Giantin-Knockout Models Reveal a Feedback Loop Between Golgi Function and Glycosyltransferase Expression Nicola L
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Supplemental Note Hominoid Fission of Chromosome 14/15 and Role Of
Supplemental Note Supplemental Note Hominoid fission of chromosome 14/15 and role of segmental duplications Giuliana Giannuzzi, Michele Pazienza, John Huddleston, Francesca Antonacci, Maika Malig, Laura Vives, Evan E. Eichler and Mario Ventura 1. Analysis of the macaque contig spanning the hominoid 14/15 fission site We grouped contig clones based on their FISH pattern on human and macaque chromosomes (Groups F1, F2, F3, G1, G2, G3, and G4). Group F2 clones (Hsa15b- and Hsa15c-positive) showed a single signal on macaque 7q and three signal clusters on human chromosome 15: at the orthologous 15q26, as expected, as well as at 15q11–14 and 15q24–25, which correspond to the actual and ancestral pericentromeric regions, respectively (Ventura et al. 2003). Indeed, this locus contains an LCR15 copy (Pujana et al. 2001) in both the macaque and human genomes. Most BAC clones were one-end anchored in the human genome (chr15:100,028–100,071 kb). In macaque this region experienced a 64 kb duplicative insertion from chromosome 17 (orthologous to human chromosome 13) (Figure 2), with the human configuration (absence of insertion) likely being the ancestral state because it is identical in orangutan and marmoset. Four Hsa15b- positive clones mapped on macaque and human chromosome 19, but neither human nor macaque assemblies report the STS Hsa15b duplicated at this locus. The presence of assembly gaps in macaque may explain why the STS is not annotated in this region. We aligned the sequence of macaque CH250-70H12 (AC187495.2) versus its human orthologous sequence (hg18 chr15:100,039k-100,170k) and found a 12 kb human expansion through tandem duplication of a ~100 bp unit corresponding to a portion of exon 20 of DNM1 (Figure S3). -
A Novel 65-Bp Indel in the GOLGB1 Gene Is Associated with Chicken Growth and Carcass Traits
animals Article A Novel 65-bp Indel in the GOLGB1 Gene Is Associated with Chicken Growth and Carcass Traits Rong Fu 1,2, Tuanhui Ren 1,2, Wangyu Li 1,2, Jiaying Liang 1,2, Guodong Mo 1,2, Wen Luo 1,2, Danlin He 1,2, Shaodong Liang 1,2 and Xiquan Zhang 1,2,* 1 Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; [email protected] (R.F.); [email protected] (T.R.); [email protected] (W.L.); [email protected] (J.L.); [email protected] (G.M.); [email protected] (W.L.); [email protected] (D.H.); [email protected] (S.L.) 2 Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China * Correspondence: [email protected] Received: 20 February 2020; Accepted: 4 March 2020; Published: 12 March 2020 Simple Summary: Many Chinese-local chickens show slow-growing and low-producing performance, which is not conductive to the development of the poultry industry. The identification of thousands of indels in the last twenty years has helped us to make progress in animal genetics and breeding. Golgin subfamily B member 1 (GOLGB1) is located on chromosome 1 in chickens. Previous study showed that a large number of QTLs on the chicken chromosome 1 were related to the important economic traits. However, the biological function of GOLGB1 gene in chickens is still unclear. In this study, we detected a novel 65-bp indel in the fifth intron of the chicken GOLGB1 gene. -
Influencers on Thyroid Cancer Onset: Molecular Genetic Basis
G C A T T A C G G C A T genes Review Influencers on Thyroid Cancer Onset: Molecular Genetic Basis Berta Luzón-Toro 1,2, Raquel María Fernández 1,2, Leticia Villalba-Benito 1,2, Ana Torroglosa 1,2, Guillermo Antiñolo 1,2 and Salud Borrego 1,2,* 1 Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; [email protected] (B.L.-T.); [email protected] (R.M.F.); [email protected] (L.V.-B.); [email protected] (A.T.); [email protected] (G.A.) 2 Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain * Correspondence: [email protected]; Tel.: +34-955-012641 Received: 3 September 2019; Accepted: 6 November 2019; Published: 8 November 2019 Abstract: Thyroid cancer, a cancerous tumor or growth located within the thyroid gland, is the most common endocrine cancer. It is one of the few cancers whereby incidence rates have increased in recent years. It occurs in all age groups, from children through to seniors. Most studies are focused on dissecting its genetic basis, since our current knowledge of the genetic background of the different forms of thyroid cancer is far from complete, which poses a challenge for diagnosis and prognosis of the disease. In this review, we describe prevailing advances and update our understanding of the molecular genetics of thyroid cancer, focusing on the main genes related with the pathology, including the different noncoding RNAs associated with the disease. -
