DOCSLIB.ORG

Mouse Dbn1 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

https://www.alphaknockout.com Mouse Dbn1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Dbn1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Dbn1 gene (NCBI Reference Sequence: NM_001177371 ; Ensembl: ENSMUSG00000034675 ) is located on Mouse chromosome 13. 15 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 15 (Transcript: ENSMUST00000021950). Exon 2~8 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Dbn1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-97L6 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 knock-out allele display impaired cued conditioning behavior. Mice homozygous for a different knock-out allele show altered neurotransmitter receptor levels in protein complexes, abnormal dendritic spine morphology, and impaired synaptic plasticity in the hippocampus. Exon 2 starts from about 4.11% of the coding region. The knockout of Exon 2~8 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 4420 bp, and the size of intron 8 for 3'-loxP site insertion: 3512 bp. The size of effective cKO region: ~2594 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 15 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Dbn1 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(9094bp) | A(22.52% 2048) | C(24.88% 2263) | T(24.49% 2227) | G(28.11% 2556) 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% chr13 - 55483693 55486692 3000 browser details YourSeq 62 2113 2271 3000 84.6% chr10 - 84065868 84066018 151 browser details YourSeq 61 2111 2252 3000 92.9% chr16 - 95731758 95731901 144 browser details YourSeq 51 2116 2252 3000 75.0% chr11 - 84720782 84720885 104 browser details YourSeq 51 2105 2170 3000 91.4% chr10 - 41231056 41231120 65 browser details YourSeq 51 2101 2181 3000 82.2% chr10 + 32787778 32787848 71 browser details YourSeq 48 2115 2170 3000 94.6% chr11 - 90205366 90205422 57 browser details YourSeq 47 2115 2171 3000 94.4% chr15 - 61334585 61334643 59 browser details YourSeq 47 2086 2146 3000 96.3% chr1 + 150072343 150072617 275 browser details YourSeq 46 2113 2181 3000 76.5% chr12 + 110719738 110719789 52 browser details YourSeq 45 2119 2252 3000 94.2% chr16 - 28345074 28345256 183 browser details YourSeq 45 2115 2181 3000 79.6% chr1 - 157725233 157725283 51 browser details YourSeq 45 2110 2165 3000 96.0% chr16 + 68362568 68362632 65 browser details YourSeq 45 2105 2252 3000 65.4% chr1 + 151018496 151018545 50 browser details YourSeq 44 2118 2271 3000 65.4% chr14 + 12087859 12087917 59 browser details YourSeq 44 2113 2179 3000 75.6% chr13 + 87272949 87272998 50 browser details YourSeq 43 2115 2181 3000 77.6% chr12 - 31974630 31974683 54 browser details YourSeq 42 2115 2164 3000 88.9% chr14 - 28277837 28277883 47 browser details YourSeq 42 2111 2179 3000 82.9% chr12 + 112089418 112089502 85 browser details YourSeq 42 2115 2181 3000 77.3% chr10 + 104236504 104236548 45 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% chr13 - 55478099 55481098 3000 browser details YourSeq 150 532 909 3000 87.0% chr4 + 150699618 150699996 379 browser details YourSeq 120 532 913 3000 83.8% chr2 - 31695744 31696300 557 browser details YourSeq 104 705 910 3000 85.2% chr2 + 154626141 154626346 206 browser details YourSeq 98 536 884 3000 77.0% chr10 + 60020900 60021212 313 browser details YourSeq 92 745 907 3000 81.0% chr7 - 116516475 116516627 153 browser details YourSeq 91 792 1229 3000 71.8% chr6 + 39212232 39212394 163 browser details YourSeq 90 543 898 3000 85.8% chr10 + 43704053 43704505 453 browser details YourSeq 89 547 905 3000 90.1% chr15 - 101120186 101120701 516 browser details YourSeq 87 737 906 3000 85.3% chr13 - 117011629 117011801 173 browser details YourSeq 85 718 906 3000 81.4% chr7 + 24621334 24621521 188 browser details YourSeq 84 799 904 3000 89.7% chr5 + 150296436 150296541 106 browser details YourSeq 83 797 907 3000 87.4% chr1 - 180184485 