Manipulation of Dietary Amino Acids Prevents and Reverses Obesity in Mice Through Multiple Mechanisms That Modulate
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
UCP1-Independent Thermogenesis in Brown/Beige Adipocytes: Classical Creatine Kinase/Phosphocreatine Shuttle Instead of “Futile Creatine Cycling”
UCP1-independent thermogenesis in brown/beige adipocytes: classical creatine kinase/phosphocreatine shuttle instead of “futile creatine cycling”. Theo Wallimann1*), Malgorzata Tokarska-Schlattner2) Laurence Kay2) and Uwe Schlattner2,3*) 1) Biology Dept. ETH-Zurich, Switzerland, emeritus, E-mail address: [email protected] 2) University Grenoble Alpes and Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics & SFR Environmental and Systems Biology, Grenoble, France, E-mail address: [email protected] 3) Institut Universitaire de France (IUF), Paris, France *) joint corresponding authors Abstract Various studies have identified creatine kinase (CK) and creatine (Cr) as important players for thermogenesis. More recently, they have been specifically linked to UCP1-independent thermogenesis in beige/brown adipocytes, and a “Cr-driven futile cycle” within mitochondria was proposed as the mechanistic basis. Here, we provide a critical appraisal of such a mechanism, which would require a rather undefined phosphocreatine phosphatase. As alternative explanation, we suggest instead that the well-known functions of the CK system, that is ATP buffering and shuttling of high-energy phosphocreatine (PCr) from sites of ATP generation to sites of ATP utilization, are also working in brown/beige adipocytes. There, the CK/PCr system would be shunted between ATP generation, at the mitochondria and/or glycolysis, and ATP hydrolysis at the ER/SR. This would largely facilitate high-throughput calcium pumping by the ATP-dependent Ca2+ pump (SERCA) as described also in skeletal and cardiac muscle. This very CK/PCr system would then support adipocyte SERCA2b function and, in tandem with adipocyte ryanodine receptor (RyR2) and/or inositol 1,4,5- 2+ triphosphate receptor (IP3-R3), facilitate thermogenic futile Ca cycling that has been described to operate in UCP1-independent, but ATP-dependent non-shivering thermogenesis. -
Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response To
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) BMJ Open Diab Res Care SUPPLEMEMTARY DATA Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response to Glucagon-like Peptide-1 Analogue Therapy in Type 2 Diabetes Mellitus Chia-Hung Lin, Yun-Shien Lee, Yu-Yao Huang, Chi-Neu Tsai List of supplemental Tables Supplemental Table S1 Demographic variables of 10 participants (training group) applied for DNA methylation chip at baselines Supplement Table S2 Demographic variables of participants (validation group) enrolled in this study Supplemental Table S3 Primers used for bisulfite sequencing primers (BSP), pyrosequencing reaction and centromeric CTCF polymorphism Supplemental Table S4 Differentially methylated regions (DMRs) in human genome and association with glycemic response of GLP-1 treatment in training group List of supplemental Figures Supplement Figure S1: A gender difference was identified in Infinium® MethylationEPIC BeadChip analysis in the training group of this study through volcano and heatmap plot. Supplemental Fig. S2: The volcano plots of the differentially methylation comparing responsive and non-responsive groups before and after GLP-1 analogue treatment. Supplemental Fig. S3: Serum level of TGF-1 as a predictor of a glycemic response to GLP-1 analogue treatment and the correlation of VTRNA2-1 RNA expression versus its promoter methylation status. Supplement Figure S4: The association between change in A1C and (A) VTRNA 2-1 methylation level, (B) TGF-beta1 levels, and (C) mRNA levels of VTRNA 2-1 Lin C-H, et al. -
Nrg4 and Gpr120 Signalling in Brown Fat Anthony Chukunweike OKOLO
