Mouse Cdk5r1 Conditional Knockout Project (CRISPR/Cas9)

Total Page:16

File Type:pdf, Size:1020Kb

Mouse Cdk5r1 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Cdk5r1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Cdk5r1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cdk5r1 gene (NCBI Reference Sequence: NM_009871 ; Ensembl: ENSMUSG00000048895 ) is located on Mouse chromosome 11. 1 exon is identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 1 (Transcript: ENSMUST00000053413). Exon 1 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Cdk5r1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP24-91N11 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: Homozygous mutation of the gene results in structural abnormalities of the brain such as a small corpus callosum and delaminated cerebral cortex. Mice show hyperactivity and decreased locomotion in response to stimulants. Exon 1 covers 100.0% of the coding region. Start codon is in exon 1, and stop codon is in exon 1. The size of effective cKO region: ~954 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy gRNA region gRNA region Wildtype allele A T G T G 5' A 3' 1 Targeting vector A T G T G A Targeted allele A T G T G A Constitutive KO allele (After Cre recombination) Legends Homology arm Exon of mouse Cdk5r1 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(6921bp) | A(20.69% 1432) | C(25.56% 1769) | T(24.78% 1715) | G(28.97% 2005) 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 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% chr11 + 80474510 80477509 3000 browser details YourSeq 77 213 473 3000 74.6% chr1 + 194831006 194831240 235 browser details YourSeq 66 239 475 3000 79.1% chr11 + 76535276 76535480 205 browser details YourSeq 54 185 267 3000 82.4% chr1 - 167812415 167812492 78 browser details YourSeq 50 204 267 3000 91.7% chrY + 17558050 17558120 71 browser details YourSeq 50 204 267 3000 91.7% chrY + 12844829 12844899 71 browser details YourSeq 49 406 475 3000 81.0% chr19 + 60591624 60591689 66 browser details YourSeq 48 217 272 3000 92.9% chr9 + 20732820 20732875 56 browser details YourSeq 46 215 272 3000 89.7% chr14 - 17163160 17163217 58 browser details YourSeq 42 214 267 3000 88.9% chr11 + 60118779 60118832 54 browser details YourSeq 39 413 474 3000 76.4% chr12 - 51124603 51124660 58 browser details YourSeq 39 215 267 3000 86.8% chr19 + 46410581 46410633 53 browser details YourSeq 39 2139 2189 3000 78.6% chr19 + 27584013 27584055 43 browser details YourSeq 38 1151 1195 3000 95.3% chr11 + 43672298 43672344 47 browser details YourSeq 37 216 266 3000 86.3% chrX + 89617061 89617111 51 browser details YourSeq 36 228 267 3000 95.0% chr5 - 101763185 101763224 40 browser details YourSeq 36 413 475 3000 85.4% chr3 - 28977339 28977399 61 browser details YourSeq 36 216 267 3000 84.7% chr1 - 141175671 141175722 52 browser details YourSeq 31 429 471 3000 86.1% chr13 - 80822051 80822093 43 browser details YourSeq 30 234 267 3000 94.2% chr14 + 46488634 46488667 34 Note: The 3000 bp section upstream of Exon 1 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% chr11 + 80478431 80481430 3000 browser details YourSeq 36 1326 1364 3000 100.0% chr1 - 185163498 185163550 53 browser details YourSeq 26 1339 1364 3000 100.0% chr4 + 148251171 148251196 26 browser details YourSeq 25 1339 1364 3000 100.0% chr11 + 116577390 116577416 27 Note: The 3000 bp section downstream of Exon 1 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Cdk5r1 cyclin-dependent kinase 5, regulatory subunit 1 (p35) [ Mus musculus (house mouse) ] Gene ID: 12569, updated on 10-Oct-2019 Gene summary Official Symbol Cdk5r1 provided by MGI Official Full Name cyclin-dependent kinase 5, regulatory subunit 1 (p35) provided by MGI Primary source MGI:MGI:101764 See related Ensembl:ENSMUSG00000048895 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 p25; p35; Cdk5r; D11Bwg0379e Orthologs human all Genomic context Location: 11 B5; 11 47.94 cM See Cdk5r1 in Genome Data Viewer Exon count: 1 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (80477023..80481184) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (80290548..80294681) Chromosome 11 - NC_000077.