Unraveling determinants of integrated farming systems adoption for sustainable livelihood and dietary diversity.

Introduction: Over the years, smallholder farmers have faced more vulnerability to risk and uncertainty in India due to their dependence on cereal crops. One way to reduce this risk is through diversified agriculture, integrating different practices for efficient resource utilization, and adopting a farming systems approach. An integrated farming system (IFS) is one such technique that provides year-round income from different components of enterprises. However, the decision to adopt IFS may be determined by several characteristics of farmers, which needs to be delineated through impact analysis to harness the benefits of a systems approach. Methods: This study analyzes the economic effects of integrated farming systems and assesses their determinants, as well as the dietary diversity patterns of farmers in two states of southern India, i.e., Kerala and Tamil Nadu. A multistage sampling technique was used to obtain cross-sectional data from 367 farmers randomly chosen from one district in Kerala and two districts in Tamil Nadu. The participants have Crop + Horticulture + Animal husbandry (45.45%) as their major system, whereas non-participants have Crop + Animal husbandry (44.35%) as their predominant system. Coarsened exact matching and logit regression methods were used to evaluate the economic impacts of IFS and its influencing factors. Results: The findings of the study indicate that age, education, livestock holding, access to credit, and plantation area have a positive and significant effect on participation by farmers in the program. The matching results show that adoption of IFS resulted in a significant economic impact, generating an additional gross income of Rs. 36,165 ha-1 and a net income of Rs. 35,852 ha-1 and improving the dietary diversity of farm households by 8.6% as compared to non-adopters. Discussion: This study suggests that IFS is a promising approach for improving farmers' livelihoods, economic gains, and nutritional security. Therefore, the integrated farming systems models need to be upscaled through the convergence of government schemes in other regions of India to support smallholder farmers' farming.

Exploring Edible Mushrooms for Diabetes: Unveiling Their Role in Prevention and Treatment.

Diabetes mellitus is a complex illness in which the body does not create enough insulin to control blood glucose levels. Worldwide, this disease is life-threatening and requires low-cost, side-effect-free medicine. Due to adverse effects, many synthetic hypoglycemic medications for diabetes fail. Mushrooms are known to contain natural bioactive components that may be anti-diabetic; thus, scientists are now targeting them. Mushroom extracts, which improve immune function and fight cancer, are becoming more popular. Mushroom-derived functional foods and dietary supplements can delay the onset of potentially fatal diseases and help treat pre-existing conditions, which leads to the successful prevention and treatment of type 2 diabetes, which is restricted to the breakdown of complex polysaccharides by pancreatic-amylase and the suppression of intestinal-glucosidase. Many mushroom species are particularly helpful in lowering blood glucose levels and alleviating diabetes symptoms. Hypoglycaemic effects have been observed in investigations on Agaricussu brufescens, Agaricus bisporus, Cordyceps sinensis, Inonotus obliqus, Coprinus comatus, Ganoderma lucidum, Phellinus linteus, Pleurotus spp., Poria cocos, and Sparassis crispa. For diabetics, edible mushrooms are high in protein, vitamins, and minerals and low in fat and cholesterol. The study found that bioactive metabolites isolated from mushrooms, such as polysaccharides, proteins, dietary fibers, and many pharmacologically active compounds, as well as solvent extracts of mushrooms with unknown metabolites, have anti-diabetic potential in vivo and in vitro, though few are in clinical trials.

Analysis of Physiological Variations and Genetic Architecture for Photosynthetic Capacity of Japanese Soybean Germplasm.

