2 to Support Spermatogenesis but Not Normal Sperm Function and Fertility†
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Maria João Abordagem À Regulação Da Mobilidade Do Martinho De Freitas Espermatozoide Através Da Caracterização E Modulação Da Via De Sinalização GSK3/PPP1R2/PPP1
Universidade de Aveiro Departamento de Biologia Ano 2018 Maria João Abordagem à regulação da mobilidade do Martinho de Freitas espermatozoide através da caracterização e modulação da via de sinalização GSK3/PPP1R2/PPP1 Addressing sperm motility regulation through characterization and modulation of the GSK3/PPP1R2/PPP1 signaling pathway Universidade de Aveiro Departamento de Biologia Ano 2018 Maria João Abordagem à regulação da mobilidade do Martinho de Freitas espermatozoide através da caracterização e modulação da via de sinalização GSK3/PPP1R2/PPP1 Addressing sperm motility regulation through characterization and modulation of the GSK3/PPP1R2/PPP1 signaling pathway Tese apresentada à Universidade de Aveiro para cumprimento dos requisitos necessários à obtenção do grau de Doutor em Biologia, realizada sob a orientação científica da Doutora Margarida de Sâncio da Cruz Fardilha, Professora Professora Auxiliar do Departamento de Ciências Médicas da Universidade de Aveiro e do Doutor Srinivasan Vijayaraghavan, Professor Professor Auxiliar do Departamento de Ciências Biológicas da Kent State University. Este trabalho é financiado por Fundos FEDER através do Programa Operacional Fatores de Competitividade-COMPETE e por Fundos Nacionais através da FCT- Fundação para a Ciência e a Tecnologia no âmbito dos projetos «PTDC/DTP-PIC/0460/2012»; «PTDB/BBB-BQB/3804/2014»; «NIH R15 HD068971-01»; da bolsa individual «SFRH/BD/84876/2012»; e do instituto de Biomedicina- iBiMED «UID/BIM/04501/2013». o júri presidente Professor Doutor Amadeu Mortágua Velho -
Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
Growth and Molecular Profile of Lung Cancer Cells Expressing Ectopic LKB1: Down-Regulation of the Phosphatidylinositol 3-Phosphate Kinase/PTEN Pathway1
[CANCER RESEARCH 63, 1382–1388, March 15, 2003] Growth and Molecular Profile of Lung Cancer Cells Expressing Ectopic LKB1: Down-Regulation of the Phosphatidylinositol 3-Phosphate Kinase/PTEN Pathway1 Ana I. Jimenez, Paloma Fernandez, Orlando Dominguez, Ana Dopazo, and Montserrat Sanchez-Cespedes2 Molecular Pathology Program [A. I. J., P. F., M. S-C.], Genomics Unit [O. D.], and Microarray Analysis Unit [A. D.], Spanish National Cancer Center, 28029 Madrid, Spain ABSTRACT the cell cycle in G1 (8, 9). However, the intrinsic mechanism by which LKB1 activity is regulated in cells and how it leads to the suppression Germ-line mutations in LKB1 gene cause the Peutz-Jeghers syndrome of cell growth is still unknown. It has been proposed that growth (PJS), a genetic disease with increased risk of malignancies. Recently, suppression by LKB1 is mediated through p21 in a p53-dependent LKB1-inactivating mutations have been identified in one-third of sporadic lung adenocarcinomas, indicating that LKB1 gene inactivation is critical in mechanism (7). In addition, it has been observed that LKB1 binds to tumors other than those of the PJS syndrome. However, the in vivo brahma-related gene 1 protein (BRG1) and this interaction is required substrates of LKB1 and its role in cancer development have not been for BRG1-induced growth arrest (10). Similar to what happens in the completely elucidated. Here we show that overexpression of wild-type PJS, Lkb1 heterozygous knockout mice show gastrointestinal hamar- LKB1 protein in A549 lung adenocarcinomas cells leads to cell-growth tomatous polyposis and frequent hepatocellular carcinomas (11, 12). suppression. To examine changes in gene expression profiles subsequent to Interestingly, the hamartomas, but not the malignant tumors, arising in exogenous wild-type LKB1 in A549 cells, we used cDNA microarrays. -