Nrg4 and Gpr120 Signalling in Brown Fat Anthony Chukunweike OKOLO Institute of Reproductive and Developmental Biology Department of Surgery and Cancer Faculty of Medicine Imperial College London A thesis submitted in fulfilment of the requirements for award of the degree of Doctor of Philosophy 1 Statement of Originality All experiments included in this thesis were performed by me unless otherwise stated in the text. 2 Copyright statement The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Directive Licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, and they do not use it for commercial purposes, and they do not alter, transform or build upon it. For any re-use or re-distribution, researchers must make clear to others the licence terms of this work. 3 Acknowledgments I would like to thank my supervisors Dr Aylin Hanyaloglu and Dr Mark Christian for giving me the great opportunity to work in their labs. Aylin put in a great deal of effort especially in area of Gpr120 signalling, including having to guide me through the critical imaging procedures. Aylin and Mark contributed a great deal towards the final edition of this thesis. I would also like to thank Dr Mark Christian for bringing me to Imperial College London to start off my PhD in his laboratory, and for being a great mentor and a continuous source of knowledge for me. I am grateful for your enduring patience in trying to bring out the best in me and ensuring that I develop the ‘critical thinking’ that is needed as a scientist. -
GRIN3A and MAPT Stimulate Nerve Overgrowth in Macrodactyly
MOLECULAR MEDICINE REPORTS 14: 5637-5643, 2016 GRIN3A and MAPT stimulate nerve overgrowth in macrodactyly XU SHI1*, LU LU2*, XIU JIN3, BIN LIU4, XIGUANG SUN4, LAIJIN LU4 and YANFANG JIANG1,5 1Department of Genetic Diagnosis Center, Central Laboratory; Departments of 2Breast Surgery, 3Burn Surgery and 4Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130000; 5Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, Jilin 130000, P.R. China Received September 30, 2015; Accepted October 12, 2016 DOI: 10.3892/mmr.2016.5923 Abstract. As an uncommon and congenital condition, to abnormal nerve proliferation and underpin the pathogenesis macrodactyly is characterized by an increase in the size of all of macrodactyly, and provide potential application targets in the elements or structures of the digits or toes; however, the nerve tissue regeneration engineering. underlying pathogenesis remains to be fully elucidated. In the present study, the gene expression profiles of abnormal nerves Introduction were examined in three patients with macrodactyly using microarray analysis to identify potential genes contributing Macrodactyly is an uncommon congenital condition character- to nerve overgrowth. Gene expression profiling in the nerve ized by an increase in the size of all the elements or structures tissue samples were scanned using the microarray and the of the digits or toes, including phalanges, tendons, vessels, differentially expressed genes were verified at the transcrip- subcutaneous fat and finger nails. The malformation often tion level using reverse transcription-quantitative polymerase occurs unilaterally or asymmetrically and affects more than chain reaction analysis. Western blot analysis was used to one digit or toe. -
Structural Basis for Phosphorylation and Lysine Acetylation Cross-Talk In
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 289, NO. 37, pp. 25890–25906, September 12, 2014 © 2014 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Structural Basis for Phosphorylation and Lysine Acetylation Cross-talk in a Kinase Motif Associated with Myocardial Ischemia and Cardioprotection*□S Received for publication, February 4, 2014, and in revised form, June 29, 2014 Published, JBC Papers in Press, July 9, 2014, DOI 10.1074/jbc.M114.556035 Benjamin L. Parker‡§¶1, Nicholas E. Shepherdʈ2, Sophie Trefely§, Nolan J. Hoffman§¶, Melanie Y. Whiteʈ**2, Kasper Engholm-Keller**, Brett D. Hambly‡**, Martin R. Larsen‡‡, David E. James§¶**, and Stuart J. Cordwell‡ʈ**3 From the ‡Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney 2006, Australia, the §Diabetes and Obesity Program, ¶Biological Mass Spectrometry Unit, Garvan Institute of Medical Research, 2010 Australia , the ʈSchool of Molecular Bioscience and the **Charles Perkins Centre, University of Sydney, Sydney 2006, Australia, and the ‡‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark Background: Myocardial ischemia and cardioprotection induce signal networks mediated by post-translational modification. Results: Phosphorylation sites altered by ischemia and/or cardioprotection were influenced by inhibition of lysine acetylation consistent with cross-talk. Conclusion: Lysine acetylation induces proximal dephosphorylation in a kinase motif by salt bridge inhibition. Significance: Cross-talk is likely to be an important aspect of signaling during ischemia and cardioprotection. Myocardial ischemia and cardioprotection by ischemic pre- Prolonged blockage of coronary blood flow (ischemia), even conditioning induce signal networks aimed at survival or cell with subsequent restoration (reperfusion), may result in death if the ischemic period is prolonged. -
