An ecological paradox: More woodland predators and less artificial nest predation in landscapes colonized by noisy miners

Many passerine bird populations, particularly those that have open‐cup nests, are in decline in agricultural landscapes. Current theory suggests that an increase in habitat generalist predators in response to landscape change is partially responsible for these declines. However, empirical tests have failed to reach a consensus on how and through what mechanisms landscape change affects nest predation. We tested one hypothesis, the Additive Predation Model, with an artificial nest experiment in fragmented landscapes in southern Queensland, Australia. We employed structural equation modelling of the influence of the relative density of woodland and habitat generalist predators and landscape features at the nest, site, patch and landscape scales on the probability of nest predation. We found little support for the Additive Predation Model, with no significant influence of the density of woodland predators on the probability of nest predation, although landscape features at different spatial scales were important. Within woodlands fragmented by agriculture in eastern Australia, the presence of noisy miner colonies appears to influence ecological processes important for nest predation such that the Additive Predation Model does not hold. In the absence of colonies of the aggressive native bird, the noisy miner, the influence of woodland predators on the risk of artificial nest predation was low compared with that of habitat generalist predators. Outside noisy miner colonies, we found significant edge effects with greater predation rates for artificial nests within woodland patches located closer to the agricultural matrix. Furthermore, the density of habitat generalist predators increased with the extent of irrigated land‐use, suggesting that in the absence of noisy miner colonies, nest predation increases with land‐use intensity at the landscape scale.     

Acute phase reactants add little to composite disease activity indices for rheumatoid arthritis: validation of a clinical activity score

Introduction  

Frequent assessments of rheumatoid arthritis (RA) disease activity allow timely adaptation of therapy, which is essential in preventing disease progression. However, values of acute phase reactants (APRs) are needed to calculate current composite activity indices, such as the Disease Activity Score (DAS)28, the DAS28-CRP (i.e. the DAS28 using C-reactive protein instead of erythrocyte sedimentation rate) and the Simplified Disease Activity Index (SDAI). We hypothesized that APRs make limited contribution to the SDAI, and that an SDAI-modification eliminating APRs – termed the Clinical Disease Activity Index (CDAI; i.e. the sum of tender and swollen joint counts [28 joints] and patient and physician global assessments [in cm]) – would have comparable validity in clinical cohorts.     

Adenovirus-5-vectored P. falciparum vaccine expressing CSP and AMA1. Part B: safety, immunogenicity and protective efficacy of the CSP component

Background

A protective malaria vaccine will likely need to elicit both cell-mediated and antibody responses. As adenovirus vaccine vectors induce both these responses in humans, a Phase 1/2a clinical trial was conducted to evaluate the efficacy of an adenovirus serotype 5-vectored malaria vaccine against sporozoite challenge.

Methodology/Principal Findings

NMRC-MV-Ad-PfC is an adenovirus vector encoding the Plasmodium falciparum 3D7 circumsporozoite protein (CSP). It is one component of a two-component vaccine NMRC-M3V-Ad-PfCA consisting of one adenovector encoding CSP and one encoding apical membrane antigen-1 (AMA1) that was evaluated for safety and immunogenicity in an earlier study (see companion paper, Sedegah et al). Fourteen Ad5 seropositive or negative adults received two doses of NMRC-MV-Ad-PfC sixteen weeks apart, at particle units per dose. The vaccine was safe and well tolerated. All volunteers developed positive ELISpot responses by 28 days after the first immunization (geometric mean 272 spot forming cells/million[sfc/m]) that declined during the following 16 weeks and increased after the second dose to levels that in most cases were less than the initial peak (geometric mean 119 sfc/m). CD8+ predominated over CD4+ responses, as in the first clinical trial. Antibody responses were poor and like ELISpot responses increased after the second immunization but did not exceed the initial peak. Pre-existing neutralizing antibodies (NAb) to Ad5 did not affect the immunogenicity of the first dose, but the fold increase in NAb induced by the first dose was significantly associated with poorer antibody responses after the second dose, while ELISpot responses remained unaffected. When challenged by the bite of P. falciparum-infected mosquitoes, two of 11 volunteers showed a delay in the time to patency compared to infectivity controls, but no volunteers were sterilely protected.

