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"Essential gene

Jia-Hsin Huang, Yun Liu, Yu-Hsien Lin, Xavier Belles, How-Jing Lee
RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool operating by disruption of essential gene expression. Although different methods, such as injection, feeding, and soaking, have been reported for successful delivery of double-stranded RNA (dsRNA), the efficiency of RNAi through oral delivery of dsRNA is highly variable among different insect groups. The German cockroach, Blattella germanica, is highly sensitive to the injection of dsRNA, as shown by many studies published previously...
May 1, 2018: Journal of Visualized Experiments: JoVE
Azat Akhmetov, Jon M Laurent, Jimmy Gollihar, Elizabeth C Gardner, Riddhiman K Garge, Andrew D Ellington, Aashiq H Kachroo, Edward M Marcotte
Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended modification. Here, we describe a CRISPR-Cas9 mediated genome editing protocol for modifying any yeast gene of interest (either essential or nonessential) in a single-step transformation without any selectable marker...
March 20, 2018: Bio-protocol
Shinsuke Ohnuki, Yoshikazu Ohya
Haploinsufficiency, a dominant phenotype caused by a heterozygous loss-of-function mutation, has been rarely observed. However, high-dimensional single-cell phenotyping of yeast morphological characteristics revealed haploinsufficiency phenotypes for more than half of 1,112 essential genes under optimal growth conditions. Additionally, 40% of the essential genes with no obvious phenotype under optimal growth conditions displayed haploinsufficiency under severe growth conditions. Haploinsufficiency was detected more frequently in essential genes than in nonessential genes...
May 2018: PLoS Biology
Michal Breker, Kristi Lieberman, Frederick Cross
We generated a large collection of temperature-sensitive lethal mutants in the unicellular green alga Chlamydomonas reinhardtii, focusing on mutations specifically affecting cell cycle regulation. We used UV mutagenesis and robotically assisted phenotypic screening to isolate candidates. To overcome the bottleneck at the critical step of molecular identification of the causative mutation ('driver'), we developed MAPS-SEQ (Meiosis-Assisted Purifying Selection Sequencing), a multiplexed genetic/bioinformatics strategy...
May 9, 2018: Plant Cell
Kevin R Roy, Justin D Smith, Sibylle C Vonesch, Gen Lin, Chelsea Szu Tu, Alex R Lederer, Angela Chu, Sundari Suresh, Michelle Nguyen, Joe Horecka, Ashutosh Tripathi, Wallace T Burnett, Maddison A Morgan, Julia Schulz, Kevin M Orsley, Wu Wei, Raeka S Aiyar, Ronald W Davis, Vytas A Bankaitis, James E Haber, Marc L Salit, Robert P St Onge, Lars M Steinmetz
Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping...
May 7, 2018: Nature Biotechnology
Min Zhang, Chengqi Wang, Thomas D Otto, Jenna Oberstaller, Xiangyun Liao, Swamy R Adapa, Kenneth Udenze, Iraad F Bronner, Deborah Casandra, Matthew Mayho, Jacqueline Brown, Suzanne Li, Justin Swanson, Julian C Rayner, Rays H Y Jiang, John H Adams
Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro...
May 4, 2018: Science
Shervi Lie, Peter Banks, Conor Lawless, David Lydall, Janni Petersen
Nutrient fluctuations in the cellular environment promote changes in cell metabolism and growth to adapt cell proliferation accordingly. The target of rapamycin (TOR) signalling network plays a key role in the coordination of growth and cell proliferation with the nutrient environment and, importantly, nutrient limitation reduces TOR complex 1 (TORC1) signalling. We have performed global quantitative fitness profiling of the collection of Schizosaccharomyces pombe strains from which non-essential genes have been deleted...
May 2018: Open Biology
Jing Zhang, Qing Lan, Jiasheng Lin
BACKGROUND: Osteosarcoma is a type of bone cancer casting huge threat to the human health worldwide. Previously, gene expression analyses were performed to identify biomarkers for cancer; however, systemic co-expression analysis for osteosarcoma is still in need. The aim of this study was to construct a gene co-expression network that predicts clusters of candidate genes associated with the pathogenesis of osteosarcoma. METHODS: Here, we extracted the large scale of datasets from the GEO database...
May 2, 2018: World Journal of Surgical Oncology
Xiaojiang Zheng, Seock Kang, Yanping Jing, Zhijie Ren, Legong Li, Jian-Min Zhou, Gerald Berkowitz, Jisen Shi, Aigen Fu, Wenzhi Lan, Fugeng Zhao, Sheng Luan
The plant elicitor peptides (Peps), a family of damage/danger-associated molecular patterns (DAMPs), are perceived by two receptors, PEPR1 and PEPR2, and contribute to plant defense against pathogen attack and abiotic stress. Here we show that the Peps-PEPR signaling pathway functions in stomatal immunity by activating guard cell anion channels in Arabidopsis thaliana. The mutant plants lacking both PEPR1 and PEPR2 (pepr1 pepr2) displayed enhanced bacterial growth after being sprayed with Pseudomonas syringae pv...
April 30, 2018: Plant Cell
Yuan Gao, Nicolás M Suárez, Gavin S Wilkie, Chuanfu Dong, Sven Bergmann, Pei-Yu Alison Lee, Andrew J Davison, Alain F C Vanderplasschen, Maxime Boutier
Cyprinid herpesvirus 3 (CyHV-3) is the archetypal fish alloherpesvirus and the etiologic agent of a lethal disease in common and koi carp. To date, the genome sequences of only four CyHV-3 isolates have been published, but no comparisons of the biologic properties of these strains have been reported. We have sequenced the genomes of a further seven strains from various geographical sources, and have compared their growth in vitro and virulence in vivo. The major findings were: (i) the existence of the two genetic lineages previously described as European and Asian was confirmed, but inconsistencies between the geographic origin and genotype of some strains were revealed; (ii) potential inter-lineage recombination was detected in one strain, which also suggested the existence of a third, as yet unidentified lineage; (iii) analysis of genetic disruptions led to the identification of non-essential genes and their potential role in virulence; (iv) comparison of the in vitro and in vivo properties of strains belonging to the two lineages revealed that inter-lineage polymorphisms do not contribute to the differences in viral fitness observed; and (v) a negative correlation was observed among strains between viral growth in vitro and virulence in vivo...
