Brag2a, a Guanine Nucleotide Exchange Factor for Arf6, Is a Component of the Dystrophin-Associated Glycoprotein Complex at the Photoreceptor Terminal
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IQSEC2 Antibody Cat
IQSEC2 Antibody Cat. No.: 8011 Western blot analysis of IQSEC2 in SK-N-SH cell lysate with IQSEC2 antibody at 1 μg/ml. Immunohistochemistry of IQSEC2 in mouse brain tissue with IQSEC2 antibody at 5 μg/ml. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat IQSEC2 antibody was raised against an 18 amino acid peptide near the carboxy terminus of human IQSEC2. IMMUNOGEN: The immunogen is located within amino acids 1380 - 1430 of IQSEC2. TESTED APPLICATIONS: ELISA, IHC-P, WB IQSEC2 antibody can be used for detection of IQSEC2 by Western blot at 1 - 2 μg/ml. Antibody can also be used for immunohistochemistry starting at 5 μg/mL. APPLICATIONS: Antibody validated: Western Blot in human samples and Immunohistochemistry in mouse samples. All other applications and species not yet tested. September 27, 2021 1 https://www.prosci-inc.com/iqsec2-antibody-8011.html IQSEC2 antibody is human, mouse and rat reactive. At least two isoforms of IQSEC2 are SPECIFICITY: known to exist; this antibody will only detect the larger isoform. IQSEC2 antibody is predicted to not cross-react with IQSEC1. POSITIVE CONTROL: 1) Cat. No. 1220 - SK-N-SH Cell Lysate Predicted: 104, 133, 141, 164 kDa PREDICTED MOLECULAR WEIGHT: Observed: 140 kDa Properties PURIFICATION: IQSEC2 antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: IQSEC2 antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL IQSEC2 antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year. -
Integrative Differential Expression and Gene Set Enrichment Analysis Using Summary Statistics for Scrna-Seq Studies
ARTICLE https://doi.org/10.1038/s41467-020-15298-6 OPEN Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies ✉ Ying Ma 1,7, Shiquan Sun 1,7, Xuequn Shang2, Evan T. Keller 3, Mengjie Chen 4,5 & Xiang Zhou 1,6 Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative 1234567890():,; and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework. By integrating DE and GSE analyses, iDEA can improve the power and consistency of DE analysis and the accuracy of GSE analysis. Importantly, iDEA uses only DE summary statistics as input, enabling effective data modeling through com- plementing and pairing with various existing DE methods. We illustrate the benefits of iDEA with extensive simulations. We also apply iDEA to analyze three scRNA-seq data sets, where iDEA achieves up to five-fold power gain over existing GSE methods and up to 64% power gain over existing DE methods. The power gain brought by iDEA allows us to identify many pathways that would not be identified by existing approaches in these data. 1 Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, P.R. China. 3 Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. 4 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. 5 Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. -
Integrating Text Mining, Data Mining, and Network Analysis for Identifying
Jurca et al. BMC Res Notes (2016) 9:236 DOI 10.1186/s13104-016-2023-5 BMC Research Notes RESEARCH ARTICLE Open Access Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends Gabriela Jurca1, Omar Addam1, Alper Aksac1, Shang Gao2, Tansel Özyer3, Douglas Demetrick4 and Reda Alhajj1,5* Abstract Background: Breast cancer is a serious disease which affects many women and may lead to death. It has received considerable attention from the research community. Thus, biomedical researchers aim to find genetic biomarkers indicative of the disease. Novel biomarkers can be elucidated from the existing literature. However, the vast amount of scientific publications on breast cancer make this a daunting task. This paper presents a framework which investigates existing literature data for informative discoveries. It integrates text mining and social network analysis in order to identify new potential biomarkers for breast cancer. Results: We utilized PubMed for the testing. We investigated gene–gene interactions, as well as novel interactions such as gene-year, gene-country, and abstract-country to find out how the discoveries varied over time and how overlapping/diverse are the discoveries and the interest of various research groups in different countries. Conclusions: Interesting trends have been identified and discussed, e.g., different genes are highlighted in relation- ship to different countries though the various genes were found to share functionality. Some text analysis based results have been validated against results from other tools that predict gene–gene relations and gene functions. Keywords: Breast cancer, Data mining, Text mining, Network analysis Background reducing the number of molecules to consider as poten- Introduction tial biomarkers. -
Research Paper Expression of the Pokemon Gene and Pikachurin Protein in the Pokémon Pikachu
