Genetic analysis of the matrix and non-structural genes of equine influenza virus (H3N8) from epizootic of 2008-2009 in India

India faced an epizootic of equine influenza in 2008-2009. The isolated viruses were typed as H3N8 and grouped with the clade 2 viruses of Florida sublineage on the basis of haemagglutinin (HA) gene sequence analysis. This report describes the genetic analysis and selection pressure of matrix (M) and non-structural 1 (NS1) genes of the Indian isolates. All isolates shared 98.41% and 99.54% homology with other clade 2 viruses of Asian origin for M1 and M2 amino acid (aa) sequences, respectively. There were 3 and 4 unique aa residue changes respectively in M1 and M2 proteins in all Asian isolates. Phylogenetic analysis revealed clustering of Indian and Chinese isolates in a separate group designated here as Asian clade for M gene. Indian and Chinese isolates shared homology ranging from 98.17% to 99.08% at aa level. The M and NS1 genes were under negative selection pressure with estimated magnitude of pressure (ω) 0.054, 0.581 and 0.30 for M1, M2 and NS1, respectively.     

Effect of selected single nucleotide polymorphisms in SLC11A1, ANKRA2, IFNG and PGLYRP1 genes on host susceptibility to Mycobacterium avium subspecies paratuberculosis infection in Indian cattle

Paratuberculosis (PTB) is a chronic infectious enteritis of ruminants, caused by Mycobacterium avium subspecies paratuberculosis (MAP) that brings huge economic loss to the dairy farmers. The study was conducted to explore the association of selected SNPs in IFNG, SLC11A1, ANKRA2 and PGLYRP1 genes with resistance to PTB disease in Indian cattle population. A case-control resource population was established based on the results of diagnostic tests used for detection of MAP infection status viz. ELISA, Johnin PPD test, faecal microscopy and IS900 blood PCR. The PCR-RFLP method was used for genotyping of SNPs. SNPs rs109453173 in SLC11A1, rs110853455 in IFNG and rs41933863 in ANKRA2 genes were significantly (P<0.05) associated with resistance to MAP infection. For SNP rs109453173, GG genotype and G allele was found to be associated with resistance against MAP infection than CC and CG genotypes and C allele, respectively. For SNP rs110853455, AG genotype was found to be associated with susceptibility to MAP infection than AA and GG genotype. For SNP rs41933863, the AG genotype provided three and six times more resistance against MAP infection than GG and AA genotype. The results of this study are suggestive of SNPs rs109453173, rs110853455 and rs41933863 as potential markers for screening MAP resistant cattle and a breeding programme favouring GG genotype and G allele for rs109453173, AG genotype for rs41933863 and against AG genotype for rs110853455 might confer resistance against MAP infection in Indian cattle. However, investigation of these SNPs in an independent and larger population will warrant the strength of association for resistance against MAP infection in cattle.

     

Landraces-potential treasure for sustainable wheat improvement

Genetic Resources and Crop Evolution - Agricultural production is facing serious threat from various biotic and abiotic stresses specifically under climatic challenges. It is becoming increasingly...     

Charcoal rot (Macrophomina phaseolina) across melon diversity: evaluating the interaction between the pathogen,plant age and environmental conditions as a step towards breeding for resistance

European Journal of Plant Pathology - Macrophomina phaseolina is a soil-borne fungal pathogen that incites charcoal rot in more than 500 plant species including melon, Cucumis melo. Disease...     

DIAGNOSIS AND RECOMMENDATION INTEGRATED SYSTEM: A TOOL FOR DETECTING NUTRIENT DEFICIENCIES IN YAM

The objective of the study carried out in the Upper Oueme Catchment in Benin (West Africa) was to assess the nutrient status in yam (Dioscorea rotundata) through the Diagnostic and Recommendation Integrated System (DRIS), to compare yield, foliar nutrient concentrations and the variance of nutrients of low-and high-yielding groups. Field experiments were carried out in 2001 and 2002 using a randomized complete block design with four treatments, 2001: n = 80, 2002: n = 109) at three sites: Beterou, Dogue, and Wewe. Nitrogen (N), followed by potassium (K), phosphorus (P), and magnesium (Mg) were identified as the most limiting nutrients in 2001 whereas sulfur (S) followed by N was identified as most limiting ones in 2002. Imbalanced nutrition was observed in both the years but was higher in 2001 compared in 2002. They may be utilized as a basis for calibrating the fertilization program of yam.     

