Somatic hypermutation leads to diversification of the heavy chain immunoglobulin repertoire in cattle

The availability of unique variable (VH), diversity (D), and joining (JH) gene segments in the vertebrate germline determines the extent to which a primary immunoglobulin (Ig) repertoire can be generated through combinatorial rearrangement. Although bovine D segments possess unusual properties, the diversity of the primary Ig heavy chain (IgH) repertoire in cattle is restricted by the dominance of a single family of germline VH genes of limited number and diversity. Cattle therefore must employ other diversification strategies in order to generate a functional IgH repertoire, the main candidates being gene conversion and somatic hypermutation. In considering these possibilities, we predicted that if somatic hypermutation was active during B lymphocyte development, the process would introduce nucleotide substitutions to the VDJ exon and also non-coding region lying downstream of the rearranged JH segment. In contrast, our expectation was that gene conversion would show a greater tendency to confine modification to the IgH coding sequence, leaving intron regions substantially unmodified. An analysis of rearranged IgH sequences from cattle of different ages revealed that the diversification of germline sequences could be observed in very young calves and that substitution frequency increased with age. The age-dependent accumulation of mutations was particularly apparent in the second IgH complementarity-determining region (CDR2). Single base substitutions were found to predominate, with purines targeted more frequently than pyrimidines and transitions favoured over transversions. In non-coding regions, mutations were detected at a normalised frequency that was indistinguishable from that observed in CDR2. These data are consistent with a process of IgH diversification driven predominantly by somatic hypermutation.     

Neuroprotective effect of naringin by modulation of endogenous biomarkers in streptozotocin induced painful diabetic neuropathy

Diabetes mellitus is a serious debilitating epidemic affecting all social strata in developing as well as developed countries. Diabetic neuropathy is most common of secondary complications associated with diabetes mellitus and is characterized by slowing of nerve conduction velocity, elevated pain, sensory loss and nerve fiber degeneration. The aim of the present investigation was to evaluate the neuroprotective effect of naringin against streptozotocin (STZ) induced diabetic neuropathic pain in laboratory rats. Four weeks after intraperitoneal injection of STZ resulted in significant decrease in mechano-tactile allodynia, mechanical hyperalgesia, thermal hyperalgesia and motor nerve conduction velocity. Activity of endogenous antioxidant like superoxide dismutase as well as membrane bound inorganic phosphate enzyme was also found to be significantly decreased. It not only caused neural cell apoptosis but also enhanced lipid peroxide, nitrite, and inflammatory mediators' (TNF-α) level. Chronic treatment with naringin (40 and 80mg/kg) for 4 weeks significantly and dose dependently attenuated the decrease in level of nociceptive threshold, endogenous antioxidant and membrane bound inorganic phosphate enzyme. It also decreased the elevated levels of oxidative-nitrosative stress, inflammatory mediators as well as apoptosis in neural cells significantly and dose dependently. The important finding of the study is that, the naringin-insulin combination not only attenuated the diabetic condition but also reversed the neuropathic pain, whereas insulin or naringin alone only improved hyperglycemia but partially reversed the pain response in diabetic rats. Thus, naringin is a potential flavonone bearing antioxidant, antiapoptotic and disease modifying property acting via modulation of endogenous biomarker to inhibit diabetes induced neuropathic pain.     

Ovipositional responses of the pulse beetle, Bruchus chinensis (Coleoptera: Bruchidae) to extracts and compounds of Capparis decidua

Extracts of Capparis decidua stems and flowers showed insecticidal and oviposition inhibitory activities against Bruchus chinensis. The LC50 values of these extracts were found to increase with the increase in the polarity of the extract at different exposure periods. For instance, after 96 h, the LC50 values were found to be 3.619, 7.319, and 10.151 microg for CD1, CD2, and CD3, respectively. Extract CD7 was effective only at higher doses. The toxicity was found to be dose- and time-dependent. The females laid lesser number of eggs, when exposed to sublethal doses of different extracts and pure compounds, as compared to control. The maximum oviposition deterrence index was found for extract CD1 followed in decreasing order by CD2, CD3, and CD7. From extract CD1, two compounds were isolated and characterized as triacontanol (C1) and 2-carboxy-1,1-dimethylpyrrolidine (C2). When the females were exposed to sublethal doses of these compounds, they laid lesser number of eggs as compared to the control. C2 was found to have a slightly greater oviposition inhibition effect than C1. From fraction CD7, one novel compound labeled as CDF1 has been isolated and identified as 6-(1-hydroxy-non-3-enyl)tetrahydropyran-2-one. CDF1 has also shown insecticidal and oviposition inhibitory activities against B. chinensis at low concentrations.     

