Influence of tillage based crop establishment and residue management practices on soil quality indices and yield sustainability in rice-wheat cropping system of Eastern Indo-Gangetic Plains.

Rice-wheat cropping system (RWCS) is the most important system occupying around 26 M ha spread over the Indo Gangetic Plains in South Asia and China. Many long-term trials were led to assess the agronomic productivity and economic profitability of various combinations of conservation agricultural (CA) practices (zero tillage, residue management and crop establishment) in RWCS of Eastern Indo-Gangetic Plains (EIGP) of India. The purpose of this study was to investigate the best management practices involving different tillage-based crop establishment and residue retention techniques and their contribution to agricultural system sustainability through improvement in soil health by developing soil quality index (SQI). We have used SQI as an instrument based on physical [macro aggregate stability (MAS), available water capacity (AWC) and soil penetration resistance (SPR)], chemical [soil organic carbon (OC), available N, available P and available K] and biological [microbial biomass carbon (MBC), fluorescein diacetate (FDA) and dehydrogenase activity (DHA)] properties of soil, because these are very useful indicators of soil's functions for agronomic productivity and soil fertility. Soil properties like MAS, OC, MBC, FDA and DHA were higher by 47, 18, 56, 48 and 53%, respectively, under ZTDSR-ZTW (T7: Zero-till direct seeded rice - Zero-till wheat) than RPTR-CTW (T1: Random puddled transplanted rice - Conventional till broadcasted wheat), at 0-10 cm. CA based treatment T7 also recorded lower SPR (126 N cm-1). SQI for different treatments were calculated by performing principal component analysis based on the total data set method. The higher system rice equivalent yield of 12.41 t ha-1 was observed at SQI value of 0.90 at 0-10 cm and 0.86 at 10-20 cm in T7. It can be concluded that crop residue retention on the surface with zero tillage is beneficial for the sustainability and productivity of the RWCS in EIGP of India.

Different subclasses and isotypes of antibodies against phosphorylcholine in haemodialysis patients: association with mortality.

The risk of premature death is high among patients on haemodialysis (HD patients). We previously determined that immunoglobulin (Ig)M antibodies against phosphorylcholine (anti-PC) are negatively associated with increased risk of cardiovascular disease (CVD), atherosclerosis, some autoimmune diseases and mortality among HD patients in this cohort. Here, we also study other subclasses and isotypes of anti-PC in HD patients in relation to mortality, inflammation and gender. The study group is a cohort of 209 prevalent HD patients [median age = 66 years, interquartile range (IQR) = 51-74], vintage time = 29 months (IQR = 15-58; 56% men) with a mean follow-up period of 41 months (IQR = 20-60). Fifty-six per cent were men. We also divided patients into inflamed C-reactive protein (CRP) > 5·6 mg/ml and non-inflamed CRP. Antibody levels were determined by in-house enzyme-linked immunosorbent assay. IgG1 anti-PC below median was significantly associated with increased all-cause mortality (after adjustment for confounders: P = 0·02), while IgG, IgA and IgG2 anti-PC were not associated with this outcome. Among non-inflamed patients, IgM and IgG1 anti-PC were significantly associated with mortality (P = 0·047 and 0·02). IgG1 anti-PC was significantly associated with mortality among men (P = 0·03) and trending among women (P = 0·26). IgM (as previously reported) and IgG1 anti-PC are negatively associated with survival among HD patients and non-inflamed HD patients, but among inflamed patients there were no associations. IgG, IgA or IgG2 anti-PC were not associated with survival in these groups and subgroups. Further studies are needed to determine if raising anti-PC levels, especially IgM and IgG1 anti-PC, through immunization is beneficial.

Evaluation of long-term conservation agriculture and crop intensification in rice-wheat rotation of Indo-Gangetic Plains of South Asia: Carbon dynamics and productivity.

