scholarly journals Creating a “Hopeful Monster”: Mouse Forward Genetic Screens

2011 ◽  
pp. 313-336 ◽  
Author(s):  
Vanessa L. Horner ◽  
Tamara Caspary
Keyword(s):  
Genetic Screens ◽  
Hopeful Monster ◽  
Forward Genetic Screens

scholarly journals Identification of plant stress-responsive determinants in arabidopsis by large-scale forward genetic screens

2006 ◽  
Vol 57 (5) ◽  
pp. 1119-1128 ◽  
Author(s):  
Hisashi Koiwa ◽  
Ray A. Bressan ◽  
Paul M. Hasegawa
Keyword(s):  
Large Scale ◽  
Plant Stress ◽  
Genetic Screens ◽  
Forward Genetic Screens

scholarly journals Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1

2019 ◽  
Author(s):  
Elizabeth R. Cebul ◽  
Ian G. McLachlan ◽  
Maxwell G. Heiman
Keyword(s):  
Glial Cell ◽  
Molecular Mechanism ◽  
Mammalian Brain ◽  
Cytoplasmic Protein ◽  
Genetic Screens ◽  
Sense Organs ◽  
Adhesion Protein ◽  
C Elegans ◽  
Dendrite Development ◽  
Forward Genetic Screens

ABSTRACTDendrites develop elaborate morphologies in concert with surrounding glia, but the molecules that coordinate dendrite and glial morphogenesis are mostly unknown.C. elegansoffers a powerful model for identifying such factors. Previous work in this system examined dendrites and glia that develop within epithelia, similar to mammalian sense organs. Here, we focus on the neurons BAG and URX, which are not part of an epithelium but instead form membranous attachments to a single glial cell at the nose, reminiscent of dendrite-glia contacts in the mammalian brain. We show that these dendrites develop by retrograde extension, in which the nascent dendrite endings anchor to the presumptive nose and then extend by stretch during embryo elongation. Using forward genetic screens, we find that dendrite development requires the adhesion protein SAX-7/L1CAM and the cytoplasmic protein GRDN-1/CCDC88C to anchor dendrite endings at the nose. SAX-7 acts in neurons and glia, while GRDN-1 acts in glia to non-autonomously promote dendrite extension. Thus, this work shows how glial factors can help to shape dendrites, and identifies a novel molecular mechanism for dendrite growth by retrograde extension.

scholarly journals Fluorescence-Based Phenotypic Selection Allows Forward Genetic Screens in Haploid Human Cells

PLoS ONE ◽  
2012 ◽  
Vol 7 (6) ◽  
pp. e39651 ◽  
Author(s):  
Lidia M. Duncan ◽  
Richard T. Timms ◽  
Eszter Zavodszky ◽  
Florencia Cano ◽  
Gordon Dougan ◽  
...  
Keyword(s):  
Phenotypic Selection ◽  
Human Cells ◽  
Genetic Screens ◽  
Forward Genetic Screens

scholarly journals Unsupervised Learning Approach for Comparing Multiple Transposon Insertion Sequencing Studies

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Troy P. Hubbard ◽  
Jonathan D. D’Gama ◽  
Gabriel Billings ◽  
Brigid M. Davis ◽  
Matthew K. Waldor
Keyword(s):  
Unsupervised Learning ◽  
Principal Component ◽  
Data Sets ◽  
Intestinal Colonization ◽  
Genetic Screens ◽  
Transposon Insertion ◽  
Screen Level ◽  
Forward Genetic Screens ◽  
Transposon Insertion Sequencing ◽  
Genome Scale

