The Influence of In Situ Chemical Oxidation on Microbial Community Composition in Groundwater Contaminated with Chlorinated Solvents

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO₄) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO₄ exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray–Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO₄ was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO₄ exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.     

Differences in dichogamy and herkogamy contribute to higher selfing in contrasting environments in the annual Blackstonia perfoliata (Gentianaceae)

Background and Aims

The establishment of plant populations in novel environments may generate pronounced shifts in floral traits and plant mating systems, particularly when pollinators are scarce. In this study, floral morphology and mating system functioning are compared between recently established and older populations of the annual plant Blackstonia perfoliata that occur in different pollinator environments.

Methods

Hand-pollination and emasculation experiments were conducted to assess the extent of pollinator-mediated pollen deposition and pollen limitation, and the contribution of autonomous selfing to total seed production. Detailed measurements of key floral traits were performed to compare the flower morphology and mating system functioning between plants from both pollination environments.

Key Results

Pollinator-mediated pollen deposition was about twice as low in the recently colonized and pollinator-poor environment compared with the old and pollinator-rich sites, but total seed set was little affected by any type of pollen limitation. The contribution of autonomous selfing to total seed production was higher in the pollinator-poor sites than in the pollinator-rich sites (index of reproductive assurance = 0·56 and 0·17, respectively), and seed production was only poorly affected by selfing, whereas in the pollinator-rich populations selfing reduced total reproductive output by about 40 % compared with outcross pollination. Plants originating from pollinator-poor environments produced smaller flowers that showed significantly lower levels of dichogamy (i.e. protogyny) and herkogamy. These reductions resulted in a 2-fold higher capacity for autonomous selfing under pollinator-free conditions (index of autonomous selfing = 0·81 and 0·41 in plants originating from the pollinator-poor and pollinator-rich environment, respectively).

Conclusions

The results illustrate that plant populations colonizing novel environments can differ markedly in floral morphology and mating system functioning. Due to a temporal shift in the male phase, the breeding system of B. perfoliata shifted from delayed selfing under pollinator-rich conditions towards competing selfing in recently established populations, providing greater reproductive assurance when pollinators and/or reproductive partners are limited.     

Absence of Complementary Sex Determination in the Parasitoid Wasp Genus Asobara (Hymenoptera: Braconidae)

An attractive way to improve our understanding of sex determination evolution is to study the underlying mechanisms in closely related species and in a phylogenetic perspective. Hymenopterans are well suited owing to the diverse sex determination mechanisms, including different types of Complementary Sex Determination (CSD) and maternal control sex determination. We investigated different types of CSD in four species within the braconid wasp genus Asobara that exhibit diverse life-history traits. Nine to thirteen generations of inbreeding were monitored for diploid male production, brood size, offspring sex ratio, and pupal mortality as indicators for CSD. In addition, simulation models were developed to compare these observations to predicted patterns for multilocus CSD with up to ten loci. The inbreeding regime did not result in diploid male production, decreased brood sizes, substantially increased offspring sex ratios nor in increased pupal mortality. The simulations further allowed us to reject CSD with up to ten loci, which is a strong refutation of the multilocus CSD model. We discuss how the absence of CSD can be reconciled with the variation in life-history traits among Asobara species, and the ramifications for the phylogenetic distribution of sex determination mechanisms in the Hymenoptera.     

CT Air Trapping Is Independently Associated with Lung Function Reduction over Time

Purpose

We aimed to study the association between lung function decline and quantitative computed tomography (CT) air trapping.

Materials and Methods

Current and former heavy smokers in a lung cancer screening trial underwent volumetric low-dose CT in inspiration and expiration. Spirometry was obtained at baseline and after 3 years. The expiratory to inspiratory ratio of mean lung density (E/I-ratio_MLD) was used to quantify air trapping. CT emphysema was defined as voxels in inspiratory CT below −950 Hounsfield Unit. Linear mixed modeling was used to determine the association between CT air trapping and lung function.