Academia Journal of Scientific Research 8(7): 235-238, July 2020 DOI: 10.15413/ajsr.2020.0503 ISSN 2315-7712 ©2020 Academia Publishing Research Paper Expression of the pokemon gene and pikachurin protein in the pokémon pikachu Accepted 13th July, 2020 ABSTRACT The proto-oncogene Pokemon is typically over expressed in cancers, and the protein Pikachurin is associated with ribbon synapses in the retina. Studying the Samuel Oak1; Ganka Joy2 and Mattan Schlomi1* former is of interest in molecular oncology and the latter in the neurodevelopment of vision. We quantified the expression levels of Pokemon and Pikachurin in the 1Okido Institute, Pallet Town, Kanto, Japan. 2Department of Opthalmology, Tokiwa City Pokémon Pikachu, where the gene and protein both act as in other vertebrates. Pokémon Center, Viridian City, Kanto, Japan. The controversy over their naming remains an issue. *Corresponding author. E-mail: [email protected]. Tel: +81 3-3529-1821 Key words: Pikachurin, EGFLAM, fibronectin, pokemon, Zbtb7, Pikachu. INTRODUCTION Pokemon is a proto-oncogene discovered in 2005 (Maeda et confusing, they do avoid the controversies associated with al., 2005). It is a “master gene” for cancer: over expression naming a disease-related gene after adorable, child-friendly of Pokemon is positively associated with multiple different creatures. [For more information, consider the forms of cancer, and some hypothesize that its expression is holoprosencephaly-associated gene sonic hedgehog and the a prerequisite for subsequent oncogenes [cancer-causing molecule that inhibits it, Robotnikin (Stanton et al., 2009)]. genes] to actually cause cancer (Gupta et al., 2020). The The gene Pokemon is thus not to be confused with name stands for POK erythroid myeloid ontogenic factor. -
Expressed Gene Fusions As Frequent Drivers of Poor Outcomes in Hormone Receptor–Positive Breast Cancer
Published OnlineFirst December 14, 2017; DOI: 10.1158/2159-8290.CD-17-0535 RESEARCH ARTICLE Expressed Gene Fusions as Frequent Drivers of Poor Outcomes in Hormone Receptor–Positive Breast Cancer Karina J. Matissek1,2, Maristela L. Onozato3, Sheng Sun1,2, Zongli Zheng2,3,4, Andrew Schultz1, Jesse Lee3, Kristofer Patel1, Piiha-Lotta Jerevall2,3, Srinivas Vinod Saladi1,2, Allison Macleay3, Mehrad Tavallai1,2, Tanja Badovinac-Crnjevic5, Carlos Barrios6, Nuran Beşe7, Arlene Chan8, Yanin Chavarri-Guerra9, Marcio Debiasi6, Elif Demirdögen10, Ünal Egeli10, Sahsuvar Gökgöz10, Henry Gomez11, Pedro Liedke6, Ismet Tasdelen10, Sahsine Tolunay10, Gustavo Werutsky6, Jessica St. Louis1, Nora Horick12, Dianne M. Finkelstein2,12, Long Phi Le2,3, Aditya Bardia1,2, Paul E. Goss1,2, Dennis C. Sgroi2,3, A. John Iafrate2,3, and Leif W. Ellisen1,2 ABSTRACT We sought to uncover genetic drivers of hormone receptor–positive (HR+) breast cancer, using a targeted next-generation sequencing approach for detecting expressed gene rearrangements without prior knowledge of the fusion partners. We identified inter- genic fusions involving driver genes, including PIK3CA, AKT3, RAF1, and ESR1, in 14% (24/173) of unselected patients with advanced HR+ breast cancer. FISH confirmed the corresponding chromo- somal rearrangements in both primary and metastatic tumors. Expression of novel kinase fusions in nontransformed cells deregulates phosphoprotein signaling, cell proliferation, and survival in three- dimensional culture, whereas expression in HR+ breast cancer models modulates estrogen-dependent growth and confers hormonal therapy resistance in vitro and in vivo. Strikingly, shorter overall survival was observed in patients with rearrangement-positive versus rearrangement-negative tumors. Cor- respondingly, fusions were uncommon (<5%) among 300 patients presenting with primary HR+ breast cancer. -
The Role of the Actin Cytoskeleton During Muscle Development In
THE ROLE OF THE ACTIN CYTOSKELETON DURING MUSCLE DEVELOPMENT IN DROSOPHILA AND MOUSE by Shannon Faye Yu A Dissertation Presented to the Faculty of the Louis V. Gerstner, Jr. Graduate School of the Biomedical Sciences in Partial Fulfillment of the Requirements of the Degree of Doctor of Philosophy New York, NY Oct, 2013 Mary K. Baylies, PhD! Date Dissertation Mentor Copyright by Shannon F. Yu 2013 ABSTRACT The actin cytoskeleton is essential for many processes within a developing organism. Unsurprisingly, actin and its regulators underpin many of the critical steps in the formation and function of muscle tissue. These include cell division during the specification of muscle progenitors, myoblast fusion, muscle elongation and attachment, and muscle maturation, including sarcomere assembly. Analysis in Drosophila has focused on regulators of actin polymerization particularly during myoblast fusion, and the conservation of many of the actin regulators required for muscle development has not yet been tested. In addition, dynamic actin processes also require the depolymerization of existing actin fibers to replenish the pool of actin monomers available for polymerization. Despite this, the role of actin depolymerization has not been described in depth in Drosophila or mammalian muscle development. ! Here, we first examine the role of the actin depolymerization factor Twinstar (Tsr) in muscle development in Drosophila. We show that Twinstar, the sole Drosophila member of the ADF/cofilin family of actin depolymerization proteins, is expressed in muscle where it is essential for development. tsr mutant embryos displayed a number of muscle defects, including muscle loss and muscle misattachment. Further, regulators of Tsr, including a Tsr-inactivating kinase, Center divider, a Tsr-activating phosphatase, Slingshot and a synergistic partner in depolymerization, Flare, are also required for embryonic muscle development. -
