DOCSLIB.ORG

Mouse Dip2b Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Dip2b Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Dip2b Knockout Project (CRISPR/Cas9) Objective: To create a Dip2b knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Dip2b gene (NCBI Reference Sequence: NM_001159361 ; Ensembl: ENSMUSG00000023026 ) is located on Mouse chromosome 15. 38 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 38 (Transcript: ENSMUST00000100203). Exon 5~10 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 5 starts from about 9.0% of the coding region. Exon 5~10 covers 18.78% of the coding region. The size of effective KO region: ~9402 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 5 6 7 8 9 10 38 Legends Exon of mouse Dip2b Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 5 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 Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 1425 bp section downstream of Exon 10 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. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(25.25% 505) | C(23.9% 478) | T(30.05% 601) | G(20.8% 416) Note: The 2000 bp section upstream of Exon 5 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. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(1425bp) | A(25.05% 357) | C(18.74% 267) | T(32.35% 461) | G(23.86% 340) Note: The 1425 bp section downstream of Exon 10 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 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr15 + 100149152 100151151 2000 browser details YourSeq 31 690 740 2000 91.2% chr19 - 28555396 28555445 50 browser details YourSeq 28 536 571 2000 93.6% chr9 + 50999681 50999718 38 browser details YourSeq 25 706 730 2000 100.0% chr4 + 128724124 128724148 25 browser details YourSeq 23 752 774 2000 100.0% chr6 + 148460551 148460573 23 browser details YourSeq 22 422 443 2000 100.0% chr13 - 22782590 22782611 22 Note: The 2000 bp section upstream of Exon 5 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 1425 1 1425 1425 100.0% chr15 + 100160554 100161978 1425 browser details YourSeq 164 633 832 1425 89.1% chr4 - 135264690 135264880 191 browser details YourSeq 160 639 835 1425 90.2% chr1 + 193206572 193206760 189 browser details YourSeq 159 634 817 1425 93.5% chr8 + 123196714 123196898 185 browser details YourSeq 156 644 818 1425 94.9% chr9 + 72844112 72844286 175 browser details YourSeq 156 633 898 1425 91.5% chr14 + 32480747 32481152 406 browser details YourSeq 156 633 814 1425 92.9% chr11 + 68478236 68478417 182 browser details YourSeq 155 633 816 1425 92.4% chr13 + 62119137 62119321 185 browser details YourSeq 154 635 819 1425 92.4% chr18 - 67507415 67507614 200 browser details YourSeq 154 633 816 1425 90.8% chr12 - 87206577 87206759 183 browser details YourSeq 153 633 817 1425 94.3% chr14 - 73799211 73799396 186 browser details YourSeq 153 633 820 1425 92.8% chr10 - 39703629 39703816 188 browser details YourSeq 153 633 816 1425 92.7% chr6 + 108681890 108682072 183 browser details YourSeq 152 632 816 1425 92.8% chr19 - 41782982 41783172 191 browser details YourSeq 152 633 817 1425 91.4% chr19 + 55235828 55236013 186 browser details YourSeq 152 633 819 1425 93.3% chr17 + 94862311 94862497 187 browser details YourSeq 151 633 814 1425 89.9% chr7 - 79823599 79823777 179 browser details YourSeq 151 639 817 1425 93.0% chr13 - 35919023 35919200 178 browser details YourSeq 151 633 818 1425 91.9% chr13 + 69544667 69544859 193 browser details YourSeq 151 640 815 1425 93.2% chr13 + 55572999 55573179 181 Note: The 1425 bp section downstream of Exon 10 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Dip2b disco interacting protein 2 homolog B [ Mus musculus (house mouse) ] Gene ID: 239667, updated on 12-Aug-2019 Gene summary Official Symbol Dip2b provided by MGI Official Full Name disco interacting protein 2 homolog B provided by MGI Primary source MGI:MGI:2145977 See related Ensembl:ENSMUSG00000023026 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 AI317237; AI854602; mKIAA1463; 4932422C22 Expression Ubiquitous expression in cerebellum adult (RPKM 10.4), whole brain E14.5 (RPKM 8.6) and 28 other tissues See more Orthologs human all Genomic context Location: 15; 15 F1 See Dip2b in Genome Data Viewer Exon count: 40 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (100037626..100219474) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (99869095..100049904) Chromosome 15 - NC_000081.