Evolutionary Conservation of Pou5f3 Genomic Organization and Its
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Product information NANOG 1-154aa Human, His-tagged, Recombinant, E.coli Cat. No. IBATGP1124 Full name: Homeobox protein NANOG NCBI Accession No.: NP_079141 Synonyms: Homeobox transcription factor Nanog, homeobox transcription factor Nanog-delta 48 Description: NANOG, also known as nanog homeobox, is a member of the homeobox family of DNA binding transcription factors that has been shown to maintain pluripotency of embryonic stem cells. Nanog expression counteracts the differentiation-promoting signals induced by the extrinsic factors LIF, Stat3 and BMP. Once NANOG expression is down-regulated, cell differentiation can proceed. Recombinant human NANOG protein, fused to His- tag at N-terminus, was expressed in E.coli and purified by using conventional chromatography. Form: Liquid. 20mM Tris-HCl buffer (pH8.0) containing 20% glycerol, 1mM DTT Molecular Weight: 19.6 kDa (174aa), confirmed by MALDI-TOF (Molecular weight on SDS-PAGE will appear higher) Purity: > 90% by SDS - PAGE Concentration: 0.25 mg/ml (determined by Bradford assay) 15% SDS-PAGE (3ug) Sequences of amino acids: MGSSHHHHHH SSGLVPRGSH MSVDPACPQS LPCFEASDCK ESSPMPVICG PEENYPSLQM SSAEMPHTET VSPLPSSMDL LIQDSPDSST SPKGKQPTSA EKSVAKKEDK VPVKKQKTRT VFSSTQLCVL NDRFQRQKYL SLQQMQELSN ILNLSYKQVK TWFQNQRMKS KRWQ General references: Clark A T., et al. (2004) Stem Cells. 22:169-179. Chambers I., et al. (2003) Cell Res. 13:499-502. Storage: Can be stored at +4°C short term (1-2 weeks). For long term storage, aliquot and store at -20°C or -70°C. Avoid repeated freezing and thawing cycles. For research use only. This product is not intended or approved for human, diagnostics or veterinary use. Immuno-Biological Laboratories, Inc. (IBL-America) 8201 Central Ave. -
Role of Mitochondrial Ribosomal Protein S18-2 in Cancerogenesis and in Regulation of Stemness and Differentiation
From THE DEPARTMENT OF MICROBIOLOGY TUMOR AND CELL BIOLOGY (MTC) Karolinska Institutet, Stockholm, Sweden ROLE OF MITOCHONDRIAL RIBOSOMAL PROTEIN S18-2 IN CANCEROGENESIS AND IN REGULATION OF STEMNESS AND DIFFERENTIATION Muhammad Mushtaq Stockholm 2017 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by E-Print AB 2017 © Muhammad Mushtaq, 2017 ISBN 978-91-7676-697-2 Role of Mitochondrial Ribosomal Protein S18-2 in Cancerogenesis and in Regulation of Stemness and Differentiation THESIS FOR DOCTORAL DEGREE (Ph.D.) By Muhammad Mushtaq Principal Supervisor: Faculty Opponent: Associate Professor Elena Kashuba Professor Pramod Kumar Srivastava Karolinska Institutet University of Connecticut Department of Microbiology Tumor and Cell Center for Immunotherapy of Cancer and Biology (MTC) Infectious Diseases Co-supervisor(s): Examination Board: Professor Sonia Lain Professor Ola Söderberg Karolinska Institutet Uppsala University Department of Microbiology Tumor and Cell Department of Immunology, Genetics and Biology (MTC) Pathology (IGP) Professor George Klein Professor Boris Zhivotovsky Karolinska Institutet Karolinska Institutet Department of Microbiology Tumor and Cell Institute of Environmental Medicine (IMM) Biology (MTC) Professor Lars-Gunnar Larsson Karolinska Institutet Department of Microbiology Tumor and Cell Biology (MTC) Dedicated to my parents ABSTRACT Mitochondria carry their own ribosomes (mitoribosomes) for the translation of mRNA encoded by mitochondrial DNA. The architecture of mitoribosomes is mainly composed of mitochondrial ribosomal proteins (MRPs), which are encoded by nuclear genomic DNA. Emerging experimental evidences reveal that several MRPs are multifunctional and they exhibit important extra-mitochondrial functions, such as involvement in apoptosis, protein biosynthesis and signal transduction. Dysregulations of the MRPs are associated with severe pathological conditions, including cancer. -
Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug
cancers Article Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug Response Genes in Pediatric Acute Myeloid Leukemia David G.J. Cucchi 1 , Costa Bachas 1 , Marry M. van den Heuvel-Eibrink 2,3, Susan T.C.J.M. Arentsen-Peters 3, Zinia J. Kwidama 1, Gerrit J. Schuurhuis 1, Yehuda G. Assaraf 4, Valérie de Haas 3 , Gertjan J.L. Kaspers 3,5 and Jacqueline Cloos 1,* 1 Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; [email protected] (D.G.J.C.); [email protected] (C.B.); [email protected] (Z.J.K.); [email protected] (G.J.S.) 2 Department of Pediatric Oncology/Hematology, Erasmus MC–Sophia Children’s Hospital, 3015 CN Rotterdam, The Netherlands; [email protected] 3 Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; [email protected] (S.T.C.J.M.A.-P.); [email protected] (V.d.H.); [email protected] (G.J.L.K.) 4 The Fred Wyszkowski Cancer Research, Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel; [email protected] 5 Emma’s Children’s Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology, 1081 HV Amsterdam, The Netherlands * Correspondence: [email protected] Received: 21 April 2020; Accepted: 12 May 2020; Published: 15 May 2020 Abstract: Novel treatment strategies are of paramount importance to improve clinical outcomes in pediatric AML. Since chemotherapy is likely to remain the cornerstone of curative treatment of AML, insights in the molecular mechanisms that determine its cytotoxic effects could aid further treatment optimization. -
