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1.
J Biol Chem ; 294(22): 8885-8893, 2019 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-31000629

RESUMO

tRNAHis guanylyltransferase (Thg1) adds a single guanine to the -1 position of tRNAHis as part of its maturation. This seemingly modest addition of one nucleotide to tRNAHis ensures translational fidelity by providing a critical identity element for the histidyl aminoacyl tRNA synthetase (HisRS). Like HisRS, Thg1 utilizes the GUG anticodon for selective tRNAHis recognition, and Thg1-tRNA complex structures have revealed conserved residues that interact with anticodon nucleotides. Separately, kinetic analysis of alanine variants has demonstrated that many of these same residues are required for catalytic activity. A model in which loss of activity with the variants was attributed directly to loss of the critical anticodon interaction has been proposed to explain the combined biochemical and structural results. Here we used RNA chemical footprinting and binding assays to test this model and further probe the molecular basis for the requirement for two critical tRNA-interacting residues, His-152 and Lys-187, in the context of human Thg1 (hThg1). Surprisingly, we found that His-152 and Lys-187 alanine-substituted variants maintain a similar overall interaction with the anticodon region, arguing against the sufficiency of this interaction for driving catalysis. Instead, conservative mutagenesis revealed a new direct function for these residues in recognition of a non-Watson-Crick G-1:A73 bp, which had not been described previously. These results have important implications for the evolution of eukaryotic Thg1 from a family of ancestral promiscuous RNA repair enzymes to the highly selective enzymes needed for their essential function in tRNAHis maturation.


Assuntos
Proteínas de Homeodomínio/metabolismo , RNA de Transferência de Histidina/metabolismo , Anticódon/química , Anticódon/metabolismo , Biocatálise , Domínio Catalítico , Evolução Molecular , Proteínas de Homeodomínio/química , Proteínas de Homeodomínio/genética , Humanos , Cinética , Mutagênese Sítio-Dirigida , Conformação de Ácido Nucleico , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética
2.
Biochemistry ; 53(8): 1380-91, 2014 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-24548272

RESUMO

In eukaryotes, the tRNA(His) guanylyltransferase (Thg1) catalyzes 3'-5' addition of a single guanosine residue to the -1 position (G-1) of tRNA(His), across from a highly conserved adenosine at position 73 (A73). After addition of G-1, Thg1 removes pyrophosphate from the tRNA 5'-end, generating 5'-monophosphorylated G-1-containing tRNA. The presence of the 5'-monophosphorylated G-1 residue is important for recognition of tRNA(His) by its cognate histidyl-tRNA synthetase. In addition to the single-G-1 addition reaction, Thg1 polymerizes multiple G residues to the 5'-end of tRNA(His) variants. For 3'-5' polymerization, Thg1 uses the 3'-end of the tRNA(His) acceptor stem as a template. The mechanism of reverse polymerization is presumed to involve nucleophilic attack of the 3'-OH from each incoming NTP on the intact 5'-triphosphate created by the preceding nucleotide addition. The potential exists for competition between 5'-pyrophosphate removal and 3'-5' polymerase reactions that could define the outcome of Thg1-catalyzed addition, yet the interplay between these competing reactions has not been investigated for any Thg1 enzyme. Here we establish transient kinetic assays to characterize the pyrophosphate removal versus nucleotide addition activities of yeast Thg1 with a set of tRNA(His) substrates in which the identity of the N-1:N73 base pair was varied to mimic various products of the N-1 addition reaction catalyzed by Thg1. We demonstrate that retention of the 5'-triphosphate is correlated with efficient 3'-5' reverse polymerization. A kinetic partitioning mechanism that acts to prevent addition of nucleotides beyond the -1 position with wild-type tRNA(His) is proposed.