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bioRxiv preprint doi: https://doi.org/10.1101/742379; this version posted August 24, 2019. 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 4.0 International license. Pathogenic impact of isoform switches in 1209 cancer samples covering 27 cancer types using an isoform-specific interaction network Abdullah Kahraman1,2,3 and Christian von Mering1,3 1 University of Zurich, Institute of Molecular Life Sciences (Zurich, Switzerland) 2 University Hospital Zurich, Department of Pathology and Molecular Pathology, Molecular Tumor Profiling lab (Zurich, Switzerland) 3 Swiss Institute of Bioinformatics Abstract Under normal conditions, cells of almost all tissues types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). But what is the pathogenic impact of these switches and how are they driving oncogenesis? To address these questions, we have developed CanIsoNet, a novel isoform-specific protein-protein interaction network that identifies binding domain losses and interaction disruptions in known alternatively spliced isoforms. We applied CanIsoNet on 1209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDTs (cMDT) between cancer types. While carcinomas of the head and neck, and brain had none or few cMDT switches, cancers of the female reproduction organs showed the highest number of cMDTs. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses 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 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
734483V2.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/734483; this version posted August 14, 2019. 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. Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells Haifeng Wang1, Muneaki Nakamura1, Dehua Zhao1, Cindy M Nguyen1, Cordelia Yu1,2, Albert Lo1, Timothy Daley1,3, Marie La Russa1, Yanxia Liu1, Lei S Qi1, 4, 5* 1Department of Bioengineering, Stanford University, Stanford, CA 94305, USA 2Castilleja School, Palo Alto, CA 94301, USA 3Department of Statistics, Stanford University, Stanford, CA 94305, USA 4Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA 5ChEM-H Institute, Stanford University, Stanford, CA 94305, USA *Correspondence to: [email protected] (L.S.Q.) 1 bioRxiv preprint doi: https://doi.org/10.1101/734483; this version posted August 14, 2019. 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 Visualizing the real-time dynamics of genome rearrangement in single living cells is core to studying genomics and diagnostics. Here, we report a robust, versatile approach named CRISPR Live-cell fluorescent in situ hybridization (LiveFISH) for multi-locus genome tracking and cytogenetic detection in a broad variety of cell types including primary cells. LiveFISH utilizes an intrinsic stability switch of CRISPR guide RNAs, which enables efficient and accurate detection of chromosomal disorders such as Patau Syndrome in prenatal amniotic fluid cells and allows multi-locus tracking in human T lymphocytes. -
Duke University Dissertation Template
Gene-Environment Interactions in Cardiovascular Disease by Cavin Keith Ward-Caviness Graduate Program in Computational Biology and Bioinformatics Duke University Date:_______________________ Approved: ___________________________ Elizabeth R. Hauser, Supervisor ___________________________ William E. Kraus ___________________________ Sayan Mukherjee ___________________________ H. Frederik Nijhout Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate Program in Computational Biology and Bioinformatics in the Graduate School of Duke University 2014 i v ABSTRACT Gene-Environment Interactions in Cardiovascular Disease by Cavin Keith Ward-Caviness Graduate Program in Computational Biology and Bioinformatics Duke University Date:_______________________ Approved: ___________________________ Elizabeth R. Hauser, Supervisor ___________________________ William E. Kraus ___________________________ Sayan Mukherjee ___________________________ H. Frederik Nijhout An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate Program in Computational Biology and Bioinformatics in the Graduate School of Duke University 2014 Copyright by Cavin Keith Ward-Caviness 2014 Abstract In this manuscript I seek to demonstrate the importance of gene-environment interactions in cardiovascular disease. This manuscript contains five studies each of which contributes to our understanding of the joint impact of genetic variation -
A Single-Cell Transcriptome Atlas of the Mouse Glomerulus
