scholarly journals Progress towards completing the mutant mouse null resource

2021 ◽  
Author(s):  
Kevin A. Peterson ◽  
Stephen A. Murray
Keyword(s):  
Large Scale ◽  
Null Allele ◽  
Mutant Mouse ◽  
Embryonic Stem ◽  
Pooled Analysis ◽  
Null Alleles ◽  
Scale Production ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Human Orthologs

AbstractThe generation of a comprehensive catalog of null alleles covering all protein-coding genes is the goal of the International Mouse Phenotyping Consortium. Over the past 20 years, significant progress has been made towards achieving this goal through the combined efforts of many large-scale programs that built an embryonic stem cell resource to generate knockout mice and more recently employed CRISPR/Cas9-based mutagenesis to delete critical regions predicted to result in frameshift mutations, thus, ablating gene function. The IMPC initiative builds on prior and ongoing work by individual research groups creating gene knockouts in the mouse. Here, we analyze the collective efforts focusing on the combined null allele resource resulting from strains developed by the research community and large-scale production programs. Based upon this pooled analysis, we examine the remaining fraction of protein-coding genes focusing on clearly defined mouse–human orthologs as the highest priority for completing the mutant mouse null resource. In summary, we find that there are less than 3400 mouse–human orthologs remaining in the genome without a targeted null allele that can be further prioritized to achieve our overall goal of the complete functional annotation of the protein-coding portion of a mammalian genome.

scholarly journals Employing single-stranded DNA donors for the high-throughput production of conditional knockout alleles in mice

2017 ◽  
Author(s):  
Denise G. Lanza ◽  
Angelina Gaspero ◽  
Isabel Lorenzo ◽  
Lan Liao ◽  
Ping Zheng ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Gene Editing ◽  
Null Allele ◽  
Conditional Knockout ◽  
Null Alleles ◽  
Protein Coding ◽  
International Mouse Phenotyping Consortium ◽  
Conditional Allele ◽  
In Cis

ABSTRACTThe International Mouse Phenotyping Consortium is generating null allele mice for every protein-coding gene in the genome and characterizing these mice to identify gene-phenotype associations. To test the feasibility of using CRISPR/Cas9 gene editing to generate conditional knockout mice for this large-scale resource, we employed Cas9-mediated homology driven repair (HDR) with short and long single-stranded oligodeoxynucleotides (ssODNs and lssODNs). Using pairs of guides and ssODNs donating loxP sites, we obtained putative conditional allele founder mice, harboring both loxP sites, for 23 of 30 genes targeted. LoxP sites integrated in cis in at least one F0 for 18 of 23 targeted genes. However, loxP sites were mutagenized in 4 of 18 in cis lines. HDR efficiency correlated with Cas9 cutting efficiency but was not influenced by ssODN homology arm symmetry. By contrast, using pairs of guides and a single lssODN to introduce a loxP-flanked exon, conditional allele founders were generated for all 4 genes targeted. Our studies demonstrate that Cas9-mediated HDR with pairs of ssODNs can generate conditional null alleles at many loci, but reveal inefficiencies when applied at scale. In contrast, lssODNs are amenable to high-throughput production of conditional alleles when they can be employed.

scholarly journals PaperBLAST: Text-mining papers for information about homologs

2017 ◽  
Author(s):  
Morgan N. Price ◽  
Adam P. Arkin
Keyword(s):  
Text Mining ◽  
Genome Sequencing ◽  
Full Text ◽  
Large Scale ◽  
Scientific Literature ◽  
Protein Sequences ◽  
Protein Coding ◽  
Link Protein ◽  
Protein Coding Genes ◽  
Link Type

AbstractLarge-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

scholarly journals Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes

2019 ◽  
Vol 116 (44) ◽  
pp. 22020-22029 ◽  
Author(s):  
Aritro Nath ◽  
Eunice Y. T. Lau ◽  
Adam M. Lee ◽  
Paul Geeleher ◽  
William C. S. Cho ◽  
...  
Keyword(s):  
Anticancer Drug ◽  
Noncoding Rna ◽  
Large Scale ◽  
Drug Response ◽  
Cancer Cell Line ◽  
Systematic Evaluation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Clinical Biomarkers ◽  
Response Predictors

Large-scale cancer cell line screens have identified thousands of protein-coding genes (PCGs) as biomarkers of anticancer drug response. However, systematic evaluation of long noncoding RNAs (lncRNAs) as pharmacogenomic biomarkers has so far proven challenging. Here, we study the contribution of lncRNAs as drug response predictors beyond spurious associations driven by correlations with proximal PCGs, tissue lineage, or established biomarkers. We show that, as a whole, the lncRNA transcriptome is equally potent as the PCG transcriptome at predicting response to hundreds of anticancer drugs. Analysis of individual lncRNAs transcripts associated with drug response reveals nearly half of the significant associations are in fact attributable to proximal cis-PCGs. However, adjusting for effects of cis-PCGs revealed significant lncRNAs that augment drug response predictions for most drugs, including those with well-established clinical biomarkers. In addition, we identify lncRNA-specific somatic alterations associated with drug response by adopting a statistical approach to determine lncRNAs carrying somatic mutations that undergo positive selection in cancer cells. Lastly, we experimentally demonstrate that 2 lncRNAs, EGFR-AS1 and MIR205HG, are functionally relevant predictors of anti-epidermal growth factor receptor (EGFR) drug response.

