DOCSLIB.ORG

Mouse Exph5 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Exph5 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Exph5 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Exph5 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Exph5 gene (NCBI Reference Sequence: NM_176846 ; Ensembl: ENSMUSG00000034584 ) is located on Mouse chromosome 9. 6 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 6 (Transcript: ENSMUST00000051014). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Exph5 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-93P8 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 2 starts from about 2.04% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 35980 bp, and the size of intron 2 for 3'-loxP site insertion: 2349 bp. The size of effective cKO region: ~661 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 2 6 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Exph5 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. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(7161bp) | A(30.08% 2154) | C(20.65% 1479) | T(28.88% 2068) | G(20.39% 1460) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr9 + 53334583 53337582 3000 browser details YourSeq 41 2215 2497 3000 78.8% chr19 + 54878858 54879129 272 browser details YourSeq 40 1955 2235 3000 95.6% chr3 + 28587625 28587955 331 browser details YourSeq 28 8 70 3000 93.8% chr19 - 12400439 12400501 63 browser details YourSeq 28 10 47 3000 96.7% chr1 + 9654613 9654651 39 browser details YourSeq 26 1955 1985 3000 82.8% chr5 + 60705236 60705264 29 browser details YourSeq 25 1955 1984 3000 82.2% chr4 - 51627331 51627358 28 browser details YourSeq 25 1295 1324 3000 82.2% chr13 + 49514839 49514866 28 browser details YourSeq 24 1953 1985 3000 88.5% chr4 + 31451001 31451032 32 browser details YourSeq 24 1955 1985 3000 84.7% chr15 + 96281725 96281753 29 browser details YourSeq 24 1953 1985 3000 88.5% chr10 + 117399820 117399851 32 browser details YourSeq 22 37 64 3000 89.3% chr16 - 97275149 97275176 28 browser details YourSeq 21 1955 1985 3000 83.9% chr18 - 34102066 34102096 31 browser details YourSeq 21 33 65 3000 81.9% chr10 + 82952109 82952141 33 Note: The 3000 bp section upstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr9 + 53338244 53341243 3000 browser details YourSeq 43 11 167 3000 92.0% chr11 + 114593503 114593666 164 browser details YourSeq 42 1372 1767 3000 57.4% chr14 + 24809059 24809202 144 browser details YourSeq 39 347 469 3000 95.3% chr1 - 157865284 157865432 149 browser details YourSeq 34 20 84 3000 94.8% chr2 - 117563031 117563096 66 browser details YourSeq 33 1313 1444 3000 94.8% chr17 + 8729552 8729728 177 browser details YourSeq 31 388 422 3000 94.3% chrX - 20731234 20731268 35 browser details YourSeq 31 8 82 3000 71.3% chr15 - 42709630 42710134 505 browser details YourSeq 28 22 79 3000 96.7% chr11 - 43756276 43756335 60 browser details YourSeq 28 445 472 3000 100.0% chr5 + 132715640 132715667 28 browser details YourSeq 28 1183 1231 3000 80.0% chr2 + 48517896 48517943 48 browser details YourSeq 27 1773 1799 3000 100.0% chr2 - 4384621 4384647 27 browser details YourSeq 27 21 80 3000 91.0% chr1 + 120560751 120560812 62 browser details YourSeq 25 69 169 3000 62.4% chr2 + 28179500 28179600 101 browser details YourSeq 25 1776 1804 3000 93.2% chr18 + 67376418 67376446 29 browser details YourSeq 24 545 571 3000 96.3% chr14 - 52578065 52578096 32 browser details YourSeq 24 553 581 3000 81.5% chr1 - 186065966 186065992 27 browser details YourSeq 24 445 470 3000 88.0% chr2 + 17168815 17168839 25 browser details YourSeq 23 21 49 3000 77.0% chr13 + 97571461 97571486 26 browser details YourSeq 23 446 470 3000 87.5% chr13 + 28790206 28790229 24 Note: The 3000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Exph5 exophilin 5 [ Mus musculus (house mouse) ] Gene ID: 320051, updated on 12-Aug-2019 Gene summary Official Symbol Exph5 provided by MGI Official Full Name exophilin 5 provided by MGI Primary source MGI:MGI:2443248 See related Ensembl:ENSMUSG00000034584 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Slac2b; slac2-b; Kiaa0624; E030050P12; B130009M24Rik; AC079869.22gm5 Expression Biased expression in cerebellum adult (RPKM 6.3), large intestine adult (RPKM 1.7) and 10 other tissues See more Orthologs human all Genomic context Location: 9; 9 A5.3 See Exph5 in Genome Data Viewer Exon count: 10 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (53301514..53381166) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (53109775..53189263) Chromosome 9 - NC_000075.