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 2 transcripts Gene: Cdk5r1 ENSMUSG00000048895 Description cyclin-dependent kinase 5, regulatory subunit 1 (p35) [Source:MGI Symbol;Acc:MGI:101764] Gene Synonyms D11Bwg0379e, p25, p35 Location Chromosome 11: 80,477,023-80,481,184 forward strand. GRCm38:CM001004.2 About this gene This gene has 2 transcripts (splice variants), 242 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 41 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Cdk5r1-201 ENSMUST00000053413.11 4162 307aa ENSMUSP00000099514.4 Protein coding CCDS25134 P61809 Q542T9 TSL:NA GENCODE basic APPRIS P1 Cdk5r1-202 ENSMUST00000147694.1 659 138aa ENSMUSP00000120964.1 Protein coding - B1AQH0 CDS 3' incomplete TSL:1 24.16 kb Forward strand 80.47Mb 80.48Mb 80.49Mb Genes (Comprehensive set... Psmd11-214 >protein coding Cdk5r1-201 >protein coding Psmd11-201 >protein coding Cdk5r1-202 >protein coding Psmd11-204 >retained intron Psmd11-209 >nonsense mediated decay Psmd11-215 >nonsense mediated decay Psmd11-205 >protein coding Psmd11-203 >protein coding Psmd11-213 >protein coding Psmd11-202 >nonsense mediated decay Contigs AL591146.21 > Genes < Myo1d-201protein coding (Comprehensive set... Regulatory Build 80.47Mb 80.48Mb 80.49Mb Reverse strand 24.16 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000053413 4.16 kb Forward strand Cdk5r1-201 >protein coding ENSMUSP00000099... MobiDB lite Low complexity (Seg) Superfamily Cyclin-like superfamily Pfam Cyclin-dependent kinase 5 activator PIRSF Cyclin-dependent kinase 5 activator PANTHER PTHR23401 PTHR23401:SF2 Gene3D 1.10.472.10 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend synonymous variant Scale bar 0 40 80 120 160 200 240 307 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Recommended publications
  • Mutations in CDK5RAP2 Cause Seckel Syndrome Go¨ Khan Yigit1,2,3,A, Karen E
    ORIGINAL ARTICLE Mutations in CDK5RAP2 cause Seckel syndrome Go¨ khan Yigit1,2,3,a, Karen E. Brown4,a,Hu¨ lya Kayserili5, Esther Pohl1,2,3, Almuth Caliebe6, Diana Zahnleiter7, Elisabeth Rosser8, Nina Bo¨ gershausen1,2,3, Zehra Oya Uyguner5, Umut Altunoglu5, Gudrun Nu¨ rnberg2,3,9, Peter Nu¨ rnberg2,3,9, Anita Rauch10, Yun Li1,2,3, Christian Thomas Thiel7 & Bernd Wollnik1,2,3 1Institute of Human Genetics, University of Cologne, Cologne, Germany 2Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany 3Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany 4Chromosome Biology Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, W12 0NN, UK 5Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey 6Institute of Human Genetics, Christian-Albrechts-University of Kiel, Kiel, Germany 7Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany 8Department of Clinical Genetics, Great Ormond Street Hospital for Children, London, WC1N 3EH, UK 9Cologne Center for Genomics, University of Cologne, Cologne, Germany 10Institute of Medical Genetics, University of Zurich, Schwerzenbach-Zurich, Switzerland Keywords Abstract CDK5RAP2, CEP215, microcephaly, primordial dwarfism, Seckel syndrome Seckel syndrome is a heterogeneous, autosomal recessive disorder marked by pre- natal proportionate short stature, severe microcephaly, intellectual disability, and Correspondence characteristic facial features. Here, we describe the novel homozygous splice-site Bernd Wollnik, Center for Molecular mutations c.383+1G>C and c.4005-9A>GinCDK5RAP2 in two consanguineous Medicine Cologne (CMMC) and Institute of families with Seckel syndrome. CDK5RAP2 (CEP215) encodes a centrosomal pro- Human Genetics, University of Cologne, tein which is known to be essential for centrosomal cohesion and proper spindle Kerpener Str.
