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1.
J Air Waste Manag Assoc ; 66(4): 412-9, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26771215

RESUMEN

UNLABELLED: A pilot study was conducted in application of the U.S. Environmental Protection Agency (EPA) Methods 325A/B variant for monitoring volatile organic compounds (VOCs) near two oil and natural gas (ONG) production well pads in the Texas Barnett Shale formation and Colorado Denver-Julesburg Basin (DJB), along with a traffic-dominated site in downtown Denver, CO. As indicated in the EPA method, VOC concentrations were measured for 14-day sampling periods using passive-diffusive tube samplers with Carbopack X sorbent at fenceline perimeter and other locations. VOCs were significantly higher at the DJB well pad versus the Barnett well pad and were likely due to higher production levels at the DJB well pad during the study. Benzene and toluene were significantly higher at the DJB well pad versus downtown Denver. Except for perchloroethylene, VOCs measured at passive sampler locations (PSs) along the perimeter of the Barnett well pad were significantly higher than PSs farther away. At the DJB well pad, most VOC concentrations, except perchloroethylene, were significantly higher prior to operational changes than after these changes were made. Though limited, the results suggest passive samplers are precise (duplicate precision usually ≤10%) and that they can be useful to assess spatial gradients and operational conditions at well pad locations over time-integrated periods. IMPLICATIONS: Recently enacted EPA Methods 325A/B use passive-diffusive tube samplers to measure benzene at multiple fenceline locations at petrochemical refineries. This pilot study presents initial data demonstrating the utility of Methods 325A/B for monitoring at ONG facilities. Measurements revealed elevated concentrations reflective of production levels and spatial gradients of VOCs relative to source proximity at the Barnett well pad, as well as operational changes at the DJB well pad. Though limited, these findings indicate that Methods 325A/B can be useful in application to characterize VOCs at well pad boundaries.


Asunto(s)
Monitoreo del Ambiente/métodos , Yacimiento de Petróleo y Gas , Compuestos Orgánicos Volátiles/análisis , Colorado , Proyectos Piloto , Texas
2.
Environ Microbiol ; 17(9): 3314-29, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25727256

RESUMEN

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound.


Asunto(s)
Butadienos/metabolismo , Ciclo del Carbono/fisiología , Hemiterpenos/metabolismo , Pentanos/metabolismo , Rhodococcus/metabolismo , Compuestos Orgánicos Volátiles/metabolismo , Secuencia de Bases , Clima , Ecosistema , Perfilación de la Expresión Génica , Genoma Bacteriano , Datos de Secuencia Molecular , Plantas/metabolismo , Plásmidos/genética , ARN Bacteriano/genética , Rhodococcus/genética , Análisis de Secuencia de ARN
3.
PLoS Pathog ; 6(9): e1001102, 2010 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-20862321

RESUMEN

A fundamental, but unanswered question in host-pathogen interactions is the timing, localization and population distribution of virulence gene expression during infection. Here, microarray and in situ single cell expression methods were used to study Vibrio cholerae growth and virulence gene expression during infection of the rabbit ligated ileal loop model of cholera. Genes encoding the toxin-coregulated pilus (TCP) and cholera toxin (CT) were powerfully expressed early in the infectious process in bacteria adjacent to epithelial surfaces. Increased growth was found to co-localize with virulence gene expression. Significant heterogeneity in the expression of tcpA, the repeating subunit of TCP, was observed late in the infectious process. The expression of tcpA, studied in single cells in a homogeneous medium, demonstrated unimodal induction of tcpA after addition of bicarbonate, a chemical inducer of virulence gene expression. Striking bifurcation of the population occurred during entry into stationary phase: one subpopulation continued to express tcpA, whereas the expression declined in the other subpopulation. ctxA, encoding the A subunit of CT, and toxT, encoding the proximal master regulator of virulence gene expression also exhibited the bifurcation phenotype. The bifurcation phenotype was found to be reversible, epigenetic and to persist after removal of bicarbonate, features consistent with bistable switches. The bistable switch requires the positive-feedback circuit controlling ToxT expression and formation of the CRP-cAMP complex during entry into stationary phase. Key features of this bistable switch also were demonstrated in vivo, where striking heterogeneity in tcpA expression was observed in luminal fluid in later stages of the infection. When this fluid was diluted into artificial seawater, bacterial aggregates continued to express tcpA for prolonged periods of time. The bistable control of virulence gene expression points to a mechanism that could generate a subpopulation of V. cholerae that continues to produce TCP and CT in the rice water stools of cholera patients.