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 3 transcripts Gene: Exph5 ENSMUSG00000034584 Description exophilin 5 [Source:MGI Symbol;Acc:MGI:2443248] Gene Synonyms AC079869.22gm5, B130009M24Rik, Slac2b, slac2-b Location Chromosome 9: 53,301,670-53,377,514 forward strand. GRCm38:CM001002.2 About this gene This gene has 3 transcripts (splice variants), 121 orthologues, is a member of 1 Ensembl protein family and is associated with 6 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Exph5-201 ENSMUST00000051014.1 5957 1960aa ENSMUSP00000062632.1 Protein coding CCDS23181 Q0VAV2 TSL:1 GENCODE basic APPRIS P1 Exph5-203 ENSMUST00000139096.1 2763 No protein - Retained intron - - TSL:1 Exph5-202 ENSMUST00000132410.1 2315 No protein - Retained intron - - TSL:1 95.84 kb Forward strand 53.30Mb 53.32Mb 53.34Mb 53.36Mb 53.38Mb Genes (Comprehensive set... Exph5-201 >protein coding Exph5-202 >retained intron Poglut3-201 >protein coding Exph5-203 >retained intron Contigs < AC160139.2 < AC079869.22 Regulatory Build 53.30Mb 53.32Mb 53.34Mb 53.36Mb 53.38Mb Reverse strand 95.84 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Non-Protein Coding processed transcript Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000051014 75.84 kb Forward strand Exph5-201 >protein coding ENSMUSP00000062... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) PROSITE profiles Rab-binding domain PANTHER Exophilin-5 Gene3D Zinc finger, RING/FYVE/PHD-type All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 200 400 600 800 1000 1200 1400 1600 1960 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Load more

Recommended publications
  • Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
    Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human.
    [Show full text]
  • Exophilin-5 Regulates Allergic Airway Inflammation by Controlling IL-33–Mediated Th2 Responses
    The Journal of Clinical Investigation RESEARCH ARTICLE Exophilin-5 regulates allergic airway inflammation by controlling IL-33–mediated Th2 responses Katsuhide Okunishi,1 Hao Wang,1 Maho Suzukawa,2,3 Ray Ishizaki,1 Eri Kobayashi,1 Miho Kihara,4 Takaya Abe,4,5 Jun-ichi Miyazaki,6 Masafumi Horie,7 Akira Saito,7 Hirohisa Saito,8 Susumu Nakae,9 and Tetsuro Izumi1 1Laboratory of Molecular Endocrinology and Metabolism, Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan. 2National Hospital Organization Tokyo National Hospital, Tokyo, Japan. 3Division of Respiratory Medicine and Allergology, Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan. 4Laboratory for Animal Resource Development and 5Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan. 6Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan. 7Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 8Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan. 9Laboratory of Systems Biology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan. A common variant in the RAB27A gene in adults was recently found to be associated with the fractional exhaled nitric oxide level, a marker of eosinophilic airway inflammation. The small GTPase Rab27 is known to regulate intracellular vesicle traffic, although its role in allergic responses is unclear. We demonstrated that exophilin-5, a Rab27-binding protein, was predominantly expressed in both of the major IL-33 producers, lung epithelial cells, and the specialized IL-5 and IL-13 producers in the CD44hiCD62LloCXCR3lo pathogenic Th2 cell population in mice.