In the context of deteriorating soil health, stagnation of yield in rice-wheat cropping system (RWCS) across Indo- Gangetic plains (IGP) and environmental pollution, a long term field experiment was conducted during 2009-2016 taking four crop scenarios with conservation agriculture (CA), crop intensification and diversified cropping as intervening technology aiming to evaluate the sustainability of the systems. Scenario 1 (S1) represented conventional farmers' practice of growing rice and wheat with summer fallow. In scenario 2 (S2) and scenario 3 (S3), legume crop was taken along with rice and wheat with partial CA and full CA, respectively. Conventional RWCS was replaced with rice-potato + maize- cowpea cropping system with partial CA in scenario 4 (S4). The S3 scenario registered highest total organic carbon (TOC) stock of 47.71 Mg C ha-1 and resulted in significant increase of 14.57% over S1 (Farmer's practice) in 0-30 cm soil depth after 7 years of field trial. The S4 scenario having intensified cropping systems recorded lowest TOC of 39.33 Mg C ha-1 and resulted in significant depletion of 17.56% in C stock with respect to S3 in 0-30 cm soil depth. The TOC enrichment was higher in S2, S3 and S4 scenario in the surface soil (0-10 cm) compared to S1. At lower depth (20-30 cm), the TOC enrichment was significantly higher in S2 (12.82 Mg C ha-1) and S3 (13.10 Mg C ha-1 soil) over S1 scenario. The S2 and S3 scenario recorded highest increased allocation of TOC (3.55 and 6.13 Mg C ha-1) to passive pool over S1. The S2 (15.72 t ha-1), S3 (16.08 t ha-1) and S4 (16.39 t ha-1) scenarios recorded significantly higher system rice equivalent yield over S1 (10.30 t ha-1). Among the scenarios, S3 scenario had greater amount of total soil organic carbon, passive pool of carbon and higher system rice equivalent yield, thus, is considered the best cropping management practice to maintain soil health and food security in the middle IGP.

Rapid spread of Vibrio cholerae O1 El Tor variant in Odisha, Eastern India, in 2008 and 2009.

The emergence and spread of Vibrio cholerae O1 El Tor variant strains causing severe diarrhea has been witnessed worldwide in recent years. In the state of Odisha, India, the spread of the V. cholerae O1 El Tor variant strains was studied during outbreaks in 2008 and 2009. Analysis of 194 V. cholerae O1 Ogawa strains revealed that V. cholerae O1 El Tor variant strains are spreading gradually throughout the state, causing outbreaks replacing typical V. cholerae O1 El Tor biotype strains.

Large outbreak of cholera caused by El Tor variant Vibrio cholerae O1 in the eastern coast of Odisha, India during 2009.

A large outbreak of cholera reported during April-July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enteriopathogens, antibiogram profile and detection of various toxic genes. The bacteriological analysis of rectal swabs and environmental water samples revealed the presence of V. cholerae O1 Ogawa biotype El Tor. The V. cholerae strains were resistant to ciprofloxacin, co-trimoxazole, chloramphenicol, streptomycin, ampicillin, furazolidone and nalidixic acid. The multiplex polymerase chain reaction (PCR) assay on V. cholerae strains revealed the presence of ctxA and tcpA genes. The mismatch amplification of mutation assay (MAMA) PCR on clinical and environmental isolates of V. cholerae revealed that the strains were El Tor biotype, which harboured the ctxB gene of the classical strain. The random amplified polymorphic DNA PCR analysis and pulsed-field gel electrophoresis results indicated that the V. cholerae isolates belonged to the same clone. This investigation gives a warning that the El Tor variant of V. cholerae has spread to the coastal district causing a large outbreak that requires close monitoring and surveillance on diarrhoeal outbreaks in Odisha.

The structure of aquareovirus shows how the different geometries of the two layers of the capsid are reconciled to provide symmetrical interactions and stabilization.

BACKGROUND: Aquareoviruses are important pathogens of aquatic animals and have severe consequences in aquaculture. These viruses belong to the family Reoviridae. A structural feature common to members of the Reoviridae is a multilayered capsid, formed by several concentric icosahedral shells with different protein compositions. How these proteins, which often are present in unequal stoichiometries, interact between icosahedral layers to stabilize the capsid is not well understood. RESULTS: We have determined the three-dimensional structure of aquareovirus to 23 A resolution using electron cryomicroscopy and computer image analysis. The protein capsid is composed of two structurally distinct icosahedral layers: an outer layer approximately 100 A thick, with incomplete T=13 left-handed symmetry, surrounds an inner layer 600 A in diameter that has T=1 symmetry and is perforated by channels near the fivefold axes. There are 120 subunits, arranged in dimers, in the inner layer, each of which interacts with two of the 600 subunits in the outer layer. A separate set of closely interacting proteins forms the fivefold axes of the virus structure, forming continuous density throughout both layers of the capsid. Comparison of full and empty (lacking RNA) virus structures reveals an RNA shell that lies directly beneath the inner layer. CONCLUSIONS: Our aquareovirus structure displays marked similarity to the mammalian reovirus intermediate subviral particles, suggesting a close evolutionary relationship. However, the noticeable distinction is that aquareovirus lacks the hemagglutinin spike observed in reovirus. The T=1 inner layer organization observed in the aquareovirus appears to be common to other members of the Reoviridae. Such organization may be of fundamental significance in the endogenous transcription of the genome in these viruses.