Asunto(s)
Proteínas Bacterianas/genética , Regulación Bacteriana de la Expresión Génica , Intestinos/microbiología , Intestinos/fisiología , Vibrio cholerae/fisiología , Virulencia/fisiología , Animales , Proteínas Bacterianas/metabolismo , Biomarcadores/metabolismo , Western Blotting , Cólera/genética , Cólera/metabolismo , Cólera/microbiología , Toxina del Cólera/genética , Toxina del Cólera/metabolismo , Proteínas Fimbrias/genética , Proteínas Fimbrias/metabolismo , Citometría de Flujo , Perfilación de la Expresión Génica , Interacciones Huésped-Patógeno , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos , Conejos , Vibrio cholerae/aislamiento & purificación
4.
Cancers (Basel) ; 14(5)2022 Mar 02.
Artículo en Inglés | MEDLINE | ID: mdl-35267599

RESUMEN

OBJECTIVE: To identify the most predictive parameters of ovarian malignancy and develop a machine learning (ML) based algorithm to preoperatively distinguish between a benign and malignant pelvic mass. METHODS: Retrospective study of 70 predictive parameters collected from 140 women with a pelvic mass. The women were split into a 3:1 "training" to "testing" dataset. Feature selection was performed using Gini impurity through an embedded random forest model and principal component analysis. Nine unique ML classifiers were assessed across a variety of model-specific hyperparameters using 25 bootstrap resamples of the training data. Model predictions were then combined into an ensemble stack by LASSO regression. The final ensemble stack and individual classifiers were then applied to the testing dataset to assess model performance. RESULTS: Feature selection identified HE4, CA125, and transferrin as three predictive parameters of malignancy. Assessment of the ensemble stack on the testing dataset outperformed all individual ML classifiers in predicting malignancy. The ensemble stack demonstrated an accuracy of 97.1%, a receiver operating characteristic (ROC) area under the curve (AUC) of 0.951, and a sensitivity of 93.3% with a specificity of 100%. CONCLUSIONS: Combining the measurement of three distinct biomarkers with the stacking of multiple ML classifiers into an ensemble can provide valuable preoperative diagnostic predictions for patients with a pelvic mass.

5.
Cancers (Basel) ; 14(21)2022 Oct 26.
Artículo en Inglés | MEDLINE | ID: mdl-36358657

RESUMEN

Circulating tumor cells (CTCs) captured from the blood of cancer patients may serve as a surrogate source of tumor material that can be obtained via a venipuncture (also known as a liquid biopsy) and used to better understand tumor characteristics. However, the only FDA-cleared CTC assay has been limited to the enumeration of surface marker-defined cells and not further characterization of the CTCs. In this study, we tested the ability of a semi-automated device capable of capturing and harvesting CTCs from peripheral blood based on cell size and deformability, agnostic of cell-surface markers (the Parsortix® PC1 System), to yield CTCs for evaluation by downstream techniques commonly available in clinical laboratories. The data generated from this study were used to support a De Novo request (DEN200062) for the classification of this device, which the FDA recently granted. As part of a multicenter clinical trial, peripheral blood samples from 216 patients with metastatic breast cancer (MBC) and 205 healthy volunteers were subjected to CTC enrichment. A board-certified pathologist enumerated the CTCs from each participant by cytologic evaluation of Wright-Giemsa-stained slides. As proof of principle, cells harvested from a concurrent parallel sample provided by each participant were evaluated using one of three additional evaluation techniques: molecular profiling by qRT-PCR, RNA sequencing, or cytogenetic analysis of HER2 amplification by FISH. The study demonstrated that the Parsortix® PC1 System can effectively capture and harvest CTCs from the peripheral blood of MBC patients and that the harvested cells can be evaluated using orthogonal methodologies such as gene expression and/or Fluorescence In Situ Hybridization (FISH).