Reproductive phenology of Calophyllum inophyllum in Yeppoon, Australia and Meegoda Western Province, Sri Lanka

Reproductive phenology of multiple use native plant Calo- phyllum inophyllum L. was studied in Yeppoon (23°7’60″ S, 150°43’60″ E), northern Australia (southern hemisphere) and in Meegoda (6o18′51″N, 80o31′3″E), Sri Lanka (northern hemisphere). C. inophyllum trees in Yeppoon, Australia had relatively shorter flowering periods, shorter floral life spans, longer fruit life spans, smaller flowers and larger fruits compared to those in Meegoda, Sri Lanka. Although the number of flower buds/ inflorescence was comparatively higher in Meegoda, C. inophyllum trees in both locations had similar mean number of mature fruits/ cluster due to the higher floral abscission in C. inophyllum trees at Meegoda. Despite having a comparatively lower fruit yield (664 000 fruts·ha 1·a 1), C. inophyllum trees in Yeppoon had higher kernel weights (2 988.0±853.2 kg·ha -1 ·a -1 ) and oil yields (1 332.6±380.5 kg·ha - 1 ·a -1 ) compared to those in Meegoda.     

Evaluation of fipronil nanoformulations for effective management of brown plant hopper (Nilaparvata lugens) in rice

In this paper, we report the development, characterization and bioefficacy evaluation of fipronil nanoformulations against brown plant hopper (BPH); Nilaparvata lugens in rice. Nanoformulations were characterized for nanosizing and stability under variable conditions. Bioefficacy of nanoformulations were evaluated under field condition at farms of Indian Agricultural Research Institute, New Delhi during Kharif 2015. At milking stage BPH populations were above economic threshold level; followed by foliar application of fipronil nanoformulations at four doses (viz., 30, 45, 60 and 90 g a.i./ha) along with commercial formulation of fipronil. The mean mortality clearly indicated that all the insecticidal treatments were significantly superior over untreated control where, highest mortalities were observed in nanodispersions followed by monolithic dispersion and commercial formulation of fipronil. Treated plots 7 days after application @ 60 g a.i./ha has shown 93.47%, 86.89% and 80.47% reduction BPH population in nanodispersion, encapsulated monolithic dispersion and commercial formulation treated plots respectively. In comparison to commercial formulation @ 60 g a.i./ha yield has increased by 0.56 t ha^?1 (28.76%) and 0.26 t ha^?1 (14.04%) in nanodispersion and monolithic dispersion.     

Fate of [14C]daminozide and [14C]maleic hydrazide in American elm (Ulmus americana L.)

Radiolabelled daminozide and maleic hydrazide (MH) were injected into American elm seedlings, kept in nutrient solution, to determine their translocation pattern and metabolic fate. Both compounds were rapidly translocated to all parts of the plant. After 21 days, 13% of the applied ¹⁴C was exuded into the nutrient solution from the roots of the plants treated with MH. Using gel-filtration and thin-layer chromatographic techniques, it was determined that daminozide did not form any metabolite, and that MH was converted into a MH-sugar complex. A significant amount of ¹⁴C was unextractable from the plant tissue.     

Novel role of photoinsensitive alleles in adaptation of soybean [Glycine max (L.) Merr.] to rainfed short growing seasons of lower latitudes

