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Mouse Nckipsd Conditional Knockout Project (CRISPR/Cas9)

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https://www.alphaknockout.com Mouse Nckipsd Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Nckipsd conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Nckipsd gene (NCBI Reference Sequence: NM_030729 ; Ensembl: ENSMUSG00000032598 ) is located on Mouse chromosome 9. 13 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 13 (Transcript: ENSMUST00000035218). Exon 3~5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Nckipsd gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP24-372F13 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: Mice homozygous for a null mutation exhibit altered protein composition of postsynaptic densities and actin cytoskeleton in hippocampal neurons. Exon 3 starts from about 13.17% of the coding region. The knockout of Exon 3~5 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 393 bp, and the size of intron 5 for 3'-loxP site insertion: 1239 bp. The size of effective cKO region: ~1607 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 8 9 10 13 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Nckipsd Homology arm cKO region loxP site Page 2 of 8 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. Tandem repeats are found in the dot plot matrix. It may be difficult to construct this targeting vector. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(8053bp) | A(21.9% 1764) | C(26.86% 2163) | T(22.96% 1849) | G(28.28% 2277) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. Significant high GC-content regions are found. It may be difficult to construct this targeting vector. Page 3 of 8 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 + 108808354 108811353 3000 browser details YourSeq 31 1865 1913 3000 85.8% chr7 - 73447825 73447871 47 browser details YourSeq 25 8 36 3000 96.3% chr2 + 147180641 147180670 30 browser details YourSeq 24 1862 1887 3000 88.0% chr10 + 126407420 126407444 25 browser details YourSeq 23 2581 2608 3000 84.0% chr5 - 98050411 98050436 26 browser details YourSeq 23 2976 3000 3000 96.0% chr17 - 87924692 87924716 25 browser details YourSeq 23 2976 3000 3000 87.5% chr1 - 36291369 36291392 24 browser details YourSeq 21 2514 2534 3000 100.0% chr4 - 66489286 66489306 21 browser details YourSeq 21 2824 2844 3000 100.0% chr15 - 99784161 99784181 21 browser details YourSeq 21 796 816 3000 100.0% chr9 + 41141266 41141286 21 browser details YourSeq 21 2513 2533 3000 100.0% chr6 + 38690586 38690606 21 browser details YourSeq 20 358 377 3000 100.0% chr1 - 41333567 41333586 20 browser details YourSeq 20 966 987 3000 95.5% chr1 - 15695836 15695857 22 Note: The 3000 bp section upstream of Exon 3 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 + 108812961 108815960 3000 browser details YourSeq 84 371 492 3000 85.6% chr9 - 66602603 66602735 133 browser details YourSeq 80 355 486 3000 83.5% chr11 + 13767902 13768037 136 browser details YourSeq 79 360 485 3000 77.9% chr1 - 182166181 182166302 122 browser details YourSeq 79 367 493 3000 85.6% chr7 + 141021816 141021953 138 browser details YourSeq 77 360 479 3000 90.8% chrX - 103377593 103378192 600 browser details YourSeq 77 360 488 3000 82.4% chr16 + 45475015 45475156 142 browser details YourSeq 76 360 461 3000 87.3% chr17 + 28926805 28926906 102 browser details YourSeq 72 360 492 3000 92.0% chr2 - 29980945 29981091 147 browser details YourSeq 71 367 461 3000 87.4% chr17 - 34942575 34942669 95 browser details YourSeq 71 366 461 3000 91.8% chr16 + 94344761 94344856 96 browser details YourSeq 70 360 461 3000 84.4% chr12 - 97302771 97302872 102 browser details YourSeq 70 360 