180184595 111 browser details YourSeq 83 567 876 3000 85.0% chrX + 48638001 48638577 577 browser details YourSeq 83 802 914 3000 83.7% chr19 + 47185534 47185643 110 browser details YourSeq 82 547 858 3000 92.8% chr14 + 60349587 60350074 488 browser details YourSeq 81 793 905 3000 81.5% chr7 - 100291420 100291527 108 browser details YourSeq 81 792 904 3000 92.8% chr2 - 121090290 121090404 115 browser details YourSeq 80 801 910 3000 86.4% chr11 + 94195861 94195970 110 browser details YourSeq 79 715 908 3000 89.9% chr3 - 9741083 9741279 197 Note: The 3000 bp section downstream of Exon 8 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Dbn1 drebrin 1 [ Mus musculus (house mouse) ] Gene ID: 56320, updated on 13-Aug-2019 Gene summary Official Symbol Dbn1 provided by MGI Official Full Name drebrin 1 provided by MGI Primary source MGI:MGI:1931838 See related Ensembl:ENSMUSG00000034675 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 Expression Biased expression in whole brain E14.5 (RPKM 193.5), CNS E14 (RPKM 184.8) and 14 other tissues See more Orthologs human all Genomic context Location: 13 B1; 13 30.06 cM See Dbn1 in Genome Data Viewer Exon count: 15 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (55473428..55488126, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (55574789..55589437, complement) Chromosome 13 - NC_000079.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 9 transcripts Gene: Dbn1 ENSMUSG00000034675 Description drebrin 1 [Source:MGI Symbol;Acc:MGI:1931838] Gene Synonyms drebrin A, drebrin E2 Location Chromosome 13: 55,473,429-55,488,111 reverse strand. GRCm38:CM001006.2 About this gene This gene has 9 transcripts (splice variants), 186 orthologues, 4 paralogues, is a member of 1 Ensembl protein family and is associated with 75 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Dbn1- ENSMUST00000021950.14 3078 706aa ENSMUSP00000021950.8 Protein coding CCDS49274 Q9QXS6 TSL:1 201 GENCODE basic APPRIS ALT2 Dbn1- ENSMUST00000109923.8 2940 660aa ENSMUSP00000105549.2 Protein coding CCDS36677 Q3TRK3 TSL:1 203 Q9QXS6 GENCODE basic APPRIS P3 Dbn1- ENSMUST00000109921.8 2378 661aa ENSMUSP00000105547.2 Protein coding CCDS49273 A0A0R4J1E3 TSL:1 202 GENCODE basic APPRIS ALT2 Dbn1- ENSMUST00000139275.7 735 169aa ENSMUSP00000122574.1 Protein coding - F7CPL2 CDS 3' 207 incomplete TSL:3 Dbn1- ENSMUST00000135705.7 2119 No - Retained - - TSL:2 206 protein intron Dbn1- ENSMUST00000127867.1 789 No - Retained - - TSL:5 205 protein intron Dbn1- ENSMUST00000175813.1 732 No - Retained - - TSL:2 209 protein intron Dbn1- ENSMUST00000139516.1 419 No - Retained - - TSL:3 208 protein intron Dbn1- ENSMUST00000124480.7 573 No - lncRNA - - TSL:3 204 protein Page 6 of 8 https://www.alphaknockout.com 34.68 kb Forward strand 55.47Mb 55.48Mb 55.49Mb Genes Prr7-201 >protein coding (Comprehensive set... Contigs < CT009762.8 Genes (Comprehensive set... < Dbn1-201protein coding < Pdlim7-211nonsense mediated decay < Dbn1-203protein coding < Pdlim7-209retained intron < Dbn1-202protein coding < Dbn1-206retained intron < Mir6944-201miRNA < Dbn1-205retained intron < Dbn1-208retained intron < Dbn1-209retained intron < Dbn1-207protein coding < Dbn1-204lncRNA Regulatory Build 55.47Mb 55.48Mb 55.49Mb Reverse strand 34.68 kb Regulation Legend CTCF Enhancer Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000021950 < Dbn1-201protein coding Reverse strand 14.68 kb ENSMUSP00000021... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF55753 SMART Actin-depolymerising factor homology domain Pfam Actin-depolymerising factor homology domain PROSITE profiles Actin-depolymerising factor homology domain PANTHER Drebrin PTHR10829 Gene3D ADF-H/Gelsolin-like domain superfamily CDD cd11281 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 480 540 600 706 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
Recommended publications
  • Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

    Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

    animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest.
  • Genetic, Cytogenetic and Physical Refinement of the Autosomal Recessive CMT Linked to 5Q31ð Q33: Exclusion of Candidate Genes I

    Genetic, Cytogenetic and Physical Refinement of the Autosomal Recessive CMT Linked to 5Q31ð Q33: Exclusion of Candidate Genes I

    European Journal of Human Genetics (1999) 7, 849–859 © 1999 Stockton Press All rights reserved 1018–4813/99 $15.00 t http://www.stockton-press.co.uk/ejhg ARTICLE Genetic, cytogenetic and physical refinement of the autosomal recessive CMT linked to 5q31–q33: exclusion of candidate genes including EGR1 Ang`ele Guilbot1, Nicole Ravis´e1, Ahmed Bouhouche6, Philippe Coullin4, Nazha Birouk6, Thierry Maisonobe3, Thierry Kuntzer7, Christophe Vial8, Djamel Grid5, Alexis Brice1,2 and Eric LeGuern1,2 1INSERM U289, 2F´ed´eration de Neurologie and 3Laboratoire de Neuropathologie R Escourolle, Hˆopital de la Salpˆetri`ere, Paris 4Laboratoire de cytog´en´etique, Villejuif 5G´en´ethon, Evry, France 6Service de Neurologie, Hˆopital des Sp´ecialit´es, Rabat, Morocco 7Service de Neurologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland 8Service D’EMG et de pathologie neuromusculaire, Hˆopital neurologique Pierre Wertheimer, Lyon, France Charcot-Marie-Tooth disease is an heterogeneous group of inherited peripheral motor and sensory neuropathies with several modes of inheritance: autosomal dominant, X-linked and autosomal recessive. By homozygosity mapping, we have identified, in the 5q23–q33 region, a third locus responsible for an autosomal recessive form of demyelinating CMT. Haplotype reconstruction and determination of the minimal region of homozygosity restricted the candidate region to a 4 cM interval. A physical map of the candidate region was established by screening YACs for microsatellites used for genetic analysis. Combined genetic, cytogenetic and physical mapping restricted the locus to a less than 2 Mb interval on chromosome 5q32. Seventeen consanguineous families with demyelinating ARCMT of various origins were screened for linkage to 5q31–q33.
  • Related ESCRT-III Subunit CHMP2B

    Related ESCRT-III Subunit CHMP2B

    The Journal of Neuroscience, February 18, 2015 • 35(7):3155–3173 • 3155 Cellular/Molecular Regulation of Postsynaptic Function by the Dementia- Related ESCRT-III Subunit CHMP2B X Romain Chassefeyre,1,2* Jose´ Martínez-Herna´ndez,1,2* Federica Bertaso,3,4,5 Nathalie Bouquier,3,4,5 Be´atrice Blot,1,2 Marine Laporte,1,2 Sandrine Fraboulet,1,2 Yohann Coute´,6,7 Anny Devoy,8 Adrian M. Isaacs,8 Karin Pernet-Gallay,1,2 Re´my Sadoul,1,2 XLaurent Fagni,3,4,5 and Yves Goldberg1,2,9 1Institut National de la Sante´ et de la Recherche Me´dicale (INSERM), Unite´ 836, F-38042 Grenoble, France, 2Universite´ Grenoble Alpes, Grenoble Institut des Neurosciences (GIN), F-38042 Grenoble, France, 3CNRS, UMR-5203, Institut de Ge´nomique Fonctionnelle, F-34094 Montpellier, France, 4Universite´s de Montpellier 1 & 2, UMR-5203, F-34094 Montpellier, France, 5INSERM, Unite´ 661, F-34094 Montpellier, France, 6INSERM, Unite´ 1038, F-38054 Grenoble, France, 7Commissariat a` l’Energie Atomique (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Laboratoire de Biologie a` Grande Echelle, F-38054 Grenoble, France, 8Department of Neurodegenerative Disease, University College London Institute of Neurology, London WC1N 3BG, United Kingdom, and 9CEA, iRTSV, Groupe Physiopathologie du Cytosquelette (GPC), F-38054 Grenoble, France The charged multivesicular body proteins (Chmp1–7) are an evolutionarily conserved family of cytosolic proteins that transiently assembles into helical polymers that change the curvature of cellular membrane domains. Mutations in human CHMP2B cause fronto- temporal dementia, suggesting that this protein may normally control some neuron-specific process.
  • In This Table Protein Name, Uniprot Code, Gene Name P-Value

