How to manage salinity in irrigated lands: a selective review with particular reference to irrigation in developing countries

Irrigation management / Irrigable land / Soil salinity / Water use efficiency / Soil degradation / Irrigated farming / Policy making / Developing countries

Model based regional estimates of soil organic carbon sequestration and greenhouse gas mitigation potentials from rice croplands in Bangladesh

Rice (Oryza sativa L.) is cultivated as a major crop in most Asian countries and its production is expected to increase to meet the demands of a growing population. This is expected to increase greenhouse gas (GHG) emissions from paddy rice ecosystems, unless mitigation measures are in place. It is therefore important to assess GHG mitigation potential whilst maintaining yield. Using the process-based ecosystem model DayCent, a spatial analysis was carried out in a rice harvested area in Bangladesh for the period 1996 to 2015, considering the impacts on soil organic carbon (SOC) sequestration, GHG emissions and yield under various mitigation options. An integrated management (IM, a best management practice) considering reduced water, tillage with residue management, reduced mineral nitrogen fertilizer and manure, led to a net offset by, on average, −2.43 t carbon dioxide equivalent (CO2-eq.) ha−1 year−1 (GHG removal) and a reduction in yield-scaled emissions intensity by −0.55 to −0.65 t CO2-eq. t−1 yield. Under integrated management, it is possible to increase SOC stocks on average by 1.7% per year in rice paddies in Bangladesh, which is nearly 4 times the rate of change targeted by the “4 per mille” initiative arising from the Paris Climate Agreement

Computational Biology Approach for Therapeutic Intervention of Alexander Disease by Post Transcriptional Gene Silencing

Alexander disease (AxD) primarily affects the white matter of the central nervous system (CNS). It is an astrogliopathy in which Astroglial cells involved in maintenance homeostasis and providing defence to the brain are affected. Therefore their dysfunction has been implicated in a number of neurological, neuropsychiatric and neurodegerative disorders. GFAP (Glial fibrillary acidic protein) is the major intermediate filament protein present in astrocytes whose heterozygous missense mutations have been reported to be a cause of AxD. In the absence of any effective therapeutic intervention of AxD, in the present study PTGS (Post transcriptional gene silencing) approach to knock down mutant gfap gene. Various mutations causing AxD were checked for their pathogenicity using various in silico tools and 13 mutations were shortlisted based on their pathogenicity and probability of occurrence. Thereafter siRNA were designed against the mutant genes to silence them and thereby preventing the accumulation of mutant gfap that causes the pathophysiology of AxD

In-silico design of an Epitope-based peptide vaccine: A Computational Biology Approach

Lymphocytic choriomeningitis, is a rodent-borne viral infectious disease caused by Lymphocytic choriomeningitis virus (LCMV), a member of the family Arenaviridae, that was initially isolated in 1933. Acquired postnatal infection ranges from asymptomatic to a brief, nonspecific flu-like illness to critical self-resolving neurological disease, predominantly consisting of aseptic meningitis or meningoencephalitis. This study was undertaken to design an epitope-based peptide vaccine against Lymphocytic choriomeningitis virus using a computational biology approach. Twenty four sequences of LCMV were retrieved from UniProt database and analyzed with various in silico tools. VaxiJen was used to identify immunogenic peptides and T-cell epitopes were analysed using NetCTL server to identify T-cell epitopes. Out of 15 immunogenic peptides analysed using NetCTL server, a conservancy of 64.28% amongst all epitopes was observed. The peptide sequence VVQNLDQLY, a non-allergen, was found to be a potent T-cell epitope that interacted with 28 human leukocyte antigens (HLAs) and its interaction with HLA-A*02:06 was studied using protein-protein docking analysis. The HLA allele and the epitope VVQNLDQLY were found to effectively interact with each other and this epitope may be used as a vaccine against LCMV. Thus immunoinformatics based approaches can be used to predict vaccine candidates against pathogens in a timely manner and usher us into an era of T-cell based novel vaccinomics approach

Investigation of Mutant GFAP Protein Associated with Alexander Disease and its Therapeutic Intervention: Structure Based Drug Design Approach

