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1.
Mol Microbiol ; 116(2): 397-415, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-33756056

RESUMEN

Endolysin enzymes from bacteriophage cause bacterial lysis by degrading the peptidoglycan cell wall. The streptococcal C1 phage endolysin PlyC, is the most potent endolysin described to date and can rapidly lyse group A, C, and E streptococci. PlyC is known to bind the Group A streptococcal cell wall, but the specific molecular target or the binding site within PlyC remain uncharacterized. Here we report for the first time, that the polyrhamnose backbone of the Group A streptococcal cell wall is the binding target of PlyC. We have also characterized the putative rhamnose binding groove of PlyC and found four key residues that were critical to either the folding or the cell wall binding action of PlyC. Based on our results, we suggest that the interaction between PlyC and the cell wall may not be a high-affinity interaction as previously proposed, but rather a high avidity one, allowing for PlyC's remarkable lytic activity. Resistance to our current antibiotics is reaching crisis levels and there is an urgent need to develop the antibacterial agents with new modes of action. A detailed understanding of this potent endolysin may facilitate future developments of PlyC as a tool against the rise of antibiotic resistance.


Asunto(s)
Bacteriófagos/metabolismo , Endopeptidasas/metabolismo , Peptidoglicano/metabolismo , Ramnosa/metabolismo , Streptococcus pyogenes/virología , Bacteriófagos/genética , Sitios de Unión/fisiología , Membrana Celular/metabolismo , Pared Celular/metabolismo , Endopeptidasas/genética , Simulación del Acoplamiento Molecular , Unión Proteica/fisiología , Streptococcus pyogenes/metabolismo
2.
Environ Sci Technol ; 55(18): 12683-12693, 2021 09 21.
Artículo en Inglés | MEDLINE | ID: mdl-34472853

RESUMEN

Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.


Asunto(s)
Hielos Perennes , Regiones Árticas , Canadá , Carbono , Metagenómica , ARN Ribosómico 16S/genética , Suelo , Microbiología del Suelo
3.
Horm Metab Res ; 50(12): 908-921, 2018 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-30360003

RESUMEN

Human thyroid peroxidase (TPO), is an important enzyme responsible for the biosynthesis of thyroid hormones and is a major autoantigen in autoimmune thyroid diseases (AITDs) such as the destructive Hashimoto's thyroiditis. Although the structure of TPO has yet to be determined, its extracellular domain consists of three regions that exhibit a high degree of sequence similarity to domains of known three-dimensional structure: the myeloperoxidase (MPO)-like domain, complement control protein (CCP)-like domain, and epidermal growth factor (EGF)-like domain. Homology models of TPO can therefore be constructed, providing some structural context to its known function, as well as facilitating the mapping of regions that are responsible for its autoantigenicity. In this review, we highlight recent progress in this area, in particular how a molecular modelling approach has advanced the visualisation and interpretation of epitope mapping studies for TPO, facilitating the dissection of the interplay between TPO protein structure, function, and autoantigenticity.


Asunto(s)
Autoantígenos/química , Autoantígenos/metabolismo , Enfermedad de Hashimoto/enzimología , Enfermedad de Hashimoto/inmunología , Yoduro Peroxidasa/química , Yoduro Peroxidasa/metabolismo , Secuencia de Aminoácidos , Animales , Epítopos/metabolismo , Humanos , Ingeniería de Proteínas , Homología Estructural de Proteína
4.
Front Microbiol ; 14: 1305967, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38075856