The culmination of conventional yield improving parameters has widened the margin between food demand and crop yield, leaving the potential yield productivity to be bridged by the manipulation of photosynthetic processes in plants. Efficient strategies to assess photosynthetic capacity in crops need to be developed to identify suitable targets that have the potential to improve photosynthetic efficiencies. Here, we assessed the photosynthetic capacity of the Japanese soybean mini core collection (GmJMC) using a newly developed high-throughput photosynthesis measurement system "MIC-100" to analyze physiological mechanisms and genetic architecture underpinning photosynthesis. K-means clustering of light-saturated photosynthesis (Asat ) classified GmJMC accessions into four distinct clusters with Cluster2 comprised of highly photosynthesizing accessions. Genome-wide association analysis based on the variation of Asat revealed a significant association with a single nucleotide polymorphism (SNP) on chromosome 17. Among the candidate genes related to photosynthesis in the genomic region, variation in expression of a gene encoding G protein alpha subunit 1 (GPA1) showed a strong correlation (r = 0.72, p < 0.01) with that of Asat . Among GmJMC accessions, GmJMC47 was characterized by the highest Asat , stomatal conductance (gs ), stomatal density (SDensity ), electron transfer rate (ETR), and light use efficiency of photosystem II (Fv'/Fm') and the lowest non-photochemical quenching [NPQ(t)], indicating that GmJMC47 has greater CO2 supply and efficient light-harvesting systems. These results provide strong evidence that exploration of plant germplasm is a useful strategy to unlock the potential of resource use efficiencies for photosynthesis.

Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat.

Global warming is a major threat for agriculture and food security, and in many cases the negative impacts are already apparent. Wheat is one of the most important staple food crops and is highly sensitive to the heat stress (HS) during reproductive and grain-filling stages. Here, whole transcriptome analysis of thermotolerant wheat cv. HD2985 was carried out at the post-anthesis stage under control (22 ± 3 °C) and HS-treated (42 °C, 2 h) conditions using Illumina Hiseq and Roche GS-FLX 454 platforms. We assembled ~24 million (control) and ~23 million (HS-treated) high-quality trimmed reads using different assemblers with optimal parameters. De novo assembly yielded 52,567 (control) and 59,658 (HS-treated) unigenes. We observed 785 transcripts to be upregulated and 431 transcripts to be downregulated under HS; 78 transcripts showed >10-fold upregulation such as HSPs, metabolic pathway-related genes, etc. Maximum number of upregulated genes was observed to be associated with processes such as HS-response, protein-folding, oxidation-reduction and photosynthesis. We identified 2008 and 2483 simple sequence repeats (SSRs) markers from control and HS-treated samples; 243 SSRs were observed to be overlying on stress-associated genes. Polymorphic study validated four SSRs to be heat-responsive in nature. Expression analysis of identified differentially expressed transcripts (DETs) showed very high fold increase in the expression of catalytic chaperones (HSP26, HSP17, and Rca) in contrasting wheat cvs. HD2985 and HD2329 under HS. We observed positive correlation between RNA-seq and qRT-PCR expression data. The present study culminated in greater understanding of the heat-response of tolerant genotype and has provided good candidate genes for the marker development and screening of wheat germplasm for thermotolerance.

Efficacy of carcinogenic embryonic antigen in differential diagnosis of diseases of pancreas and liver--a comparative study in a tertiary care hospital of Western Nepal.

OBJECTIVE: The objective of our present study was to assess the efficacy of carcinoembryonic antigen (CEA) for differentiating and diagnosis of pancreatic and liver diseases in Pokhara valley. MATERIALS AND METHODS: A hospital based retrospective study was carried out using data retrieved from the register maintained in the Department of Biochemistry of the Manipal Teaching Hospital, Pokhara, Nepal between 1st January, 2011 and 31st October, 2011. Estimation of CEA was performed by ELISA reader for all cases. Approval for the study was obtained from the institutional research ethical committee. RESULTS: Of the 771 subjects, 208 (27%), 60(7.8%), 240(31.1%), 54(7.0%) , 75(9.7%), 59(7.7%), 75(9.7%) cases were of active chronic hepatitis , cryptogenic cirrhosis, alcoholic cirrhosis, primary biliary cirrhosis, hepatoma, acute or chronic pancreatitis, carcinoma of pancreas respectively. The majority of cases (104) of active chronic hepatitis had CEA levels <5 ng/ml(50%). CEA levels were found to be increased in cases of alcoholic cirrhosis with maximum number of cases (106) in range of 10 to 20 ng/ml (44%). There were no cases having more than 20 ng/ml of CEA in primary biliary cirrhosis and acute or chronic pancreatitis. In cases of pancreatic cancer, maximum number of cases (35) were having CEA >20 ng/ml(47%). CONCLUSION: High levels of CEA are associated with advanced stage of disease. CEA can thus provide an important improvement in the diagnosis by differentiating pancreatic cancer especially from chronic pancreatitis when there is a high suspicion of malignancy. Increased CEA levels may also signify progression from benign to malignant transformation in the liver.

