Recent advances in gel-based proteome profiling techniques

This review focuses on recent developments in gel-based proteomics techniques. By combining traditional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoretic techniques with recent advances in protein labeling using different classes of molecules (i.e., fluorescent dyes, chemical probes, radioisotopes), new technologies have been developed that allow for high-throughput studies of proteins at the whole-proteome scale.     

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids

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Trophic niche similarities of sympatric Turdus thrushes determined by fecal contents,stable isotopes,and bipartite network approaches

An ecological niche has been defined as an n‐dimensional hypervolume formed by conditions and resources that species need to survive, grow, and reproduce. In practice, such niche dimensions are measurable and describe how species share resources, which has been thought to be a crucial mechanism for coexistence and a major driver of broad biodiversity patterns. Here, we investigate resource partitioning and trophic interactions of three sympatric, phylogenetically related and morphologically similar species of thrushes (Turdus spp.). Based on one year of data collected in southern Brazil, we investigated niche partitioning using three approaches: diet and trophic niche assessed by fecal analysis, diet and niche estimated by stable isotopes in blood and mixing models, and bipartite network analysis derived from direct diet and mixing model outputs. Approaches revealed that the three sympatric thrushes are generalists that feed on similar diets, demonstrating high niche overlap. Fruits from C3 plants were one of the most important food items in their networks, with wide links connecting the three thrush species. Turdus amaurochalinus and T. albicollis had the greatest trophic and isotopic niche overlap, with 90% and 20% overlap, respectively. There was partitioning of key resources between these two species, with a shared preference for fig tree fruits—Ficus cestrifolia (T. amaurochalinus PSIRI% = 11.3 and T. albicollis = 11.5), which was not present in the diet of T. rufiventris. Results added a new approach to the network analysis based on values from the stable isotope mixing models, allowing comparisons between traditional dietary analysis and diet inferred by isotopic mixing models, which reflects food items effectively assimilated in consumer tissues. Both are visualized in bipartite networks and show food‐consumers link strengths. This approach could be useful to other studies using stable isotopes coupled to network analysis, particularly useful in sympatric species with similar niches.     

The role of male accessory-gland substance on female reproduction with some observations of spermatogenesis in the stable fly

The bulbous tubular portion of the median ejaculatory duct functions as the accessory gland in the male stable fly, Stomoxys calcitrans. The gland started to enlarge after emergence when the fly was fed on sugar-water or blood. Implants of accessory glands from sugar-water or blood-fed males were effective in stimulating oviposition in virgin females. The injection into females of accessory-gland extracts from males fed blood prevented insemination; this extract was effective in concentration as low as 0.25 gland per female. Accessory-gland extracts from sugar-water fed males were only partially effective in preventing female insemination. However, the accessory-gland extracts of male stable flies had little effect on insemination when injected into three other species of female dipterans.Spermatogenesis was completed by the time of emergence, or shortly thereafter, a process independent of blood feeding. Three types of spermatids were identified, forming a continuum of spermiogenesis stages. Fat, fusiform spermatozoa elongated to become thin, elongate and mature spermatozoa.     

Nitronate monooxygenase, a model for anionic flavin semiquinone intermediates in oxidative catalysis

Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase, is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Over the past 5 years, a resurgence of interest on the enzymology of NMO has driven several studies aimed at the elucidation of the mechanistic and structural properties of the enzyme. This review article summarizes the knowledge gained from these studies on NMO, which has been emerging as a model system for the investigation of anionic flavosemiquinone intermediates in the oxidative catalysis of organic molecules, and for the effect that branching of reaction intermediates has on both the kinetic parameters and isotope effects associated with enzymatic reactions. A comparison of the catalytic mechanism of NMO with other flavin-dependent enzymes that oxidize nitroalkane and nitronates is also presented.     

Minimizing the effect of mineral nitrogen on biological nitrogen fixation in common bean by increasing nutrient levels

Although common bean (Phaseolus vulgaris L.) has good potential for N₂ fixation, some additional N provided through fertilizer usually is required for a maximum yield. In this study the suppressive effect of N on nodulation and N₂ fixation was evaluated in an unfertile soil under greenhouse conditions with different levels of soil fertility (low=no P, K and S additions; medium = 50, 63 and 10 mg kg^–1 soil and high = 200, 256 and 40 mg kg^–1 soil, respectively) and combined with 5, 15, 60 and 120 mg N kg^–1 soil of ¹⁵N-labelled urea. The overall average nodule number and weight increased under high fertility levels. At low N applications, nitrogen had a synergistic effect on N₂ fixation, by stimulating nodule formation, nitrogenase activity and plant growth. At high fertility and at the highest N rate (120 mg kg^–1 soil), the stimulatory effect of N fertilizer on N₂ fixation was still observed, increasing the amounts of N₂ fixed from 88 up to 375 mg N plant^–1. These results indicate that a suitable balance of soil nutrients is essential to obtain high N₂ fixation rates and yield in common beans.     

