The Role and Robustness of the Gini Coefficient As an Unbiased Tool For
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Ovulation-Selective Genes: the Generation and Characterization of an Ovulatory-Selective Cdna Library
531 Ovulation-selective genes: the generation and characterization of an ovulatory-selective cDNA library A Hourvitz1,2*, E Gershon2*, J D Hennebold1, S Elizur2, E Maman2, C Brendle1, E Y Adashi1 and N Dekel2 1Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA 2Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel (Requests for offprints should be addressed to N Dekel; Email: [email protected]) *(A Hourvitz and E Gershon contributed equally to this paper) (J D Hennebold is now at Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon 97006, USA) Abstract Ovulation-selective/specific genes, that is, genes prefer- (FAE-1) homolog, found to be localized to the inner entially or exclusively expressed during the ovulatory periantral granulosa and to the cumulus granulosa cells of process, have been the subject of growing interest. We antral follicles. The FAE-1 gene is a -ketoacyl-CoA report herein studies on the use of suppression subtractive synthase belonging to the fatty acid elongase (ELO) hybridization (SSH) to construct a ‘forward’ ovulation- family, which catalyzes the initial step of very long-chain selective/specific cDNA library. In toto, 485 clones were fatty acid synthesis. All in all, the present study accom- sequenced and analyzed for homology to known genes plished systematic identification of those hormonally with the basic local alignment tool (BLAST). Of those, regulated genes that are expressed in the ovary in an 252 were determined to be nonredundant. -
18S Rrna Is a Reliable Normalisation Gene for Real Time PCR Based On
Kuchipudi et al. Virology Journal 2012, 9:230 http://www.virologyj.com/content/9/1/230 METHODOLOGY Open Access 18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells Suresh V Kuchipudi1*, Meenu Tellabati1, Rahul K Nelli1, Gavin A White2, Belinda Baquero Perez1, Sujith Sebastian1, Marek J Slomka3, Sharon M Brookes3, Ian H Brown3, Stephen P Dunham1 and Kin-Chow Chang1 Abstract Background: One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. However, ACTB and GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. To date no detailed study has been described that compares the suitability of commonly used housekeeping genes in influenza virus infections. The present study evaluated several commonly used housekeeping genes [ACTB, GAPDH, 18S ribosomal RNA (18S rRNA), ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B) and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) (ATP5G1)] to identify the most stably expressed gene in human, pig, chicken and duck cells infected with a range of influenza A virus subtypes. Results: The relative expression stability of commonly used housekeeping genes were determined in primary human bronchial epithelial cells (HBECs), pig tracheal epithelial cells (PTECs), and chicken and duck primary lung-derived cells infected with five influenza A virus subtypes. -
Supplementary Materials
Supplementary Materials Identification of Compounds The connectivity map concept (C-Map) is based on gene expression profiles, also known as gene fingerprints, and is used to analyze similar effects of compounds and to find drugs for treating diseases [1]. The gene expression profiles in both the C-Map and the CLUE [2] websites were derived from the treatment of human cells with thousands of drugs. Therefore, the gene expression signatures of interest in any induced or organic cell state could be compared with one another to determine similar mechanisms or reverse signatures of drugs and shRNA. Pattern-matching algorithms were used to score each gene expression profile and provide strength of enrichment through query signatures. The results were ranked by “connectivity score (τ)”; a positive score of a signature denoted a similar effect, whereas a negative score indicated a contrary effect. A τ of 90 indicated that only 10% of all perturbations exhibited strong connectivity to the query [2]. Methodology of perturbagen classes (PCLs) To render the CLUE database relatively easy for users to quickly find the mechanism of action (MOA) of a target drug, codifying the class-level annotation required considerable effort. MOAs were adopted to identify groups of compounds with distinct chemical structures, and genetic perturbagens were grouped on the basis of their belonging to the same 1 gene family or being commonly targeted by the same compounds. Ultimately, CLUE named PCLs for their class-level annotations and further connected these cognate class members according to the results of L1000 connectivity analyses to predict the mechanism [2]. 2 A B 3 C D 4 E 5 Figure S1. -
Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct Cpg Island Methylation State
RESEARCH ARTICLE Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State Steve Pells1,2*, Eirini Koutsouraki1, Sofia Morfopoulou1, Sara Valencia-Cadavid1, Simon R. Tomlinson1, Ravi Kalathur3, Matthias E. Futschik3, Paul A. De Sousa1,2* 1 MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom, 2 Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom, 3 Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal * [email protected] (PDS); [email protected] (SP) Abstract Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may com- OPEN ACCESS promise function, so an epigenetic pluripotency “signature” would be invaluable for line vali- Citation: Pells S, Koutsouraki E, Morfopoulou S, dation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by Valencia-Cadavid S, Tomlinson SR, Kalathur R, et al. genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation (2015) Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG between lines. Comparison of hESC CGI methylation profiles to corresponding somatic Island Methylation State. PLoS ONE 10(7): tissue data and hESC mRNA expression profiles identified a conserved hESC-specific e0131102. doi:10.1371/journal.pone.0131102 methylation pattern associated with expressed genes. Transcriptional repressors and acti- Editor: Jason Glenn Knott, Michigan State University, vators were over-represented amongst genes whose associated CGIs were methylated or UNITED STATES unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional Received: March 10, 2015 regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic Accepted: May 27, 2015 expression in fibroblasts modulated iPSC colony formation. -
Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach
Mafalda Rita Avó Bacalhau Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach Tese de doutoramento do Programa de Doutoramento em Ciências da Saúde, ramo de Ciências Biomédicas, orientada pela Professora Doutora Maria Manuela Monteiro Grazina e co-orientada pelo Professor Doutor Henrique Manuel Paixão dos Santos Girão e pela Professora Doutora Lee-Jun C. Wong e apresentada à Faculdade de Medicina da Universidade de Coimbra Julho 2017 Faculty of Medicine Establishing the pathogenicity of novel mitochondrial DNA sequence variations: a cell and molecular biology approach Mafalda Rita Avó Bacalhau Tese de doutoramento do programa em Ciências da Saúde, ramo de Ciências Biomédicas, realizada sob a orientação científica da Professora Doutora Maria Manuela Monteiro Grazina; e co-orientação do Professor Doutor Henrique Manuel Paixão dos Santos Girão e da Professora Doutora Lee-Jun C. Wong, apresentada à Faculdade de Medicina da Universidade de Coimbra. Julho, 2017 Copyright© Mafalda Bacalhau e Manuela Grazina, 2017 Esta cópia da tese é fornecida na condição de que quem a consulta reconhece que os direitos de autor são pertença do autor da tese e do orientador científico e que nenhuma citação ou informação obtida a partir dela pode ser publicada sem a referência apropriada e autorização. This copy of the thesis has been supplied on the condition that anyone who consults it recognizes that its copyright belongs to its author and scientific supervisor and that no quotation from the -
Frontiers in Integrative Genomics and Translational Bioinformatics
BioMed Research International Frontiers in Integrative Genomics and Translational Bioinformatics Guest Editors: Zhongming Zhao, Victor X. Jin, Yufei Huang, Chittibabu Guda, and Jianhua Ruan Frontiers in Integrative Genomics and Translational Bioinformatics BioMed Research International Frontiers in Integrative Genomics and Translational Bioinformatics Guest Editors: Zhongming Zhao, Victor X. Jin, Yufei Huang, Chittibabu Guda, and Jianhua Ruan Copyright © òýÔ Hindawi Publishing Corporation. All rights reserved. is is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Frontiers in Integrative Genomics and Translational Bioinformatics, Zhongming Zhao, Victor X. Jin, Yufei Huang, Chittibabu Guda, and Jianhua Ruan Volume òýÔ , Article ID Þò ¥ÀÔ, ç pages Building Integrated Ontological Knowledge Structures with Ecient Approximation Algorithms, Yang Xiang and Sarath Chandra Janga Volume òýÔ , Article ID ýÔ ò, Ô¥ pages Predicting Drug-Target Interactions via Within-Score and Between-Score, Jian-Yu Shi, Zun Liu, Hui Yu, and Yong-Jun Li Volume òýÔ , Article ID ç ýÀç, À pages RNAseq by Total RNA Library Identies Additional RNAs Compared to Poly(A) RNA Library, Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian Lehmann, Jennifer Pietenpol, David C. Samuels, and Yu Shyr Volume òýÔ , Article ID âòÔçý, À pages Construction of Pancreatic Cancer Classier Based on SVM Optimized by Improved FOA, Huiyan Jiang, Di Zhao, Ruiping Zheng, and Xiaoqi Ma Volume òýÔ , Article ID ÞÔýòç, Ôò pages OperomeDB: A Database of Condition-Specic Transcription Units in Prokaryotic Genomes, Kashish Chetal and Sarath Chandra Janga Volume òýÔ , Article ID çÔòÔÞ, Ôý pages How to Choose In Vitro Systems to Predict In Vivo Drug Clearance: A System Pharmacology Perspective, Lei Wang, ChienWei Chiang, Hong Liang, Hengyi Wu, Weixing Feng, Sara K. -