RAPID COMMUNICATION www.jasn.org A Single-Cell Transcriptome Atlas of the Mouse Glomerulus Nikos Karaiskos,1 Mahdieh Rahmatollahi,2 Anastasiya Boltengagen,1 Haiyue Liu,1 Martin Hoehne ,2 Markus Rinschen,2,3 Bernhard Schermer,2,4,5 Thomas Benzing,2,4,5 Nikolaus Rajewsky,1 Christine Kocks ,1 Martin Kann,2 and Roman-Ulrich Müller 2,4,5 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Three different cell types constitute the glomerular filter: mesangial depending on cell location relative to the cells, endothelial cells, and podocytes. However, to what extent cellular heteroge- glomerular vascular pole.3 Because BP ad- neity exists within healthy glomerular cell populations remains unknown. aptation and mechanoadaptation of glo- merular cells are key determinants of kidney Methods We used nanodroplet-based highly parallel transcriptional profiling to function and dysregulated in kidney disease, characterize the cellular content of purified wild-type mouse glomeruli. we tested whether glomerular cell type sub- Results Unsupervised clustering of nearly 13,000 single-cell transcriptomes identi- sets can be identified by single-cell RNA fied the three known glomerular cell types. We provide a comprehensive online sequencing in wild-type glomeruli. This atlas of gene expression in glomerular cells that can be queried and visualized using technique allows for high-throughput tran- an interactive and freely available database. Novel marker genes for all glomerular scriptome profiling of individual cells and is cell types were identified and supported by immunohistochemistry images particularly suitable for identifying novel obtained from the Human Protein Atlas. -
IGF1R Deficiency Attenuates Acute Inflammatory Response in A
www.nature.com/scientificreports OPEN IGF1R deficiency attenuates acute inflammatory response in a bleomycin-induced lung injury Received: 7 November 2016 Accepted: 17 May 2017 mouse model Published: xx xx xxxx Sergio Piñeiro-Hermida1, Icíar P. López1, Elvira Alfaro-Arnedo1, Raquel Torrens1, María Iñiguez2, Lydia Alvarez-Erviti3, Carlos Ruíz-Martínez4 & José G. Pichel 1 IGF1R (Insulin-like Growth Factor 1 Receptor) is a tyrosine kinase with pleiotropic cellular functions. IGF activity maintains human lung homeostasis and is implicated in pulmonary diseases such as cancer, ARDS, COPD, asthma and fibrosis. Here we report that lung transcriptome analysis in mice with a postnatally-induced Igf1r gene deletion showed differentially expressed genes with potentially protective roles related to epigenetics, redox and oxidative stress. After bleomycin-induced lung injury, IGF1R-deficient mice demonstrated improved survival within a week. Three days post injury, IGF1R- deficient lungs displayed changes in expression of IGF system-related genes and reduced vascular fragility and permeability. Mutant lungs presented reduced inflamed area, down-regulation of pro- inflammatory markers and up-regulation of resolution indicators. Decreased inflammatory cell presence in BALF was reflected in diminished lung infiltration mainly affecting neutrophils, also corroborated by reduced neutrophil numbers in bone marrow, as well as reduced lymphocyte and alveolar macrophage counts. Additionally, increased SFTPC expression together with hindered HIF1A expression and augmented levels of Gpx8 indicate that IGF1R deficiency protects against alveolar damage. These findings identify IGF1R as an important player in murine acute lung inflammation, suggesting that targeting IGF1R may counteract the inflammatory component of many lung diseases. Inflammation is a relevant component of many lung diseases including ARDS, COPD, asthma, cancer, fibrosis and pneumonia1–5. -
Gene Expression Differences Associated with Human Papillomavirus Status in Head and Neck Squamous Cell Carcinoma Robbertj.C