6.
Appl Environ Microbiol ; 77(21): 7772-8, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21908638

RESUMEN

The mevalonate pathway is utilized for the biosynthesis of isoprenoids in many bacterial, eukaryotic, and archaeal organisms. Based on previous reports of its feedback inhibition, mevalonate kinase (MVK) may play an important regulatory role in the biosynthesis of mevalonate pathway-derived compounds. Here we report the purification, kinetic characterization, and inhibition analysis of the MVK from the archaeon Methanosarcina mazei. The inhibition of the M. mazei MVK by the following metabolites derived from the mevalonate pathway was explored: dimethylallyl diphosphate (DMAPP), geranyl pyrophosphate (GPP), farnesyl pyrophosphate (FPP), isopentenyl monophosphate (IP), and diphosphomevalonate. M. mazei MVK was not inhibited by DMAPP, GPP, FPP, diphosphomevalonate, or IP, a proposed intermediate in an alternative isoprenoid pathway present in archaea. Our findings suggest that the M. mazei MVK represents a distinct class of mevalonate kinases that can be differentiated from previously characterized MVKs based on its inhibition profile.


Asunto(s)
Proteínas Arqueales/metabolismo , Retroalimentación Fisiológica , Methanosarcina/enzimología , Fosfotransferasas (Aceptor de Grupo Alcohol)/metabolismo , Terpenos/metabolismo , Proteínas Arqueales/genética , Proteínas Arqueales/aislamiento & purificación , Vías Biosintéticas , Análisis por Conglomerados , Cinética , Methanosarcina/genética , Fosfotransferasas (Aceptor de Grupo Alcohol)/genética , Fosfotransferasas (Aceptor de Grupo Alcohol)/aislamiento & purificación , Filogenia , Homología de Secuencia de Aminoácido
7.
J Air Waste Manag Assoc ; 61(8): 834-42, 2011 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-21874954

RESUMEN

In 2009, the U.S. Environmental Protection Agency (EPA) executed a year-long field study at a refinery in Corpus Christi, TX, to evaluate the use of passive diffusive sampling technology for assessing time-averaged benzene concentrations at the facility fence line. The purpose of the study was to investigate the implementation viability and performance of this type of monitoring in a real-world setting as part of EPA's fence-line measurement research program. The study utilized 14-day, time-integrated Carbopack X samplers deployed at 18 locations on the fence line and at two nearby air monitoring sites equipped with automated gas chromatographs. The average fence-line benzene concentration during the study was 1075 parts per trillion by volume (pptv) with a standard deviation of 1935 pptv. For a 6-month period during which wind direction was uniform, the mean concentration value for a group of downwind sites exceeded the mean value of a similar upwind group by 1710 pptv. Mean value differences for these groups were not statistically significant for the remaining 6-month time period when wind directions were mixed. The passive sampling approach exhibited acceptable performance with a data completeness value of 97.1% (n = 579). Benzene concentration comparisons with automated gas chromatographs yielded an r2 value of 0.86 and a slope of 0.90 (n = 50). A linear regression of duplicate pairs yielded an r2 of 0.97, unity slope, and zero intercept (n = 56). In addition to descriptions of technique performance and general results, time-series analyses are described, providing insight into the utility of 2-week sampling for source apportionment under differing meteorological conditions. The limitations of the approach and recommendations for future measurement method development work are also discussed.


