DOCSLIB.ORG

Genome-Scale Detection of Positive Selection in Nine Primates Predicts Human-Virus Evolutionary Conflicts Robin Van Der Lee1,*, Laurens Wiel1,2, Teunis J.P

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome-Scale Detection of Positive Selection in Nine Primates Predicts Human-Virus Evolutionary Conflicts Robin Van Der Lee1,*, Laurens Wiel1,2, Teunis J.P 10634–10648 Nucleic Acids Research, 2017, Vol. 45, No. 18 Published online 11 August 2017 doi: 10.1093/nar/gkx704 Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts Robin van der Lee1,*, Laurens Wiel1,2, Teunis J.P. van Dam1 and Martijn A. Huynen1 1Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands and 2Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Received May 02, 2017; Revised July 26, 2017; Editorial Decision July 30, 2017; Accepted August 02, 2017 ABSTRACT able at https://github.com/robinvanderlee/positive- selection. Hotspots of rapid genome evolution hold clues about human adaptation. We present a compara- tive analysis of nine whole-genome sequenced pri- INTRODUCTION mates to identify high-confidence targets of posi- Conservation of structure and sequence often indicate bi- tive selection. We find strong statistical evidence ological function. Rapidly evolving sequence features may for positive selection in 331 protein-coding genes however also indicate function, as they may reveal molecu- (3%), pinpointing 934 adaptively evolving codons lar adaptations to new selection pressures. But what drives (0.014%). Our new procedure is stringent and re- these rapid genetic changes during evolution? Can these changes explain the specific phenotypes of species or indi- veals substantial artefacts (20% of initial predic- viduals, such as a differential susceptibility to viruses? tions) that have inflated previous estimates. The fi- Immunity genes contain the strongest signatures of nal 331 positively selected genes (PSG) are strongly rapid evolution due to positive Darwinian selection (1–13). enriched for innate and adaptive immunity, secreted Pathogens continuously invent new ways to evade, coun- and cell membrane proteins (e.g. pattern recognition, teract and suppress the immune response of their hosts, complement, cytokines, immune receptors, MHC, thereby acting as major drivers of the observed adaptive Siglecs). We also find evidence for positive selection evolution of immune systems (14,15). In line with this, the in reproduction and chromosome segregation (e.g. structural interfaces of human proteins directly involved centromere-associated CENPO, CENPT), apolipopro- in virus interactions show accelerated evolution (16). Nu- teins, smell/taste receptors and mitochondrial pro- merous proteins involved in the virus–host interaction have teins. Focusing on the virus–host interaction, we been demonstrated to be in genetic conflict with their inter- acting viral proteins, a phenomenon that has been likened retrieve most evolutionary conflicts known to influ- to a virus–host ‘arms race’ (15). Such studies have generally ence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, focused on a single gene or gene family of interest sequenced tetherin) and predict 70 novel cases through integra- across a large number of species. Evolutionary analyses can tion with virus–human interaction data. Protein struc- then predict which genes and codons may be involved in ture analysis further identifies positive selection in virus interactions. For example, mitochondrial antiviral sig- the interaction interfaces between viruses and their naling protein (MAVS) is a central signaling hub in the cellular receptors (CD4-HIV; CD46-measles, ade- RIG-I-like receptor (RLR) pathway, which recognizes in- noviruses; CD55-picornaviruses). Finally, primate fections of a wide range of viruses from the presence of their PSG consistently show high sequence variation in RNA in the cytosol. Analysis of the MAVS gene in 21 pri- human exomes, suggesting ongoing evolution. Our mates identified several positions that have evolved under curated dataset of positive selection is a rich source recurrent strong positive selection and turned out to be crit- ical for resisting cleavage by Hepatitis C virus (17). Other ex- for studying the genetics underlying human (an- amples of immunity genes showing evolutionary divergence tiviral) phenotypes. Procedures and data are avail- that directly impacts the ability to restrict viral replication include TRIM5␣ (18), PKR (19)andMxA(20). *To whom correspondence should be addressed. Tel: +1 604 875 2345 (Ext 5273); Email: [email protected] Present addresses: Robin van der Lee, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. Teunis J.P. van Dam, Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, The Netherlands. C The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Downloaded from https://academic.oup.com/nar/article-abstract/45/18/10634/4080662 by Universiteitsbibliotheek Utrecht user on 16 January 2018 Nucleic Acids Research, 2017, Vol. 45, No. 18 10635 Positive selection can be detected through comparative tholog