Stephen B. Cox

Evidence that miRNAs are different from other RNAs

Abstract.An examination of 513 known pre-miRNAs and 237 other RNAs (tRNA, rRNA, and mRNA) revealed that miRNAs were significantly different from other RNAs (p < 0.001). miRNA genes were less conserved than other RNA genes, although their mature miRNA sequences were highly conserved. The A+U content of pre-miRNAs was higher than non-coding RNA (p < 0.001), but lower than mRNAs. The nucleotides in pre-miRNAs formed more hydrogen bonds and base pairs than in other RNAs. miRNAs had higher negative adjusted minimal folding free energies than other RNAs except tRNAs (p < 0.001). The MFE index (MFEI) was a sufficient criterion to distinguish miRNAs from all coding and non-coding RNAs (p < 0.001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies.

Linking Microbial Community Structure and Function to Seasonal Differences in Soil Moisture and Temperature in a Chihuahuan Desert Grassland

Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.

Etiological study of esophageal squamous cell carcinoma in an endemic region: a population-based case control study in Huaian, China

BackgroundContinuous exposure to various environmental carcinogens and genetic polymorphisms of xenobiotic-metabolizing enzymes (XME) are associated with many types of human cancers, including esophageal squamous cell carcinoma (ESCC). Huaian, China, is one of the endemic regions of ESCC, but fewer studies have been done in characterizing the risk factors of ESCC in this area. The aims of this study is to evaluate the etiological roles of demographic parameters, environmental and food-borne carcinogens exposure, and XME polymorphisms in formation of ESCC, and to investigate possible gene-gene and gene-environment interactions associated with ESCC in Huaian, China.MethodsA population based case-control study was conducted in 107 ESCC newly diagnosed cases and 107 residency- age-, and sex-matched controls in 5 townships of Huaian. In addition to regular epidemiological and food frequency questionnaire analyses, genetic polymorphisms of phase I enzymes CYP1A1, CYP1B1, CYP2A6, and CYP2E1, and phase II enzymes GSTM1, GSTT1, GSTP1, and microsomal epoxide hydrolase (EPHX) were assessed from genomic DNA using PCR based techniques.ResultsConsuming acrid food, fatty meat, moldy food, salted and pickled vegetables, eating fast, introverted personality, passive smoking, a family history of cancer, esophageal lesion, and infection with Helicobacter pylori were significant risk factors for ESCC (P < 0.05). Regular clean up of food storage utensils, green tea consumption, and alcohol abstinence were protective factors for ESCC (P < 0.01). The frequency of the GSTT1 null genotype was higher in cases (59.4%) compared to controls (47.2%) with an odds ratio (OR) of 1.68 and 95% confidence interval (CI) from 0.96 to 2.97 (P = 0.07), especially in males (OR = 2.78; 95% CI = 1.22–6.25; P = 0.01). No associations were found between polymorphisms of CYP1A1, CYP1B1, CYP2A6, CYP2E1, GSTM1, GSTP1, and EPHX and ESCC (P > 0.05).ConclusionOur results demonstrated that dietary and environmental exposures, some demographic parameters and genetic polymorphism of GSTT1 may play important roles in the development of ESCC in Huaian area, China.

Modulation of aflatoxin biomarkers in human blood and urine by green tea polyphenols intervention

To evaluate the efficacy of green tea polyphenols (GTPs) in modulating aflatoxin B(1) (AFB(1)) biomarkers, a total of 352 serum samples and 352 urine samples collected from a 3 month chemoprevention trial with 500 mg GTPs, 1000 mg GTPs and a placebo were measured for AFB(1)-albumin adducts (AFB-AA), aflatoxin M(1) (AFM(1)) and aflatoxin B(1)-mercapturic acid (AFB-NAC). Levels of AFB-AA at baseline were comparable for all three dose groups (P = 0.506). No significant differences were observed in AFB-AA levels in the placebo group over the 3 month period (P = 0.252). However, a significant reduction in AFB-AA levels was observed in the 500 mg group (P = 0.002). A marginally significant reduction in AFB-AA levels was also found in the 1000 mg group over the 3 month intervention period (P = 0.051). An analysis using a mixed-effects model indicated that the reduction in AFB-AA levels over time was dose and time dependent (dose-time interaction P = 0.049). There were no significant differences in median AFM(1) levels among the three study groups at the baseline (P = 0.832), 1 month (P = 0.188) and 3 months (P = 0.132) of the GTP intervention; however, reduction of 42 and 43% in median AFM(1) levels, as compared with the placebo, were found in 500 mg (P = 0.096) and 1000 mg (P = 0.072) groups at 3 months of the intervention. Significant elevations in median AFB-NAC levels and the ratio of AFB-NAC:AFM(1) were found in both 500 and 1000 mg groups compared with the placebo group at both 1 month (P < 0.001) and 3 months (P < 0.001) of GTPs intervention. These results demonstrate that GTPs effectively modulate AFB(1) metabolism and metabolic activation.

Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter.

Background: Emergence and spread of antibiotic resistance has become a global health threat and is often linked with overuse and misuse of clinical and veterinary chemotherapeutic agents. Modern industrial-scale animal feeding operations rely extensively on veterinary pharmaceuticals, including antibiotics, to augment animal growth. Following excretion, antibiotics are transported through the environment via runoff, leaching, and land application of manure; however, airborne transport from feed yards has not been characterized. Objectives: The goal of this study was to determine the extent to which antibiotics, antibiotic resistance genes (ARG), and ruminant-associated microbes are aerially dispersed via particulate matter (PM) derived from large-scale beef cattle feed yards. Methods: PM was collected downwind and upwind of 10 beef cattle feed yards. After extraction from PM, five veterinary antibiotics were quantified via high-performance liquid chromatography with tandem mass spectrometry, ARG were quantified via targeted quantitative polymerase chain reaction, and microbial community diversity was analyzed via 16S rRNA amplification and sequencing. Results: Airborne PM derived from feed yards facilitated dispersal of several veterinary antibiotics, as well as microbial communities containing ARG. Concentrations of several antibiotics in airborne PM immediately downwind of feed yards ranged from 0.5 to 4.6 μg/g of PM. Microbial communities of PM collected downwind of feed yards were enriched with ruminant-associated taxa and were distinct when compared to upwind PM assemblages. Furthermore, genes encoding resistance to tetracycline antibiotics were significantly more abundant in PM collected downwind of feed yards as compared to upwind. Conclusions: Wind-dispersed PM from feed yards harbors antibiotics, bacteria, and ARGs. Citation: McEachran AD, Blackwell BR, Hanson JD, Wooten KJ, Mayer GD, Cox SB, Smith PN. 2015. Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environ Health Perspect 123:337–343; http://dx.doi.org/10.1289/ehp.1408555

An evaluation of the impact of multiwalled carbon nanotubes on soil microbial community structure and functioning

This study evaluated the impacts of multiwalled carbon nanotubes (MWNTs) on microbial community composition and functioning in a sandy loam soil over 90 d. We used test concentrations in the range of lower MWNT concentrations (10mg/kg) to extremely high MWNT concentrations (10,000 mg/kg) as a worst case scenario. We observed no effects of MWNTs on soil respiration, enzymatic activities, and microbial community composition at 10, 100 and 1,000 mg/kg. However, increases in fungal fatty acid methyl ester markers were observed at the highest treatment. In addition, pyrosequencing demonstrated a decreased abundance of some bacterial genera like Derxia, Holophaga, Opitutus and Waddlia at the highest treatment while bacterial genera that are considered potential degraders of recalcitrant contaminants (such as polycyclic aromatic hydrocarbons) like Rhodococcus, Cellulomonas, Nocardioides and Pseudomonas increased. These results suggest a shift in soil microbial community composition to more tolerant microbial populations in the presence of extremely high MWNT concentrations. It is unlikely that the change observed at 10,000 mg/kg is due to metal or carbon impurities as the MWNTs used in this study were of high purity. Given the need for wide-ranging data for regulation and risk assessment of nanomaterials, this study provides valuable data.

SCALE-DEPENDENT RESPONSES OF PLANT BIODIVERSITY TO NITROGEN ENRICHMENT

Experimental studies demonstrating that nitrogen (N) enrichment reduces plant diversity within individual plots have led to the conclusion that anthropogenic N enrichment is a threat to global biodiversity. These conclusions overlook the influence of spatial scale, however, as N enrichment may alter beta diversity (i.e., how similar plots are in their species composition), which would likely alter the degree to which N-induced changes in diversity within localities translate to changes in diversity at larger scales that are relevant to policy and management. Currently, it is unclear how N enrichment affects biodiversity at scales larger than a small plot. We synthesized data from 18 N-enrichment experiments across North America to examine the effects of N enrichment on plant species diversity at three spatial scales: small (within plots), intermediate (among plots), and large (within and among plots). We found that N enrichment reduced plant diversity within plots by an average of 25% (ranging from a reduction of 61% to an increase of 5%) and frequently enhanced beta diversity. The extent to which N enrichment altered beta diversity, however, varied substantially among sites (from a 22% increase to an 18% reduction) and was contingent on site productivity. Specifically, N enrichment enhanced beta diversity at low-productivity sites but reduced beta diversity at high-productivity sites. N-induced changes in beta diversity generally reduced the extent of species loss at larger scales to an average of 22% (ranging from a reduction of 54% to an increase of 18%). Our results demonstrate that N enrichment often reduces biodiversity at both local and regional scales, but that a focus on the effects of N enrichment on biodiversity at small spatial scales may often overestimate (and sometimes underestimate) declines in regional biodiversity by failing to recognize the effects of N on beta diversity.

