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  1 / 18 MEDLINE  
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[PMID]:28115382
[Au] Autor:Matteau D; Pepin ME; Baby V; Gauthier S; Arango Giraldo M; Knight TF; Rodrigue S
[Ad] Endereço:Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.
[Ti] Título:Development of -Based Plasmids for Mesoplasma florum.
[So] Source:Appl Environ Microbiol;83(7), 2017 Apr 01.
[Is] ISSN:1098-5336
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The near-minimal bacterium constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted chromosomal origin of replication ( ) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both and intergenic regions, interspaced or not with a copy of the gene, resulted in a frequency of ∼4.1 × 10 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one intergenic region or the heterologous region of , , or failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from , reaching frequencies up to 7.87 × 10 and 8.44 × 10 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in Taken together, these valuable genetic tools will facilitate efforts toward building an -based near-minimal cellular chassis for synthetic biology. constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, shows higher growth rates than other , has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of in order to modify its genome. To address this issue, we have evaluated the susceptibility of to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.
[Mh] Termos MeSH primário: Entomoplasmataceae/genética
Plasmídeos/genética
Origem de Replicação
[Mh] Termos MeSH secundário: Antibacterianos/farmacologia
Proteínas de Bactérias/genética
Replicação do DNA
DNA Bacteriano/genética
DNA Intergênico
Proteínas de Ligação a DNA/genética
Farmacorresistência Bacteriana Múltipla
Entomoplasmataceae/efeitos dos fármacos
Escherichia coli/genética
Vetores Genéticos
Mycoplasma/genética
Recombinação Genética
Biologia Sintética
Transformação Bacteriana
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (DNA, Intergenic); 0 (DNA-Binding Proteins); 0 (DnaA protein, Bacteria)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171109
[Lr] Data última revisão:
171109
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170125
[St] Status:MEDLINE


  2 / 18 MEDLINE  
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[PMID]:28185583
[Au] Autor:Khan MA; Mahmudi O; Ullah I; Arvestad L; Lagergren J
[Ad] Endereço:KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, Solna, 171 21, Sweden.
[Ti] Título:Probabilistic inference of lateral gene transfer events.
[So] Source:BMC Bioinformatics;17(Suppl 14):431, 2016 Nov 11.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. CONCLUSIONS: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.
[Mh] Termos MeSH primário: Transferência Genética Horizontal/genética
Modelos Genéticos
[Mh] Termos MeSH secundário: Evolução Biológica
Entomoplasmataceae/classificação
Entomoplasmataceae/genética
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[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:170211
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-016-1268-2


  3 / 18 MEDLINE  
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[PMID]:26197065
[Au] Autor:Matteau D; Baby V; Pelletier S; Rodrigue S
[Ad] Endereço:Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.
[Ti] Título:A Small-Volume, Low-Cost, and Versatile Continuous Culture Device.
[So] Source:PLoS One;10(7):e0133384, 2015.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Continuous culture devices can be used for various purposes such as establishing reproducible growth conditions or maintaining cell populations under a constant environment for long periods. However, commercially available instruments are expensive, were not designed to handle small volumes in the milliliter range, and can lack the flexibility required for the diverse experimental needs found in several laboratories. METHODOLOGY/PRINCIPAL FINDINGS: We developed a versatile continuous culture system and provide detailed instructions as well as a graphical user interface software for potential users to assemble and operate their own instrument. Three culture chambers can be controlled simultaneously with the proposed configuration, and all components are readily available from various sources. We demonstrate that our continuous culture device can be used under different modes, and can easily be programmed to behave either as a turbidostat or chemostat. Addition of fresh medium to the culture vessel can be controlled by a real-time feedback loop or simply calibrated to deliver a defined volume. Furthermore, the selected light-emitting diode and photodetector enable the use of phenol red as a pH indicator, which can be used to indirectly monitor the bulk metabolic activity of a cell population rather than the turbidity. CONCLUSIONS/SIGNIFICANCE: This affordable and customizable system will constitute a useful tool in many areas of biology such as microbial ecology as well as systems and synthetic biology.
[Mh] Termos MeSH primário: Divisão Celular/fisiologia
Técnicas Microbiológicas/instrumentação
Técnicas Microbiológicas/métodos
Modelos Teóricos
[Mh] Termos MeSH secundário: Entomoplasmataceae/citologia
Entomoplasmataceae/crescimento & desenvolvimento
Desenho de Equipamento
Escherichia coli/citologia
Escherichia coli/crescimento & desenvolvimento
Concentração de Íons de Hidrogênio
Técnicas Microbiológicas/economia
Reprodutibilidade dos Testes
Saccharomyces cerevisiae/citologia
Saccharomyces cerevisiae/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1605
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150722
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0133384