was annotated (likely a combination of suboptimal analysis of protein-coding DNA sequences from multiple genome annotation and lineage-specific gene loss), while species (9,21). Markov models of codon evolution com- another 3798 were discarded because they were part of one- bined with maximum likelihood (ML) methods (22)can to-many or many-to-many relationships. Human genes part analyze alignments of orthologous sequences to identify of the one-to-one ortholog clusters are generally a good genes, codons and lineages that show an excess of nonsyn- representation of all protein-coding human genes, as only onymous substitutions (mutations in the DNA that cause functions related to olfactory signaling and sensory percep- changes to the protein) compared to synonymous (‘silent’) tion of smell are strongly underrepresented among them. substitutions (dN/dS ratio or ␻, see Text S1 for a detailed A number of other categories are moderately underrepre- explanation). Successful application requires many steps sented (antigen presentation and MHC; translation and ri- (15,23) (Text S1), including: (i) the identification of orthol- bosome) or overrepresented (development and differentia- ogous sequences, sampled from species across an appropri- tion, including neuron, synapse and nervous system devel- ate evolutionary distance (distant enough to show variation, opment; kinases and phosphatases; cell motility and migra- but not too divergent to prevent saturation); (ii) accurate tion). Note that our analyses of PSG functions (below) cor- alignment and phylogenetic tree reconstruction; (iii) param- rect for these patterns by using the one-to-one orthologs as eterization of the ML model. While studies of positive se- a background. lection on individual genes have achieved reliable results, estimates of positive selection in whole genomes have been Initial alignments substantially affected by unreliabilities in sequencing, gene models, annotation and misalignment (24–30). In addition We first obtained multiple alignments of the clusters ofor- to the analysis of genomes from different species, the in- thologous primate protein sequences using MUSCLE (34) creasing availability of individual human genomes and pop- and Mafft (35), and from the Compara pipeline (i.e. filter- ulations provides new opportunities to systematically ana- ing the larger vertebrate alignment for primate sequences) lyze more recent sequence variation (9,31). (33). Inspections revealed that misalignment of nonhomol- In this study, we performed comparative evolution- ogous codons affects virtually all alignments, as was ob- ary analyses of recent whole-genome sequenced primates served in previous studies (25–29). This is probably the re- as well as of human genetic variation to identify high- sult of the tendency of alignment algorithms to overalign, confidence targets of positive selection. Our findings pro- i.e. produce alignments that are shorter than the true solu- vide insights into the biological systems that have under- tion due to collapsed insertions in an attempt to avoid gap gone molecular adaptation in primate evolution, which goes penalties (26,36). The PRANK algorithm to some extent beyond immunity genes. Interrogation of the positively se- prevents alignment of nonhomologous regions by flagging lected genes with structural and genomic data describing gaps made during different stages of progressive alignment virus–host interactions provides insights into potential de- and permitting their reuse without further penalties (36). terminants of viral infection and predicts new virus–human As PRANK has been shown to provide better initial align- evolutionary conflicts. ments for large-scale positive selection detection (25–30), we obtained multiple alignments of the primate ortholog MATERIALS AND METHODS clusters using the PRANK codon mode (prank +F -codon; v.140603). We used the default settings of (i) obtaining a Genes, orthologs and sequences guide tree from MAFFT for the progressive alignment pro- We obtained protein-coding DNA sequences of all nine cedure and (ii) selecting the best alignment from five itera- simian primates
Load more

Recommended publications
  • CSE642 Final Version
    Eindhoven University of Technology MASTER Dimensionality reduction of gene expression data Arts, S. Award date: 2018 Link to publication Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain Eindhoven University of Technology MASTER THESIS Dimensionality Reduction of Gene Expression Data Author: S. (Sako) Arts Daily Supervisor: dr. V. (Vlado) Menkovski Graduation Committee: dr. V. (Vlado) Menkovski dr. D.C. (Decebal) Mocanu dr. N. (Nikolay) Yakovets May 16, 2018 v1.0 Abstract The focus of this thesis is dimensionality reduction of gene expression data. I propose and test a framework that deploys linear prediction algorithms resulting in a reduced set of selected genes relevant to a specified case. Abstract In cancer research there is a large need to automate parts of the process of diagnosis, this is mainly to reduce cost, make it faster and more accurate.
