DOCSLIB.ORG

The Title of the Article

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Title of the Article Identifying Interacting Environmental Factor – Gene Pairs Chad Kimmel, MS1, Jonathan Lustgarten, PhD3, An-Kwok Ian Wong, MS2, Shyam Visweswaran, MD, PhD1,2 1Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 2Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA 3 University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA ABSTRACT underlying the disease (based on the already characterized mechanisms in the similar diseases) or in investigating Most diseases are caused by a combination of new therapies (based on the therapies in use in the similar environmental and genetic etiological factors, and these diseases). factors may interact in causing disease. We conjectured that an environmental factor and a gene that are Several papers have described innovative methods for associated with the same set of diseases are likely to extracting environmental factors of disease and in interact. We extracted environmental factor – disease analyzing environmental factors in combination with associations and gene – disease associations from freely genetic factors. Liu et. al. extracted a comprehensive list accessible online databases and the research literature, of associations between disease and environmental factors and identified environmental factor – gene pairs that were using the Medical Subject Headings (MeSH) annotations similar in being associated with a common set of diseases. of MEDLINE articles and combined it with genetic For several of these pairs that we examined, we found factors of disease to characterize the “etiome” profile of evidence for plausible biological interactions in the over 800 diseases [3]. Patel et. al. developed a new literature. We postulate that that the remaining pairs may method called an Environment-Wide Association Study represent novel interactions between an environmental (EWAS) - similar to a Genome Wide Association Study factor and a gene. (GWAS) - to extract environmental factors of disease and applied it to Diabetes mellitus type 2 [4]. Gohlke et. al. INTRODUCTION extracted environmental factors of disease by identifying key molecular pathways that are jointly associated with The etiological factors associated with the development of genetic and environmental factors using a gene-centric human disease are broadly categorized into environmental database, and validated their new-found associations with and genetic factors. While infections like community- known chemical-disease relationships and transcriptional acquired pneumonia are predominantly influenced by regulation data [5]. We followed the strategies used by environmental factors and Mendelian diseases like sickle Liu et. al. to compile datasets of environmental factor – cell anemia are predominantly influenced by genetic disease and gene – disease associations. factors, many of the common diseases like coronary heart disease are influenced by both environmental and genetic We conjectured that an environmental factor and a gene factors that likely interact with each other. that are associated with the same set of diseases are likely to have a biological interaction. In this paper, we Several freely accessible online databases are now computed a similarity measure for an environmental available that collate information on genetic factors factor and a gene. We then investigated the most similar associated with disease, such as the Online Mendelian environmental factor - gene pairs for plausible biological Inheritance in Man (OMIM), the Genetic Association interactions. We defined an interaction as either the Database [1], and GeneCards. Fewer sources of environmental factor having a direct influence on the information are available on environmental factors gene, or the environmental factor and the gene (along associated with diseases. A freely accessible database is with the protein product) having a direct influence on a the CHE Toxicant and Disease Database [2] that contains common biological molecule (e.g., gene, protein, curated information on chemicals/toxins associated with metabolite). disease, and another source is the dataset provided by Liu et. al. in their paper on the “etiome” [3]. METHODS Collated data on environmental factor – disease In this section, we briefly describe the extraction of associations and gene – disease associations can provide a environmental and genetic factors of diseases, the wealth of information. For example, identifying similarity measure we used and the method we followed etiologically similar diseases to a disease of interest may for the selection of promising environmental factor – gene be useful in unraveling the biological mechanisms pairs. Environmental Factors. We obtained environmental Environmental Factor – Gene Pairs. We examined factors of human diseases from two sources. We obtained environmental factor – gene pairs with a Jaccard chemical-disease associations from the CHE Toxicant and similarity measure of 0.4 or greater for plausible Disease Database [2]. In addition, we extracted interactions between members of the pair. We chose a