    [Show full text]
  • (P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
    Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds.
    [Show full text]
  • Microarray Analysis of Novel Genes Involved in HSV- 2 Infection
    Microarray analysis of novel genes involved in HSV- 2 infection Hao Zhang Nanjing University of Chinese Medicine Tao Liu ( [email protected] ) Nanjing University of Chinese Medicine https://orcid.org/0000-0002-7654-2995 Research Article Keywords: HSV-2 infection,Microarray analysis,Histospecic gene expression Posted Date: May 12th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-517057/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background: Herpes simplex virus type 2 infects the body and becomes an incurable and recurring disease. The pathogenesis of HSV-2 infection is not completely clear. Methods: We analyze the GSE18527 dataset in the GEO database in this paper to obtain distinctively displayed genes(DDGs)in the total sequential RNA of the biopsies of normal and lesioned skin groups, healed skin and lesioned skin groups of genital herpes patients, respectively.The related data of 3 cases of normal skin group, 4 cases of lesioned group and 6 cases of healed group were analyzed.The histospecic gene analysis , functional enrichment and protein interaction network analysis of the differential genes were also performed, and the critical components were selected. Results: 40 up-regulated genes and 43 down-regulated genes were isolated by differential performance assay. Histospecic gene analysis of DDGs suggested that the most abundant system for gene expression was the skin, immune system and the nervous system.Through the construction of core gene combinations, protein interaction network analysis and selection of histospecic distribution genes, 17 associated genes were selected CXCL10,MX1,ISG15,IFIT1,IFIT3,IFIT2,OASL,ISG20,RSAD2,GBP1,IFI44L,DDX58,USP18,CXCL11,GBP5,GBP4 and CXCL9.The above genes are mainly located in the skin, immune system, nervous system and reproductive system.
    [Show full text]
  • Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition
    HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition Charles Richard Bradshaw1¤a, Vineeth Surendranath1, Robert Henschel2,3, Matthias Stefan Mueller2, Bianca Hermine Habermann1,4*¤b 1 Bioinformatics Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony, Germany, 2 Center for Information Services and High Performance Computing (ZIH), Technical University, Dresden, Saxony, Germany, 3 High Performance Applications, Pervasive Technology Institute, Indiana University, Bloomington, Indiana, United States of America, 4 Bioinformatics Laboratory, Scionics c/o Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony, Germany Abstract Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes.
    [Show full text]
  • Exophilin-5 Regulates Allergic Airway Inflammation by Controlling IL-33-Mediated Th2 Responses
    Exophilin-5 regulates allergic airway inflammation by controlling IL-33-mediated Th2 responses Katsuhide Okunishi, … , Susumu Nakae, Tetsuro Izumi J Clin Invest. 2020. https://doi.org/10.1172/JCI127839. Research In-Press Preview Immunology Graphical abstract Find the latest version: https://jci.me/127839/pdf Exophilin-5 regulates allergic airway inflammation by controlling IL-33-mediated Th2 responses Katsuhide Okunishi1*, Hao Wang1, Maho Suzukawa2,3, Ray Ishizaki1, Eri Kobayashi1, Miho Kihara4, Takaya Abe4,5, Jun-ichi Miyazaki6, Masafumi Horie7, Akira Saito7, Hirohisa Saito8, Susumu Nakae9 and Tetsuro Izumi1* 1Laboratory of Molecular Endocrinology and Metabolism, Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan; 2National Hospital Organization Tokyo National Hospital, Tokyo, Japan; 3Division of Respiratory Medicine and Allergology, Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan; 4Laboratory for Animal Resource Development and 5Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; 6 The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan; 7Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; 8Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan. 9Laboratory of Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Authorship note: K.O. and H.W. have contributed equally. *Correspondence: Katsuhide Okunishi, 3-39-15 Showa-machi, Maebashi, Gunma 371-8512, Japan; Phone: +81-27-220-8877; E-mail: [email protected]. Or to Tetsuro Izumi, 3-39-15 Showa-machi, Maebashi, Gunma 371-8512, Japan; Phone: +81-27-220-8856; E-mail: 1 [email protected].
