The Intra-Mitochondrial O-Glcnacylation System Acutely Regulates OXPHOS Capacity and ROS Dynamics in the Heart
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The Functional Profiles of Chicken Eggs Incubated Under
THE FUNCTIONAL PROFILES OF CHICKEN EGGS INCUBATED UNDER MONOCHROMATIC LIGHTING A Dissertation by MOHAMED MAGDY ABDELFATTAH IBRAHIM Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Giridhar Athrey Committee Members, John B. Carey Luc R. Berghman Gregory S. Archer Head of Department, Audrey McElroy May 2021 Major Subject: Poultry Science Copyright 2021 Mohamed Magdy Abdelfattah Ibrahim ABSTRACT Poultry production remains susceptible to significant infectious disease threats such as Avian Flu, and Newcastle Disease Virus (NDV), which threaten the supply of poultry production. My dissertation research addresses this challenge by leveraging avian circadian biology to improve responses to vaccines to enhance poultry performance. The central hypothesis is that specific visible light wavelengths would enhance circadian rhythm development in ovo, leading to improved immune responses. I addressed an essential question regarding the effect of providing photoperiods with different wavelengths (Blue, Green, and White) on circadian rhythm development and its interplay with the immune response following the NDV challenge in chick embryos using the RNAseq technology. Our results showed that incubating chicken embryos under blue light 450nm was most efficient in entraining the circadian rhythm in lung tissue, compared to white light or dark treatment. Blue light showed a specific impact on skeletal muscle, regulation of striated muscle contraction, Glycerolipid metabolism, and development of neurons. The white light incubation led to a photo-acceleration stimulant effect on epidermal growth factor receptor signaling pathway, ErbB signaling pathway, MAPK signaling pathway, and Insulin signaling pathway were upregulated in white light non-challenged treatment. -
The Interplay Between Dysregulated Ion Transport and Mitochondrial Architecture As a Dangerous Liaison in Cancer
International Journal of Molecular Sciences Review The Interplay between Dysregulated Ion Transport and Mitochondrial Architecture as a Dangerous Liaison in Cancer Stine F. Pedersen 1,* , Mette Flinck 1 and Luis A. Pardo 2,* 1 Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark; mette.fl[email protected] 2 Oncophysiology Group, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany * Correspondence: [email protected] (S.F.P.); [email protected] (L.A.P.) Abstract: Transport of ions and nutrients is a core mitochondrial function, without which there would be no mitochondrial metabolism and ATP production. Both ion homeostasis and mitochondrial phenotype undergo pervasive changes during cancer development, and both play key roles in driving the malignancy. However, the link between these events has been largely ignored. This review comprehensively summarizes and critically discusses the role of the reciprocal relationship between ion transport and mitochondria in crucial cellular functions, including metabolism, signaling, and cell fate decisions. We focus on Ca2+,H+, and K+, which play essential and highly interconnected roles in mitochondrial function and are profoundly dysregulated in cancer. We describe the transport and roles of these ions in normal mitochondria, summarize the changes occurring during cancer development, and discuss how they might impact tumorigenesis. Keywords: mitochondrial fission; mitochondrial fusion; calcium; pH; potassium; membrane potential; metabolism; apoptosis; cell cycle; metastasis Citation: Pedersen, S.F.; Flinck, M.; Pardo, L.A. The Interplay between Dysregulated Ion Transport and Mitochondrial Architecture as a 1. Introduction Dangerous Liaison in Cancer. Int. J. Since the first observation of mitochondria in the 1840s, a century had to pass until it Mol. -
Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
NICU Gene List Generator.Xlsx