461 3000 84.4% chr14 + 47482676 47482777 102 browser details YourSeq 70 360 463 3000 83.7% chr10 + 80869999 80870102 104 browser details YourSeq 69 367 461 3000 86.4% chr12 - 24967234 24967328 95 browser details YourSeq 68 368 461 3000 86.2% chrX + 155221079 155221172 94 browser details YourSeq 67 362 464 3000 82.6% chr16 + 50459734 50459836 103 browser details YourSeq 66 368 461 3000 82.8% chr1 + 162459171 162459263 93 browser details YourSeq 65 368 461 3000 85.2% chr18 - 42496348 42496443 96 browser details YourSeq 65 367 463 3000 83.6% chr16 - 73609456 73609552 97 Note: The 3000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Nckipsd NCK interacting protein with SH3 domain [ Mus musculus (house mouse) ] Gene ID: 80987, updated on 12-Aug-2019 Gene summary Official Symbol Nckipsd provided by MGI Official Full Name NCK interacting protein with SH3 domain provided by MGI Primary source MGI:MGI:1931834 See related Ensembl:ENSMUSG00000032598 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 DIP1; ORF1; WISH; Wasbp; AF3P21; SPIN90; WASLBP Expression Ubiquitous expression in adrenal adult (RPKM 18.3), cerebellum adult (RPKM 18.0) and 28 other tissues See more Orthologs human all Genomic context Location: 9; 9 F2 See Nckipsd in Genome Data Viewer Exon count: 14 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (108808346..108818839) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (108710711..108720697) Chromosome 9 - NC_000075.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 6 transcripts Gene: Nckipsd ENSMUSG00000032598 Description NCK interacting protein with SH3 domain [Source:MGI Symbol;Acc:MGI:1931834] Gene Synonyms AF3P21, DIP1, ORF1, SPIN90, WISH, Wasbp Location Chromosome 9: 108,808,368-108,818,844 forward strand. GRCm38:CM001002.2 View alleles of this gene on alternative sequences About this gene This gene has 6 transcripts (splice variants), 1 gene allele, 196 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Nckipsd- ENSMUST00000035218.8 3360 714aa ENSMUSP00000035218.7 Protein coding CCDS23538 Q9ESJ4 TSL:1 201 GENCODE basic APPRIS P1 Nckipsd- ENSMUST00000195323.1 467 76aa ENSMUSP00000141728.1 Protein coding - A0A0A6YWW3 TSL:3 206 GENCODE basic Nckipsd- ENSMUST00000194819.1 367 101aa ENSMUSP00000141702.1 Protein coding - A0A0A6YWU4 CDS 3' incomplete 205 TSL:3 Nckipsd- ENSMUST00000192678.1 178 45aa ENSMUSP00000141857.1 Protein coding - A0A0A6YX64 CDS 5' incomplete 203 TSL:1 Nckipsd- ENSMUST00000192180.1 1089 No - Retained - - TSL:2 202 protein intron Nckipsd- ENSMUST00000194413.1 754 No - Retained - - TSL:3 204 protein intron Page 6 of 8 https://www.alphaknockout.com 30.48 kb Forward strand 108.80Mb 108.81Mb 108.82Mb Genes (Comprehensive set... Ip6k2-206 >protein coding Nckipsd-201 >protein coding Celsr3-207 >protein coding Ip6k2-207 >retained intron Nckipsd-206 >protein coding Nckipsd-204 >retained intron Celsr3-201 >protein coding Ip6k2-201 >protein coding Nckipsd-205 >protein coding Nckipsd-202 >retained intron Gm37714-201 >TEC Ip6k2-211 >protein coding Nckipsd-203 >protein coding Ip6k2-208 >retained intron Contigs AC168054.4 > Genes < Gm35025-202lncRNA (Comprehensive set... < Gm35025-203lncRNA < Gm35025-201TEC Regulatory Build 108.80Mb 108.81Mb 108.82Mb Reverse strand 30.48 kb Regulation Legend CTCF Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000035218 10.48 kb Forward strand Nckipsd-201 >protein coding ENSMUSP00000035... MobiDB lite Low complexity (Seg) Superfamily SH3-like domain superfamily SMART SH3 domain Pfam SH3 domain Domain of unknown function DUF2013 PROSITE profiles SH3 domain PANTHER PTHR13357 Gene3D 2.30.30.40 CDD SPIN90, SH3 domain All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend stop gained