Cell Cycle and Pluripotency: Convergence on Octamer‑Binding Transcription Factor 4 (Review)
MOLECULAR MEDICINE REPORTS 16: 6459-6466, 2017 Cell cycle and pluripotency: Convergence on octamer‑binding transcription factor 4 (Review) SHIQI SHE1*, QUCHENG WEI2*, BO KANG1 and YING-JIE WANG1 1State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003; 2Cardiovascular Key Lab of Zhejiang, Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China Received December 17, 2016; Accepted July 14, 2017 DOI: 10.3892/mmr.2017.7489 Abstract. Embryonic stem cells (ESCs) have unlimited expan- 1. Introduction sion potential and the ability to differentiate into all somatic cell types for regenerative medicine and disease model studies. Embryonic stem cells (ESCs) are characterized by unlimited Octamer-binding transcription factor 4 (OCT4), encoded by proliferation (self-renewal) and the ability to differentiate into the POU domain, class 5, transcription factor 1 gene, is a tran- three primary germ layers, namely the endoderm, mesoderm scription factor vital for maintaining ESC pluripotency and and ectoderm (pluripotency) (1-4). It has been established somatic reprogramming. Many studies have established that that complicated regulatory networks are present in ESCs the cell cycle of ESCs is featured with an abbreviated G1 phase that critically maintain the state of self-renewal and pluri- and a prolonged S phase. Changes in cell cycle dynamics are potency for later development (5,6). Several transcription intimately associated with the state of ESC pluripotency, and factors (TFs), including octamer-binding transcription factor manipulating cell-cycle regulators could enable a controlled 4 (OCT4), SRY-box 2 (SOX2) and homeobox protein NANOG differentiation of ESCs. -
The Genomic Organization and Expression Pattern of the Low-Affinity Fc Gamma Receptors (Fcγr) in the Göttingen Minipig
Immunogenetics (2019) 71:123–136 https://doi.org/10.1007/s00251-018-01099-1 ORIGINAL ARTICLE The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig Jerome Egli1 & Roland Schmucki1 & Benjamin Loos1 & Stephan Reichl1 & Nils Grabole1 & Andreas Roller1 & Martin Ebeling1 & Alex Odermatt2 & Antonio Iglesias1 Received: 9 August 2018 /Accepted: 24 November 2018 /Published online: 18 December 2018 # The Author(s) 2018 Abstract Safety and efficacy of therapeutic antibodies are often dependent on their interaction with Fc receptors for IgG (FcγRs). The Göttingen minipig represents a valuable species for biomedical research but its use in preclinical studies with therapeutic antibodies is hampered by the lack of knowledge about the porcine FcγRs. Genome analysis and sequencing now enabled the localization of the previously described FcγRIIIa in the orthologous location to human FCGR3A. In addition, we identified nearby the gene coding for the hitherto undescribed putative porcine FcγRIIa. The 1′241 bp long FCGR2A cDNA translates to a 274aa transmembrane protein containing an extracellular region with high similarity to human and cattle FcγRIIa. Like in cattle, the intracellular part does not contain an immunoreceptor tyrosine-based activation motif (ITAM) as in human FcγRIIa. Flow cytometry of the whole blood and single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) of Göttingen minipigs revealed the expression profile of all porcine FcγRs which is compared to human and mouse. The new FcγRIIa is mainly expressed on platelets making the minipig a good model to study IgG-mediated platelet activation and aggregation. In contrast to humans, minipig blood monocytes were found to express inhibitory FcγRIIb that could lead to the underestimation of FcγR-mediated effects of monocytes observed in minipig studies with therapeutic antibodies. -
Identification and Characterization of Tissue-Resident Memory T Cells in Humans Brahma Vencel Kumar
Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2018 ©2017 Brahma Vencel Kumar All rights reserved ABSTRACT Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar Memory T cells are critical for maintaining lifelong immunity by protecting against reinfection with previously encountered pathogens. In recent years, a subset of memory T cells termed tissue-resident memory T cells (TRM) has emerged as the primary mediator of protection at many tissue sites. Numerous studies in mice have demonstrated that TRM accelerate pathogen clearance compared with other subsets of memory T cells. The defining characteristic of TRM is that they are retained within tissues and do not circulate in the blood. The lack of TRM in blood has proved to be a barrier for investigating the role of TRM in healthy humans. As a result, there are many outstanding questions about TRM biology in humans, including which phenotypic markers identify TRM, if TRM represent a unique memory subset, as well as defining transcriptional and functional characteristics of this subset. Through a unique collaboration with the local organ procurement agency, we obtained samples from >15 tissue sites from healthy organ donors of all ages. We found that the surface marker CD69 was expressed by memory CD4 + and CD8 + T cells in multiple tissues including spleen and other lymphoid tissues, lung, and intestines, but not in blood, suggesting that this marker may identify TRM in human tissues. -
Gene Expression Profiling in Human Fetal Liver and Identification of Tissue
Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Gene Expression Profiling in Human Fetal Liver and Identification of Tissue- and Developmental-Stage-Specific Genes through Compiled Expression Profiles and Efficient Cloning of Full-Length cDNAs Yongtao Yu, Chenggang Zhang, Gangqiao Zhou, Songfeng Wu, Xianghu Qu, Handong Wei, Guichun Xing, Chunna Dong, Yun Zhai, Jinghong Wan, Shuguang Ouyang, Li Li, Shaowen Zhang, Kaixin Zhou, Yinan Zhang, Chutse Wu, and Fuchu He1 Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Chinese National Human Genome Center at Beijing, Beijing 100850, China Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) and by analyzing the compiled expression profiles of liver at different developmental stages. A total of 13,077 ESTs were sequenced from a 3Ј-directed cDNA library of HFL22w, and classified as follows: 5819 (44.5%) matched to known genes; 5460 (41.8%) exhibited no significant homology to known genes; and the remaining 1798 (13.7%) were genomic sequences of unknown function, mitochondrial genomic sequences, or repetitive sequences. Integration of ESTs of known human genes generated a profile including 1660 genes that could be divided into 15 gene categories according to their functions. Genes related to general housekeeping, ESTs associated with hematopoiesis, and liver-specific genes were highly expressed. -
Chain Locus Heavy Genomic Organization of the Variable
Antibody Repertoire Development in Fetal and Neonatal Piglets. XI. The Relationship of Variable Heavy Chain Gene Usage and the Genomic Organization of the Variable Heavy This information is current as Chain Locus of September 27, 2021. Tomoko Eguchi-Ogawa, Nancy Wertz, Xiu-Zhu Sun, Francois Puimi, Hirohide Uenishi, Kevin Wells, Patrick Chardon, Gregory J. Tobin and John E. Butler J Immunol published online 5 March 2010 Downloaded from http://www.jimmunol.org/content/early/2010/03/05/jimmun ol.0903616 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2010/03/05/jimmunol.090361 Material 6.DC1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 27, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts Errata An erratum has been published regarding this article. Please see next page or: /content/190/3/1383.full.pdf The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published March 5, 2010, doi:10.4049/jimmunol.0903616 The Journal of Immunology Antibody Repertoire Development in Fetal and Neonatal Piglets. -
Functional Analysis of Structural Variation in the 2D and 3D Human Genome
FUNCTIONAL ANALYSIS OF STRUCTURAL VARIATION IN THE 2D AND 3D HUMAN GENOME by Conor Mitchell Liam Nodzak A dissertation submitted to the faculty of The University of North Carolina at Charlotte in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics and Computational Biology Charlotte 2019 Approved by: Dr. Xinghua Mindy Shi Dr. Rebekah Rogers Dr. Jun-tao Guo Dr. Adam Reitzel ii c 2019 Conor Mitchell Liam Nodzak ALL RIGHTS RESERVED iii ABSTRACT CONOR MITCHELL LIAM NODZAK. Functional analysis of structural variation in the 2D and 3D human genome. (Under the direction of DR. XINGHUA MINDY SHI) The human genome consists of over 3 billion nucleotides that have an average distance of 3.4 Angstroms between each base, which equates to over two meters of DNA contained within the 125 µm3 volume diploid cell nuclei. The dense compaction of chromatin by the supercoiling of DNA forms distinct architectural modules called topologically associated domains (TADs), which keep protein-coding genes, noncoding RNAs and epigenetic regulatory elements in close nuclear space. It has recently been shown that these conserved chromatin structures may contribute to tissue-specific gene expression through the encapsulation of genes and cis-regulatory elements, and mutations that affect TADs can lead to developmental disorders and some forms of cancer. At the population-level, genomic structural variation contributes more to cumulative genetic difference than any other class of mutation, yet much remains to be studied as to how structural variation affects TADs. Here, we study the func- tional effects of structural variants (SVs) through the analysis of chromatin topology and gene activity for three trio families sampled from genetically diverse popula- tions from the Human Genome Structural Variation Consortium. -