Asunto(s)
Contaminantes Ocupacionales del Aire/análisis , Monitoreo del Ambiente/instrumentación , Contaminantes Atmosféricos/análisis , Benceno/análisis , Monitoreo del Ambiente/métodos , Industrias , Petróleo , Reproducibilidad de los Resultados , Estados Unidos , United States Environmental Protection Agency
8.
Environ Monit Assess ; 172(1-4): 663-87, 2011 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-20221800

RESUMEN

The impact of urbanization on stream ecosystems is linked by land cover changes to the alteration of the natural hydrology and subsequent physical disruption of stream biota and habitat. Seasonal floods are part of the natural disturbance regime of many streams, but urbanization increases their frequency and magnitude. This study evaluated the impact of hydrologic disturbance on fish and aquatic macroinvertebrates in 81 (56 urban/25 reference) Ohio streams. Hydrologic variables included annual and monthly 24-h rainfall maxima and computed annual peak discharge, with computation supported by GIS-based drainage area delineation and land cover characterization. Ohio biological criteria for fish and macroinvertebrates measured during the late spring and summer were negatively impacted by annual peak discharge in urban streams as compared to reference streams. Results support the application of stormwater best management practices as part of stream restoration efforts to mitigate urbanization impacts to fish and macroinvertebrates.


Asunto(s)
Monitoreo del Ambiente/métodos , Ríos , Animales , Biodiversidad , Peces , Invertebrados , Movimientos del Agua
9.
PLoS Pathog ; 2(10): e109, 2006 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-17054394

RESUMEN

Vibrio cholerae causes a severe diarrhoeal disease by secreting a toxin during colonization of the epithelium in the small intestine. Whereas the initial steps of the infectious process have been intensively studied, the last phases have received little attention. Confocal microscopy of V. cholerae O1-infected rabbit ileal loops captured a distinctive stage in the infectious process: 12 h post-inoculation, bacteria detach from the epithelial surface and move into the fluid-filled lumen. Designated the "mucosal escape response," this phenomenon requires RpoS, the stationary phase alternative sigma factor. Quantitative in vivo localization assays corroborated the rpoS phenotype and showed that it also requires HapR. Expression profiling of bacteria isolated from ileal loop fluid and mucus demonstrated a significant RpoS-dependent upregulation of many chemotaxis and motility genes coincident with the emigration of bacteria from the epithelial surface. In stationary phase cultures, RpoS was also required for upregulation of chemotaxis and motility genes, for production of flagella, and for movement of bacteria across low nutrient swarm plates. The hapR mutant produced near-normal numbers of flagellated cells, but was significantly less motile than the wild-type parent. During in vitro growth under virulence-inducing conditions, the rpoS mutant produced 10- to 100-fold more cholera toxin than the wild-type parent. Although the rpoS mutant caused only a small over-expression of the genes encoding cholera toxin in the ileal loop, it resulted in a 30% increase in fluid accumulation compared to the wild-type. Together, these results show that the mucosal escape response is orchestrated by an RpoS-dependent genetic program that activates chemotaxis and motility functions. This may furthermore coincide with reduced virulence gene expression, thus preparing the organism for the next stage in its life cycle.


Asunto(s)
Proteínas Bacterianas/fisiología , Cólera/microbiología , Mucosa Intestinal/microbiología , Factor sigma/fisiología , Vibrio cholerae/fisiología , Animales , Cólera/patología , Modelos Animales de Enfermedad , Eliminación de Gen , Regulación Bacteriana de la Expresión Génica , Íleon/microbiología , Íleon/fisiopatología , Mucosa Intestinal/fisiopatología , Microscopía Confocal , Movimiento/fisiología , Análisis de Secuencia por Matrices de Oligonucleótidos , ARN Bacteriano/análisis , Conejos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Factor sigma/deficiencia , Vibrio cholerae/ultraestructura
10.
FEMS Microbiol Lett ; 275(2): 199-206, 2007 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-17697110

RESUMEN

The natural life cycle of Vibrio cholerae involves the transitioning of cells between different environmental surfaces such as the chitinous shell of Crustaceae and the epithelial layer of the human intestine. Previous studies using static biofilm systems showed a strict dependence of biofilm formation on the vps and lux genes, which are essential for exopolysaccharide formation and cell-cell signaling, respectively. The authors' report here that in biofilms grown under hydrodynamic conditions, DeltavpsA and DeltaluxO mutants of V. cholerae do form pronounced, three-dimensional biofilms that resemble all aspects of wild-type biofilms. By genetic experiments, it was shown that in hydrodynamically grown biofilms this independence of vpsA is due to the expression of rpoS, which is a negative regulator of vpsA expression. Biofilms also underwent substantial dissolution after 96 h that could be induced by a simple stop of medium flow. The studies indicate that metabolic conditions control the reversible attachment of cells to the biofilm matrix and are key in regulating biofilm cell physiology via RpoS. Furthermore, the results redefine the roles of vps and quorum-sensing in V. cholerae biofilms.