In vitro and in vivo evaluation of Assam Bora rice starch-based bioadhesive microsphere as a drug carrier for colon targeting.

OBJECTIVE: The aim of this study is to develop, characterize and evaluate (in vitro and in vivo) a novel colon-targeted bioadhesive microsphere (BAM) containing metronidazole (MTZ). METHODS: BAMs are prepared using Assam Bora rice starch as a natural bioadhesive polymer by a double emulsion solvent evaporation method. RESULTS: The prepared microspheres showed a uniform spherical shape, with excellent retention time. The in vitro drug release study of the optimized formulations, in different physiological environments, confirmed the insignificant release of metronidazole in the physiological conditions of the stomach (10 - 12.5%) and small intestine (< 25%). Further, fast and major drug release in cecal content (> 90) indicated that the release of the drug was unaffected by the hostile environment of the gastrointestinal tract (GIT). In vitro bacterial inhibition studies illustrated that MTZ loaded BAMs, inhibiting metronidazole-sensitive Bacteroides fragilis and selected BAMs (F1 - F7), have an equivalent or higher zone of inhibition than the marketed formulation. An in vivo organ distribution study of MTZ revealed that Assam Bora rice starch-based microspheres were relatively intact in the upper part of GIT, and the drug was released only after reaching the colon, owing to the microbial degradation of Assam Bora rice starch by microflora residing in the colon. CONCLUSION: MTZ release patterns exhibited slow and extended release over longer periods of time, which shows the potential of Assam Bora rice starch microspheres as a drug carrier for an effective colon-targeted delivery system.

Diagnostic significance of alpha fetoprotein in carcinomas of liver and biliary tract - a comparative study from the western region of Nepal.

OBJECTIVE: To assess the diagnostic significance of α-fetoprotein in carcinomas of liver and biliary tract with the overall goal of reducing morbidity and mortality in Pokhara valley. MATERIALS AND METHODS: It was a hospital based comparative study carried out in the Department of Biochemistry of Manipal Teaching Hospital, Pokhara, Nepal between 1st January 2009 and 31st December 2010. The variables collected were age, gender, serum alpha feto protein. Approval for the study was obtained from the institutional research ethical committee. Estimation of AFP was performed by ELISA reader for all cases. The standard procedure was followed as per manufacturer's instructions for ELISA. All these laboratory parameters were analyzed using Human reagent kits and with the help of ELISA and semi autoanalyser (Humalyser 3500, Germany). RESULTS: Out of 1200 patients, there were 348(29%) cases of HCC. Out of that, 285 cases were found to be AFP positive with significant elevation. Furthermore, diagnosed cases were of cholangiocarcinomas (96, 8%) and secondary carcinomas of liver (216, 18%). In both of these clinical conditions, there was insignificant elevation of AFP. Another commonly diagnosed condition was cirrhosis (480, 40%) and in 90 cases, AFP values were moderately raised from the upper limit of normal reference range. The last diagnosed cases were of either Hepatitis A/E(60, 5%) and did not show any rise in levels of AFP. CONCLUSION: Serological markers for hepatocellular carcinoma (HCC) are imperative for early identification, as well as scrutinizing of tumour aggressiveness, treatment responsiveness, reappearance and endurance. It is consequently justifiable to carry out the test for serum AFP to detect and differentiate at early stage of liver cell carcinomas.

