Identification of a UDP-glucosyltransferase conferring deoxynivalenol resistance in Aegilops tauschii and wheat

Aegilops tauschii is the diploid progenitor of the wheat D subgenome and a valuable resource for wheat breeding, yet, genetic analysis of resistance against Fusarium head blight (FHB) and the major Fusarium mycotoxin deoxynivalenol (DON) is lacking. We treated a panel of 147 Ae. tauschii accessions with either Fusarium graminearum spores or DON solution and recorded the associated disease spread or toxin-induced bleaching. A k-mer-based association mapping pipeline dissected the genetic basis of resistance and identified candidate genes. After DON infiltration nine accessions revealed severe bleaching symptoms concomitant with lower conversion rates of DON into the non-toxic DON-3-O-glucoside. We identified the gene AET5Gv20385300 on chromosome 5D encoding a uridine diphosphate (UDP)-glucosyltransferase (UGT) as the causal variant and the mutant allele resulting in a truncated protein was only found in the nine susceptible accessions. This UGT is also polymorphic in hexaploid wheat and when expressed in Saccharomyces cerevisiae only the full-length gene conferred resistance against DON. Analysing the D subgenome helped to elucidate the genetic control of FHB resistance and identified a UGT involved in DON detoxification in Ae. tauschii and hexaploid wheat. This resistance mechanism is highly conserved since the UGT is orthologous to the barley UGT HvUGT13248 indicating descent from a common ancestor of wheat and barley.     

Plant growth promoting rhizobacteria for sustainable agricultural practices with special reference to biotic and abiotic stresses

The most common, devastating problem in agriculture is plant (pathogenic) diseases and abiotic conditions which have a profound effect on growth and yield of the plant resulting in heavy losses. In order to prevent losses, different chemicals are used indiscriminately, which in turn lead to environmental pollution due to their persistence and toxicity yet employed to meet consumer demand. To fight ever increasing demand and indiscriminate use of chemical agents along with their devastating after effects in agriculture, we need less invasive, eco-friendly and most importantly sustainable practices. Plant growth promoting rhizobacteria (PGPR) influence different physiological activities of the plant through various mechanisms (metabolites, antibiotics, Induced Systemic Resistance and enzymes) and impart protection from pathogens as well as environmental stress factors. But, current applications are limited in this regard as mechanisms involved, field applications variance and lack of farmer awareness contributing majorly. Current review tries to provide comprehensive knowledge on the PGPR’s applications as plant protectant against pathogens & abiotic factors leading to sustainable agricultural practices.     

Surface Plasmon Assisted Luminescence Enhancement of Ag NP/NWs-Doped SiO2-TiO2-ZrO2:Eu3+ Ternary System

Plasmonics - Non-hydrolytic sol-gel process was employed to prepare Eu3+-doped and silver nanoparticles/nanowires (Ag NP/NWs) co-doped SiO2-TiO2-ZrO2 ternary matrix. XRD, TEM, and SAED analyses...     

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

Rapid development of next generation sequencing technology has enabled the identification of genomic alterations from short sequencing reads. There are a number of software pipelines available for calling single nucleotide variants from genomic DNA but, no comprehensive pipelines to identify, annotate and prioritize expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data. We have developed the eSNV-Detect, a novel computational system, which utilizes data from multiple aligners to call, even at low read depths, and rank variants from RNA-Seq. Multi-platform comparisons with the eSNV-Detect variant candidates were performed. The method was first applied to RNA-Seq from a lymphoblastoid cell-line, achieving 99.7% precision and 91.0% sensitivity in the expressed SNPs for the matching HumanOmni2.5 BeadChip data. Comparison of RNA-Seq eSNV candidates from 25 ER+ breast tumors from The Cancer Genome Atlas (TCGA) project with whole exome coding data showed 90.6–96.8% precision and 91.6–95.7% sensitivity. Contrasting single-cell mRNA-Seq variants with matching traditional multicellular RNA-Seq data for the MD-MB231 breast cancer cell-line delineated variant heterogeneity among the single-cells. Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.     