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Dip2b ENSMUSG00000023026 Description disco interacting protein 2 homolog B [Source:MGI Symbol;Acc:MGI:2145977] Location Chromosome 15: 100,038,664-100,219,473 forward strand. GRCm38:CM001008.2 About this gene This gene has 5 transcripts (splice variants), 262 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 3 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Dip2b-202 ENSMUST00000100203.9 8914 1574aa ENSMUSP00000097777.3 Protein coding CCDS49731 Q3UH60 TSL:1 GENCODE basic APPRIS P1 Dip2b-201 ENSMUST00000023768.13 4320 1340aa ENSMUSP00000023768.7 Protein coding CCDS27831 B2RQC7 TSL:5 GENCODE basic Dip2b-204 ENSMUST00000230619.1 743 No protein - Retained intron - - - Dip2b-203 ENSMUST00000135658.2 714 No protein - Retained intron - - TSL:5 Dip2b-205 ENSMUST00000230733.1 371 No protein - Retained intron - - - Page 7 of 9 https://www.alphaknockout.com 200.81 kb Forward strand 100.05Mb 100.10Mb 100.15Mb 100.20Mb Genes (Comprehensive set... Dip2b-202 >protein coding Dip2b-201 >protein coding Dip2b-205 >retained intron Dip2b-204 >retained intron Dip2b-203 >retained intron Atf1-201 >protein coding Atf1-202 >protein coding Atf1-208 >protein coding Contigs < AC133868.10 < AC125526.4 < AC124479.4 Genes < Gm49474-201TEC < Gm49475-201lncRNA (Comprehensive set... < 4930478M13Rik-201lncRNA Regulatory Build 100.05Mb 100.10Mb 100.15Mb 100.20Mb Reverse strand 200.81 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000100203 180.81 kb Forward strand Dip2b-202 >protein coding ENSMUSP00000097... MobiDB lite Low complexity (Seg) Superfamily SSF56801 SMART DMAP1-binding domain Pfam DMAP1-binding domain AMP-dependent synthetase/ligase PANTHER PTHR22754:SF38 PTHR22754 Gene3D AMP-dependent synthetase-like superfamily 3.30.300.30 CDD Dip2-like domain All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend frameshift variant missense variant synonymous variant Scale bar 0 200 400 600 800 1000 1200 1574 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
Load more

Recommended publications
  • Datasheet Blank Template
    SAN TA C RUZ BI OTEC HNOL OG Y, INC . DIP2A (L-16): sc-67555 BACKGROUND APPLICATIONS DIP2A (Disco-interacting protein 2 homolog A), also known as DIP2, is a 1,571 DIP2A (L-16) is recommended for detection of DIP2A of human origin by amino acid nuclear protein. It is one of three human homologs (DIP2A, DIP2B Western Blotting (starting dilution 1:200, dilution range 1:100-1:1000), and DIP2C) of the Drosophila dip2 (disconnected-interacting protein 2) protein. immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml of cell In Drosophila , dip2 interacts with disco, a protein required for neuronal con - lysate)], immunofluorescence (starting dilution 1:50, dilution range 1:50- nections in the visual systems of larvae and adults. The closest vertebrate 1:500) and solid phase ELISA (starting dilution 1:30, dilution range 1:30- homologs to disco are the basonuclin genes. In mice, DIP2 homologs show 1:3000). restricted expression to the brain. This suggests that, similar to the function DIP2A (L-16) is also recommended for detection of DIP2A, also designated of Drosphila dip2, vertebrate DIP2 homologs may play a role in the develop - Disco-interacting protein 2 homolog A, in additional species, including ment of the nervous system. Expressed ubiquitously with highest expression canine. in the brain, DIP2A is thought to function in signaling throughout the central nervous system by providing positional clues for axon patterning and pathfind - Suitable for use as control antibody for DIP2A siRNA (h): sc-62212, DIP2A ing . Four isoforms of DIP2A exist due to alternative splicing events.
    [Show full text]
  • Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
    Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Loss of DIP2C in RKO Cells Stimulates Changes in DNA
    Larsson et al. BMC Cancer (2017) 17:487 DOI 10.1186/s12885-017-3472-5 RESEARCH ARTICLE Open Access Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial- mesenchymal transition Chatarina Larsson1, Muhammad Akhtar Ali1,2, Tatjana Pandzic1, Anders M. Lindroth3, Liqun He1,4 and Tobias Sjöblom1* Abstract Background: The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells. Methods: We engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C. Effects on cell death pathways and epithelial-mesenchymal transition traits were studied based on the results from expression profiling. Results: Knockout of DIP2C in RKO cells resulted in cell enlargement and growth retardation. Expression profiling revealed 780 genes for which the expression level was affected by the loss of DIP2C, including the tumour-suppressor encoding CDKN2A gene, the epithelial-mesenchymal transition (EMT) regulator-encoding ZEB1,andCD44 and CD24 that encode breast cancer stem cell markers. Analysis of DNA methylation showed more than 30,000 sites affected by differential methylation, the majority of which were hypomethylated following loss of DIP2C. Changes in DNA methylation at promoter regions were strongly correlated to changes in gene expression, and genes involved with EMT and cell death were enriched among the differentially regulated genes.