Large-scale production of murine embryonic stem cell-derived osteoblasts and chondrocytes on microcarriers in serum-free media

Biomaterials ◽  
2011 ◽  
Vol 32 (26) ◽  
pp. 6006-6016 ◽  
Author(s):  
Roz Alfred ◽  
Jaymi T. Taiani ◽  
Roman J. Krawetz ◽  
Akihiro Yamashita ◽  
Derrick E. Rancourt ◽  
...  
Keyword(s):  
Stem Cell ◽  
Embryonic Stem Cell ◽  
Large Scale ◽  
Embryonic Stem ◽  
Scale Production ◽  
Serum Free ◽  
Murine Embryonic Stem Cell ◽  
Large Scale Production ◽  
Free Media

scholarly journals Human Fetal Liver: AnIn VitroModel of Erythropoiesis

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Guillaume Pourcher ◽  
Christelle Mazurier ◽  
Yé Yong King ◽  
Marie-Catherine Giarratana ◽  
Ladan Kobari ◽  
...  
Keyword(s):  
Stem Cells ◽  
Large Scale ◽  
Adult Stem Cells ◽  
Fetal Liver ◽  
Es Cells ◽  
Embryonic Stem ◽  
Scale Production ◽  
Cloning Efficiency ◽  
Hematopoietic Stem

We previously described the large-scale production of RBCs from hematopoietic stem cells (HSCs) of diverse sources. Our present efforts are focused to produce RBCs thanks to an unlimited source of stem cells. Human embryonic stem (ES) cells or induced pluripotent stem cell (iPS) are the natural candidates. Even if the proof of RBCs production from these sources has been done, their amplification ability is to date not sufficient for a transfusion application. In this work, our protocol of RBC production was applied to HSC isolated from fetal liver (FL) as an intermediate source between embryonic and adult stem cells. We studied the erythroid potential of FL-derived CD34+cells. In thisin vitromodel, maturation that is enucleation reaches a lower level compared to adult sources as observed for embryonic or iP, but, interestingly, they (i) displayed a dramaticin vitroexpansion (100-fold more when compared to CB CD34+) and (ii) 100% cloning efficiency in hematopoietic progenitor assays after 3 days of erythroid induction, as compared to 10–15% cloning efficiency for adult CD34+cells. This work supports the idea that FL remains a model of study and is not a candidate forex vivoRBCS production for blood transfusion as a direct source of stem cells but could be helpful to understand and enhance proliferation abilities for primitive cells such as ES cells or iPS.

scholarly journals An Exploration of the Sequence of a 2.9-Mb Region of the Genome of Drosophila melanogaster: The Adh Region

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 179-219 ◽  
Author(s):  
M Ashburner ◽  
S Misra ◽  
J Roote ◽  
S E Lewis ◽  
R Blazej ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Large Scale ◽  
Chromosome Region ◽  
Complete Sequence ◽  
Test Methods ◽  
P Element ◽  
Cdna Libraries ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized “Adh region.” A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.

scholarly journals High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola)

2021 ◽  
Author(s):  
Yun-Xia Luan ◽  
Yingying Cui ◽  
Wan-Jun Chen ◽  
Jianfeng Jin ◽  
Ai-Min Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Test Organism ◽  
Gene Families ◽  
Species Differentiation ◽  
Folsomia Candida ◽  
Cryptic Speciation ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Soil Arthropod

The collembolan Folsomia candida Willem, 1902, is an important representative soil arthropod that is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we present two high-quality chromosome-level genomes of F. candida, for the parthenogenetic Danish strain (FCDK, 219.08 Mb, N50 of 38.47 Mb, 25,139 protein-coding genes) and the sexual Shanghai strain (FCSH, 153.09 Mb, N50 of 25.75 Mb, 21,609 protein-coding genes). The seven chromosomes of FCDK are each 25–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to its broader environmental adaptation. In addition, the overall sequence identity of the two mitogenomes is only 78.2%, and FCDK has fewer strain-specific microRNAs than FCSH. In conclusion, FCDK and FCSH have accumulated independent genetic changes and evolved into distinct species since diverging 10 Mya. Our work shows that F. candida represents a good model of rapidly cryptic speciation. Moreover, it provides important genomic resources for studying the mechanisms of species differentiation, soil arthropod adaptation to soil ecosystems, and Wolbachia-induced parthenogenesis as well as the evolution of Collembola, a pivotal phylogenetic clade between Crustacea and Insecta.

