The food-energy-water-carbon nexus of the rice-wheat production system in the western Indo-Gangetic Plain of India: An impact of irrigation system, conservational tillage and residue management

The conventional rice-wheat system in the western Indo-Gangetic plain of India is energy and water intensive with high carbon footprint. The transition towards resource-efficient eco-friendly production technologies with lower footprint is required for inclusive ecological sustenance. A five-year (2016-17 to 2020-21) field experiment was conducted in RWS with hypothesis that pressurized irrigation systems [drip (DRIP) and mini-sprinkler (MSIS)] in conservation tillage [reduced (RT)/zero (ZT)] and crop residue management [incorporation (RI)/mulch (RM)] might result in higher resource use efficiency with lesser carbon footprint compared to conventional system. Experiment consisted five treatments namely (1) puddled transplanted rice followed by conventionally tilled wheat (PTR/CTW), (2) DRIP irrigated reduced till direct seeded rice (RTDSR) followed by zero-till wheat with 100 % rice residue mulching (ZTW + RM) (DRIP-RTDSR/ZTW + RM), (3) surface irrigated RTDSR followed by ZTW + RM (SIS-RTDSR/ZTW + RM), (4) MSIS irrigated RTDSR followed by ZTW + RM (MSIS-RTDSR/ZTW + RM), and (5) MSIS irrigated RTDSR with 1/3rd wheat residue incorporation followed by ZTW + RM (MSIS-RTDSR + RI/ZTW + RM). The pressurized irrigation system in RWS established under conservational tillage and residue management (DRIP-RTDSR/ZTW + RM and MSIS-DSR + RI/ZTW + RM) produced at par system productivity compared to PTR/CTW. Substantial nitrogen (79-114 ka ha^-1) and irrigation water (536-680 mm) savings under pressurized irrigation systems resulted in 41-64 % higher partial factor productivity of nitrogen with 48-61 % lower water footprint. These systems had lower energy consumption attaining 15-21 % higher net energy, 44-61 % higher energy use efficiency, and 31-38 % lower specific energy. Efficient utilization of farm inputs caused lower greenhouse gas emission (39-44 %) and enhanced carbon sequestration (35-62 %) resulting 63-76 % lower carbon footprint over PTR/CTW. The information generated here might useful in developing policies for resource and climate-smart food production system aiming livelihood security and ecological sustainability in the region. Further, trials are needed for wider adaptability under different climate, soil and agronomic practices to develop site-specific climate smart practices.

Climate-smart agricultural practices influence the fungal communities and soil properties under major agri-food systems

Fungal communities in agricultural soils are assumed to be affected by climate, weather, and anthropogenic activities, and magnitude of their effect depends on the agricultural activities. Therefore, a study was conducted to investigate the impact of the portfolio of management practices on fungal communities and soil physical-chemical properties. The study comprised different climate-smart agriculture (CSA)-based management scenarios (Sc) established on the principles of conservation agriculture (CA), namely, ScI is conventional tillage-based rice-wheat rotation, ScII is partial CA-based rice-wheat-mungbean, ScIII is partial CSA-based rice-wheat-mungbean, ScIV is partial CSA-based maize-wheat-mungbean, and ScV and ScVI are CSA-based scenarios and similar to ScIII and ScIV, respectively, except for fertigation method. All the scenarios were flood irrigated except the ScV and ScVI where water and nitrogen were given through subsurface drip irrigation. Soils of these scenarios were collected from 0 to 15 cm depth and analyzed by Illumina paired-end sequencing of Internal Transcribed Spacer regions (ITS1 and ITS2) for the study of fungal community composition. Analysis of 5 million processed sequences showed a higher Shannon diversity index of 1.47 times and a Simpson index of 1.12 times in maize-based CSA scenarios (ScIV and ScVI) compared with rice-based CSA scenarios (ScIII and ScV). Seven phyla were present in all the scenarios, where Ascomycota was the most abundant phyla and it was followed by Basidiomycota and Zygomycota. Ascomycota was found more abundant in rice-based CSA scenarios as compared to maize-based CSA scenarios. Soil organic carbon and nitrogen were found to be 1.62 and 1.25 times higher in CSA scenarios compared with other scenarios. Bulk density was found highest in farmers' practice (Sc1); however, mean weight diameter and water-stable aggregates were found lowest in ScI. Soil physical, chemical, and biological properties were found better under CSA-based practices, which also increased the wheat grain yield by 12.5% and system yield by 18.8%. These results indicate that bundling/layering of smart agricultural practices over farmers' practices has tremendous effects on soil properties, and hence play an important role in sustaining soil quality/health.