RESUMEN

Inadequate sampling approaches to wastewater analyses can introduce biases, leading to inaccurate results such as false negatives and significant over- or underestimation of average daily viral concentrations, due to the sporadic nature of viral input. To address this challenge, we conducted a field trial within the University of Tennessee residence halls, employing different composite sampling modes that encompassed different time intervals (1 h, 2 h, 4 h, 6 h, and 24 h) across various time windows (morning, afternoon, evening, and late-night). Our primary objective was to identify the optimal approach for generating representative composite samples of SARS-CoV-2 from raw wastewater. Utilizing reverse transcription-quantitative polymerase chain reaction, we quantified the levels of SARS-CoV-2 RNA and pepper mild mottle virus (PMMoV) RNA in raw sewage. Our findings consistently demonstrated that PMMoV RNA, an indicator virus of human fecal contamination in water environment, exhibited higher abundance and lower variability compared to pathogenic SARS-CoV-2 RNA. Significantly, both SARS-CoV-2 and PMMoV RNA exhibited greater variability in 1 h individual composite samples throughout the entire sampling period, contrasting with the stability observed in other time-based composite samples. Through a comprehensive analysis of various composite sampling modes using the Quade Nonparametric ANCOVA test with date, PMMoV concentration and site as covariates, we concluded that employing a composite sampler during a focused 6 h morning window for pathogenic SARS-CoV-2 RNA is a pragmatic and cost-effective strategy for achieving representative composite samples within a single day in wastewater-based epidemiology applications. This method has the potential to significantly enhance the accuracy and reliability of data collected at the community level, thereby contributing to more informed public health decision-making during a pandemic.

5.
Environ Microbiome ; 18(1): 33, 2023 Apr 13.
Artículo en Inglés | MEDLINE | ID: mdl-37055869

RESUMEN

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

6.
Front Microbiol ; 14: 1144026, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37187532

RESUMEN

Introduction: Although severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA has been frequently detected in sewage from many university dormitories to inform public health decisions during the COVID-19 pandemic, a clear understanding of SARS-CoV-2 RNA persistence in site-specific raw sewage is still lacking. To investigate the SARS-CoV-2 RNA persistence, a field trial was conducted in the University of Tennessee dormitories raw sewage, similar to municipal wastewater. Methods: The decay of enveloped SARS-CoV-2 RNA and non-enveloped Pepper mild mottle virus (PMMoV) RNA was investigated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in raw sewage at 4°C and 20°C. Results: Temperature, followed by the concentration level of SARS-CoV-2 RNA, was the most significant factors that influenced the first-order decay rate constants (k) of SARS-CoV-2 RNA. The mean k values of SARS-CoV-2 RNA were 0.094 day-1 at 4°C and 0.261 day-1 at 20°C. At high-, medium-, and low-concentration levels of SARS-CoV-2 RNA, the mean k values were 0.367, 0.169, and 0.091 day-1, respectively. Furthermore, there was a statistical difference between the decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA at different temperature conditions. Discussion: The first decay rates for both temperatures were statistically comparable for SARS-CoV-2 RNA, which showed sensitivity to elevated temperatures but not for PMMoV RNA. This study provides evidence for the persistence of viral RNA in site-specific raw sewage at different temperature conditions and concentration levels.

7.
Environ Sci Technol ; 46(3): 1361-70, 2012 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-22191430

RESUMEN

Ponds receiving latrine effluents may serve as sources of fecal contamination to shallow aquifers tapped by millions of tube-wells in Bangladesh. To test this hypothesis, transects of monitoring wells radiating away from four ponds were installed in a shallow sandy aquifer underlying a densely populated village and monitored for 14 months. Two of the ponds extended to medium sand. Another pond was sited within silty sand and the last in silt. The fecal indicator bacterium E. coli was rarely detected along the transects during the dry season and was only detected near the ponds extending to medium sand up to 7 m away during the monsoon. A log-linear decline in E. coli and Bacteroidales concentrations with distance along the transects in the early monsoon indicates that ponds excavated in medium sand were the likely source of contamination. Spatial removal rates ranged from 0.5 to 1.3 log(10)/m. After the ponds were artificially filled with groundwater to simulate the impact of a rain storm, E. coli levels increased near a pond recently excavated in medium sand, but no others. These observations show that adjacent sediment grain-size and how recently a pond was excavated influence the how much fecal contamination ponds receiving latrine effluents contribute to neighboring groundwater.