Assuntos
Difosfatos/metabolismo , Nucleotídeos/metabolismo , Nucleotidiltransferases/metabolismo , RNA de Transferência/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimologia , Pareamento Incorreto de Bases , Pareamento de Bases , Biocatálise , Guanosina Trifosfato/metabolismo , Cinética , RNA de Transferência/química , RNA de Transferência/genética , Reprodutibilidade dos Testes
3.
Plasmid ; 73: 16-25, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24792221

RESUMO

BACKGROUND: Horizontal gene transfer (HGT) is a widespread process that enables the acquisition of genes and metabolic pathways in single evolutionary steps. Previous reports have described fitness costs of HGT, but have largely focused on the acquisition of relatively small plasmids. We have previously shown that a Pseudomonas syringae pv. lachrymans strain recently acquired a cryptic megaplasmid, pMPPla107. This extrachromosomal element contributes hundreds of new genes to P. syringae and increases total genomic content by approximately 18%. However, this early work did not directly explore transmissibility, stability, or fitness costs associated with acquisition of pMPPla107. RESULTS: Here, we show that pMPPla107 is self-transmissible across a variety of diverse pseudomonad strains, on both solid agar and within shaking liquid cultures, with conjugation dependent on a type IV secretion system. To the best of our knowledge, this is the largest self-transmissible megaplasmid known outside of Sinorhizobium. This megaplasmid can be lost from all novel hosts although the rate of loss depends on medium type and genomic background. However, in contrast, pMPPla107 is faithfully maintained within the original parent strain (Pla107) even under direct negative selection during laboratory assays. These results suggest that Pla107 specific stabilizing mutations have occurred either on this strain's chromosome or within the megaplasmid. Lastly, we demonstrate that acquisition of pMPPla107 by strains other than Pla107 imparts severe (20%) fitness costs under competitive conditions in vitro. CONCLUSIONS: We show that pMPPla107 is capable of transmitting and maintaining itself across multiple Pseudomonas species, rendering it one of the largest conjugative elements discovered to date. The relative stability of pMPPla107, coupled with extensive fitness costs, makes it a tractable model system for investigating evolutionary and genetic mechanisms of megaplasmid maintenance and a unique testing ground to explore evolutionary dynamics after HGT of large secondary elements.


Assuntos
Evolução Biológica , Doenças das Plantas/genética , Plasmídeos/genética , Infecções por Pseudomonas/transmissão , Pseudomonas syringae/genética , Pseudomonas/genética , Virulência/genética , Conjugação Genética , Doenças das Plantas/microbiologia , Pseudomonas/classificação , Pseudomonas/patogenicidade , Infecções por Pseudomonas/genética , Pseudomonas syringae/patogenicidade
4.
Proc Natl Acad Sci U S A ; 107(47): 20305-10, 2010 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-21059936

RESUMO

All known DNA and RNA polymerases catalyze the formation of phosphodiester bonds in a 5' to 3' direction, suggesting this property is a fundamental feature of maintaining and dispersing genetic information. The tRNA(His) guanylyltransferase (Thg1) is a member of a unique enzyme family whose members catalyze an unprecedented reaction in biology: 3'-5' addition of nucleotides to nucleic acid substrates. The 2.3-Å crystal structure of human THG1 (hTHG1) reported here shows that, despite the lack of sequence similarity, hTHG1 shares unexpected structural homology with canonical 5'-3' DNA polymerases and adenylyl/guanylyl cyclases, two enzyme families known to use a two-metal-ion mechanism for catalysis. The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases.


Assuntos
Guanosina/metabolismo , Modelos Moleculares , Nucleotidiltransferases/química , RNA de Transferência de Histidina/metabolismo , DNA Polimerase Dirigida por RNA/química , Cristalografia , Evolução Molecular , Humanos , Estrutura Molecular , Nucleotidiltransferases/metabolismo , DNA Polimerase Dirigida por RNA/metabolismo
5.
ISME J ; 17(12): 2270-2278, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37865718

