Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop’ to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.     

Characterization of ZnO nanoparticles grown in presence of Folic acid template

ABSTRACT: BACKGROUND: ZnO nanoparticles (grown in the template of folic acid) are biologically useful, luminescent material. It can be used for multifunctional purposes, e.g., as biosensor, bioimaging, targeted drug delivery and as growth promoting medicine. METHODS: Sol-gel chemical method was used to develop the uniform ZnO nanoparticles, in a folic acid template at room temperature and pH ~ 7.5. Agglomeration of the particles was prevented due to surface charge density of folic acid in the medium. ZnO nanoparticle was further characterized by different physical methods. RESULTS: Nanocrystalline, wurtzite ZnO particles thus prepared show interesting structural as well as band gap properties due to capping with folic acid. CONCLUSIONS: A rapid, easy and chemical preparative method for the growth of ZnO nanoparticles with important surface physical properties is discussed. Emphatically, after capping with folic acid, its photoluminescence properties are in the visible region. Therefore, the same can be used for monitoring local environmental properties of biosystems.     

Effect of Concomitant Administration of L-Glutamine and Cycloart-23-ene-3β, 25-diol (B2) with Sitagliptin in GLP-1 (7–36) Amide Secretion,Biochemical and Oxidative Stress in Streptozotocin - Nicotinamide Induced Diabetic Sprague Dawley Rats

Previously we have reported that, cycloart-23-ene-3β, 25-diol (called as B2) and L-glutamine stimulated glucagon like peptide-1 (GLP-1) (7–36) amide secretion diabetic rats. The objective of present investigation was to investigate the concomitant administration of cycloart-23-ene-3β, 25-diol+sitagliptin and L-glutamine+sitagliptin in streptozotocin - nicotinamide induced diabetic Sprague Dawley. Type 2 diabetes was induced in overnight fasted male Sprague Dawley rats pre-treated with nicotinamide (100 mg/kg, i.p.) followed by administration of streptozotocin (55 mg/kg, i.p.) 20 min after. The rats were divided into; I- non-diabetic, II- diabetic control, III- Sitagliptin (5 mg/kg, p.o.)+cycloart-23-ene-3β, 25-diol (1 mg/kg, p.o.), IV- Sitagliptin (5 mg/kg, p.o.)+L-glutamine (1000 mg/kg, p.o.). The concomitant treatment of cycloart-23-ene-3β, 25-diol and L-glutamine with sitagliptin was 8 weeks. Plasma glucose, body weight, food and water intake were determined every week. Glycosylated haemoglobin, lipid profile, plasma and colonic active (GLP-1) (7–36) amide, plasma and pancreatic insulin, histology of pancreata and biomarkers of oxidative stress were measured after 8^th week treatment. Concomitant administration of cycloart-23-ene-3β, 25-diol and L-glutamine with sitagliptin significantly (p<0.001) reduced plasma glucose, glyoxylated haemoglobin, lipid profile and oxidative stress parameters compared to diabetic control groups. Both concomitant treatment increased plasma and pancreatic insulin as well as plasma and colonic active (GLP-1) (7–36) amide secretion. Histological analysis by Gomori staining observed less destruction of pancreatic β cells. The result obtained from this study; it is concluded that concomitant administration of cycloart-23-ene-3β, 25-diol+sitagliptin and L-glutamine+sitagliptin showed additive antihyperglycaemic effect in diabetic rats.     

Purification and characterization of enolase from neuroblastoma cell line NG108

Neuroblastoma Cell line NG108 (a hybrid from Chinese hamster and mouse) produces high levels of enolase. Using ion-exchange chromatography and gel filtration, we have purified the enzyme (about 19 fold purification) and characterized it. The purified enzyme is a dimer of 90,000 m.wt. and is stable at room temperature. At higher temperatures (e.g., 50 degrees, 60 degrees C etc.) it gets inactivated. Enolase requires Mg++ for its activity and is resistant to urea. The optimum pH for the enzyme is 7, and Km values for Mg++ and 2-phosphoglycerate were found to be 3.1 and 1.1 mM, respectively. Fluorophosphate is a strong inhibitor of the enzyme. The clinical applications of the enzyme have been discussed.     

