Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India

We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune evasion cluster appear to be different from those of strain ST772 on preliminary examination.

Serodiagnosis of Tuberculosis in Asian Elephants (Elephas maximus) in Southern India: A Latent Class Analysis

Background: Mycobacterium tuberculosis, a causative agent of chronic tuberculosis disease, is widespread among some animal species too. There is paucity of information on the distribution, prevalence and true disease status of tuberculosis in Asian elephants (Elephas maximus). The aim of this study was to estimate the sensitivity and specificity of serological tests to diagnose M. tuberculosis infection in captive elephants in southern India while simultaneously estimating sero-prevalence. Methodology/Principal Findings: Health assessment of 600 elephants was carried out and their sera screened with a commercially available rapid serum test. Trunk wash culture of select rapid serum test positive animals yielded no animal positive for M. tuberculosis isolation. Under Indian field conditions where the true disease status is unknown, we used a latent class model to estimate the diagnostic characteristics of an existing (rapid serum test) and new (four in-house ELISA) tests. One hundred and seventy nine sera were randomly selected for screening in the five tests. Diagnostic sensitivities of the four ELISAs were 91.3-97.6% (95% Credible Interval (CI): 74.8-99.9) and diagnostic specificity were 89.6-98.5% (95% CI: 79.4-99.9) based on the model we assumed. We estimate that 53.6% (95% CI: 44.6-62.8) of the samples tested were free from infection with M. tuberculosis and 15.9% (97.5% CI: 9.8 - to 24.0) tested positive on all five tests. Conclusions/Significance: Our results provide evidence for high prevalence of asymptomatic M. tuberculosis infection in Asian elephants in a captive Indian setting. Further validation of these tests would be important in formulating area-specific effective surveillance and control measures.

Algal biofuel production and mitigation potential in India

Energy and energy services are the backbone of growth and development in India and is increasingly dependent upon the use of fossil based fuels that lead to greenhouse gases (GHG) emissions and related concerns. Algal biofuels are being evolved as carbon (C)-neutral alternative biofuels. Algae are photosynthetic microorganisms that convert sunlight, water and carbon dioxide (CO2) to various sugars and lipids Tri-Acyl-Glycols (TAG) and show promise as an alternative, renewable and green fuel source for India. Compared to land based oilseed crops algae have potentially higher yields (5-12 g/m(2)/d) and can use locations and water resources not suited for agriculture. Within India, there is little additional land area for algal cultivation and therefore needs to be carried out in places that are already used for agriculture, e.g. flooded paddy lands (20 Mha) with village level technologies and on saline wastelands (3 Mha). Cultivating algae under such conditions requires novel multi-tier, multi-cyclic approaches of sharing land area without causing threats to food and water security as well as demand for additional fertilizer resources by adopting multi-tier cropping (algae-paddy) in decentralized open pond systems. A large part of the algal biofuel production is possible in flooded paddy crop land before the crop reaches dense canopies, in wastewaters (40 billion litres per day), in salt affected lands and in nutrient/diversity impoverished shallow coastline fishery. Mitigation will be achieved through avoidance of GHG, C-capture options and substitution of fossil fuels. Estimates made in this paper suggest that nearly half of the current transportation petro-fuels could be produced at such locations without disruption of food security, water security or overall sustainability. This shift can also provide significant mitigation avenues. The major adaptation needs are related to socio-technical acceptance for reuse of various wastelands, wastewaters and waste-derived energy and by-products through policy and attitude change efforts.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

Impact of pit-toilet leachate on groundwater chemistry and role of vadose zone in removal of nitrate and E-coli pollutants in Kolar District, Karnataka, India

Assessment of chemistry of groundwater infiltrated by pit-toilet leachate and contaminant removal by vadose zone form the focus of this study. The study area is Mulbagal Town in Karnataka State, India. Groundwater level measurements and estimation of unsaturated permeability indicated that the leachate recharged the groundwater inside the town at the rate of 1 m/day. The average nitrate concentration of groundwater inside the town (148 mg/L) was three times larger than the permissible limit (45 mg/L), while the average nitrate concentration of groundwater outside the town (30 mg/L) was below the permissible limit. The groundwater inside the town exhibited E. coli contamination, while groundwater outside the town was free of pathogen contamination. Infiltration of alkalis (Na+, K+) and strong acids (Cl-, SO4 (2-)) caused the mixed Ca-Mg-Cl type (60 %) and Na-Cl type (28 %) facies to predominate groundwater inside the town, while, Ca-HCO3 (35 %), mixed Ca-Mg-Cl type (35 %) and mixed Ca-Na-HCO3 type (28 %) facies predominated groundwater outside/periphery of town. Reductions in E. coli and nitrate concentrations with vadose zone thickness indicated its participation in contaminant removal. A 4-m thickness of unsaturated sand + soft, disintegrated weathered rock deposit facilitates the removal of 1 log of E. coli pathogen. The anoxic conditions prevailing in the deeper layers of the vadose zone (> 19 m thickness) favor denitrification resulting in lower nitrate concentrations (28-96 mg/L) in deeper water tables (located at depths of -29 to -39 m).