RESUMO

Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects for a focal population would enhance our ability to predict evolution. Specifically, does the type of ecological interaction, such as mutualism or competition, change the average effect of a mutation (i.e., the mean of the distribution of fitness effects)? Furthermore, how often does increasing community complexity alter the impact of species interactions on mutant fitness? To address these questions, we created a transposon mutant library in Salmonella enterica and measured the fitness of loss of function mutations in 3,550 genes when grown alone versus competitive co-culture or mutualistic co-culture with Escherichia coli and Methylorubrum extorquens. We found that mutualism reduces the average impact of mutations, while competition had no effect. Additionally, mutant fitness in the 3-species communities can be predicted by averaging the fitness in each 2-species community. Finally, we discovered that in the mutualism S. enterica obtained vitamins and more amino acids than previously known. Our results suggest that species interactions can predictably impact fitness effect distributions, in turn suggesting that evolution may ultimately be predictable in multi-species communities.


Assuntos
Microbiota , Salmonella enterica , Humanos , Simbiose/genética , Escherichia coli/genética , Aminoácidos/metabolismo , Salmonella enterica/metabolismo
6.
bioRxiv ; 2023 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-37214994

RESUMO

Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects for a focal population would enhance our ability to predict evolution. Specifically, it would be useful to know if the type of ecological interaction, such as mutualism or competition, changes the average effect of a mutation (i.e., the mean of the distribution of fitness effects). Furthermore, how often does increasing community complexity alter the impact of species interactions on mutant fitness? To address these questions, we created a transposon mutant library in Salmonella enterica and measured the fitness of loss of function mutations in 3,550 genes when grown alone versus competitive co-culture or mutualistic co-culture with Escherichia coli and Methylorubrum extorquens. We found that mutualism reduces the average impact of mutations, while competition had no effect. Additionally, mutant fitness in the 3-species communities can be predicted by averaging the fitness in each 2-species community. Finally, the fitness effects of several knockouts in the mutualistic communities were surprising. We discovered that S. enterica is obtaining a different source of carbon and more vitamins and amino acids than we had expected. Our results suggest that species interactions can predictably impact fitness effect distributions, in turn suggesting that evolution may ultimately be predictable in multi-species communities.

7.
Biochemistry ; 51(1): 453-65, 2012 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-22136300

RESUMO

The tRNA(His) guanylyltransferase (Thg1) catalyzes the incorporation of a single guanosine residue at the -1 position (G(-1)) of tRNA(His), using an unusual 3'-5' nucleotidyl transfer reaction. Thg1 and Thg1 orthologs known as Thg1-like proteins (TLPs), which catalyze tRNA repair and editing, are the only known enzymes that add nucleotides in the 3'-5' direction. Thg1 enzymes share no identifiable sequence similarity with any other known enzyme family that could be used to suggest the mechanism for catalysis of the unusual 3'-5' addition reaction. The high-resolution crystal structure of human Thg1 revealed remarkable structural similarity between canonical DNA/RNA polymerases and eukaryotic Thg1; nevertheless, questions regarding the molecular mechanism of 3'-5' nucleotide addition remain. Here, we use transient kinetics to measure the pseudo-first-order forward rate constants for the three steps of the G(-1) addition reaction catalyzed by yeast Thg1: adenylylation of the 5' end of the tRNA (k(aden)), nucleotidyl transfer (k(ntrans)), and removal of pyrophosphate from the G(-1)-containing tRNA (k(ppase)). This kinetic framework, in conjunction with the crystal structure of nucleotide-bound Thg1, suggests a likely role for two-metal ion chemistry in all three chemical steps of the G(-1) addition reaction. Furthermore, we have identified additional residues (K44 and N161) involved in adenylylation and three positively charged residues (R27, K96, and R133) that participate primarily in the nucleotidyl transfer step of the reaction. These data provide a foundation for understanding the mechanism of 3'-5' nucleotide addition in tRNA(His) maturation.


