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"Essential gene

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https://www.readbyqxmd.com/read/28434086/the-inability-of-bacillus-licheniformis-perr-mutant-to-grow-is-mainly-due-to-the-lack-of-perr-mediated-fur-repression
#1
Jung-Hoon Kim, Yoon-Mo Yang, Chang-Jun Ji, Su-Hyun Ryu, Young-Bin Won, Shin-Yeong Ju, Yumi Kwon, Yeh-Eun Lee, Hwan Youn, Jin-Won Lee
PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes involved in peroxide stress response. Industrially important bacterium Bacillus licheniformis contains three PerR-like proteins (PerRBL, PerR2, and PerR3) compared to its close relative Bacillus subtilis. Interestingly, unlike other bacteria including B. subtilis, no authentic perR BL null mutant could be established for B. licheniformis. Thus, we constructed a conditional perR BL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28431907/telomere-shortening-during-aging-attenuation-by-antioxidants-and-anti-inflammatory-agents
#2
REVIEW
Kedar N Prasad, Meixia Wu, Stephen C Bondy
Telomeres are a repeated sequence -of bases found at the ends of chromosomes. In humans, this sequence is TTAGGG, which is repeated over 2000 times. Telomeres protect the ends chromosomes from fusion with nearby chromosomes, and allow effective replication of DNA. Each time a cell divides, 25-200 base pairs are lost from the terminal sequence of chromosomes. By becoming truncated during cell division, telomeres protect essential genes from being shortened and thus inactivated. In addition, telomeres are sensitive to inflammation and oxidative stress, which can further promote telomere shortening...
April 18, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28429771/crispr-cas9-mediated-genome-editing-in-one-blastomere-of-two-cell-embryos-reveals-a-novel-tet3-function-in-regulating-neocortical-development
#3
Lingbo Wang, Min-Yin Li, Chao Qu, Wan-Ying Miao, Qi Yin, Jiaoyang Liao, Hua-Teng Cao, Min Huang, Kai Wang, Erwei Zuo, Guangdun Peng, Shu-Xin Zhang, Guodong Chen, Qing Li, Ke Tang, Qian Yu, Zhoujie Li, Catherine Cl Wong, Guoliang Xu, Naihe Jing, Xiang Yu, Jinsong Li
Studying the early function of essential genes is an important and challenging problem in developmental biology. Here, we established a method for rapidly inducing CRISPR-Cas9-mediated mutations in one blastomere of two-cell stage embryos, termed 2-cell embryo-CRISPR-Cas9 injection (2CC), to study the in vivo function of essential (or unknown) genes in founder chimeric mice. By injecting both Cre mRNA and CRISPR-Cas9 targeting the gene of interest into fluorescent reporter mice, the 2CC method can trace both wild-type and mutant cells at different developmental stages, offering internal control for phenotypic analyses of mutant cells...
April 21, 2017: Cell Research
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#4
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28423708/targeting-the-centriolar-replication-factor-stil-synergizes-with-dna-damaging-agents-for-treatment-of-ovarian-cancer
#5
Noa Rabinowicz, Lingegowda S Mangala, Kevin R Brown, Cintia Checa-Rodriguez, Asher Castiel, Oren Moskovich, Giulia Zarfati, Luba Trakhtenbrot, Adva Levy-Barda, Dahai Jiang, Cristian Rodriguez-Aguayo, Sunila Pradeep, Yael van Praag, Gabriel Lopez-Berestein, Ahuvit David, Ilya Novikov, Pablo Huertas, Robert Rottapel, Anil K Sood, Shai Izraeli
Advanced ovarian cancer is an incurable disease. Thus, novel therapies are required. We wished to identify new therapeutic targets for ovarian cancer. ShRNA screen performed in 42 ovarian cancer cell lines identified the centriolar replication factor STIL as an essential gene for ovarian cancer cells. This was verified in-vivo in orthotopic human ovarian cancer mouse models. STIL depletion by administration of siRNA in neutral liposomes resulted in robust anti-tumor effect that was further enhanced in combination with cisplatin...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28411883/horning-cell-self-digestion-autophagy-wins-the%C3%A2-2016-nobel-prize-in-physiology-or-medicine
#6
EDITORIAL
Po-Yuan Ke
Autophagy is an evolutionarily conserved process by which eukaryotic cells eliminate intracellular components via the lysosomal degradation process. This cell self-digestion process was first discovered and morphologically characterized in the late 1950s and early 1960s. The genetic screen studies in baker's yeast in the 1990s further identified the essential genes functioning in the autophagic process. In the past two decades, the detailed molecular process involved in the completion of autophagy was delineated...
February 2017: Biomedical Journal
https://www.readbyqxmd.com/read/28411216/construction-of-a-dcas9-based-gene-knockdown-system-in-staphylococcus-aureus
#7
Changlong Zhao, Xueqin Shu, Baolin Sun
There has been constant absence of an efficient gene knockdown method in the important human pathogen Staphylococcus aureus like RNA interference in eukaryotes. The early developed antisense RNA technology is mainly applied for forward genetic screen, but is rather limiting in specific gene knockdown for the lack of rational antisense RNA design strategies. Here we report an efficient and specific gene knockdown system in S. aureus based on type II clustered regularly interspaced short palindromic repeats (CRISPR) system from Streptococcus pyogenes...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28407093/non-random-inversion-landscapes-in-prokaryotic-genomes-are-shaped-by-heterogeneous-selection-pressures
#8
Jelena Repar, Tobias Warnecke
Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased towards (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favouring symmetric rearrangements in archaea with a single origin of replication...
April 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28399968/tuberculosis-resistance-conferring-mutations-with-fitness-cost-among-hiv-positive-individuals-in-uganda
#9
W Ssengooba, D Lukoye, C J Meehan, D P Kateete, M L Joloba, B C de Jong, F G Cobelens, F van Leth
BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) is considered to be less transmissible due to the fitness cost associated with drug resistance-conferring mutations in essential genes. OBJECTIVE: To test the hypothesis that TB drug resistance-conferring mutations with fitness cost are more frequent among human immunodeficiency virus (HIV) positive than among HIV-negative patients. DESIGN: We analysed all strains from the two TB drug resistance surveys conducted in Uganda between 2008 and 2011...
May 1, 2017: International Journal of Tuberculosis and Lung Disease
https://www.readbyqxmd.com/read/28398605/identification-of-key-gene-modules-for-in-human-osteosarcoma-by-co-expression-analysis-weighted-gene-coexpression-network-analysis-wgcna
#10
Xiangsheng Liu, Ai-Xin Hu, Jia-Li Zhao, Feng-Li Chen
Osteosarcoma is the eighth-most common form of childhood cancer, comprising about 20% of all primary bone cancers. To date, systemic co-expression analysis for this cancer is still insufficient to explain the pathogenesis of poorly understood OC. The objective of this study was to construct a gene co-expression network to predict clusters of candidate genes involved in the pathogenesis of osteosarcoma. First, we contributed co-expression modules via weighted gene co-expression network analysis (WGCNA) and investigated the functional enrichment analysis of co-expression genes in terms of GO and KEGG...
April 11, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28397356/links-between-critical-proteins-drive-the-controllability-of-protein-interaction-networks
#11
Stefan Wuchty, Toni Boltz, Hande Küçük-McGinty
Focusing on the interactomes of H. sapiens, S. cerevisiae, and E. coli, we investigated interactions between controlling proteins. In particular, we determined critical, intermittent, and redundant proteins based on their tendency to participate in minimum dominating sets (MDSets). Independently of the organisms considered, we found that interactions that involved critical nodes had the most prominent effects on the topology of their corresponding networks. Furthermore, we observed that phosphorylation and regulatory events were considerably enriched when the corresponding transcription factors and kinases were critical proteins, while such interactions were depleted when they were redundant proteins...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28386168/differences-between-flocculating-yeast-and-regular-industrial-yeast-in-transcription-and-metabolite-profiling-during-ethanol-fermentation
#12
Lili Li, Xiaoning Wang, Xudong Jiao, Song Qin
Objectives: To improve ethanolic fermentation performance of self-flocculating yeast, difference between a flocculating yeast strain and a regular industrial yeast strain was analyzed by transcriptional and metabolic approaches. Results: The number of down-regulated (industrial yeast YIC10 vs. flocculating yeast GIM2.71) and up-regulated genes were 4503 and 228, respectively. It is the economic regulation for YIC10 that non-essential genes were down-regulated, and cells put more "energy" into growth and ethanol production...
March 2017: Saudi Journal of Biological Sciences
https://www.readbyqxmd.com/read/28375518/generation-and-validation-of-the-ikp1289-metabolic-model-for-klebsiella-pneumoniae-kppr1
#13
Christopher S Henry, Ella Rotman, Wyndham W Lathem, Keith E J Tyo, Alan R Hauser, Mark J Mandel
Klebsiella pneumoniae has a reputation for causing a wide range of infectious conditions, with numerous highly virulent and antibiotic-resistant strains. Metabolic models have the potential to provide insights into the growth behavior, nutrient requirements, essential genes, and candidate drug targets in these strains. Here we develop a metabolic model for KPPR1, a highly virulent strain of K. pneumoniae. We apply a combination of Biolog phenotype data and fitness data to validate and refine our KPPR1 model...