scholarly journals A resource of targeted mutant mouse lines for 5,061 genes

2019 ◽  
Author(s):  
Marie-Christine Birling ◽  
Atsushi Yoshiki ◽  
David J Adams ◽  
Shinya Ayabe ◽  
Arthur L Beaudet ◽  
...  
Keyword(s):  
Mutant Mouse ◽  
Embryonic Stem ◽  
Null Alleles ◽  
Mouse Mutant ◽  
International Mouse Phenotyping Consortium ◽  
Number Of Genes ◽  
Mutant Strains ◽  
Community Effort ◽  
Mutant Mouse Line ◽  
Public Repositories

AbstractThe International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This nearly triples the number of genes with reporter alleles and almost doubles the number of conditional alleles available to the scientific community. When combined with more than 30 years of community effort, the total mutant allele mouse resource covers more than half of the genome. The extensively validated collection is archived and distributed through public repositories, facilitating availability to the worldwide biomedical research community, and expanding our understanding of gene function and human disease.

293 MASS PRODUCTION OF Nkx2.5-POSITIVE CARDIAC PROGENITOR CELLS DERIVED FROM MOUSE EMBRYONIC STEM CELLS IN SLOW-TURNING LATERAL VESSEL FOR CELL TRANSPLANTATION AND DRUG TESTING

2011 ◽  
Vol 23 (1) ◽  
pp. 244
Author(s):  
S. Rungarunlert ◽  
N. Klincumhom ◽  
C. Nemes ◽  
M. Techakumphu ◽  
M. K. Pirity ◽  
...  
Keyword(s):  
Suspension Culture ◽  
Progenitor Cells ◽  
Mass Production ◽  
Large Scale ◽  
Es Cells ◽  
Embryonic Stem ◽  
Cardiac Progenitor Cells ◽  
Scale Production ◽  
Culture Methods ◽  
Mouse Es Cells

Regenerative cell therapy against cardiovascular disease would require mass production and purification of specific cell types before transplantation. To enable large-scale production of embryonic stem (ES)-derived pure cardiomyocytes, we developed an animal model for a single-step scalable bioprocess that allows direct embryoid body (EB) formation in a fully controlled slow-turning lateral vessel (STLV, Synthecon, Inc., Houston, TX, USA) bioreactor following inoculation with a single cell suspension of mouse ES cells. To enhance the yield of cardiac progenitor cells, mouse ES cells (HM1; 129Sv/Ola, Magin et al. 1992 Nucl. Acids Res. 20, 3795–3796) were targeted with the cardiac-specific mouse Nkx2.5 promoter driven enhanced fluorescent green protein (EGFP). Among 15 targeted colonies, which were characterised based on morphology, the ability to form EB, EGFP expression, and in vitro differentiation ability toward cardiomyocytes, 3 lines were further evaluated for the efficiency of cardiomyocyte production. The 3 lines were cultured in STLV bioreactor and compared with classical hanging drop (HD) and static suspension culture methods. Embryonic bodies at day 3 to 8 were collected and analysed by using fluorescence-activated cell sorting for markers of pluripotency (e.g. Oct-4, SSEA1, Nanog) and cardiac (e.g. Nkx2.5, Troponin T) lineage commitments. Data was analysed by one-way ANOVA and t-tests. The results showed that both level and kinetics of Nkx2.5 expression was dependent on culture conditions. The STLV and static suspension culture methods produced higher rates of Nkx2.5-positive cells on day 5 than that of HD (70 and 54 v. 30%, respectively). The STLV method produced a highly uniform population of efficiently differentiating EB in large quantities and resulted in the highest, 108 yield of cardiomyocytes in a single 110-mL STLV on day 4. In conclusion, the STLV method provides a technological platform for controlled large-scale generation of ES-cell-derived cardiomyocytes for clinical and industrial applications. In vivo transplantation tests of cardiomyocytes produced via STLV are currently underway. This study was financed by EU FP6 (CLONET, MRTN-CT-2006-035468), EU FP7 (PartnErS, PIAP-GA-2008-218205; InduHeart, PEOPLE-IRG-2008-234390; InduStem, PIAP-GA-2008-230675; PluriSys, HEALTH-2007-B-223485); NKTH-OTKA-EU FP7-HUMAN-2009-MB08-C 80205 and NKTH/KPI (NKFP_07_1-ES2HEART-HU OM-00202-2007), CHE-TRF senior scholarship, No. RTA 5080010 (M.T.), and the Thailand Commission on Higher Education [CHE-PhD-SW-2005-100 (S.R.), CHE-PhD-SW-RG-2007 (N.K.)].

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