Asunto(s)
Monitoreo del Ambiente/estadística & datos numéricos , Escherichia coli/aislamiento & purificación , Aguas del Alcantarillado/microbiología , Cuartos de Baño , Abastecimiento de Agua , Pozos de Agua/microbiología , Bangladesh , Monitoreo del Ambiente/métodos , Sedimentos Geológicos , Tamaño de la Partícula
8.
J Water Health ; 10(4): 565-78, 2012 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-23165714

RESUMEN

Bangladesh is underlain by shallow aquifers in which millions of drinking water wells are emplaced without annular seals. Fecal contamination has been widely detected in private tubewells. To evaluate the impact of well construction on microbial water quality 35 private tubewells (11 with intact cement platforms, 19 without) and 17 monitoring wells (11 with the annulus sealed with cement, six unsealed) were monitored for culturable Escherichia coli over 18 months. Additionally, two 'snapshot' sampling events were performed on a subset of wells during late-dry and early-wet seasons, wherein the fecal indicator bacteria (FIB) E. coli, Bacteroidales and the pathogenicity genes eltA (enterotoxigenic E. coli; ETEC), ipaH (Shigella) and 40/41 hexon (adenovirus) were detected using quantitative polymerase chain reaction (qPCR). No difference in E. coli detection frequency was found between tubewells with and without platforms. Unsealed private wells, however, contained culturable E. coli more frequently and higher concentrations of FIB than sealed monitoring wells (p < 0.05), suggestive of rapid downward flow along unsealed annuli. As a group the pathogens ETEC, Shigella and adenovirus were detected more frequently (10/22) during the wet season than the dry season (2/20). This suggests proper sealing of private tubewell annuli may lead to substantial improvements in microbial drinking water quality.


Asunto(s)
Monitoreo del Ambiente/métodos , Heces/microbiología , Pozos de Agua/microbiología , Adenoviridae/genética , Adenoviridae/aislamiento & purificación , Proteínas Bacterianas/genética , Bangladesh , Proteínas de la Cápside/genética , Agua Potable/microbiología , Escherichia coli Enterotoxigénica/genética , Escherichia coli Enterotoxigénica/aislamiento & purificación , Proteínas de Escherichia coli/genética , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Shigella/genética , Shigella/aislamiento & purificación , Calidad del Agua
9.
J Bacteriol ; 193(18): 5009-10, 2011 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-21742869

RESUMEN

Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ∼6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.


Asunto(s)
ADN Bacteriano/química , ADN Bacteriano/genética , Genoma Bacteriano , Pseudomonas fluorescens/genética , Análisis de Secuencia de ADN , Genes Reporteros , Ingeniería Genética , Islas Genómicas , Luciferasas/genética , Luciferasas/metabolismo , Datos de Secuencia Molecular , Plásmidos , Hidrocarburos Policíclicos Aromáticos/metabolismo , Profagos/genética , Pseudomonas fluorescens/metabolismo
10.
FEMS Microbiol Ecol ; 96(12)2020 11 25.
Artículo en Inglés | MEDLINE | ID: mdl-33181853

RESUMEN

This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01-0.45% and Chlorophyta (green algae) 0.01-0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.


Asunto(s)
Chlorella , Hielos Perennes , Regiones Árticas , Suelo , Microbiología del Suelo
11.
Endocrinology ; 161(2)2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-32022847

RESUMEN

Thyroid peroxidase (TPO) is a critical membrane-bound enzyme involved in the biosynthesis of multiple thyroid hormones, and is a major autoantigen in autoimmune thyroid diseases such as destructive (Hashimoto) thyroiditis. Here we report the biophysical and structural characterization of a novel TPO construct containing only the ectodomain of TPO and lacking the propeptide. The construct was enzymatically active and able to bind the patient-derived TR1.9 autoantibody. Analytical ultracentrifugation data suggest that TPO can exist as both a monomer and a dimer. Combined with negative stain electron microscopy and molecular dynamics simulations, these data show that the TR1.9 autoantibody preferentially binds the TPO monomer, revealing conformational changes that bring together previously disparate residues into a continuous epitope. In addition to providing plausible structural models of a TPO-autoantibody complex, this study provides validated TPO constructs that will facilitate further characterization, and advances our understanding of the structural, functional, and antigenic characteristics of TPO, an autoantigen implicated in some of the most common autoimmune diseases.


Asunto(s)
Autoanticuerpos/metabolismo , Yoduro Peroxidasa/metabolismo , Tiroiditis Autoinmune/enzimología , Dimerización , Células HEK293 , Humanos , Yoduro Peroxidasa/química , Yoduro Peroxidasa/aislamiento & purificación , Yoduro Peroxidasa/ultraestructura , Multimerización de Proteína , Estructura Cuaternaria de Proteína
12.
Front Plant Sci ; 11: 180, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32180783

RESUMEN

Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.

