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1 / 1964

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[PMID]: 29391275 [Au] Autor: Yang X; Wang J; Bing G; Bie P; De Y; Lyu Y; Wu Q [Ad] Endereço: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China. [Ti] Título: Ortholog-based screening and identification of genes related to intracellular survival. [So] Source: Gene;651:134-142, 2018 Apr 20. [Is] ISSN: 1879-0038 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival. Only 19 clusters were present in facultative intracellular pathogens, and not all were present in extracellular pathogens. Construction of a phylogenetic tree selected 18 of these 19 clusters. Comparisons with the DEG database and previous research revealed that seven other clusters are considered essential gene clusters and that seven other clusters are associated with intracellular survival. Moreover, this study confirmed that clusters screened by orthologs with similar function could be replaced with an approved uvrY gene and its orthologs, and the results revealed that the usg gene is associated with intracellular survival. The study improves the current understanding of intracellular pathogens characteristics and allows further exploration of the intracellular survival-related gene modules in these pathogens. [Mh] Termos MeSH primário: Bactérias/genética Fenômenos Fisiológicos Bacterianos Células/microbiologia Genes Bacterianos [Mh] Termos MeSH secundário: Animais Proteínas de Bactérias/genética Proteínas de Bactérias/fisiologia Células Cultivadas Genes Essenciais Interações Hospedeiro-Patógeno Camundongos Família Multigênica Filogenia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180203 [St] Status: MEDLINE

2 / 1964

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[PMID]: 28454689 [Au] Autor: Steinhauser CB; Wing TT; Gao H; Li X; Burghardt RC; Wu G; Bazer FW; Johnson GA [Ad] Endereço: Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, TX 77843-4458, USA. [Ti] Título: Identification of appropriate reference genes for qPCR analyses of placental expression of SLC7A3 and induction of SLC5A1 in porcine endometrium. [So] Source: Placenta;52:1-9, 2017 Apr. [Is] ISSN: 1532-3102 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: INTRODUCTION: Endometria and placentae undergo developmental changes that affect the stability of genes used as references for normalization of qPCR data. We identified genes that are stable within the porcine endometrium and placenta throughout pregnancy, and elucidated the temporal/spatial mRNA localization of the glucose and arginine transporters, solute carrier family (SLC) 5A1 and SLC7A3, respectively. MATERIALS AND METHODS: qPCR was performed for 10 genes within porcine endometria from Days 5, 11, and 15 of the estrous cycle and 11, 15, 25, 40, 60, and 85 of pregnancy; and chorioallantois from Days 30, 35, 45, 50, 60, and 85. Gene stability was analyzed using GeNorm and NormFinder algorithms. qPCR and in situ hybridization determined temporal/spatial localization of SLC5A1 and SLC7A3 at the uterine-placental interface. RESULTS: The geometric mean of TATA-binding protein (TBP), hypoxanthine phosphoribosyl transferase 1 (HPRT1), and tubulin alpha 1B (TUBA1B) provides acceptable reference values for porcine placenta. The geometric mean of TBP, beta actin (ACTB), and succinate dehydrogenase complex subunit A flavoprotein (SDHA) is acceptable for endometria. SLC5A1 is induced by estrogen in endometrial luminal epithelium (LE) on Days 12 and 13 of pregnancy. SLC7A3 is expressed in the chorion. DISCUSSION AND CONCLUSION: Using appropriate reference genes resulted in complementary results between qPCR and in situ hybridization techniques for SLC5A1 and SLC7A3 mRNAs. SLC5A1 is induced in uterine LE by estrogen of trophectoderm origin when the blastocyst is free-floating and dependent on glucose from the endometrium, and SLC7A3 is expressed by the established placenta to support fetal growth. [Mh] Termos MeSH primário: Sistemas de Transporte de Aminoácidos Básicos/metabolismo Endométrio/metabolismo Genes Essenciais Placenta/metabolismo Reação em Cadeia da Polimerase em Tempo Real/métodos Transportador 1 de Glucose-Sódio/metabolismo [Mh] Termos MeSH secundário: Sistemas de Transporte de Aminoácidos Básicos/genética Animais Feminino Gravidez Transportador 1 de Glucose-Sódio/genética Suínos [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Amino Acid Transport Systems, Basic); 0 (Sodium-Glucose Transporter 1) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180305 [Lr] Data última revisão: 180305 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170430 [St] Status: MEDLINE