Effects of landuse and precipitation on pesticides and water quality in playa lakes of the southern high plains

The 25000 playa wetlands within the Southern High Plains (SHP) of the United States of America (USA) are the dominant hydrogeomorphic feature in the region, providing habitat for numerous plants and wildlife. The SHP are among the most intensively cultivated regions; there are concerns over the degradation and/or loss of playa wetland habitat. We examined water quality in playa wetlands surrounded by both grassland and agriculture and measured water concentrations of pesticides used on cotton (acephate, trifluralin, malathion, pendimethalin, tribufos, bifenthrin, λ-cyhalothrin, acetamiprid, and thiamethoxam), the dominant crop in the SHP. Pesticides used on cotton were detected in water samples collected from all playas. Precipitation events and the amount of cultivation were related to pesticide concentrations in sediment and water. Our results show that pesticide concentrations were related in some circumstances to time, precipitation, and tilled-index for some but not all pesticides. We further compared measured pesticide concentrations in playas to toxicity benchmarks used by the US EPA in pesticide ecological risk assessments to obtain some insight into the potential for ecological effects. For all pesticides in water, the maximum measured concentrations exceeded at least one toxicity benchmark, while median concentrations did not exceed any benchmarks. This analysis indicates that there is a potential for adverse effects of pesticides to aquatic organisms.

Analysis of the chronic wound microbiota of 2,963 patients by 16S rDNA pyrosequencing

The extent to which microorganisms impair wound healing is an ongoing controversy in the management of chronic wounds. Because the high diversity and extreme variability of the microbiota between individual chronic wounds lead to inconsistent findings in small cohort studies, evaluation of a large number of chronic wounds using identical sequencing and bioinformatics methods is necessary for clinicians to be able to select appropriate empiric therapies. In this study, we utilized 16S rDNA pyrosequencing to analyze the composition of the bacterial communities present in samples obtained from patients with chronic diabetic foot ulcers (N = 910), venous leg ulcers (N = 916), decubitus ulcers (N = 767), and nonhealing surgical wounds (N = 370). The wound samples contained a high proportion of Staphylococcus and Pseudomonas species in 63 and 25% of all wounds, respectively; however, a high prevalence of anaerobic bacteria and bacteria traditionally considered commensalistic was also observed. Our results suggest that neither patient demographics nor wound type influenced the bacterial composition of the chronic wound microbiome. Collectively, these findings indicate that empiric antibiotic selection need not be based on nor altered for wound type. Furthermore, the results provide a much clearer understanding of chronic wound microbiota in general; clinical application of this new knowledge over time may help in its translation to improved wound healing outcomes.

Functional Diversity of Soil Bacterial Communities in the Tabonuco Forest: Interaction of Anthropogenic and Natural Disturbance1

Anthropogenic and natural disturbances play critical roles in affecting the structure and function of Caribbean ecosystems, where hurricanes represent important disturbances superimposed on a landscape modified by human agricultural and forestry practices. Based on the differential catabolism of a suite of 128 carbon sources by soil bacterial communities, we focus on four aspects of functional diversity (total substrate activity, substrate richness, substrate evenness, substrate diversity) in the tabonuco forest of Puerto Rico, and assess the degree to which their spatial variability is a consequence of historical landuse or impacts of Hurricane Hugo. Considerable microspatial heterogeneity characterizes the functional diversity of forest soil communities, but the degree of hurricane damage to aboveground plant communities is positively related to all four indexes of functional diversity 5yr after the hurricane. No differences in functional diversity were detected with respect to historical landuse, after controlling for the effects of hurricane damage. However, this lack of significance may be an artifact because the spatial distribution of hurricane damage is not independent of historical landuse. As a consequence, contemporary studies of spatial heterogeneity that do not account for historical patterns of anthropogenic or natural disturbance may yield spurious or incorrect conclusions. Long-term studies help to rectify this problem and are especially important within the context of evaluating the impacts of increasing human demands on natural ecosystems.