A Transcriptional Signature of Postmitotic Maintenance in Neural Tissues
Neurobiology of Aging 74 (2019) 147e160 Contents lists available at ScienceDirect Neurobiology of Aging journal homepage: www.elsevier.com/locate/neuaging Postmitotic cell longevityeassociated genes: a transcriptional signature of postmitotic maintenance in neural tissues Atahualpa Castillo-Morales a,b, Jimena Monzón-Sandoval a,b, Araxi O. Urrutia b,c,*, Humberto Gutiérrez a,** a School of Life Sciences, University of Lincoln, Lincoln, UK b Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK c Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico article info abstract Article history: Different cell types have different postmitotic maintenance requirements. Nerve cells, however, are Received 11 April 2018 unique in this respect as they need to survive and preserve their functional complexity for the entire Received in revised form 3 October 2018 lifetime of the organism, and failure at any level of their supporting mechanisms leads to a wide range of Accepted 11 October 2018 neurodegenerative conditions. Whether these differences across tissues arise from the activation of Available online 19 October 2018 distinct cell typeespecific maintenance mechanisms or the differential activation of a common molecular repertoire is not known. To identify the transcriptional signature of postmitotic cellular longevity (PMCL), Keywords: we compared whole-genome transcriptome data from human tissues ranging in longevity from 120 days Neural maintenance Cell longevity to over 70 years and found a set of 81 genes whose expression levels are closely associated with Transcriptional signature increased cell longevity. Using expression data from 10 independent sources, we found that these genes Functional genomics are more highly coexpressed in longer-living tissues and are enriched in specific biological processes and transcription factor targets compared with randomly selected gene samples. -
Studies Relating to the Differentiation of Human Embryonic Stem Cells
Studies relating to the differentiation of human embryonic stem cells A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 Georgios Anyfantis List of Figures .................................................................................................... 10 List of Tables ...................................................................................................... 13 Declaration ........................................................................................................ 15 Copyright statement .......................................................................................... 15 Acknowledgements ........................................................................................... 16 Abbreviations .................................................................................................... 17 Chapter 1: Introduction ...................................................................................... 23 1.1 Diabetes Mellitus ......................................................................................... 23 1.2 Pancreatic function and Organogenesis ........................................................ 24 1.2.1 Pancreatic Function .................................................................................... 24 1.2.2 Pancreatic Organogenesis ........................................................................... 26 1.3 Signalling Pathways associated with pancreas development ....................... -
Genomic Insights Into Drug Resistance Determinants in Cedecea Neteri, a Rare Opportunistic Pathogen
microorganisms Article Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen Dorothea K. Thompson * and Stephen M. Sharkady Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Campbell University, Buies Creek, NC 27506, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-910-893-7463 Abstract: Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, Citation: Thompson, D.K.; Sharkady, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new S.M. Genomic Insights into Drug insights into drug resistance mechanisms of an environmental microorganism capable of behaving as Resistance Determinants in Cedecea a clinically relevant opportunistic pathogen.