    [Show full text]
  • Neuroprotective Role of Intermittent Fasting in Senescence-Accelerated Mice P8 (SAMP8) M
    Neuroprotective role of intermittent fasting in senescence-accelerated mice P8 (SAMP8) M. Tajes, J. Gutierrez-Cuesta, J. Folch, D. Ortuño-Sahagun, E. Verdaguer, A. Jiménez, F. Junyent, A. Lau, A. Camins, M. Pallàs To cite this version: M. Tajes, J. Gutierrez-Cuesta, J. Folch, D. Ortuño-Sahagun, E. Verdaguer, et al.. Neuroprotective role of intermittent fasting in senescence-accelerated mice P8 (SAMP8). Experimental Gerontology, Elsevier, 2010, 45 (9), pp.702. 10.1016/j.exger.2010.04.010. hal-00615111 HAL Id: hal-00615111 https://hal.archives-ouvertes.fr/hal-00615111 Submitted on 18 Aug 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ÔØ ÅÒÙ×Ö ÔØ Neuroprotective role of intermittent fasting in senescence-accelerated mice P8 (SAMP8) M. Tajes, J. Gutierrez-Cuesta, J. Folch, D. Ortu˜no-Sahagun, E. Verda- guer, A. Jim´enez,F. Junyent, A. Lau, A. Camins, M. Pall`as PII: S0531-5565(10)00188-9 DOI: doi: 10.1016/j.exger.2010.04.010 Reference: EXG 8747 To appear in: Experimental Gerontology Received date: 25 December 2009 Revised date: 23 April 2010 Accepted date: 29 April 2010 Please cite this article as: Tajes, M., Gutierrez-Cuesta, J., Folch, J., Ortu˜no-Sahagun, D., Verdaguer, E., Jim´enez, A., Junyent, F., Lau, A., Camins, A., Pall`as, M., Neuroprotec- tive role of intermittent fasting in senescence-accelerated mice P8 (SAMP8), Experimental Gerontology (2010), doi: 10.1016/j.exger.2010.04.010 This is a PDF file of an unedited manuscript that has been accepted for publication.
    [Show full text]
  • Transcriptomic and Open Chromatin Atlas of High-Resolution Anatomical Regions in the Rhesus Macaque Brain
    ARTICLE https://doi.org/10.1038/s41467-020-14368-z OPEN Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain Senlin Yin1,7, Keying Lu1,7, Tao Tan2,3,4,7, Jie Tang 1,7, Jingkuan Wei3, Xu Liu5, Xinlei Hu1, Haisu Wan5, Wei Huang6, Yong Fan4*, Dan Xie 1* & Yang Yu 2* 1234567890():,; The rhesus macaque is a prime model animal in neuroscience. A comprehensive tran- scriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque. 1 Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China. 2 Department of Obstetrics and Gynecology, Peking University Third Hospital, 100191 Beijing, China. 3 Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500 Kunming, Yunnan, China.