Structure and sequence comparison of bovine respiratory syncytial virus fusion protein.

The fusion (F) proteins of 10 strains of bovine respiratory syncytial virus (BRSV) were compared by radioimmunoprecipitation with fractionation on SDS-polyacrylamide gels. Two different molecular weights (15 kDa and 20 kDa) of the F2 proteins were demonstrated among the BRSV strains tested. To delineate the molecular basis for differences in the molecular weights of F2 subunits among the BRSV strains, the nucleotide sequences of the F genes of FS1 and VC464 strains were determined from cDNA clones. The deduced amino acid sequences were then compared to those of BRSV strains RB94, 391-2 and A51908. The F gene was highly conserved (> 95%) among BRSV strains. Comparison of the deduced F2 amino acid sequences showed that the strain with F2 subunits of 20 kDa had three N-linked glycosylation sites, whereas the strains with F2 subunits of 15 kDa had two N-linked glycosylation sites. Analysis of F2 subunits in their deglycosylated forms indicated that the difference in the molecular weights of the F2 subunits was due to the difference in the extent of glycosylation.

Gene junction sequences of bovine respiratory syncytial virus.

The nucleotide sequences of seven gene junctions (N-P, P-M, M-SH, SH-G, G-F, F-M2 and M2-L) of bovine respiratory syncytial virus (BRSV) strain A51908 were determined by dideoxynucleotide sequencing of cDNAs from polytranscript mRNAs and from genomic RNA. By comparison with the consensus sequences derived from human respiratory syncytial virus (HRSV) mRNAs, gene-start and gene-end sequences were found in all BRSV mRNAs. There was a perfect match between the BRSV and HRSV in all gene-start sequences, except for the sequence of the SH gene which contained one nucleotide difference compared to HRSV A2; and the gene-start sequence of the L gene, which was one nucleotide shorter than the corresponding sequence of HRSV. Analysis of the intergenic regions showed a high degree of divergence in the nucleotide sequence between BRSV and HRSV. However, the length of the nucleotides in the intergenic sequences was similar for a given gene junction. As in the case of HRSV, the M2 and L genes of BRSV overlap by 68 nucleotides, suggesting a similar transcription attenuation mechanism. The sequences of the overlap, corresponding to the 3' end of the L gene, were almost identical between BRSV and HRSV.

Structural difference in the fusion protein among strains of bovine respiratory syncytial virus.

The polypeptides of different strains of bovine respiratory syncytial virus (RSV) were compared. Altered electrophoretic migrations were observed in the G, F, P, M and 22 kDa polypeptides. The molecular weight of the F2 fragment in human RSV (Long strain) and bovine RSV (A51908 and Md-X strains) was approximately 20 kDa whereas it was approximately 15.5 kDa in caprine RSV and bovine RSV (FS-1 and VC-464 strains). The size difference of the F2 subunit was due to difference in the extent of glycosylation.

Analysis of the bovine respiratory syncytial virus fusion protein (F) using monoclonal antibodies.

Seven monoclonal antibodies (MAbs) directed against bovine respiratory syncytial virus (BRSV) fusion (F) protein were produced and characterized by radioimmunoprecipitation and immunofluorescence assays. These seven MAbs together with the previously described MAbs (Beeler and Van Wyke Coelingh, 1989) to the F protein of human respiratory syncytial virus (HRSV) were used to study the antigenic variation of 12 strains of ungulate RSV. All except one MAbs specific for the HRSV-F protein reacted with ungulate RSV strains less efficiently, indicating that some epitopes are conserved, and others are not conserved on the F proteins of HRSV and BRSV strains. Three MAbs specific to the BRSV-F protein neutralized virus infectivity and reacted with all the ungulate RSV strains, suggesting that these epitopes are well conserved. Based on the reactivity of three other MAbs specific to the BRSV-F protein, ungulate RSVs could be grouped into two subgroups. The results indicated that there are antigenic variations in the F protein among ungulate RSV strains.

Genetic analysis of the G and P genes in ungulate respiratory syncytial viruses by RNase A mismatch cleavage method.

