Sperm Differentiation
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Towards the Understanding of Ccnb1ip1 As a Co-Regulator of Meiotic Crossing-Over in the Mouse
TOWARDS THE UNDERSTANDING OF CCNB1IP1 AS A CO-REGULATOR OF MEIOTIC CROSSING-OVER IN THE MOUSE 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 Edward Remco Strong January 2014 © 2014 Edward Remco Strong TOWARDS THE UNDERSTANDING OF CCNB1IP1 AS A CO-REGULATOR OF MEIOTIC CROSSING-OVER IN THE MOUSE Edward Remco Strong, Ph. D. Cornell University 2014 It is clear that there are many genes required for meiosis in mammals that are not present in the more tractable model organisms. To identify such genes, our lab has performed forward genetic chemical (ENU) mutagenesis screens for alleles conferring infertility in mice. A novel allele, Ccnb1ip1mei4, generated in these screens is of interest because it is defective in a form of recombination called crossing-over. Ccnb1ip1mei4/mei4 results in male and female infertility of otherwise normal-appearing animals. CCNB1IP1 is finely regulated in both timing and localization to the events of meiotic crossover formations. Towards understanding the molecular functions of CCNB1IP1 and how the defect in Ccnb1ip1me4i/mei4 animals leads to meiotic arrest, studies of CCNB1IP1 within meiocytes implicate a role for CCNB1IP1 in SUMOylation. Remarkably little is understood about SUMO-modification consequences to meiosis. Protein-protein interactions with CCNB1IP1 identify a number of putative targets of SUMOylation, and subsequent in vivo biochemical interrogations reveal the CCNB1IP1-interacting proteins 4930455F23RIK and GGN as targets of posttranslational modification dependent upon a putative SUMO E3 ligase. In totality, these studies support the hypothesis that CCNB1IP1 performs as a meiotic co- regulator, mediating the SUMO-modification of proteins essential to the stabilization and maturation of crossover intermediates. -
UCSD MOLECULE PAGES Doi:10.6072/H0.MP.A002549.01 Volume 1, Issue 2, 2012 Copyright UC Press, All Rights Reserved
UCSD MOLECULE PAGES doi:10.6072/H0.MP.A002549.01 Volume 1, Issue 2, 2012 Copyright UC Press, All rights reserved. Review Article Open Access WAVE2 Tadaomi Takenawa1, Shiro Suetsugu2, Daisuke Yamazaki3, Shusaku Kurisu1 WASP family verprolin-homologous protein 2 (WAVE2, also called WASF2) was originally identified by its sequence similarity at the carboxy-terminal VCA (verprolin, cofilin/central, acidic) domain with Wiskott-Aldrich syndrome protein (WASP) and N-WASP (neural WASP). In mammals, WAVE2 is ubiquitously expressed, and its two paralogs, WAVE1 (also called suppressor of cAMP receptor 1, SCAR1) and WAVE3, are predominantly expressed in the brain. The VCA domain of WASP and WAVE family proteins can activate the actin-related protein 2/3 (Arp2/3) complex, a major actin nucleator in cells. Proteins that can activate the Arp2/3 complex are now collectively known as nucleation-promoting factors (NPFs), and the WASP and WAVE families are a founding class of NPFs. The WAVE family has an amino-terminal WAVE homology domain (WHD domain, also called the SCAR homology domain, SHD) followed by the proline-rich region that interacts with various Src-homology 3 (SH3) domain proteins. The VCA domain located at the C-terminus. WAVE2, like WAVE1 and WAVE3, constitutively forms a huge heteropentameric protein complex (the WANP complex), binding through its WHD domain with Abi-1 (or its paralogs, Abi-2 and Abi-3), HSPC300 (also called Brick1), Nap1 (also called Hem-2 and NCKAP1), Sra1 (also called p140Sra1 and CYFIP1; its paralog is PIR121 or CYFIP2). The WANP complex is recruited to the plasma membrane by cooperative action of activated Rac GTPases and acidic phosphoinositides. -
Genome Sequence, Population History, and Pelage Genetics of the Endangered African Wild Dog (Lycaon Pictus) Michael G
Campana et al. BMC Genomics (2016) 17:1013 DOI 10.1186/s12864-016-3368-9 RESEARCH ARTICLE Open Access Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus) Michael G. Campana1,2*, Lillian D. Parker1,2,3, Melissa T. R. Hawkins1,2,3, Hillary S. Young4, Kristofer M. Helgen2,3, Micaela Szykman Gunther5, Rosie Woodroffe6, Jesús E. Maldonado1,2 and Robert C. Fleischer1 Abstract Background: The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. Results: We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. Conclusions: We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage. Keywords: Lycaon pictus, Genome, Population history, Selection, Pelage Background Primarily a hunter of antelopes, the African wild dog is a The African wild dog (Lycaon pictus) is an endangered highly distinct canine. -
Leveraging Mouse Chromatin Data for Heritability Enrichment Informs Common Disease Architecture and Reveals Cortical Layer Contributions to Schizophrenia
Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia Paul W. Hook1 and Andrew S. McCallion1,2,3 1McKusick-Nathans Department of Genetic Medicine, 2Department of Comparative and Molecular Pathobiology, 3Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA Genome-wide association studies have implicated thousands of noncoding variants across common human phenotypes. However, they cannot directly inform the cellular context in which disease-associated variants act. Here, we use open chro- matin profiles from discrete mouse cell populations to address this challenge. We applied stratified linkage disequilibrium score regression and evaluated heritability enrichment in 64 genome-wide association studies, emphasizing schizophrenia. We provide evidence that mouse-derived human open chromatin profiles can serve as powerful proxies for difficult to ob- tain human cell populations, facilitating the illumination of common disease heritability enrichment across an array of hu- man phenotypes. We demonstrate that signatures from discrete subpopulations of cortical excitatory and inhibitory neurons are significantly enriched for schizophrenia heritability with maximal enrichment in cortical layer V excitatory neu- rons. We also show that differences between schizophrenia and bipolar disorder are concentrated in excitatory neurons in cortical layers II-III, IV, and V, as well as the dentate gyrus. Finally, we leverage these data to fine-map variants in 177 schiz- ophrenia loci nominating variants in 104/177. We integrate these data with transcription factor binding site, chromatin in- teraction, and validated enhancer data, placing variants in the cellular context where they may modulate risk. -
047605V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. 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 Assembly and Activation of Dynein-Dynactin by the Cargo Adaptor Protein Hook3 Courtney M. Schroeder1,2 and Ronald D. Vale1,2 1The Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA 2Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA. Corresponding Author: Ronald D. Vale Dept. of Cellular and Molecular Pharmacology University of California, San Francisco Genentech Hall, MC 2200, Room N312A 600-16th Street San Francisco, CA 94158-2517 E-mail: [email protected] Phone: 415-476-6380 Fax: 415-514-4412 bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. 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. 2 Abstract Metazoan cytoplasmic dynein moves processively along microtubules with the aid of dynactin and an adaptor protein that joins dynein and dynactin into a stable ternary complex. Here, we have examined how Hook3, a cargo adaptor involved in Golgi and endosome transport, forms a motile dynein-dynactin complex. We show that the conserved Hook domain interacts directly with the dynein light intermediate chain 1 (LIC1). -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
The Intrinsically Disordered Protein SPE-18 Promotes Localized Assembly of MSP in Caenorhabditis Elegans Spermatocytes Kari L
© 2021. Published by The Company of Biologists Ltd | Development (2021) 148, dev195875. doi:10.1242/dev.195875 RESEARCH ARTICLE The intrinsically disordered protein SPE-18 promotes localized assembly of MSP in Caenorhabditis elegans spermatocytes Kari L. Price*,¶, Marc Presler‡,¶, Christopher M. Uyehara§ and Diane C. Shakes ABSTRACT Buracco et al., 2019; Brouhard and Rice, 2018; Bodakuntla et al., Many specialized cells use unconventional strategies of cytoskeletal 2019; de Forges et al., 2012). However, a full understanding of control. Nematode spermatocytes discard their actin and tubulin cytoskeletal control requires consideration of less-studied proteins following meiosis, and instead employ the regulated assembly/ whose properties challenge our standard assumptions. disassembly of the Major Sperm Protein (MSP) to drive sperm One such protein is the nematode Major Sperm Protein (MSP), motility. However, prior to the meiotic divisions, MSP is sequestered assembly/disassembly dynamics of which power the crawling through its assembly into paracrystalline structures called fibrous motility of nematode spermatozoa (Klass and Hirsh, 1981; bodies (FBs). The accessory proteins that direct this sequestration Sepsenwol et al., 1989; Italiano et al., 1996; reviewed by Roberts process have remained mysterious. This study reveals SPE-18 as an and Stewart, 2012; Smith, 2014). Although MSP-based motility intrinsically disordered protein that is essential for MSP assembly appears superficially similar to its actin-based counterpart, the within FBs. In spe-18 mutant spermatocytes, MSP forms disorganized molecular mechanisms are distinct. Much of what we know about cortical fibers, and the cells arrest in meiosis without forming haploid MSP dynamics was gleaned from the parasitic nematode Ascaris, sperm. -
The Kinesin Walk: a Dynamic Model with Elastically Coupled Heads
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 6775-6779, June 1996 Biophysics The kinesin walk: A dynamic model with elastically coupled heads IMRE DERENYI AND TAMA'S VICSEK Department of Atomic Physics, Eotvos University, Budapest, Puskin u 5-7, 1088 Hungary Communicated by Leo P. Kadanoff, University of Chicago, Chicago, IL, February 26, 1996 (received for review November 28, 1995) ABSTRACT Recently individual two-headed kinesin mol- of the related transport phenomena. These models (12-19), ecules have been studied in in vitro motility assays revealing a except that of Ajdari (20), consider cases in which the internal number of their peculiar transport properties. In this paper degree of freedom of the molecular motors is not taken into we propose a simple and robust model for the kinesin stepping account. The purpose of the present work is to define and process with elastically coupled Brownian heads that show all investigate a dynamic model for the kinesin walk that has an of these properties. The analytic and numerical treatment of internal degree of freedom and results in a full agreement with our model results in a very good fit to the experimental data the experimental data for the range of its parameters allowed and practically has no free parameters. Changing the values by the known estimates for the lower and upper bounds of ofthe parameters in the restricted range allowed by the related these parameters. experimental estimates has almost no effect on the shape of There are two basic classes of possible models for the the curves and results mainly in a variation of the zero load stepping of kinesin (21). -
