New Genotype of Dengue Type 3 Virus Circulating in Brazil and Colombia Showed a Close Relationship to Old Asian Viruses

Dengue type 3 genotype V viruses have been recently detected in Brazil and Colombia. In this study, we described another Brazilian isolate belonging to this genotype. Phylogenetic analysis including dengue type 3 viruses isolated worldwide showed that Brazilian and Colombian viruses were closely related to viruses isolated in Asia more than two decades ago. The characteristic evolutionary pattern of dengue type 3 virus cannot explain the close similarity of new circulating viruses with old viruses. Further studies are needed to confirm the origin of the new dengue type III genotype circulating in Brazil and Colombia.     

ApoA-I cleaved by transthyretin has reduced ability to promote cholesterol efflux and increased amyloidogenicity

A fraction of plasma transthyretin (TTR) circulates in HDL through binding to apolipoprotein A-I (apoA-I). Moreover, TTR is able to cleave the C terminus of lipid-free apoA-I. In this study, we addressed the relevance of apoA-I cleavage by TTR in lipoprotein metabolism and in the formation of apoA-I amyloid fibrils. We determined that TTR may also cleave lipidated apoA-I, with cleavage being more effective in the lipid-poor prebeta-HDL subpopulation. Upon TTR cleavage, discoidal HDL particles displayed a reduced capacity to promote cholesterol efflux from cholesterol-loaded THP-1 macrophages. In similar assays, TTR-containing HDL from mice expressing human TTR in a TTR knockout background had a decreased ability to perform reverse cholesterol transport compared with similar particles from TTR knockout mice, reinforcing the notion that cleavage by TTR reduces the ability of apoA-I to promote cholesterol efflux. As amyloid deposits composed of N-terminal apoA-I fragments are common in the atherosclerotic intima, we assessed the impact of TTR cleavage on apoA-I aggregation and fibrillar growth. We determined that TTR-cleaved apoA-I has a high propensity to form aggregated particles and that it formed fibrils faster than full-length apoA-I, as assessed by electron microscopy. Our results show that apoA-I cleavage by TTR may affect HDL biology and the development of atherosclerosis by reducing cholesterol efflux and increasing the apoA-I amyloidogenic potential.     

Comparison of sand fly trapping approaches for vector surveillance of Leishmania and Bartonella species in ecologically distinct,endemic regions of Peru

BackgroundIn Peru, the information regarding sand fly vectors of leishmaniasis and bartonellosis in the Amazon region is limited. In this study, we carried out sand fly collections in Peruvian lowland and highland jungle areas using different trap type configurations and screened them for Leishmania and Bartonella DNA.Methodology/Principal findingsPhlebotomine sand flies were collected in Peruvian Amazon jungle and inter Andean regions using CDC light trap, UV and color LED traps, Mosquito Magnet trap, BG Sentinel trap, and a Shannon trap placed outside the houses. Leishmania spp. screening was performed by kDNA PCR and confirmed by a nested cytochrome B gene (cytB) PCR. Bartonella spp. screening was performed by ITS PCR and confirmed by citrate synthase gene (gltA). The PCR amplicons were sequenced to identify Leishmania and Bartonella species.UV and Blue LED traps collected the highest average number of sand flies per hour in low jungle; UV, Mosquito Magnet and Shannon traps in high jungle; and Mosquito Magnet in inter Andean region. Leishmania guyanensis in Lutzomyia carrerai carrerai and L. naiffi in Lu. hirsuta hirsuta were identified based on cytB sequencing. Bartonella spp. related to Bartonella bacilliformis in Lu. whitmani, Lu. nevesi, Lu. hirsuta hirsuta and Lu. sherlocki, and a Bartonella sp. related to Candidatus B. rondoniensis in Lu. nevesi and Lu. maranonensis were identified based on gltA gene sequencing.Conclusions/SignificanceUV, Blue LED, Mosquito Magnet and Shannon traps were more efficient than the BG-Sentinel, Green, and Red LED traps. This is the first report of L. naiffi and of two genotypes of Bartonella spp. related to B. bacilliformis and Candidatus B. rondoniensis infecting sand fly species from the Amazon region in Peru.     