    [Show full text]
  • WES Gene Package Multiple Congenital Anomalie.Xlsx
    Whole Exome Sequencing Gene package Multiple congenital anomalie, version 5, 1‐2‐2018 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A4GALT [Blood group, P1Pk system, P(2) phenotype], 111400 607922 101 100 100 99 [Blood group, P1Pk system, p phenotype], 111400 NOR polyagglutination syndrome, 111400 AAAS Achalasia‐addisonianism‐alacrimia syndrome, 231550 605378 73 100 100 100 AAGAB Keratoderma, palmoplantar,
    [Show full text]
  • 2016 Yet Idil 1167460 Ethesis
    This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ INTEGRATED EPIGENOMICS AND METABOLOMICS ANALYSIS IN TWINS Yet, Idil Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 01. Oct. 2021 INTEGRATED EPIGENOMICS AND METABOLOMICS ANALYSIS IN TWINS IDIL YET KING’S COLLEGE LONDON FACULTY OF LIFE SCIENCES & MEDICINE DIVISION OF GENETICS & MOLECULAR MEDICINE DEPARTMENT OF TWIN RESEARCH AND GENETIC EPIDEMIOLOGY Submitted in particular fulfilment of the requirements for the degree of Doctor of Philosophy 2016 1 ABSTRACT Epigenetics and metabolomics are rapidly growing areas of research, in part due to recent advances in technology that have allowed for a wide coverage of the human genome.
    [Show full text]
  • 1 Mutational Heterogeneity in Cancer Akash Kumar a Dissertation
    Mutational Heterogeneity in Cancer Akash Kumar A dissertation Submitted in partial fulfillment of requirements for the degree of Doctor of Philosophy University of Washington 2014 June 5 Reading Committee: Jay Shendure Pete Nelson Mary Claire King Program Authorized to Offer Degree: Genome Sciences 1 University of Washington ABSTRACT Mutational Heterogeneity in Cancer Akash Kumar Chair of the Supervisory Committee: Associate Professor Jay Shendure Department of Genome Sciences Somatic mutation plays a key role in the formation and progression of cancer. Differences in mutation patterns likely explain much of the heterogeneity seen in prognosis and treatment response among patients. Recent advances in massively parallel sequencing have greatly expanded our capability to investigate somatic mutation. Genomic profiling of tumor biopsies could guide the administration of targeted therapeutics on the basis of the tumor’s collection of mutations. Central to the success of this approach is the general applicability of targeted therapies to a patient’s entire tumor burden. This requires a better understanding of the genomic heterogeneity present both within individual tumors (intratumoral) and amongst tumors from the same patient (intrapatient). My dissertation is broadly organized around investigating mutational heterogeneity in cancer. Three projects are discussed in detail: analysis of (1) interpatient and (2) intrapatient heterogeneity in men with disseminated prostate cancer, and (3) investigation of regional intratumoral heterogeneity in
    [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]
  • Transcriptome-Wide Association Study of Attention Deficit Hyperactivity Disorder Identifies Associated Genes and Phenotypes
    bioRxiv preprint doi: https://doi.org/10.1101/642231; this version posted May 20, 2019. 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-NC-ND 4.0 International license. Transcriptome-wide association study of attention deficit hyperactivity disorder identifies associated genes and phenotypes Calwing Liao1,2, Alexandre D. Laporte2, Dan Spiegelman2, Fulya Akçimen1,2, Ridha Joober3, Patrick A. Dion2,4, Guy A. Rouleau1,2,4 1Department of Human Genetics, McGill University, Montréal, Quebec, Canada 2Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada 3Department of Psychiatry, McGill University, Montréal, Quebec, Canada 4Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada Word count: 2,619 excluding abstract and references Figures: 2 Tables: 3 Keywords: ADHD, transcriptome-wide association study, KAT2B, TMEM161B, amygdala, prefrontal cortex *Correspondence: Dr. Guy A. Rouleau Montreal Neurological Institute and Hospital Department of Neurology and Neurosurgery 3801 University Street, Montreal, QC Canada H3A 2B4. Tel: +1 514 398 2690 Fax: +1 514 398 8248 E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/642231; this version posted May 20, 2019. 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-NC-ND 4.0 International license. Abstract Attention deficit/hyperactivity disorder (ADHD) is one of the most common neurodevelopmental psychiatric disorders.