    [Show full text]
  • Looking for Missing Proteins in the Proteome Of
    Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update Yves Vandenbrouck, Lydie Lane, Christine Carapito, Paula Duek, Karine Rondel, Christophe Bruley, Charlotte Macron, Anne Gonzalez de Peredo, Yohann Coute, Karima Chaoui, et al. To cite this version: Yves Vandenbrouck, Lydie Lane, Christine Carapito, Paula Duek, Karine Rondel, et al.. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. Journal of Proteome Research, American Chemical Society, 2016, 15 (11), pp.3998-4019. 10.1021/acs.jproteome.6b00400. hal-02191502 HAL Id: hal-02191502 https://hal.archives-ouvertes.fr/hal-02191502 Submitted on 19 Mar 2021 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. Journal of Proteome Research 1 2 3 Looking for missing proteins in the proteome of human spermatozoa: an 4 update 5 6 Yves Vandenbrouck1,2,3,#,§, Lydie Lane4,5,#, Christine Carapito6, Paula Duek5, Karine Rondel7, 7 Christophe Bruley1,2,3, Charlotte Macron6, Anne Gonzalez de Peredo8, Yohann Couté1,2,3, 8 Karima Chaoui8, Emmanuelle Com7, Alain Gateau5, AnneMarie Hesse1,2,3, Marlene 9 Marcellin8, Loren Méar7, Emmanuelle MoutonBarbosa8, Thibault Robin9, Odile Burlet- 10 Schiltz8, Sarah Cianferani6, Myriam Ferro1,2,3, Thomas Fréour10,11, Cecilia Lindskog12,Jérôme 11 1,2,3 7,§ 12 Garin , Charles Pineau .
    [Show full text]
  • Cellular and Molecular Aspects of the Response of the Testis to Nutrition In
    Cellular and molecular aspects of the response of the testis to nutrition in sexually mature sheep Yongjuan Guan 21004548 This thesis is presented for the degree of Doctor of Philosophy of The University of Western Australia School of Animal Biology Institute of Agriculture March 2015 Declaration Declaration The work presented in this thesis is original work of the author, and none of the material in this thesis has been submitted either in full, or part, for a degree at this university or any other universities or institutions before. The experimental designs and manuscript preparation were carried out by myself after discussion with my supervisors Prof Graeme Martin, A/Prof Irek Malecki and Dr Penny Hawken. Yongjuan Guan March 2015 1 Contents Contents Summary ....................................................................................................................................... 4 Acknowledgements ....................................................................................................................... 8 Publications ................................................................................................................................. 10 Chapter 1: General Introduction ................................................................................................. 12 Chapter 2: Literature Review ...................................................................................................... 16 2.1 Male reproduction ............................................................................................................