A transgenic RNAi approach for developing tomato plants immune to Pepino mosaic virus

RNA interference (RNAi) or gene silencing is a natural defence response of plants to invading viruses. Here, we applied this approach against pepino mosaic virus (PepMV) isolates in their natural host, tomato. PepMV isolates differ in their genetic sequences, the severity of the disease they induce, and their worldwide distribution. PepMV causes heavy crop losses, mainly due to impaired tomato fruit quality. Resistant varieties are not yet available, despite many years of resistance breeding efforts within the tomato seed industry. To generate broad resistance to PepMV strains, conserved sequences from three different strains of PepMV (US1, LP, and CH2) were synthesized as a single insert and cloned in a hairpin configuration into a binary vector, which was used to transform tomato plants. Transgenic tomato lines that expressed a high level of transgene-siRNA exhibited immunity to PepMV strains, including a new Israeli isolate. This immunity was maintained even after graft inoculation, in which a transgenic scion was grafted onto nontransgenic infected rootstocks. However, an immune transgenic rootstock was unable to induce resistance in a nontransformed scion. These results provide the first example of engineered immunity to diverse PepMV strains in transgenic tomato based on gene silencing.     

Application of Native Lactic Acid Bacteria (LAB) for Fermentative Recovery of Lipids and Proteins from Fish Processing Wastes: Bioactivities of Fermentation Products

Fermentation using native lactic acid bacteria (LAB) was evaluated for its effectiveness in recovering lipids and proteins simultaneously from freshwater fish visceral waste (FVW). Five different LAB isolated from fish processing waste were employed in a fermentation process that involved 10% (w/w) glucose, 2% (w/w) NaCl, and 10% (v/w) LAB. Cultures evaluated included four native isolates (Pediococcus acidilactici NCIM5368, Enterococcus faecalis NCIM5367, Pediococcus acidilactici FM37, and Pediococcus acidilactici MW2) from FVW with E. faecium NCIM5335 as the reference culture. Fermentation with native LAB resulted in recovery of > 90% oil present in the material as against no recovery in case of raw (unfermented) viscera and resulted in > 50% of degree of hydrolysis of proteins. The fatty acid profile of lipids was not affected by the fermentation process. The fermentation liquor, rich in hydrolyzed protein, exhibited antioxidant as well as antagonistic properties against several bacterial pathogens. The results clearly demonstrate the usefulness of fermentation using native isolates for simultaneous recovery of lipids and proteins from fish processing waste. It also asserts the value of fermentation as an eco-friendly method and aids in minimizing disposal/pollution problems associated with these solid wastes.     

Laboratory Wet Milling of Corn: Milling Fraction Correlations and Variations Among Crop Years

Several coproducts result from fractionating corn in the wet‐milling process. Because small changes in product composition and milling characteristics can have a major impact on coproduct yields and values, testing is done to anticipate final product yields. Using small sample size and controlled conditions, a laboratory wet‐milling method proved to be a useful tool for wet milling and genetics industries. A wet‐milling process (100‐g batches) was used for data collection. Data collected during 11 years (1994–2004) were observed for samples used as benchmarks to verify process precision and accuracy and determine correlations among wet‐milling yields. More than 400 milling tests were performed on benchmark samples. Data from benchmark samples also were pooled. Coefficients of variation were low (<6%) for mean yields; year‐to‐year standard deviations of benchmark sample yield means were homogenous and implied precision of the procedure. Some differences were detected in mean yields among years (P ≤ 0.05) for benchmark data due to combined effects of hybrid and environment. A negative correlation (r = –0.58) was observed between starch and gluten yield for pooled benchmark data. Four years (2002–2005) of milling data from commercially available hybrids were analyzed using the milling procedure. For pooled commercial data, the correlation between starch and fiber yield was (r = –0.80); correlation between starch and gluten was (r = –0.76).     

λ-cyhalothrin and cypermethrin induced in vivo alterations in the activity of acetylcholinesterase in a freshwater fish, Channa punctatus (Bloch)

In the present study, the in vivo effects of λ-cyhalothrin and cypermethrin on the activity of acetylcholinesterase (AChE, EC 3.1.1.7) were evaluated for 96 h in brain, muscle and gills of Channa punctatus. Both compounds exhibited tissue specific as well as dose dependent decrease in the activity of AChE. The treated fish showed a significant decrease in the activity of AChE in brain and a lesser inhibition in muscle and gills in response to the increasing concentrations of λ-cyhalothrin as well as cypermethrin. Our results indicated that the brain was the main target organ for both insecticides, followed by muscle and gills, as determined by AChE inhibition study. However, these organs showed variations in the degree of AChE inhibition for separate treatments of both insecticides. The λ-cyhalothrin was a more potent AChE inhibitor as compared to cypermethrin. These findings indicated that apart from the established mechanism of delayed closure of sodium ion channels, these pyrethroids inhibit the activity of AChE in C. punctatus which could further aggravate their neurotoxic effects.