    [Show full text]
  • Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis
    Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis by Valbona Luga A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy, Department of Molecular Genetics, University of Toronto © Copyright by Valbona Luga, 2013 Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis Valbona Luga Doctor of Philosophy Department of Molecular Genetics University of Toronto 2013 Abstract The tumour-associated stroma, consisting of fibroblasts, inflammatory cells, vasculature and extracellular matrix proteins, plays a critical role in tumour growth, but how it regulates cancer cell migration and metastasis is poorly understood. The Wnt-planar cell polarity (PCP) pathway regulates convergent extension movements in vertebrate development. However, it is unclear whether this pathway also functions in cancer cell migration. In addition, the factors that mobilize long-range signalling of Wnt morphogens, which are tightly associated with the plasma membrane, have yet to be completely characterized. Here, I show that fibroblasts secrete membrane microvesicles of endocytic origin, termed exosomes, which promote tumour cell protrusive activity, motility and metastasis via the exosome component Cd81. In addition, I demonstrate that fibroblast exosomes activate autocrine Wnt-PCP signalling in breast cancer cells as detected by the association of Wnt with Fzd receptors and the asymmetric distribution of Fzd-Dvl and Vangl-Pk complexes in exosome-stimulated cancer cell protrusive structures. Moreover, I show that Pk expression in breast cancer cells is essential for fibroblast-stimulated cancer cell metastasis. Lastly, I reveal that trafficking in cancer cells promotes tethering of autocrine Wnt11 to fibroblast exosomes. These studies further our understanding of the role of ii the tumour-associated stroma in cancer metastasis and bring us closer to a more targeted approach for the treatment of cancer spread.
    [Show full text]
  • Novel Targets of Apparently Idiopathic Male Infertility
    International Journal of Molecular Sciences Review Molecular Biology of Spermatogenesis: Novel Targets of Apparently Idiopathic Male Infertility Rossella Cannarella * , Rosita A. Condorelli , Laura M. Mongioì, Sandro La Vignera * and Aldo E. Calogero Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; [email protected] (R.A.C.); [email protected] (L.M.M.); [email protected] (A.E.C.) * Correspondence: [email protected] (R.C.); [email protected] (S.L.V.) Received: 8 February 2020; Accepted: 2 March 2020; Published: 3 March 2020 Abstract: Male infertility affects half of infertile couples and, currently, a relevant percentage of cases of male infertility is considered as idiopathic. Although the male contribution to human fertilization has traditionally been restricted to sperm DNA, current evidence suggest that a relevant number of sperm transcripts and proteins are involved in acrosome reactions, sperm-oocyte fusion and, once released into the oocyte, embryo growth and development. The aim of this review is to provide updated and comprehensive insight into the molecular biology of spermatogenesis, including evidence on spermatogenetic failure and underlining the role of the sperm-carried molecular factors involved in oocyte fertilization and embryo growth. This represents the first step in the identification of new possible diagnostic and, possibly, therapeutic markers in the field of apparently idiopathic male infertility. Keywords: spermatogenetic failure; embryo growth; male infertility; spermatogenesis; recurrent pregnancy loss; sperm proteome; DNA fragmentation; sperm transcriptome 1. Introduction Infertility is a widespread condition in industrialized countries, affecting up to 15% of couples of childbearing age [1]. It is defined as the inability to achieve conception after 1–2 years of unprotected sexual intercourse [2].
    [Show full text]
  • Phenotyping Structural Abnormalities in Mouse Embryos Using High-Resolution Episcopic Microscopy Wolfgang J
    © 2014. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2014) 7, 1143-1152 doi:10.1242/dmm.016337 RESEARCH ARTICLE Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy Wolfgang J. Weninger1,*, Stefan H. Geyer1, Alexandrine Martineau2, Antonella Galli3, David J. Adams3, Robert Wilson2 and Timothy J. Mohun2 ABSTRACT genetic manipulation with the ability to study uterine embryo The arrival of simple and reliable methods for 3D imaging of mouse development that more closely resembles that of humans. embryos has opened the possibility of analysing normal and Until recently, the majority of advances in understanding genetic abnormal development in a far more systematic and comprehensive controls of murine cellular differentiation and organogenesis have manner than has hitherto been possible. This will not only help to come from studies targeting individual genes or individual genetic extend our understanding of normal tissue and organ development pathways for genetic perturbation. However, it has now become but, by applying the same approach to embryos from genetically feasible to adopt a more systematic approach to such studies. Since modified mouse lines, such imaging studies could also transform our 2007, the International Knockout Mouse Consortium (IKMC, knowledge of gene function in embryogenesis and the aetiology of www.mousephenotype.org) has been coordinating an international developmental disorders. The International Mouse Phenotyping effort to produce knockout lines in which every gene in the mouse Consortium is coordinating efforts to phenotype single gene genome is individually targeted. This work is now well advanced knockouts covering the entire mouse genome, including and attention is now focused on the goal of phenotyping adult characterising developmental defects for those knockout lines that mice from the knockout lines, an ambitious task overseen by prove to be embryonic lethal.
    [Show full text]