Short- and long-term temporal variations in salinity and the oxygen, carbon and hydrogen isotopic compositions of the Hooghly Estuary water, India

The Hooghly River estuary provides a unique experimental site to understand the effect of monsoonal river discharge on freshwater and seawater mixing. Water samples collected bi-weekly for a duration of 17 months were analyzed for salinity, delta O-18,delta C-13(DIC), as well as delta D to investigate the differential mixing of freshwater and seawater. The differences in salinity and delta O-18 of samples collected during low and high tides on the same day are strongly correlated suggesting a well mixed water column at our sampling site. Low salinity and depleted delta O-18 during monsoon is consistent with increased river discharge as well as high rainfall. We identified different slopes in a delta O-18 versus salinity plot for the estuary water samples collected during monsoon and non-monsoon seasons. This is driven by composition of the freshwater source which is dominated by rainwater during monsoon and rivers during non-monsoon months. Selected delta D analyses of samples indicate that groundwater contributes significantly to the Hooghly Estuary during low rainfall times of the year. delta C-13(DIC) measured in the water recorded low values towards the end of monsoon indicating low productivity (i.e. increased organic respiration) while progressively increasing delta C-13(DIC) values from October till January as well as during some of the pre-monsoon months can be explained by increasing productivity. Very low delta C-13(DIC) (similar to-20%0) suggests involvement of carbon derived from anaerobic oxidation of organics and/or methane with potential contribution from increased anthropogenic water supply. An estimate of seawater incursion into the Hooghly Estuary at different times of the year is obtained by using salinity data in a two-component mixing model. Presence of seawater was found maximum (31-37%) during February till July and lowest (less than or equal to 6%) from September till November. We notice a temporal offset between Ganges River discharge farther upstream at Farakka and salinity variation at the Hooghly Estuary. We believe that this time lag is a result of the physical distance between Farakka and Kakdweep (our sampling location) and put constraints on the travel time of river water during early monsoon. (c) 2012 Published by Elsevier B.V.

A study of vertical cloud structure of the Indian summer monsoon using CloudSat data

Precise specification of the vertical distribution of cloud optical properties is important to reduce the uncertainty in quantifying the radiative impacts of clouds. The new global observations of vertical profiles of clouds from the CloudSat mission provide opportunities to describe cloud structures and to improve parameterization of clouds in the weather and climate prediction models. In this study, four years (2007-2010) of observations of vertical structure of clouds from the CloudSat cloud profiling radar have been used to document the mean vertical structure of clouds associated with the Indian summer monsoon (ISM) and its intra-seasonal variability. Active and break monsoon spells associated with the intra-seasonal variability of ISM have been identified by an objective criterion. For the present analysis, we considered CloudSat derived column integrated cloud liquid and ice water, and vertically profiles of cloud liquid and ice water content. Over the South Asian monsoon region, deep convective clouds with large vertical extent (up to 14 km) and large values of cloud water and ice content are observed over the north Bay of Bengal. Deep clouds with large ice water content are also observed over north Arabian Sea and adjoining northwest India, along the west coast of India and the south equatorial Indian Ocean. The active monsoon spells are characterized by enhanced deep convection over the Bay of Bengal, west coast of India and northeast Arabian Sea and suppressed convection over the equatorial Indian Ocean. Over the Bay of Bengal, cloud liquid water content and ice water content is enhanced by similar to 90 and similar to 200 % respectively during the active spells. An interesting feature associated with the active spell is the vertical tilting structure of positive CLWC and CIWC anomalies over the Arabian Sea and the Bay of Bengal, which suggests a pre-conditioning process for the northward propagation of the boreal summer intra-seasonal variability. It is also observed that during the break spells, clouds are not completely suppressed over central India. Instead, clouds with smaller vertical extent (3-5 km) are observed due to the presence of a heat low type of circulation. The present results will be useful for validating the vertical structure of clouds in weather and climate prediction models.

Microearthquake activity near the Idukki Reservoir, south India: A rare example of renewed triggered seismicity

Earthquakes triggered by artificial reservoirs have been documented for more than seven decades and the processes leading to this phenomenon are fairly well understood. Larger among such earthquakes are known to occur within a few years of reservoir impoundment and usually the activity decreases with time. A documented example of Reservoir Triggered Seismicity (RTS), the Idukki Reservoir in Kerala, south India, impounded in 1975, is an exception wherein the triggered activity has been revived in 2011, nearly 35 years after the initial burst of activity in 1977, two years after the dam was filled. The magnitude of the largest shock in the 2011 sequence exceeded that of the previously documented largest microearthquake. Presence of faults that are close to failure and vulnerable to increase in pore pressure due to reservoir loading or increased rainfall, or a combination of both seems to trigger shocks in this area. The renewed burst of earthquakes after a prolonged period of reduced activity at the Idukki Reservoir is a rare example of RTS. (C) 2012 Elsevier B.V. All rights reserved.

Trends and Variability of AVHRR-Derived NPP in India

In this paper, we estimate the trends and variability in Advanced Very High Resolution Radiometer (AVHRR)-derived terrestrial net primary productivity (NPP) over India for the period 1982-2006. We find an increasing trend of 3.9% per decade (r = 0.78, R-2 = 0.61) during the analysis period. A multivariate linear regression of NPP with temperature, precipitation, atmospheric CO2 concentration, soil water and surface solar radiation (r = 0.80, R-2 = 0.65) indicates that the increasing trend is partly driven by increasing atmospheric CO2 concentration and the consequent CO2 fertilization of the ecosystems. However, human interventions may have also played a key role in the NPP increase: non-forest NPP growth is largely driven by increases in irrigated area and fertilizer use, while forest NPP is influenced by plantation and forest conservation programs. A similar multivariate regression of interannual NPP anomalies with temperature, precipitation, soil water, solar radiation and CO2 anomalies suggests that the interannual variability in NPP is primarily driven by precipitation and temperature variability. Mean seasonal NPP is largest during post-monsoon and lowest during the pre-monsoon period, thereby indicating the importance of soil moisture for vegetation productivity.

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.