    [Show full text]
  • Expanding the Clinical Spectrum of COL1A1 Mutations in Different Forms of Glaucoma
    Mauri et al. Orphanet Journal of Rare Diseases (2016) 11:108 DOI 10.1186/s13023-016-0495-y RESEARCH Open Access Expanding the clinical spectrum of COL1A1 mutations in different forms of glaucoma Lucia Mauri1, Steffen Uebe2, Heinrich Sticht3, Urs Vossmerbaeumer4,NicoleWeisschuh5, Emanuela Manfredini1, Edoardo Maselli6, Mariacristina Patrosso1,RobertN.Weinreb7, Silvana Penco1,AndréReis2 and Francesca Pasutto2* Abstract Background: Primary congenital glaucoma (PCG) and early onset glaucomas are one of the major causes of children and young adult blindness worldwide. Both autosomal recessive and dominant inheritance have been described with involvement of several genes including CYP1B1, FOXC1, PITX2, MYOC and PAX6. However, mutations in these genes explain only a small fraction of cases suggesting the presence of further candidate genes. Methods: To elucidate further genetic causes of these conditions whole exome sequencing (WES) was performed in an Italian patient, diagnosed with PCG and retinal detachment, and his unaffected parents. Sanger sequencing of the complete coding region of COL1A1 was performed in a total of 26 further patients diagnosed with PCG or early onset glaucoma. Exclusion of pathogenic variations in known glaucoma genes as CYP1B1, MYOC, FOXC1, PITX2 and PAX6 was additionally done per Sanger sequencing and Multiple Ligation-dependent Probe Amplification (MLPA) analysis. Results: In the patient diagnosed with PCG and retinal detachment, analysis of WES data identified compound heterozygous variants in COL1A1 (p.Met264Leu; p.Ala1083Thr). Targeted COL1A1 screening of 26 additional patients detected three further heterozygous variants (p.Arg253*, p.Gly767Ser and p.Gly154Val) in three distinct subjects: two of them diagnosed with early onset glaucoma and mild form of osteogenesis imperfecta (OI), one patient with a diagnosis of PCG at age 4 years.
    [Show full text]
  • WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12N 1/19 (2006.01) C12Q 1/02 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, C12N 15/81 (2006.01) C07K 14/47 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US20 15/049674 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 11 September 2015 ( 11.09.201 5) SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/050,045 12 September 2014 (12.09.2014) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: WHITEHEAD INSTITUTE FOR BIOMED¬ DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, ICAL RESEARCH [US/US]; Nine Cambridge Center, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Cambridge, Massachusetts 02142-1479 (US).
    [Show full text]
  • Population and Family Based Studies of Consanguinity: Genetic And
    Population and family based studies of consanguinity: Genetic and computational approaches Abdullah Mesut Erzurumluoğlu A dissertation submitted to the University of Bristol in accordance with the requirements for award of degree of Doctor of Philosophy (PhD) in the Faculty of Medicine and Dentistry October 2015 Word Count = ~65,000* *Excluding preface, tables, footnotes, references and appendices Thesis Abstract Consanguinity is the union of closely related individuals – which can have genetic implications on the health of offspring(s). Consanguineous families with disorders have been extensively analysed by geneticists and this has led to the identification of many autosomal recessive disorder causal variants and genes. Two copies of the ‘inactivating’ or loss of function (LoF) allele are required to cause an autosomal recessive disorder, one inherited from the mother and the other from the father. In outbreeding populations these LoF alleles very rarely meet their counterpart (as it requires both parents to possess the allele), thus are passed down the generations silently – sometimes for millennia. However, consanguineous and/or endogamous offspring have elevated levels of homozygosity, which dramatically increases the probability of any allele to be in a homozygous (or more correctly autozygous) state. This increase in probability applies to LoF mutations also; and this elevation of levels of homozygosity is the main reason why extremely rare autosomal recessive disorders are usually only seen in populations where consanguinity (and/or endogamy) levels are high. With the ever decreasing prices of DNA sequencing, whole-genome sequencing is becoming a reality for many laboratories. However, for now, whole-exome sequencing (WES) is the most feasible sequencing technique mostly due to cost factors.