    In This Table Protein Name, Uniprot Code, Gene Name P-Value

    Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2-
  • DBN1 Monoclonal Antibody (M03), Clone 2E11

    DBN1 Monoclonal Antibody (M03), Clone 2E11

    DBN1 monoclonal antibody (M03), clone 2E11 Catalog # : H00001627-M03 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a full-length recombinant Western Blot (Recombinant protein) Description: DBN1. Sandwich ELISA (Recombinant Immunogen: DBN1 (AAH00283, 1 a.a. ~ 649 a.a) full-length recombinant protein with protein) GST tag. MW of the GST tag alone is 26 KDa. Sequence: MAGVSFSGHRLELLAAYEEVIREESAADWALYTYEDGSDDLKLAASGEG GLQELSGHFENQKVMYGFCSVKDSQAALPKYVLINWVGEDVPDARKCA CASHVAKVAEFFQGVDVIVNASSVEDIDAGAIGQRLSNGLARLSSPVLHR LRLREDENAEPVGTTYQKTDAAVEMKRINREQFWEQAKKEEELRKEEER KKALDERLRFEQERMEQERQEQEERERRYREREQQIEEHRRKQQTLEA enlarge EEAKRRLKEQSIFGDHRDEEEETHMKKSESEVEEAAAIIAQRPDNPREFF KQQERVASASAGSCDVPSPFNHRPGSHLDSHRRMAPTPIPTRSPSDSST ELISA ASTPVAEQIERALDEVTSSQPPPLPPPPPPAQETQEPSPILDSEETRAAA PQAWAGPMEEPPQAQAPPRGPGSPAEDLMFMESAEQAVLAAPVEPAT ADATEVHDAADTIETDTATADTTVANNVPPAATSLIDLWPGNGEGASTLQ GEPRAPTPPSGTEVTLAEVPLLDEVAPEPLLPAGEGCATLLNFDELPEPP ATFCDPEEVEGEPLAAPQTPTLPSALEELEQEQEPEPHLLTNGETTQKE GTQASEGYFSQSQEEEFAQSEELCAKAPPPVFYNKPPEIDITCWDADPV PEEEEGFEGGD Host: Mouse Reactivity: Human Isotype: IgG2a Kappa Quality Control Antibody Reactive Against Recombinant Protein. Testing: Western Blot detection against Immunogen (97.13 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Page 1 of 2 2016/5/20 Western Blot (Recombinant protein) Protocol Download Sandwich ELISA (Recombinant
  • A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases

    A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases

    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. 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 4.0 International license. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. 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 4.0 International license. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer.
  • Transdifferentiation of Human Mesenchymal Stem Cells

    Transdifferentiation of Human Mesenchymal Stem Cells

    Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone
  • Functional Genomic Annotation of Genetic Risk Loci Highlights Inflammation and Epithelial Biology Networks in CKD

    Functional Genomic Annotation of Genetic Risk Loci Highlights Inflammation and Epithelial Biology Networks in CKD