Asunto(s)
Proteínas Bacterianas/metabolismo , Biopelículas/crecimiento & desarrollo , Regulación Bacteriana de la Expresión Génica , Factor sigma/metabolismo , Vibrio cholerae/crecimiento & desarrollo , Proteínas Bacterianas/genética , Técnicas Bacteriológicas , Medios de Cultivo , Microscopía Confocal , Mutación , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Factor sigma/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Vibrio cholerae/genética , Vibrio cholerae/metabolismo , Vibrio cholerae/ultraestructura
19.
Prostate ; 68(10): 1097-104, 2008 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-18459105

RESUMEN

BACKGROUND: p300 impacts the transcription of several genes involved in key pathways critical to PCa progression. Therefore, we evaluated the prognostic value of p300 expression and its correlation with nuclear alterations seen in tumor cells in men with long-term follow-up after radical prostatectomy (RP). METHODS: NCI Cooperative Prostate Cancer Tissue Resource tissue microarray cores of 92 RP cases (56 non-recurrences and 36 PSA recurrences) were utilized for the study. p300 expression was assessed by quantitative immunohistochemistry and nuclear alterations in Feulgen-stained nuclei were evaluated by digital image analysis using the AutoCyte Pathology Workstation. Cox proportional hazards regression, Spearman's rank correlation, and Kaplan-Meier plots were employed to analyze the data. RESULTS: p300 expression significantly correlated with nuclear alterations seen in tumor cells; specifically with circular form factor (P = 0.012) and minimum feret (P = 0.048). p300 expression in high grade tumors (Gleason score >or=7) was significantly higher compared to low grade tumors (Gleason score <7) [17.7% versus 13.7%, respectively, P = 0.03]. TNM stage, Gleason score, and p300 expression were univariately significant in the prediction of PCa biochemical recurrence-free survival (P or=7 and p300 expression >24% showed the highest risk for PCa biochemical recurrence (P = 0.002). CONCLUSIONS: p300 expression correlates with nuclear alterations seen in tumor cells and has prognostic value in predicting long-term PCa biochemical recurrence-free survival.


Asunto(s)
Biomarcadores de Tumor/metabolismo , Neoplasias de la Próstata/metabolismo , Neoplasias de la Próstata/patología , Factores de Transcripción p300-CBP/metabolismo , Adulto , Anciano , Forma del Núcleo Celular , Supervivencia sin Enfermedad , Células Epiteliales/metabolismo , Células Epiteliales/patología , Humanos , Masculino , Persona de Mediana Edad , Recurrencia Local de Neoplasia/metabolismo , Recurrencia Local de Neoplasia/patología , Estadificación de Neoplasias , Valor Predictivo de las Pruebas , Pronóstico , Modelos de Riesgos Proporcionales
20.
Appl Environ Microbiol ; 73(11): 3705-14, 2007 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-17449702

RESUMEN

Studies of Vibrio cholerae diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of V. cholerae. Comparative genome hybridization using microarrays constructed from the fully sequenced V. cholerae O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence V. cholerae population structure in aquatic environments.


Asunto(s)
ADN Bacteriano/genética , Variación Genética , Genoma Bacteriano/genética , Agua de Mar/microbiología , Vibrio cholerae/genética , Vibrio cholerae/aislamiento & purificación , California , Secuencia Conservada , ADN Bacteriano/aislamiento & purificación , Ecosistema , Genes Bacterianos , Redes y Vías Metabólicas/genética , Hibridación de Ácido Nucleico , Análisis de Secuencia por Matrices de Oligonucleótidos , Fenotipo , Filogenia , Vibrio cholerae/metabolismo
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