Human T-Complex Protein 11 (TCP11), a Testis-Specific Gene Product, Is a Potential Determinant of the Sperm Morphology
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Computational Genome-Wide Identification of Heat Shock Protein Genes in the Bovine Genome [Version 1; Peer Review: 2 Approved, 1 Approved with Reservations]
F1000Research 2018, 7:1504 Last updated: 08 AUG 2021 RESEARCH ARTICLE Computational genome-wide identification of heat shock protein genes in the bovine genome [version 1; peer review: 2 approved, 1 approved with reservations] Oyeyemi O. Ajayi1,2, Sunday O. Peters3, Marcos De Donato2,4, Sunday O. Sowande5, Fidalis D.N. Mujibi6, Olanrewaju B. Morenikeji2,7, Bolaji N. Thomas 8, Matthew A. Adeleke 9, Ikhide G. Imumorin2,10,11 1Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria 2International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA 3Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico 5Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria 6Usomi Limited, Nairobi, Kenya 7Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria 8Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA 9School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa 10School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA 11African Institute of Bioscience Research and Training, Ibadan, Nigeria v1 First published: 20 Sep 2018, 7:1504 Open Peer Review https://doi.org/10.12688/f1000research.16058.1 Latest published: 20 Sep 2018, 7:1504 https://doi.org/10.12688/f1000research.16058.1 Reviewer Status Invited Reviewers Abstract Background: Heat shock proteins (HSPs) are molecular chaperones 1 2 3 known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, version 1 we carried out a computational genome-wide survey of the bovine 20 Sep 2018 report report report genome. -
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UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Asha Marie Miles December 2019 © 2019 Asha Marie Miles UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH Asha Marie Miles, Ph. D. Cornell University 2019 This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic cell score (SCS). Composite milk samples were collected across 6 sampling periods representing key lactation stages: 0-1 day in milk (DIM), 3- 5 DIM, 10-14 DIM, 50-60 DIM, 90-110 DIM, and 210-230 DIM. Cows were scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Independent multivariable logistic regression models were used to generate odds ratios for elevated SCC (≥ 200,000 cells/ml) and farm-diagnosed clinical mastitis. Within our study cohort, loose fore udder attachment, flat teat ends, low rear udder height, and wide rear teats were associated with increased odds of mastitis. Principal component analysis was performed on these traits to create a single new phenotype describing mastitis susceptibility based on these high-risk phenotypes. Cows (N = 471) were genotyped on the Illumina BovineHD 777K SNP chip and considering all 14 traits of interest, a total of 56 genome-wide associations (GWA) were performed and 28 significantly associated quantitative trait loci (QTL) were identified. -
Taf7l Cooperates with Trf2 to Regulate Spermiogenesis
Taf7l cooperates with Trf2 to regulate spermiogenesis Haiying Zhoua,b, Ivan Grubisicb,c, Ke Zhengd,e, Ying Heb, P. Jeremy Wangd, Tommy Kaplanf, and Robert Tjiana,b,1 aHoward Hughes Medical Institute and bDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720; cUniversity of California Berkeley–University of California San Francisco Graduate Program in Bioengineering, University of California, Berkeley, CA 94720; dDepartment of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104; eState Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, People’s Republic of China; and fSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel Contributed by Robert Tjian, September 11, 2013 (sent for review August 20, 2013) TATA-binding protein (TBP)-associated factor 7l (Taf7l; a paralogue (Taf4b; a homolog of Taf4) (9), TBP-related factor 2 (Trf2) (10, of Taf7) and TBP-related factor 2 (Trf2) are components of the core 11), and Taf7l (12, 13). For example, mice bearing mutant or promoter complex required for gene/tissue-specific transcription deficient CREM showed decreased postmeiotic gene expression of protein-coding genes by RNA polymerase II. Previous studies and defective spermiogenesis (14). Mice deficient in Taf4b, reported that Taf7l knockout (KO) mice exhibit structurally abnor- a testis-specific homolog of Taf4, are initially normal but undergo mal sperm, reduced sperm count, weakened motility, and compro- progressive germ-cell loss and become infertile by 3 mo of age −/Y mised fertility. -
Co-Expression Module Analysis Reveals Biological Processes