Antimicrobial Resistance,Virulence Profiles and Molecular Subtypes of Salmonella enterica Serovars Typhi and Paratyphi A Blood Isolates from Kolkata,India during 2009-2013

Enteric fever, caused by Salmonella enterica, remains an unresolved public health problem in India and antimicrobial therapy is the main mode of treatment. The objective of this study was to characterize the Salmonella enterica isolates from Kolkata with respect to their antimicrobial resistance (AMR), virulence profiles and molecular subtypes. Salmonella enterica blood isolates were collected from clinically suspected enteric fever patients attending various hospitals in Kolkata, India from January 2009 to June 2013 and were tested for AMR profiles by standard protocols; for resistance gene transfer by conjugation; for resistance and virulence genes profiles by PCR; and for molecular subtypes by Pulsed Field Gel Electrophoresis (PFGE). A total of 77 Salmonella enterica serovar Typhi (S. Typhi) and 25 Salmonella enterica serovar Paratyphi A (S. Paratyphi A) from Kolkata were included in this study. Although multidrug resistance (resistance to chloramphenicol, ampicillin, co-trimoxazole) was decreasing in S. Typhi (18.2%) and absent in S. Paratyphi A, increased resistance to fluoroquinolone, the current drug of choice, caused growing concern for typhoid treatment. A single, non-conjugative non-IncHI1 plasmid of 180 kb was found in 71.4% multidrug resistant (MDR) S. Typhi; the remaining 28.6% isolates were without plasmid. Various AMR markers (bla _TEM-1, catA, sul1, sul2, dfrA15, strA-strB) and class 1 integron with dfrA7 gene were detected in MDR S. Typhi by PCR and sequencing. Most of the study isolates were likely to be virulent due to the presence of virulence markers. Major diversity was not noticed among S. Typhi and S. Paratyphi A from Kolkata by PFGE. The observed association between AMR profiles and S. Typhi pulsotypes might be useful in controlling the spread of the organism by appropriate intervention. The study reiterated the importance of continuous monitoring of AMR and molecular subtypes of Salmonella isolates from endemic regions for better understanding of the disease epidemiology.     

Crystal structure of a Chlamydomonas reinhardtii flagellar RabGAP TBC‐domain at 1.8 Å resolution

Rab GTPases play a crucial role in the regulation of many intracellular membrane trafficking pathways including endocytosis and ciliogenesis. Rab GTPase activating proteins (RabGAPs) increase the GTP hydrolysis rate of Rab GTPases and turn them into guanine nucleotide diphosphate (GDP) bound inactive form. Here, we determined the crystal structure of the putative catalytic domain of a RabGAP (which we name CrfRabGAP) that is found in the flagellar proteome of the unicellular green alga Chlamydomonas reinhardtii. BLAST searches revealed potential human orthologues of CrfRabGAP as TBC1D3 and TBC1D26. Sequence and structural comparison with other canonical RabGAPs revealed that the CrfRabGAP does not contain the canonical catalytic residues required for the activation of Rab GTPases. The function of noncanonical RabGAPs‐like CrfRabGAP might be to serve as Rab effectors rather than activators. Proteins 2014; 82:2282–2287. © 2014 Wiley Periodicals, Inc.     

Potential bio-control agent for management of post-flowering stalk rot complex and maize plant health

The of aim of this study was to evaluate the potentiality of the native isolate of Trichoderma harzianum from IARI farm for the management of post-flowering stalk rot of maize and improvement of plant health. The treatment was tried as a seed treatment with the potent commercial formulation Kalisena SD (Aspergillus niger), neem kernel powder and effective fungicides (Thiram, Carbendazim, Captan) for comparison of its efficacy. The minimum disease was recorded in plots treated with native isolate both due to Fusarium moniliforme and Macrophomina phaseolina. The fungicides Carbendazim and Thiram ranked second in controlling the disease due to F. moniliforme and M. phaseolina, respectively. Plant health with respect to vigour and plant stand were found to be better than those of all the other treatments. It is concluded that the native isolate of T. harzianum may be used for maintaining good plant health and managing post-flowering stalk rot of maize.     

Predicting the risk of soybean rust in Minnesota based on an integrated atmospheric model

To minimize crop loss by assisting in timely disease management and reducing fungicide use, an integrated atmospheric model was developed and tested for predicting the risk of occurrence of soybean rust in Minnesota. The model includes a long-range atmospheric spore transport and deposition module coupled to a leaf wetness module. The latter is required for spore germination and infection. Predictions are made on a daily basis for up to 7 days in advance using forecast data from the United States National Weather Service. Complementing the transport and leaf wetness modules, bulk (wet plus dry) atmospheric deposition samples from Minnesota were examined for soybean rust spores using a specific DNA test and sequence analysis. Overall, the risk prediction worked satisfactorily within the bounds of the uncertainty associated with the use of modeled 7-day weather forecasts, with more than 65% agreement between the model forecast and the DNA test results. The daily predictions are available as an advisory to the user community through the University of Minnesota Extension. However, users must take the actual decision to implement the disease management strategy.