  4 / 18 MEDLINE  
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[PMID]:25750180
[Au] Autor:Sung W; Ackerman MS; Gout JF; Miller SF; Williams E; Foster PL; Lynch M
[Ad] Endereço:Department of Biology, Indiana University, Bloomington waysung@indiana.edu.
[Ti] Título:Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments.
[So] Source:Mol Biol Evol;32(7):1672-83, 2015 Jul.
[Is] ISSN:1537-1719
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) mutation-accumulation (MA) lines of the gram-positive model organism Bacillus subtilis. We then analyzed>7,500 spontaneous base-substitution mutations across B. subtilis, Escherichia coli, and Mesoplasma florum WT and MMR(-) MA lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighboring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighboring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on genome architecture is strongest in M. florum, consistent with the reduced efficiency of selection in organisms with low effective population size. If not properly accounted for, the disparities arising from patterns of context-dependent mutation can significantly influence interpretations of positive and purifying selection.
[Mh] Termos MeSH primário: Bactérias/genética
Reparo de Erro de Pareamento de DNA/genética
Acúmulo de Mutações
Taxa de Mutação
[Mh] Termos MeSH secundário: Bacillus subtilis/genética
Entomoplasmataceae/genética
Escherichia coli/genética
Genoma Bacteriano
Nucleotídeos/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Nucleotides)
[Em] Mês de entrada:1603
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150310
[St] Status:MEDLINE
[do] DOI:10.1093/molbev/msv055


  5 / 18 MEDLINE  
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[PMID]:25402616
[Au] Autor:Cameron DE; Collins JJ
[Ad] Endereço:1] Howard Hughes Medical Institute, Boston University, Boston, Massachusetts, USA. [2] Center of Synthetic Biology, Boston University, Boston, Massachusetts, USA. [3] Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
[Ti] Título:Tunable protein degradation in bacteria.
[So] Source:Nat Biotechnol;32(12):1276-81, 2014 Dec.
[Is] ISSN:1546-1696
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Tunable control of protein degradation in bacteria would provide a powerful research tool. Here we use components of the Mesoplasma florum transfer-messenger RNA system to create a synthetic degradation system that provides both independent control of steady-state protein level and inducible degradation of targeted proteins in Escherichia coli. We demonstrate application of this system in synthetic circuit development and control of core bacterial processes and antibacterial targets, and we transfer the system to Lactococcus lactis to establish its broad functionality in bacteria. We create a 238-member library of tagged essential proteins in E. coli that can serve as both a research tool to study essential gene function and an applied system for antibiotic discovery. Our synthetic protein degradation system is modular, does not require disruption of host systems and can be transferred to diverse bacteria with minimal modification.
[Mh] Termos MeSH primário: Escherichia coli/metabolismo
Proteólise
RNA Mensageiro/genética
[Mh] Termos MeSH secundário: Entomoplasmataceae/química
Entomoplasmataceae/metabolismo
Regulação Bacteriana da Expressão Gênica
Lactococcus lactis/química
Lactococcus lactis/genética
Dados de Sequência Molecular
RNA Mensageiro/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Messenger)
[Em] Mês de entrada:1508
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:141118
[St] Status:MEDLINE
[do] DOI:10.1038/nbt.3053