    [Show full text]
  • Mouse Ssmem1 Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ssmem1 Knockout Project (CRISPR/Cas9) Objective: To create a Ssmem1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ssmem1 gene (NCBI Reference Sequence: NM_027073 ; Ensembl: ENSMUSG00000029784 ) is located on Mouse chromosome 6. 3 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 3 (Transcript: ENSMUST00000031797). Exon 2~3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 6.8% of the coding region. Exon 2~3 covers 93.37% of the coding region. The size of effective KO region: ~2401 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 Legends Exon of mouse Ssmem1 Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Mouse Tmem209 Conditional Knockout Project (CRISPR/Cas9)
    http://www.alphaknockout.com/ Mouse Tmem209 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Tmem209 conditional knockout mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Tmem209 gene ( NCBI Reference Sequence: NM_178625 ; Ensembl: ENSMUSG00000029782 ) is located on mouse chromosome 6. 15 exons are identified , with the ATG start codon in exon 1 and the TAG stop codon in exon 15 (Transcript Tmem209-204: ENSMUST00000115160). Exon 4~5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the mouse Tmem209 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-317G5 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: The knockout of Exon 4~5 will result in frameshift of the gene, and covers 22.22% of the coding region. The size of effective cKO region: ~2246 bp. Page 1 of 8 http://www.alphaknockout.com/ Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 15 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Tmem209 Homology arm cKO region loxP site Page 2 of 8 http://www.alphaknockout.com/ Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Genome-Scale Detection of Positive Selection in 9 Primates Predicts Human-Virus Evolutionary Conflicts
    bioRxiv preprint doi: https://doi.org/10.1101/131680; this version posted April 27, 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-ND 4.0 International license. Genome-scale detection of positive selection in 9 primates predicts human-virus evolutionary conflicts Robin van der Lee1,*,^, Laurens Wiel1,2, Teunis J.P. van Dam1,#, Martijn A. Huynen1 1Centre for Molecular and Biomolecular Informatics, 2Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands *Correspondence: [email protected] ^Current address: Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada #Current address: Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, The Netherlands bioRxiv preprint doi: https://doi.org/10.1101/131680; this version posted April 27, 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-ND 4.0 International license. Abstract Hotspots of rapid genome evolution hold clues about human adaptation. Here, we present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection acting on 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%).
    [Show full text]
  • Investigating Polyphosphate Biology: from Post-Translational Modification to Rare Disease
    Investigating polyphosphate biology: From post-translational modification to rare disease Amanda Bentley-DeSousa A thesis submitted to the Faulty of Graduate and Postdoctoral Studies in partial fulfillment of requirements for the Doctorate in Philosophy degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa Ó Amanda Bentley-DeSousa, Ottawa, Canada, 2021 Authorizations Manuscript #1 Bentley-DeSousa, A., Holinier, C., Moteshareie, H., Tseng, Y-C., Kajjo, S., Nwosu, C., Amodeo, G.F., Bondy-Chorney, E., Sai, Y., Rudner A., Golshani, A., Davey, N.E., and Downey, M. (2018). A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Reports 22, 3427-3439. This is an open access article distributed under the terms of the Creative Commons CC-BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Manuscript #2 McCarthy, L.*, Bentley-DeSousa, A.*, Denoncourt, A., Tseng, Y-C., Gabriel, M., and Downey M. (2020). Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast. FEBS Letters 594, 21-30. *Authors contributed equally License number: 5011081359570 License date: February 16, 2021 License content published: John Wiley and Sons License content publication: FEBS Letters Manuscript #3 Bentley-DeSousa, A., and Downey, M. Vtc5 is localized to the vacuole membrane by the conserved AP-3 complex to regulate polyphosphate synthesis in budding yeast. Manuscript submitted to BioRxiv and in review at mBio Manuscript #4 (Review – Appendix C) Bentley-DeSousa, A., and Downey, M. (2019). From underlying chemistry to therapeutic potential: open questions in the new field of lysine polyphosphorylation.