February 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28369650/genome-urbanization-clusters-of-topologically-co-regulated-genes-delineate-functional-compartments-in-the-genome-of-saccharomyces-cerevisiae
#14
Maria Tsochatzidou, Maria Malliarou, Nikolas Papanikolaou, Joaquim Roca, Christoforos Nikolaou
The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II (topoII). By analyzing a genome-wide transcription run-on experiment upon thermal inactivation of topoII in Saccharomyces cerevisiae we were able to define 116 gene clusters of consistent response (either positive or negative) to topological stress...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28368806/analysis-of-organization-of-the-interactome-using-dominating-sets-a-case-study-on-cell-cycle-interaction-networks
#15
Huiru Zheng, Chaoyang Wang, Haiying Wang
In this study, a minimum dominating set based approach was developed and implemented as a Cytoscape plugin to identify critical and redundant proteins in a protein interaction network. We focused on the investigation of the properties associated with critical proteins in the context of the analysis of interaction networks specific to cell cycle in both yeast and human. A total of 132 yeast genes and 129 human proteins have been identified as critical nodes while 950 in yeast and 980 in human have been categorized as redundant nodes...
March 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28367572/a-systematic-reconstruction-and-constraint-based-analysis-of-leishmania-donovani-metabolic-network-identification-of-potential-antileishmanial-drug-targets
#16
Mahesh Sharma, Naeem Shaikh, Shailendra Yadav, Sushma Singh, Prabha Garg
Visceral leishmaniasis, a lethal parasitic disease, is caused by the protozoan parasite Leishmania donovani. The absence of an effective vaccine, drug toxicity and parasite resistance necessitates the identification of novel drug targets. Reconstruction of genome-scale metabolic models and their simulation has been established as an important tool for systems-level understanding of a microorganism's metabolism. In this work, amalgamating the tools and techniques of computational systems biology with rigorous manual curation, a constraint-based metabolic model for Leishmania donovani BPK282A1 has been developed...
April 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28360929/talen-mediated-genome-editing-approaches-in-the-liverwort-marchantia-polymorpha-yield-high-efficiencies-for-targeted-mutagenesis
#17
Sarah Kopischke, Esther Schüßler, Felix Althoff, Sabine Zachgo
BACKGROUND: The liverwort Marchantia polymorpha occupies a crucial position in land plant evolution and provides the opportunity to investigate adaptations to a terrestrial plant life style. Marchantia reverse genetic analyses have thus far been conducted by employing a homologous recombination approach, which yields an efficiency of around 3%. Availability of the characterized and suitable endogenous MpEF1α promoter prompted us to establish the TALEN gene targeting technique for Marchantia...
2017: Plant Methods
https://www.readbyqxmd.com/read/28358836/selection-of-key-sequence-based-features-for-prediction-of-essential-genes-in-31-diverse-bacterial-species
#18
Xiao Liu, Bao-Jin Wang, Luo Xu, Hong-Ling Tang, Guo-Qing Xu
Genes that are indispensable for survival are essential genes. Many features have been proposed for computational prediction of essential genes. In this paper, the least absolute shrinkage and selection operator method was used to screen key sequence-based features related to gene essentiality. To assess the effects, the selected features were used to predict the essential genes from 31 bacterial species based on a support vector machine classifier. For all 31 bacterial objects (21 Gram-negative objects and ten Gram-positive objects), the features in the three datasets were reduced from 57, 59, and 58, to 40, 37, and 38, respectively, without loss of prediction accuracy...
2017: PloS One
https://www.readbyqxmd.com/read/28357319/phylogenetic-profiles-of-all-membrane-transport-proteins
#19
January Weiner, Taco W A Kooij
In order to combat the on-going malaria epidemic, discovery of new drug targets remains vital. Proteins that are essential to survival and specific to malaria parasites are key candidates. To survive within host cells, the parasites need to acquire nutrients and dispose of waste products across multiple membranes. Additionally, like all eukaryotes, they must redistribute ions and organic molecules between their various internal membrane bound compartments. Membrane transport proteins mediate all of these processes and are considered important mediators of drug resistance as well as drug targets in their own right...
August 30, 2016: Microbial Cell
https://www.readbyqxmd.com/read/28348033/minimal-cells-real-and-imagined
#20
John I Glass, Chuck Merryman, Kim S Wise, Clyde A Hutchison, Hamilton O Smith
A minimal cell is one whose genome only encodes the minimal set of genes necessary for the cell to survive. Scientific reductionism postulates the best way to learn the first principles of cellular biology would be to use a minimal cell in which the functions of all genes and components are understood. The genes in a minimal cell are, by definition, essential. In 2016, synthesis of a genome comprised of only the set of essential and quasi-essential genes encoded by the bacterium Mycoplasma mycoides created a near-minimal bacterial cell...
March 27, 2017: Cold Spring Harbor Perspectives in Biology
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