Shi et al. BMC Systems Biology 2010, 4:74 http://www.biomedcentral.com/1752-0509/4/74 RESEARCH ARTICLE Open Access Co-expressionResearch article module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression Zhiao Shi1,2, Catherine K Derow3 and Bing Zhang*3 Abstract Background: Gene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest. However, individual gene-based signatures usually suffer from low reproducibility and interpretability. Results: We have developed a novel algorithm Iterative Clique Enumeration (ICE) for identifying relatively independent maximal cliques as co-expression modules and a module-based approach to the analysis of gene expression data. Applying this approach on a public breast cancer dataset identified 19 modules whose expression levels were significantly correlated with tumor grade. The correlations were reproducible for 17 modules in an independent breast cancer dataset, and the reproducibility was considerably higher than that based on individual genes or modules identified by other algorithms. Sixteen out of the 17 modules showed significant enrichment in certain Gene Ontology (GO) categories. Specifically, modules related to cell proliferation and immune response were up-regulated in high- grade tumors while those related to cell adhesion was down-regulated. Further analyses showed that transcription factors NYFB, E2F1/E2F3, NRF1, and ELK1 were responsible for the up-regulation of the cell proliferation modules. IRF family and ETS family proteins were responsible for the up-regulation of the immune response modules. Moreover, inhibition of the PPARA signaling pathway may also play an important role in tumor progression. -
35Th International Society for Animal Genetics Conference 7
35th INTERNATIONAL SOCIETY FOR ANIMAL GENETICS CONFERENCE 7. 23.16 – 7.27. 2016 Salt Lake City, Utah ABSTRACT BOOK https://www.asas.org/meetings/isag2016 INVITED SPEAKERS S0100 – S0124 https://www.asas.org/meetings/isag2016 epigenetic modifications, such as DNA methylation, and measuring different proteins and cellular metab- INVITED SPEAKERS: FUNCTIONAL olites. These advancements provide unprecedented ANNOTATION OF ANIMAL opportunities to uncover the genetic architecture GENOMES (FAANG) ASAS-ISAG underlying phenotypic variation. In this context, the JOINT SYMPOSIUM main challenge is to decipher the flow of biological information that lies between the genotypes and phe- notypes under study. In other words, the new challenge S0100 Important lessons from complex genomes. is to integrate multiple sources of molecular infor- T. R. Gingeras* (Cold Spring Harbor Laboratory, mation (i.e., multiple layers of omics data to reveal Functional Genomics, Cold Spring Harbor, NY) the causal biological networks that underlie complex traits). It is important to note that knowledge regarding The ~3 billion base pairs of the human DNA rep- causal relationships among genes and phenotypes can resent a storage devise encoding information for be used to predict the behavior of complex systems, as hundreds of thousands of processes that can go on well as optimize management practices and selection within and outside a human cell. This information is strategies. Here, we describe a multi-step procedure revealed in the RNAs that are composed of 12 billion for inferring causal gene-phenotype networks underly- nucleotides, considering the strandedness and allelic ing complex phenotypes integrating multi-omics data. content of each of the diploid copies of the genome. -
Spermatozoa Protein Alterations in Infertile Men with Bilateral Varicocele
Asian Journal of Andrology (2016) 18, 43–53 © 2016 AJA, SIMM & SJTU. All rights reserved 1008-682X www.asiaandro.com; www.ajandrology.com Open Access ORIGINAL ARTICLE Spermatozoa protein alterations in infertile men with bilateral varicocele Male Infertility Ashok Agarwal1,*, Rakesh Sharma1,*, Damayanthi Durairajanayagam1,2, Zhihong Cui1, Ahmet Ayaz1, Sajal Gupta1, Belinda Willard3, Banu Gopalan3, Edmund Sabanegh1 Among infertile men, a diagnosis of unilateral varicocele is made in 90% of varicocele cases and bilateral in the remaining varicocele cases. However, there are reports of under‑diagnosis of bilateral varicocele among infertile men and that its prevalence is greater than 10%. In this prospective study, we aimed to examine the differentially expressed proteins (DEP) extracted from spermatozoa cells of patients with bilateral varicocele and fertile donors. Subjects consisted of 17 men diagnosed with bilateral varicocele and 10 proven fertile men as healthy controls. Using the LTQ‑orbitrap elite hybrid mass spectrometry system, proteomic analysis was done on pooled samples from 3 patients with bilateral varicocele and 5 fertile men. From these samples, 73 DEP were identified of which 58 proteins were differentially expressed, with 7 proteins unique to the bilateral varicocele group and 8 proteins to the fertile control group. Majority of the DEPs were observed to be associated with metabolic processes, stress responses, oxidoreductase activity, enzyme regulation, and immune system processes. Seven DEP were involved in sperm function such as capacitation, motility, and sperm‑zona binding. Proteins TEKT3 and TCP11 were validated by Western blot analysis and may serve as potential biomarkers for bilateral varicocele. In this study, we have demonstrated for the first time the presence of DEP and identified proteins with distinct reproductive functions which are altered in infertile men with bilateral varicocele. -