Enhanced Mineralization of [U-14C]2,4-Dichlorophenoxyacetic Acid in Soil from the Rhizosphere of Trifolium pratense

Enhanced biodegradation in the rhizosphere has been reported for many organic xenobiotic compounds, although the mechanisms are not fully understood. The purpose of this study was to discover whether rhizosphere-enhanced biodegradation is due to selective enrichment of degraders through growth on compounds produced by rhizodeposition. We monitored the mineralization of [U-¹⁴C]2,4-dichlorophenoxyacetic acid (2,4-D) in rhizosphere soil with no history of herbicide application collected over a period of 0 to 116 days after sowing of Lolium perenne and Trifolium pratense. The relationships between the mineralization kinetics, the number of 2,4-D degraders, and the diversity of genes encoding 2,4-D/α-ketoglutarate dioxygenase (tfdA) were investigated. The rhizosphere effect on [¹⁴C]2,4-D mineralization (50 μg g⁻¹) was shown to be plant species and plant age specific. In comparison with nonplanted soil, there were significant (P < 0.05) reductions in the lag phase and enhancements of the maximum mineralization rate for 25- and 60-day T. pratense soil but not for 116-day T. pratense rhizosphere soil or for L. perenne rhizosphere soil of any age. Numbers of 2,4-D degraders in planted and nonplanted soil were low (most probable number, <100 g⁻¹) and were not related to plant species or age. Single-strand conformational polymorphism analysis showed that plant species had no impact on the diversity of α-Proteobacteria tfdA-like genes, although an impact of 2,4-D application was recorded. Our results indicate that enhanced mineralization in T. pratense rhizosphere soil is not due to enrichment of 2,4-D-degrading microorganisms by rhizodeposits. We suggest an alternative mechanism in which one or more components of the rhizodeposits induce the 2,4-D pathway.     

Rhizodeposition and the enhanced mineralization of 2,4-dichlorophenoxyacetic acid in soil from the Trifolium pratense rhizosphere

Enhanced biodegradation of organic xenobiotic compounds in the rhizosphere is frequently recorded although the specific mechanisms are poorly understood. We have shown that the mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) is enhanced in soil collected from the rhizosphere of Trifolium pratense[e.g. maximum mineralization rate=7.9 days-1 and time at maximum rate (t1)=16.7 days for 12-day-old T. pratense soil in comparison with 4.7 days-1 and 25.4 days, respectively, for non-planted controls). The purpose of this study was to gain a better understanding of the plant-microbe interactions involved in rhizosphere-enhanced biodegradation by narrowing down the identity of the T. pratense rhizodeposit responsible for stimulating the microbial mineralization of 2,4-D. Specifically, we investigated the distribution of the stimulatory component(s) among rhizodeposit fractions (exudates or root debris) and the influence of soil properties and plant species on its production. Production of the stimulatory rhizodeposit was dependent on soil pH (e.g. t1 for roots grown at pH 6.5 was significantly lower than for those grown at pH 4.4) but independent of soil inorganic N concentration. Most strikingly, the stimulatory rhizodeposit was only produced by T. pratense grown in non-sterile soil and was present in both exudates and root debris. Comparison of the effect of root debris from plant species (three each) from the classes monocotyledon, dicotyledon (non-legume) and dicotyledon (legume) revealed that legumes had by far the greatest positive impact on 2,4-D mineralization kinetics. We discuss the significance of these findings with respect to legume-rhizobia interactions in the rhizosphere.     