    [Show full text]
  • 1471-2105-8-S9-S6.Pdf
    BMC Bioinformatics BioMed Central Proceedings Open Access Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations Hyunsoo Kim, Haesun Park* and Barry L Drake Address: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA Email: Hyunsoo Kim - [email protected]; Haesun Park* - [email protected]; Barry L Drake - [email protected] * Corresponding author from First International Workshop on Text Mining in Bioinformatics (TMBio) 2006 Arlington, VA, USA. 10 November 2006 Published: 27 November 2007 BMC Bioinformatics 2007, 8(Suppl 9):S6 doi:10.1186/1471-2105-8-S9-S6 <supplement> <title> <p>First International Workshop on Text Mining in Bioinformatics (TMBio) 2006</p> </title> <editor>Min Song and Zoran Obradovic</editor> <note>Proceedings</note> </supplement> This article is available from: http://www.biomedcentral.com/1471-2105/8/S9/S6 © 2007 Kim et al; licensee BioMed Central Ltd. Abstract Background: The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical literature may be helpful in building biological hypotheses that can be explored further experimentally. Recently, latent semantic indexing based on the singular value decomposition (LSI/SVD) has been applied to gene retrieval. However, the determination of the number of factors k used in the reduced rank matrix is still an open problem. Results: In this paper, we introduce a way to incorporate a priori knowledge of gene relationships into LSI/SVD to determine the number of factors. We also explore the utility of the non-negative matrix factorization (NMF) to extract unrecognized gene relationships from the biomedical literature by taking advantage of known gene relationships.
    [Show full text]
  • Downloaded from in December 2015)
    cells Article Proteomic Analysis of Hydromethylthionine in the Line 66 Model of Frontotemporal Dementia Demonstrates Actions on Tau-Dependent and Tau-Independent Networks Karima Schwab 1,2, Valeria Melis 1, Charles R. Harrington 1,3 , Claude M. Wischik 1,3, Mandy Magbagbeolu 2, Franz Theuring 2,† and Gernot Riedel 1,*,† 1 School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; [email protected] (K.S.); [email protected] (V.M.); [email protected] (C.R.H.); [email protected] (C.M.W.) 2 Charité—Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany; [email protected] (M.M.); [email protected] (F.T.) 3 TauRx Therapeutics Ltd., 395 King Street, Aberdeen AB24 5RP, UK * Correspondence: [email protected] † Equal contribution (co-last author). Abstract: Abnormal aggregation of tau is the pathological hallmark of tauopathies including fron- totemporal dementia (FTD). We have generated tau-transgenic mice that express the aggregation- prone P301S human tau (line 66). These mice present with early-onset, high tau load in brain and FTD-like behavioural deficiencies. Several of these behavioural phenotypes and tau pathology are reversed by treatment with hydromethylthionine but key pathways underlying these corrections Citation: Schwab, K.; Melis, V.; Harrington, C.R.; Wischik, C.M.; remain elusive. In two proteomic experiments, line 66 mice were compared with wild-type mice Magbagbeolu, M.; Theuring, F.; and then vehicle and hydromethylthionine treatments of line 66 mice were compared. The brain Riedel, G. Proteomic Analysis of proteome was investigated using two-dimensional electrophoresis and mass spectrometry to iden- Hydromethylthionine in the Line 66 tify protein networks and pathways that were altered due to tau overexpression or modified by Model of Frontotemporal Dementia hydromethylthionine treatment.