Assuntos
Células Eucarióticas/enzimologia , Guanosina/química , Nucleotidiltransferases/química , RNA Nucleotidiltransferases/química , Aminoacil-RNA de Transferência/química , Catálise , Proteínas de Homeodomínio/química , Humanos , Saccharomyces cerevisiae/enzimologia , Proteínas de Saccharomyces cerevisiae/química
8.
Philos Trans R Soc Lond B Biol Sci ; 377(1842): 20200474, 2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34839711

RESUMO

Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the Pseudomonas syringae megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of Pseudomonas stutzeri populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.


Assuntos
Pseudomonas stutzeri , Transferência Genética Horizontal , Plasmídeos/genética , Pseudomonas stutzeri/genética , Pseudomonas syringae/genética , Análise de Sequência de DNA
9.
mSystems ; 7(2): e0009122, 2022 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-35293790

RESUMO

Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. strain 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. strain 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. To begin to understand such symbioses, we developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in coculture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in coculture was greater than in axenic culture, but the opposite was true for Pestalotiopsis sp. Dual-transcriptome sequencing (RNA-seq) data demonstrate that growing in coculture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. IMPORTANCE Interactions between microbes and their hosts have important outcomes for host and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual-RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together versus separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and the potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.


Assuntos
Ascomicetos , Fungos não Classificados , Gammaproteobacteria , Sistemas de Secreção Tipo VI , Xanthomonadaceae , Simbiose , Endófitos , Pestalotiopsis , Ascomicetos/genética , Bactérias/genética , Plantas , Metionina
10.
Perspect Biol Med ; 54(2): 121-31, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21532128

RESUMO

Loss of consciousness in pilots during rapid ascent after bombing missions was a major problem in World War II, and experiments were undertaken to study the cause of this phenomenon. Postulating impaired cerebral blood flow as a likely mechanism, the investigators developed a neck device, the KRA Cuff, which when inflated could shut off blood supply to the brain. With cessation of blood flow for up to 100 seconds, the investigators observed a sequence of responses, including unconsciousness, followed by dilated pupils, tonic/clonic movements, loss of bladder and eventually bowel control, and appearance of pathological reflexes. This study, carried out in prisoners and patients with schizophrenia in 1941-42, largely disappeared from public discourse for a number of years. It has received occasional attention subsequently and been considered controversial. Recently discovered records, including extensive written and photographic data from the studies, shed new light on the methods and motives of the research team. We describe here this new information and its implications for the scientific and ethical assessment of the study.


Assuntos
Pesquisa Biomédica/história , Encéfalo/irrigação sanguínea , Circulação Cerebrovascular , Hipóxia Encefálica/fisiopatologia , Fisiologia/história , Aeronaves , Doença da Altitude/fisiopatologia , Piscadela , Tempo de Circulação Sanguínea , Ética Médica , História do Século XX , Humanos , Pressão , Prisioneiros , Esquizofrenia/fisiopatologia , Estresse Fisiológico , Inconsciência/fisiopatologia , II Guerra Mundial
11.
J Sleep Res ; 18(3): 291-303, 2009 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-19552702

RESUMO

Few studies have investigated waking electrophysiological measures of arousal during sleep restriction. This study examined electroencephalogram (EEG) activity and performance during a 96-hour laboratory protocol where participants slept a baseline night (8 h), were randomly assigned to 3-, 5-, or 8-hour sleep groups for the next two nights sleep restriction (SR1, SR2), and then slept a recovery night (8 h). There were dose-dependent deficits on measures of mood, sleepiness, and reaction time that were apparent during this short-term bout of sleep restriction. The ratio of alpha to theta EEG recorded at rest indicated dose-dependent changes in CNS arousal. At 9:00 hours, both the 3- and 5-hour groups showed EEG slowing (sleepiness) during restriction, with the 3-hour group exhibiting greater deficits. Later in the day at 13:00 hours, the 5-hour group no longer exhibited EEG slowing, but the extent of slowing was more widespread across the scalp for the 3-hour group. High-frequency EEG, a measure of effort, was greater on the mornings following sleep restriction. The 5-hour group had increased beta EEG at central-parietal sites following both nights of restriction, whereas the 3-hour group had increased beta and gamma EEG at occipital regions following the first night only. Short-term sleep restriction leads to deficits in performance as well as EEG slowing that correspond to the amount and duration of sleep loss. High-frequency EEG may be a marker of effort or compensation.