  6 / 18 MEDLINE  
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[PMID]:24673892
[Au] Autor:Helmling C; Bessi I; Wacker A; Schnorr KA; Jonker HR; Richter C; Wagner D; Kreibich M; Schwalbe H
[Ad] Endereço:Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt , Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany.
[Ti] Título:Noncovalent spin labeling of riboswitch RNAs to obtain long-range structural NMR restraints.
[So] Source:ACS Chem Biol;9(6):1330-9, 2014 Jun 20.
[Is] ISSN:1554-8937
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Paramagnetic relaxation enhancement (PRE) NMR is a powerful method to study structure, dynamics and function of proteins. Up to now, the application of PRE NMR on RNAs is a significant challenge due to the limited size of chemically synthesized RNA. Here, we present a noncovalent spin labeling strategy to spin label RNAs in high yields required for NMR studies. The approach requires the presence of a helix segment composed of about 10 nucleotides (nt) but is not restricted by the size of the RNA. We show successful application of this strategy on the 2'dG sensing aptamer domain of Mesoplasma florum (78 nt). The aptamer domain was prepared in two fragments. A larger fragment was obtained by biochemical means, while a short spin labeled fragment was prepared by chemical solid-phase synthesis. The two fragments were annealed noncovalently by hybridization. We performed NMR, cw-EPR experiments and gel shift assays to investigate the stability of the two-fragment complex. NMR analysis in (15)N-TROSY and (1)H,(1)H-NOESY spectra of both unmodified and spin labeled aptamer domain show that the fragmented system forms a stable hybridization product, is in structural agreement with the full length aptamer domain and maintains its function. Together with structure modeling, experimentally determined (1)H-Γ2 rates are in agreement with reported crystal structure data and show that distance restraints up to 25 Å can be obtained from NMR PRE data of RNA.
[Mh] Termos MeSH primário: Aptâmeros de Nucleotídeos/genética
Entomoplasmataceae/genética
RNA Bacteriano/química
RNA Bacteriano/genética
Riboswitch/genética
[Mh] Termos MeSH secundário: Aptâmeros de Nucleotídeos/química
Pareamento de Bases
Sequência de Bases
Espectroscopia de Ressonância de Spin Eletrônica
Entomoplasmataceae/metabolismo
Espectroscopia de Ressonância Magnética
Modelos Moleculares
Dados de Sequência Molecular
Conformação de Ácido Nucleico
Marcadores de Spin
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Aptamers, Nucleotide); 0 (RNA, Bacterial); 0 (Riboswitch); 0 (Spin Labels)
[Em] Mês de entrada:1508
[Cu] Atualização por classe:140814
[Lr] Data última revisão:
140814
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140329
[St] Status:MEDLINE
[do] DOI:10.1021/cb500050t