Tracing water uptake by jarrah (Eucalyptus marginata) trees using natural abundances of deuterium

 Seasonal change in the δ²H content of water from twig sap, soil, rainfall and groundwater were measured to determine the water sources accessed by jarrah (Eucalyptus marginata) trees at three sites in Western Australia with differing soils and depths to water table. During winter and spring the main contributor to the water uptake of the trees was stored water in the surface layers of the soil replenished by predominantly winter rainfall. With the onset of summer drought jarrah became more reliant on water from deeper down the profile. There was no clear evidence that jarrah could tap water from groundwater more than 14 m deep in deep sands. Defining the source of water for trees in deep lateritic soils using stable isotopes is hampered by the uniform deuterium profiles down most of the unsaturated zone and into the groundwater. There was a limited response in the δ²H values of sapwater in twigs to changes in the δ²H of the upper layers of the deep sand following input of rainfall in autumn. The damped response was related to the small variation in the δ²H composition of rainfall in most events during the year and the mixing in the tree of water extracted from different locations in the soil profile. Received: 21 August 1995 / Accepted: 3 December 1995     

Red bat fatality: Geographic extents through deuterium and niche models

Bat fatality at wind energy facilities is a conservation issue, but its effect on bat populations is difficult to estimate. We have little understanding of wind turbine effects on bat population persistence, in part because we have poor knowledge of bat migration pathways and hence the source populations for individual fatalities. We used deuterium ratio analysis combined with genetic algorithm for rule-set prediction and the web-based isoscapes modeling, analysis, and prediction in a geographic information system environment as a novel approach. Our objectives were to explore the utility of these methods together and map the geographic extents of eastern red bat (Lasiurus borealis) specimens salvaged in 2008–2010 from a single, 92-km² wind energy facility in Illinois, USA. Results indicate that combining these methods can be successful and support their use with species where ranges may be less well defined. Because of the migratory nature of this species and the range of deuterium values of pixels in our isotope model, we predicted that 18% and 82% of the specimens would have isotope results inside and outside of the wind facility's isocline respectively. We concluded that 71.4% of the specimens had isotope signatures placing them outside the wind facility's isocline. It could be argued that the wide distribution of bat fatalities dilutes the overall effect of those fatalities on the bat species; however, if other facilities show a similar pattern, each facility could have cumulative and far reaching population-level effects. © 2019 The Wildlife Society.     

Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1–N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

Density functional theory calculations of isolated Watson–Crick A:U and A:T base pairs predict that adenine ¹³C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, ^2hΔ¹³C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that ^2hΔ¹³C2 is sensitive to hydrogen-bond strength. Calculated ^2hΔ¹³C2 values at a given N1–N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical ^2hΔ¹³C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on ^2hΔ¹³C2 values. Furthermore, ^2hΔ¹³C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that ^2hΔ¹³C2 is context dependent and that this dependence is similar for RNA and DNA. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Variation in δ13C among species and sexes in the family Restionaceae along a fine‐scale hydrological gradient

Consistent, repeatable segregation of plant species along hydrological gradients is an established phenomenon that must in some way reflect a trade‐off between plants' abilities to tolerate the opposing constraints of drought and waterlogging. In C₃ species tissue carbon isotope discrimination (δ¹³C) is known to vary sensitively in response to stomatal behaviour, reflecting stomatal limitation of photosynthesis during the period of active growth. However, this has not been studied at fine‐spatial scale in natural communities. We tested how δ¹³C varied between species and sexes of individuals in the family Restionaceae growing along a monitored hydrological gradient. Twenty Restionaceae species were investigated using species‐level phylogeny at two sites in the Cape Floristic Region, a biodiversity hotspot. A spatial overlap analysis showed the Restionaceae species segregated significantly (P < 0.001) at both sites. Moreover, there were significant differences in δ¹³C values among the Restionaceae species (P < 0.001) and between male and female individuals of each species (P < 0.01). However, after accounting for phylogeny, species δ¹³C values did not show any significant correlation with the hydrological gradient. We suggest that some other variable (e.g. plant phenology) could be responsible for masking a simple response to water availability.