Neonatal Crisis Sequencing Panel Gene List Genes: A2ML1 - B3GLCT A2ML1 ADAMTS9 ALG1 ARHGEF15 AAAS ADAMTSL2 ALG11 ARHGEF9 AARS1 ADAR ALG12 ARID1A AARS2 ADARB1 ALG13 ARID1B ABAT ADCY6 ALG14 ARID2 ABCA12 ADD3 ALG2 ARL13B ABCA3 ADGRG1 ALG3 ARL6 ABCA4 ADGRV1 ALG6 ARMC9 ABCB11 ADK ALG8 ARPC1B ABCB4 ADNP ALG9 ARSA ABCC6 ADPRS ALK ARSL ABCC8 ADSL ALMS1 ARX ABCC9 AEBP1 ALOX12B ASAH1 ABCD1 AFF3 ALOXE3 ASCC1 ABCD3 AFF4 ALPK3 ASH1L ABCD4 AFG3L2 ALPL ASL ABHD5 AGA ALS2 ASNS ACAD8 AGK ALX3 ASPA ACAD9 AGL ALX4 ASPM ACADM AGPS AMELX ASS1 ACADS AGRN AMER1 ASXL1 ACADSB AGT AMH ASXL3 ACADVL AGTPBP1 AMHR2 ATAD1 ACAN AGTR1 AMN ATL1 ACAT1 AGXT AMPD2 ATM ACE AHCY AMT ATP1A1 ACO2 AHDC1 ANK1 ATP1A2 ACOX1 AHI1 ANK2 ATP1A3 ACP5 AIFM1 ANKH ATP2A1 ACSF3 AIMP1 ANKLE2 ATP5F1A ACTA1 AIMP2 ANKRD11 ATP5F1D ACTA2 AIRE ANKRD26 ATP5F1E ACTB AKAP9 ANTXR2 ATP6V0A2 ACTC1 AKR1D1 AP1S2 ATP6V1B1 ACTG1 AKT2 AP2S1 ATP7A ACTG2 AKT3 AP3B1 ATP8A2 ACTL6B ALAS2 AP3B2 ATP8B1 ACTN1 ALB AP4B1 ATPAF2 ACTN2 ALDH18A1 AP4M1 ATR ACTN4 ALDH1A3 AP4S1 ATRX ACVR1 ALDH3A2 APC AUH ACVRL1 ALDH4A1 APTX AVPR2 ACY1 ALDH5A1 AR B3GALNT2 ADA ALDH6A1 ARFGEF2 B3GALT6 ADAMTS13 ALDH7A1 ARG1 B3GAT3 ADAMTS2 ALDOB ARHGAP31 B3GLCT Updated: 03/15/2021; v.3.6 1 Neonatal Crisis Sequencing Panel Gene List Genes: B4GALT1 - COL11A2 B4GALT1 C1QBP CD3G CHKB B4GALT7 C3 CD40LG CHMP1A B4GAT1 CA2 CD59 CHRNA1 B9D1 CA5A CD70 CHRNB1 B9D2 CACNA1A CD96 CHRND BAAT CACNA1C CDAN1 CHRNE BBIP1 CACNA1D CDC42 CHRNG BBS1 CACNA1E CDH1 CHST14 BBS10 CACNA1F CDH2 CHST3 BBS12 CACNA1G CDK10 CHUK BBS2 CACNA2D2 CDK13 CILK1 BBS4 CACNB2 CDK5RAP2 -
Discovery of Genes by Phylocsf Supplemental
Supplemental Materials for Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci Supplemental Methods ....................................................................................................................... 2 Supplemental annotation methods ........................................................................................................... 2 Manual annotation overview ...................................................................................................................................... 2 Summary diagram for the workflow used in this study ................................................................................. 3 Transcriptomics analysis ............................................................................................................................................. 3 Comparative annotation ............................................................................................................................................... 4 Overlap of novel annotations with transposon sequences ........................................................................... 6 Assessing the novelty of annotations ...................................................................................................................... 7 Additional considerations for the annotation of PCCRs in other species ............................................... 7 PhyloCSF and browser tracks .................................................................................................................... -
Pan-Cancer Analysis Identifies Mutations in SUGP1 That Recapitulate Mutant SF3B1 Splicing Dysregulation
Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation Zhaoqi Liua,b,c,1, Jian Zhangd,1, Yiwei Suna,c, Tomin E. Perea-Chambleea,b,c, James L. Manleyd,2, and Raul Rabadana,b,c,2 aProgram for Mathematical Genomics, Columbia University, New York, NY 10032; bDepartment of Systems Biology, Columbia University, New York, NY 10032; cDepartment of Biomedical Informatics, Columbia University, New York, NY 10032; and dDepartment of Biological Sciences, Columbia University, New York, NY 10027 Contributed by James L. Manley, March 2, 2020 (sent for review January 2, 2020; reviewed by Kristen Lynch and Gene Yeo) The gene encoding the core spliceosomal protein SF3B1 is the most also resulted in the same splicing defects observed in SF3B1 frequently mutated gene encoding a splicing factor in a variety of mutant cells (11). hematologic malignancies and solid tumors. SF3B1 mutations in- In addition to SF3B1, other SF-encoding genes have also been duce use of cryptic 3′ splice sites (3′ss), and these splicing errors found to be mutated in hematologic malignancies, e.g., U2AF1, contribute to tumorigenesis. However, it is unclear how wide- SRSF2, and ZRSR2. However, these SF gene mutations do not spread this type of cryptic 3′ss usage is in cancers and what is share common alterations in splicing (1, 3), suggesting that dif- the full spectrum of genetic mutations that cause such missplicing. ferent splicing patterns may contribute to different phenotypes To address this issue, we performed an unbiased pan-cancer anal- of cancers. Because SF3B1 is the most frequently mutated ysis to identify genetic alterations that lead to the same aberrant splicing gene, the splicing defects caused by mutant SF3B1 may SF3B1 splicing as observed with mutations. -
Crystal Structure of Histidine Triad Nucleotide- Binding Protein from the Pathogenic Fungus Candida Albicans
