Modification of Crocodile Spermatozoa Refutes the Tenet That Post-Testicular Sperm Maturation Is Restricted to Mammals
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Gene Expression and Splicing Alterations Analyzed by High Throughput RNA Sequencing of Chronic Lymphocytic Leukemia Specimens
Liao et al. BMC Cancer (2015) 15:714 DOI 10.1186/s12885-015-1708-9 RESEARCH ARTICLE Open Access Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens Wei Liao1, Gwen Jordaan1, Phillipp Nham2, Ryan T. Phan2, Matteo Pelegrini3 and Sanjai Sharma1,4* Abstract Background: To determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed. Methods: Ten CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system. Results: An average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). -
Astrin-SKAP Complex Reconstitution Reveals Its Kinetochore
RESEARCH ARTICLE Astrin-SKAP complex reconstitution reveals its kinetochore interaction with microtubule-bound Ndc80 David M Kern1,2, Julie K Monda1,2†, Kuan-Chung Su1†, Elizabeth M Wilson-Kubalek3, Iain M Cheeseman1,2* 1Whitehead Institute for Biomedical Research, Cambridge, United States; 2Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 3Department of Cell Biology, The Scripps Research Institute, La Jolla, United States Abstract Chromosome segregation requires robust interactions between the macromolecular kinetochore structure and dynamic microtubule polymers. A key outstanding question is how kinetochore-microtubule attachments are modulated to ensure that bi-oriented attachments are selectively stabilized and maintained. The Astrin-SKAP complex localizes preferentially to properly bi-oriented sister kinetochores, representing the final outer kinetochore component recruited prior to anaphase onset. Here, we reconstitute the 4-subunit Astrin-SKAP complex, including a novel MYCBP subunit. Our work demonstrates that the Astrin-SKAP complex contains separable kinetochore localization and microtubule binding domains. In addition, through cross-linking analysis in human cells and biochemical reconstitution, we show that the Astrin-SKAP complex binds synergistically to microtubules with the Ndc80 complex to form an integrated interface. We propose a model in which the Astrin-SKAP complex acts together with the Ndc80 complex to stabilize correctly formed kinetochore-microtubule interactions. *For correspondence: DOI: https://doi.org/10.7554/eLife.26866.001 [email protected] †These authors contributed equally to this work Introduction Competing interests: The The macromolecular kinetochore complex links chromosomes to dynamic microtubule polymers and authors declare that no harnesses the forces generated by microtubule growth and depolymerization to facilitate accurate competing interests exist. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Produktinformation
Produktinformation Diagnostik & molekulare Diagnostik Laborgeräte & Service Zellkultur & Verbrauchsmaterial Forschungsprodukte & Biochemikalien Weitere Information auf den folgenden Seiten! See the following pages for more information! Lieferung & Zahlungsart Lieferung: frei Haus Bestellung auf Rechnung SZABO-SCANDIC Lieferung: € 10,- HandelsgmbH & Co KG Erstbestellung Vorauskassa Quellenstraße 110, A-1100 Wien T. +43(0)1 489 3961-0 Zuschläge F. +43(0)1 489 3961-7 [email protected] • Mindermengenzuschlag www.szabo-scandic.com • Trockeneiszuschlag • Gefahrgutzuschlag linkedin.com/company/szaboscandic • Expressversand facebook.com/szaboscandic MYCBP monoclonal antibody (M13), clone 1B12 Catalog # : H00026292-M13 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Transfected lysate) Description: MYCBP. Immunogen: MYCBP (NP_036465.2, 34 a.a. ~ 103 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: LYEEPEKPNSALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENK KLKAKLAQYEPPQEEKRAE enlarge Host: Mouse Western Blot (Recombinant protein) Reactivity: Human Sandwich ELISA (Recombinant Isotype: IgG2a Kappa protein) Quality Control Antibody Reactive Against Recombinant Protein. Testing: enlarge ELISA Western Blot detection against Immunogen (33.44 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Western Blot (Transfected lysate) Page 1 of 3 2016/5/23 Western Blot analysis of MYCBP expression in transfected 293T cell line by MYCBP monoclonal antibody (M13), clone 1B12. Lane 1: MYCBP transfected lysate(12 KDa). Lane 2: Non-transfected lysate. Protocol Download Western Blot (Recombinant protein) Protocol Download Sandwich ELISA (Recombinant protein) Detection limit for recombinant GST tagged MYCBP is 0.1 ng/ml as a capture antibody. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
© Copyright 2021 Heather Raquel Dahlin