Significance

The NMRC-MV-Ad-PfC vaccine expressing CSP was safe and well tolerated given as two doses, but did not provide sterile protection.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00392015","term_id":"NCT00392015"}}NCT00392015     

湖南邵东中泥盆统棋梓桥组层孔虫生物群及其生态环境

湖南中部泥盆纪地层和生物礁相当发育。湖南邵东中泥盆世棋梓桥期的泥质石灰岩中层孔虫广泛分布,本文共描述邵东廉桥马鞍山棋梓桥期层孔虫12属18种,其中Stromatopora wenshanensis为一新名,代替1982年根据一个云南标本定名为Stromatopora irregularis的种名。 马鞍山礁是—发育在海底平台上的厚度稍有变化的层状礁,马鞍山礁的沉积相变化过程,是由近岸浅海到展状礁普遍发育的开阔台地,再到封闭或半封闭的泻湖或潮坪环境。生物组合和沉积物也随沉积环境的变化而发生相应的变化。     

A phospho-proteomic screen identifies novel S6K1 and mTORC1 substrates revealing additional complexity in the signaling network regulating cell growth

S6K1, a critical downstream substrate of mTORC1, has been implicated in regulating protein synthesis and a variety of processes that impinge upon cell growth and proliferation. While the role of the cytoplasmic p70^S6K1 isoform in the regulation of translation has been intensively studied, the targets and function of the nuclear p85^S6K1 isoform remain unclear. Therefore, we carried out a phospho-proteomic screen to identify novel p85^S6K1 substrates. Four novel putative p85^S6K1 substrates, GRP75, CCTβ, PGK1 and RACK1, and two mTORC1 substrates, ANXA4 and PSMA6 were identified, with diverse roles in chaperone function, ribosome maturation, metabolism, vesicle trafficking and the proteasome, respectively. The chaperonin subunit CCTβ was further investigated and the site of phosphorylation mapped to serine 260, a site located in the chaperonin apical domain. Consistent with this domain being involved in folding substrate interactions, we found that phosphorylation of serine 260 modulates chaperonin folding activity.     

Early Archean planktonic mode of life: Implications from fluid dynamics of lenticular microfossils

Lenticular, and commonly flanged, microfossils in 3.0–3.4 Ga sedimentary deposits in Western Australia and South Africa are unusually large (20–80 μm across), robust, and widespread in space and time. To gain insight into the ecology of these organisms, we performed simulations of fluid dynamics of virtual cells mimicking lenticular forms of variable sizes, oblateness, flange presence, and flange thickness. Results demonstrate that (a) the flange reduces sedimentation velocity, (b) this flange function works more effectively in larger cells, and (c) modest oblateness lowers sedimentation rate. These observations support interpretations that the lenticular microbes were planktonic—a lifestyle that could have been advantageous in an early Earth harsh environment including violent volcanic activities, repeated asteroid impacts, and relatively high UV‐radiation. Although the robustness of these organisms could have provided additional protection on the early Earth, this architecture may have impeded a planktonic lifestyle by increasing cell density. However, our data suggest that this disadvantage could have been compensated by enlargement of cell volume, which could have enhanced the ability of the flange to slow sedimentation rate, especially if coupled with vacuolation. The results of this simulation study may help to explain the unique morphology and unusually large size of these Archean microfossils.     

Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes

The Brazos-Trinity Basin on the slope of the Gulf of Mexico passive margin was drilled during Integrated Ocean Drilling Progam Expedition 308. The buried anaerobic sediments of this basin are largely organic-poor and have few microbial inhabitants compared with the organic-rich sediments with high cell counts from the Peru Margin that were drilled during Ocean Drilling Program Leg 201. Nucleic acids were extracted from Brazos-Trinity Basin sediments and were subjected to whole-genome amplification and pyrosequencing. A comparison of the Brazos-Trinity Basin metagenome, consisting of 105 Mbp, and the existing Peru Margin metagenome revealed trends linking gene content, phylogenetic content, geological location and geochemical regime. The major microbial groups (Proteobacteria, Firmicutes, Euryarchaeota and Chloroflexi) occur consistently throughout all samples, yet their shifting abundances allow for discrimination between samples. The cluster of orthologous groups category abundances for some classes of genes are correlated with geochemical factors, such as the level of ammonia. Here we describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 likely represents the subsurface microbial inhabitants of turbiditic slopes that lack substantial upwelling.     

Patterns of daily behaviour in two lizard species Lacerta agilis L. and Lacerta vivipara Jacquin

Summary During the period May to August 1978, individuals of both Lacerta agilis and Lacerta vivipara were observed in a specially constructed out-door vivarium. The daily patterns of behaviour of the two species were recorded along with surface and air temperatures. Daily activity of both species followed a similar basic pattern but was modified by variations in the local weather. Adults of L. vivipara reached a thermal preferendum more quickly and had a longer daily activity period than adults of L. agilis. The larger L. agilis can increase its period of activity by making use of different thermal conditions in a diverse habitat with varied vegetation structure under conditions of high solar radiation. The status of viable populations of L. agilis could be maintained or enhanced by management aimed at modifying the microenvironment of the lizard's habitat.