3 / 1964

MEDLINE

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[PMID]: 29385205 [Au] Autor: Di Paola N; Freire CCM; Zanotto PMA [Ad] Endereço: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil. [Ti] Título: Does adaptation to vertebrate codon usage relate to flavivirus emergence potential? [So] Source: PLoS One;13(1):e0191652, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher CAI towards the host has been associated with higher viral titers, we explored temporal trends of several historic and extensively sequenced zoonotic flaviviruses and relationships within the genus itself. To showcase evolutionary and epidemiological relationships associated with silent, adaptive synonymous changes of viruses, we used codon usage tables from human housekeeping and antiviral immune genes, as well as tables from arthropod vectors and vertebrate species involved in the flavivirus maintenance cycle. We argue that temporal trends of CAI changes could lead to a better understanding of zoonotic emergences, evolutionary dynamics, and host adaptation. CAI appears to help illustrate historically relevant trends of well-characterized viruses, in different viral species and genetic diversity within a single species. CAI can be a useful tool together with in vivo and in vitro kinetics, phylodynamics, and additional functional genomics studies to better understand species trafficking and viral emergence in a new host. [Mh] Termos MeSH primário: Códon/genética Flavivirus/genética Flavivirus/patogenicidade [Mh] Termos MeSH secundário: Adaptação Fisiológica Aedes/genética Aedes/virologia Animais Culex/genética Culex/virologia Vírus da Dengue/genética Vírus da Dengue/patogenicidade Vírus da Dengue/fisiologia Evolução Molecular Flavivirus/fisiologia Genes Essenciais Genoma Viral Interações Hospedeiro-Patógeno/genética Seres Humanos Mosquitos Vetores/genética Mosquitos Vetores/virologia Filogenia Vírus do Mosaico do Tabaco/genética Vírus do Mosaico do Tabaco/patogenicidade Vírus do Mosaico do Tabaco/fisiologia Vertebrados/genética Vertebrados/virologia Vírus do Nilo Ocidental/genética Vírus do Nilo Ocidental/patogenicidade Vírus do Nilo Ocidental/fisiologia Vírus da Febre Amarela/genética Vírus da Febre Amarela/patogenicidade Vírus da Febre Amarela/fisiologia [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Codon) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180302 [Lr] Data última revisão: 180302 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180201 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0191652

4 / 1964

MEDLINE

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[PMID]: 29329327 [Au] Autor: Singh S; Gupta M; Pandher S; Kaur G; Rathore P; Palli SR [Ad] Endereço: Punjab Agricultural University, Regional Station, Faridkot, Punjab, India. [Ti] Título: Selection of housekeeping genes and demonstration of RNAi in cotton leafhopper, Amrasca biguttula biguttula (Ishida). [So] Source: PLoS One;13(1):e0191116, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Amrasca biguttula biguttula (Ishida) commonly known as cotton leafhopper is a severe pest of cotton and okra. Not much is known on this insect at molecular level due to lack of genomic and transcriptomic data. To prepare for functional genomic studies in this insect, we evaluated 15 common housekeeping genes (Tub, B-Tub, EF alpha, GADPH, UbiCF, RP13, Ubiq, G3PD, VATPase, Actin, 18s, 28s, TATA, ETF, SOD and Cytolytic actin) during different developmental stages and under starvation stress. We selected early (1st and 2nd), late (3rd and 4th) stage nymphs and adults for identification of stable housekeeping genes using geNorm, NormFinder, BestKeeper and RefFinder software. Based on the different algorithms, RP13 and VATPase are identified as the most suitable reference genes for quantification of gene expression by reverse transcriptase quantitative PCR (RT-qPCR). Based on RefFinder which comprehended the results of three algorithms, RP13 in adults, Tubulin (Tub) in late nymphs, 28S in early nymph and UbiCF under starvation stress were identified as the most stable genes. We also developed methods for feeding double-stranded RNA (dsRNA) incorporated in the diet. Feeding dsRNA targeting Snf7, IAP, AQP1, and VATPase caused 56.17-77.12% knockdown of targeted genes compared to control and 16 to 48% mortality of treated insects when compared to control. [Mh] Termos MeSH primário: Genes Essenciais Genes de Insetos Gossypium/parasitologia Hemípteros/genética Interferência de RNA [Mh] Termos MeSH secundário: Animais Perfilação da Expressão Gênica [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180215 [Lr] Data última revisão: 180215 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180113 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0191116

5 / 1964

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[PMID]: 29293080 [Au] Autor: Larssen KW; Nor A; Bergh K [Ad] Endereço: 1​Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway. [Ti] Título: Rapid discrimination of Staphylococcus epidermidis genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes. [So] Source: J Med Microbiol;67(2):169-182, 2018 Feb. [Is] ISSN: 1473-5644 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: PURPOSE: Staphylococcus epidermidis colonies often display several morphologies and antimicrobial susceptibility patterns when cultured from device-related infections, and may represent one or multiple genotypes. Genotyping may be helpful in the clinical interpretation, but is time consuming and expensive. We wanted to establish a method for rapid discrimination of S. epidermidis genotypes for use in a routine microbiology laboratory. METHODOLOGY: A real-time PCR targeting eight discriminatory class I or II single-nucleotide polymorphisms (SNPs) in six of the seven housekeeping genes was constructed. Post PCR, high-resolution melt (HRM) analysis using EvaGreen as fluorophore discriminated amplicons based on their percentage GC content. RESULTS: In silico, 42 representative sequence types (STs), including all major MLST group and subgroup founders, were separated into 23 different cluster profiles with a Simpson's index of diversity of 0.97. By HRM-PCR, 11 commonly encountered hospital and outbreak STs were separated into eight HRM patterns. CONCLUSION: This method can rapidly establish whether S. epidermidis strains belong to different genotypes. It can be used in patients with S. epidermidis infections, as an aid in outbreak investigations and to select strains for investigation with more discriminatory methods, saving workload and costs. Results may be obtained the same day as culture results. Its strength lies mainly in indicating differences, as some STs may have the same melt profile. Changes in S. epidermidis epidemiology may warrant alterations in the inclusion of SNPs. We believe this method can reduce the threshold for performing genotyping analysis on an increasingly important nosocomial pathogen. [Mh] Termos MeSH primário: Técnicas de Tipagem Bacteriana/métodos Polimorfismo de Nucleotídeo Único Reação em Cadeia da Polimerase em Tempo Real Infecções Estafilocócicas/microbiologia Staphylococcus epidermidis/genética [Mh] Termos MeSH secundário: Infecção Hospitalar/diagnóstico Infecção Hospitalar/microbiologia DNA Bacteriano Genes Essenciais Genótipo Seres Humanos Tipagem de Sequências Multilocus Infecções Estafilocócicas/diagnóstico Staphylococcus epidermidis/classificação Staphylococcus epidermidis/isolamento & purificação [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Bacterial) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180206 [Lr] Data última revisão: 180206 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180103 [St] Status: MEDLINE [do] DOI: 10.1099/jmm.0.000663

6 / 1964

MEDLINE

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[PMID]: 29219067 [Au] Autor: Fan Y; Tang X; Hu X; Wu W; Ping Q [Ad] Endereço: School of Mathematics, Liaoning University, Shenyang, 110036, China. [Ti] Título: Prediction of essential proteins based on subcellular localization and gene expression correlation. [So] Source: BMC Bioinformatics;18(Suppl 13):470, 2017 Dec 01. [Is] ISSN: 1471-2105 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: BACKGROUND: Essential proteins are indispensable to the survival and development process of living organisms. To understand the functional mechanisms of essential proteins, which can be applied to the analysis of disease and design of drugs, it is important to identify essential proteins from a set of proteins first. As traditional experimental methods designed to test out essential proteins are usually expensive and laborious, computational methods, which utilize biological and topological features of proteins, have attracted more attention in recent years. Protein-protein interaction networks, together with other biological data, have been explored to improve the performance of essential protein prediction. RESULTS: The proposed method SCP is evaluated on Saccharomyces cerevisiae datasets and compared with five other methods. The results show that our method SCP outperforms the other five methods in terms of accuracy of essential protein prediction. CONCLUSIONS: In this paper, we propose a novel algorithm named SCP, which combines the ranking by a modified PageRank algorithm based on subcellular compartments information, with the ranking by Pearson correlation coefficient (PCC) calculated from gene expression data. Experiments show that subcellular localization information is promising in boosting essential protein prediction. [Mh] Termos MeSH primário: Algoritmos Biologia Computacional/métodos Regulação Fúngica da Expressão Gênica Genes Essenciais Mapas de Interação de Proteínas Proteínas de Saccharomyces cerevisiae/metabolismo Saccharomyces cerevisiae/metabolismo [Mh] Termos MeSH secundário: Saccharomyces cerevisiae/genética Proteínas de Saccharomyces cerevisiae/genética Frações Subcelulares [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Saccharomyces cerevisiae Proteins) [Em] Mês de entrada: 1801 [Cu] Atualização por classe: 180130 [Lr] Data última revisão: 180130 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171209 [St] Status: MEDLINE [do] DOI: 10.1186/s12859-017-1876-5

7 / 1964

MEDLINE

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[PMID]: 28963003 [Au] Autor: Mukherjee RP; Fruchtl MS; Beitle RR; Brune EM [Ad] Endereço: Ralph E. Martin Department of Chemical Engineering, Bell Engineering Center, University of Arkansas, Fayetteville, AR 72701, USA. [Ti] Título: Development of a novel engineered E. coli host cell line platform with improved column capacity performance for ion-exchange chromatography. [So] Source: Protein Expr Purif;142:32-36, 2018 Feb. [Is] ISSN: 1096-0279 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: This article reports on the analysis of an engineered Escherichia coli designed to reduce the host cell protein (HCP) burden on recombinant protein purification by column chromatography. Since downstream purification accounts for a major portion of production costs when using a recombinant platform, minimization of HCPs that are initially captured or otherwise interfere during chromatography will positively impact the entire purification process. Such a strategy, of course, would also require the cell line to grow, and express recombinant proteins, at levels comparable to, or better than, its parent strain. An E. coli strain with a small number of strategic deletions (LTSF06) was transformed to produce three different recombinant biologics to examine growth and expression, and with another model protein to assess growth and the effect of selectively reduced HCPs on target product capture on DEAE ion exchange medium. Cell growth levels were maintained or increased for all constructs, and a significant reduction in HCP adsorption was realized. Indeed, a breakthrough analysis indicated that as a result of reducing adsorption of particular HCPs, a 37% increase in target protein capture was observed. This increase in product capture efficiency was achieved by focusing not on HCPs that co-elute with the recombinant target, but rather on those possessing particular column adsorption and elution characteristics. [Mh] Termos MeSH primário: Escherichia coli/genética Deleção de Genes Genes Bacterianos Engenharia Metabólica/métodos [Mh] Termos MeSH secundário: Adsorção Técnicas de Cultura Celular por Lotes Cromatografia por Troca Iônica Escherichia coli/metabolismo Expressão Gênica Genes Essenciais Vetores Genéticos/química Vetores Genéticos/metabolismo Proteínas Recombinantes/biossíntese Proteínas Recombinantes/genética Proteínas Recombinantes/isolamento & purificação [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Recombinant Proteins) [Em] Mês de entrada: 1711 [Cu] Atualização por classe: 171128 [Lr] Data última revisão: 171128 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171001 [St] Status: MEDLINE