© Copyright 2021 Heather Raquel Dahlin The Structure of Sperm Autoantigenic Protein (SPA17): An R2D2 Protein Critical to Cilia and Implicated in Oncogenesis Heather Raquel Dahlin A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2021 Reading Committee: John D. Scott, Chair Ning Zheng Linda Wordeman Program Authorized to Offer Degree: Pharmacology University of Washington Abstract Structure of SPA17: An R2D2 Protein Critical to Cilia and Implicated in Oncogenesis Heather Raquel Dahlin Chair of the Supervisory Committee: John D. Scott, Ph.D., Edwin G. Krebs- Speights Professor of Cell Signaling and Cancer Biology Pharmacology A-Kinase Anchoring proteins (AKAPs) localize the activity of cyclic AMP (cAMP)-Dependent Protein Kinase (PKA) through interaction of an amphipathic helix that binds to a conserved RIIα docking and dimerization (R2D2) domain on the N-terminus of PKA. Genome analysis indicates that at least thirteen other RIIα superfamily proteins exist in humans, which are not coupled to cyclic nucleotide binding domains and are largely localized to cilia and flagella. The newly reported R2D2 proteins exist in two lineages differing by their similarity to Type I or Type II PKA. Moreover, R2D2 domains bind to AKAPs and can contain extra regulatory sequences conferring novel functions and binding specificity. Here we detail the structure of one such domain comprising the N-terminus of Sperm Autoantigenic Protein 17 (SPA17) resolved to 1.72 Å. The structure of core hydrophobic sites for dimerization and AKAP binding are highly conserved between PKA and SPA17. Additional flanking sequences outside of the core R2D2 domain occlude the AKAP binding site and reduce the affinity for AKAP helices in the absence of heterodimerization with another R2D2 protein, ROPN1L. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Structural Capacitance in Protein Evolution and Human Diseases
Structural Capacitance in Protein Evolution and Human Diseases Adrian Woolfson, Ashley Buckle, Natalie Borg, Geoffrey Webb, Itamar Kass, Malcolm Buckle, Jiangning Song, Chen Li, Liah Clark, Rory Zhang, et al. To cite this version: Adrian Woolfson, Ashley Buckle, Natalie Borg, Geoffrey Webb, Itamar Kass, et al.. Structural Ca- pacitance in Protein Evolution and Human Diseases. Journal of Molecular Biology, Elsevier, 2018, 10.1016/j.jmb.2018.06.051. hal-02368321 HAL Id: hal-02368321 https://hal.archives-ouvertes.fr/hal-02368321 Submitted on 20 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Structural Capacitance in Protein Evolution and Human Diseases Chen Li, Liah Clark, Rory Zhang, Benjamin Porebski, Julia Mccoey, Natalie Borg, Geoffrey Webb, Itamar Kass, Malcolm Buckle, Jiangning Song, etal. To cite this version: Chen Li, Liah Clark, Rory Zhang, Benjamin Porebski, Julia Mccoey, et al.. Structural Capaci- tance in Protein Evolution and Human Diseases. Journal of Molecular Biology, Elsevier, 2018, 10.1016/j.jmb.2018.06.051. hal-02368321 HAL Id: hal-02368321 https://hal.archives-ouvertes.fr/hal-02368321 Submitted on 20 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. -
Modifications of H3K4 Methylation Levels Are Associated with DNA Hypermethylation in Acute Myeloid Leukemia
Modifications of H3K4 methylation levels are associated with DNA hypermethylation in Acute Myeloid Leukemia Stefania Scalea1, Carmen Maresca2 , Caterina Catalanotto3, Rachele Marino3, Carlo Cogoni3, Anna Reale1, Michele Zampieri1 and Giuseppe Zardo1 1 Department of Experimental Medicine University of Rome “Sapienza” Italy: [email protected];[email protected]; [email protected]; [email protected] 2 Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome, Italy: [email protected] 3 Department of Molecular Medicine University of Rome “Sapienza” Italy [email protected]; [email protected]; [email protected] Correspondence: [email protected] Running Title: H3K4me3 modifications and DNA methylation in AML Keywords: DNA methylation; histone modifications; Acute Myeloid Leukemia Abbreviations: H3K4me3, Histone 3 Lysine 4 trimethylated; H3K27me3, Histone 3 Lysine 27 trimethylated; H3K4me0, Histone 3 Lysine 4 unmethylated; hESC, Human Embryonic Stem Cells; hHSC/MPP, human Hematopoietic Stem or Progenitor cells; AML, Acute Myeloid Leukemia; CpGis, CpG islands; RLGS, Restriction Landmark Genome Scanning; TSS, Transcriptional Start Site; IRX2, Iroquois homeobox 2 gene; CABYR, Calcium-binding tyrosine phosphorylation-regulated gene; NKX6-1, Homeobox Protein NK-6 Homolog A gene; FOXE1, Forkhead Box E1 gene; NRG1, Neuregulin 1 gene; RA, retinoic acid; CSF1, Colony Stimulating Factor 1; CSF2, Colony Stimulating Factor 2; CSF3, Colony Stimulating Factor 3. Abstract The “instructive model” of aberrant DNA methylation in human tumors is based on the observation that CpG islands prone to hypermethylation in cancers are embedded in chromatin enriched in H3K27me3 in human embryonic stem cells (hESC). Recent studies also link methylation of CpG islands to the methylation status of H3K4, where H3K4me3 is inversely correlated with DNA methylation. -
TCTE1 Is a Conserved Component of the Dynein Regulatory Complex and Is Required for Motility and Metabolism in Mouse Spermatozoa
