Maturation of West Nile virus modulates sensitivity to antibody-mediated neutralization

West Nile virions incorporate 180 envelope (E) proteins that orchestrate the process of virus entry and are the primary target of neutralizing antibodies. The E proteins of newly synthesized West Nile virus (WNV) are organized into trimeric spikes composed of pre-membrane (prM) and E protein heterodimers. During egress, immature virions undergo a protease-mediated cleavage of prM that results in a reorganization of E protein into the pseudo-icosahedral arrangement characteristic of mature virions. While cleavage of prM is a required step in the virus life cycle, complete maturation is not required for infectivity and infectious virions may be heterogeneous with respect to the extent of prM cleavage. In this study, we demonstrate that virion maturation impacts the sensitivity of WNV to antibody-mediated neutralization. Complete maturation results in a significant reduction in sensitivity to neutralization by antibodies specific for poorly accessible epitopes that comprise a major component of the human antibody response following WNV infection or vaccination. This reduction in neutralization sensitivity reflects a decrease in the accessibility of epitopes on virions to levels that fall below a threshold required for neutralization. Thus, in addition to a role in facilitating viral entry, changes in E protein arrangement associated with maturation modulate neutralization sensitivity and introduce an additional layer of complexity into humoral immunity against WNV.     

Polyhydroxybutyrate accumulation by a Serratia sp.

A strain of Serratia sp. showed intracellular electron-transparent inclusion bodies when incubated in the presence of citrate and glycerol 2-phosphate without nitrogen source following pre-growth under carbon-limitation in continuous culture. About 1.3 mmol citrate were consumed per 450 mg biomass, giving a calculated yield of maximally 55% of stored material per g of biomass dry wt. The inclusion bodies were stained with Sudan Black and Nile Red (NR), suggesting a lipid material, which was confirmed as polyhydroxybutyrate (PHB) by analysis of molecular fragments by GC and by FTIR spectroscopy of isolated bio-PHB in comparison with reference material. Multi-parameter flow cytometry in conjunction with NR fluorescence, and electron microscopy, showed that not all cells contained heavy PHB bodies, suggesting the potential for increasing the overall yield. The economic attractiveness is enhanced by the co-production of nanoscale hydroxyapatite (HA), a possible high-value precursor for bone replacement materials.     

An untargeted metabolomics method for archived newborn dried blood spots in epidemiologic studies

Introduction

For pediatric diseases like childhood leukemia, a short latency period points to in-utero exposures as potentially important risk factors. Untargeted metabolomics of small molecules in archived newborn dried blood spots (DBS) offers an avenue for discovering early-life exposures that contribute to disease risks.

Objectives

The purpose of this study was to develop a quantitative method for untargeted analysis of archived newborn DBS for use in an epidemiological study (California Childhood Leukemia Study, CCLS).

Methods

Using experimental DBS from the blood of an adult volunteer, we optimized extraction of small molecules and integrated measurement of potassium as a proxy for blood hematocrit. We then applied this extraction method to 4.7-mm punches from 106 control DBS samples from the CCLS. Sample extracts were analyzed with liquid chromatography—high resolution mass spectrometry (LC-HRMS) and an untargeted workflow was used to screen for metabolites that discriminate population characteristics such as sex, ethnicity, and birth weight.

Results

Thousands of small molecules were measured in extracts of archived DBS. Normalizing for potassium levels removed variability related to varying hematocrit across DBS punches. Of the roughly 1000 prevalent small molecules that were tested, multivariate linear regression detected significant associations with ethnicity (three metabolites) and birth weight (15 metabolites) after adjusting for multiple testing.

Conclusions

This untargeted workflow can be used for analysis of small molecules in archived DBS to discover novel biomarkers, to provide insights into the initiation and progression of diseases, and to provide guidance for disease prevention.

     

Comparison of sample preparation techniques for large‐scale proteomics

Numerous workflows exist for large‐scale bottom‐up proteomics, many of which achieve exceptional proteome depth. Herein, we evaluated the performance of several commonly used sample preparation techniques for proteomic characterization of HeLa lysates [unfractionated in‐solution digests, SDS‐PAGE coupled with in‐gel digestion, gel‐eluted liquid fraction entrapment electrophoresis (GELFrEE) technology, SCX StageTips and high‐/low‐pH reversed phase fractionation (HpH)]. HpH fractionation was found to be superior in terms of proteome depth (>8400 proteins detected) and fractionation efficiency compared to other techniques. SCX StageTip fractionation required minimal sample handling and was also a substantial improvement over SDS‐PAGE separation and GELFrEE technology. Sequence coverage of the HeLa proteome increased to 38% when combining all workflows, however, total proteins detected improved only slightly to 8710. In summary, HpH fractionation and SCX StageTips are robust techniques and highly suited for complex proteome analysis.     

Scales drive detection,attention, and memory of snakes in wild vervet monkeys (<Emphasis Type="Italic">Chlorocebus pygerythrus</Emphasis>)

Predatory snakes are argued to have been largely responsible for the origin of primates via selection favoring expansion of the primate visual system, and even today snakes can be deadly to primates. Neurobiological research is now beginning to reveal the mechanisms underlying the ability of primates (including humans) to detect snakes more rapidly than other stimuli. However, the visual cues allowing rapid detection of snakes, and the cognitive and ecological conditions contributing to faster detection, are unclear. Since snakes are often partially obscured by vegetation, the more salient cues are predicted to occur in small units. Here we tested for the salience of snake scales as the smallest of potential visual cues by presenting four groups of wild vervet monkeys (Chlorocebus pytherythrus) with a gopher snake (Pituophis catenifer) skin occluded except for no more than 2.7 cm, in natural form and flat, the latter to control for even small curvilinear cues from their unusual body shape. Each of these treatments was preceded by a treatment without the snakeskin, the first to provide a baseline, and the second, to test for vigilance and memory recall after exposure to the snakeskin. We found that (1) vervets needed only a small portion of snakeskin for detection, (2) snake scales alone were sufficient for detection, (3) latency to detect the snakeskin was longer with more extensive and complex ground cover, and (4) vervets that were exposed to the snakeskin remembered where they last saw “snakes”, as indicated by increased wariness near the occluding landmarks in the absence of the snakeskin and more rapid detection of the next presented snakeskin. Unexpectedly, adult males did not detect the snakeskin as well as adult females and juveniles. These findings extend our knowledge of the complex ecological and evolutionary relationships between snakes and primates.     

