Coherent synthesis of genomic associations with phenotypes and home environments

Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome‐wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade‐offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.     

Environmental factors affecting the degradation of Dyfonate by soil fungi.

The ability of selected fungi to degrade the soil insecticide Dyfonate (O-ethyl S-phenyl ethylphosphonodithioate) into water-soluble, noninsecticidal metabolites was found to be dependent on the supply of nutrients, incubation time, temperature, pH, as well as other factors. With yeast extract as the carbon source (5 g/liter) and ammonium nitrate (1 g/liter) as the nitrogen source, both Rhizopus arrhizus and Penicillium notatum degraded the insecticide to a larger extent than with any other combination of nutrients used. With glucose as the carbon source, concentrations of ammonium nitrate above 5 g/liter inhibited the degradation of Dyfonate by R. arrhizus. Time-course studies on the metabolism of the insecticide indicated that Dyfonate was first absorbed by the fungal mycelium, where it was metabolized followed by the release of water-soluble, noninsecticidal, breakdown products into the culture media. The degradation appeared to involve the breakdown of Dyfonate into ethyl acetate soluble metabolites, such as ethylethoxyphosphonothioic acid, ethylethoxyphosphonic acid, methyl phenyl sulfoxide, and methyl phenyl sulfone. These compounds were then further degraded into water-soluble products. The optimum conditions for the degradation of the insecticide by R. arrhizus were observed at pH 6.0 to 7.0 and at 15-25 degrees C. Aged fungal mycelia were as active as mycelia in the logarithmic growth phase.     

Control of the Balb/c-3T3 cell cycle by nutrients and serum factors: analysis using platelet-derived growth factor and platelet-poor plasma.

Much controversy regarding the relationship between nutrients and serum in regulation of cell growth can be reconciled by recognizing that serum contains multiple factors which regulate different events in the cell cycle. Serum was fractionated into a platelet-derived growth factor (PDGF), which induces cells to become competent to synthesize DNA, and plasma which allows competent cells to traverse G0/G1 and enter the S phase. Nutrients are not required for the cellular response to PDGF; however amino acids are required for plasma to promote the entry of PDGF-treated, competent cells into S phase. The nutrient independent, PDGF-modulated, growth regulatory event (competence) is located 12 hours prior to the G1/S phase boundary in quiescent, density-arrested Balb/c-3T3 cells. The nutrient dependent, plasma-modulated event is located six hours prior to the G1/S phase boundary and corresponds in concentration of amino acids required for DNA synthesis. Infection of density-arrested Balb/c3T3 cells with SV40 overrides both the nutrient independent and the nutrient dependent growth regulatory events.     

A factor analysis of associations among self-reported immune related symptoms in a large twin sample.

We examined the cumulative prevalences of 22 symptoms thought to reflect immune system function reported in a questionnaire mailed to 7616 Australian twins. The associations between symptoms and demographic variables were expressed in terms of polychoric or polyserial correlations, and a principal components analysis performed. Factors representing underlying propensities respectively to allergic disease, various minor infections, diseases associated with aging such as arthritis, skin disease, and respiratory tract infection were extracted. Possible processes underlying these symptom clusters and the relative strengths and weaknesses of this type of analysis are discussed.     

Risk factors for contamination of domestic hot water systems by legionellae.

To assess risk factors associated with the contamination of the domestic environment by legionellae, 211 houses in the Quebec City area were randomly selected and water samples were collected from the hot water tank, the shower heads, and the most frequently used faucet. After centrifugation, concentrated samples were seeded in triplicate on BCYE and GPV media. Data on the characteristics of the hot water system and plumbing in the house and on the personal habits of the occupants were collected for each house. Among these 211 houses, hot water was provided by either an oil or gas heater in 33 and by an electric heater in 178. Legionellae were isolated from none of the samples from houses with oil or gas heaters and from 39% (69 of 178) of those with electric water heaters (P less than 0.0001). This association remained highly significant after control for water temperature and other variables in a stratified analysis. In the 178 houses with an electric heater, 12% of the faucets, 15% of the shower heads, and 37% of the water heaters were contaminated. Legionella pneumophila serogroups 2 and 4 were the most frequently isolated strains. Logistic regression showed that factors associated with electric water heater contamination were (i) location of the house in older districts of the city (P less than 0.0001), (ii) old age of the water heater (P = 0.003), and (iii) low water temperature (P = 0.05). Contamination of the water heater was the only factor significantly associated with the contamination of peripheral outlets (P less than 0.0001).(ABSTRACT TRUNCATED AT 250 WORDS)     

Risk factors for contamination of domestic hot water systems by legionellae.