Kinesin Motility Is Driven by Subdomain Dynamics Wonmuk Hwang1,2,3*, Matthew J Lang4,5*, Martin Karplus6,7*
RESEARCH ARTICLE Kinesin motility is driven by subdomain dynamics Wonmuk Hwang1,2,3*, Matthew J Lang4,5*, Martin Karplus6,7* 1Department of Biomedical Engineering, Texas A&M University, College Station, United States; 2Department of Materials Science & Engineering, Texas A&M University, College Station, United States; 3School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea; 4Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States; 5Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, United States; 6Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States; 7Laboratoire de Chimie Biophysique, ISIS, Universite´ de Strasbourg, Strasbourg, France Abstract The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are ’pulled’ by switch-I, and a new ATP is ’captured’ by a concerted motion of the a0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed *For correspondence: mechanism provides the flexibility necessary for walking in the crowded cellular environment. [email protected] (WH); DOI: https://doi.org/10.7554/eLife.28948.001 [email protected] (MJL); [email protected] (MK) Competing interests: The authors declare that no Introduction competing interests exist. -
Actin Nucleator Spire 1 Is a Regulator of Ectoplasmic Specialization in the Testis Qing Wen1,Nanli1,Xiangxiao 1,2,Wing-Yeelui3, Darren S
Wen et al. Cell Death and Disease (2018) 9:208 DOI 10.1038/s41419-017-0201-6 Cell Death & Disease ARTICLE Open Access Actin nucleator Spire 1 is a regulator of ectoplasmic specialization in the testis Qing Wen1,NanLi1,XiangXiao 1,2,Wing-yeeLui3, Darren S. Chu1, Chris K. C. Wong4, Qingquan Lian5,RenshanGe5, Will M. Lee3, Bruno Silvestrini6 and C. Yan Cheng 1 Abstract Germ cell differentiation during the epithelial cycle of spermatogenesis is accompanied by extensive remodeling at the Sertoli cell–cell and Sertoli cell–spermatid interface to accommodate the transport of preleptotene spermatocytes and developing spermatids across the blood–testis barrier (BTB) and the adluminal compartment of the seminiferous epithelium, respectively. The unique cell junction in the testis is the actin-rich ectoplasmic specialization (ES) designated basal ES at the Sertoli cell–cell interface, and the apical ES at the Sertoli–spermatid interface. Since ES dynamics (i.e., disassembly, reassembly and stabilization) are supported by actin microfilaments, which rapidly converts between their bundled and unbundled/branched configuration to confer plasticity to the ES, it is logical to speculate that actin nucleation proteins play a crucial role to ES dynamics. Herein, we reported findings that Spire 1, an actin nucleator known to polymerize actins into long stretches of linear microfilaments in cells, is an important regulator of ES dynamics. Its knockdown by RNAi in Sertoli cells cultured in vitro was found to impede the Sertoli cell tight junction (TJ)-permeability barrier through changes in the organization of F-actin across Sertoli cell cytosol. Unexpectedly, Spire 1 knockdown also perturbed microtubule (MT) organization in Sertoli cells cultured in vitro. -
Applying Expression Profile Similarity for Discovery of Patient-Specific
bioRxiv preprint doi: https://doi.org/10.1101/172015; this version posted September 17, 2017. 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. Applying expression profile similarity for discovery of patient-specific functional mutations Guofeng Meng Partner Institute of Computational Biology, Yueyang 333, Shanghai, China email: [email protected] Abstract The progress of cancer genome sequencing projects yields unprecedented information of mutations for numerous patients. However, the complexity of mutation profiles of patients hinders the further understanding of mechanisms of oncogenesis. One basic question is how to uncover mutations with functional impacts. In this work, we introduce a computational method to predict functional somatic mutations for each of patient by integrating mutation recurrence with similarity of expression profiles of patients. With this method, the functional mutations are determined by checking the mutation enrichment among a group of patients with similar expression profiles. We applied this method to three cancer types and identified the functional mutations. Comparison of the predictions for three cancer types suggested that most of the functional mutations were cancer-type-specific with one exception to p53. By checking prediction results, we found that our method effectively filtered non-functional mutations resulting from large protein sizes. In addition, this methods can also perform functional annotation to each patient to describe their association with signalling pathways or biological processes. In breast cancer, we predicted "cell adhesion" and other mutated gene associated terms to be significantly enriched among patients. -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes.