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[PMID]:27770357
[Au] Autor:Bilichak A; Kovalchuk I
[Ad] Endereço:Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada. andrii.bilichak@agr.gc.ca.
[Ti] Título:The Combined Bisulfite Restriction Analysis (COBRA) Assay for the Analysis of Locus-Specific Changes in Methylation Patterns.
[So] Source:Methods Mol Biol;1456:63-71, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA methylation is a heritable but reversible epigenetic mechanism of control over gene expression. The level of DNA methylation of specific genomic regions correlates with chromatin condensation, the level of gene expression, and in some cases genome stability and the frequency of homologous recombination. Here, we describe the combined bisulfite restriction analysis (COBRA) assay that allows analyzing the methylation status at a specific locus. The protocol consists of the following major steps: bisulfite conversion of non-methylated cytosines to uracils, the locus-specific PCR amplification of converted DNA, restriction digestion, the analysis of restriction patterns on the gel, and the quantification of these restriction patterns using ImageJ or a similar program.
[Mh] Termos MeSH primário: Metilação de DNA
Epigenômica
Loci Gênicos
Mapeamento por Restrição/métodos
Análise de Sequência de DNA
Sulfitos
[Mh] Termos MeSH secundário: Epigenômica/métodos
Reação em Cadeia da Polimerase
Análise de Sequência de DNA/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Sulfites); OJ9787WBLU (hydrogen sulfite)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


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[PMID]:28468906
[Au] Autor:Dou J; Dou H; Mu C; Zhang L; Li Y; Wang J; Li T; Li Y; Hu X; Wang S; Bao Z
[Ad] Endereço:Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
[Ti] Título:Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding.
[So] Source:Genetics;206(3):1237-1250, 2017 07.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based " " linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6-14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1-98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies.
[Mh] Termos MeSH primário: Ligação Genética
Genoma de Planta
Mapeamento por Restrição/métodos
Software
[Mh] Termos MeSH secundário: Arabidopsis/genética
Mapeamento por Restrição/normas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171213
[Lr] Data última revisão:
171213
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.117.200303


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[PMID]:28873431
[Au] Autor:Barrera GP; Villamizar LF; Espinel C; Quintero EM; Belaich MN; Toloza DL; Ghiringhelli PD; Vargas G
[Ad] Endereço:Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria CORPOICA, Mosquera, Cundinamarca, Colombia.
[Ti] Título:Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II.
[So] Source:PLoS One;12(9):e0184053, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.
[Mh] Termos MeSH primário: Complexo IV da Cadeia de Transporte de Elétrons/genética
Lepidópteros/enzimologia
[Mh] Termos MeSH secundário: Animais
DNA de Cadeia Simples/química
Genitália Masculina/anatomia & histologia
Lepidópteros/anatomia & histologia
Masculino
Conformação de Ácido Nucleico
Nucleotídeos/genética
Filogenia
Reação em Cadeia da Polimerase
Polimorfismo Conformacional de Fita Simples
Mapeamento por Restrição
Análise de Sequência de DNA
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (Nucleotides); EC 1.9.3.- (cytochrome C oxidase subunit II); EC 1.9.3.1 (Electron Transport Complex IV)
[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.0184053


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[PMID]:28669404
[Au] Autor:Acuna-Hidalgo R; Sengul H; Steehouwer M; van de Vorst M; Vermeulen SH; Kiemeney LALM; Veltman JA; Gilissen C; Hoischen A
[Ad] Endereço:Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands.
[Ti] Título:Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life.
[So] Source:Am J Hum Genet;101(1):50-64, 2017 Jul 06.
[Is] ISSN:1537-6605
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals ≥65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.
[Mh] Termos MeSH primário: Análise Mutacional de DNA/métodos
Hematopoese/genética
Mutação/genética
[Mh] Termos MeSH secundário: Adulto
Idoso
Sequência de Bases
Células Clonais
Loci Gênicos
Seres Humanos
Meia-Idade
Sondas Moleculares/metabolismo
Fases de Leitura Aberta/genética
Reprodutibilidade dos Testes
Mapeamento por Restrição
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Molecular Probes)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170802
[Lr] Data última revisão:
170802
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170704
[St] Status:MEDLINE


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[PMID]:28334749
[Au] Autor:Zaghloul EM; Gissberg O; Moreno PMD; Siggens L; Hällbrink M; Jørgensen AS; Ekwall K; Zain R; Wengel J; Lundin KE; Smith CIE
[Ad] Endereço:Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.
[Ti] Título:CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression.
[So] Source:Nucleic Acids Res;45(9):5153-5169, 2017 May 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease. In addition, it has been suggested that the muHTT transcript contributes to the toxicity. Thus, reduction of both muHTT mRNA and protein levels would ideally be the most useful therapeutic option. We herein present a novel strategy for HD treatment using oligonucleotides (ONs) directly targeting the HTT trinucleotide repeat DNA. A partial, but significant and potentially long-term, HTT knock-down of both mRNA and protein was successfully achieved. Diminished phosphorylation of HTT gene-associated RNA-polymerase II is demonstrated, suggestive of reduced transcription downstream the ON-targeted repeat. Different backbone chemistries were found to have a strong impact on the ON efficiency. We also successfully use different delivery vehicles as well as naked uptake of the ONs, demonstrating versatility and possibly providing insights for in vivo applications.
[Mh] Termos MeSH primário: Regulação para Baixo/efeitos dos fármacos
Proteína Huntingtina/genética
Oligonucleotídeos Fosforotioatos/farmacologia
Expansão das Repetições de Trinucleotídeos/genética
[Mh] Termos MeSH secundário: Alelos
DNA/metabolismo
Fibroblastos/efeitos dos fármacos
Fibroblastos/metabolismo
Técnicas de Silenciamento de Genes
Seres Humanos
Proteína Huntingtina/metabolismo
Desnaturação de Ácido Nucleico/efeitos dos fármacos
Peptídeos/metabolismo
Fosforilação/efeitos dos fármacos
Fosfosserina/metabolismo
RNA Polimerase II/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Mapeamento por Restrição
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Huntingtin Protein); 0 (Peptides); 0 (Phosphorothioate Oligonucleotides); 0 (RNA, Messenger); 17885-08-4 (Phosphoserine); 9007-49-2 (DNA); EC 2.7.7.- (RNA Polymerase II)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170919
[Lr] Data última revisão:
170919
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170324
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx111


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[PMID]:28190200
[Au] Autor:Bald-Blume N; Bergervoet JHW; Maiss E
[Ad] Endereço:Section of Phytomedicine, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany.
[Ti] Título:Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species.
[So] Source:Arch Virol;162(6):1519-1528, 2017 Jun.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:A Luminex xTAG-based assay for plant-infecting tospoviruses was developed. The test enables the detection of tospoviruses in general and the differentiation of the four important member species of this genus: Tomato spotted wilt virus, Impatiens necrotic spot virus, the proposed 'Capsicum chlorosis virus' and Watermelon silver mottle virus. The generic tospovirus primers used in this method are also applicable for detection of tospoviruses by basic RT-PCR. We also describe an economic alternative method for the distinction of the four tospoviruses mentioned and of additional member viruses, based on a restriction fragment length polymorphism (RFLP). The sophisticated Luminex xTAG technology allows the simultaneous detection of various targets. This study is part of a project that aims to develop a method for the simultaneous detection of various plant pathogens (viral, bacterial and fungal) in plant material.
[Mh] Termos MeSH primário: Imunoensaio/métodos
Reação em Cadeia da Polimerase Multiplex/métodos
Tospovirus/genética
Tospovirus/isolamento & purificação
[Mh] Termos MeSH secundário: Primers do DNA
Doenças das Plantas/virologia
Plantas/virologia
Polimorfismo de Fragmento de Restrição
RNA Viral/análise
Mapeamento por Restrição/métodos
Tospovirus/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Primers); 0 (RNA, Viral)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170720
[Lr] Data última revisão:
170720
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170213
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3256-x


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[PMID]:28135327
[Au] Autor:Nowakiewicz A; Ziólkowska G; Zieba P; Gnat S; Troscianczyk A; Adaszek L
[Ad] Endereço:Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland.
[Ti] Título:Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis.
[So] Source:PLoS One;12(1):e0171160, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The aim of this study was to characterize multidrug resistant E. faecalis strains from pigs of local origin and to analyse the relationship between resistance and genotypic and proteomic profiles by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI -TOF MS). From the total pool of Enterococcus spp. isolated from 90 pigs, we selected 36 multidrug resistant E. faecalis strains, which represented three different phenotypic resistance profiles. Phenotypic resistance to tetracycline, macrolides, phenicols, and lincomycin and high-level resistance to aminoglycosides were confirmed by the occurrence of at least one corresponding resistance gene in each strain. Based on the analysis of the genotypic and phenotypic resistance of the strains tested, five distinct resistance profiles were generated. As a complement of this analysis, profiles of virulence genes were determined and these profiles corresponded to the phenotypic resistance profiles. The demonstration of resistance to a wide panel of antimicrobials by the strains tested in this study indicates the need of typing to determine the spread of resistance also at the local level. It seems that in the case of E. faecalis, type and scope of resistance strongly determines the genotypic pattern obtained with the ADSRRS-fingerprinting method. The ADSRRS-fingerprinting analysis showed consistency of the genetic profiles with the resistance profiles, while analysis of data with the use of the MALDI- TOF MS method did not demonstrate direct reproduction of the clustering pattern obtained with this method. Our observations were confirmed by statistical analysis (Simpson's index of diversity, Rand and Wallace coefficients). Even though the MALDI -TOF MS method showed slightly higher discrimination power than ADSRRS-fingerprinting, only the latter method allowed reproduction of the clustering pattern of isolates based on phenotypic resistance and analysis of resistance and virulence genes (Wallace coefficient 1.0). This feature seems to be the most useful for epidemiological purposes and short-term analysis.
[Mh] Termos MeSH primário: Impressões Digitais de DNA/métodos
Farmacorresistência Bacteriana Múltipla/genética
Enterococcus faecalis/genética
Mapeamento por Restrição
Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
Sus scrofa/microbiologia
[Mh] Termos MeSH secundário: Animais
Antibacterianos/farmacologia
Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos
Enterococcus faecalis/efeitos dos fármacos
Enterococcus faecalis/patogenicidade
Genes Bacterianos
Testes de Sensibilidade Microbiana
Fenótipo
Filogenia
Virulência/efeitos dos fármacos
Virulência/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170814
[Lr] Data última revisão:
170814
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170131
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0171160


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[PMID]:28111453
[Au] Autor:Liu X; Xue M
[Ad] Endereço:Genetics Diagnostic Lab, Tai'an Maternity and Child Care Hospital, Tai'an, Shandong, China (mainland).
[Ti] Título:Noninvasive Prenatal Diagnosis Significance of ERG Methylation as a Biomarker in Down's Syndrome.
[So] Source:Med Sci Monit;23:398-404, 2017 Jan 23.
[Is] ISSN:1643-3750
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND Down's syndrome (DS) is a genetic disease with chromosome abnormality due to the increasing chromosome 21. This study focused on the clinical application value of ERG methylation level in blood of pregnant women as a biomarker in Down's syndrome. MATERIAL AND METHODS The sham group consisted of 210 nonpregnant women, the positive control group consisted of 33 women with a delivery history of DS fetus, and the negative control group consisted of 60 women with eutocia history. A combination of restriction enzyme digestion experiment and PCR was performed to examine ERG methylation levels, methylation sites, and distribution in blood of pregnant women and in chorion tissues from abortion samples. Gene sequencing was performed to determine the ERG sequence in chromosome 21. Homology between normal tissues and chorion tissues from abortion samples was analyzed with bioinformatics technology. RESULTS ERG methylation in chorion tissues from 210 abortion samples at 8, 9, and 10 weeks gestational age were determined; however, no ERG methylation was determined in blood of pregnant women. Gene sequencing indicated that normal ERG sequence in chromosome 21 was in fetus chorion tissues, and these ERG sequences were aberrantly methylated. Bioinformatics result showed that homology and DNA methylation level was discrepancy in normal tissues and chorion tissues from abortion samples. CONCLUSIONS It was worthwhile to use ERG methylation as biomarker in noninvasive prenatal diagnosis, and ERG methylation should be applied with consent of pregnancy and her relatives.
[Mh] Termos MeSH primário: Biomarcadores/sangue
Metilação de DNA/genética
Síndrome de Down/sangue
Síndrome de Down/genética
Diagnóstico Pré-Natal/métodos
[Mh] Termos MeSH secundário: Adulto
Sequência de Bases
Córion/metabolismo
DNA Complementar/genética
Eletroforese em Gel de Ágar
Feminino
Genoma Humano
Idade Gestacional
Seres Humanos
Reação em Cadeia da Polimerase
Gravidez
Mapeamento por Restrição
Análise de Sequência de DNA
Regulador Transcricional ERG/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers); 0 (DNA, Complementary); 0 (ERG protein, human); 0 (Transcriptional Regulator ERG)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170627
[Lr] Data última revisão:
170627
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170124
[St] Status:MEDLINE


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[PMID]:27900459
[Au] Autor:Han H; Wei X; Wei Y; Zhang X; Li X; Jiang J; Wang R
[Ad] Endereço:Key Laboratory of Guizhou Bioresource Development and Utilization, Guizhou Education University, Guiyang, 550018, Guizhou, China.
[Ti] Título:Isolation, Characterization, and Bioinformatic Analyses of Lytic Salmonella Enteritidis Phages and Tests of Their Antibacterial Activity in Food.
[So] Source:Curr Microbiol;74(2):175-183, 2017 Feb.
[Is] ISSN:1432-0991
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Salmonella Enteritidis remains a major threat for food safety. To take efforts to develop phage-based biocontrol for S. Enteritidis contamination in food, in this study, the phages against S. Enteritidis were isolated from sewage samples, characterized by host range assays, DNA restriction enzyme pattern analyses, and transmission electron microscope observations, and tested for antibacterial activity in food; some potent phages were further characterized by bioinformatic analyses. Results showed that based on the plaque quality and host range, seven lytic phages targeting S. Enteritidis were selected, considered as seven distinct phages through DNA physical maps, and classified as Myoviridae or Siphoviridae family by morphologic observations; the combined use of such seven strain phages as a "food additive" could succeed in controlling the artificial S. Enteritidis contamination in the different physical forms of food at a range of temperatures; by bioinformatic analyses, both selected phage BPS Q and BPS Q seemed to be newfound obligate lytic phage strains with no indications for any potentially harmful genes in their genomes. In conclusion, our results showed a potential of isolated phages as food additives for controlling S. Enteritidis contamination in some salmonellosis outbreak-associated food vehicles, and there could be minimized potential risk associated with using BPS Q and BPS Q in food.
[Mh] Termos MeSH primário: Biologia Computacional
Microbiologia de Alimentos
Fagos de Salmonella/isolamento & purificação
Fagos de Salmonella/fisiologia
Salmonella enteritidis/virologia
[Mh] Termos MeSH secundário: Bacteriólise
DNA Viral/genética
Ordem dos Genes
Genes Virais
Genoma Viral
Especificidade de Hospedeiro
Microscopia Eletrônica de Transmissão
Myoviridae/genética
Myoviridae/isolamento & purificação
Myoviridae/fisiologia
Myoviridae/ultraestrutura
Mapeamento por Restrição
Fagos de Salmonella/genética
Fagos de Salmonella/ultraestrutura
Salmonella enteritidis/crescimento & desenvolvimento
Esgotos/virologia
Siphoviridae/genética
Siphoviridae/isolamento & purificação
Siphoviridae/fisiologia
Siphoviridae/ultraestrutura
Ensaio de Placa Viral
Vírion/ultraestrutura
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Viral); 0 (Sewage)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161201
[St] Status:MEDLINE
[do] DOI:10.1007/s00284-016-1169-7


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[PMID]:28155644
[Au] Autor:Abbas MM; Bahig HM
[Ad] Endereço:Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar. mohamza@hbku.edu.qa.
[Ti] Título:A fast exact sequential algorithm for the partial digest problem.
[So] Source:BMC Bioinformatics;17(Suppl 19):510, 2016 Dec 22.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the lengths of the cut DNA. Using different reaction times with a single enzyme to cut DNA is a technique known as a partial digestion. Determining the exact locations of restriction sites following a partial digestion is challenging due to the computational time required even with the best known practical algorithm. RESULTS: In this paper, we introduce an efficient algorithm to find the exact solution for the partial digest problem. The algorithm is able to find all possible solutions for the input and works by traversing the solution tree with a breadth-first search in two stages and deleting all repeated subproblems. Two types of simulated data, random and Zhang, are used to measure the efficiency of the algorithm. We also apply the algorithm to real data for the Luciferase gene and the E. coli K12 genome. CONCLUSION: Our algorithm is a fast tool to find the exact solution for the partial digest problem. The percentage of improvement is more than 75% over the best known practical algorithm for the worst case. For large numbers of inputs, our algorithm is able to solve the problem in a suitable time, while the best known practical algorithm is unable.
[Mh] Termos MeSH primário: Algoritmos
Biologia Computacional/métodos
DNA Bacteriano/genética
Escherichia coli/genética
Genoma Bacteriano
Luciferases/genética
Mapeamento por Restrição/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); EC 1.13.12.- (Luciferases)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170817
[Lr] Data última revisão:
170817
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170204
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-016-1365-2



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