missense variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 480 540 600 714 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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    Mammalian Genome (2018) 29:523–538 https://doi.org/10.1007/s00335-018-9765-4 Human genetics of mycobacterial disease Monica Dallmann‑Sauer1,2,3 · Wilian Correa‑Macedo1,2,4 · Erwin Schurr1,2,3,4 Received: 30 March 2018 / Accepted: 23 July 2018 / Published online: 16 August 2018 © The Author(s) 2018 Abstract Mycobacterial diseases are caused by members of the genus Mycobacterium, acid-fast bacteria characterized by the presence of mycolic acids within their cell walls. Claiming almost 2 million lives every year, tuberculosis (TB) is the most common mycobacterial disease and is caused by infection with M. tuberculosis and, in rare cases, by M. bovis or M. africanum. The second and third most common mycobacterial diseases are leprosy and buruli ulcer (BU), respectively. Both diseases affect the skin and can lead to permanent sequelae and deformities. Leprosy is caused by the uncultivable M. leprae while the etiological agent of BU is the environmental bacterium M. ulcerans. After exposure to these mycobacterial species, a majority of individuals will not progress to clinical disease and, among those who do, inter-individual variability in disease manifestation and outcome can be observed. Susceptibility to mycobacterial diseases carries a human genetic component and intense efforts have been applied over the past decades to decipher the exact nature of the genetic factors controlling disease susceptibility. While for BU this search was mostly conducted on the basis of candidate genes association studies, genome-wide approaches have been widely applied for TB and leprosy. In this review, we summarize some of the findings achieved by genome-wide linkage, association and transcriptome analyses in TB disease and leprosy and the recent genetic findings for BU susceptibility.
  • (12) Patent Application Publication (10) Pub. No.: US 2011/0098188 A1 Niculescu Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2011/0098188 A1 Niculescu Et Al

    US 2011 0098188A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0098188 A1 Niculescu et al. (43) Pub. Date: Apr. 28, 2011 (54) BLOOD BOMARKERS FOR PSYCHOSIS Related U.S. Application Data (60) Provisional application No. 60/917,784, filed on May (75) Inventors: Alexander B. Niculescu, Indianapolis, IN (US); Daniel R. 14, 2007. Salomon, San Diego, CA (US) Publication Classification (51) Int. Cl. (73) Assignees: THE SCRIPPS RESEARCH C40B 30/04 (2006.01) INSTITUTE, La Jolla, CA (US); CI2O I/68 (2006.01) INDIANA UNIVERSITY GOIN 33/53 (2006.01) RESEARCH AND C40B 40/04 (2006.01) TECHNOLOGY C40B 40/10 (2006.01) CORPORATION, Indianapolis, IN (52) U.S. Cl. .................. 506/9: 435/6: 435/7.92; 506/15; (US) 506/18 (57) ABSTRACT (21) Appl. No.: 12/599,763 A plurality of biomarkers determine the diagnosis of psycho (22) PCT Fled: May 13, 2008 sis based on the expression levels in a sample Such as blood. Subsets of biomarkers predict the diagnosis of delusion or (86) PCT NO.: PCT/US08/63539 hallucination. The biomarkers are identified using a conver gent functional genomics approach based on animal and S371 (c)(1), human data. Methods and compositions for clinical diagnosis (2), (4) Date: Dec. 22, 2010 of psychosis are provided. Human blood Human External Lines Animal Model External of Evidence changed in low vs. high Lines of Evidence psychosis (2pt.) Human postmortem s Animal model brai brain data (1 pt.) > Cite go data (1 p. Biomarker For Bonus 1 pt. Psychosis Human genetic 2 N linkage? association A all model blood data (1 pt.) data (1 p.