Assuntos
Afeto/fisiologia , Nível de Alerta/fisiologia , Atenção/fisiologia , Córtex Cerebral/fisiopatologia , Eletroencefalografia , Fadiga/fisiopatologia , Tempo de Reação/fisiologia , Processamento de Sinais Assistido por Computador , Privação do Sono/fisiopatologia , Vigília/fisiologia , Adolescente , Mapeamento Encefálico , Dominância Cerebral/fisiologia , Potenciais Evocados/fisiologia , Feminino , Análise de Fourier , Humanos , Masculino , Rememoração Mental/fisiologia , Testes Neuropsicológicos , Lobo Occipital/fisiopatologia , Lobo Parietal/fisiopatologia , Polissonografia , Adulto Jovem
12.
Biochem J ; 410(3): 455-62, 2008 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-18031291

RESUMO

The OXA-1 beta-lactamase is one of the few class D enzymes that has an aspartate residue at position 66, a position that is proximal to the active-site residue Ser(67). In class A beta-lactamases, such as TEM-1 and SHV-1, residues adjacent to the active-site serine residue play a crucial role in inhibitor resistance and substrate selectivity. To probe the role of Asp(66) in substrate affinity and catalysis, we performed site-saturation mutagenesis at this position. Ampicillin MIC (minimum inhibitory concentration) values for the full set of Asp(66) mutants expressed in Escherichia coli DH10B ranged from < or =8 microg/ml for cysteine, proline and the basic amino acids to > or =256 microg/ml for asparagine, leucine and the wild-type aspartate. Replacement of aspartic acid by asparagine at position 66 also led to a moderate enhancement of extended-spectrum cephalosporin resistance. OXA-1 shares with other class D enzymes a carboxylated residue, Lys(70), that acts as a general base in the catalytic mechanism. The addition of 25 mM bicarbonate to Luria-Bertani-broth agar resulted in a > or =16-fold increase in MICs for most OXA-1 variants with amino acid replacements at position 66 when expressed in E. coli. Because Asp(66) forms hydrogen bonds with several other residues in the OXA-1 active site, we propose that this residue plays a role in stabilizing the CO2 bound to Lys(70) and thereby profoundly affects substrate turnover.


Assuntos
Ácido Aspártico/metabolismo , Carbamatos/metabolismo , beta-Lactamases/metabolismo , Sequência de Bases , Sítios de Ligação , Western Blotting , Primers do DNA , Cinética , Testes de Sensibilidade Microbiana , Mutagênese Sítio-Dirigida , Especificidade por Substrato , beta-Lactamases/biossíntese , beta-Lactamases/química
13.
Genome Biol Evol ; 11(4): 1192-1206, 2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30918968

RESUMO

Pseudomonads are ubiquitous group of environmental proteobacteria, well known for their roles in biogeochemical cycling, in the breakdown of xenobiotic materials, as plant growth promoters, and as pathogens of a variety of host organisms. We have previously identified a large megaplasmid present within one isolate of the plant pathogen Pseudomonas syringae, and here we report that a second member of this megaplasmid family is found within an environmental Pseudomonad isolate most closely related to Pseudomonas putida. Many of the shared genes are involved in critical cellular processes like replication, transcription, translation, and DNA repair. We argue that presence of these shared pathways sheds new light on discussions about the types of genes that undergo horizontal gene transfer (i.e., the complexity hypothesis) as well as the evolution of pangenomes. Furthermore, although both megaplasmids display a high level of synteny, genes that are shared differ by over 50% on average at the amino acid level. This combination of conservation in gene order despite divergence in gene sequence suggests that this Pseudomonad megaplasmid family is relatively old, that gene order is under strong selection within this family, and that there are likely many more members of this megaplasmid family waiting to be found in nature.