The G and P genes of bovine, ovine and caprine respiratory syncytial (RS) viruses were analyzed by RNase A one-dimensional fingerprinting, using A 51908 as the reference strain. Antisense G or P RNA probes of bovine RS virus strain A 51908 were hybridized to total RNA extracted from bovine turbinate cells infected with bovine, ovine or caprine RS virus strains. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products were analyzed by gel electrophoresis. Comparative analysis of the cleavage patterns revealed heterogeneity among bovine, ovine and caprine RS virus isolates. Ovine RS virus strains generated RNA cleavage patterns more distantly related to the bovine or caprine RS virus strains, particularly in the G gene. Statistical analysis of the results obtained indicated that genetic differences between bovine and ovine viruses were larger, compared with the ones among bovine strains themselves. The same analysis also revealed a close genetic relation among bovine and caprine strains. These results are discussed in terms of ungulate RS virus genetic variation and vaccine development.

Bovine respiratory syncytial virus can induce apoptosis in MDBK cultured cells.

Bovine respiratory syncytial virus (BRSV) is a major cause of respiratory disease in calves. BRSV infection is associated with epithelial cell death and inflammation. Over the past few years, a growing number of viruses have been found to induce apoptosis. In order to determine the ability of BRSV to induce apoptosis, we studied the effect of BRSV infection in cultured MDBK cells. We used ligation-mediated PCR assay to detect specific blunt-end cellular DNA fragments produced by cellular endonucleases cleaving the genomic DNA between the nucleosomes during apoptosis. We found that BRSV infection resulted in apoptosis in MDBK cells. This data demonstrates for the first time that BRSV can induce apoptosis. This data also may contribute to delineate the mechanisms that regulate tissue injury and potential lung repair following BRSV infection.

Recombinant Newcastle disease virus as a vaccine vector.

Veterinary vaccines remained conventional for more than fifty years. Recent advances in the recombinant genetic engineering techniques brought forward a leap in designing vaccines for veterinary use. A novel approach of delivering protective immunogens of many different pathogens in a single virus vector was made possible with the introduction of a "reverse genetics" system for nonsegmented negative-sense RNA viruses. Newcastle disease virus (NDV), a nonsegmented negative-sense virus, is one of the major viruses of economic importance in the poultry industry throughout the world. Despite the availability of live virus vaccines of good potency, the intrinsic ability of attenuated strains to revert in virulence makes control of this disease by vaccination difficult. Armed with the knowledge of virulence factors of this virus, it is now possible to produce genetically stable vaccines and to engineer mutations that enhance immunogenicity. The modular nature of the genome of this virus facilitates engineering additional genes from several different pathogens or tumor-specific antigens to design contemporary vaccines for animals and humans. This review will summarize the developments in using NDV as a vaccine vector and the potential of this approach in designing next generation vaccines for veterinary use.

Role of envelope glycoproteins of bovine respiratory syncytial virus in cell fusion.

To investigate the requirements for bovine respiratory syncytial virus (BRSV) cell fusion, the fusion (F), the attachment (G) and the small hydrophobic (SH) glycoproteins were expressed individually or coexpressed, using the vaccinia virus-T7 polymerase transient expression system. The contribution of individual glycoproteins in cell fusion was studied by a reporter gene activation assay. Activation of a reporter gene, beta-galactosidase, was assessed by colorimetric assay of detergent cell lysates or by in situ staining. Quantitative measurements indicated much higher sensitivity compared with analysis of syncytium formation. Our results showed that expression of any individual BRSV envelope gene or coexpression of F + G genes, did not induce significant cell fusion; however, coexpression of F + G + SH genes induced extensive cell fusion. To examine the role of N-linked glycosylation, each of the four potential glycosylation sites were individually removed by mutagenesis. The fusogenic activities of these F glycosylation mutants was examined using the reporter gene activation assay. Our results showed removal of individual carbohydrate chains on F2 subunit had no significant deleterious effects on cell fusion.

Efficient fluorescence-based imaging methods for quantitating infectivity and oncolytic efficacy of Newcastle disease virus.

A high throughput quantitation protocol is desired to determine the replication of various recombinant oncolytic viruses in vitro. Plaque assay is the classic method for viral infectivity quantitation but is laborious and time consuming; moreover it does not report the oncolytic efficacy of a virus. In this paper, three new imaging methods for quantitating viral infectivity are derived and evaluated: fluorescence intensity, infection counts, and infection degree. Infection of oncolytic Newcastle disease virus in human tumor and normal cells was followed over a time course by plaque assay and the imaging methods. For the latter, brightfield and green channel images were acquired at various fixed locations in the cell culture, and later analyzed. One of the imaging methods was found to be highly correlated with viral titer; the other methods are complementary to plaque assay and provide additional information like oncolytic efficacy, syncytium formation etc. The new methods significantly reduce the time and material costs required by plaque assay, and provide an efficient system for quantitating and characterizing infectivity and efficacy of oncolytic viruses.