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • LAMB3 Missense Variant in Australian Shepherd Dogs with Junctional Epidermolysis Bullosa
    G C A T T A C G G C A T genes Article LAMB3 Missense Variant in Australian Shepherd Dogs with Junctional Epidermolysis Bullosa 1,2, 3, 4 1,2 Sarah Kiener y , Aurore Laprais y, Elizabeth A. Mauldin , Vidhya Jagannathan , Thierry Olivry 5,* and Tosso Leeb 1,2,* 1 Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; [email protected] (S.K.); [email protected] (V.J.) 2 Dermfocus, University of Bern, 3001 Bern, Switzerland 3 The Ottawa Animal Emergency and Specialty Hospital, Ottawa, ON K1K 4C1, Canada; [email protected] 4 School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] 5 Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA * Correspondence: [email protected] (T.O.); [email protected] (T.L.); Tel.: +41-31-631-2326 (T.L.) These authors contributed equally to this work (shared first authors). y Received: 10 August 2020; Accepted: 3 September 2020; Published: 7 September 2020 Abstract: In a highly inbred Australian Shepherd litter, three of the five puppies developed widespread ulcers of the skin, footpads, and oral mucosa within the first weeks of life. Histopathological examinations demonstrated clefting of the epidermis from the underlying dermis within or just below the basement membrane, which led to a tentative diagnosis of junctional epidermolysis bullosa (JEB) with autosomal recessive inheritance. Endoscopy in one affected dog also demonstrated separation between the epithelium and underlying tissue in the gastrointestinal tract. As a result of the severity of the clinical signs, all three dogs had to be euthanized.
    [Show full text]
  • Association of Single Nucleotide Polymorphism In
    PROCEEDINGS OF THE LATVIAN ACADEMY OF SCIENCES. Section B, Vol. 67 (2013), No. 6 (687), pp. 453–456. DOI: 10.2478/prolas-2013-0079 ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISM IN CHROMOSOME 11 WITH AUTISM SPECTRUM DISORDER Daiga Bauze*, **, Linda Piekuse***, Laura Kevere*, Zane Kronberga*, Arnis Riþevs*, Iveta Vaivade****, Kristîne Vîksne****, Raisa Andrçziòa*, ***, and Baiba Lâce**** * Children’s University Hospital, Child Psychiatry Clinic, Juglas iela 20, Rîga, LV–1079, LATVIA; [email protected] ** Children’s University Hospital, Medical Genetics Clinic, Juglas iela 20, Rîga, LV–1079, LATVIA *** Rîga Stradiòð University, Dzirciema 16, Rîga, LV-1007, LATVIA **** Latvian Biomedical Research and Study Centre, Râtsupîtes iela 1, Rîga, LV-1067, LATVIA Communicated by Isaak Rashal Several genetic loci in chromosomes 11 and 15 have recently been associated with non-syndromic autism spectrum disorder (ASD) in populations from North America and Europe. The aim of the present study was to investigate whether such an association exists in a Latvian population. Ninety-five patients with ASD in the age range 3–20 years (mean age 8 years, SD 3.18) participated in the study. The control group consisted of 161 healthy, non-related individuals without ASD randomly selected from the Latvian Genome Database. Four single nucleotide poly- morphisms (SNPs) — rs11212733, SNP rs1394119, rs2421826, rs1454985 — were genotyped by the TaqMan method. Allele frequency differences between ASD patients and control subjects were compared for each SNP using a standard chi-square test with Bonferroni correction. The level of statistical significance was set at 0.05 for nominal association. Only the genetic marker rs11212733, localised on the long arm of chromosome 11 in locus 22.3, was found to be strongly 2 associated with the ASD patient group (c 6.982, Padjusted 0.033, odds ratio 1.625).
    [Show full text]