13.
Chemosphere ; 255: 126951, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32417512

RESUMEN

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.


Asunto(s)
Sedimentos Geológicos/química , Uranio/química , Contaminantes Radiactivos del Agua/química , Bacterias , Agua Subterránea/química , Nitratos/análisis , Compuestos Orgánicos , Sulfatos/análisis , Uranio/análisis , Contaminantes Radiactivos del Agua/análisis
14.
Atmos Environ (1994) ; 43(12): 2018-2030, 2009 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-20161318

RESUMEN

Particulate matter less than 2.5 microns in diameter (PM(2.5)) has been shown to have a wide range of adverse health effects and consequently is regulated in accordance with the US-EPA's National Ambient Air Quality Standards. PM(2.5) originates from multiple primary sources and is also formed through secondary processes in the atmosphere. It is plausible that some sources form PM(2.5) that is more toxic than PM(2.5) from other sources. Identifying the responsible sources could provide insight into the biological mechanisms causing the observed health effects and provide a more efficient approach to regulation. This is the goal of the Denver Aerosol Sources and Health (DASH) study, a multi-year PM(2.5) source apportionment and health study.The first step in apportioning the PM(2.5) to different sources is to determine the chemical make-up of the PM(2.5). This paper presents the methodology used during the DASH study for organic speciation of PM(2.5). Specifically, methods are covered for solvent extraction of non-polar and semi-polar organic molecular markers using gas chromatography-mass spectrometry (GC-MS). Vast reductions in detection limits were obtained through the use of a programmable temperature vaporization (PTV) inlet along with other method improvements. Results are presented for the first 1.5 years of the DASH study revealing seasonal and source-related patterns in the molecular markers and their long-term correlation structure. Preliminary analysis suggests that point sources are not a significant contributor to the organic molecular markers measured at our receptor site. Several motor vehicle emission markers help identify a gasoline/diesel split in the ambient data. Findings show both similarities and differences when compared with other cities where similar measurements and assessments have been made.

15.
J Exp Ther Oncol ; 5(2): 111-23, 2005.
Artículo en Inglés | MEDLINE | ID: mdl-16471037

RESUMEN

Prostate cancer is a leading cause of death from cancer in American men and metastasis the main cause of death. To better understand the disease and accelerate development of new therapies, in vivo models that reflect different disease stages are needed. A family of cell lines that mimics multiple steps in cancer development and tumor progression has been developed in our laboratory from the parent, non-tumorigenic, RWPE-1 cell line by transformation with N-methyl-N-nitrosourea (MNU). The MNU cell lines mimic multiple steps in tumor progression where WPE1-NB26 is the most malignant cell line. WPE1-NB26 cells form metastases in the lungs of athymic, male, nude mice after intravenous injection. Two new cell lines, WPE1-NB26-64 and WPE1-NB26-65, showing more malignant characteristics than the parent WPE1-NB26 cell line, were derived from tumors after subcutaneous injection of WPE1-NB26 cells into nude mice. The WPE1-NB26-64 and WPE1-NB26-65 cell lines show an increase in anchorage-dependent growth and invasive ability as compared to the parent WPE1-NB26 cells. While the parent WPE1-NB26 cells express barely detectable levels, the new cell lines produce high levels of matrix metalloproteinase MMP-2 and detectable levels of MMP-9. By immunostaining, all three cell lines were positive for cytokeratins CK18 and CK5/14. These cell lines, having the same lineage, represent additional steps in the multi-step process of tumor progression and provide novel and useful cell models for studies on tumor progression and for drug development for the treatment of prostate cancer.