Molecules and Cells Minireview Crystal Structure of Histidine Triad Nucleotide- Binding Protein from the Pathogenic Fungus Candida albicans Ahjin Jung1,6, Ji-Sook Yun1,6, Shinae Kim1, Sang Ryong Kim2, Minsang Shin3, Dong Hyung Cho2, Kwang Shik Choi2,4,5,*, and Jeong Ho Chang1,5,* 1Department of Biology Education, 2School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, 3Department of Mi- crobiology, School of Medicine, 4Research Institute for Dokdo and Ulleungdo Island, Kyungpook National University, 5Research Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Korea, 6These authors contributed equally to this work. *Correspondence: [email protected] (KSC); [email protected] (JHC) http://dx.doi.org/10.14348/molcells.2018.0377 www.molcells.org Histidine triad nucleotide-binding protein (HINT) is a member of evolution. Further studies are required to address the func- of the histidine triad (HIT) superfamily, which has hydrolase tional significance of variations in the C-terminal region. This activity owing to a histidine triad motif. The HIT superfamily structural analysis of CaHINT provided important insights into can be divided to five classes with functions in galactose me- the molecular aspects of evolution within the HIT superfamily. tabolism, DNA repair, and tumor suppression. HINTs are high- ly conserved from archaea to humans and function as tumor Keywords: Candida albicans, crystal structure, histidine triad, suppressors, translation regulators, and neuropathy inhibitors. HIT family, HINT Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features INTRODUCTION and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albi- Histidine triad nucleotide-binding protein (HINT), which con- cans (CaHINT) in complex with zinc ions at a resolution of 2.5 tains three highly conserved histidines as catalytic residues, is Å. -
An Integrated Approach to Comprehensively Map the Molecular Context of Proteins
bioRxiv preprint doi: https://doi.org/10.1101/264788; this version posted February 13, 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. Liu et al. An integrated approach to comprehensively map the molecular context of proteins Xiaonan Liu1,2, Kari Salokas1,2, Fitsum Tamene1,2,3 and Markku Varjosalo1,2,3* 1Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland 2Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland 3Proteomics Unit, University of Helsinki, Helsinki 00014, Finland *Corresponding author Abstract: Protein-protein interactions underlie almost all cellular functions. The comprehensive mapping of these complex cellular networks of stable and transient associations has been made available by affi nity purifi cation mass spectrometry (AP-MS) and more recently by proximity based labelling methods such as BioID. Due the advancements in both methods and MS instrumentation, an in-depth analysis of the whole human proteome is at grasps. In order to facilitate this, we designed and optimized an integrated approach utilizing MAC-tag combining both AP-MS and BioID in a single construct. We systematically applied this approach to 18 subcellular localization markers and generated a molecular context database, which can be used to defi ne molecular locations for any protein of interest. In addition, we show that by combining the AP-MS and BioID results we can also obtain interaction distances within a complex. Taken together, our combined strategy off ers comprehensive approach for mapping physical and functional protein interactions. Introduction: Majority of proteins do not function in isolation geting the endogenous bait protein, allowing and their interactions with other proteins defi ne purifi cation of the bait protein together with the their cellular functions. -
Protein Network Analyses of Pulmonary Endothelial Cells In
www.nature.com/scientificreports OPEN Protein network analyses of pulmonary endothelial cells in chronic thromboembolic pulmonary hypertension Sarath Babu Nukala1,8,9*, Olga Tura‑Ceide3,4,5,9, Giancarlo Aldini1, Valérie F. E. D. Smolders2,3, Isabel Blanco3,4, Victor I. Peinado3,4, Manuel Castell6, Joan Albert Barber3,4, Alessandra Altomare1, Giovanna Baron1, Marina Carini1, Marta Cascante2,7,9 & Alfonsina D’Amato1,9* Chronic thromboembolic pulmonary hypertension (CTEPH) is a vascular disease characterized by the presence of organized thromboembolic material in pulmonary arteries leading to increased vascular resistance, heart failure and death. Dysfunction of endothelial cells is involved in CTEPH. The present study describes for the frst time the molecular processes underlying endothelial dysfunction in