ABSTRACT Transposon insertion sequencing (TIS) is a widely used technique for conducting genome-scale forward genetic screens in bacteria. However, few methods enable comparison of TIS data across multiple replicates of a screen or across independent screens, including screens performed in different organisms. Here, we introduce a post hoc analytic framework, comparative TIS (CompTIS), which utilizes unsupervised learning to enable meta-analysis of multiple TIS data sets. CompTIS first implements screen-level principal-component analysis (PCA) and clustering to identify variation between the TIS screens. This initial screen-level analysis facilitates the selection of related screens for additional analyses, reveals the relatedness of complex environments based on growth phenotypes measured by TIS, and provides a useful quality control step. Subsequently, PCA is performed on genes to identify loci whose corresponding mutants lead to concordant/discordant phenotypes across all or in a subset of screens. We used CompTIS to analyze published intestinal colonization TIS data sets from two vibrio species. Gene-level analyses identified both pan-vibrio genes required for intestinal colonization and conserved genes that displayed species-specific requirements. CompTIS is applicable to virtually any combination of TIS screens and can be implemented without regard to either the number of screens or the methods used for upstream data analysis. IMPORTANCE Forward genetic screens are powerful tools for functional genomics. The comparison of similar forward genetic screens performed in different organisms enables the identification of genes with similar or different phenotypes across organisms. Transposon insertion sequencing is a widely used method for conducting genome-scale forward genetic screens in bacteria, yet few bioinformatic approaches have been developed to compare the results of screen replicates and different screens conducted across species or strains. Here, we used principal-component analysis (PCA) and hierarchical clustering, two unsupervised learning approaches, to analyze the relatedness of multiple in vivo screens of pathogenic vibrios. This analytic framework reveals both shared pan-vibrio requirements for intestinal colonization and strain-specific dependencies. Our findings suggest that PCA-based analytics will be a straightforward widely applicable approach for comparing diverse transposon insertion sequencing screens.

scholarly journals David Bilder: Getting to know epithelia inside and out

2011 ◽  
Vol 193 (6) ◽  
pp. 956-957
Author(s):  
Caitlin Sedwick
Keyword(s):  
Genetic Screens ◽  
Form And Function ◽  
Forward Genetic Screens ◽  
And Function

Bilder explores epithelial form and function in Drosophila using forward genetic screens.

scholarly journals Zebrafish embryonic development is induced by carp sperm

2016 ◽  
Vol 12 (11) ◽  
pp. 20160628 ◽  
Author(s):  
Thomas A. Delomas ◽  
Konrad Dabrowski
Keyword(s):  
Nervous System ◽  
Linkage Analysis ◽  
Embryonic Development ◽  
Common Carp ◽  
Genetic Screens ◽  
Characteristic Set ◽  
Zebrafish Development ◽  
Functional Development ◽  
Forward Genetic Screens

Haploid gynogenetic screens increase the efficiency of forward genetic screens and linkage analysis in fish. Typically, UV-irradiated zebrafish sperm is used to activate zebrafish oocytes for haploid screens. We describe the use of UV-irradiated common carp sperm to activate haploid gynogenetic zebrafish development. Carp × zebrafish hybrids are shown to have a characteristic set of features during embryonic development and exhibit functional development of several tissues (muscle, heart and nervous system). Hybrids become inviable past the embryonic stages. This technique eliminates the possibility of incompletely irradiated zebrafish spermatozoa contaminating haploid progenies. While developing this protocol, one unique zebrafish female was identified which, upon insemination with UV-irradiated carp spermatozoa, repeatedly displayed spontaneous diploidization of the maternal chromosomes in her offspring.

scholarly journals Forward genetic screens in mice uncover mediators and suppressors of metastatic reactivation

2014 ◽  
Vol 111 (46) ◽  
pp. 16532-16537 ◽  
Author(s):  
Hua Gao ◽  
Goutam Chakraborty ◽  
Ai Ping Lee-Lim ◽  
Konstantinos J. Mavrakis ◽  
Hans-Guido Wendel ◽  
...  
Keyword(s):  
Genetic Screens ◽  
Forward Genetic Screens

scholarly journals Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway

2015 ◽  
Vol 84 (2) ◽  
pp. 257-266 ◽  
Author(s):  
Govinda Rizal ◽  
Vivek Thakur ◽  
Jacqueline Dionora ◽  
Shanta Karki ◽  
Samart Wanchana ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Genetic Screens ◽  
Cytochrome P450 Gene ◽  
P450 Gene ◽  
Vein Density ◽  
Forward Genetic Screens
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