Climate resilient integrated soil-crop management (CRISCM) for salt affected wheat agri-food production systems

Maximizing opportunities for climate resilient agriculture is vital for global food security, and ecological sustainability. To explore the improvement potential of mitigation and adaptation strategies in stabilizing wheat production and increasing farm income in sodicity-prone Ghaghar Basin of Haryana, India, participatory research trials on land reclamation (gypsum/pressmud) and crop management (varieties, nutrient management and weed control) practices were undertaken during 2016-2020. Results indicated that combining gypsum and pressmud together accelerated the reclamation process (soil pH: -3.3% and ESP: -22.1%) and improved plant adaptability (RWC: 10%; MI: -15%; Pn: 40%; gS: 36%; NaK_S: -38% and NaK_R: -42%), which in turn increased wheat yield by 20% compared to unamended control. With increasing sodicity stress, salt tolerant wheat variety KRL 210 exhibited better morpho-physiological adaptation, lesser yield reduction (0.8-1.1 t ha^-1) and attained 4.1% mean yield advantage compared to traditionally cultivated HD 2967. There were genotypic differences for N requirements in sodicity stressed wheat, with 173 kg ha^-1 in KRL 210 and 188 kg ha^-1 in HD 2967 as the economically optimum dose; further advocating for upward revision of current N recommendations beyond 150 kg N ha^-1. Balanced nutrition through foliage applied K compensated the sodicity hazards with lower proportion of Na⁺/K⁺ in leaf tissues (13%), and attained higher grain yield (4%) and incremental income (34 US$ ha^-1) compared to farmers' practice. Sequential use of herbicides provided affordable solution to check Phalaris minor infestation (84% WCE) and enhanced wheat productivity (5.7% higher) with incremental income of 48 US$ ha^-1 compared to farmers' sole dependency on post-emergence herbicides. Synergistic integration of gypsum and pressmud-mediated sodic land reclamation, usage of stress tolerant wheat variety, 15% higher N application, foliar K-nutrition and effective P. minor control substantiate appreciable reduction in soil sodicity, improved crop resilience, and ultimately translated into 5% and 26% higher yields over the recommended and local farm practices, respectively. The key insights of this study suggest a range of opportunities wherein inputs of CRISCM could potentially stabilize the wheat production, improve farm economy and reduce environmental risks beyond what is currently being achieved with existing farm practices.

Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice

Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm^-1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs. Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm^-1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Mono-oxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.

Climate-smart agriculture practices influence weed density and diversity in cereal-based agri-food systems of western Indo-Gangetic plains