To assess risk factors associated with the contamination of the domestic environment by legionellae, 211 houses in the Quebec City area were randomly selected and water samples were collected from the hot water tank, the shower heads, and the most frequently used faucet. After centrifugation, concentrated samples were seeded in triplicate on BCYE and GPV media. Data on the characteristics of the hot water system and plumbing in the house and on the personal habits of the occupants were collected for each house. Among these 211 houses, hot water was provided by either an oil or gas heater in 33 and by an electric heater in 178. Legionellae were isolated from none of the samples from houses with oil or gas heaters and from 39% (69 of 178) of those with electric water heaters (P less than 0.0001). This association remained highly significant after control for water temperature and other variables in a stratified analysis. In the 178 houses with an electric heater, 12% of the faucets, 15% of the shower heads, and 37% of the water heaters were contaminated. Legionella pneumophila serogroups 2 and 4 were the most frequently isolated strains. Logistic regression showed that factors associated with electric water heater contamination were (i) location of the house in older districts of the city (P less than 0.0001), (ii) old age of the water heater (P = 0.003), and (iii) low water temperature (P = 0.05). Contamination of the water heater was the only factor significantly associated with the contamination of peripheral outlets (P less than 0.0001).(ABSTRACT TRUNCATED AT 250 WORDS)     

Investigation into the production of bacteriostatic substances by fungi VI. Examination of the larger Basidiomycetes

The present paper, the sixth of the series, gives the results of testing some 700 species of the larger Basidiomycetes for bacteriostatic properties. Initially, the 'juice' extracted from the sporophore was tested and this was followed in certain cases by a test of the metabolism solution produced by the fungus in culture. The results indicate that the larger Basidiomycetes are among the more promising fungus groups which produce antibiotics and that they compare favourably in this respect with the Aspergilli and the Penicillia. Of the 700 species tested approximately 70 are strongly and approximately 100 weakly positive against Staphylococcus aureus and/or Bacterium colt.     

中国白酒发酵过程中的核心微生物群及其与环境因子的关系

【目的】揭示白酒酿造过程复杂微生物群落中的核心微生物群(core microbiota),定量分析核心微生物群的环境调控因素。【方法】通过高通量测序揭示发酵过程中的微生物群落结构,使用气相色谱-质谱联仪(GC-MS)测定发酵过程中的挥发性化合物。采用微生物群落与挥发性化合物轮廓关联分析获得风味代谢的功能微生物群(functional microbiota);通过微生物共现性网络分析,获得群落组成中的共现微生物群(co-occurring microbiota),两类微生物群的集合即为白酒酿造的核心微生物群。利用冗余分析(redundancy analysis)和蒙特卡洛置换检验(Monte Carlo permutation test)研究每个环境因素对该核心微生物群的影响。【结果】白酒发酵过程中的核心微生物群主要包含10个属,分别是Lactobacillus、Saccharomyces、Candida、Rhizopus、Saccharomycopsis、Pichia、Dipodascus、Bacillus、Thermoascus和Lactococcus。冗余分析和蒙特卡洛置换检验表明,化学因素(还原糖和乙醇)对核心微生物群的变化比物理因素(水分、温度和酸度)具有更加重要的影响作用,此外物理-化学因素的相互作用对核心微生物群的驱动也有很大的影响。【结论】本研究揭示了白酒发酵过程中的微生物群落组成和代谢物轮廓的变化规律及其二者之间的相关关系,确立了发酵过程中的核心微生物群并量化了影响核心微生物群变化的环境因素,为实现合成微生物组生产白酒及其定向调控奠定理论基础。     

Blood lead in children and associations with trace elements and sociodemographic factors

BackgroundNo safe blood lead concentration in children has been identified. Lead can affect nearly every system in the body and is especially harmful to the developing central nervous system of children.The aim of this study is to analyze blood lead in a population of children and its association with sociodemographic variables, biochemical parameters, copper, iron, selenium and zinc.MethodsWe recruited 155 children (86 boys and 69 girls) with a mean age of 7.3 (SD:4.1). Blood lead and serum selenium concentrations were measured by electrothermal atomic absorption spectrometry. Serum copper and zinc concentrations were measured by flame atomic absorption spectrometry. Serum iron levels were determined by colorimetric assay. A risk exposure questionnaire for lead was administered to the participants.ResultsThe median blood lead level was 1.1 (IQR 0.7–1.6) μg/dL. Regarding risk exposure factors, the youngest children (<2 years) who played outdoors presented a median blood lead concentration of 1.1 μg/dL IQR: 0.48–1.48, compared to the median of 0.3 μg/dL IQR:0.2-0.48 in the children who stated they played at home (p = 0.024). Significant differences were also found when taking into account those parents who smoked (median 1.3 IQR 0.8–1.9 μg/dL vs 0.9 IQR 0.5–1.4 μg/dL of non-smokers, p = 0.002). Children who drank tap water had higher blood lead levels (median 1.2 IQR 0.7–1.6 μg/dL) than those who drank bottled water (median 0.7 IQR 0.2–1.3 μg/dL p = 0.014). In addition, children whose mothers had not finished school had higher blood lead levels (median 1.7 IQR 1.2–2.3 μg/dL) than those whose mothers had finished school (median 1.2 IQR 0.7–1.7 μg/dL) and those whose mothers had gone to university (median 0.9 IQR 0.5–1.4 μg/dL) p = 0.034. In the multivariate lineal regression analysis we continue to observe the association between mother’s higher level of education and lower blood levels (p = 0.04) and the interaction between age and outdoor play (p = 0.0145).ConclusionsIn spite of the decline in blood lead concentrations, associated risk factors continue to exist in vulnerable populations such as children.     

