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1.
J Biomol Tech ; 28(1): 31-39, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28337070

RESUMO

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.


Assuntos
Microbiologia Ambiental , Microbiota/genética , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Ambientes Extremos , Metagenoma , Tipagem Molecular/normas , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , Padrões de Referência , Análise de Sequência de DNA/normas
2.
J Wildl Dis ; 53(2): 248-257, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28118558

RESUMO

Hereditary disorders and genetic predispositions to disease are rarely reported in captive and free-ranging wildlife, and none have been definitively identified and characterized in elephants. A wild-caught, 41-yr-old male Asian elephant ( Elephas maximus ) without an apparent increased bleeding tendency was consistently found to have prolonged prothrombin times (PTs, mean=55±35 s) compared to 17 other elephants (PT=10±2 s). This elephant's partial thromboplastin times (PTT) fell within the normal range of the other elephants (12-30 s). A prolonged PT in the presence of a normal PTT suggests disruption of the extrinsic pathway via deficiency of coagulation Factor VII (FVII). This elephant's plasma FVII activity was very low (2%) compared to that of 15 other elephants (57-80%), but other coagulation factors' activities did not differ from the control elephants. Sequencing of genomic DNA from ethylenediaminetetraacetic acid blood revealed a single homozygous point mutation (c.202A>G) in the F7 gene of the FVII deficient elephant that was not present in unrelated elephants. This mutation causes an amino acid substitution (p.Arg68Gly) that is predicted to be deleterious. Two living offspring of the affected elephant were heterozygous for the mutation and had normal plasma FVII activities and coagulation profiles. Tissue from a third offspring, a deceased calf, was utilized to show that it was also a heterozygote. A DNA test has been developed to enable the screening of additional elephants for this mutation. Consistent with FVII deficiency investigations in other species, the condition did not cause a serious bleeding tendency in this individual elephant.


Assuntos
Elefantes/genética , Deficiência do Fator VII/veterinária , Mutação de Sentido Incorreto , Animais , Animais Selvagens , Masculino , Mutação
3.
NPJ Microgravity ; 2: 16035, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-28725742

RESUMO

Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space.

5.
Appl Environ Microbiol ; 76(21): 7161-70, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20851978

RESUMO

Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N2O. A total of 109 genes displayed expression that differed significantly between soils with low and high N2O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.


Assuntos
Análise de Sequência com Séries de Oligonucleotídeos/métodos , Microbiologia do Solo , Biota , DNA Bacteriano/análise , DNA Bacteriano/genética , DNA Complementar/genética , Genes Bacterianos/genética , Fixação de Nitrogênio/genética , RNA Bacteriano/análise , RNA Bacteriano/genética , Solo/análise
6.
J Microbiol Methods ; 75(2): 172-6, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18582973

RESUMO

The advent of metagenomics has revealed that our planet harbors millions of previously undiscovered microbial species. However, functional insights into the activities of microbial communities cannot easily be obtained using metagenomics. Using transcriptional analyses to study microbial gene functions is currently problematic due to difficulties working with unstable microbial mRNA as a small fraction of total cellular RNA. Current techniques can be expensive and time consuming, and still result in significant levels of rRNA contamination. We have adapted techniques to rapidly isolate high high-quality RNA from environmental samples and developed a simple method for specific isolation of mRNA by size separation. This new technique was evaluated by constructing cDNA libraries directly from uncultured environmental microbial communities, including agricultural soil samples, aquatic flocculants, organic composts, mammalian oral and faecal samples, and wastewater sludge. The sequencing of a fraction of these cDNA clones revealed a high degree of novelty, demonstrating the potential of this approach to capture a large number of unique transcripts directly from the environment. To our knowledge, this is the first study that uses gel electrophoresis to isolate mRNA from microbial communities. We conclude that this method could be used to provide insights into the microbial 'metatranscriptome' of entire microbial communities. Coupled with high-throughput sequencing or the construction of cDNA microarrays, this approach will provide a useful tool to study the transcriptional activities of microorganisms, including those of entire microbial communities and of non-culturable microorganisms.


Assuntos
Microbiologia Ambiental , Perfilação da Expressão Gênica , RNA Mensageiro , Animais , Bovinos , Clonagem Molecular , Ecossistema , Fezes/microbiologia , Água Doce/microbiologia , Biblioteca Gênica , Humanos , Boca/microbiologia , RNA Mensageiro/análise , RNA Mensageiro/genética , RNA Mensageiro/isolamento & purificação , RNA Ribossômico 16S/genética , Rúmen/microbiologia , Análise de Sequência de DNA , Microbiologia do Solo
7.
Plant Physiol ; 139(2): 949-59, 2005 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-16183832

RESUMO

To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance.