  7 / 18 MEDLINE  
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[PMID]:24534435
[Au] Autor:Chang TH; Lo WS; Ku C; Chen LL; Kuo CH
[Ad] Endereço:Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
[Ti] Título:Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species.
[So] Source:Genome Biol Evol;6(3):500-9, 2014 Mar.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Comparative genomics provides a powerful tool to characterize the genetic differences among species that may be linked to their phenotypic variations. In the case of mosquito-associated Spiroplasma species, such approach is useful for the investigation of their differentiations in substrate utilization strategies and putative virulence factors. Among the four species that have been assessed for pathogenicity by artificial infection experiments, Spiroplasma culicicola and S. taiwanense were found to be pathogenic, whereas S. diminutum and S. sabaudiense were not. Intriguingly, based on the species phylogeny, the association with mosquito hosts and the gain or loss of pathogenicity in these species appears to have evolved independently. Through comparison of their complete genome sequences, we identified the genes and pathways that are shared by all or specific to one of these four species. Notably, we found that a glycerol-3-phosphate oxidase gene (glpO) is present in S. culicicola and S. taiwanense but not in S. diminutum or S. sabaudiense. Because this gene is involved in the production of reactive oxygen species and has been demonstrated as a major virulence factor in Mycoplasma, this distribution pattern suggests that it may be linked to the observed differences in pathogenicity among these species as well. Moreover, through comparative analysis with other Spiroplasma, Mycoplasma, and Mesoplasma species, we found that the absence of glpO in S. diminutum and S. sabaudiense is best explained by independent losses. Finally, our phylogenetic analyses revealed possible recombination of glpO between distantly related lineages and local rearrangements of adjacent genes.
[Mh] Termos MeSH primário: Evolução Molecular
Genes Bacterianos
Spiroplasma/genética
Fatores de Virulência/genética
[Mh] Termos MeSH secundário: Animais
Culicidae/microbiologia
DNA Bacteriano/genética
Entomoplasmataceae/genética
Genômica
Glicerolfosfato Desidrogenase/genética
Dados de Sequência Molecular
Mycoplasma/genética
Filogenia
Análise de Sequência de DNA
Especificidade da Espécie
Spiroplasma/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Virulence Factors); EC 1.1.- (Glycerolphosphate Dehydrogenase); EC 1.1.3.21 (glycerol-3-phosphate oxidase)
[Em] Mês de entrada:1410
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140219
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evu033


  8 / 18 MEDLINE  
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[PMID]:23593647
[Au] Autor:Sung W; Ackerman MS; Miller SF; Doak TG; Lynch M
[Ti] Título:Reply to Massey: Drift does influence mutation-rate evolution.
[So] Source:Proc Natl Acad Sci U S A;110(10):E860, 2013 Mar 05.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Evolução Biológica
Chlamydomonas reinhardtii/genética
Entomoplasmataceae/genética
Deriva Genética
Modelos Genéticos
Taxa de Mutação
Isolamento Reprodutivo
[Pt] Tipo de publicação:COMMENT; LETTER
[Em] Mês de entrada:1305
[Cu] Atualização por classe:161025
[Lr] Data última revisão:
161025
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130418
[St] Status:MEDLINE


  9 / 18 MEDLINE  
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[PMID]:23428322
[Au] Autor:Sniegowski P; Raynes Y
[Ad] Endereço:Department of Biology, University of Pennsylvania, Philadelphia, PA 19063, USA. paulsnie@sas.upenn.edu
[Ti] Título:Mutation rates: how low can you go?
[So] Source:Curr Biol;23(4):R147-9, 2013 Feb 18.
[Is] ISSN:1879-0445
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Two recent reports combine mutation accumulation and whole-genome sequencing to measure mutation rates in microbes with unusual genome sizes and life cycles. The results are broadly consistent with the hypothesis that genetic drift plays a role in shaping genomic mutation rates across a wide range of taxa.
[Mh] Termos MeSH primário: Deriva Genética
Tamanho do Genoma/genética
Taxa de Mutação
[Mh] Termos MeSH secundário: Chlamydomonas reinhardtii/genética
Entomoplasmataceae/genética
Evolução Molecular
Variação Genética
Genoma
Paramecium tetraurellia/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1308
[Cu] Atualização por classe:130222
[Lr] Data última revisão:
130222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130223
[St] Status:MEDLINE


  10 / 18 MEDLINE  
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[PMID]:23407172
[Au] Autor:Massey SE
[Ti] Título:Proteome size as the major factor determining mutation rates.
[So] Source:Proc Natl Acad Sci U S A;110(10):E858-9, 2013 Mar 05.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Evolução Biológica
Chlamydomonas reinhardtii/genética
Entomoplasmataceae/genética
Deriva Genética
Modelos Genéticos
Taxa de Mutação
Isolamento Reprodutivo
[Pt] Tipo de publicação:COMMENT; LETTER
[Em] Mês de entrada:1305
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130215
[St] Status:MEDLINE
[do] DOI:10.1073/pnas.1219306110



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