Parallel High Throughput RNA Interference Screens Identify PINK1
Author Manuscript Published OnlineFirst on January 17, 2011; DOI: 10.1158/0008-5472.CAN-10-2836 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Parallel High Throughput RNA interference Screens Identify PINK1 as a Potential Therapeutic Target for the Treatment of DNA Mismatch Repair Deficient Cancers Sarah A. Martin1,2,3,4 Madeleine Hewish1,2,4, David Sims2, 2 1,2 Christopher J. Lord * and Alan Ashworth * 1Cancer Research UK Gene Function and Regulation Group 2The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK 3Current address: Centre for Molecular Oncology and Imaging, Institute of Cancer, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, EC1M 6BQ 4Authors contributed equally to this work *Corresponding Authors: Christopher J. Lord & Alan Ashworth Email: [email protected], [email protected] Keywords: PINK1, oxidative damage, mitochondria, MLH1, MSH2, MSH6 Downloaded from cancerres.aacrjournals.org on October 1, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on January 17, 2011; DOI: 10.1158/0008-5472.CAN-10-2836 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. MMR and PINK1 synthetic lethality 2 Abstract Synthetic lethal approaches to cancer treatment have the potential to deliver relatively large therapeutic windows and therefore significant patient benefit. To identify potential therapeutic approaches for cancers deficient in DNA mismatch repair (MMR), we have carried out parallel high throughput RNA interference screens using tumour cell models of MSH2 and MLH1-related MMR deficiency. -
Bioinformatics Analysis of Mitochondrial Disease
BIOINFORMATICS ANALYSIS OF MITOCHONDRIAL DISEASE By Kieren Lythgow Bsc (Hons), MRes Thesis submitted to the University of Newcastle upon Tyne in candidature for the degree of Doctor of Philosophy 2010 Abstract Several bioinformatic methods have been developed to aid the identification of novel nuclear-mitochondrial genes involved in disease. Previous research has aimed to increase the sensitivity and specificity of these predictions through a combination of available techniques. This investigation shows the optimum sensitivity and specificity can be achieved by carefully selecting seven specific classifiers in combination. The results also show that increasing the number of classifiers even further can paradoxically decrease the sensitivity and specificity of a prediction. Additionally, text mining applications are playing a huge role in disease candidate gene identification providing resources for interpreting the vast quantities of biomedical literature currently available. A work- flow resource was developed identifying a number of genes potentially associated with Lebers Hereditary Optic Neuropathy (LHON). This included specific orthologues in mouse displaying a potential association to LHON not annotated as such in humans. Mitochondrial DNA (mtDNA) fragments have been transferred to the human nu- clear genome over evolutionary time. These insertions were compared to an existing database of 263 mtDNA deletions to highlight any associated mechanisms governing DNA loss from mitochondria. Flanking regions were also screened within the nuclear genome that surrounded these insertions for transposable elements, GC content and mitochondrial genes. No obvious association was found relating NUMTs to mtDNA deletions. NUMTs do not appear to be distributed throughout the genome via trans- position and integrate predominantly in areas of low %GC with low gene content. -
Association of Sequence Alterations in the Putative Promoter of RAB7L1 with a Reduced Parkinson Disease Risk