Assuntos
Evolução Molecular , Plasmídeos/genética , Pseudomonas putida/genética , Pseudomonas syringae/genética , Genes Essenciais , Família Multigênica , RNA de Transferência/genética
14.
Pediatrics ; 141(6)2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29793986

RESUMO

Antibiotic-resistant infections pose a growing threat to public health. Antibiotic use, regardless of whether it is warranted, is a primary factor in the development of resistance. In the United States, the majority of antibiotic health care expenditures are due to prescribing in outpatient settings. Much of this prescribing is inappropriate, with research showing that at least 30% of antibiotic use in outpatient settings is unnecessary. In this State of the Art Review article, we provide an overview of the latest research on outpatient antibiotic prescribing practices in the United States. Although many of the researchers in these studies describe antibiotic prescribing across all patient age groups, we highlight prescribing in pediatric populations when data are available. We then describe the various factors that can influence a physician's prescribing decisions and drive inappropriate antibiotic use and the potential role of behavioral science in enhancing stewardship interventions to address these drivers. Finally, we highlight the role that a wide range of health care stakeholders can play in aiding the expansion of outpatient stewardship efforts that are needed to fully address the threat of antibiotic resistance.


Assuntos
Assistência Ambulatorial , Gestão de Antimicrobianos , Prescrição Inadequada/prevenção & controle , Antibacterianos/uso terapêutico , Tomada de Decisão Clínica , Prescrições de Medicamentos/estatística & dados numéricos , Farmacorresistência Bacteriana Múltipla , Humanos , Preferência do Paciente , Satisfação do Paciente , Padrões de Prática Médica , Fatores de Tempo , Carga de Trabalho
15.
J Mol Biol ; 430(12): 1745-1759, 2018 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-29660326

RESUMO

Ribosomal RNA (rRNA) is a major component of ribosomes and is fundamental to the process of translation. In bacteria, 16S rRNA is a component of the small ribosomal subunit and plays a critical role in mRNA decoding. rRNA maturation entails the removal of intervening spacer sequences contained within the pre-rRNA transcript by nucleolytic enzymes. Enzymatic activities involved in maturation of the 5'-end of 16S rRNA have been identified, but those involved in 3'-end maturation of 16S rRNA are more enigmatic. Here, we investigate molecular details of 16S rRNA maturation using purified in vivo-formed small subunit (SSU) assembly intermediates (pre-SSUs) from wild-type Escherichia coli that contain precursor 16S rRNA (17S rRNA). Upon incubation of pre-SSUs with E. coli S100 cell extracts or purified enzymes implicated in 16S rRNA processing, the 17S rRNA is processed into additional intermediates and mature 16S rRNA. These results illustrate that exonucleases RNase R, RNase II, PNPase, and RNase PH can process the 3'-end of pre-SSUs in vitro. However, the endonuclease YbeY did not exhibit nucleolytic activity with pre-SSUs under these conditions. Furthermore, these data demonstrate that multiple pathways facilitate 16S rRNA maturation with pre-SSUs in vitro, with the dominant pathways entailing complete processing of the 5'-end of 17S rRNA prior to 3'-end maturation or partial processing of the 5'-end with concomitant processing of the 3'-end. These results reveal the multifaceted nature of SSU biogenesis and suggest that E. coli may be able to escape inactivation of any one enzyme by using an existing complementary pathway.


Assuntos
Escherichia coli/genética , RNA Ribossômico 16S/genética , Subunidades Ribossômicas Menores de Bactérias/metabolismo , Proteínas de Escherichia coli/metabolismo , Metaloproteínas/metabolismo , Processamento Pós-Transcricional do RNA , RNA Bacteriano/genética , RNA Ribossômico 16S/metabolismo , Proteínas S100/metabolismo
16.
FEMS Microbiol Lett ; 365(9)2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29579234

RESUMO

Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.


