ANALYZING THE EXPERIENCE OF ONLINE USERS USING B2C WEBSITES

Volume 2 Issue 1 (January 2014

Selection of Housekeeping Genes and Demonstration of RNAi in Cotton Leafhopper, \u3cem\u3eAmrasca biguttula biguttula\u3c/em\u3e (Ishida)

Amrasca biguttula biguttula (Ishida) commonly known as cotton leafhopper is a severe pest of cotton and okra. Not much is known on this insect at molecular level due to lack of genomic and transcriptomic data. To prepare for functional genomic studies in this insect, we evaluated 15 common housekeeping genes (Tub, B-Tub, EF alpha, GADPH, UbiCF, RP13, Ubiq, G3PD, VATPase, Actin, 18s, 28s, TATA, ETF, SOD and Cytolytic actin) during different developmental stages and under starvation stress. We selected early (1st and 2nd), late (3rd and 4th) stage nymphs and adults for identification of stable housekeeping genes using geNorm, NormFinder, BestKeeper and RefFinder software. Based on the different algorithms, RP13 and VATPase are identified as the most suitable reference genes for quantification of gene expression by reverse transcriptase quantitative PCR (RT-qPCR). Based on RefFinder which comprehended the results of three algorithms, RP13 in adults, Tubulin (Tub) in late nymphs, 28S in early nymph and UbiCF under starvation stress were identified as the most stable genes. We also developed methods for feeding double-stranded RNA (dsRNA) incorporated in the diet. Feeding dsRNA targeting Snf7, IAP, AQP1, and VATPase caused 56.17–77.12% knockdown of targeted genes compared to control and 16 to 48% mortality of treated insects when compared to control

RNA Sequencing, Selection of Reference Genes and Demonstration of Feeding RNAi in \u3cem\u3eThrips tabaci\u3c/em\u3e (Lind.) (Thysanoptera: Thripidae)

Background: Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time. Results: From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified. About 85.4% of CDS identified showed positive Blast hits. The homologs of most of the core RNAi machinery genes were identified in this transcriptome. To select reference genes for reverse-transcriptase real-time quantitative PCR (RT-qPCR) experiments, 14 housekeeping genes were identified in the transcriptome and their expression was analyzed by (RT-qPCR). UbiCE in adult, 28s in nymphs and SOD under starvation stress were identified as the most stable reference genes for RT-qPCR. Feeding dsSNF7 and dsAQP caused 16.4- and 14.47-fold reduction in SNF7 and AQP mRNA levels respectively, when compared to their levels in dsGFP fed control insects. Feeding dsSNF7 or dsAQP also caused 62 and 72% mortality in T. tabaci. Interestingly, simultaneous feeding of dsRNAs targeting SNF7 or AQP and one of the RNAi pathway genes (Dicer-2/Aubergine/Staufen) resulted in a significant reduction in RNAi of target genes. These data suggest the existence of robust RNAi machinery in T. tabaci. Conclusion: The current research is the first report of the assembled, analyzed and annotated RNAseq resource for T. tabaci, which may be used for future molecular studies in this insect. Reference genes validated across stages and starvation stress provides first-hand information on stable genes in T. tabaci. The information on RNAi machinery genes and significant knockdown of the target gene through dsRNA feeding in synthetic diet confirms the presence of efficient RNAi in this insect. These data provide a solid foundation for further research on developing RNAi as a method to manage this pest

NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India

The North-East region of India is one of the twelve mega biodiversity region, containing many rare and endangered species. A curated database of medicinal and aromatic plants from the regions called NeMedPlant is developed. The database contains traditional, scientific and medicinal information about plants and their active constituents, obtained from scholarly literature and local sources. The database is cross-linked with major biochemical databases and analytical tools. The integrated database provides resource for investigations into hitherto unexplored medicinal plants and serves to speed up the discovery of natural productsbased drugs

Sustainability of maize (Zea mays)-wheat (Triticum aestivum) cropping system under legumes intercropping and effect of nitrogen level on light distribution, soil temperature and crop productivity