ORIGINAL CONTRIBUTION Association of Sequence Alterations in the Putative Promoter of RAB7L1 With a Reduced Parkinson Disease Risk Ziv Gan-Or, BMedSci; Anat Bar-Shira, PhD; Dvir Dahary, MSc; Anat Mirelman, PhD; Merav Kedmi, PhD; Tanya Gurevich, MD; Nir Giladi, MD; Avi Orr-Urtreger, MD, PhD Objective: To examine whether PARK16, which was re- Results: All tested SNPs were significantly associated with cently identified as a protective locus for Parkinson dis- PD (odds ratios=0.64-0.76; P=.0002-.014). Two of them, ease (PD) in Asian, white, and South American popula- rs1572931 and rs823144, were localized to the putative pro- tions, is also associated with PD in the genetically moter region of RAB7L1 and their sequence variations al- homogeneous Ashkenazi Jewish population. teredthepredictedtranscriptionfactorbindingsitesofCdxA, p300, GATA-1, Sp1, and c-Ets-1. Only 0.4% of patients were Design: Case-control study. homozygous for the protective rs1572931 genotype (T/T), comparedwith3.0%amongcontrols(P=5ϫ10−5).ThisSNP was included in a haplotype that reduced the risk for PD by Setting: A medical center affiliated with a university. 10- to 12-fold (P=.002-.01) in all patients with PD and in a subgroupofpatientswhodonotcarrytheAshkenazifounder Subjects: Five single-nucleotide polymorphisms (SNPs) mutations in the GBA or LRRK2 genes. located between RAB7L1 and SLC41A1 were analyzed in 720 patients with PD and 642 controls, all of Ashkenazi Conclusions: Our data demonstrate that specific SNP Jewish origin. variations and haplotypes in the PARK16 locus are asso- ciated with reduced risk for PD in Ashkenazim. Al- Main Outcome Measures: Haplotypes were defined though it is possible that alterations in the putative pro- and risk estimates were determined for each SNP and hap- moter of RAB7L1 are associated with this effect, the role lotype. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential
International Journal of Molecular Sciences Review Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential Bruna B. Brandão 1,†, Ankita Poojari 2,† and Atefeh Rabiee 2,* 1 Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; [email protected] 2 Department of Physiology & Pharmacology, Thomas J. Long School of Pharmacy & Health Sciences, University of the Pacific, Stockton, CA 95211, USA; [email protected]fic.edu * Correspondence: arabiee@pacific.edu † These authors contributed equally to this work. Abstract: The concerning worldwide increase of obesity and chronic metabolic diseases, such as T2D, dyslipidemia, and cardiovascular disease, motivates further investigations into preventive and alternative therapeutic approaches. Over the past decade, there has been growing evidence that the formation and activation of thermogenic adipocytes (brown and beige) may serve as therapy to treat obesity and its associated diseases owing to its capacity to increase energy expenditure and to modulate circulating lipids and glucose levels. Thus, understanding the molecular mechanism of brown and beige adipocytes formation and activation will facilitate the development of strategies to combat metabolic disorders. Here, we provide a comprehensive overview of pathways and players involved in the development of brown and beige fat, as well as the role of thermogenic adipocytes in energy homeostasis and metabolism. Furthermore, we discuss the alterations in brown and beige adipose tissue function during obesity and explore the therapeutic potential of thermogenic activation to treat metabolic syndrome. Citation: Brandão, B.B.; Poojari, A.; Rabiee, A. Thermogenic Fat: Keywords: adipose tissue; development; molecular circuits; secretome; thermogenesis; metabolism; Development, Physiological Function, obesity; therapy and Therapeutic Potential. -
Mendelian Randomization Analysis Identified Potential Genes Pleiotropically Associated with Polycystic Ovary Syndrome Qian Sun
medRxiv preprint doi: https://doi.org/10.1101/2021.06.29.21259512; this version posted July 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Mendelian randomization analysis identified potential genes pleiotropically associated with polycystic ovary syndrome Qian Sun1*, Gao Yuan1*, Jingyun Yang2,3, Jiayi Lu4, Wen Feng1, Wen Yang1 1Department of Gynecology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, Jiangsu, China 2Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA 3Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA 4Department of Finance, School of Economics, Shanghai University, Shanghai, China *The two authors contributed equally to this paper and share the first authorship Corresponding to Wen Yang Department of Gynecology The First Affiliated Hospital of Kangda College of Nanjing Medical University 6 Zhenhua Road Lianyungang, Jiangsu 222061 China Tel: 86-18961325910 E-mail: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2021.06.29.21259512; this version posted July 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. ABSTRACT Research question: Polycystic ovary syndrome (PCOS) is a common endocrine disorder with unclear etiology.