Climate-smart agriculture (CSA)-based management practices are getting popular across South-Asia as an alternative to the conventional system for particular weed suppression, resources conservation and environmental quality. An 8-year study (2012-2013 to 2019-2020) was conducted to understand the shift in weed density and diversity under different CSA-based management practices called scenarios (Sc). These Sc involved: Sc1, conventional tillage (CT)-based rice-wheat system with flood irrigation (farmers' practice); Sc2, CT-rice, zero tillage (ZT)-wheat-mungbean with flood irrigation (partial CA-based); Sc3, ZT rice-wheat-mungbean with flood irrigation (partial CSA-based rice); Sc4, ZT maize-wheat-mungbean with flood irrigation (partial CSA-based maize); Sc5, ZT rice-wheat-mungbean with subsurface drip irrigation (full CSA-based rice); and Sc6, ZT maize-wheat-mungbean with subsurface drip irrigation (full CSA-based maize). The most abundant weed species were P. minor > A. arvensis > M. indicus > C. album and were favored by farmers' practice. However, CSA-based management practices suppressed these species and favored S. nigrum and R. dentatus and the effect of CSAPs was more evident in the long-term. Maximum total weed density was observed for Sc1, while minimum value was recorded under full CSA-based maize systems, where seven weed-species vanished, and P. minor density declined to 0.33 instead of 25.93 plant m-2 after 8-years of continuous cultivation. Full CSA-based maize-wheat system could be a promising alternative for the conveniently managed rice-wheat system in weed suppression in north-west India.

Agricultural labor, COVID-19, and potential implications for food security and air quality in the breadbasket of India

To contain the COVID-19 pandemic, India imposed a national lockdown at the end of March 2020, a decision that resulted in a massive reverse migration as many workers across economic sectors returned to their home regions. Migrants provide the foundations of the agricultural workforce in the 'breadbasket' states of Punjab and Haryana in Northwest India.There are mounting concerns that near and potentially longer-term reductions in labor availability may jeopardize agricultural production and consequently national food security. The timing of rice transplanting at the beginning of the summer monsoon season has a cascading influence on productivity of the entire rice-wheat cropping system. To assess the potential for COVID-related reductions in the agriculture workforce to disrupt production of the dominant rice-wheat cropping pattern in these states, we use a spatial ex ante modelling framework to evaluate four scenarios representing a range of plausible labor constraints on the timing of rice transplanting. Averaged over both states, results suggest that rice productivity losses under all delay scenarios would be low as compare to those for wheat, with total system productivity loss estimates ranging from 9%, to 21%, equivalent to economic losses of USD $674 m to $1.48 billion. Late rice transplanting and harvesting can also aggravate winter air pollution with concomitant health risks. Technological options such as direct seeded rice, staggered nursery transplanting, and crop diversification away from rice can help address these challenges but require new approaches to policy and incentives for change.

Topsoil Bacterial Community Changes and Nutrient Dynamics Under Cereal Based Climate-Smart Agri-Food Systems

Soil microorganisms play a critical role in soil biogeochemical processes, nutrient cycling, and resilience of agri-food systems and are immensely influenced by agronomic management practices. Understanding soil bacterial community and nutrient dynamics under contrasting management practices is of utmost importance for building climate-smart agri-food systems. Soil samples were collected at 0–15 cm soil depth from six management scenarios in long-term conservation agriculture (CA) and climate-smart agriculture (CSA) practices. These scenarios (Sc) involved; ScI-conventional tillage based rice-wheat rotation, ScII- partial CA based rice-wheat-mungbean, ScIII- partial CSA based rice-wheat-mungbean, ScIV is partial CSA based maize-wheat-mungbean, ScV and ScVI are CSA based scenarios, were similar to ScIII and ScIV respectively, layered with precision water & nutrient management. The sequencing of soil DNA results revealed that across the six scenarios, a total of forty bacterial phyla were observed, with Proteobacteria as dominant in all scenarios, followed by Acidobacteria and Actinobacteria. The relative abundance of Proteobacteria was 29% higher in rice-based CSA scenarios (ScIII and ScV) and 16% higher in maize-based CSA scenarios (ScIV and ScVI) compared to conventional-till practice (ScI). The relative abundance of Acidobacteria and Actinobacteria was respectively 29% and 91% higher in CT than CSA based rice and 27% and 110% higher than maize-based scenarios. Some taxa are present relatively in very low abundance or exclusively in some scenarios, but these might play important roles there. Three phyla are exclusively present in ScI and ScII i.e., Spirochaetes, Thermi, and Euryarchaeota. Shannon diversity index was 11% higher in CT compared to CSA scenarios. Maize based CSA scenarios recorded higher diversity indices than rice-based CSA scenarios. Similar to changes in soil bacterial community, the nutrient dynamics among the different scenarios also varied significantly. After nine years of continuous cropping, the soil organic carbon was improved by 111% and 31% in CSA and CA scenarios over the CT scenario. Similarly, the available nitrogen, phosphorus, and potassium were improved by, respectively, 38, 70, and 59% in CSA scenarios compared to the CT scenario. These results indicate that CSA based management has a positive influence on soil resilience in terms of relative abundances of bacterial groups, soil organic carbon & available plant nutrients and hence may play a critical role in the sustainability of the intensive cereal based agri-food systems.