Human Cancer Biology Gene Expression Differences Associated with Human Papillomavirus Status in Head and Neck Squamous Cell Carcinoma RobbertJ.C. Slebos,1, 2 Yajun Yi, 7 Kim Ely,3 Jesse Carter,8 Amy Evjen,1Xueqiong Zhang,4 Yu Shyr,4 Barbara M. Murphy,8 Anthony J. Cmelak,5 Brian B. Burkey,2 James L. Netterville,2 Shawn Levy,6 Wendell G. Yarbrough,1, 2 and Christine H. Chung8 Abstract Human papillomavirus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC). Between 15% and 35% of HNSCCs harbor HPV DNA. Demographic and exposure differences between HPV-positive (HPV+) and negative (HPVÀ) HNSCCs suggest that HPV + tumors may constitute a subclass with different biology, whereas clinical differences have also been observed. Gene expression profiles of HPV+ and HPVÀ tumors were compared with further exploration of the biological effect of HPV in HNSCC. Thirty-six HNSCC tumors were analyzed using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV by PCR and real-time PCR. Eight of 36 (22%) tumors were positive for HPV subtype 16. Statistical analysis using Significance Analysis of Microarrays based on HPV status as a supervising variable resulted in a list of 91genes that were differentially expressed with statistical significance. Results for a subset of these genes were verified by real-time PCR. Genes highly expressed in HPV+ samples included cell cycle regulators (p16INK4A, p18, and CDC7) and transcription factors (TAF7L, RFC4, RPA2, andTFDP2).The microarray data were also investigated by mapping genes by chromosomal loca- tion (DIGMAP).A large number of genes on chromosome 3q24-qter had high levels of expression in HPV+ tumors. -
Coordinated Downregulation of Spinophilin and the Catalytic Subunits of PP1, PPP1CA/B/C, Contributes to a Worse Prognosis in Lung Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 62), pp: 105196-105210 Research Paper Coordinated downregulation of Spinophilin and the catalytic subunits of PP1, PPP1CA/B/C, contributes to a worse prognosis in lung cancer Eva M. Verdugo-Sivianes1,2, Lola Navas1,2, Sonia Molina-Pinelo1,2, Irene Ferrer2,3, Alvaro Quintanal-Villalonga3, Javier Peinado1,4, Jose M. Garcia-Heredia1,2,5, Blanca Felipe-Abrio1,2, Sandra Muñoz-Galvan1,2, Juan J. Marin1,2,6, Luis Montuenga2,7, Luis Paz-Ares2,3 and Amancio Carnero1,2 1Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain 2CIBER de Cáncer, Instituto de Salud Carlos III, Pabellón 11, Planta 0, Madrid, Spain 3H120-CNIO Lung Cancer Clinical Research Unit, Instituto de Investigación Hospital 12 de Octubre and CNIO, Madrid, Spain 4Radiation Oncology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain 5Department of Vegetal Biochemistry and Molecular Biology, University of Seville, Seville, Spain 6Department of Predictive Medicine and Public Health, Universidad de Sevilla, Sevilla, Spain 7Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Pamplona, Spain Correspondence to: Amancio Carnero, email: [email protected] Keywords: Spinophilin; PP1; biomarker; lung cancer; therapy Received: May 13, 2017 Accepted: September 03, 2017 Published: October 26, 2017 Copyright: Verdugo-Sivianes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. -
TXNDC5, a Newly Discovered Disulfide Isomerase with a Key Role in Cell Physiology and Pathology
Int. J. Mol. Sci. 2014, 15, 23501-23518; doi:10.3390/ijms151223501 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review TXNDC5, a Newly Discovered Disulfide Isomerase with a Key Role in Cell Physiology and Pathology Elena Horna-Terrón 1, Alberto Pradilla-Dieste 1, Cristina Sánchez-de-Diego 1 and Jesús Osada 2,3,* 1 Grado de Biotecnología, Universidad de Zaragoza, Zaragoza E-50013, Spain; E-Mails: [email protected] (E.H.-T.); [email protected] (A.P.-D.); [email protected] (C.S.-D.) 2 Departamento Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS), Universidad de Zaragoza, Zaragoza E-50013, Spain 3 CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid E-28029, Spain * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +34-976-761-644; Fax: +34-976-761-612. External Editor: Johannes Haybaeck Received: 16 September 2014; in revised form: 1 December 2014 / Accepted: 5 December 2014 / Published: 17 December 2014 Abstract: Thioredoxin domain-containing 5 (TXNDC5) is a member of the protein disulfide isomerase family, acting as a chaperone of endoplasmic reticulum under not fully characterized conditions As a result, TXNDC5 interacts with many cell proteins, contributing to their proper folding and correct formation of disulfide bonds through its thioredoxin domains. Moreover, it can also work as an electron transfer reaction, recovering the functional isoform of other protein disulfide isomerases, replacing reduced glutathione in its role. Finally, it also acts as a cellular adapter, interacting with the N-terminal domain of adiponectin receptor.