Cell surface expression of the vaccinia virus complement control protein is mediated by interaction with the viral A56 protein and protects infected cells from complement attack.

The vaccinia virus (VACV) complement control protein (VCP) is the major protein secreted from VACV-infected cells. It has been reported that VCP binds to the surfaces of uninfected cells by interacting with heparan sulfate proteoglycans (HSPGs). In this study, we show that VCP is also expressed on the surfaces of infected cells and demonstrate that surface localization occurs independently of HSPGs. Since VCP does not contain a transmembrane domain, we hypothesized that VCP interacts with a membrane protein that localizes to the infected-cell surface. We show that the VACV A56 membrane protein is necessary for the cell surface expression of VCP and demonstrate that VCP and A56 interact in VACV-infected cells. Since the surface expression of VCP was abrogated by reducing agents, we examined the contribution of an unpaired cysteine residue on VCP to VCP surface expression and VCP's interaction with A56. To do this, we mutated the unpaired cysteine in VCP and generated a recombinant virus expressing the altered form of VCP. Following the infection of cells with the mutant virus, VCP was neither expressed on the cell surface nor able to interact with A56. Importantly, the cell surface expression of VCP was found to protect infected cells from complement-mediated lysis. Our findings suggest a new function for VCP that may be important for poxvirus pathogenesis and impact immune responses to VACV-based vaccines.

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

MOTIVATION: Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. RESULTS: We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. AVAILABILITY: Dataset and stand-alone program are available upon request.

The identification and characterization of a monoclonal antibody to the vaccinia virus E3 protein.

Monoclonal antibodies with reactivity to vaccinia virus specific proteins are useful reagents to study the proteins as well as to help understand aspects of the poxvirus life cycle. Using a vaccinia virus proteomics microarray, we found a hybridoma (MAb 3015B2) from a vaccinia virus vaccinated mouse that reacted with the product of the E3L gene. The specificity to the E3 protein was confirmed by Western blotting and immunofluorescence of cells infected with either wild-type vaccinia virus or a mutant virus with the E3L gene deleted. Antibody reactivity with E3 was also seen in cells transfected with a plasmid expressing the E3 protein. A panel of mutated vaccinia viruses with truncations in the E3L gene revealed that while MAb 3015B2 reacted with E3 lacking the C-terminal 7 amino acids, it lost reactivity with a mutant E3 lacking the C-terminal 26 amino acids. This indicates that the antigenic site recognized by 3015B2 is on the C-terminus, somewhere between amino acids 164 through 183. The antibody also recognizes the E3 protein encoded by other orthopoxviruses. This antibody will be useful for further investigations of the E3 protein as well as a useful reagent to indicate vaccinia virus early protein expression.

Trivalent vaccine against botulinum toxin serotypes A, B, and E that can be administered by the mucosal route.

Most reports dealing with vaccines against botulinum toxin have focused on the injection route of administration. This is unfortunate, because a mucosal vaccine is likely to be more efficacious for patients and pose fewer risks to health care workers and to the environment. Therefore, efforts were made to generate a mucosal vaccine that provides protection against the botulinum serotypes that typically cause human illness (serotypes A, B, and E). This work demonstrated that carboxy-terminal peptides derived from each of the three serotypes were able to bind to and penetrate human epithelial barriers in vitro, and there was no cross inhibition of membrane binding and transcytosis. The three polypeptides were then tested in vivo as a trivalent vaccine that could be administered to mice by the intranasal route. The results indicated that the mucosal vaccine evoked high secretory titers of immunoglobulin A (IgA), as well as high circulating titers of IgG and IgA, and it also evoked a high level of resistance to challenge with toxin. The immunoglobulin responses and the levels of resistance to challenge were increased by coadministration of adjuvants, such as chitosan and vitamin E. At least three mechanisms were identified to account for the antibody-induced resistance: (i) blockade of toxin absorption across epithelial cells, (ii) enhanced clearance of toxin from the circulation, and (iii) blockade of toxin action at the neuromuscular junction. These results are a compelling demonstration that a mucosal vaccine against multiple serotypes of botulinum toxin has been identified.