Systems Biology approach involves integration of experimental and computational research to understand complex biological systems. Alexander's Disease (AxD) was first described by W. S. Alexander in 1949, and is a rare, but often fatal neurological disorder that has been divided into three subtypes based on the age of onset: the infantile, juvenile and adult forms that are shown to be caused by mutations in the gfap gene. The infantile form, with onset between birth and about two years of age, is currently the most common form of the disease. The characteristic neuropathological feature of all forms of AxD is the presence of Rosenthal fibers. In present study, the mutant GFAP protein associated with AxD was investigated by predicting the structure of wild type and mutant GFAP protein. It was found that due to the reported single point mutation, the mutant protein adopted a left handed α-helix structure in sharp contrast to the predicted right handed α-helix of the wt GFAP indicating large conformational change which may be the cause of aggregation of GFAP forming Rosenthal Fibers. In the absence of any commercially available drug to alleviate the symptoms of AxD, the therapeutic intervention of mutant GFAP protein was done using structure based drug design approach. The drug dibutyryl cyclic AMP identified through data mining from STITCH 4.0 was found to be toxic and therefore its structural analogs were generated using GAUSSIAN 09. Each of the 20 structural analogs of dbcAMP were docked with mutant GFAP using Discovery Studio 2.5 and analysed for their toxicity potential using OSIRIS Property Explorer. Three structural analogs i.e. DBCM12, DBCM17 and DBCM20 were found to have favourable docking, druglikeness and did not pose any toxicity risk. These structural analogs identified may be further analysed for therapeutic intervention of AxD by their role in prevention of aggregation of mutant GFAP.

Error caused by carbon dioxide in determination of ammonium by direct steam distillation of tropical wetland rice soils

Abstract A study was made with eight Philippine wetland rice soils to quantify the possible error caused by the CO2 evolved during direct distillation of soil suspensions in aerobic and anaerobic conditions with MgO. The error caused by CO2 was eliminated by absorbing the ammonia distilled in H2SO4, which was gently boiled to derive off the CO2 absorbed. The possible error caused by CO2 was not eliminated when boric acid was used for absorbing ammonia. The difference in NH4 + values determined by using sulfuric acid and boric acid methods gave an estimate of the error caused by CO2. It was found that CO2 evolved caused negative error in the NH4 + values obtained using the direct distillation of soil suspensions with MgO in presence of KCl. The magnitude of error was higher and significant with anaerobic soil samples but this error was negligible with aerobic soils

Managing iron toxicity in lowland rice: the role of tolerant genotypes and plant nutrients

This paper critically reviews the recent research on the role of tolerant genotypes and plant nutrients in reducing iron toxicity. The ultimate goal is to provide information that can be used for the increase of rice productivity in iron-toxic wetlands on a sustainable basis. Some tolerant genotypes that can be used for reducing iron toxicity are presented. The role of other nutrients in reducing iron toxicity is mentioned

Effect of biuret content on transformation of urea nitrogen in soil

The effect of the biuret content (0.0, 1.0, 2.5, 5.0 and 10.0% of urea) on transformations of urea-N was studied in a sandy loam (pH 7.7). While biuret did not affect urea hydrolysis, it inhibited the conversion of NH+4 to NO−2 and the subsequent oxidation of NO−2 to NO−3. This resulted in the accumulation of larger amounts of both NH+4-N and NO−2-N in soil as compared to soil receiving urea alone. The results suggest that biuret impurity in urea fertilizer is likely to enhance nitrite toxicity. ∗Present address: Soil Chemistry Department, International Rice Research Institute, Los Baños (Mail address: P.O. Box 933, Manila, Philippines), Philippines

Nitrification in some tropical soils

Nitrification of soil N in 8 mineral and 2 histosols having a wide range in pH (3.4 to 8.6), organic C (1.22 to 22.70%) and total N (0.09 to 1.20%) was studied by measuring nitrate fromation under aerobic incubation of the soil samples at 30°C for 4 weeks. The amounts of NO3-N produced in the soils varied from 0 to 123 μg/g of soil. Soil N in the two acid sulfate soils and one other acid soil did not nitrify under conditions that stimulate nitrification. Soils having pH more than 6.0 nitrified at a rapid rate and released NO3-N ranging from 98 to 123 μg/g. The two organic soils differed considerably in their capacity to nitrify though the total amounts of mineral N released were similar in these soils. The amounts of NO3-N formed in the soils was highly positively correlated with the soil pH but was not significantly correlated with the organic C of total N content of the soils. Statistical analysis also showed that nitrate formation was not significantly correlated with soil pH in soils having pH higher than 6.0

Effect of carbofuran on transformation of urea nitrogen in soil

THE effect of Carbofuran at 10 and 50 ppm of soil on transformation of urea nitrogen in a sandy loam (PH 7-7) was studied in laboratory. The insecticide had no effect on urea hydrolysis but moderately inhibited both conversion of NH4+ to N02- and N02- to N03-, the effect being pronounced at the higher rate but lasted upto 2 weeks only. The results 0'£ the study along with other evidences suggest that under normal field application rates, carbofuran may have little effect on the hydrolysis as well as nitrification of urea nitrogen in soils with pH in the alkaline rang