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Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9
TLDR
An effective and inexpensive method for genome DNA editing in Drosophila melanogaster whereby plasmid DNAs encoding short sgRNAs under the control of the U6b promoter are injected into transgenic flies in which Cas9 is specifically expressed in the germ line via the nanos promoter. Expand
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets
TLDR
It is found that 21% of the proteins in the PPI network are indispensable, Interestingly, these indispensable proteins are the primary targets of disease-causing mutations, human viruses, and drugs, suggesting that altering a network’s control property is critical for the transition between healthy and disease states. Expand
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.
TLDR
The sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages, provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects. Expand
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions
TLDR
A computational framework to integrate protein-protein interaction (PPI) networks and genetic screens to predict the 'signs' of interactions and identified an unexpected role for the metabolic enzymes enolase and aldo-keto reductase as positive and negative regulators of proteolysis, respectively. Expand
Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi
TLDR
A CRISPR-based method to generate homogeneous mutant Drosophila cell lines is developed and individual knockdown of three candidate genes had similar growth-inhibiting effects in mammalian TSC2-deficient cell lines, illustrating the power of this cross-species screening strategy to identify potential drug targets. Expand
Protein Complex–Based Analysis Framework for High-Throughput Data Sets
TLDR
An analysis framework based on protein complexes, which are at the core of network reorganization, is reported, which generated a protein complex resource for human, Drosophila, and yeast from the literature and databases of protein-protein interaction networks, with each species having thousands of complexes. Expand
UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents
TLDR
UP-TORR allows users to choose the mostappropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies. Expand
Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus
TLDR
Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome‐wide gene expression for both symbiotic and aposymbiotic anemones, but the genetic links between the anthozoan–algal symbioses and immunity in a two‐factor RNA‐Seq experiment did not observe strong interactions between symbiotic state and Vibri exposure. Expand
FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update
TLDR
Recent changes reflect a shift in the focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches. Expand
Transcriptomics reveals specific molecular mechanisms underlying transgenerational immunity in Manduca sexta
TLDR
It is shown that maternal exposure to both heat‐killed and live S. marcescens has strong and significant transgenerational impacts on gene expression patterns in their offspring, including upregulation of peptidoglycan recognition protein, toll‐like receptor 9, and the antimicrobial peptide cecropin. Expand
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