Sevoflurane-induced structural changes in a four-alpha-helix bundle protein.

The mechanisms whereby volatile general anesthetics reversibly alter protein function in the central nervous system remain obscure. Using three different spectroscopic approaches, evidence is presented that binding of the modern general anesthetic sevoflurane to the hydrophobic core of a model four-alpha-helix bundle protein results in structural changes. Aromatic residues in the hydrophobic core reorient into new environments upon anesthetic binding, and the protein as a whole becomes less dynamic and exhibits structural tightening. Comparable structural changes in the predicted in vivo protein targets, such as the gamma-aminobutyric acid type A receptor and the N-methyl-D-aspartate receptor, may underlie some, or all, of the behavioral effects of these widely used clinical agents.

Expression and characterization of a four-alpha-helix bundle protein that binds the volatile general anesthetic halothane.

The structural features of volatile anesthetic binding sites on proteins are being investigated with the use of a defined model system consisting of a four-alpha-helix bundle scaffold with a hydrophobic core. The current study describes the bacterial expression, purification, and initial characterization of the four-alpha-helix bundle (Aalpha(2)-L1M/L38M)(2). The alpha-helical content and stability of the expressed protein are comparable to that of the chemically synthesized four-alpha-helix bundle (Aalpha(2)-L38M)(2) reported earlier. The affinity for binding halothane is somewhat improved with a K(d) = 120 +/- 20 microM as determined by W15 fluorescence quenching, attributed to the L1M substitution. Near-UV circular dichroism spectroscopy demonstrated that halothane binding changes the orientation of the aromatic residues in the four-alpha-helix bundle. Nuclear magnetic resonance experiments reveal that halothane binding results in narrowing of the peaks in the amide region of the one-dimensional proton spectrum, indicating that bound anesthetic limits protein dynamics. This expressed protein should prove to be amenable to nuclear magnetic resonance structural studies on the anesthetic complexes, because of its relatively small size (124 residues) and the high affinities for binding volatile anesthetics. Such studies will provide much needed insight into how volatile anesthetics interact with biological macromolecules and will provide guidelines regarding the general architecture of binding sites on central nervous system proteins.

Metastatic melanoma of mesentery.

A case of malignant melanoma metastatic to small bowel mesentery in an old female is reported. Her primary malignant melanoma of nasal mucosa was already treated. She presented with intestinal obstruction, underwent surgical excision of the tumour and was tumour-free postoperatively.

Antibodies against the extracellular enveloped virus B5R protein are mainly responsible for the EEV neutralizing capacity of vaccinia immune globulin.

In the event of smallpox bioterrorism, widespread vaccination may be required. Vaccinia immune globulin (VIG) has been used to treat complications from the smallpox vaccine. While the potency of VIG was defined by its ability to neutralize intracellular mature virus, a second form of vaccinia called the extracellular enveloped virus (EEV) is critical for virus spread in the host. The B5R-protein is one of many EEV-specific proteins. Immunoprecipitation and ELISA revealed that VIG recognizes the B5R-protein. An EEV plaque-reduction assay using a recombinant vaccinia that lacks the majority of the extracellular domain of B5R showed that the ability of VIG to neutralize EEV is principally directed at B5R. In addition, absorbing out the anti-B5R antibody present in VIG through the addition of recombinant B5R protein abrogated VIG's ability to significantly neutralize wild-type EEV. This work demonstrates the prominent role of B5R as a target of EEV-neutralizing activity of human antibodies.