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Barlow et al. BMC Biology (2018) 16:27 https://doi.org/10.1186/s12915-018-0492-9 RESEARCHARTICLE Open Access A sophisticated, differentiated Golgi in the ancestor of eukaryotes Lael D. Barlow1, Eva Nývltová2,3, Maria Aguilar1, Jan Tachezy2 and Joel B. Dacks1,4* Abstract Background: The Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle’s dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear. Various proteins have roles in organizing the Golgi, chief among them being the golgins. Results: We address Golgi evolution by analyzing genome sequences from organisms which have lost stacked cisternae as a feature of their Golgi and those that have not. Using genomics and immunomicroscopy, we first identify Golgi in the anaerobic amoeba Mastigamoeba balamuthi. We then searched 87 genomes spanning eukaryotic diversity for presence of the most prominent proteins implicated in Golgi structure, focusing on golgins. We show some candidates as animal specific and others as ancestral to eukaryotes. Conclusions: None of the proteins examined show a phyletic distribution that correlates with the morphology of stacked cisternae, suggesting the possibility of stacking as an emergent property. Strikingly, however, the combination of golgins conserved among diverse eukaryotes allows for the most detailed reconstruction of the organelle to date, showing a sophisticated Golgi with differentiated compartments and trafficking pathways in the common eukaryotic ancestor. -
Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases. -
Meta-Analysis of Nasopharyngeal Carcinoma
BMC Genomics BioMed Central Research article Open Access Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation Xia Chen†1,2, Shuang Liang†1, WenLing Zheng1,3, ZhiJun Liao1, Tao Shang1 and WenLi Ma*1 Address: 1Institute of Genetic Engineering, Southern Medical University, Guangzhou, PR China, 2Xiangya Pingkuang associated hospital, Pingxiang, Jiangxi, PR China and 3Southern Genomics Research Center, Guangzhou, Guangdong, PR China Email: Xia Chen - [email protected]; Shuang Liang - [email protected]; WenLing Zheng - [email protected]; ZhiJun Liao - [email protected]; Tao Shang - [email protected]; WenLi Ma* - [email protected] * Corresponding author †Equal contributors Published: 7 July 2008 Received: 16 February 2008 Accepted: 7 July 2008 BMC Genomics 2008, 9:322 doi:10.1186/1471-2164-9-322 This article is available from: http://www.biomedcentral.com/1471-2164/9/322 © 2008 Chen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Epstein-Barr virus (EBV) presumably plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC), but the molecular mechanism of EBV-dependent neoplastic transformation is not well understood. The combination of bioinformatics with evidences from biological experiments paved a new way to gain more insights into the molecular mechanism of cancer. Results: We profiled gene expression using a meta-analysis approach. Two sets of meta-genes were obtained. Meta-A genes were identified by finding those commonly activated/deactivated upon EBV infection/reactivation. -
RCAN2 Isoform 2 Recombinant Protein Cat
RCAN2 Isoform 2 Recombinant Protein Cat. No.: 95-114 RCAN2 Isoform 2 Recombinant Protein Specifications SPECIES: Mouse SOURCE SPECIES: E. coli SEQUENCE: aa 2 - 197 FUSION TAG: Fusion Partner: C-terminal His-tag TESTED APPLICATIONS: ELISA, WB APPLICATIONS: This recombinant protein can be used for WB and ELISA. For research use only. PREDICTED MOLECULAR 26 kDa (Calculated) WEIGHT: Properties PURITY: ~95% PHYSICAL STATE: Liquid 100mM sodium phosphate, 10mM Tris, 500mM NaCl, 25 mM imidazole, 2mM MgCl2, 10% BUFFER: gycerol Store in working aliquots at -70˚C. Avoid freeze/thaw cycles. When working with proteins STORAGE CONDITIONS: care should be taken to keep recombinant protein at a cool and stable temperature. September 29, 2021 1 https://www.prosci-inc.com/rcan2-isoform-2-recombinant-protein-95-114.html Additional Info OFFICIAL SYMBOL: Rcan2 RCAN2 Antibody: Csp2, MCIP2, ZAKI-4, Dscr1l1, Zaki4, Calcipressin-2, Calcineurin inhibitory ALTERNATE NAMES: protein ZAKI-4 ACCESSION NO.: AAH62141 PROTEIN GI NO.: 38328420 GENE ID: 53901 Background and References Regulator of calcineurin 2 (RCAN2), also known as ZAKI4 and DSCR1L1, is expressed as two isoforms differing at their N-terminus. The longer of the two (isoform 1) is expressed exclusively in the brain, while isoform 2 is ubiquitously expressed, with highest expression in brain, heart, and muscle (1,2). Both isoforms bind to the catalytic subunit of calcineurin, a Ca++-dependent protein phosphatase involved in several neuronal functions, though BACKGROUND: their C-terminal region and inhibit calcineurin’s activity (3). Unlike isoform 1 of RCAN2, the expression of the second isoform is not induced by the thyroid hormone T3 (3). -
Genotyping of Breech Flystrike Resource – Update
