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"Essential gene"

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https://www.readbyqxmd.com/read/28213355/chd1-is-a-synthetic-essential-gene-in-pten-deficient-prostate-cancer
#1
(no author information available yet)
CHD1 is required for the growth of PTEN-deficient prostate cancer cells in vitro and in vivo.
February 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28212095/identifying-bacterial-essential-genes-based-on-a-feature-integrated-method
#2
Yan Lin, Fa-Zhan Zhang, Kai Xue, Yi-Zhou Gao, Feng-Biao Guo
Essential genes are those genes of an organism that are considered to be crucial for its survival. Identification of essential genes is therefore of great significance to advance our understanding of the principles of cellular life. We have developed a novel computational method, which can effectively predict bacterial essential genes by extracting and integrating homologous features, protein domain feature, gene intrinsic features and network topological features. By performing the principal component regression (PCR) analysis for Escherichia coli MG1655, we established a classification model with the average area under curve (AUC) value of 0...
February 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28209762/identification-of-genes-in-saccharomyces-cerevisiae-that-are-haploinsufficient-for-overcoming-amino-acid-starvation
#3
Nancy S Bae, Andrew P Seberg, Leslie P Carroll, Mark J Swanson
The yeast Saccharomyces cerevisiae responds to amino acid deprivation by activating a pathway conserved in eukaryotes to overcome the starvation stress. We have screened the entire yeast heterozygous deletion collection to identify strains haploinsufficient for growth in the presence of sulfometuron methyl, which causes starvation for isoleucine and valine. We have discovered that cells devoid of MET15 are sensitive to sulfometuron methyl, and loss of heterozygosity at the MET15 locus can complicate screening the heterozygous deletion collection...
February 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#4
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196871/identification-of-a-transcriptional-activation-domain-in-yeast-repressor-activator-protein-1-rap1-using-an-altered-dna-binding-specificity-variant
#5
Amanda N Johnson, P Anthony Weil
Repressor Activator Protein 1 (Rap1) performs multiple vital cellular functions in the budding yeast Saccharomyces cerevisiae. These include regulation of telomere length, transcriptional repression of both telomere-proximal genes and the silent mating type loci, and transcriptional activation of hundreds of mRNA-encoding genes, including the highly transcribed ribosomal protein- and glycolytic enzyme-encoding genes. Studies of the contributions of Rap1 to telomere length regulation and transcriptional repression have yielded significant mechanistic insights...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193780/an-essential-gene-dataset-defines-functional-gene-networks
#6
(no author information available yet)
Gene essentiality pattern analysis can identify gene interactions and synthetic lethal interactions.
February 13, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28193152/a-fast-method-for-analyzing-essential-protein-mutants-in-human-cells
#7
Frank Dietsch, Mariel Donzeau, Agnes M Cordonnier, Etienne Weiss, Bruno Chatton, Marc Vigneron
Here we developed a complementation method for the study of essential genes in live human cells using the CRISPR/Cas9 system. Proteins encoded by essential genes were expressed using a derivative of the pCEP4 compensating plasmid in combination with Cas9 endonuclease targeting of the chromosomal genes. We show that this strategy can be applied to essential genes, such as those coding for proliferating cell nuclear antigen (PCNA) and DNA polymerase delta subunit 2 (POLD2). As demonstrated for the PCNA protein, our method allows mutational analysis of essential protein-coding sequences in live cells...
February 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28187184/the-finr-regulated-essential-gene-fpra-encoding-ferredoxin-nadp-reductase-roles-in-superoxide-mediated-stress-protection-and-virulence-of-pseudomonas-aeruginosa
#8
Siriwan Boonma, Adisak Romsang, Jintana Duang-Nkern, Sopapan Atichartpongkul, Wachareeporn Trinachartvanit, Paiboon Vattanaviboon, Skorn Mongkolsuk
Pseudomonas aeruginosa has two genes encoding ferredoxin NADP(+) reductases, denoted fprA and fprB. We show here that P. aeruginosa fprA is an essential gene. However, the ΔfprA mutant could only be successfully constructed in PAO1 strains containing an extra copy of fprA on a mini-Tn7 vector integrated into the chromosome or carrying it on a temperature-sensitive plasmid. The strain containing an extra copy of the ferredoxin gene (fdx1) could suppress the essentiality of FprA. Other ferredoxin genes could not suppress the requirement for FprA, suggesting that Fdx1 mediates the essentiality of FprA...
