Determination of biologically significant hydrologic condition metrics in urbanizing watersheds: an empirical analysis over a range of environmental settings

We investigated the relations among 83 hydrologic condition metrics (HCMs) and changes in algal, invertebrate, and fish communities in five metropolitan areas across the continental United States. We used a statistical approach that employed Spearman correlation and regression tree analysis to identify five HCMs that are strongly associated with observed biological variation along a gradient of urbanization. The HCMs related to average flow magnitude, high-flow magnitude, high-flow event frequency, high-flow duration, and rate of change of stream cross-sectional area were most consistently associated with changes in aquatic communities. Although our investigation used an urban gradient design with short hydrologic periods of record (≤1 year) of hourly cross-sectional area time series, these five HCMs were consistent with previous investigations using long-term daily-flow records. The ecological sampling day often was included in the hydrologic period. Regression tree models explained up to 73, 92, and 79% of variance for specific algal, invertebrate, and fish community metrics, respectively. National models generally were not as statistically significant as models for individual metropolitan areas. High-flow event frequency, a hydrologic metric found to be transferable across stream type and useful for classifying habitat by previous research, was found to be the most ecologically relevant HCM; transformation by precipitation increased national-scale applicability. We also investigated the relation between measures of stream flashiness and land-cover indicators of urbanization and found that land-cover characteristic and pattern variables, such as road density, percent wetland, and proximity of developed land, were strongly related to HCMs at both a metropolitan and national scale and, therefore, may be effective land-use management options in addition to wholesale impervious-area reduction.     

Characterization of microsatellite loci for the Argentine ant,Linepithema humile,and their potential for analysis of colony structure in invading Hawaiian populations

We developed primers for five polymorphic microsatellite loci to analyse the genetic structure of colonies in an invading Argentine ant population located in Haleakala National Park on the island of Maui, Hawaii. Microsatellite loci were isolated using both a polymerase chain reaction‐based and a cloning‐based method. With a range of 3–18 alleles and expected levels of heterozygosity of 0.46–0.77, these loci provide useful markers for the detection of colony and population structure in new or expanding populations of this species.     

Effect of migration and environmental heterogeneity on the maintenance of quantitative genetic variation: a simulation study

The paradox of high genetic variation observed in traits under stabilizing selection is a long‐standing problem in evolutionary theory, as mutation rates appear too low to explain observed levels of standing genetic variation under classic models of mutation–selection balance. Spatially or temporally heterogeneous environments can maintain more standing genetic variation within populations than homogeneous environments, but it is unclear whether such conditions can resolve the above discrepancy between theory and observation. Here, we use individual‐based simulations to explore the effect of various types of environmental heterogeneity on the maintenance of genetic variation (V_A) for a quantitative trait under stabilizing selection. We find that V_A is maximized at intermediate migration rates in spatially heterogeneous environments and that the observed patterns are robust to changes in population size. Spatial environmental heterogeneity increased variation by as much as 10‐fold over mutation–selection balance alone, whereas pure temporal environmental heterogeneity increased variance by only 45% at max. Our results show that some combinations of spatial heterogeneity and migration can maintain considerably more variation than mutation–selection balance, potentially reconciling the discrepancy between theoretical predictions and empirical observations. However, given the narrow regions of parameter space required for this effect, this is unlikely to provide a general explanation for the maintenance of variation. Nonetheless, our results suggest that habitat fragmentation may affect the maintenance of V_A and thereby reduce the adaptive capacity of populations.     

Functional insights from proteome-wide structural modeling of <Emphasis Type="Italic">Treponema pallidum</Emphasis> subspecies <Emphasis Type="Italic">pallidum</Emphasis>, the causative agent of syphilis

Background

Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale.

Results

Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens.

Conclusions

Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T. pallidum proteome-wide structural modeling study and is one of few studies to apply this approach for the functional annotation of a whole proteome.

     

Dose effects of modified alternate-day fasting regimens on in vivo cell proliferation and plasma insulin-like growth factor-1 in mice.