the development of the CTEPH. The advanced analytical approach and the protein network analyses of patient derived CTEPH endothelial cells allowed the quantitation of 3258 proteins. The 673 diferentially regulated proteins were associated with functional and disease protein network modules. The protein network analyses resulted in the characterization of dysregulated pathways associated with endothelial dysfunction, such as mitochondrial dysfunction, oxidative phosphorylation, sirtuin signaling, infammatory response, oxidative stress and fatty acid metabolism related pathways. In addition, the quantifcation of advanced oxidation protein products, total protein carbonyl content, and intracellular reactive oxygen species resulted increased -
Role and Mechanisms of Mitophagy in Liver Diseases
cells Review Role and Mechanisms of Mitophagy in Liver Diseases Xiaowen Ma 1, Tara McKeen 1, Jianhua Zhang 2 and Wen-Xing Ding 1,* 1 Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA; [email protected] (X.M.); [email protected] (T.M.) 2 Department of Pathology, Division of Molecular Cellular Pathology, University of Alabama at Birmingham, 901 19th street South, Birmingham, AL 35294, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-913-588-9813 Received: 13 February 2020; Accepted: 28 March 2020; Published: 31 March 2020 Abstract: The mitochondrion is an organelle that plays a vital role in the regulation of hepatic cellular redox, lipid metabolism, and cell death. Mitochondrial dysfunction is associated with both acute and chronic liver diseases with emerging evidence indicating that mitophagy, a selective form of autophagy for damaged/excessive mitochondria, plays a key role in the liver’s physiology and pathophysiology. This review will focus on mitochondrial dynamics, mitophagy regulation, and their roles in various liver diseases (alcoholic liver disease, non-alcoholic fatty liver disease, drug-induced liver injury, hepatic ischemia-reperfusion injury, viral hepatitis, and cancer) with the hope that a better understanding of the molecular events and signaling pathways in mitophagy regulation will help identify promising targets for the future treatment of liver diseases. Keywords: alcohol; autophagy; mitochondria; NAFLD; Parkin; Pink1 1. Introduction Autophagy (or macroautophagy) involves the formation of a double membrane structure called an autophagosome. Autophagosomes bring the enveloped cargoes to the lysosomes to form autolysosomes where the lysosomal enzymes consequently degrade the cargos [1,2]. -
OXPHOS Remodeling in High-Grade Prostate Cancer Involves Mtdna Mutations and Increased Succinate Oxidation
ARTICLE https://doi.org/10.1038/s41467-020-15237-5 OPEN OXPHOS remodeling in high-grade prostate cancer involves mtDNA mutations and increased succinate oxidation Bernd Schöpf 1, Hansi Weissensteiner 1, Georg Schäfer2, Federica Fazzini1, Pornpimol Charoentong3, Andreas Naschberger1, Bernhard Rupp1, Liane Fendt1, Valesca Bukur4, Irina Giese4, Patrick Sorn4, Ana Carolina Sant’Anna-Silva 5, Javier Iglesias-Gonzalez6, Ugur Sahin4, Florian Kronenberg 1, ✉ Erich Gnaiger 5,6 & Helmut Klocker 7 1234567890():,; Rewiring of energy metabolism and adaptation of mitochondria are considered to impact on prostate cancer development and progression. Here, we report on mitochondrial respiration, DNA mutations and gene expression in paired benign/malignant human prostate tissue samples. Results reveal reduced respiratory capacities with NADH-pathway substrates glu- tamate and malate in malignant tissue and a significant metabolic shift towards higher succinate oxidation, particularly in high-grade tumors. The load of potentially deleterious mitochondrial-DNA mutations is higher in tumors and associated with unfavorable risk factors. High levels of potentially deleterious mutations in mitochondrial Complex I-encoding genes are associated with a 70% reduction in NADH-pathway capacity and compensation by increased succinate-pathway capacity. Structural analyses of these mutations reveal amino acid alterations leading to potentially deleterious effects on Complex I, supporting a causal relationship. A metagene signature extracted from the transcriptome of tumor samples exhibiting a severe mitochondrial phenotype enables identification of tumors with shorter survival times. 1 Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University Innsbruck, Schöpfstraße 41, A-6020 Innsbruck, Austria. 2 Institute of Pathology, Neuropathology and Molecular Pathology, Medical University Innsbruck, Müllerstraße 44, A-6020 Innsbruck, Austria.