Fire effects and ecological recovery pathways of tropical montane cloud forests along a time chronosequence

Tropical montane cloud forests (TMCFs) harbour high levels of biodiversity and large carbon stocks. Their location at high elevations make them especially sensitive to climate change, because a warming climate is enhancing upslope species migration, but human disturbance (especially fire) may in many cases be pushing the treeline downslope. TMCFs are increasingly being affected by fire, and the long‐term effects of fire are still unknown. Here, we present a 28‐year chronosequence to assess the effects of fire and recovery pathways of burned TMCFs, with a detailed analysis of carbon stocks, forest structure and diversity. We assessed rates of change of carbon (C) stock pools, forest structure and tree‐size distribution pathways and tested several hypotheses regarding metabolic scaling theory (MST), C recovery and biodiversity. We found four different C stock recovery pathways depending on the selected C pool and time since last fire, with a recovery of total C stocks but not of aboveground C stocks. In terms of forest structure, there was an increase in the number of small stems in the burned forests up to 5–9 years after fire because of regeneration patterns, but no differences on larger trees between burned and unburned plots in the long term. In support of MST, after fire, forest structure appears to approximate steady‐state size distribution in less than 30 years. However, our results also provide new evidence that the species recovery of TMCF after fire is idiosyncratic and follows multiple pathways. While fire increased species richness, it also enhanced species dissimilarity with geographical distance. This is the first study to report a long‐term chronosequence of recovery pathways to fire suggesting faster recovery rates than previously reported, but at the expense of biodiversity and aboveground C stocks.     

Horizon scan of global conservation issues for 2011

This review describes outcomes of a 2010 horizon-scanning exercise building upon the first exercise conducted in 2009. The aim of both horizon scans was to identify emerging issues that could have substantial impacts on the conservation of biological diversity, and to do so sufficiently early to encourage policy-relevant, practical research on those issues. Our group included professional horizon scanners and researchers affiliated with universities and non- and inter-governmental organizations, including specialists on topics such as invasive species, wildlife diseases and coral reefs. We identified 15 nascent issues, including new greenhouse gases, genetic techniques to eradicate mosquitoes, milk consumption in Asia and societal pessimism.     

Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs

Objective

To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers.

Methods and Materials

Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT) associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact.

Results

Shortly after publication, 62 (9%) of the 687 research papers were determined to describe at least a ‘major addition to knowledge’ –6 were thought to be ‘landmark’ papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications.

Conclusion

When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.     

Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization

Receptor signaling in the growth hormone (GH)-growth hormone receptor (GHR) system is controlled through a sequential two-step hormone-induced dimerization of two copies of the extracellular domain (ECD) of the receptor. The regulatory step of this process is the binding of the second ECD (ECD2) to the stable preassociated 1 : 1 GH/ECD1 complex on the cell surface. To determine the energetics that governs this step, the binding kinetics of 38 single- and double-alanine mutants in the hGH Site2 contact with ECD2 were measured by using trimolecular surface plasmon resonance (TM-SPR). We find that the Site2 interface of hGH does not have a distinct binding hot-spot region, and the most important residues are not spatially clustered, but rather are distributed over the whole binding surface. In addition, it was determined through analysis of a set of pairwise double alanine mutations that there is a significant degree of negative cooperativity among Site2 residues. Residues that show little effect or even improved binding on substitution with alanine, when paired with D116A-hGH, display significant negative cooperativity. Because most of these pairwise mutated residues are spatially separated by >or=10 A, this indicates that the Site2 binding interface of the hGH-hGHR ternary complex displays both structural and energetic malleability.     

Cartilage oligomeric matrix protein-deficient mice have normal skeletal development

Cartilage oligomeric matrix protein (COMP) belongs to the thrombospondin family and is a homopentamer primarily expressed in cartilage. Mutations in the COMP gene result in the autosomal dominant chondrodysplasias pseudoachondroplasia (PSACH) and some types of multiple epiphyseal dysplasia (MED), which are characterized by mild to severe short-limb dwarfism and early-onset osteoarthritis. We have generated COMP-null mice to study the role of COMP in vivo. These mice show no anatomical, histological, or ultrastructural abnormalities and show none of the clinical signs of PSACH or MED. Northern blot analysis and immunohistochemical analysis of cartilage indicate that the lack of COMP is not compensated for by any other member of the thrombospondin family. The results also show that the phenotype in PSACH/MED cartilage disorders is not caused by the reduced amount of COMP.