    [Show full text]
  • 1 Supplementary Table 1. List (Akronym and Description) Of
    Supplementary Table 1. List (akronym and description) of differentially expressed genes (P < 0.05) solely related to copulation, in in pig endocervix (Cvx) up- or down-regulated. UP Description DOWN AGT angiotensinogen (serpin peptidase inhibitor, clade A, member 8) ABHD2 abhydrolase domain containing 2(ABHD2) AKAP13 A kinase (PRKA) anchor protein 13; A-kinase anchor protein 13-like AGPAT2 1-acylglycerol-3-phosphate O-acyltransferase 2(AGPAT2) AKAP9 A kinase (PRKA) anchor protein 9; A-kinase anchor protein 9-like ANXA5 annexin A5(ANXA5) ankyrin repeat domain 33B; ankyrin repeat domain-containing ANKRD33B protein 33B-like ATP6V0C ATPase H+ transporting V0 subunit c(ATP6V0C) C2H5orf45 chromosome 2 open reading frame, human C5orf45 B3GALT2 beta-1,3-galactosyltransferase 2(B3GALT2) C4H1orf110 chromosome 4 open reading frame, human C1orf110 B4GALT1 beta-1,4-galactosyltransferase 1(B4GALT1) CCDC130 coiled-coil domain containing 130(CCDC130) BRINP2 BMP/retinoic acid inducible neural specific 2(BRINP2) CCDC92 coiled-coil domain containing 92(CCDC92) C7H14orf119 chromosome 7 open reading frame, human C14orf119(C7H14orf119) CDKAL1 CDK5 regulatory subunit associated protein 1 like 1(CDKAL1) C8H4orf32 chromosome 8 open reading frame, human C4orf32 COLCA2 colorectal cancer associated 2(COLCA2) CD47 CD47 molecule CPD carboxypeptidase D(CPD) CDH7 cadherin 7(CDH7) CRTC1 CREB regulated transcription coactivator 1(CRTC1) CMPK2 cytidine/uridine monophosphate kinase 2(CMPK2) cap methyltransferase 1; cap-specific mRNA (nucleoside-2-O-)- methyltransferase 1-like;
    [Show full text]
  • Preclinical Evaluation of TEX101 Protein As a Male Infertility Biomarker and Identification of Its Functional Interactome
    Preclinical Evaluation of TEX101 Protein as a Male Infertility Biomarker and Identification of its Functional Interactome by Christina Schiza A thesis submitted in conformity with the requirements for the degree of Doctorate of Philosophy Laboratory Medicine and Pathobiology University of Toronto © Copyright by Christina Schiza 2017 Preclinical Evaluation of TEX101 Protein as a Male Infertility Biomarker and Identification of its Functional Interactome Christina Schiza Doctor of Philosophy Laboratory Medicine and Pathobiology University of Toronto 2017 Abstract TEX101 is a testis-specific cell surface protein expressed exclusively in the male germ cells, and it was previously suggested as a biomarker for the differential diagnosis of male infertility. Molecular function of TEX101 is not known, but previous studies demonstrated that murine TEX101 was a cell membrane chaperone, essential for fertilization. In this work, we employed quantitative proteomic strategies to investigate the clinical and the functional aspects of human TEX101 protein. To facilitate translation of TEX101 into clinic, we first developed and optimized an immunoassay for TEX101 measurement in biological fluids. We then evaluated the performance of TEX101 ELISA in 805 seminal plasma samples of fertile, sub-fertile, and infertile men. We demonstrated the clinical utility of TEX101 to evaluate vasectomy success, to stratify azoospermia forms and subtypes, and to predict the success of sperm retrieval in patients diagnosed with non-obstructive azoospermia. To gain insights into human TEX101 function, we employed mass spectrometry approaches to investigate the physical and the transient TEX101 interactome. Co-immunoprecipitation-mass spectrometry revealed a testis-specific complex TEX101-DPEP3 which was validated by hybrid immunoassay in testicular tissues and spermatozoa.