Results

We included 985 subjects with a mean age of 61.3 years. Independent of CT emphysema, CT air trapping was significantly associated with a reduction in forced expiratory volume in one second (FEV₁) and the ratio of FEV₁ over the forced vital capacity (FEV₁/FVC); FEV₁ declines with 33 mL per percent increase in CT air trapping, while FEV₁/FVC declines 0.58% per percent increase (both p<0.001). CT air trapping further elicits accelerated loss of FEV₁/FVC (additional 0.24% reduction per percent increase; p = 0.014).

Conclusion

In a lung cancer screening cohort, quantitatively assessed air trapping on low-dose CT is independently associated with reduced lung function and accelerated decline of FEV₁/FVC.     

Semi-Automatic Quantification of Subsolid Pulmonary Nodules: Comparison with Manual Measurements

Rationale

Accurate measurement of subsolid pulmonary nodules (SSN) is becoming increasingly important in the management of these nodules. SSNs were previously quantified with time-consuming manual measurements. The aim of the present study is to test the feasibility of semi-automatic SSNs measurements and to compare the results to the manual measurements.

Methods

In 33 lung cancer screening participants with 33 SSNs, the nodules were previously quantified by two observers manually. In the present study two observers quantified these nodules by using semi-automated nodule volumetry software. Nodules were quantified for effective diameter, volume and mass. The manual and semi-automatic measurements were compared using Bland-Altman plots and paired T tests. Observer agreement was calculated as an intraclass correlation coefficient. Data are presented as mean (SD).

Results

Semi-automated measurements were feasible in all 33 nodules. Nodule diameter, volume and mass were 11.2 (3.3) mm, 935 (691) ml and 379 (311) milligrams for observer 1 and 11.1 (3.7) mm, 986 (797) ml and 399 (344) milligrams for observer 2, respectively. Agreement between observers and within observer 1 for the semi-automatic measurements was good with an intraclass correlation coefficient >0.89. For observer 1 and observer 2, measured diameter was 8.8% and 10.3% larger (p<0.001), measured volume was 24.3% and 26.5% larger (p<0.001) and measured mass was 10.6% and 12.0% larger (p<0.001) with the semi-automatic program compared to the manual measurements.

Conclusion

Semi-automated measurement of the diameter, volume and mass of SSNs is feasible with good observer agreement. Semi-automated measurement makes quantification of mass and volume feasible in daily practice.     

Recombinant human lecithin‐cholesterol acyltransferase Fc fusion: Analysis of N‐ and O‐linked glycans and identification and elimination of a xylose‐based O‐linked tetrasaccharide core in the linker region

Recombinant human lecithin‐cholesterol acyltransferase Fc fusion (huLCAT‐Fc) is a chimeric protein produced by fusing human Fc to the C‐terminus of the human enzyme via a linker sequence. The huLCAT‐Fc homodimer contains five N‐linked glycosylation sites per monomer. The heterogeneity and site‐specific distribution of the various glycans were examined using enzymatic digestion and LC‐MS/MS, followed by automatic processing. Almost all of the N‐linked glycans in human LCAT are fucosylated and sialylated. The predominant LCAT N‐linked glycoforms are biantennary glycans, followed by triantennary sugars, whereas the level of tetraantennary glycans is much lower. Glycans at the Fc N‐linked site exclusively contain typical asialobiantennary structures. HuLCAT‐Fc was also confirmed to have mucin‐type glycans attached at T₄₀₇ and S₄₀₉. When LCAT‐Fc fusions were constructed using a G‐S‐G‐G‐G‐G linker, an unexpected +632 Da xylose‐based glycosaminoglycan (GAG) tetrasaccharide core of Xyl‐Gal‐Gal‐GlcA was attached to S₄₁₈. Several minor intermediate species including Xyl, Xyl‐Gal, Xyl‐Gal‐Gal, and a phosphorylated GAG core were also present. The mucin‐type O‐linked glycans can be effectively released by sialidase and O‐glycanase; however, the GAG could only be removed and localized using chemical alkaline β‐elimination and targeted LC‐MS/MS. E₄₁₆ (the C‐terminus of LCAT) combined with the linker sequence is likely serving as a substrate for peptide O‐xylosyltransferase. HuLCAT‐Fc shares some homology with the proposed consensus site near the linker sequence, in particular, the residues underlined PPP E₄₁₆GS₄₁₈G G G GDK. GAG incorporation can be eliminated through engineering by shifting the linker Ser residue downstream in the linker sequence.     