    [Show full text]
  • CDK5R1(P35) Antibody (C-Term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # Ap7743b
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 CDK5R1(p35) Antibody (C-term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP7743b Specification CDK5R1(p35) Antibody (C-term) - Product Information Application WB, IHC-P,E Primary Accession Q15078 Other Accession P61810, P61809, Q28199 Reactivity Human Predicted Bovine, Mouse, Rat Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Calculated MW 34060 Antigen Region 272-301 CDK5R1 Antibody (C-term) (Cat. #AP7743b) CDK5R1(p35) Antibody (C-term) - Additional western blot analysis in A2058 cell line Information lysates (35ug/lane).This demonstrates the CDK5R1 antibody detected the CDK5R1 Gene ID 8851 protein (arrow). Other Names Cyclin-dependent kinase 5 activator 1, CDK5 activator 1, Cyclin-dependent kinase 5 regulatory subunit 1, TPKII regulatory subunit, Cyclin-dependent kinase 5 activator 1, p35, p35, Cyclin-dependent kinase 5 activator 1, p25, p25, Tau protein kinase II 23 kDa subunit, p23, CDK5R1, CDK5R, NCK5A Target/Specificity This CDK5R1(p35) antibody is generated from rabbits immunized with a KLH conjugated synthetic peptide between Formalin-fixed and paraffin-embedded 272-301 amino acids from the C-terminal human brain tissue reacted with region of human CDK5R1(p35). CDK5R1(p35) Antibody (C-term) (Cat.#AP7743b), which was Dilution peroxidase-conjugated to the secondary WB~~1:1000 antibody, followed by DAB staining. This data IHC-P~~1:10~50 demonstrates the use of this antibody for immunohistochemistry; clinical relevance has Format not been evaluated. Purified polyclonal antibody supplied in PBS with 0.09% (W/V) sodium azide. This antibody is purified through a protein A CDK5R1(p35) Antibody (C-term) - column, followed by peptide affinity Background Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 purification.
    [Show full text]
  • Extracting Unrecognized Gene Relationships from the Biomedical Literature Via Matrix Factorizations
    Extracting Unrecognized Gene Relationships from the Biomedical Literature via Matrix Factorizations Hyunsoo Kim∗1, Haesun Park∗1 and Barry L. Drake1 1 College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. Email: H. Kim∗- [email protected]; H. Park∗- [email protected]; B. L. Drake - [email protected]; ∗Corresponding author Abstract Background: The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical literature may be helpful in building biological hypotheses that can be explored further experimentally. Recently, latent semantic indexing based on the singular value decomposition (LSI/SVD) has been applied to gene retrieval. However, the determination of the number of factors k used in the reduced rank matrix is still an open problem. Results: In this paper, we introduce a way to incorporate a priori knowledge of gene relationships into LSI/SVD to determine the number of factors. We also explore the utility of the non-negative matrix factorization (NMF) to extract unrecognized gene relationships from the biomedical literature by taking advantage of known gene relationships. A gene retrieval method based on NMF (GR/NMF) showed comparable performance with LSI/SVD. Conclusions: Using known gene relationships of a given gene, we can determine the number of factors used in the reduced rank matrix and retrieve unrecognized genes related with the given gene by LSI/SVD or GR/NMF. 1 Background Latent semantic indexing based on the singular value decomposition (LSI/SVD) [1, 2] uses the truncated singular value decomposition as a low-rank approximation of a term-by-document matrix.
    [Show full text]
  • SUPPLEMENTARY MATERIALS and METHODS PBMC Transcriptomics
    BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut SUPPLEMENTARY MATERIALS AND METHODS PBMC transcriptomics identifies immune-metabolism disorder during the development of HBV-ACLF Contents l Supplementary methods l Supplementary Figure 1 l Supplementary Figure 2 l Supplementary Figure 3 l Supplementary Figure 4 l Supplementary Figure 5 l Supplementary Table 1 l Supplementary Table 2 l Supplementary Table 3 l Supplementary Table 4 l Supplementary Tables 5-14 l Supplementary Table 15 l Supplementary Table 16 l Supplementary Table 17 Li J, et al. Gut 2021;0:1–13. doi: 10.1136/gutjnl-2020-323395 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut SUPPLEMENTARY METHODS Test for HBV DNA The levels of HBV DNA were detected using real-time PCR with a COBAS® AmpliPrep/COBAS® TaqMan 48 System (Roche, Basel, Switzerland) and HBV Test v2.0. Criteria for diagnosing cirrhosis Pathology The gold standard for the diagnosis of cirrhosis is a liver biopsy obtained through a percutaneous or transjugular approach.1 Ultrasonography was performed 2-4 hours before biopsy. Liver biopsy specimens were obtained by experienced physicians. Percutaneous transthoracic puncture of the liver was performed according to the standard criteria. After biopsy, patients were monitored in the hospital with periodic analyses of haematocrit and other vital signs for 24 hours. Cirrhosis was diagnosed according to the globally agreed upon criteria.2 Cirrhosis is defined based on its pathological features under a microscope: (a) the presence of parenchymal nodules, (b) differences in liver cell size and appearance, (c) fragmentation of the biopsy specimen, (d) fibrous septa, and (d) an altered architecture and vascular relationships.