Soybean is a temperate photosensitive crop but has adapted to sub-tropical and tropical countries of lower latitudes also. Photoperiodic and maturity genes confer latitudinal adaptation in this crop. Genotyping of accessions of higher latitudes have shown the role of photoinsensitivity, conferred by recessive photoperiodic alleles (e1/e2/e3/e4), in adaptation of the crop to high latitudes but information is not available for lower latitudinal countries like India. We genotyped and calculated the photosensitivity of 101 cultivated Indian soybean varieties and found that majority of the varieties (86) were photosensitive and had the dominant alleles at these loci. Four genotypic classes (e1-as/E2/E3/E4, E1/e2/e3/E4, E1/e2/E3/E4 and E1/E2/e3/E4) were observed for varieties with recessive alleles. Photoinsensitive alleles at E1 and E2 loci significantly reduced the days to flower, maturity and photosensitivity percentage. Adaptive role of photoperiodic alleles was inferred from breeder seed requirement of these varieties for 35 years. Although the photosensitive class contributed 81% to the total seed requirement the weighted mean contribution of this class (380 Q/year) was far less than that of photoinsensitive class (648 Q/year). Photoinsensitivity is essential for perpetuation of crop in higher latitudes. Present report highlights the novel role of photoinsensitive alleles in adaptation of soybean to rainfed, short growing and sub-tropical conditions of lower latitudes by conferring earliness.

     

Chirality index, molecular overlay and biological activity of diastereoisomeric mosquito repellents

Both 1-methylisopropyl 2-(2-hydroxyethyl)piperidine-1-carboxylate, (Picaridin((R))) and cyclohex-3-enyl 2-methylpiperidin-1-yl ketone (AI3-37220; 220) have two asymmetric centers, and the four diastereoisomers of each compound are known to have differing degrees of mosquito-repellent activity according to quantitative behavioral assays conducted at the United States Department of Agriculture. Computational chemistry was used to identify the structural and configurational basis for repellent activity. Molecular overlay of the optimized geometries of the lowest energy conformers of the diastereoisomers was investigated to elucidate the role of chiral centers in 220 and Picaridin. It was found that the presence of a chiral carbon alpha to the nitrogen with the S configuration in the piperidine ring is essential to the three-dimensional arrangement of the atoms of the pharmacophore for effective repellent activity.     

Nutrient Management for Sustaining Productivity of Sunflower-Based Cropping Sequence in Indian Semiarid Regions

A comprehensive long-term study (2006–2010) was undertaken to develop a balanced and integrated nutrient supply system for sunflower-based cropping sequence considering the efficient utilization of residual and cumulative soil nutrient balance along with added fertilizers by the crops grown in rotation. The fertilizer application was done in potato and sunflower while greengram was raised as such on their residual effect. Significant response in yield was observed with 150% of the recommended nitrogen, phosphorus and potassium (NPK) or inclusion of farmyard manure (FYM) with the recommended NPK in the cropping sequence indicating 6.2–7.0% gain in system productivity over the existing recommendations. Each additional unit of P and K nutrition prompted system productivity by 18.9 and 11.0 kg kg^?1 of applied nutrient, respectively. Apparent yield decline was observed in K and PK omission plots to the extent of 15.8 and 27.4% in potato, 10.5 and 23.9% in sunflower and 4.2 and 8.3% in greengram, respectively, compared to the recommended fertilization. The superiority of the FYM along with the recommended NPK (potato/sunflower) was evident on the overall profitability and sustainability of the system, highlighted by the significantly higher productivity (7.16 t SFEY ha^?1), sustainability yield index (SYI; 0.76), production efficiency (PE; 27.85 kg SFEY ha^?1 day^?1) and net returns (2520 USD ha^?1) with a B:C ratio of 2.91. Apparent change in potassium permanganate (KMnO₄)-N was negative in all the treatments while N and P balance was positive with 150% NPK fertilization. Nutrient uptake exceeded the replenishment with 100% NPK application and maintained net negative soil nutrient stock for all the primary nutrients, indicating the need for revalidation of the existing recommendations in the system perspective. Conspicuous improvement in residual soil fertility in terms of maximum buildup of soil organic carbon (14%) and enhancement in soil KMnO₄-N (4.2%), Olsen-P (19.4%), ammonium acetate (NH4OAc)-K (5.8%) and dehydrogenase enzyme activity (44.4%) was observed in FYM-treated plots over the initial values. The study suggested that the inclusion of legumes and FYM application with the recommended NPK in potato-sunflower cropping sequence will sustain the system’s productivity through the efficient use of nutrients, enhanced microbial activity and improved soil health while combating escalating prices of fertilizers as well as environmental issues in the Indo-Gangetic plains of India and similar environments.     

Complete genome sequence analysis of chicken astrovirus isolate from India

Objective

Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens.

Methods

Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein.

Results

The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.