limb development, and shows how perceived wisdom about the process was incomplete. An international group of clinicians and researchers from Singapore, Turkey, France, Portugal and India, studied five families with either limb malformations, or tetra-amelia syndrome that is characterised by the absence of lungs and all four limbs. They found that mutations in the RSPO2 gene lead to incomplete limb development. Until now, the RSPO proteins were believed to only work with their receptors called LGRs. Together, RSPO and LGRs were thought to allow limb formation by blocking two key enzymes ZNRF3 and RNF43. Or so we thought. The team then studied mice lacking all three LGRs required for RSPO2’s function, and found that contrary to what was expected they still developed limbs and lungs normally. This indicates that RSPO2 does not need LGRs — disproving the established understanding of how this is happening. “Our results establish that even without the LGR receptors, RSPO2, can bind to other molecules and constitute a master switch that governs limb development,” says Dr Emmanuelle Szenker-Ravi, a co-first author of the study based at Agency of Science, Technology and Research’s (A*STAR) Institute of Medical Biology (IMB) in Singapore. -
Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods
fgene-12-651485 May 6, 2021 Time: 11:28 # 1 MINI REVIEW published: 06 May 2021 doi: 10.3389/fgene.2021.651485 Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods Ravi Tharakan1* and Akira Sawa2,3 1 National Institute on Aging, National Institutes of Health, Baltimore, MD, United States, 2 Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States, 3 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and Edited by: conceptual challenges facing future micropeptide endeavors. Liangliang Sun, Keywords: micropeptides, miniproteins, proteogenomics, sORF, ribosome profiling, proteomics, genomics, RNA Michigan State University, sequencing United States Reviewed by: Yanbao Yu, INTRODUCTION J. Craig Venter Institute (Rockville), United States The sequencing and publication of complete genomic sequences of many organisms have aided Hongqiang Qin, the medical sciences greatly, allowing advances in both human genetics and the biology of human Dalian Institute of Chemical Physics, Chinese Academy of Sciences, China disease, as well as a greater understanding of the biology of human pathogens (Firth and Lipkin, 2013). -
Reduced ELABELA Expression Attenuates Trophoblast Invasion Through the PI3K/AKT/Mtor Pathway in Early Onset Preeclampsia T
Placenta 87 (2019) 38–45 Contents lists available at ScienceDirect Placenta journal homepage: www.elsevier.com/locate/placenta Reduced ELABELA expression attenuates trophoblast invasion through the PI3K/AKT/mTOR pathway in early onset preeclampsia T Lijing Wanga,b, Yan Zhangc, Hongmei Qud, Fengsen Xub, Haiyan Hub, Qian Zhangb, ∗ Yuanhua Yea,c, a Department of Obstetrics and Gynecology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266000, China b Department of Obstetrics, Qingdao Municipal Hospital, Qingdao, 266000, China c Department of Obstetrics, Affiliated Hospital of Qingdao University, Qingdao, 266000, China d Department of Obstetrics, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, China ARTICLE INFO ABSTRACT Keywords: Introduction: Early onset preeclampsia is linked to abnormal trophoblast invasion, leading to insufficient re- ELA casting of uterine spiral arteries and shallow placental implantation. This study investigated ELABELA (ELA) PI3K expression and its involvement in the pathogenesis of early onset preeclampsia. AKT Methods: We used immunohistochemistry, quantitative PCR and Western blot to calculate ELA levels in the Invasion placentas. Transwell assays were utilize to assess the invasion and migration of trophoblastic Cells. Western blot Preeclampsia was used to identify the concentrations of vital kinases in PI3K/AKT/mTOR pathways and invasion-related proteins in trophoblast cells. Results: ELA was expressed in villous cytotrophoblasts and syncytiotrophoblasts in placental tissue. Compared with the normal pregnancies, ELA mRNA and protein expression was significantly reduced in early onset pre- eclampsia placentas. In the HTR-8/SVneo cells, when ELA was knocked down, the invasion and migration capability of cells decreased significantly, with MMP2 and MMP9 expression downregulated and the expression of important kinases in the PI3K/AKT/mTOR pathways being significantly decreased compared to the control group. -
Neuralization of Dissociated Xenopus Cells Is Mediated by Ras/MAPK Activation
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION tive signals that act through Receptor Tyrosine kinases Default neural induction: (RTKs). Growth factors that signal via RTKs, such as neuralization of dissociated Fibroblast Growth Factor (FGF), Insulin-like Growth Factor (IGF), and Hepatocyte Growth Factor (HGF), are Xenopus cells is mediated potent neural inducers in vertebrates (Wilson and Edlund by Ras/MAPK activation 2001; De Robertis and Kuroda 2004; Stern 2004). RTK signaling activates the mitogen-activated protein kinase Hiroki Kuroda,1 Luis Fuentealba, Atsushi Ikeda, (MAPK) known as extracellular signal-regulated protein 2 kinase (ERK) via the Ras pathway, and in this way causes Bruno Reversade, and E.M. De Robertis neural induction. Howard Hughes Medical Institute and Department Two disparate views dominate the neural induction of Biological Chemistry, University of California, field at present. Work in the chick embryo has stressed Los Angeles, California 90095-1662, USA the importance of FGF signaling, whereas work in Xeno- pus has tended to emphasize the requirement for anti- Xenopus embryonic ectodermal cells dissociated for BMPs in neural induction (Harland 2000; Stern 2004). three or more hours differentiate into neural tissue in- We have argued that these apparently conflicting obser- stead of adopting their normal epidermal fate. This de- vations can be reconciled through a molecular mecha- nism in which Ras/MAPK phosphorylation regulates the fault type of neural induction occurs in the absence of BMP transducers Smad1/5/8 (De Robertis and Kuroda Spemann’s organizer signals and is thought to be caused 2004). -
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