May 2, 2018: Veterinary Research
Mitra Ataei, Fatemeh Akbarian, Mahba Ataei Talebi, Peyman Dolati, Maryam Mobaraki, Abolfazl Faraji, Massoud Houshmand
Background/aim: Infertility is a main health issue. The human Y chromosome contains essential genes for spermatogenesis, especially those located on four major intervals defined as AZFa, AZFb, AZFc, and AZFd. A partial deletion of the AZFc region is reported as a significant risk factor for oligo-/azoospermia. The main purpose of this study was to investigate the prevalence of partial deletions in the AZFc region (gr/gr, b1/b3, and b2/b3) in Iranian oligozoospermic candidates for intracytoplasmic sperm injection...
April 30, 2018: Turkish Journal of Medical Sciences
Aaron Seo, Orna Steinberg-Shemer, Sule Unal, Silvia Casadei, Tom Walsh, Fatma Gumruk, Stavit Shalev, Akiko Shimamura, Nurten Ayse Akarsu, Hannah Tamary, Mary-Claire King
BRCA1 is essential for repair of DNA double-strand breaks by homologous recombination, and hence for survival. Complete loss of its function is lethal during early embryonic development. Patients who are compound heterozygous for BRCA1 truncating mutations and missense alleles that retain some DNA repair capacity may survive, albeit with very high risk of early onset breast or ovarian cancer and features of Fanconi anemia. However, a mechanism enabling survival of patients homozygous for BRCA1 truncating mutations has not been described...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
M Carda-Diéguez, F X Silva-Hernández, T P Hubbard, M C Chao, M K Waldor, C Amaro
Vibrio vulnificus can be a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death. To survive and proliferate in blood, the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. We created a high-density transposon mutant library in YJ016, a strain representative of the most virulent V. vulnificus lineage (or phylogroup) and used transposon insertion sequencing (TIS) screens to identify loci that enable the pathogen to survive and proliferate in human serum...
April 26, 2018: Virulence
Kohei Taniguchi, Nobuhiko Sugito, Haruka Shinohara, Yuki Kuranaga, Yosuke Inomata, Kazumasa Komura, Kazuhisa Uchiyama, Yukihiro Akao
Pyruvate kinase is known as the glycolytic enzyme catalyzing the final step in glycolysis. In mammals, two different forms of it exist, i.e., pyruvate kinase M1/2 ( PKM ) and pyruvate kinase L/R ( PKLR ). Also, PKM has two isoforms, i.e., PKM1 and PKM2 . These genes have tissue-specific distribution. Namely, PKM1 is distributed in high-energy-demanding organs, such as brain and muscle. Also, PKM2 is distributed in various other organs, such as the colon. On the other hand, PKLR is distributed in liver and red blood cells (RBCs)...
April 24, 2018: International Journal of Molecular Sciences
Adi Yannai, Sophia Katz, Ruth Hershberg
Codon usage bias affects the genomes of organisms from all kingdoms of life, and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared to lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function...
April 23, 2018: Genome Biology and Evolution
Yan Zhu, Tobias Czauderna, Jinxin Zhao, Matthias Klapperstueck, Mohd Hafidz Mahamad Maifiah, Mei-Ling Han, Jing Lu, Björn Sommer, Tony Velkov, Trevor Lithgow, Jiangning Song, Falk Schreiber, Jian Li
Background: Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients, and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics, it is necessary to systematically understand how P. aeruginosa alters its metabolism in response to polymyxin treatment, thereby facilitating the development of effective therapies. To this end, a genome-scale metabolic model (GSMM) was used to analyze bacterial metabolic changes at the systems level...
April 1, 2018: GigaScience
Maddalena Dilucca, Giulio Cimini, Andrea Giansanti
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias...
April 17, 2018: Gene
Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda van Leeuwen, Elizabeth N Koch, Carles Pons, Andrius J Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo, Robbie Loewith, Amy Caudy, Daniel Bolnick, Grant W Brown, Brenda J Andrews, Charles Boone, Chad L Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions...
April 20, 2018: Science
Olivier Christiaens, Myriam G Tardajos, Zarel L Martinez Reyna, Mamoni Dash, Peter Dubruel, Guy Smagghe
Lepidoptera comprise some of the most devastating herbivorous pest insects worldwide. One of the most promising novel pest control strategies is exploiting the RNA interference (RNAi) mechanism to target essential genes for knockdown and incite toxic effects in the target species without harming other organisms in the ecosystem. However, many insects are refractory to oral RNAi, often due to rapid degradation of ingested dsRNA in their digestive system. This is the case for many lepidopteran insects, including the beet armyworm Spodoptera exigua , which is characterized by a very alkaline gut environment (pH > 9...
2018: Frontiers in Physiology
Darya Ausiannikava, Laura Mitchell, Hannah Marriott, Victoria Smith, Michelle Hawkins, Kira S Makarova, Eugene V Koonin, Conrad A Nieduszynski, Thorsten Allers
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: (1) mutational diversification of a multi-copy chromosome; (2) capture of a new chromosome by horizontal transfer; (3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination...
April 16, 2018: Molecular Biology and Evolution
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