    BASIC RESEARCH www.jasn.org Functional Genomic Annotation of Genetic Risk Loci Highlights Inflammation and Epithelial Biology Networks in CKD Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Hyun-Mi Kang, Sang-Youb Han, Peter Choi, and Katalin Susztak Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania ABSTRACT Genome-wide association studies (GWASs) have identified multiple loci associated with the risk of CKD. Almost all risk variants are localized to the noncoding region of the genome; therefore, the role of these variants in CKD development is largely unknown. We hypothesized that polymorphisms alter transcription factor binding, thereby influencing the expression of nearby genes. Here, we examined the regulation of transcripts in the vicinity of CKD-associated polymorphisms in control and diseased human kidney samples and used systems biology approaches to identify potentially causal genes for prioritization. We interro- gated the expression and regulation of 226 transcripts in the vicinity of 44 single nucleotide polymorphisms using RNA sequencing and gene expression arrays from 95 microdissected control and diseased tubule samples and 51 glomerular samples. Gene expression analysis from 41 tubule samples served for external validation. 92 transcripts in the tubule compartment and 34 transcripts in glomeruli showed statistically significant correlation with eGFR. Many novel genes, including ACSM2A/2B, FAM47E, and PLXDC1, were identified. We observed that the expression of multiple genes in the vicinity of any single CKD risk allele correlated with renal function, potentially indicating that genetic variants influence multiple transcripts. Network analysis of GFR-correlating transcripts highlighted two major clusters; a positive correlation with epithelial and vascular functions and an inverse correlation with inflammatory gene cluster.
  • Datasheet: VPA00848 Product Details

    Datasheet: VPA00848 Product Details

    Datasheet: VPA00848 Description: RABBIT ANTI DREBRIN 1 Specificity: DREBRIN 1 Format: Purified Product Type: PrecisionAb™ Polyclonal Isotype: Polyclonal IgG Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Product Form Purified IgG - liquid Preparation Rabbit polyclonal antibody purified by affinity chromatography on immunogen Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide Stabilisers Immunogen KLH conjugated synthetic peptide corresponding to amino acids 1-28 of human drebrin 1 External Database Links UniProt: Q16643 Related reagents Entrez Gene: 1627 DBN1 Related reagents Synonyms D0S117E Specificity Rabbit anti Human drebrin 1 antibody recognizes drebrin 1, also known as developmentally- regulated brain protein-drebrin, drebrin E, DBN1 and drebrin E2. The protein encoded by DBN1 is a cytoplasmic actin-binding protein thought to play a role in the Page 1 of 2 process of neuronal growth. It is a member of the drebrin family of proteins that are developmentally regulated in the brain.
  • S-Palmitoylation of Synaptic Proteins As a Novel Mechanism Underlying Sex-Dependent Differences in Neuronal Plasticity

    S-Palmitoylation of Synaptic Proteins As a Novel Mechanism Underlying Sex-Dependent Differences in Neuronal Plasticity

    International Journal of Molecular Sciences Article S-Palmitoylation of Synaptic Proteins as a Novel Mechanism Underlying Sex-Dependent Differences in Neuronal Plasticity Monika Zar˛eba-Kozioł 1,*,† , Anna Bartkowiak-Kaczmarek 1,†, Matylda Roszkowska 1, Krystian Bijata 1,2, Izabela Figiel 1 , Anup Kumar Halder 3 , Paulina Kami ´nska 1, Franziska E. Müller 4, Subhadip Basu 3 , Weiqi Zhang 5, Evgeni Ponimaskin 4 and Jakub Włodarczyk 1,* 1 Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, Pasteur Str. 3, 02-093 Warsaw, Poland; [email protected] (A.B.-K.); [email protected] (M.R.); [email protected] (K.B.); i.fi[email protected] (I.F.); [email protected] (P.K.) 2 Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland 3 Department of Computer Science and Engineering, Jadvapur University, Kolkata 700032, India; [email protected] (A.K.H.); [email protected] (S.B.) 4 Cellular Neurophysiology, Hannover Medical School, Carl-Neuberg Str. 1, 30625 Hannover, Germany; [email protected] (F.E.M.); [email protected] (E.P.) 5 Department of Mental Health, University of Münster, Albert-Schweitzer-Campus 1/A9, 48149 Munster, Germany; [email protected] * Correspondence: [email protected] (M.Z.-K.); [email protected] (J.W.) † These authors contributed equally. Abstract: Although sex differences in the brain are prevalent, the knowledge about mechanisms Citation: Zar˛eba-Kozioł,M.; underlying sex-related effects on normal and pathological brain functioning is rather poor. It is Bartkowiak-Kaczmarek, A.; known that female and male brains differ in size and connectivity.
  • A CRISPR Screen to Identify Combination Therapies of Cytotoxic