Assuntos
Arabidopsis/genética , Arabidopsis/metabolismo , Ciclopentanos/metabolismo , Etilenos/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Expressão Gênica , Genes de Plantas , Genoma de Planta , Oxilipinas , Filogenia , Doenças das Plantas/genética , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Transdução de Sinais , Transativadores/genética , Transativadores/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
8.
Pain ; 111(3): 313-22, 2004 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-15363875

RESUMO

We investigated adverse events (AEs) associated with perioperative tenoxicam in a double-blind, prospective, randomised study. Patients undergoing surgery, screened for contraindications to non-steroidal anti-inflammatory drug, received tenoxicam (n=750) on 2843 days or placebo (n=251) on 988 days, in courses of 1-12 days. There was no increase in the overall incidence of side effects with tenoxicam (33 vs 38% with placebo: P=0.15), or in major side effects (3.9 vs 2.0% with placebo: P=0.11). Of major side effects possibly or probably related to tenoxicam (2.1 vs 1.2% with placebo: P=0.26), all but one involved post-operative surgical site bleeding. However, in the subgroup of patients undergoing otorhinolaryngology surgery, surgical site bleeding occurred in 18 of 171 (10.5%) patients on tenoxicam and one of 57 (1.8%) on placebo (P=0.026); of these, nine in the tenoxicam group and 0 in the placebo were classified as major (P=0.07). One patient on tenoxicam experienced endoscopically proven duodenal ulceration with malaena. In conclusion, perioperative tenoxicam is well tolerated in comparison with placebo and the incidence of drug-related major AEs (other than post-operative bleeding) is no greater than 1 in 150 in low risk patients, but in patients undergoing otorhinolaryngological surgery there may be an increased risk of post-operative bleeding.


Assuntos
Assistência Perioperatória/métodos , Piroxicam/análogos & derivados , Piroxicam/efeitos adversos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Intervalos de Confiança , Método Duplo-Cego , Feminino , Gastroenteropatias/induzido quimicamente , Humanos , Masculino , Pessoa de Meia-Idade , Assistência Perioperatória/estatística & dados numéricos , Piroxicam/uso terapêutico , Estudos Prospectivos
9.
Plant Physiol ; 132(2): 1020-32, 2003 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-12805630

RESUMO

The PDF1.2 gene of Arabidopsis encoding a plant defensin is commonly used as a marker for characterization of the jasmonate-dependent defense responses. Here, using PDF1.2 promoter-deletion lines linked to the beta-glucoronidase-reporter gene, we examined putative promoter elements associated with jasmonate-responsive expression of this gene. Using stably transformed plants, we first characterized the extended promoter region that positively regulates basal expression from the PDF1.2 promoter. Second, using promoter deletion constructs including one from which the GCC-box region was deleted, we observed a substantially lower response to jasmonate than lines carrying this motif. In addition, point mutations introduced into the core GCC-box sequence substantially reduced jasmonate responsiveness, whereas addition of a 20-nucleotide-long promoter element carrying the core GCC-box and flanking nucleotides provided jasmonate responsiveness to a 35S minimal promoter. Taken together, these results indicated that the GCC-box plays a key role in conferring jasmonate responsiveness to the PDF1.2 promoter. However, deletion or specific mutations introduced into the core GCC-box did not completely abolish the jasmonate responsiveness of the promoter, suggesting that the other promoter elements lying downstream from the GCC-box region may also contribute to jasmonate responsiveness. In other experiments, we identified a jasmonate- and pathogen-responsive ethylene response factor transcription factor, AtERF2, which when overexpressed in transgenic Arabidopsis plants activated transcription from the PDF1.2, Thi2.1, and PR4 (basic chitinase) genes, all of which contain a GCC-box sequence in their promoters. Our results suggest that in addition to their roles in regulating ethylene-mediated gene expression, ethylene response factors also appear to play important roles in regulating jasmonate-responsive gene expression, possibly via interaction with the GCC-box.


Assuntos
Arabidopsis/genética , Ciclopentanos/farmacologia , Defensinas , Regulação da Expressão Gênica de Plantas/genética , Proteínas de Plantas/genética , Arabidopsis/efeitos dos fármacos , Proteínas de Arabidopsis/genética , Sequência de Bases , Northern Blotting , Primers do DNA , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Cinética , Oxilipinas , Reguladores de Crescimento de Planta/farmacologia , Plantas Geneticamente Modificadas/efeitos dos fármacos , Plantas Geneticamente Modificadas/genética , Reação em Cadeia da Polimerase , Regiões Promotoras Genéticas/efeitos dos fármacos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transcrição Genética/efeitos dos fármacos
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