environmental factor – disease associations from the threshold of 0.4 rather arbitrarily so that we had a MeSH annotations of MEDLINE articles using the manageable number of high scoring environmental factor strategies developed by Liu et. al. [3]. MeSH is a – gene pairs to examine. We used the research literature comprehensive controlled vocabulary that contains over and Ingenuity (Ingenuity Systems©, www.ingenuity.com) 25,000 descriptors (also known as subject headings) and to identify interactions. Ingenuity is a systems biology over 80 qualifiers (also known as subheadings). An article database that contains manually annotated relationships in MEDLINE is typically annotated with several between biological agents such as chemicals, drugs, descriptor/qualifier pairs. For example, "peptic ulcer" is a genes, and proteins. In Ingenuity, we searched for descriptor and "chemically induced" is a qualifier and evidence that the environmental factor in a pair directly "peptic ulcer/chemically induced" describes articles on influences the gene. We also searched for biological peptic ulcer that are chemically induced (e.g., by a drug molecules (genes, metabolites, etc.) that are related to like indomethacin). Liu et al. identified several patterns of both the environmental factor and the gene in a pair. pairs of MeSH qualifiers to infer environmental factor → disease associations. For example, the association RESULTS indomethacin → peptic ulcer is induced from the We extracted 51,994 disease-environmental associations following two annotations of an article: peptic ulcer / between 1,911 diseases and 5,801 environmental agents chemically induced and indomethacin / adverse effect from the CHE Toxicant and Disease Database and (MeSH descriptors are in bold and MeSH qualifiers are in MEDLINE. We extracted 8,872 disease-gene associations italics). between 889 diseases and 1,891 genes from the GAD. The CHE Toxicant and Disease Database and MEDLINE Genetic Factors. We obtained genetic factors of human annotations were downloaded in May 2009. After diseases from the Genetic Association Database (GAD) etiological factors with less than three associated diseases which contains gene-disease associations that have been were excluded the number of environmental factors curated from the literature [1]. The GAD uses decreased to 2,459 and the number of genes decreased to standardized identifiers for genes (NCBI Entrez Gene 1,469. This resulted in more than three and a half million identifiers) and diseases (Medical Subject Headings environmental factor – gene pairs for which we computed (MeSH) identifiers) that enable easy machine processing. the Jaccard similarity measure. Similarity Measure. A similarity measure indicates the We identified a total of 63 environmental factor – gene strength of commonality between a pair of entities (e.g., pairs with a similarity of measure of 0.4 or greater. Table an environmental factor and a genetic factor) based on 1 gives a list of the 63 pairs and the common associated their properties (e.g., associated diseases). We used the diseases. The maximum number of common diseases for Jaccard similarity measure to calculate the similarity a pair was three. between an environmental factor E and a genetic factor G, as follows: We found evidence for an interaction for 10 of the 63 environmental factor – gene pairs. We now summarize ( ) some of this evidence. For the sodium salicylate – KCNQ4 gene pair, Wu et al. [6] showed that salicytate blocks the action of the KCNQ4 gene resulting in hearing where S11 is the number of diseases associated with both loss. For the antithrombins – F3 pair, antithrombin G and E, S10 is the number of diseases associated with E inhibits the complex consisting of coagulation factors III but not G, and S01 is the number of diseases associated and VII that are produced by genes F3 and F7 [7]. with G but not E. The Jaccard similarity measure varies between 0 and 1 where 1 denotes that E and G are Several of the environmental factor – gene pairs had an associated with exactly the same set of diseases, and 0 influence on the same biological molecule. For instance, denotes that E and G have no common associated in the pair piperonyl butoxide – SMYD3, both piperonyl diseases. We computed the Jaccard similarity measure butoxide, and SMYD3 have an influence on the c-Myc only for those genetic and environmental factors that were oncogene which has been implicated in the
Load more

Recommended publications
  • Diagnostic Value of PRND Gene Expression Profiles in Astrocytomas: Relationship to Tumor Grades of Malignancy