Reduced cell proliferation is associated with lower cancer risk. Alternate-day fasting (ADF), defined as alternating 24-h periods of ad libitum feeding and fasting, decreases cell proliferation. The effect of modified regimens of ADF on cell proliferation, however, has not been examined. This study measured the effects of modified ADF regimens on prostate and splenic T-cell proliferation and circulating insulin-like growth factor-1 (IGF-1) levels in mice. In a 4-wk study, 24 male C57BL/6J mice were randomized to one of four interventions: 1) ADF-25% [25% calorie restriction (CR) on fast day], 2) ADF-50% (50% CR on fast day), 3) ADF-100% (100% CR on fast day), and 4) control. Body weight of the ADF-100% group was less (P < 0.005) than that of the ADF-25% and ADF-50% groups posttreatment. On the feast day, the ADF-100% and ADF-50% groups ate 85% and 45% more food, respectively, than controls, indicating a hyperphagic response to fasting. Proliferation rates of T-cells were 6% and 30% lower (P < 0.05) in the ADF-50% and ADF-100% groups, respectively, relative to controls. Prostate cell proliferation was reduced (P < 0.05) by 49% in the ADF-100% group, relative to controls, but did not change in the other groups. IGF-1 levels were reduced (P < 0.05) by 40%, relative to controls, in the ADF-100% group. These findings confirm the beneficial effects of ADF-100% on cancer risk by decreasing cell proliferation and IGF-1 levels and suggest that modified ADF regimens comprising 25-50% CR on the fast day do not replicate these effects.     

Permafrost thaw and intense thermokarst activity decreases abundance of stream benthic macroinvertebrates

Intensification of permafrost thaw has increased the frequency and magnitude of large permafrost slope disturbances (mega slumps) in glaciated terrain of northwestern Canada. Individual thermokarst disturbances up to 40 ha in area have made large volumes of previously frozen sediments available for leaching and transport to adjacent streams, significantly increasing sediment and solute loads in these systems. To test the effects of this climate‐sensitive disturbance regime on the ecology of Arctic streams, we explored the relationship between physical and chemical variables and benthic macroinvertebrate communities in disturbed and undisturbed stream reaches in the Peel Plateau, Northwest Territories, Canada. Highly disturbed and undisturbed stream reaches differed with respect to taxonomic composition and invertebrate abundance. Minimally disturbed reaches were not differentiated by these variables but rather were distributed along a disturbance gradient between highly disturbed and undisturbed sites. In particular, there was evidence of a strong negative relationship between macroinvertebrate abundance and total suspended solids, and a positive relationship between abundance and the distance from the disturbance. Increases in both sediments and nutrients appear to be the proximate cause of community differences in highly disturbed streams. Declines in macroinvertebrate abundance in response to slump activity have implications for the food webs of these systems, potentially leading to negative impacts on higher trophic levels, such as fish. Furthermore, the disturbance impacts on stream health can be expected to intensify as climate change increases the frequency and magnitude of thermokarst.     

Insulin Stimulates S100B Secretion and These Proteins Antagonistically Modulate Brain Glucose Metabolism

Neurochemical Research - Brain metabolism is highly dependent on glucose, which is derived from the blood circulation and metabolized by the astrocytes and other neural cells via several pathways....     

The role of soil conditions in fine root ecomorphology in Norway spruce (Picea abies (L.) Karst.)

The present study is an attempt to investigate the pattern of morphological variability of the short roots of Norway spruce (Picea abies (L.) Karst.) growing in different soils. Five root parameters – diameter, length and dry weight of the root tip, root density (dry weight per water-saturated volume) and specific root area (absorbing area of dry weight unit) were studied with respect to 11 soil characteristics using CANOCO RDA analysis. The investigation was conducted in seven study areas in Estonia differing in site quality class and soil type. Ten root samples per study area were collected randomly from the forest floor and from the 20 cm soil surface layer. Eleven soil parameters were included in the study: humus content, specific soil surface area, field capacity, soil bulk density, pH (KCl and H₂O dilution's), N and Ca concentrations, Ca/Al and C/N ratios, and the decomposition rate of fine roots (<2 mm dia.). Root morphological characteristics most strongly related to the measured soil characteristics in the different sites were specific root area, root density and diameter of the short roots, the means varying from 29 to 42 m² kg⁻¹, from 310 to 540 kg m⁻³ and from 0.26 to 0.32 mm, respectively; root density being most sensitive. The most favourable site and soil types resulting in fine roots with morphological characteristics for optimizing nutrient uptake (e.g. low short root density and high specific root area) were Umbric Luvisol (Oxalis), Dystric Gleysol (Oxalis) and Gleyic Luvisol (Hepatica). These soil types correspond to highly productive natural forest stands of Norway spruce in Estonia. All measured soil variables explained 28% of total variance of the root characteristics. The most important variables related to root morphology were the humus content, field capacity and specific soil surface area. This revised version was published online in June 2006 with corrections to the Cover Date.