Monsoon sensitivity to aerosol direct radiative forcing in the community atmosphere model

Aerosol forcing remains a dominant uncertainty in climate studies. The impact of aerosol direct radiative forcing on Indian monsoon is extremely complex and is strongly dependent on the model, aerosol distribution and characteristics specified in the model, modelling strategy employed as well as on spatial and temporal scales. The present study investigates (i) the aerosol direct radiative forcing impact on mean Indian summer monsoon when a combination of quasi-realistic mean annual cycles of scattering and absorbing aerosols derived from an aerosol transport model constrained with satellite observed Aerosol Optical Depth (AOD) is prescribed, (ii) the dominant feedback mechanism behind the simulated impact of all-aerosol direct radiative forcing on monsoon and (iii) the relative impacts of absorbing and scattering aerosols on mean Indian summer monsoon. We have used CAM3, an atmospheric GCM (AGCM) that has a comprehensive treatment of the aerosol-radiation interaction. This AGCM has been used to perform climate simulations with three different representations of aerosol direct radiative forcing due to the total, scattering aerosols and black carbon aerosols. We have also conducted experiments without any aerosol forcing. Aerosol direct impact due to scattering aerosols causes significant reduction in summer monsoon precipitation over India with a tendency for southward shift of Tropical Convergence Zones (TCZs) over the Indian region. Aerosol forcing reduces surface solar absorption over the primary rainbelt region of India and reduces the surface and lower tropospheric temperatures. Concurrent warming of the lower atmosphere over the warm oceanic region in the south reduces the land-ocean temperature contrast and weakens the monsoon overturning circulation and the advection of moisture into the landmass. This increases atmospheric convective stability, and decreases convection, clouds, precipitation and associated latent heat release. Our analysis reveals a defining negative moisture-advection feedback that acts as an internal damping mechanism spinning down the regional hydrological cycle and leading to significant circulation changes in response to external radiative forcing perturbations. When total aerosol loading (both absorbing and scattering aerosols) is prescribed, dust and black carbon aerosols are found to cause significant atmospheric heating over the monsoon region but the aerosol-induced weakening of meridional lower tropospheric temperature gradient (leading to weaker summer monsoon rainfall) more than offsets the increase in summer-time rainfall resulting from the atmospheric heating effect of absorbing aerosols, leading to a net decrease of summer monsoon rainfall. Further, we have carried out climate simulations with globally constant AODs and also with the constant AODs over the extended Indian region replaced by realistic AODs. Regional aerosol radiative forcing perturbations over the Indian region is found to have impact not only over the region of loading but over remote tropical regions as well. This warrants the need to prescribe realistic aerosol properties in strategic regions such as India in order to accurately assess the aerosol impact.

Game theoretic, decentralized, local information based algorithm for community detection in social graphs

Motivated by the observation that communities in real world social networks form due to actions of rational individuals in networks, we propose a novel game theory inspired algorithm to determine communities in networks. The algorithm is decentralized and only uses local information at each node. We show the efficacy of the proposed algorithm through extensive experimentation on several real world social network data sets.

Infection of Human Endothelial Cells by Japanese Encephalitis Virus: Increased Expression and Release of Soluble HLA-E

Japanese encephalitis virus (JEV) is a single stranded RNA virus that infects the central nervous system leading to acute encephalitis in children. Alterations in brain endothelial cells have been shown to precede the entry of this flavivirus into the brain, but infection of endothelial cells by JEV and their consequences are still unclear. Productive JEV infection was established in human endothelial cells leading to IFN-beta and TNF-alpha production. The MHC genes for HLA-A, -B, -C and HLA-E antigens were upregulated in human brain microvascular endothelial cells, the endothelial-like cell line, ECV 304 and human foreskin fibroblasts upon JEV infection. We also report the release/shedding of soluble HLA-E (sHLA-E) from JEV infected human endothelial cells for the first time. This shedding of sHLA-E was blocked by an inhibitor of matrix metalloproteinases (MMP). In addition, MMP-9, a known mediator of HLA solubilisation was upregulated by JEV. In contrast, human fibroblasts showed only upregulation of cell-surface HLA-E. Addition of UV inactivated JEV-infected cell culture supernatants stimulated shedding of sHLA-E from uninfected ECV cells indicating a role for soluble factors/cytokines in the shedding process. Antibody mediated neutralization of TNF-alpha as well as IFNAR receptor together not only resulted in inhibition of sHLA-E shedding from uninfected cells, it also inhibited HLA-E and MMP-9 gene expression in JEV-infected cells. Shedding of sHLA-E was also observed with purified TNF-alpha and IFN-beta as well as the dsRNA analog, poly (I:C). Both IFN-beta and TNF-alpha further potentiated the shedding when added together. The role of soluble MHC antigens in JEV infection is hitherto unknown and therefore needs further investigation.

RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Levels of Alpha-Toxin Correlate with Distinct Phenotypic Response Profiles of Blood Mononuclear Cells and with agr Background of Community-Associated Staphylococcus aureus Isolates

Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of alpha-toxin than did the proliferative supernatants. Addition of alpha-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, delta-toxin or phenol soluble modulin alpha-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

Community-managed forests and wildlife-friendly agriculture play a subsidiary but not substitutive role to protected areas for the endangered Asian elephant

Global conservation policy is increasingly debating the feasibility of reconciling wildlife conservation and human resource requirements in land uses outside protected areas (PAs). However, there are few quantitative assessments of whether or to what extent these `wildlife-friendly' land uses fulfill a fundamental function of PAs-to separate biodiversity from anthropogenic threats. We distinguish the role of wildlife-friendly land uses as being (a) subsidiary, whereby they augment PAs with secondary habitat, or (b) substitutive, wherein they provide comparable habitat to PAs. We tested our hypotheses by investigating the influence of land use and human presence on space-use intensity of the endangered Asian elephant (Elephas maximus) in a fragmented landscape comprising PAs and wildlife-friendly land uses. We applied multistate occupancy models to spatial data on elephant occurrence to estimate and model the overall probability of elephants using a site, and the conditional probability of high-intensity use given that elephants use a site. The probability of elephants using a site regardless of intensity did not vary between PAs and wildlife-friendly land uses. However, high-intensity use declined with distance to PM, and this effect was accentuated by an increase in village density. Therefore, while wildlife-friendly land uses did play a subsidiary conservation role, their potential to substitute for PAs was offset by a strong human presence. Our findings demonstrate the need to evaluate the role of wildlife-friendly land uses in landscape-scale conservation; for species that have conflicting resource requirements with people, PAs are likely to provide crucial refuge from growing anthropogenic threats. (C) 2014 Elsevier Ltd. All rights reserved.

Decentralized demand-supply matching using community microgrids and consumer demand response: A scenario analysis

Developing countries constantly face the challenge of reliably matching electricity supply to increasing consumer demand. The traditional policy decisions of increasing supply and reducing demand centrally, by building new power plants and/or load shedding, have been insufficient. Locally installed microgrids along with consumer demand response can be suitable decentralized options to augment the centralized grid based systems and plug the demand-supply gap. The objectives of this paper are to: (1) develop a framework to identify the appropriate decentralized energy options for demand supply matching within a community, and, (2) determine which of these options can suitably plug the existing demand-supply gap at varying levels of grid unavailability. A scenario analysis framework is developed to identify and assess the impact of different decentralized energy options at a community level and demonstrated for a typical urban residential community Vijayanagar, Bangalore in India. A combination of LPG based CHP microgrid and proactive demand response by the community is the appropriate option that enables the Vijayanagar community to meet its energy needs 24/7 in a reliable, cost-effective manner. The paper concludes with an enumeration of the barriers and feasible strategies for the implementation of community microgrids in India based on stakeholder inputs. (C) 2014 Elsevier Ltd. All rights reserved.

Importance of intraspecifically gregarious species in a tropical bird community

In both single- and mixed-species social groups, certain participants are known to play important roles in providing benefits. Identifying these participants is critical for understanding group dynamics, but is often difficult with large roving social groups in the wild. Here, we develop a new approach to characterize roles in social groups and apply it to mixed-species bird flocks (flocks hereafter) in an Indian tropical evergreen forest. Two types of species, namely intraspecifically gregarious and sallying species, are thought to play important roles in flocks because studies have shown they attract other flock participants. However, it is unclear why these types are attractive and whether they are essential for flock formation. We address these questions by focusing on the composition of the subset of flocks containing only two species each. In two-species flocks, it is reasonable to assume that at least one species obtains some kind of benefit. Therefore, only those species combinations that result in benefit to at least one species should occur as two-species flocks. Using data from 540 flocks overall, of which 158 were two-species flocks, we find that intraspecifically gregarious species are disproportionately represented in two-species flocks and always lead flocks when present, and that flocks containing them are joined significantly more by other species. Our results suggest that intraspecifically gregarious species are likely to be the primary benefit providers in flocks and are important for tropical flock formation. Our study also provides a new approach to understanding importance in other mixed-species and single-species social groups.

Infection of human amniotic and endothelial cells by Japanese encephalitis virus: Increased expression of HLA-F

Productive infection of human amniotic and endothelial cell lines with Japanese encephalitis virus (JEV) was established leading to the induction of NF kappa B and HLA-F, a non-classical MHC molecule. Induction of the HLA-F gene and protein in JEV-infected cells was shown to be NF kappa B dependent since it was blocked by inhibitors of NF kappa B activation. ShRNA targeting lentivirus-mediated stable knockdown of the p65 subunit of NF kappa B inhibited JEV-mediated induction of HLA-F both in the amniotic cell line, AV-3 as well as the human brain microendothelial cell line, HBMEC. The induction of HLA-F by treatment of AV-3 with TNF-alpha was also inhibited by ShRNA mediated knockdown of NF kappa B. TNF-alpha treatment of HEK293T cells that were transfected with reporter plasmids under the control of HLA-F enhancer A elements resulted in significant transactivation of the luciferase reporter gene. NF kappa B-mediated induction of HLA-F following JEV infection and TNF-alpha exposure is being suggested for the first time. (C) 2014 Elsevier Inc. All rights reserved.