Mouse Egflam Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Egflam Knockout Project (CRISPR/Cas9) Objective: To create a Egflam knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Egflam gene (NCBI Reference Sequence: NM_001289496 ; Ensembl: ENSMUSG00000042961 ) is located on Mouse chromosome 15. 23 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 23 (Transcript: ENSMUST00000096494). Exon 2~3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous null mutants are viable and fertile under normal conditions. They exhibit abnormal photoreceptor ribbon synapses, resulting in alteration in synaptic signal transmission and visual function. Exon 2 starts from about 3.21% of the coding region. Exon 2~3 covers 6.36% of the coding region. The size of effective KO region: ~1952 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 23 Legends Exon of mouse Egflam Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. -
The Roles of A-Dystroglycan in the Central Nervous System- Man Qi Li1 and Yi Luo2*
International Journal of Neurological Disorders Review Article The Roles of A-Dystroglycan in the Central Nervous System- Man Qi Li1 and Yi Luo2* 1Department of Foreign Language, Yangtze University College of Arts and Science, Jing zhou 434000, China 2Department of Neurology, The First People’s Hospital of Jingzhou, the First Affiliated Hospital of Yangtze University, Jing zhou 434000, China *Address for Correspondence: Yi Luo, Department of Neurology, The First People’s Hospital of Jingzhou, the First Affiliated Hospital of Yangtze University, Jing zhou 434000, China, E-mail: Submitted: 12 December 2019; Approved: 02 January 2020; Published: 04 January 2020 Cite this article: Li MQ, Luo Y. The Roles of Α-Dystroglycan in the Central Nervous System. Int J Neurol Dis. 2020;4(1): 001-004. Copyright: © 2020 Li MQ, et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ISSN: 2639-7021 International Journal of Neurological Disorders ISSN: 2639-7021 ABSTRACT Dystroglycan is a membrane protein, which is related to extracellular matrix in various mammalian tissues. α-subunit of Dystroglycan (α-DG) is highly glycosylated, including a special O-mannose group, depending on this unique glycosylation to bind its ligands. Diff erent groups of muscular dystrophies are caused by a low glycosylation of α-DG, accompanied by the involvement of the central nervous system, from the brain malformation to intellectual retardation. More and more literatures discuss α-DG in the central nervous system, from the brain development to the maintenance of synapses. -
GATA2 Regulates Mast Cell Identity and Responsiveness to Antigenic Stimulation by Promoting Chromatin Remodeling at Super- Enhancers
ARTICLE https://doi.org/10.1038/s41467-020-20766-0 OPEN GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super- enhancers Yapeng Li1, Junfeng Gao 1, Mohammad Kamran1, Laura Harmacek2, Thomas Danhorn 2, Sonia M. Leach1,2, ✉ Brian P. O’Connor2, James R. Hagman 1,3 & Hua Huang 1,3 1234567890():,; Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage- determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes. 1 Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA. 2 Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA. 3 Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, ✉ CO 80045, USA. email: [email protected] NATURE COMMUNICATIONS | (2021) 12:494 | https://doi.org/10.1038/s41467-020-20766-0 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-20766-0 ast cells (MCs) are critical effectors in immunity that at key MC genes. -
Dystroglycan Is a Scaffold for Extracellular Axon Guidance Decisions L Bailey Lindenmaier1, Nicolas Parmentier2, Caiying Guo3, Fadel Tissir2, Kevin M Wright1*