Agriculture designs for cropping system with legume intercropping for increased resource use efficiency profitability, productivity and reduced adverse environmental impact are urgently required. A three years field experiment consisting of six cropping treatments applied during both seasons was conducted during 2008-09 to 2010-11 to study the effect of nitrogen and legumes intercropping with maize (Zea mays L.) for sustainability of maize-wheat (Triticum aestivum L.) cropping system. Results indicate that the photosynthetic active radiation had highest values at noon reaching nearly 1940 µmol/m2/s for maize and 1620 µmol/m2/s for intercropped legumes. Intercropping can increase light interception, shading and reduce water evaporation as compared to sole maize. Maize intercropped had higher values of stomatal condutance and leaf temperature than sole crop. The grain yield and yield attributing characters of wheat crop increased significantly under intercropping treatments over respective check. Wheat yield significantly increased up to 160 kg N/ha. However, there was no significant increase in yield of maize beyond 120 kg N/ha.Sole maize-wheat rotation showed a decline in soil organic carbon by 3.7%,while blackgram and cowpea intercropping with maize in paired rows (2:2 row ratio) followed by wheat increased contents of percent organic carbon in soil as 0.63 and 0.67 respectively, compared to initial values of 0.54 percent. Plots treated with intercrops/FYM during the rainy season sustained the wheat yield while the check plot showed a decline in wheat yield by 4-9%

Crop Ontology Governance and Stewardship Framework

A governance & stewardship framework for the Crop Ontology Project is required as this is a collaborative tool developed by a Community of Practice. Over the last 12 years of its existence, it has increased significantly in scope and use. Collecting and storing plant trait data and annotating the data with ontology terms is widely accepted by the crop science community to be critical to enable data interoperability and interexchange through tools such as the Breeding API (BrAPI). The Crop Ontology Community of Practice is organised around roles, curation principles and validation processes that require a formal description. A governance framework is defined by the various actors involved in the asset’s design, development and maintenance. It is complemented by a quality assurance process to ensure that trust levels, value creation, and sustainability objectives meet appropriate quality levels. The general principles underlying data governance are integrity, transparency, accountability and ownership, stewardship, standardization, change management and a robust data audit

The ontologies community of practice: a CGIAR initiative for Big Data in agrifood systems

Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams

Living kidney donor with monoclonal gammopathy of undetermined significance: Is it a contraindication for kidney donation?

Kidney transplantation is the treatment of choice for patients suffering from end-stage renal disease. We report a case of living kidney transplantation in which the donor had monoclonal gammopathy of undetermined significance, a condition having possible implication for both donor and recipient. Both donor and recipient had an uneventful course in short-term follow-up of 1 year following kidney transplantation

Reduced dose coupled with improved method of neem-coated urea application and foliar sprays of KNO₃ enhance cotton yield and fiber parameters under semi-arid climates

Choice of source, nitrogen rate, and its application method affect cotton productivity. In absence of new recommendations for recently introduced neem-coated urea (NCU) in India, farmers have been applying either similar or above optimal levels of NCU in cotton just like conventional urea. The present study aimed to evaluate the optimum dose and better method of NCU application to improve cotton productivity and profitability under arid climates. A total of eight different treatments were evaluated in a randomized complete block design. Two NCU doses [i.e., 112.5 kg ha−1 (75% of conventional nitrogen [urea] recommendation-CNR) and 150 kg ha−1 (100% of CNR)] were applied using three methods, i.e., (a) band application, (b) spot application, and (c) broadcasting constituted six treatments. In addition, foliar sprays of NCU@1% and KNO3@2% were also evaluated to study their effect in improving seed cotton yield (SCY) and fiber parameters. These findings elucidated that the spot method of NCU application proved better than the broadcasting and band application method owing to better nitrogen use efficiency (NUE). NCU@ 112.5 kg N ha−1 applied through spot application along with three foliar sprays of KNO3@2% resulted in similar profitability as that of broadcasting 150 kg NCU ha−1 along with four foliar sprays of KNO3. Improved physiological parameters like net photosynthesis and chlorophyll coupled with higher NUE played a decisive role for at par SCY despite 25% low nutrient input besides enhanced environment safety. Therefore, under semi-arid climates, 37.5 kg N ha−1 could be saved without compromising cotton productivity.</p

Red eye: Rule out Ophthalmomyiasis too

Ophthalmomyiasis is the infestation of human eye by the larvae of certain flies. Sheep botfly commonly manifests as Ophthalmomyiasis externa when there is conjunctival involvement or rarely as Opthalmomyiasis interna when there is larval penetration into the eyeball. It appears to be more common than what has been indicated by previously published reports. We present a report of seven cases of Ophthalmomyiasis by Oestrus ovis, from central India who presented with features of conjunctivitis varying between mild to severe. The larvae were seen in bulbar and palpebral conjunctiva and also entangled in lashes with discharge. Since the larvae are photophobic, it is prudent to look for them in the fornices and also in discharge. Prompt removal of the larvae from the conjunctiva helps in relieving the symptoms and also prevents serious complications. Taxonomic identification of the species is important to estimate the risk of globe penetration by the larvae