Assuntos
Doenças dos Peixes/microbiologia , Genômica/métodos , Infecções por Pseudomonas/veterinária , Pseudomonas/genética , Análise de Sequência de DNA/métodos , Animais , Genoma Bacteriano , Genômica/instrumentação , Nanoporos , Fenótipo , Filogenia , Pseudomonas/classificação , Pseudomonas/isolamento & purificação , Infecções por Pseudomonas/microbiologia , Semicondutores , Análise de Sequência de DNA/instrumentação
17.
Cancer Res ; 65(21): 9834-42, 2005 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-16267006

RESUMO

The p14 alternate reading frame (ARF) tumor suppressor plays a central role in cancer by binding to mdm2 (Hdm2 in humans) and enhancing p53-mediated apoptosis following DNA damage and oncogene activation. It is unclear, however, how ARF initiates its involvement in the p53/mdm2 pathway, as p53 and mdm2 are located in the nucleoplasm, whereas ARF is largely nucleolar in tumor cells. We have used immunofluorescence and coimmunoprecipitation to examine how the subnuclear distribution and protein-protein interactions of ARF change immediately after DNA damage and over the time course of the DNA damage response in human tumor cells. We find that DNA damage disrupts the interaction of ARF with the nucleolar protein B23(nucleophosmin) and promotes a transient p53-independent translocation of ARF to the nucleoplasm, resulting in a masking of the ARF NH2 terminus that correlates with the appearance of ARF-Hdm2 complexes. The translocation also results in an unmasking of the ARF COOH terminus, suggesting that redistribution disrupts a nucleolar interaction of ARF involving this region. By 24 hours after irradiation, DNA repair has ceased and the pretreatment immunofluorescence patterns and complexes of ARF have been restored. Although the redistribution of ARF is independent of p53 and likely to be regulated by interactions other than Hdm2, ARF does not promote UV sensitization unless p53 is expressed. The results implicate the nucleolus and nucleolar interactions of the ARF, including potentially novel interactions involving its COOH terminus as sites for early DNA damage and stress-mediated cellular events.


Assuntos
Nucléolo Celular/metabolismo , Dano ao DNA/fisiologia , Proteínas Nucleares/metabolismo , Proteína Supressora de Tumor p14ARF/metabolismo , Sequência de Aminoácidos , Linhagem Celular Tumoral , Sobrevivência Celular/fisiologia , Sobrevivência Celular/efeitos da radiação , Humanos , Microscopia de Fluorescência , Dados de Sequência Molecular , Nucleofosmina , Nucleoplasminas , Fosfoproteínas/metabolismo , Proteína Supressora de Tumor p53/metabolismo , Raios Ultravioleta
18.
J Orthop Res ; 35(7): 1523-1531, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-27556250

RESUMO

Several surgically corrective procedures are considered to treat Adult Acquired Flatfoot Deformity (AAFD) patients, relieve pain, and restore function. Procedure selection is based on best practices and surgeon preference. Recent research created patient specific models of AAFD to explore their predictive capabilities and examine effectiveness of the surgical procedure used to treat the deformity. The models' behavior was governed solely by patient bodyweight, soft tissue constraints, muscle loading, and joint contact without the assumption of idealized joints. The current work expanded those models to determine if an alternate procedure would be more effective for the individual. All procedures incorporated first a tendon transfer and then included one hindfoot procedure, the Medializing Calcaneal Osteotomy (MCO), and one of three lateral column procedures: Evans osteotomy, Calcaneocuboid Distraction Arthrodesis (CCDA), Z osteotomy, and the combination procedures MCO & Evans osteotomy, MCO & CCDA, and MCO & Z osteotomy. The combination MCO & Evans and MCO & Z procedures were shown to provide the greatest amount of correction for both forefoot abduction and hindfoot valgus. However, these two procedures significantly increased joint contact force, specifically at the calcaneocuboid joint, and ground reaction force along the lateral column. With exception to the lateral bands of the plantar fascia and middle spring ligament, the strain present in the plantar fascia, spring, and deltoid ligaments decreased after all procedures. The use of patient specific computational models provided the ability to investigate effects of alternate surgical corrections on restoring biomechanical function in these flatfoot patients. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1523-1531, 2017.