    989-996 29/3/07 11:35 Page 989 ONCOLOGY REPORTS 17: 989-996, 2007 989 Diagnostic value of PRND gene expression profiles in astrocytomas: Relationship to tumor grades of malignancy S. COMINCINI1, V. FERRARA1, A. ARIAS1, A. MALOVINI1, A. AZZALIN1, L. FERRETTI1, E. BENERICETTI2, M. CARDARELLI3, M. GEROSA3, M.G. PASSARIN4, S. TURAZZI3 and R. BELLAZZI5 1Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, Pavia; 2Azienda Ospedaliera - Universitaria di Parma, Parma; 3Clinica Neurochirurgica Università di Verona; 4U.O. Neurologia, Azienda Ospedaliera - Universitaria di Verona, Verona; 5Dipartimento di Informatica e Sistemistica, Università degli Studi di Pavia, Pavia, Italy Received December 14, 2006; Accepted January 24, 2007 Abstract. Doppel (PRND) is a paralogue of the mammalian grade astrocytomas have an inherent tendency to progress prion (PRNP) gene. It is abundant in testis and, unlike PRNP, toward more malignant forms. This progression has been it is expressed at low levels in the adult central nervous system thought to result from an accumulation of genetic events (CNS). Besides, doppel overexpression correlates with some that leads to the clonal expansion of a malignant cell (4). prion-disease pathological features, such as ataxia and death Some of these events, such as the inactivation of the p53 of cerebellar neurons. Recently, ectopic expression of doppel tumor suppressor gene in the initial steps of carcinogenesis was found in two different tumor types, specifically in glial and amplification of the epidermal growth factor receptor and haematological cancers. In order to address clinical (EGFR) gene in the late stages have been identified (reviewed important issues, PRND mRNA expression was investigated in ref.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Identification of Multiple Quantitative Trait Loci Linked to Prion Disease Incubation Period in Mice
    Identification of multiple quantitative trait loci linked to prion disease incubation period in mice Sarah E. Lloyd†, Obia N. Onwuazor†, Jonathan A. Beck†, Gary Mallinson‡, Martin Farrall§, Paul Targonski§, John Collinge†‡¶, and Elizabeth M. C. Fisher‡ †Medical Research Council Prion Unit and ‡Department of Neurogenetics, Imperial College School of Medicine at St Mary’s, Norfolk Place, London W2 1PG, United Kingdom; and §Department of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom Communicated by Charles Weissmann, Imperial College of Science, Technology, and Medicine, London, United Kingdom, March 14, 2001 (received for review January 15, 2001) Polymorphisms in the prion protein gene are known to affect prion identify prion ligands and biochemical pathways that will allow disease incubation times and susceptibility in humans and mice. a better understanding of prion pathogenesis and the develop- However, studies with inbred lines of mice show that large dif- ment of rational therapeutics. ferences in incubation times occur even with the same amino acid Direct identification of human quantitative trait loci (QTL) is sequence of the prion protein, suggesting that other genes may both technically challenging and expensive because of the large contribute to the observed variation. To identify these loci we sample sizes that are necessary to detect alleles of modest effect analyzed 1,009 animals from an F2 intercross between two strains in randomly mating populations. The advantages of studying of mice, CAST͞Ei and NZW͞OlaHSd, with significantly different organisms in which breeding designs are under experimental incubation periods when challenged with RML scrapie prions.
    [Show full text]
  • "The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
    The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses.
    [Show full text]
  • The Vascular Endothelial Cell-Expressed Prion Protein Doppel Promotes Angiogenesis and Blood-Brain Barrier Development Zhihua Chen1, John E
    © 2020. Published by The Company of Biologists Ltd | Development (2020) 147, dev193094. doi:10.1242/dev.193094 RESEARCH ARTICLE The vascular endothelial cell-expressed prion protein doppel promotes angiogenesis and blood-brain barrier development Zhihua Chen1, John E. Morales1, Naze Avci1, Paola A. Guerrero1, Ganesh Rao1, Je Hoon Seo2 and Joseph H. McCarty1,* ABSTRACT linked to activation of Notch-Dll4 signaling in vascular endothelial The central nervous system (CNS) contains a complex network of tip cells (Jakobsson et al., 2009; Siekmann et al., 2008). VEGF-A blood vessels that promote normal tissue development and physiology. signaling is also linked to Slit signaling through Robo receptors and Abnormal control of blood vessel morphogenesis and maturation is is crucial for developmental CNS angiogenesis (Rama et al., 2015). linked to the pathogenesis of various neurodevelopmental diseases. Furthermore, the Slit2-Robo complex in endothelial cells is The CNS-specific genes that regulate blood vessel morphogenesis in involved in VEGFR2 internalization and signaling (Genet et al., β development and disease remain largely unknown. Here, we have 2019). Integrin-mediated activation of TGF- signaling is also characterized functions for the gene encoding prion protein 2 (Prnd) crucially involved in control of sprouting angiogenesis and NVU in CNS blood vessel development and physiology. Prnd encodes the development (Arnold et al., 2014; Hirota et al., 2015, 2011; Ma glycosylphosphatidylinositol (GPI)-linked protein doppel, which is et al., 2017; McCarty, 2020; Mobley et al., 2009). In addition, Wnts expressed on the surface of angiogenic vascular endothelial cells, secreted by radial glial cells also promote angiogenesis and blood- but is absent in quiescent endothelial cells of the adult CNS.