Comparative Genomics Reveals Gene-Specific and Shared Regulatory Sequences in the Spermatid-Expressed Mammalian Odf1, Prm1, Prm2
Genomics 92 (2008) 101–106 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Comparative genomics reveals gene-specific and shared regulatory sequences in the spermatid-expressed mammalian Odf1, Prm1, Prm2, Tnp1, and Tnp2 genes☆ Kenneth C. Kleene ⁎, Jana Bagarova Department of Biology, University of Massachusetts at Boston, Boston, MA 02125, USA ARTICLE INFO ABSTRACT Article history: The comparative genomics of the Odf1, Prm1, Prm2, Tnp1, and Tnp2 genes in 13–21 diverse mammalian Received 6 January 2008 species reveals striking similarities and differences in the sequences that probably function in the Accepted 1 May 2008 transcriptional and translational regulation of gene expression in haploid spermatogenic cells, spermatids. Available online 17 June 2008 The 5′ flanking regions contain putative TATA boxes and cAMP-response elements (CREs), but the TATA boxes and CREs exhibit gene-specific sequences, and an overwhelming majority of CREs differ from the consensus Keywords: ′ ′ fi Comparative genomics sequence. The 5 and 3 UTRs contain highly conserved gene-speci c sequences including canonical and Translational regulation noncanonical poly(A) signals and a suboptimal context for the Tnp2 translation initiation codon. The Spermatid conservation of the 5′ UTR is unexpected because mRNA translation in spermatids is thought to be regulated Protamine primarily by the 3′ UTR. Finally, all of the genes contain a single intron, implying that retroposons are rarely Transition protein created from mRNAs that are expressed in spermatids. Outer dense fiber 1 © 2008 Elsevier Inc. All rights reserved. TATA box CREMτ Noncanonical poly(A) signal Retroposon Introduction [4]. The importance of delaying translation is demonstrated by reports that premature translation of the Prm1 and Tnp2 mRNAs in round The haploid, differentiation phase of spermatogenesis in mammals spermatids in transgenic mice impairs male fertility [5,6]. -
(QQ) Plot of the Discovery Meta-Analysis P
1. SUPPLEMENTARY FIGURES Supplementary Figure 1. Quantile-quantile (Q-Q) plot of the discovery meta-analysis p-values before (red) (lambda=1.028) and after removing any SNPs within 500 kb of a previously established locus (green). Supplementary Figure 2. Manhattan plot of the discovery meta-analysis –log10 p-values by chromosome position. Each chromosome is plotted with a different color. The dashed horizontal line indicates genome-wide significance (5x10-8). a. b. Supplementary Figure 3. Regional plots of the suggestive loci, 4q24 (a) and 3p22.2 (b), are plotted by position on chromosome against the association with CLL (-log P-value) from the discovery fixed effects meta-analysis (dots) and for the lead SNP, the combined discovery and replication fixed effects meta-analysis (purple diamond). The lead SNPs, rs10028805 at 4q24 and rs1274963 at 3p22.2, are shown in purple. Estimated recombination rates (from 1000 Genomes) are plotted in blue. The SNPs surrounding the most significant SNP are color-coded to reflect their correlation with this SNP. Pairwise r2 values are from 1000 Genomes European data (March 2012 release). Genes, position of exons, and direction of transcription from UCSC genome browser (genome.ucsc.edu) are noted. Plots were generated using LocusZoom (http://csg.sph.umich.edu/locuszoom). Supplementary Figure 4. Chromatin states at new and suggestive CLL SNPs and proxies (r2>0.8) Supplementary Figure 5. Pathways identified by Webgestalt 2. SUPPLEMENTARY TABLES Supplementary Table 1. Description and study design of studies -
Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo -
Reproductionresearch