    A CRISPR Screen to Identify Combination Therapies of Cytotoxic

    CRISPRi Screens to Identify Combination Therapies for the Improved Treatment of Ovarian Cancer By Erika Daphne Handly B.S. Chemical Engineering Brigham Young University, 2014 Submitted to the Department of Biological Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY February 2021 © 2020 Massachusetts Institute of Technology. All rights reserved. Signature of author………………………………………………………………………………… Erika Handly Department of Biological Engineering February 2021 Certified by………………………………………………………………………………………… Michael Yaffe Director MIT Center for Precision Cancer Medicine Department of Biological Engineering and Biology Thesis Supervisor Accepted by………………………………………………………………………………………... Katharina Ribbeck Professor of Biological Engineering Chair of Graduate Program, Department of Biological Engineering Thesis Committee members Michael T. Hemann, Ph.D. Associate Professor of Biology Massachusetts Institute of Technology Douglas A. Lauffenburger, Ph.D. (Chair) Ford Professor of Biological Engineering, Chemical Engineering, and Biology Massachusetts Institute of Technology Michael B. Yaffe, M.D., Ph.D. (Thesis Supervisor) David H. Koch Professor of Science Prof. of Biology and Biological Engineering Massachusetts Institute of Technology 2 CRISPRi Screens to Identify Combination Therapies for the Improved Treatment of Ovarian Cancer By Erika Daphne Handly B.S. Chemical Engineering Brigham Young University, 2014 Submitted to the Department of Biological Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering ABSTRACT Ovarian cancer is the fifth leading cause of cancer death for women in the United States, with only modest improvements in patient survival in the past few decades. Standard-of-care consists of surgical debulking followed by a combination of platinum and taxane agents, but relapse and resistance frequently occur.
  • Developmental Retardation Due to Paternal 5Q/11Q Translocation in a Chinese Infant: Clinical, Chromosomal and Microarray Characterization

    Developmental Retardation Due to Paternal 5Q/11Q Translocation in a Chinese Infant: Clinical, Chromosomal and Microarray Characterization

    Journal of Genetics (2019) 98:77 © Indian Academy of Sciences https://doi.org/10.1007/s12041-019-1120-3 RESEARCH ARTICLE Developmental retardation due to paternal 5q/11q translocation in a Chinese infant: clinical, chromosomal and microarray characterization XIANGYU ZHAO1 , HONGYAN XU1, CHEN ZHAO2 and LIN LI1∗ 1Department of Medical Genetics, Linyi People’s Hospital, Linyi 276003, Shandong, People’s Republic of China 2Department of Neurology, Weifang People’s Hospital, Weifang 261000, Shandong, People’s Republic of China *For correspondence. E-mail: [email protected]. Received 12 June 2018; revised 18 April 2019; accepted 19 May 2019 Abstract. Although it is known that the parental carriers of chromosomal translocation are considered to be at high risk for spontaneous abortion and embryonic death, normal gestation and delivery remain possible. This study aims to investigate the genetic factors of a Chinese infant with multiple malformations and severe postnatal development retardation. In this study, the routine cytogenetic analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) analysis were performed. Conventional karyotype analyses revealed normal karyotypes of all family members. CMA of the DNA of the proband revealed a 8.3 Mb duplication of 5q35.1-qter and a 6.9 Mb deletion of 11q24.3-qter. FISH analyses verified a paternal tiny translocation between the long arm of chromosomes 5 and 11. Our investigation serves to provide important information on genetic counselling for the patient and future pregnancies in this family. Moreover, the combined use of CMA and FISH is effective for clarifying pathogenically submicroscopic copy number variants. Keywords. 5q/11q translocation; karyotyping; chromosomal microarray analysis; fluorescence in situ hybridization; growth retardation.