    [Show full text]
  • PDF Datasheet
    Product Datasheet SSMEM1 Overexpression Lysate NBL1-08557 Unit Size: 0.1 mg Store at -80C. Avoid freeze-thaw cycles. Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBL1-08557 Updated 3/17/2020 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBL1-08557 Page 1 of 2 v.20.1 Updated 3/17/2020 NBL1-08557 SSMEM1 Overexpression Lysate Product Information Unit Size 0.1 mg Concentration The exact concentration of the protein of interest cannot be determined for overexpression lysates. Please contact technical support for more information. Storage Store at -80C. Avoid freeze-thaw cycles. Buffer RIPA buffer Target Molecular Weight 28 kDa Product Description Description Transient overexpression lysate of chromosome 7 open reading frame 45 (C7orf45) The lysate was created in HEK293T cells, using Plasmid ID RC205412 and based on accession number NM_145268. The protein contains a C- MYC/DDK Tag. Gene ID 136263 Gene Symbol C7ORF45 Species Human Notes HEK293T cells in 10-cm dishes were transiently transfected with a non-lipid polymer transfection reagent specially designed and manufactured for large volume DNA transfection. Transfected cells were cultured for 48hrs before collection. The cells were lysed in modified RIPA buffer (25mM Tris-HCl pH7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 1xProteinase inhibitor cocktail mix, 1mM PMSF and 1mM Na3VO4, and then centrifuged to clarify the lysate. Protein concentration was measured by BCA protein assay kit.This product is manufactured by and sold under license from OriGene Technologies and its use is limited solely for research purposes.
    [Show full text]
  • Genome-Scale Detection of Positive Selection in Nine Primates Predicts Human-Virus Evolutionary Conflicts
    10634–10648 Nucleic Acids Research, 2017, Vol. 45, No. 18 Published online 11 August 2017 doi: 10.1093/nar/gkx704 Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts Robin van der Lee1,*, Laurens Wiel1,2, Teunis J.P. van Dam1 and Martijn A. Huynen1 1Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands and 2Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Received May 02, 2017; Revised July 26, 2017; Editorial Decision July 30, 2017; Accepted August 02, 2017 ABSTRACT able at https://github.com/robinvanderlee/positive- selection. Hotspots of rapid genome evolution hold clues about human adaptation. We present a compara- tive analysis of nine whole-genome sequenced pri- INTRODUCTION mates to identify high-confidence targets of posi- Conservation of structure and sequence often indicate bi- tive selection. We find strong statistical evidence ological function. Rapidly evolving sequence features may for positive selection in 331 protein-coding genes however also indicate function, as they may reveal molecu- (3%), pinpointing 934 adaptively evolving codons lar adaptations to new selection pressures. But what drives (0.014%). Our new procedure is stringent and re- these rapid genetic changes during evolution? Can these changes explain the specific phenotypes of species or indi- veals substantial artefacts (20% of initial predic- viduals, such as a differential susceptibility to viruses? tions) that have inflated previous estimates. The fi- Immunity genes contain the strongest signatures of nal 331 positively selected genes (PSG) are strongly rapid evolution due to positive Darwinian selection (1–13).
    [Show full text]
  • Identification of PDL1 Drivers in Models of Head and Neck Squamous Cell Carcinoma by Genome Wide Screening
    Identification of PDL1 Drivers in Models of Head and Neck Squamous Cell Carcinoma by Genome Wide Screening by Jacqueline Mann A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2020 Doctoral Committee: Assistant Professor J.Chad Brenner, Co-Chair Professor Alexey Nesvizhskii, Co-Chair Professor Thomas Carey Professor Nicholas Lukacs Jacqueline Mann [email protected] ORCID iD: 0000-0002-6786-7990 Dedication For my friends, my family members, and all others who suffer from cancer. ii Acknowledgements First, I would like to thank Dr. Chad Brenner for welcoming me into his lab, for his encouragement and guidance along this journey, and for his enduring optimism in the face of any challenge, as this was often exactly what I needed in a mentor. I would also like to thank my committee members for their support throughout this process. Dr. Tom Carey, Dr. Nick Lukacs, and my co-mentor Dr. Alexey Nesvizhskii have all encouraged and helped me in finding my way through graduate school and beyond, and I am so grateful they Were willing to take the time to help mold my scientific thinking and advise me as I transition to the next phase of my career. Thank you to the Molecular and Cellular Pathology Program, especially Dr. Zaneta Nikolovska- Coleska and Laura Labut, for the support and resources they work so tirelessly to provide in order to create such a strong training environment. Thank you also to the Proteome Informatics of Cancer Training Program, which expanded the scope of my learning tremendously.
    [Show full text]