    [Show full text]
  • Doppel Antibody / PRND (RQ4601)
    Doppel Antibody / PRND (RQ4601) Catalog No. Formulation Size RQ4601 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human, Mouse, Rat Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Antigen affinity purified Buffer Lyophilized from 1X PBS with 2% Trehalose and 0.025% sodium azide UniProt Q9UKY0 Localization Cytoplasm, plasma membrane Applications Western blot : 0.5-1ug/ml IHC (FFPE) : 1-2ug/ml Western blot testing of 1) human SHG-44, 2) rat testis, 3) rat kidney, 4) mouse testis, 5) mouse kidney and 6) mouse brain lysate with Doppel antibody at 0.5ug/ml. Predicted molecular weight ~20 kDa. IHC staining of FFPE human testis with Doppel antibody at 1ug/ml. HIER: boil tissue sections in pH6, 10mM citrate buffer, for 10-20 min followed by cooling at RT for 20 min. IHC staining of FFPE mouse testis with Doppel antibody at 1ug/ml. HIER: boil tissue sections in pH6, 10mM citrate buffer, for 10-20 min followed by cooling at RT for 20 min. Description Prion protein 2 (dublet), also known as PRND, or Doppel protein, is a protein which in humans is encoded by the PRND gene. It is mapped to 20p13. This gene is found on chromosome 20, approximately 20 kbp downstream of the gene encoding cellular prion protein, to which it is biochemically and structurally similar. The protein encoded by this gene is a membrane glycosylphosphatidylinositol-anchored glycoprotein that is found predominantly in testis. Mutations in this gene may lead to neurological disorders.
    [Show full text]
  • The DNA Sequence and Comparative Analysis of Human Chromosome 20
    articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M.
    [Show full text]
  • Heterogeneity Between Primary Colon Carcinoma and Paired Lymphatic and Hepatic Metastases
    MOLECULAR MEDICINE REPORTS 6: 1057-1068, 2012 Heterogeneity between primary colon carcinoma and paired lymphatic and hepatic metastases HUANRONG LAN1, KETAO JIN2,3, BOJIAN XIE4, NA HAN5, BINBIN CUI2, FEILIN CAO2 and LISONG TENG3 Departments of 1Gynecology and Obstetrics, and 2Surgical Oncology, Taizhou Hospital, Wenzhou Medical College, Linhai, Zhejiang; 3Department of Surgical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang; 4Department of Surgical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang; 5Cancer Chemotherapy Center, Zhejiang Cancer Hospital, Zhejiang University of Chinese Medicine, Hangzhou, Zhejiang, P.R. China Received January 26, 2012; Accepted May 8, 2012 DOI: 10.3892/mmr.2012.1051 Abstract. Heterogeneity is one of the recognized characteris- Introduction tics of human tumors, and occurs on multiple levels in a wide range of tumors. A number of studies have focused on the Intratumor heterogeneity is one of the recognized charac- heterogeneity found in primary tumors and related metastases teristics of human tumors, which occurs on multiple levels, with the consideration that the evaluation of metastatic rather including genetic, protein and macroscopic, in a wide range than primary sites could be of clinical relevance. Numerous of tumors, including breast, colorectal cancer (CRC), non- studies have demonstrated particularly high rates of hetero- small cell lung cancer (NSCLC), prostate, ovarian, pancreatic, geneity between primary colorectal tumors and their paired gastric, brain and renal clear cell carcinoma (1). Over the past lymphatic and hepatic metastases. It has also been proposed decade, a number of studies have focused on the heterogeneity that the heterogeneity between primary colon carcinomas and found in primary tumors and related metastases with the their paired lymphatic and hepatic metastases may result in consideration that the evaluation of metastatic rather than different responses to anticancer therapies.
    [Show full text]
  • Mouse Prn Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Prn Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Prn conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Prn gene (NCBI Reference Sequence: NM_001278258 ; Ensembl: ENSMUSG00000098754 ) is located on Mouse chromosome 2. 4 exons are identified, with the ATG start codon in exon 3 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000136783). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Prn gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-401J24 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: Exon 3 starts from about 0.51% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 34078 bp, and the size of intron 3 for 3'-loxP site insertion: 6535 bp. The size of effective cKO region: ~547 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 4 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Prn Homology arm cKO region loxP site Page 2 of 7 https://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]
  • The Role of the Prion Protein in the Immune System