Epidemics of severe cholera caused by El Tor Vibrio cholerae O1 Ogawa possessing the ctxB gene of the classical biotype in Orissa, India.

BACKGROUND: We investigated the epidemic of cholera that occurred in Kashipur and Dasmantpur blocks of Orissa, reported during July-September 2007. METHODS: Sixty-two rectal swabs and 28 water samples collected from diarrhea patients at different hospitals and villages were bacteriologically analyzed for the identification, antibiogram, and detection of toxic genes of Vibrio cholerae. RESULTS: The cholera outbreaks were caused by V. cholerae O1 Ogawa biotype El Tor in both Kashipur and Dasmantpur blocks. All the V. cholerae isolates from the clinical and environmental samples were sensitive to tetracycline, gentamicin, azithromycin, and chloramphenicol, but were resistant to ampicillin, ciprofloxacin, norfloxacin, co-trimoxazole, nalidixic acid, neomycin, and furazolidone, except the water isolates, which were sensitive to ciprofloxacin and norfloxacin. The multiplex PCR assay revealed that all the clinical and environmental V. cholerae isolates were positive for the ctxA and tcpA genes, showing biotype El Tor. Interestingly, 88% of the clinical and environmental isolates of V. cholerae were El Tor biotype with mutation at the ctxB gene of the classical strain, as confirmed by mismatch amplification of mutation (MAMA)-PCR assay. CONCLUSIONS: This is the first report of the El Tor variant of V. cholerae O1 Ogawa having the ctxB gene of the classical strain with altered antibiogram causing epidemics of cholera in Orissa, India.

Analysis of the ovine respiratory syncytial virus (RSV) G glycoprotein gene defines a subgroup of ungulate RSV.

Respiratory syncytial virus (RSV) has been isolated from sheep suffering from respiratory tract disease. Since the greatest differences between bovine RSV and human RSV are found on the attachment G protein, we have determined the nucleotide and deduced amino acid sequences of the G gene of ovine RSV. The latter contained 838 nucleotides and had a major open reading frame encoding a protein of 263 residues, and shared 73% nucleotide sequence identity with that of bovine RSV. The deduced amino acid sequence of the ovine RSV G protein showed only 60% amino acid identity with the G protein of bovine RSV. Despite the low level of identity, there were similarities in the predicted hydropathy profiles of the G proteins of ovine and bovine RSV. The intergenic sequences for the SH-G and G-F gene junctions of ovine RSV showed 64 and 57% identity respectively with the corresponding regions of the bovine RSV. Our results indicate that ovine and bovine RSV might be classified as two subgroups of an ungulate RSV.

Nucleotide sequence analysis of a matrix and small hydrophobic protein dicistronic mRNA of bovine respiratory syncytial virus demonstrates extensive sequence divergence of the small hydrophobic protein from that of human respiratory syncytial virus.

The nucleotide and deduced amino acid sequences of the matrix (M) and small hydrophobic (SH) proteins of bovine respiratory syncytial virus (BRSV) have been determined from a dicistronic mRNA. Comparison of these sequences with the corresponding published sequences of human respiratory syncytial virus (HRSV) revealed extensive overall homology at both the nucleotide and amino acid levels in the M protein, but low overall homology at both the nucleotide and amino acid levels in the SH protein. There was only 16 to 22% identity between the BRSV SH protein and the HRSV SH proteins at the C terminus. There were also an additional eight amino acids at the C terminus of BRSV. Despite the low level of identity, there were similarities in the predicted hydropathy profiles of BRSV and HRSV SH proteins. The transcription start and stop signals, which are conserved among HRSV mRNAs, were also identified in the M-SH dicistronic mRNA of BRSV. In addition, the intergenic sequence for the M-SH gene junction of BRSV was determined.

Sequence variability of the glycoprotein gene of bovine respiratory syncytial virus.

Sequence variation in the attachment glycoprotein G of bovine respiratory syncytial virus (BRSV) was determined. The nucleotide sequences of the G mRNAs of the A51908, VC464 and FS-1 strains of BRSV were compared with the published sequence of the BRSV strain 391-2. Nucleotide sequence alignment showed that overall they are highly conserved, with 90 to 97% identity. In addition, the coding region of strain A51908 was longer by 18 nucleotides at the 3' end. An 84 to 95% level of identity was observed among the deduced amino acid sequences of the G proteins of BRSV strains. A maximum divergence of 19% was found when the extracellular domains of the G proteins were compared. The level of diversity would be consistent, by analogy to the human respiratory syncytial viruses, with these BRSV strains forming a single subgroup.