3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach

3D domain swapping is a protein structural phenomenon that mediates the formation of the higher order oligomers in a variety of proteins with different structural and functional properties. 3D domain swapping is associated with a variety of biological functions ranging from oligomerization to pathological conformational diseases. 3D domain swapping is realised subsequent to structure determination where the protein is observed in the swapped conformation in the oligomeric state. This is a limiting step to understand this important structural phenomenon in a large scale from the growing sequence data. A new machine learning approach, 3dswap-pred, has been developed for the prediction of 3D domain swapping in protein structures from mere sequence data using the Random Forest approach. 3Dswap-pred is implemented using a positive sequence dataset derived from literature based structural curation of 297 structures. A negative sequence dataset is obtained from 462 SCOP domains using a new sequence data mining approach and a set of 126 sequencederived features. Statistical validation using an independent dataset of 68 positive sequences and 313 negative sequences revealed that 3dswap-pred achieved an accuracy of 63.8%. A webserver is also implemented using the 3dswap-pred Random Forest model. The server is available from the URL: http://caps.ncbs.res.in/3dswap-pred.     

PURE: A webserver for the prediction of domains in unassigned regions in proteins

Background  

Protein domains are the structural and functional units of proteins. The ability to parse proteins into different domains is important for effective classification, understanding of protein structure, function, and evolution and is hence biologically relevant. Several computational methods are available to identify domains in the sequence. Domain finding algorithms often employ stringent thresholds to recognize sequence domains. Identification of additional domains can be tedious involving intense computation and manual intervention but can lead to better understanding of overall biological function. In this context, the problem of identifying new domains in the unassigned regions of a protein sequence assumes a crucial importance.     

Does exposure of male Drosophila melanogaster to acute gamma radiation influence egg to adult development time and longevity of F1–F3 offspring?

Two‐ to three‐day‐old male Drosophila melanogaster flies were irradiated with 1, 2, 4, 6, 8, 10, 20, 25, 30, 40 and 50 Gy doses of gamma radiation. The longevity and rate of development were observed for three successive generations to assess the impact of irradiation. The mean lifespan of irradiated flies was significantly increased at 1, 2 and 8 Gy, while it was vice versa for high doses at 30, 40 and 50 Gy. Paternal irradiation had an impact on F₁ generation, with significantly increased mean longevity at 2 (female), 4, 6, 8 and 10 and decreased mean longevity at 40 and 50 Gy (male and female). Significant increase in the longevity was observed in the F₂ generation of the 8 (male and female) and 10 Gy (male) irradiated groups, while decreased longevity was observed in F₂ female progeny at 40 Gy. In the case of F₃ progeny of irradiated flies, longevity did not show significant difference with the control. Paternal exposure to radiation had a significant impact on the mean egg to adult developmental time of the F₁ generation; it was shortened at 2 Gy and extended at 25, 30, 40 and 50 Gy compared to the control. Mean development time at 30, 40 and 50 Gy was significantly increased in the F₂ generation, while there were no significant changes in the F₃ generation. The present study concludes that the effect of acute gamma irradiation on longevity and “egg to adult” development time of D. melanogaster may persist to following generations.     

IWS: integrated web server for protein sequence and structure analysis

Rapid increase in protein sequence information from genome sequencing projects demand the intervention of bioinformatics tools to recognize interesting gene-products and associated function. Often, multiple algorithms need to be employed to improve accuracy in predictions and several structure prediction algorithms are on the public domain. Here, we report the availability of an Integrated Web-server as a bioinformatics online package dedicated for in-silico analysis of protein sequence and structure data (IWS). IWS provides web interface to both in-house and widely accepted programs from major bioinformatics groups, organized as 10 different modules. IWS also provides interactive images for Analysis Work Flow, which will provide transparency to the user to carry out analysis by moving across modules seamlessly and to perform their predictions in a rapid manner. AVAILABILITY: IWS IS AVAILABLE FROM THE URL: http://caps.ncbs.res.in/iws.