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2013 The role of the prion protein in the immune system Kana, V Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-79331 Dissertation Published Version Originally published at: Kana, V. The role of the prion protein in the immune system. 2013, University of Zurich, Faculty of Science. The Role of the Prion Protein in the Immune System Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Veronika Kana von Chur GR Promotionskomitee Prof. Dr. Adriano Aguzzi (Vorsitz) Prof. Dr. Cornelia Halin Winter Prof. Dr. Christian Grimm Prof. Dr. Christian Münz Zürich, 2013 TABLE OF CONTENTS 1 SUMMARY ........................................................................................................................................ 3 2 ZUSAMMENFASSUNG .................................................................................................................... 6 3 ABBREVIATIONS ............................................................................................................................. 9 4 THE ROLE OF THE PRION PROTEIN IN THE IMMUNE SYSTEM .............................................. 11 4.1 INTRODUCTION ...................................................................................................................... 12 4.1.1
    [Show full text]
  • Restoring Spermatogenesis: Lentiviral Gene Therapy for Male Infertility in Mice
    RESTORING SPERMATOGENESIS: LENTIVIRAL GENE THERAPY FOR MALE INFERTILITY IN MICE by Randall J Beadling BS Biology, University of Georgia, 2012 Submitted to the Graduate Faculty of Human Genetics, Genetic Counseling Graduate School of Public Health in partial fulfillment of the requirements for the degree of Master of Science University of Pittsburgh 2015 UNIVERSITY OF PITTSBURGH Graduate School of Public Health This thesis was presented by Randall Beadling It was defended on April 14th, 2015 and approved by Candace Kammerer PhD, Associate Professor, Human Genetics Graduate School of Public Health, University of Pittsburgh Daniel E. Weeks PhD, Professor, Human Genetics Graduate School of Public Health, University of Pittsburgh Committee Chair: Alex Yatsenko MD, PhD, Assistant Professor, Obstetrics, Gynecology & Reproducitve Sciences, Magee-Womens Research Institute and Foundation, University of Pittsburgh Medical Center ii Copyright © by Randall Beadling 2015 iii Alex Yatsenko MD, PhD RESTORING SPERMATOGENESIS: LENTIVIRAL GENE THERAPY FOR MALE INFERTILITY IN MICE Randall Beadling, MS University of Pittsburgh, 2015 ABSTRACT Background: Male infertility of genetic origin affects nearly 1 in 40 men. Yet 80% of men with low sperm production are considered idiopathic due to negative genetic testing. Based on mouse studies there are several hundred possible candidate genes for causing isolated idiopathic male infertility due to their involvement in spermatogenesis and male germline-specific expression. Although little is known about their pathophysiology and epidemiology in human males, these genes represent vast potential for diagnosing and treating infertility. Lentiviral vector gene therapy has recently been shown to be effective in restoring gene expression, and has the potential to serve as treatment in male infertility caused by gene defects.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials 1 Supplementary Figure S1. Expression of BPIFB4 in murine hearts. Representative immunohistochemistry images showing the expression of BPIFB4 in the left ventricle of non-diabetic mice (ND) and diabetic mice (Diab) given vehicle or LAV-BPIFB4. BPIFB4 is shown in green, nuclei are identified by the blue fluorescence of DAPI. Scale bars: 1 mm and 100 μm. 2 Supplementary Table S1 – List of PCR primers. Target gene Primer Sequence NCBI Accession number / Reference Forward AAGTCCCTCACCCTCCCAA Actb [1] Reverse AAGCAATGCTGTCACCTTC Forward TCTAGGCAATGCCGTTCAC Cpt1b [2] Reverse GAGCACATGGGCACCATAC Forward GGAAATGATCAACAAAAAAAGAAGTATTT Acadm (Mcad) [2] Reverse GCCGCCACATCAGA Forward TGATGGTTTGGAGGTTGGGG Acot1 NM_012006.2 Reverse TGAAACTCCATTCCCAGCCC Forward GGTGTCCCGTCTAATGGAGA Hmgcs2 NM_008256.4 Reverse ACACCCAGGATTCACAGAGG Forward CAAGCAGCAACATGGGAAGA Cs [2] Reverse GTCAGGATCAAGAACCGAAGTCT Forward GCCATTGTCAACTGTGCTGA Ucp3 NM_009464.3 Reverse TCCTGAGCCACCATCTTCAG Forward CGTGAGGGCAATGATTTATACCAT Atp5b [2] Reverse TCCTGGTCTCTGAAGTATTCAGCAA Pdk4 Forward CCGCTGTCCATGAAGCA [2] 3 Reverse GCAGAAAAGCAAAGGACGTT Forward AGAGTCCTATGCAGCCCAGA Tomm20 NM_024214.2 Reverse CAAAGCCCCACATCTGTCCT Forward GCCTCAGATCGTCGTAGTGG Drp1 NM_152816.3 Reverse TTCCATGTGGCAGGGTCATT Forward GGGAAGGTGAAGAAGCTTGGA Mfn2 NM_001285920.1 Reverse ACAACTGGAACAGAGGAGAAGTT Forward CGGAAATCATATCCAACCAG [2] Ppargc1a (Pgc1α) Reverse TGAGAACCGCTAGCAAGTTTG Forward AGGCTTGGAAAAATCTGTCTC [2] Tfam Reverse TGCTCTTCCCAAGACTTCATT Forward TGCCCCAGAGCTGTTAATGA Bcl2l1 NM_001289716.1
    [Show full text]