TCTE1 is a conserved component of the dynein PNAS PLUS regulatory complex and is required for motility and metabolism in mouse spermatozoa Julio M. Castanedaa,b,1, Rong Huac,d,1, Haruhiko Miyatab, Asami Ojib,e, Yueshuai Guoc,d, Yiwei Chengc,d, Tao Zhouc,d, Xuejiang Guoc,d, Yiqiang Cuic,d, Bin Shenc, Zibin Wangc, Zhibin Huc,f, Zuomin Zhouc,d, Jiahao Shac,d, Renata Prunskaite-Hyyrylainena,g,h, Zhifeng Yua,i, Ramiro Ramirez-Solisj, Masahito Ikawab,e,k,2, Martin M. Matzuka,g,i,l,m,n,2, and Mingxi Liuc,d,2 aDepartment of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030; bResearch Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan; cState Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, People’s Republic of China; dDepartment of Histology and Embryology, Nanjing Medical University, Nanjing 210029, People’s Republic of China; eGraduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 5650871, Japan; fAnimal Core Facility of Nanjing Medical University, Nanjing 210029, People’s Republic of China; gCenter for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030; hFaculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland; iCenter for Drug Discovery, Baylor College of Medicine, Houston, TX 77030; jWellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; kThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; lDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; mDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; and nDepartment of Pharmacology, Baylor College of Medicine, Houston, TX 77030 Contributed by Martin M. -
Lncrna LUNAR1 Accelerates Colorectal Cancer Progression by Targeting the Mir‑495‑3P/MYCBP Axis
INTERNATIONAL JOURNAL OF ONCOLOGY 57: 1157-1168, 2020 lncRNA LUNAR1 accelerates colorectal cancer progression by targeting the miR‑495‑3p/MYCBP axis JIAJIE QIAN1, ALOK GARG2, FUQIANG LI3, QIANYUN SHEN1 and KE XIAO4 1Department of Gastrointestinal Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China; 2Department of Surgery, City Hospital Braunschweig, D-38118 Braunschweig, Germany; 3Department of Thyroid Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China; 4Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, D-30625 Hannover, Lower Saxony, Germany Received April 16, 2020; Accepted September 14, 2020 DOI: 10.3892/ijo.2020.5128 Abstract. Colorectal cancer (CRC) is a tumor type and functional research showed that LUNAR1 accelerated characterized by high patient morbidity and mortality. It has CRC progression via the miR-495-3p/MYCBP axis. In been reported that long non-coding (lncRNA) LUNAR1 conclusion, LUNAR1 accelerates CRC progression via the (LUNAR1) participates in the regulation of tumor progression, miR-495-3p/MYCBP axis, indicating that LUNAR1 may such as diffuse large B-cell lymphoma. However, its role and serve as a prognostic biomarker for CRC patients. underlying mechanisms in CRC progression have not been elucidated. The present study was designed to investigate Introduction the underlying mechanisms by which LUNAR1 regulates CRC progression. RT-qPCR and Pearson's correlation Colorectal cancer (CRC) is a tumor type characterized by analysis revealed that LUNAR1 was highly expressed and high patient morbidity and mortality (1). At present, surgery, was negatively associated with the overall survival of CRC radiotherapy and chemotherapy are the primary strategies for patients. -
Hippo and Sonic Hedgehog Signalling Pathway Modulation of Human Urothelial Tissue Homeostasis
Hippo and Sonic Hedgehog signalling pathway modulation of human urothelial tissue homeostasis Thomas Crighton PhD University of York Department of Biology November 2020 Abstract The urinary tract is lined by a barrier-forming, mitotically-quiescent urothelium, which retains the ability to regenerate following injury. Regulation of tissue homeostasis by Hippo and Sonic Hedgehog signalling has previously been implicated in various mammalian epithelia, but limited evidence exists as to their role in adult human urothelial physiology. Focussing on the Hippo pathway, the aims of this thesis were to characterise expression of said pathways in urothelium, determine what role the pathways have in regulating urothelial phenotype, and investigate whether the pathways are implicated in muscle-invasive bladder cancer (MIBC). These aims were assessed using a cell culture paradigm of Normal Human Urothelial (NHU) cells that can be manipulated in vitro to represent different differentiated phenotypes, alongside MIBC cell lines and The Cancer Genome Atlas resource. Transcriptomic analysis of NHU cells identified a significant induction of VGLL1, a poorly understood regulator of Hippo signalling, in differentiated cells. Activation of upstream transcription factors PPARγ and GATA3 and/or blockade of active EGFR/RAS/RAF/MEK/ERK signalling were identified as mechanisms which induce VGLL1 expression in NHU cells. Ectopic overexpression of VGLL1 in undifferentiated NHU cells and MIBC cell line T24 resulted in significantly reduced proliferation. Conversely, knockdown of VGLL1 in differentiated NHU cells significantly reduced barrier tightness in an unwounded state, while inhibiting regeneration and increasing cell cycle activation in scratch-wounded cultures. A signalling pathway previously observed to be inhibited by VGLL1 function, YAP/TAZ, was unaffected by VGLL1 manipulation.