Do the beneficial fungi manage phytosanitary problems in the tea agro-ecosystem?

BioControl - In recent years, Fungal Biocontrol Agents (FBCAs) have played a significant role in the biological control of pests and plant pathogens of several economically important crops,...     

WindowMasker: window-based masker for sequenced genomes

MOTIVATION: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase library, that may not exist for newly sequenced genomes. RESULTS: We have developed a software tool called WindowMasker (WM) that identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. WM is orders of magnitude faster than RM because WM uses a few linear-time scans of the genome sequence, rather than local alignment methods that compare each library sequence with each piece of the genome. We validate WM by comparing BLAST outputs from large sets of queries applied to two versions of the same genome, one masked by WM, and the other masked by RM. Even for genomes such as the human genome, where a good RepBase library is available, searching the database as masked with WM yields more matches that are apparently non-repetitive and fewer matches to repetitive sequences. We show that these results hold for transcribed regions as well. WM also performs well on genomes for which much of the sequence was in draft form at the time of the analysis. AVAILABILITY: WM is included in the NCBI C++ toolkit. The source code for the entire toolkit is available at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/. Once the toolkit source is unpacked, the instructions for building WindowMasker application in the UNIX environment can be found in file src/app/winmasker/README.build. SUPPLEMENTARY INFORMATION: Supplementary data are available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/windowmasker_suppl.pdf     

DDT and HCH (Organochlorine Pesticides) in Residential Soils and Health Assessment for Human Populations in Korba,India

Dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), and their isomers’ levels in residential soils were determined for the assessment of health risk in Korba, India. Observed concentrations of total HCH and total DDT in soils were more or less comparable with other parts of India and the world. ΣHCH and ΣDDT concentrations ranged between 0.9–20 μg kg^?1 and 2–315 μg kg^?1, respectively, which were lower than recommended soil quality guidelines indicating low ecotoxicological risk. Carcinogenic and non-carcinogenic impacts of HCH and DDT on human populations through soil ingestion were evaluated and presented. The incremental lifetime cancer risk (ILCR) for adults and children ranged between 7.8 × 10^?10–1.6 × 10^?7 and 4.1 × 10^?9–8.2 × 10^?7, respectively. Non-cancer health hazard quotient (HQ) ranged between 5.9 × 10^?7–1.8 × 10^?3 and 3.1 × 10^?6–9.4 × 10^?3, respectively, for adults and children. The estimated ILCR and HQ were within the safe acceptable limits of 10^?6–10^?4 and ≤1.0, respectively, indicating low risk to human populations from exposure to organochlorine pesticides (HCH and DDT) in the study area.     

Wolbachia infection can bias estimates of intralocus sexual conflict

Males and females share most of their genome and develop many of the same traits. However, each sex frequently has different optimal values for these shared traits, creating intralocus sexual conflict. This conflict has been observed in wild and laboratory populations of insects and affects important evolutionary processes such as sexual selection, the maintenance of genetic variation, and possibly even speciation. Given the broad impacts of intralocus conflict, accurately detecting and measuring it is important. A common way to detect intralocus sexual conflict is to calculate the intersexual genetic correlation for fitness, with negative values suggesting conflict. Here, we highlight a potential confounder of this measure—cytoplasmic incompatibility caused by the intracellular parasite Wolbachia. Infection with Wolbachia can generate negative intersexual genetic correlations for fitness in insects, suggestive of intralocus sexual conflict. This is because cytoplasmic incompatibility reduces the fitness of uninfected females mated to infected males, while uninfected males will not suffer reductions in fitness if they mate with infected females and may even be fitter than infected males. This can lead to strong negative intersexual genetic correlations for fitness, mimicking intralocus conflict. We illustrate this issue using simulations and then present Drosophila simulans data that show how reproductive incompatibilities caused by Wolbachia infection can generate signals of intralocus sexual conflict. Given that Wolbachia infection in insect populations is pervasive, but populations usually contain both infected and uninfected individuals providing scope for cytoplasmic incompatibility, this is an important consideration for sexual conflict research but one which, to date, has been largely underappreciated.     