2017: PloS One
https://www.readbyqxmd.com/read/28179021/switch-a-dynamic-crispr-tool-for-genome-engineering-and-metabolic-pathway-control-for-cell-factory-construction-in-saccharomyces-cerevisiae
#9
Katherina García Vanegas, Beata Joanna Lehka, Uffe Hasbro Mortensen
BACKGROUND: The yeast Saccharomyces cerevisiae is increasingly used as a cell factory. However, cell factory construction time is a major obstacle towards using yeast for bio-production. Hence, tools to speed up cell factory construction are desirable. RESULTS: In this study, we have developed a new Cas9/dCas9 based system, SWITCH, which allows Saccharomyces cerevisiae strains to iteratively alternate between a genetic engineering state and a pathway control state...
February 8, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28178517/meiotic-knockdown-and-complementation-reveals-essential-role-of-rad51-in-mouse-spermatogenesis
#10
Jieqiong Dai, Oleg Voloshin, Svetlana Potapova, R Daniel Camerini-Otero
Meiotic homologous recombination (HR) is important for proper chromosomal segregation during gametogenesis and facilitates evolutionary adaptation via genomic reshuffling. In most eukaryotes, HR is mediated by two recombinases, the ubiquitous RAD51 and the meiosis-specific DMC1. The role of RAD51 in mammalian meiosis is unclear and study of its function is limited due to embryonic lethality of RAD51 knockouts. Here, we developed an in vivo meiotic knockdown and protein complementation system to study RAD51 during mouse spermatogenesis...
February 7, 2017: Cell Reports
https://www.readbyqxmd.com/read/28174266/low-escape-rate-genome-safeguards-with-minimal-molecular-perturbation-of-saccharomyces-cerevisiae
#11
Neta Agmon, Zuojian Tang, Kun Yang, Ben Sutter, Shigehito Ikushima, Yizhi Cai, Katrina Caravelli, James A Martin, Xiaoji Sun, Woo Jin Choi, Allen Zhang, Giovanni Stracquadanio, Haiping Hao, Benjamin P Tu, David Fenyo, Joel S Bader, Jef D Boeke
As the use of synthetic biology both in industry and in academia grows, there is an increasing need to ensure biocontainment. There is growing interest in engineering bacterial- and yeast-based safeguard (SG) strains. First-generation SGs were based on metabolic auxotrophy; however, the risk of cross-feeding and the cost of growth-controlling nutrients led researchers to look for other avenues. Recent strategies include bacteria engineered to be dependent on nonnatural amino acids and yeast SG strains that have both transcriptional- and recombinational-based biocontainment...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28167532/identification-of-a-membrane-protein-required-for-lipomannan-maturation-and-lipoarabinomannan-synthesis-in-corynebacterineae
#12
Tamaryn J Cashmore, Stephan Klatt, Yoshiki Yamaryo-Botte, Rajini Brammananth, Arek K Rainczuk, Malcolm J McConville, Paul K Crellin, Ross L Coppel
Mycobacterium tuberculosis and related Corynebacterineae synthesize a family of lipomannans (LM) and lipoarabinomannans (LAM) that are abundant components of the multilaminate cell wall and essential virulence factors in pathogenic species. Here we describe a new membrane protein, highly conserved in all Corynebacterineae, that is required for synthesis of full length LM and LAM. Deletion of the Corynebacterium glutamicum NCgl2760 gene resulted in a complete loss of mature LM/LAM, and the appearance of a truncated LM (t-LM)...
February 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28166537/synthetic-essentiality-of-chromatin-remodelling-factor-chd1-in-pten-deficient-cancer
#13
Di Zhao, Xin Lu, Guocan Wang, Zhengdao Lan, Wenting Liao, Jun Li, Xin Liang, Jasper Robin Chen, Sagar Shah, Xiaoying Shang, Ming Tang, Pingna Deng, Prasenjit Dey, Deepavali Chakravarti, Peiwen Chen, Denise J Spring, Nora M Navone, Patricia Troncoso, Jianhua Zhang, Y Alan Wang, Ronald A DePinho
Synthetic lethality and collateral lethality are two well-validated conceptual strategies for identifying therapeutic targets in cancers with tumour-suppressor gene deletions. Here, we explore an approach to identify potential synthetic-lethal interactions by screening mutually exclusive deletion patterns in cancer genomes. We sought to identify 'synthetic-essential' genes: those that are occasionally deleted in some cancers but are almost always retained in the context of a specific tumour-suppressor deficiency...