    [Show full text]
  • Tissue-Type Plasminogen Activator Regulates P35-Mediated Cdk5
    © 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs224196. doi:10.1242/jcs.224196 RESEARCH ARTICLE Tissue-type plasminogen activator regulates p35-mediated Cdk5 activation in the postsynaptic terminal Ariel Diaz1,*, Valerie Jeanneret2,*, Paola Merino1, Patrick McCann1 and Manuel Yepes1,2,3,‡ ABSTRACT functional and structural changes in the synapse required for the Neuronal depolarization induces the synaptic release of tissue-type development of long-term potentiation (Qian et al., 1993), learning plasminogen activator (tPA). Cyclin-dependent kinase-5 (Cdk5) is a (Seeds et al., 1995), stress-induced anxiety (Pawlak et al., 2003) and member of the family of cyclin-dependent kinases that regulates cell visual cortex plasticity (Müller and Griesinger, 1998). Interestingly, migration and synaptic function in postmitotic neurons. Cdk5 is activated recent studies indicate that the release of tPA into the synaptic cleft by its binding to p35 (also known as Cdk5r1), a membrane-anchored also modulates the response of the postsynaptic terminal to the protein that is rapidly degraded by the proteasome. Here, we show that presynaptic release of glutamate (Jeanneret et al., 2016), and has a tPA prevents the degradation of p35 in the synapse by a plasminogen- direct effect on the structure and receptor composition of the dependent mechanism that requires open synaptic N-methyl-D- postsynaptic density (PSD) (Jeanneret et al., 2018). aspartate (NMDA) receptors. We show that tPA treatment increases Cyclin-dependent kinase-5 (Cdk5) is a member of the family of the abundance of p35 and its binding to Cdk5 in the postsynaptic density cyclin-dependent kinases found in postmitotic neurons (Dhavan and (PSD).
    [Show full text]
  • Altered Resting-State Functional Connectivity in Hipsc-Derived Neuronal Networks from Schizophrenia Patients
    medRxiv preprint doi: https://doi.org/10.1101/2021.08.26.21262277; this version posted August 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Manuscript Title: Altered resting-state functional connectivity in hiPSC-derived neuronal networks from schizophrenia patients Short Title: Altered neuronal network dynamics in schizophrenia Authors: Sofía Puvogel1,2,3 a, Kris Blanchard1,2 a, Bárbara S. Casas1, Robyn Miller4,5, Delia Garrido1, Magdalena Sanhueza2#, Verónica Palma1# a These authors contributed equally to this work # Co-Corresponding Authors: Verónica Palma ([email protected]), Phone number (56-2) 2978 7221, Las Encinas 3370. Milenio Building, Floor 3, Ñuñoa, Santiago, Chile. 7800024. Magdalena Sanhueza ([email protected]). Phone number (56-2) 2978 7344. Las Encinas 3370. Milenio Building, Floor 3, Ñuñoa, Santiago, Chile. 7800024 1. Laboratory of Stem Cells and Developmental Biology, Department of Biology, Faculty of Sciences. Universidad de Chile. Santiago, Chile. 2. Cell Physiology Laboratory, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile. 3. Current affiliation: Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, Groningen, The Netherlands. 4. Georgia State University, Dept of Computer Science, Atlanta GA, USA. 5. Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS Center), Atlanta, GA, USA 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
    [Show full text]
  • Kinome Expression Profiling to Target New Therapeutic Avenues in Multiple Myeloma