A Molecular and Genetic Analysis of Otosclerosis
A molecular and genetic analysis of otosclerosis Joanna Lauren Ziff Submitted for the degree of PhD University College London January 2014 1 Declaration I, Joanna Ziff, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Where work has been conducted by other members of our laboratory, this has been indicated by an appropriate reference. 2 Abstract Otosclerosis is a common form of conductive hearing loss. It is characterised by abnormal bone remodelling within the otic capsule, leading to formation of sclerotic lesions of the temporal bone. Encroachment of these lesions on to the footplate of the stapes in the middle ear leads to stapes fixation and subsequent conductive hearing loss. The hereditary nature of otosclerosis has long been recognised due to its recurrence within families, but its genetic aetiology is yet to be characterised. Although many familial linkage studies and candidate gene association studies to investigate the genetic nature of otosclerosis have been performed in recent years, progress in identifying disease causing genes has been slow. This is largely due to the highly heterogeneous nature of this condition. The research presented in this thesis examines the molecular and genetic basis of otosclerosis using two next generation sequencing technologies; RNA-sequencing and Whole Exome Sequencing. RNA–sequencing has provided human stapes transcriptomes for healthy and diseased stapes, and in combination with pathway analysis has helped identify genes and molecular processes dysregulated in otosclerotic tissue. Whole Exome Sequencing has been employed to investigate rare variants that segregate with otosclerosis in affected families, and has been followed by a variant filtering strategy, which has prioritised genes found to be dysregulated during RNA-sequencing. -
Université De La Méditerranée Faculte De Médecine De Marseille École Doctorale Des Sciences De La Vie Et De La Santé Centre De Recherche En Cancérologie De Marseille
UNIVERSITÉ DE LA MÉDITERRANÉE FACULTE DE MÉDECINE DE MARSEILLE ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ CENTRE DE RECHERCHE EN CANCÉROLOGIE DE MARSEILLE T H È S E Pour l’obtention du Diplôme de DOCTEUR de L’UNIVERSITÉ de la MÉDITERRANÉE SPÉCIALITÉ : Oncologie : Pharmacologie et Thérapeutique Présentée et soutenue publiquement par Mme Laetitia STUHL-GOURMAND Le 30 Mars 2010 ROLE DE NACA ET DE SES PARTENAIRES MOLÉCULAIRES DANS LA DIFFÉRENCIATION ÉRYTHROÏDE NORMALE ET PATHOLOGIQUE DES SYNDROMES MYÉLODYSPLASIQUES Directeur de Thèse : Dr Sophie GOMEZ Membres du Jury de Thèse : Pr Daniel Olive Président Pr Catherine Lacombe Rapporteur Dr Dominique Duménil Rapporteur Dr Christian Chabannon Examinateur 1 A mes deux hommes, mes deux amours : mon fils Anthony et mon mari Sébastien 2 REMERCIEMENTS Je remercie les membres du jury d’avoir accepté de juger ce travail: les Pr Catherine Lacombe, Dr Christian Chabannon, Dr Dominique Duménil et le Pr Daniel Olive de présider ce jury. Je remercie Françoise Birg de m’avoir accueillie au centre de Recherche en Cancérologie de Marseille UMR891. Je remercie ma directrice de thèse Dr Sophie Gomez a qui je dois beaucoup. Merci de m’avoir toujours soutenue tout au long de cette thèse, et de m’avoir accompagné avec patience dans l’aboutissement de ce travail à mon rythme de jeune maman. Je remercie le Dr Patrice Dubreuil de m’avoir accueilli dans son équipe, d’avoir toujours été à l’écoute, et de m’avoir soutenu pour la finalisation de mon projet. Je remercie Véronique Gelsi-Boyer, Virginie Trouplin, Daniel Birnbaum et Norvert Vey, sans qui le projet MDS n’aurait pas existé. -