Asunto(s)
Neoplasias de la Próstata/patología , Animales , Línea Celular Tumoral , Proliferación Celular , Humanos , Queratinas/análisis , Masculino , Metaloproteinasa 2 de la Matriz/metabolismo , Metaloproteinasa 9 de la Matriz/metabolismo , Ratones , Ratones Desnudos , Invasividad Neoplásica , Metástasis de la Neoplasia , Trasplante de Neoplasias , Fenotipo , Trasplante Heterólogo
16.
J Forensic Sci ; 60(4): 844-50, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25808627

RESUMEN

Bacteria are taphonomic agents of human decomposition, potentially useful for estimating postmortem interval (PMI) in late-stage decomposition. Bone samples from 12 individuals and three soil samples were analyzed to assess the effects of decomposition and advancing time on bacterial communities. Results indicated that partially skeletonized remains maintained a presence of bacteria associated with the human gut, whereas bacterial composition of dry skeletal remains maintained a community profile similar to soil communities. Variation in the UniFrac distances was significantly greater between groups than within groups (p < 0.001) for the unweighted metric and not the weighted metric. The members of the bacterial communities were more similar within than between decomposition stages. The oligotrophic environment of bone relative to soft tissue and the physical protection of organic substrates may preclude bacterial blooms during the first years of skeletonization. Therefore, community membership (unweighted) may be better for estimating PMI from skeletonized remains than community structure (weighted).


Asunto(s)
Bacterias/aislamiento & purificación , ADN Bacteriano/aislamiento & purificación , Cambios Post Mortem , Costillas/microbiología , Microbiología del Suelo , Anciano , Anciano de 80 o más Años , Bacterias/genética , Femenino , Humanos , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa , ARN Ribosómico 16S/metabolismo , Análisis de Secuencia de ADN
17.
Environ Toxicol Chem ; 21(11): 2385-93, 2002 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-12389918

RESUMEN

We have applied a method for quantifying relative levels of messenger RNA (mRNA) transcription to assess chemically induced gene expression in fathead minnows (Pimephales promelas). Synthetic oligonucleotides designed for the fathead minnow vitellogenin gene transcription product were used in a reverse transcription polymerase chain reaction (RT-PCR) protocol. This sensitive and rapid strategy detected vitellogenin gene transcription in livers of male fathead minnows exposed to concentrations as low as 2 ng/L of the endocrine-disrupting compound 17alpha-ethynylestradiol for 24 h. Surprisingly, vitellogenin transcription products also were detected in gill tissue and in 48-h-old posthatch fathead minnow larvae. Relative levels of vitellogenin gene induction among individuals were quantified in a single-step reaction (PCR multiplex) with 18S rRNA universal primers and Competimers concurrently with fathead minnow vitellogenin oligonucleotides. This quantitative approach will markedly enhance detection of the first cellular event of estrogenic exposure to aquatic ecosystems in both field and laboratory systems. Use of the model provides sensitivity of detection at a concentration below those that cause mortality or visible signs of stress in fish or other aquatic organisms. The model may also provide an in vivo screening method for estrogenlike endocrine-disrupting compounds.


Asunto(s)
Cyprinidae/metabolismo , Monitoreo del Ambiente/métodos , Etinilestradiol/toxicidad , Hígado/efectos de los fármacos , Vitelogeninas/biosíntesis , Contaminantes Químicos del Agua/toxicidad , Animales , Cyprinidae/genética , Electroforesis en Gel de Agar , Branquias , Larva , Hígado/metabolismo , Masculino , ARN Mensajero/análisis , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Transcripción Genética/efectos de los fármacos , Vitelogeninas/genética
18.
Genome Announc ; 2(6)2014 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-25414497

RESUMEN

The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport.

19.
FEMS Microbiol Ecol ; 87(1): 217-30, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24102625

RESUMEN

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed ß- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.


Asunto(s)
Bacterias/aislamiento & purificación , Reacción en Cadena de la Polimerasa/métodos , Microbiología del Suelo , Regiones Árticas , Bacterias/clasificación , Bacterias/genética , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Datos de Secuencia Molecular , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/aislamiento & purificación , Juego de Reactivos para Diagnóstico/economía
20.
Sci Total Environ ; 431: 314-22, 2012 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-22705866

RESUMEN

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.


Asunto(s)
Heces/microbiología , Agua Subterránea/microbiología , Rotavirus/patogenicidad , Bacteroides/patogenicidad , Bangladesh , Colifagos/patogenicidad , Agua Potable/microbiología , Enterobacteriaceae/patogenicidad , Escherichia coli/genética , Escherichia coli/patogenicidad , Heces/virología , Agua Subterránea/virología , Humanos , Shigella/patogenicidad , Vibrio/patogenicidad , Microbiología del Agua
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