    Plasma Cell DIsorders SUPPLEMENTARY APPENDIX Kinome expression profiling to target new therapeutic avenues in multiple myeloma Hugues de Boussac, 1 Angélique Bruyer, 1 Michel Jourdan, 1 Anke Maes, 2 Nicolas Robert, 3 Claire Gourzones, 1 Laure Vincent, 4 Anja Seckinger, 5,6 Guillaume Cartron, 4,7,8 Dirk Hose, 5,6 Elke De Bruyne, 2 Alboukadel Kassambara, 1 Philippe Pasero 1 and Jérôme Moreaux 1,3,8 1IGH, CNRS, Université de Montpellier, Montpellier, France; 2Department of Hematology and Immunology, Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium; 3CHU Montpellier, Laboratory for Monitoring Innovative Therapies, Department of Biologi - cal Hematology, Montpellier, France; 4CHU Montpellier, Department of Clinical Hematology, Montpellier, France; 5Medizinische Klinik und Poliklinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany; 6Nationales Centrum für Tumorerkrankungen, Heidelberg , Ger - many; 7Université de Montpellier, UMR CNRS 5235, Montpellier, France and 8 Université de Montpellier, UFR de Médecine, Montpel - lier, France ©2020 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2018.208306 Received: October 5, 2018. Accepted: July 5, 2019. Pre-published: July 9, 2019. Correspondence: JEROME MOREAUX - [email protected] Supplementary experiment procedures Kinome Index A list of 661 genes of kinases or kinases related have been extracted from literature9, and challenged in the HM cohort for OS prognostic values The prognostic value of each of the genes was computed using maximally selected rank test from R package MaxStat. After Benjamini Hochberg multiple testing correction a list of 104 significant prognostic genes has been extracted. This second list has then been challenged for similar prognosis value in the UAMS-TT2 validation cohort.
    [Show full text]
  • Dishevelled Is a NEK2 Kinase Substrate Controlling Dynamics of Centrosomal Linker Proteins
    Dishevelled is a NEK2 kinase substrate controlling dynamics of centrosomal linker proteins Igor Cervenkaa, Jana Valnohovaa,1, Ondrej Bernatika,b, Jakub Harnosa, Matej Radsetoulala, Katerina Sedovac, Katerina Hanakovac, David Potesilc, Miroslava Sedlackovad, Alena Salasovaa,e, Zachary Steinhartf, Stephane Angersf, Gunnar Schultea,g, Ales Hampld, Zbynek Zdrahalc,h, and Vitezslav Bryjaa,b,2 aDepartment of Experimental Biology, Faculty of Science, Masaryk University, 61 137 Brno, Czech Republic; bInstitute of Biophysics, Academy of Sciences of Czech Republic, 61 200 Brno, Czech Republic; cResearch Group Proteomics, Central European Institute of Technology, 62 500 Brno, Czech Republic; dDepartment of Histology and Embryology, Faculty of Medicine, Masaryk University, 62 500 Brno, Czech Republic; eDepartment of Biochemistry and Biophysics, Karolinska Institutet Stockholm, 171 77, Sweden; fDepartment of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; gReceptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, 17 177 Stockholm, Sweden; and hNational Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic Edited by Roeland Nusse, Stanford University School of Medicine, Stanford, CA, and approved June 23, 2016 (received for review May 31, 2016) Dishevelled (DVL) is a key scaffolding protein and a branching point cleavage of Rootletin (14) and displacement of C-NAP1 from cen- in Wnt signaling pathways. Here, we present conclusive evidence trosomes (18). Interference with linker proteins or their phosphor- that DVL regulates the centrosomal cycle. We demonstrate that DVL ylation has a drastic effect on cell division (19) and on genome dishevelled and axin (DIX) domain, but not DIX domain-mediated integrity caused by chromosome segregation errors (20).
    [Show full text]