Inhibition of ERK and proliferation in NK cell lines by soluble HLA-E released from Japanese encephalitis virus infected cells

Productive infection of human endothelial cells with Japanese encephalitis virus (JEV), a single stranded RNA virus induces shedding of sHLA-E. We show here that sHLA-E that is released upon infection with this flavivirus can inhibit IL-2 and PMA mediated ERK 1/2 phosphorylation in two NK cell lines, Nishi and NKL. Virus infected or IFN-gamma treated cell culture supernatants containing sHLA-E were found to partially inhibit IL-2 mediated induction of CD25 molecules on NKL cells. It was also found that sHLA-E could inhibit IL-2 induced H-3]-thymidine incorporation suggesting that, similar to cell surface expressed HLA-E, sHLA-E could also inhibit NK cell responses. Hence JEV-induced shedding of sHLA-E needs further investigation to better understand immune responses in JEV infections since it may have a role in viral evasion of NK cell responses. (C) 2014 Elsevier B.V. All rights reserved.

Long-term effects of Macroternies termites, herbivores and annual early fire on woody undergrowth community in Sudanian woodland, Burkina Faso

Termites, herbivores and fire are recognized as major guilds that structure woody plant communities in African savanna and woodland ecosystems. An understanding of their interaction is crucial to design appropriate management regimes. The aim of this study was to evaluate the long-term impacts of herbivore, fire and termite activities on regeneration of trees. Permanent experimental quadrats were established in 1992 in the Sudanian woodland of Burkina Faso subjected to grazing by livestock and annual early fire and the control. Within the treatment quadrats, an inventory of the woody undergrowth community was conducted on termitaria occupied by Macrotermes subhyalinus, extended termitosphere (within 5 m radius from the mound base) and adjacent area (beyond 5 m from the mound base). Hierarchical analysis was performed to determine significant differences in species richness, abundance and diversity indices among vegetation patches within fire and herbivory treatments. Grazed quadrats had significantly (P < 0.001) more species and stem density of woody undergrowth than non-grazed quadrats but maintained similar level of species richness and stem density of woody undergrowth on termitaria. There were not significant differences (P>0.05) in species richness and stem density between burnt and unburnt quadrats. Termitaria supported a highly diverse woody undergrowth with higher stem density than either the extended termitosphere or rest of quadrats. The density of woody undergrowth was significantly related with mature trees of selected species on termitaria (R-2 = 0.593; P<0.001) than that on the extended termitosphere (R-2 = 0.333; P<0.001) and adjacent area (R-2 = 0.197; P<0.001). It can be concluded that termites facilitate the regeneration of woody species while grazing and annual early fire play a minor role in the regeneration of woody species. The current policy that prohibits grazing should be revised to accommodate the interests of livestock herders. (C) 2014 Elsevier GmbH. All rights reserved.

Lizards of the Thar Desert - Resource partitioning and community composition

How similar species co-exist in nature is a fundamental question in community ecology. Resource partitioning has been studied in desert lizard communities across four continents, but data from South Asia is lacking. We used area-constrained visual encounter surveys to study community composition and spatial and temporal resource partitioning in a lizard community during summer in the Thar Desert, western India, addressing an important biogeographic gap in knowledge. Twelve one-hectare grids divided into 25 m x 25 m plots were placed across four habitats barren dunes, stabilized dunes, grassland, and rocky hills. We recorded 1039 sightings of 12 species during 84 sampling sessions. Lizard abundance decreased in the order stabilized dunes > grassland > barren dunes > rocky hills; richness was in roughly the opposite order. Resource partitioning was examined for the seven commonest species. Overall spatial overlap was low (<0.6) between species pairs. Overlap was higher within habitats, but species showed finer separation through use of different microhabitat categories and specific spatial resources, as well as by positioning at different distances to vegetation. Diurnal species were also separated by peak time of activity. Space appears to be an important resource dimension facilitating coexistence in this desert lizard community. (C) 2015 Elsevier Ltd. All rights reserved.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects

Healthy human skin harbours a diverse array of microbes that comprise the skin microbiome. Commensal bacteria constitute an important component of resident microbiome and are intricately linked to skin health. Recent studies describe an association between altered skin microbial community and epidemiology of diseases, like psoriasis, atopic dermatitis etc. In this study, we compare the differences in bacterial community of lesional and non-lesional skin of vitiligo subjects. Our study reveals dysbiosis in the diversity of microbial community structure in lesional skin of vitiligo subjects. Although individual specific signature is dominant over the vitiligo-specific microbiota, a clear decrease in taxonomic richness and evenness can be noted in lesional patches. Investigation of community specific correlation networks reveals distinctive pattern of interactions between resident bacterial populations of the two sites (lesional and non-lesional). While Actinobacterial species constitute the central regulatory nodes (w.r.t. degree of interaction) in non-lesional skin, species belonging to Firmicutes dominate on lesional sites. We propose that the changes in taxonomic characteristics of vitiligo lesions, as revealed by our study, could play a crucial role in altering the maintenance and severity of disease. Future studies would elucidate mechanistic relevance of these microbial dynamics that can provide new avenues for therapeutic interventions.