RESEARCH ARTICLE Dystroglycan is a scaffold for extracellular axon guidance decisions L Bailey Lindenmaier1, Nicolas Parmentier2, Caiying Guo3, Fadel Tissir2, Kevin M Wright1* 1Vollum Institute, Oregon Health & Science University, Portland, United States; 2Institiute of Neuroscience, Universite´ Catholique de Louvain, Brussels, Belgium; 3Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States Abstract Axon guidance requires interactions between extracellular signaling molecules and transmembrane receptors, but how appropriate context-dependent decisions are coordinated outside the cell remains unclear. Here we show that the transmembrane glycoprotein Dystroglycan interacts with a changing set of environmental cues that regulate the trajectories of extending axons throughout the mammalian brain and spinal cord. Dystroglycan operates primarily as an extracellular scaffold during axon guidance, as it functions non-cell autonomously and does not require signaling through its intracellular domain. We identify the transmembrane receptor Celsr3/ Adgrc3 as a binding partner for Dystroglycan, and show that this interaction is critical for specific axon guidance events in vivo. These findings establish Dystroglycan as a multifunctional scaffold that coordinates extracellular matrix proteins, secreted cues, and transmembrane receptors to regulate axon guidance. DOI: https://doi.org/10.7554/eLife.42143.001 Introduction During neural circuit development, extending axons encounter distinct combinations of cues and *For correspondence: growth substrates that guide their trajectory. These cues can be attractive or repulsive, secreted [email protected] and/or anchored to cell membranes, and signal through cell surface receptors on the growth cones of axons (Kolodkin and Tessier-Lavigne, 2011). Receptors also recognize permissive and non-per- Competing interest: See missive growth substrates formed by the extracellular matrix (ECM), surrounding cells, and other page 21 axons (Raper and Mason, 2010). -
Promoter Alteration Causes Transcriptional Repression of the POMGNT1 Gene in Limb-Girdle Muscular Dystrophy Type 2O
European Journal of Human Genetics (2012) 20, 945–952 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Promoter alteration causes transcriptional repression of the POMGNT1 gene in limb-girdle muscular dystrophy type 2O Madalina Raducu1, Jonathan Baets2,3, Oihane Fano1, Rudy Van Coster4 and Jesu´s Cruces*,1 Limb-girdle muscular dystrophy type 2O (LGMD2O) belongs to a group of rare muscular dystrophies named dystroglycanopathies, which are characterized molecularly by hypoglycosylation of a-dystroglycan (a-DG). Here, we describe the first dystroglycanopathy patient carrying an alteration in the promoter region of the POMGNT1 gene (protein O-mannose b-1,2-N-acetylglucosaminyltransferase 1), which involves a homozygous 9-bp duplication (-83_-75dup). Analysis of the downstream effects of this mutation revealed a decrease in the expression of POMGNT1 mRNA and protein because of negative regulation of the POMGNT1 promoter by the transcription factor ZNF202 (zinc-finger protein 202). By functional analysis of various luciferase constructs, we localized a proximal POMGNT1 promoter and we found a 75% decrease in luciferase activity in the mutant construct when compared with the wild type. Electrophoretic mobility shift assay (EMSA) revealed binding sites for the Sp1, Ets1 and GATA transcription factors. Surprisingly, the mutation generated an additional ZNF202 binding site and this transcriptional repressor bound strongly to the mutant promoter while failing to recognize the wild-type promoter. Although the genetic causes of dystroglycanopathies are highly variable, they account for only 50% of the cases described. Our results emphasize the importance of extending the mutational screening outside the gene-coding region in dystroglycanopathy patients of unknown aetiology, because mutations in noncoding regions may be the cause of disease. -
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation Chip-Sequencing Data Processing Pipeline
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Processing Pipeline Erinija Pranckeviciene Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa c Erinija Pranckeviciene, Ottawa, Canada, 2015 Abstract The rapidly advancing high-throughput and next generation sequencing technologies facilitate deeper insights into the molecular mechanisms underlying the expression of phenotypes in living organisms. Experimental data and scientific publications following this technological advance- ment have rapidly accumulated in public databases. Meaningful analysis of currently avail- able data in genomic databases requires sophisticated computational tools and algorithms, and presents considerable challenges to molecular biologists without specialized training in bioinfor- matics. To study their phenotype of interest molecular biologists must prioritize large lists of poorly characterized genes generated in high-throughput experiments. To date, prioritization tools have primarily been designed to work with phenotypes of human diseases as defined by the genes known to be associated with those diseases. There is therefore a need for more prioritiza- tion tools for phenotypes which are not related with diseases generally or diseases with which no genes have yet been associated in particular. Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) is a method of choice to study the gene regulation processes responsible for the expression of cellular phenotypes. Among publicly available computational pipelines for the processing of ChIP-Seq data, there is a lack of tools for the downstream analysis of composite motifs and preferred binding distances of the DNA binding proteins.