Project No: ON-00515 Contract No: PO4500010753 AWI Project Manager: Bridget Peachey Contractor Name: CSIRO Agriculture and Food Prepared by: Dr Sonja Dominik Publication Date: July 2019 Genotyping of breech flystrike resource – update Published by Australian Wool Innovation Limited, Level 6, 68 Harrington Street, THE ROCKS, NSW, 2000 This publication should only be used as a general aid and is not a substitute for specific advice. To the extent permitted by law, we exclude all liability for loss or damage arising from the use of the information in this publication. AWI invests in research, development, innovation and marketing activities along the global supply chain for Australian wool. AWI is grateful for its funding, which is primarily provided by Australian woolgrowers through a wool levy and by the Australian Government which provides a matching contribution for eligible R&D activities © 2019 Australian Wool Innovation Ltd. All rights reserved. Contents Executive Summary .................................................................................................................... 3 1 Introduction/Hypothesis .................................................................................................... 5 2 Literature Review ............................................................................................................... 6 3 Project Objectives .............................................................................................................. 8 4 Success in Achieving Objectives ........................................................................................ -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Retinal Pigment Epithelium Protein of 65 Kda Gene
Molecular Vision 2013; 19:2312-2320 <http://www.molvis.org/molvis/v19/2312> © 2013 Molecular Vision Received 31 July 2013 | Accepted 14 November 2013 | Published 16 November 2013 Retinal pigment epithelium protein of 65 kDA gene-linked retinal degeneration is not modulated by chicken acidic leucine-rich epidermal growth factor-like domain containing brain protein/ Neuroglycan C/ chondroitin sulfate proteoglycan 5 Sandra Cottet,1,2 René Jüttner,3 Nathalie Voirol,1 Pierre Chambon,4 Fritz G. Rathjen,3 Daniel F. Schorderet,1,2,5 Pascal Escher1,2 1Institute for Research in Ophthalmology, Sion, Switzerland; 2Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland; 3Max-Delbrück-Centrum, Berlin, Germany; 4Institut de Génétique et de Biologie Moléculaire et Cellulaire, Collège de France, Strasbourg, France; 5EPFL-Ecole Polytechnique Fédérale, Lausanne, Switzerland Purpose: To analyze in vivo the function of chicken acidic leucine-rich epidermal growth factor-like domain containing brain protein/Neuroglycan C (gene symbol: Cspg5) during retinal degeneration in the Rpe65−/− mouse model of Leber congenital amaurosis. Methods: We resorted to mice with targeted deletions in the Cspg5 and retinal pigment epithelium protein of 65 kDa (Rpe65) genes (Cspg5−/−/Rpe65−/−). Cone degeneration was assessed with cone-specific peanut agglutinin staining. Tran- scriptional expression of rhodopsin (Rho), S-opsin (Opn1sw), M-opsin (Opn1mw), rod transducin α subunit (Gnat1), and cone transducin α subunit (Gnat2) genes was assessed with quantitative PCR from 2 weeks to 12 months. The retinal pigment epithelium (RPE) was analyzed at P14 with immunodetection of the retinol-binding protein membrane receptor Stra6. Results: No differences in the progression of retinal degeneration were observed between the Rpe65−/− and Cspg5−/−/ Rpe65−/− mice. -
RCAN2 Antibody Cat
RCAN2 Antibody Cat. No.: 5051 RCAN2 Antibody Immunohistochemistry of RCAN2 in mouse brain tissue Immunofluorescence of RCAN2 in mouse brain tissue with with RCAN2 antibody at 2.5 μg/mL. RCAN2 antibody at 20 μg/mL. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat HOMOLOGY: Predicted species reactivity based on immunogen sequence: Bovine: (100%) RCAN2 antibody was raised against a 14 amino acid synthetic peptide near the center of human RCAN2. IMMUNOGEN: The immunogen is located within amino acids 70 - 120 of RCAN2. TESTED APPLICATIONS: ELISA, IF, IHC-P, WB September 26, 2021 1 https://www.prosci-inc.com/rcan2-antibody-5051.html RCAN2 antibody can be used for detection of RCAN2 by Western blot at 1 - 2 μg/mL. Antibody can also be used for immunohistochemistry starting at 2.5 μg/mL. For immunofluorescence start at 20 μg/mL. APPLICATIONS: Antibody validated: Western Blot in mouse samples; Immunohistochemistry in mouse samples and Immunofluorescence in mouse samples. All other applications and species not yet tested. POSITIVE CONTROL: 1) Cat. No. 1282 - 3T3 (NIH) Cell Lysate Properties PURIFICATION: RCAN2 Antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: RCAN2 Antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL RCAN2 antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year. As with all antibodies care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: Rcan2 RCAN2 Antibody: Csp2, MCIP2, ZAKI-4, Dscr1l1, Zaki4, Calcipressin-2, Calcineurin inhibitory ALTERNATE NAMES: protein ZAKI-4 ACCESSION NO.: AAH62141 PROTEIN GI NO.: 38328420 GENE ID: 53901 USER NOTE: Optimal dilutions for each application to be determined by the researcher.