Cultivation-independent analysis of bacteria in IDEXX Quanti-Tray/2000 fecal indicator assays

Monitoring microbiological water quality is important for protecting water resources and the health of swimmers. Routine monitoring relies on cultivating fecal indicator bacteria (FIB), frequently using defined substrate technology. Defined substrate technology is designed to specifically enrich for FIB, but a complete understanding of the assay microbiology requires culture-independent analysis of the enrichments. This study aimed to identify bacteria in positive wells of Colilert and Enterolert Quanti-Tray/2000 (IDEXX Laboratories) FIB assays in environmental water samples and to quantify the degree of false-positive results for samples from an urban creek by molecular methods. Pooled Escherichia coli- and Enterococcus-positive Quanti-Tray/2000 enrichments, either from urban creek dry weather flow or municipal sewage, harbored diverse bacterial populations based on 16S rRNA gene sequences and terminal restriction fragment length polymorphism analyses. Target taxa (coliforms or enterococci) and nontarget taxa (Vibrio spp., Shewanella spp., Bacteroidetes, and Clostridium spp.) were identified in pooled and individual positive Colilert and Enterolert wells based on terminal restriction fragments that were in common with those generated in silico from clone sequences. False-positive rates of between 4 and 23% occurred for the urban creek samples, based on the absence of target terminal restriction fragments in individual positive wells. This study suggests that increased selective inhibition of nontarget bacteria could improve the accuracy of the Colilert and Enterolert assays.     

Soil water content, maize yield and its stability as affected by tillage and crop residue management in rainfed semi-arid highlands

Rainfed crop management systems need to be optimized to provide more resilient options to cope with projected climatic scenarios forecasting a decrease in mean precipitation and more frequent extreme drought periods in Mexico. Soil water content (0?C60 cm) was measured during three crop cycles in maize plots with different agronomic management practices in a long-term rainfed experiment (established in 1991) in the highlands of Mexico. Maize yields of 1997?C2009 were reported. Crop management practices varied in (1) tillage (conventional [CT] vs. zero tillage [ZT]) and (2) residue management (full or partial retention and removal). ZT with residue retention had higher soil water content than management practices involving CT and ZT with residue removal which provided a buffer for drought periods during the growing seasons. In 2009, a cycle with a prolonged drought during vegetative growth, this resulted in yield differences of up to 4.7 Mg ha^?1 between ZT with (partial) residue retention and the other practices. Averaged over 1997?C2009, these practices had a yield advantage of approximately 1.5 Mg ha^?1 over practices involving CT and ZT with residue removal. ZT with (partial) residue retention used rainfall more efficiently and resulted in a more resilient agronomic system than practices involving either CT or ZT with residue removal.     

Perception of Interannual Covariation and Strategies for Risk Reduction among Mikea of Madagascar

This paper begins with the hypothesis that Mikea, participants in a mixed foraging–fishing–farming–herding economy of southwestern Madagascar, may attempt to reduce interannual variance in food supply caused by unpredictable rainfall by following a simple rule-of-thumb: Practice an even mix of activities that covary positively with rainfall and activities that covary negatively with rainfall. Results from a historical matrix participatory exercise confirm that Mikea perceive that foraging and farming outcomes covary positively or negatively with rainfall. This paper further considers whether Mikea learn about covariation through personal observation and memory recall (individual learning) or through socially transmitted ethnotheory (social learning). Dual inheritance theory models by Boyd and Richerson (1988) predict that individual learning is more effective in spatially and temporally variable environments such as the Mikea Forest. In contrast, the psychological literature suggests that individuals judge covariation poorly when memory of past events is required, unless they share a socially learned theory that a covariation should exist (Nisbett and Ross 1980). Results suggest that Mikea rely heavily on shared ethnotheory when judging covariation, but individuals continually strive to improve their judgment through individual observation.