Assuntos
Calcâneo/cirurgia , Pé Chato/cirurgia , Ligamentos/fisiologia , Modelos Teóricos , Medicina de Precisão , Pé Chato/diagnóstico por imagem , Articulações do Pé/diagnóstico por imagem , Articulações do Pé/fisiologia , Humanos , Radiografia , Transferência Tendinosa
19.
Cancer Res ; 63(14): 4239-43, 2003 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-12874032

RESUMO

Elucidation of the mechanisms of hormone-independent metastatic prostate cancer remains a significant and highly relevant challenge. We report here that hormone-refractory human prostate carcinoma growing orthotopically efficiently deliver viable metastatic cells in the host circulation. This is in contrast to the ectopic tumors of the same lineage, which do not deliver live cells into the circulation. To investigate the malignant potential of viable circulating carcinoma cells, we developed a novel dual-color orthotopic coimplantation model of human prostate cancer metastasis in nude mice. This model is comprised of coinjection of an equivalent mixture of isolated and cultured circulating green fluorescent protein-expressing clones and parental red fluorescent protein-expressing human prostate carcinoma cells. In the dual-color model, the selected green fluorescent protein-labeled viable circulating cells have an increased metastatic propensity relative to the red fluorescent protein-labeled parental cells. The identification and isolation of highly malignant viable circulating human prostate carcinoma cells from orthotopic but not ectopic models will enable important new insights into the metastatic process including the role of the tumor microenvironment.


Assuntos
Células Neoplásicas Circulantes/patologia , Neoplasias da Próstata/patologia , Animais , Humanos , Masculino , Camundongos , Camundongos Nus , Microscopia de Fluorescência , Metástase Neoplásica , Transplante de Neoplasias , Neoplasias da Próstata/sangue , Transplante Heterólogo
20.
Orthop J Sports Med ; 3(12): 2325967115617932, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26779551

RESUMO

BACKGROUND: Females experience greater overall rates of athletic anterior cruciate ligament (ACL) injury than males. The specific mechanisms of the predisposition remain unclear. HYPOTHESIS: Modeling of knee kinematics has shown that the more extended the knee joint, the greater the strain on the ACL. The authors hypothesized that female athletes would have a lesser degree of knee flexion than male athletes at initial ground contact while performing change-of-direction cutting maneuvers. STUDY DESIGN: Controlled laboratory study. METHODS: Twenty female and 20 male high school soccer athletes with at least 1 year of experience were recruited for the study. Athletes were excluded if they had a history of any major lower limb injury or current knee pain causing a reduction in training and/or competition. Reflective markers were attached at the greater trochanter of the femur, the lateral epicondyle of the knee, and the lateral malleolus of the ankle to enable motion capture. Each athlete performed 6 change-of-direction maneuvers in random order in front of 2 cameras. Multiple regression analysis was used to determine differences between the sexes from the motion data captured; P < .05 defined significance. RESULTS: Statistically significant differences existed in knee flexion angles between male and female participants at the 90° and 135° cutting angles. At 90°, males and females showed initial contact knee flexion angles (mean ± SD) of 39.0° ± 6.8° and 29.3° ± 6.2°, respectively (P < .0001), and mean maximum flexion angles of 56.4° ± 6.9° and 49.7° ± 7.0°, respectively (P = .0036). At 135°, males and females showed mean initial contact knee flexion angles of 36.8° ± 7.9° and 29.7° ± 7.8°, respectively (P = .0053), and mean maximum flexion angles of 60.7° ± 8.1° and 51.6° ± 9.4°, respectively (P = .0017). CONCLUSION: The research conducted is intended to foster an awareness of injury disposition in female athletes and guide future endeavors to develop, test, and implement a proactive approach in lowering female noncontact athletic ACL injury rates. This project adds to the literature as wider side-cut maneuvers (≥90°) were studied, as compared with previous studies using small side-cut angles (<90°), offering a model for alternative sports actions.

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