Unsuccessful introduced biocontrol agents can act as pollinators of invasive weeds: Bitou Bush (Chrysanthemoides monilifera ssp. rotundata) as an example

The extent of self‐compatibility and reliance on pollinators for seed set are critical determinants of reproductive success in invasive plant species. Seed herbivores are commonly used as biocontrol agents but may also act as flower visitors, potentially resulting in pollination. However, such contrasting or potentially counterproductive interaction effects are rarely considered or evaluated for biological control programs. We investigated the breeding system and pollinators of Bitou Bush (Chrysanthemoides monilifera ssp. rotundata), an invasive species in Australia that has been the subject of biocontrol programs since 1987. We found the species to be obligate outcrossing in all six populations tested. From 150 video hours, we found 21 species of potential pollinators, including Mesoclanis polana, the Bitou Seedfly, native to South Africa and released in Australia as a biocontrol agent in 1996. Mesoclanis polana transferred pollen to stigmas and was the most common pollinator (52% of pollinator visits), followed by the syrphid fly Simosyrphus grandicornis (9%) and introduced honeybee, Apis mellifera (6.5%). Fruit‐to‐flower ratios ranged from 0.12 to 0.45 and were highest in the population with the greatest proportion of Mesoclanis polana visits. In an experimental trial, outside the naturalized range, the native bee Homalictus sphecodoides and the native syrphid Melangyna viridiceps were the primary pollinators, and fruit‐to‐flower ratios were 0.35, indicating that Bitou Bush would have ready pollinators if its range expanded inland. Synthesis. Invasive Bitou Bush requires pollinators, and this is effected by a range of generalist pollinators in eastern Australia including the Bitou Seedfly, introduced as a biocontrol agent, and the major pollinator detected in this study. Fruit‐to‐flower ratios were highest when the Bitou Seedfly was in high abundance. This study underscores the importance of evaluating the pollination biology of invasive species in their native ranges and prior to the introduction of biocontrol agents.     

Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase.

The major soluble avian eye lens protein, delta crystallin, is highly homologous to the housekeeping enzyme argininosuccinate lyase (ASL). ASL is part of the urea and arginine-citrulline cycles and catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate. In duck lenses, there are two delta crystallin isoforms that are 94% identical in amino acid sequence. Only the delta2 isoform has maintained ASL activity and has been used to investigate the enzymatic mechanism of ASL. The role of the active site residues Ser-29, Asp-33, Asp-89, Asn-116, Thr-161, His-162, Arg-238, Thr-281, Ser-283, Asn-291, Asp-293, Glu-296, Lys-325, Asp-330, and Lys-331 have been investigated by site-directed mutagenesis, and the structure of the inactive duck delta2 crystallin (ddeltac2) mutant S283A with bound argininosuccinate was determined at 1.96 A resolution. The S283A mutation does not interfere with substrate binding, because the 280's loop (residues 270-290) is in the open conformation and Ala-283 is more than 7 A from the substrate. The substrate is bound in a different conformation to that observed previously indicating a large degree of conformational flexibility in the fumarate moiety when the 280's loop is in the open conformation. The structure of the S283A ddeltac2 mutant and mutagenesis results reveal that a complex network of interactions of both protein residues and water molecules are involved in substrate binding and specificity. Small changes even to residues not involved directly in anchoring the argininosuccinate have a significant effect on catalysis. The results suggest that either His-162 or Thr-161 are responsible for proton abstraction and reinforce the putative role of Ser-283 as the catalytic acid, although we cannot eliminate the possibility that arginine is released in an uncharged form, with the solvent providing the required proton. A detailed enzymatic mechanism of ASL/ddeltac2 is presented.     

Male Demography,Female Mating Behavior,and Infanticide in Wild Patas Monkeys (Erythrocebus patas)

Infanticide by males has been hypothesized to be a naturally selected behavioral strategy that increases the infanticidal male's reproductive success. The sexual selection hypothesis has been challenged via alternative, nonadaptive hypotheses that dispute its empirical and theoretical bases. Two of the most widely recognized alternatives are the social pathology hypothesis, in which infanticide results from overcrowding or recent human disturbance, and the generalized aggression hypothesis, in which infanticide is an epiphenomenon of increased male aggression. We report the first case of infanticide in wild, seasonally breeding patas monkeys (Erythrocebus patas) living at a low population density in a stable habitat, conditions which do not support the social pathology hypothesis. Its exceptional occurrence is consistent with the sexual selection hypothesis: over a 7-year period the infanticidal male was the only one of 13 resident males that was not present during the actual conception season but was present during the following birth season. Also consistent with this hypothesis, mothers were differentially targeted for male aggression, which increased sevenfold during the days surrounding the infanticide and then decreased to baseline levels after the infanticide. Aggression targeted at mothers does not support the generalized aggression hypothesis. As predicted by the sexual selection hypothesis, females began soliciting mating immediately after the infanticide, despite its occurrence in the nonconceptive season.