Molecular characterization of distinct YMV (Yellow mosaic virus) isolates affecting pulses in India with the aid of coat protein gene as a marker for identification

The present study was carried out to find out the variations present in different isolates of yellow mosaic virus (YMV) causing yellow mosaic disease of pulses in southern parts of India. The coat protein gene of YMV was amplified using gene specific and deng universal primers with DNA isolated from YMV infected samples. Further, cloning and DNA sequencing of CP gene was carried out. CP gene decrypt sequences revealed that YMV infected samples of Black gram, Cowpea and Green gram were similar to the MYMV-Tamil Nadu isolates. Whereas the YMV infected sample of Horse gram was found to be similar with HYMV. Hence, in the present study, two distinct YMV infecting pulses in Tamil Nadu (MYMV and HYMV species) were identified and it was observed that there exists considerable genetic variation among these species. In addition, Cowpea crop which was earlier supposed not to be susceptible for YMV infection also showed the presence of this virus similar to the MYMV. Overall, the findings of the present study indicate that the CP region is efficient enough to provide a simple, rapid, and reliable method for early detection of YMV infections in pulses, which would help to develop proper management strategies to control these viruses.     

GroEL Mediates Folding of <Emphasis Type="Italic">Bacillus anthracis</Emphasis> Serine/Threonine Protein Kinase,PrkC

Bacillus anthracis causes anthrax in human and animals. Both, signaling system such as two component system and endogenous chaperone system such as GroEL–GroES help bacteria to cope with the environmental challenges. Such molecular chaperones are the stress induced proteins that help bacteria to override unfavorable conditions by their moonlighting functions. Previous reports showed that PrkC and PrpC, the Ser/Thr kinase–phosphatase pair in B. anthracis, control phosphorylation of GroEL and regulate biofilm formation. In this study, we show that GroEL is involved in the folding of PrkC to active form. The proteins (GroEL, PrkC and PrpC) were expressed and purified by affinity chromatography. Purified GroEL was used for refolding of denatured PrkC and PrpC and observed that GroEL refolds PrkC but not PrpC as measured by their enzymatic activity. We also observed that purification of GroEL with six histidine tag using Cobalt-Agarose resin yielded superior quality GroEL protein with negligible contamination of non-specific proteins. Thus, cobalt resin can be a better choice for purification of many histidine tagged proteins, where Ni-NTA does not work very well.     

Environmental trade-offs across cascading lithium-ion battery life cycles

Purpose

The purpose of this study was to analyze the environmental trade-offs of cascading reuse of electric vehicle (EV) lithium-ion batteries (LIBs) in stationary energy storage at automotive end-of-life.

Methods

Two systems were jointly analyzed to address the consideration of stakeholder groups corresponding to both first (EV) and second life (stationary energy storage) battery applications. The environmental feasibility criterion was defined by an equivalent-functionality lead-acid (PbA) battery. A critical methodological challenge addressed was the allocation of environmental impacts associated with producing LIBs across the EV and stationary use systems. The model also tested sensitivity to parameters such as the fraction of battery cells viable for reuse, service life of refurbished cells, and PbA battery efficiency.

Results and discussion

From the perspective of EV applications, cascading reuse of an LIB in stationary energy storage can reduce net cumulative energy demand and global warming potential by 15 % under conservative estimates and by as much as 70 % in ideal refurbishment and reuse conditions. When post-EV LIB cells were compared directly to a new PbA system for stationary energy storage, the reused cells generally had lower environmental impacts, except in scenarios where very few of the initial battery cells and modules could be reused and where reliability was low (e.g., life span of 1 year or less) in the secondary application.

Conclusions

These findings demonstrate that EV LIB reuse in stationary application has the potential for dual benefit—both from the perspective of offsetting initial manufacturing impacts by extending battery life span as well as avoiding production and use of a less-efficient PbA system. It is concluded that reuse decisions and diversion of EV LIBs toward suitable stationary applications can be based on life cycle centric studies. However, technical feasibility of these systems must still be evaluated, particularly with respect to the ability to rapidly analyze the reliability of EV LIB cells, modules, or packs for refurbishment and reuse in secondary applications.