REPRODUCTIONRESEARCH Haplo-deficiency of ODF1/HSPB10 in mouse sperm causes relaxation of head-to-tail linkage Kefei Yang, Pawel Grzmil1,2, Andreas Meinhardt3 and Sigrid Hoyer-Fender Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, Georg-August-Universita¨tGo¨ttingen, 37077 Go¨ttingen, Germany, 1Institute of Human Genetics, University Medicine, Heinrich-Du¨ker-Weg 12, Georg-August-Universita¨tGo¨ttingen, 37077 Go¨ttingen, Germany, 2Department of Genetics and Evolution, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Krako´w, Poland and 3Department of Anatomy and Cell Biology, Aulweg 123, Justus-Liebig-University Gießen, 35392 Gießen, Germany Correspondence should be addressed to S Hoyer-Fender; Email: [email protected] Abstract The small heat shock protein ODF1/HSPB10 is essential for male fertility in mice. Targeted deletion of Odf1 resulted in acephalic sperm in homozygous mice of mixed background (C57BL/6J//129/Sv), whereas heterozygous animals are fully fertile. To further elucidate the function of ODF1, we generated incipient congenic mice with targeted deletion of Odf1 by successive backcrossing on the 129/Sv C K background. We observed that fecundity of heterozygous Odf1 / male mice was severely reduced over backcross generations. However, neither aberrant sperm parameters nor sperm anomalies could be observed. Ultra-structural analyses of sperm from incipient C K congenic heterozygous Odf1 / males of backcross generation N7 revealed no obvious pathological findings. However, we observed an enlargement of the distance between nuclear membrane and capitulum, indicating a weakening of the sperm head-to-tail coupling. Severe male subfertility provoked by haplo-deficiency of ODF1 is therefore most probably caused by impaired head-to-tail coupling that eventually might induce sperm decapitation on the specific conditions of in vivo fertilisation. -
The ZNF76 Rs10947540 Polymorphism Associated With
www.nature.com/scientificreports OPEN The ZNF76 rs10947540 polymorphism associated with systemic lupus erythematosus risk in Chinese populations Yuan‑yuan Qi1,4, Yan Cui1,4, Hui Lang2, Ya‑ling Zhai1, Xiao‑xue Zhang1, Xiao‑yang Wang1, Xin‑ran Liu1, Ya‑fei Zhao1, Xiang‑hui Ning3 & Zhan‑zheng Zhao1* Systemic lupus erythematosus (SLE) is a typical autoimmune disease with a strong genetic disposition. Genetic studies have revealed that single‑nucleotide polymorphisms (SNPs) in zinc fnger protein (ZNF)‑coding genes are associated with susceptibility to autoimmune diseases, including SLE. The objective of the current study was to evaluate the correlation between ZNF76 gene polymorphisms and SLE risk in Chinese populations. A total of 2801 individuals (1493 cases and 1308 controls) of Chinese Han origin were included in this two‑stage genetic association study. The expression of ZNF76 was evaluated, and integrated bioinformatic analysis was also conducted. The results showed that 28 SNPs were associated with SLE susceptibility in the GWAS cohort, and the association of rs10947540 was successfully replicated in the independent replication cohort −2 (Preplication = 1.60 × 10 , OR 1.19, 95% CI 1.03–1.37). After meta‑analysis, the association between −6 rs10947540 and SLE was pronounced (Pmeta = 9.62 × 10 , OR 1.29, 95% CI 1.15–1.44). Stratifed analysis suggested that ZNF76 rs10947540 C carriers were more likely to develop relatively high levels of serum creatinine (Scr) than noncarriers (CC + CT vs. TT, p = 9.94 × 10−4). The bioinformatic analysis revealed that ZNF76 rs10947540 was annotated as an eQTL and that rs10947540 was correlated with decreased expression of ZNF76. -
(12) United States Patent (10) Patent No.: US 7,671,085 B2 Downes Et Al
USOO7671085B2 (12) United States Patent (10) Patent No.: US 7,671,085 B2 DOWnes et al. (45) Date of Patent: Mar. 2, 2010 (54) NON-STEROIDAL FARNESOIDX RECEPTOR 4,265,874 A 5/1981 Bonsen et al. MODULATORS AND METHODS FOR THE 5,151,442 A 9, 1992 Garcia et al. USE THEREOF FOREIGN PATENT DOCUMENTS (75) Inventors: Michael R. Downes, San Diego, CA WO WOOO/37077 6, 2000 (US); Ronald M. Evans, La Jolla, CA WO WOOOf 76.523 12/2000 (US) WO WO 2004/046.162 6, 2004 OTHER PUBLICATIONS (73) Assignee: The Salk Institute for Biological Fi1Orucci iS. S, RizzoRIZZO (J,G. DoniniJonini A,A. DistruttiJS 1 E.E, and SanlucciSantucci L.L, “Targetilargeting Studies, La Jolla, CA (US) farnesoid X receptor for liver and metabolic disorders.” Trends in c - r Molecular Medicine, Jul. 2007. 13(7) 298–309.* (*) Notice: Subj ect to any disclaimer, the term of this Scotti E, Gilardi F. Godio C, Gers E, Krneta J. Mitro N. De Fabiani E. patent is extended or adjusted under 35 Caruso D, and Crestani M. "Bile acids and their signaling pathways: U.S.C. 154(b) by 907 days. eclectic regulators of diverse cellular functions.” Cellular and Molecular Life Sciences, Oct. 2007, 64(19-20), 2477-2491.* (21) Appl. No.: 10/535,043 Laffitte et al., “Identification of the DNA binding specificity and potential target genes for the farnesoid X-activated receptor.” Journal (22) PCT Filed: Nov. 14, 2003 of Biological Chemistry, 275: 10638-10647, 2000. Nicolaou et al., “Natural product-like combinatorial libraries based (86).