8 / 1964

MEDLINE

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[PMID]: 28976972 [Au] Autor: Hammond AM; Kyrou K; Bruttini M; North A; Galizi R; Karlsson X; Kranjc N; Carpi FM; D'Aurizio R; Crisanti A; Nolan T [Ad] Endereço: Dept. of Life Sciences, Imperial College London, London, United Kingdom. [Ti] Título: The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito. [So] Source: PLoS Genet;13(10):e1007039, 2017 Oct. [Is] ISSN: 1553-7404 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Gene drives have enormous potential for the control of insect populations of medical and agricultural relevance. By preferentially biasing their own inheritance, gene drives can rapidly introduce genetic traits even if these confer a negative fitness effect on the population. We have recently developed gene drives based on CRISPR nuclease constructs that are designed to disrupt key genes essential for female fertility in the malaria mosquito. The construct copies itself and the associated genetic disruption from one homologous chromosome to another during gamete formation, a process called homing that ensures the majority of offspring inherit the drive. Such drives have the potential to cause long-lasting, sustainable population suppression, though they are also expected to impose a large selection pressure for resistance in the mosquito. One of these population suppression gene drives showed rapid invasion of a caged population over 4 generations, establishing proof of principle for this technology. In order to assess the potential for the emergence of resistance to the gene drive in this population we allowed it to run for 25 generations and monitored the frequency of the gene drive over time. Following the initial increase of the gene drive we observed a gradual decrease in its frequency that was accompanied by the spread of small, nuclease-induced mutations at the target gene that are resistant to further cleavage and restore its functionality. Such mutations showed rates of increase consistent with positive selection in the face of the gene drive. Our findings represent the first documented example of selection for resistance to a synthetic gene drive and lead to important design recommendations and considerations in order to mitigate for resistance in future gene drive applications. [Mh] Termos MeSH primário: Anopheles/genética Genes Essenciais Genética Populacional Seleção Genética [Mh] Termos MeSH secundário: Alelos Sequência de Aminoácidos Animais Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética Feminino Fertilidade/genética Frequência do Gene Biblioteca Gênica Engenharia Genética Haplótipos Sequenciamento de Nucleotídeos em Larga Escala Insetos Vetores/genética Malária/prevenção & controle Masculino Modelos Genéticos Controle de Mosquitos/métodos Mutação Análise de Sequência de RNA [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171116 [Lr] Data última revisão: 171116 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171005 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pgen.1007039

9 / 1964

MEDLINE

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[PMID]: 28910375 [Au] Autor: Maheshwari Y; Selvaraj V; Hajeri S; Yokomi R [Ad] Endereço: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America. [Ti] Título: Application of droplet digital PCR for quantitative detection of Spiroplasma citri in comparison with real time PCR. [So] Source: PLoS One;12(9):e0184751, 2017. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Droplet digital polymerase chain reaction (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD) in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative) PCR (qPCR) for S. citri detection in citrus tissues. Standard curve analyses on tenfold dilution series showed that both ddPCR and qPCR exhibited good linearity and efficiency. However, ddPCR had a tenfold greater sensitivity than qPCR and accurately quantified up to one copy of spiralin gene. Receiver operating characteristic analysis indicated that the ddPCR methodology was more robust for diagnosis of CSD and the area under the curve was significantly broader compared to qPCR. Field samples were used to validate ddPCR efficacy and demonstrated that it was equal or better than qPCR to detect S. citri infection in fruit columella due to a higher pathogen titer. The ddPCR assay detected both the S. citri spiralin and the SpV1 ORF1 targets quantitatively with high precision and accuracy compared to qPCR assay. The ddPCR was highly reproducible and repeatable for both the targets and showed higher resilience to PCR inhibitors in citrus tissue extract for the quantification of S. citri compare to qPCR. [Mh] Termos MeSH primário: Proteínas de Bactérias/genética Citrus/microbiologia Reação em Cadeia da Polimerase/métodos Spiroplasma citri/isolamento & purificação [Mh] Termos MeSH secundário: Primers do DNA/genética Genes Essenciais Doenças das Plantas/microbiologia Curva ROC Sensibilidade e Especificidade Spiroplasma citri/genética [Pt] Tipo de publicação: COMPARATIVE STUDY; JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (DNA Primers) [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171017 [Lr] Data última revisão: 171017 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170915 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0184751

10 / 1964

MEDLINE

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[PMID]: 28873455 [Au] Autor: Chen L; Zhang YH; Wang S; Zhang Y; Huang T; Cai YD [Ad] Endereço: School of Life Sciences, Shanghai University, Shanghai, People's Republic of China. [Ti] Título: Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. [So] Source: PLoS One;12(9):e0184129, 2017. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems. [Mh] Termos MeSH primário: Ontologia Genética Genes Essenciais Transdução de Sinais/genética [Mh] Termos MeSH secundário: Reprodutibilidade dos Testes Máquina de Vetores de Suporte [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171016 [Lr] Data última revisão: 171016 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170906 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0184129

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