Proteasome Subunit Beta Type 2 (PSMB2) Rabbit Polyclonal Antibody Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TA332716 Proteasome subunit beta type 2 (PSMB2) Rabbit Polyclonal Antibody Product data: Product Type: Primary Antibodies Applications: IF, IHC, WB Recommended Dilution: WB 1:500 - 1:2000, IHC 1:50- 1:200, IF 1:50- 1:200 Reactivity: Human, Mouse, Rat Host: Rabbit Isotype: IgG Clonality: Polyclonal Immunogen: Recombinant protein of human PSMB2 Formulation: Store at -20°C (regular) and -80°C (long term). Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide, 50% glycerol, pH7.3. Concentration: lot specific Purification: Affinity purification Conjugation: Unconjugated Storage: Store at -20°C as received. Stability: Stable for 12 months from date of receipt. Predicted Protein Size: 201 Gene Name: proteasome subunit beta 2 Database Link: NP_002785 Entrez Gene 26445 MouseEntrez Gene 29675 RatEntrez Gene 5690 Human P49721 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 Proteasome subunit beta type 2 (PSMB2) Rabbit Polyclonal Antibody – TA332716 Background: The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. -
Prediction of Meiosis-Essential Genes Based Upon the Dynamic Proteomes Responsive to Spermatogenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.05.936435; this version posted February 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Prediction of meiosis-essential genes based upon the dynamic proteomes responsive to spermatogenesis Kailun Fang1,2,3,8, Qidan Li3,4,5,8, Yu Wei2,3,8, Jiaqi Shen6,8, Wenhui Guo3,4,5,7,8, Changyang Zhou2,3,8, Ruoxi Wu1, Wenqin Ying2, Lu Yu1,2, Jin Zi5, Yuxing Zhang3,4,5, Hui Yang2,3,9*, Siqi Liu3,4,5,9*, Charlie Degui Chen1,3,9* 1. State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. 2. State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. 3. University of the Chinese Academy of Sciences, Beijing 100049, China. 4. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. 5. BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China. 6. United World College Changshu China, Jiangsu 215500, China. 7. Malvern College Qingdao, Shandong, 266109, China 8. -
Gene Expression Profiling of Corpus Luteum Reveals the Importance Of
bioRxiv preprint doi: https://doi.org/10.1101/673558; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Gene expression profiling of corpus luteum reveals the 2 importance of immune system during early pregnancy in 3 domestic sheep. 4 Kisun Pokharel1, Jaana Peippo2 Melak Weldenegodguad1, Mervi Honkatukia2, Meng-Hua Li3*, Juha 5 Kantanen1* 6 1 Natural Resources Institute Finland (Luke), Jokioinen, Finland 7 2 Nordgen – The Nordic Genetic Resources Center, Ås, Norway 8 3 College of Animal Science and Technology, China Agriculture University, Beijing, China 9 * Correspondence: MHL, [email protected]; JK, [email protected] 10 Abstract: The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus 11 the most critical period determining reproductive success. While ovulation rate is the major determinant of 12 litter size in sheep, interactions among the conceptus, corpus luteum and endometrium are essential for 13 pregnancy success. Here, we performed a comparative transcriptome study by sequencing total mRNA from 14 corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 15 crosses, and mapping the RNA-Seq reads to the latest Rambouillet reference genome. A total of 21,287 genes 16 were expressed in our dataset. Highly expressed autosomal genes in the CL were associated with biological 17 processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (eg. -
Naca Mouse Shrna Plasmid (Locus ID 17938) – TL501429 | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TL501429 Naca Mouse shRNA Plasmid (Locus ID 17938) Product data: Product Type: shRNA Plasmids Product Name: Naca Mouse shRNA Plasmid (Locus ID 17938) Locus ID: 17938 Synonyms: AL022831; AL024382; Gm1878; mKIAA0363; skNAC Vector: pGFP-C-shLenti (TR30023) Format: Lentiviral plasmids Components: Naca - Mouse, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 17938). 5µg purified plasmid DNA per construct Non-effective 29-mer scrambled shRNA cassette in pGFP-C-shLenti Vector, TR30021, included for free. RefSeq: BC083340, BC099375, NM_001113199, NM_001282976, NM_013608, BC029830 Summary: Prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). Binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER. Also reduces the inherent affinity of ribosomes for protein translocation sites in the ER membrane (M sites) (By similarity). Isoform 1 and isoform 2 appear to bind DNA and play roles in transcription. Isoform 1 may function as a specific coactivator for JUN, acting to stabilize the interaction of JUN homodimers with promoter elements. [UniProtKB/Swiss-Prot Function] shRNA Design: These shRNA constructs were designed against multiple splice variants at this gene locus. To be certain that your variant of interest is targeted, please contact [email protected]. If you need a special design or shRNA sequence, please utilize our custom shRNA service.