February 6, 2017: Nature
https://www.readbyqxmd.com/read/28165493/a-noise-trimming-and-positional-significance-of-transposon-insertion-system-to-identify-essential-genes-in-yersinia-pestis
#14
Zheng Rong Yang, Helen L Bullifent, Karen Moore, Konrad Paszkiewicz, Richard J Saint, Stephanie J Southern, Olivia L Champion, Nicola J Senior, Mitali Sarkar-Tyson, Petra C F Oyston, Timothy P Atkins, Richard W Titball
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28162770/gene-essentiality-profiling-reveals-gene-networks-and-synthetic-lethal-interactions-with-oncogenic-ras
#15
Tim Wang, Haiyan Yu, Nicholas W Hughes, Bingxu Liu, Arek Kendirli, Klara Klein, Walter W Chen, Eric S Lander, David M Sabatini
The genetic dependencies of human cancers widely vary. Here, we catalog this heterogeneity and use it to identify functional gene interactions and genotype-dependent liabilities in cancer. By using genome-wide CRISPR-based screens, we generate a gene essentiality dataset across 14 human acute myeloid leukemia (AML) cell lines. Sets of genes with correlated patterns of essentiality across the lines reveal new gene relationships, the essential substrates of enzymes, and the molecular functions of uncharacterized proteins...
February 1, 2017: Cell
https://www.readbyqxmd.com/read/28159753/requirements-for-driving-anti-pathogen-effector-genes-into-populations-of-disease-vectors-by-homing
#16
Andrea Beaghton, Andrew Hammond, Tony Nolan, Andrea Crisanti, H Charles J Godfray, Austin Burt
There is a need for new interventions against the on-going burden of vector-borne diseases such as malaria and dengue. One suggestion has been to develop genes encoding effector molecules that block parasite development within the vector, and then use the nuclease-based homing reaction as a form of gene drive to spread those genes through target populations. If the effector gene reduces the fitness of the mosquito and does not contribute to the drive, then loss-of-function mutations in the effector will eventually replace functional copies, but protection may nonetheless persist sufficiently long to provide a public health benefit...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28158612/accurate-prediction-of-human-essential-genes-using-only-nucleotide-composition-and-association-information
#17
Feng-Biao Guo, Chuan Dong, Hong-Li Hua, Shuo Liu, Hao Luo, Hong-Wan Zhang, Yan-Ting Jin, Kai-Yue Zhang
No abstract text is available yet for this article.
January 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28158450/infantile-neurodegenerative-disorder-associated-with-mutations-in-tbcd-an-essential-gene-in-the-tubulin-heterodimer-assembly-pathway
#18
Shimon Edvardson, Guoling Tian, Hayley Cullen, Hannah Vanyai, Linh Ngo, Saiuj Bhat, Adi Aran, Muhannad Daana, Naderah Da'amseh, Bassam Abu-Libdeh, Nicholas J Cowan, Julian Ik-Tsen Heng, Orly Elpeleg
No abstract text is available yet for this article.
November 1, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28154519/mining-the-proteome-of-fusobacterium-nucleatum-subsp-nucleatum-atcc-25586-for-potential-therapeutics-discovery-an-in-silico-approach
#19
Abdul Musaweer Habib, Md Saiful Islam, Md Sohel, Md Habibul Hasan Mazumder, Mohd Omar Faruk Sikder, Shah Md Shahik
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28148789/extreme-mutation-tolerance-nearly-half-of-the-archaeal-fusellovirus-ssv1-genes-are-not-required-for-virus-function-including-the-minor-capsid-protein-gene-vp3
#20
Eric A Iverson, David A Goodman, Madeline E Gorchels, Kenneth M Stedman
: Viruses infecting the Archaea harbor a tremendous amount of genetic diversity. This is especially true for the spindle-shaped viruses of the family Fuselloviridae, where >90% of the viral genes do not have detectable homologs in public databases. This significantly limits our ability to elucidate the role of viral proteins in the infection cycle. To address this, we have developed genetic techniques to study the well-characterized fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1) which infects Sulfolobus solfataricus in volcanic hot springs at 80°C and pH 3...
February 1, 2017: Journal of Virology
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