刺槐与环境因子相关性的缩元递阶矢量分析

为了研究环境因子对刺槐综合影响,揭示其重要影响因子,研究设置了水分适宜、干旱、严重干旱3种不同生境,从环境因子--刺槐生理变化--刺槐生长状况3个层次采用多个指标进行了实验观测.根据实验结果,利用缩元递阶矢量分析法对层与层间的关系进行分析.分析结果表明:土壤有效供水量和温度是两个重要的因子.在水分适宜的条件下,环境因子对叶水势和WUE有一定的影响,对其它生理指标没有明显影响,刺槐基本上不受环境因子的制约,能够按自身生理发展.但随着干旱加重,环境因子对刺槐的影响加重,刺槐的生理变化受环境因子的制约.在干旱、严重干旱的条件下,光合速率,蒸腾速率,WUE是3个重要指标,生理变化对枝条生长有制约性.刺槐在生长季内的生物总量明显下降,土壤水分对刺槐的生长、成活有重要影响.由此得出:刺槐的生长与土壤水分、土壤有效供水量、温度等环境因子关系密切,种植刺槐时要注意它的生存环境,特别是土壤的水分含量.缩元递阶矢量分析法是一种值得应用的好方法.     

Examination of microbial fuel cell start-up times with domestic wastewater and additional amendments

Rapid startup of microbial fuel cells (MFCs) and other bioreactors is desirable when treating wastewaters. The startup time with unamended wastewater (118 h) was similar to that obtained by adding acetate or fumarate (110-115 h), and less than that with glucose (181 h) or Fe(III) (353 h). Initial current production took longer when phosphate buffer was added, with startup times increasing with concentration from 149 h (25 mM) to 251 h (50 mM) and 526 h (100 mM). Microbial communities that developed in the reactors contained Betaproteobacteria, Acetoanaerobium noterae, and Chlorobium sp. Anode biomass densities ranged from 200 to 600 μg/cm² for all amendments except Fe(Ш) (1650 μg/cm²). Wastewater produced 91 mW/m², with the other MFCs producing 50 mW/m² (fumarate) to 103 mW/m² (Fe(III)) when amendments were removed. These experiments show that wastewater alone is sufficient to acclimate the reactor without the need for additional chemical amendments.     

Cleft lip with or without cleft palate: associations with transforming growth factor alpha and retinoic acid receptor loci.

The first association study of cleft lip with or without cleft palate (CL/P), with candidate genes, found an association with the transforming growth-factor alpha (TGFA) locus. This finding has since been replicated, in whole or in part, in three independent studies. Here we extend our original analysis of the TGFA TaqI RFLP to two other TGFA RFLPs and seven other RFLPs at five candidate genes in 117 nonsyndromic cases of CL/P and 113 controls. The other candidate genes were the retinoic acid receptor (RARA), the bcl-2 oncogene, and the homeobox genes 2F, 2G, and EN2. Significant associations with the TGFA TaqI and BamHI RFLPs were confirmed, although associations of clefting with previously reported haplotypes did not reach significance. Of particular interest, in view of the known teratogenic role of retinoic acid, was a significant association with the RARA PstI RFLP (P = .016; not corrected for multiple testing). The effect on risk of the A2 allele appears to be additive, and although the A2A2 homozygote only has an odds ratio of about 2 and recurrence risk to first-degree relatives (lambda 1) of 1.06, because it is so common it may account for as much as a third of the attributable risk of clefting. There is no evidence of interaction between the TGFA and RARA polymorphisms on risk, and jointly they appear to account for almost half the attributable risk of clefting.     

Spatiotemporal variation in home range size of female polar bears and correlations with individual contaminant load

We quantified the effect of multiple environmental and biological determinants on variation in home range size across multiple spatial (total-home range–core-home range areas) and temporal (seasonal and all seasons combined) scales for 22 adult female polar bears (Ursus maritimus) from Svalbard, Norway (2003–2011). We also evaluated if considering spatiotemporal variation in home range size and location is valuable to assess variation in concentrations of persistent organic pollutants (POPs). In general, home range size was negatively related to the proportion of land within the home range and sea ice concentration, but positively to snow depth. However, effects typically differed between seasons and total, and core-home range size, providing evidence that home range size is scale dependent in this large Arctic mammal. Females accompanied by dependent offspring had smaller home ranges during the breeding season and spring compared to solitary females, while age and body mass did not explain variation in home range size. Correlations between POP concentration and space use were marginally significant, but consistently stronger at fine spatiotemporal resolutions (i.e. core-home ranges during the breeding season) compared to coarse resolution (i.e. total-home ranges over the entire year). We also found that the geographic location of the home range is a stronger ecological correlate of POP concentration than home range size. To improve our understanding of the relation between POPs and animal space use, we recommend increasing the temporal frequency of POP measurements to evaluate how POP concentrations vary during a year and across areas.