Conservation Agriculture-based Sustainable Intensification of Cereal Systems Leads to Energy Conservation, Higher Productivity and Farm Profitability

In the Indo-Gangetic Plains of South Asia, the quadruple challenges of deteriorating soil quality, declining groundwater, energy shortages, and diminishing farm profitability threaten sustainability of conventional till (CT)-based cereal production systems. A 5-year study was conducted to evaluate the effect of conservation agriculture (CA)-based management (tillage, crop establishment, residue management, and system intensification through mungbean integration) on energy budget, water productivity, and economic profitability in cereal (rice-wheat, RW/maize-wheat, MW)-based systems compared with CT-based management. In CA systems, crop residues contributed the maximum (~76%) in total energy input (167,995 MJ ha^-1); however, fertilizer application (nonrenewable energy source) contributed the maximum (43%) in total energy input (47,760 MJ ha^-1) in CT-based systems. CA-based cereal (rice/maize) systems recorded higher net energy and energy-intensiveness (EI) levels of 251% and 300%, respectively, compared with those of the CT-based rice-wheat system (RW/CT) (295,217 MJ ha^-1 and 46.05 MJ USD^-1), irrespective of mungbean integration. MWMb/ZT+R utilized 204% more input energy, which resulted in 14% higher net energy and 229% higher EI compared with RW/CT. CA-based RW and MW systems enhanced the crop productivity by 10 and 16%, water productivity by 56 and 33%, and profitability by 34 and 36%, while saving in irrigation water by 38 and 32%, compared with their respective CT-based systems, respectively. CA-based system improved net energy, crop productivity, and profitability; therefore, it should be outscaled to improve the soil and environmental quality in north-west India.

Re-designing irrigated intensive cereal systems through bundling precision agronomic innovations for transitioning towards agricultural sustainability in North-West India

A study was conducted to design productive, profitable, irrigation water¸ nitrogen and energy use efficient intensive cereal systems (rice-wheat; RW and maize-wheat; MW) in North-West India. Bundling of conservation agriculture (CA) with sub-surface drip irrigation termed as CA⁺ were compared with CA alone and conventional tillage based and flood irrigated RW rotation (farmer’s practice; ScI). In contrast to conventional till RW rotation which consumed 1889 mm ha⁻¹ irrigation water (2-yr mean), CA⁺ system saved 58.4 and 95.5% irrigation water in RW and MW rotations, respectively. CA⁺ practices saved 45.8 and 22.7% of irrigation water in rice and maize, respectively compared to CA with flood irrigation. On a system basis, CA⁺ practices saved 46.7 and 44.7% irrigation water under RW (ScV) and MW (ScVI) systems compared to their respective CA-based systems with flood irrigation (ScIII and ScIV). CA⁺ in RW system recorded 11.2% higher crop productivity and improved irrigation water productivity by 145% and profitability by 29.2% compared to farmers’ practice. Substitution of rice with maize (MW system; ScVI) recorded 19.7% higher productivity, saved 84.5% of irrigation water and increased net returns by 48.9% compared to farmer’s practice. CA⁺ RW and MW system improved energy productivity by 75 and 169% and partial factor productivity of N by 44.6 and 49.6%, respectively compared to ScI. The sub-surface drip irrigation system saved the fertilizer N by 20% under CA systems. CA⁺ in RW and MW systems recorded ~13 and 5% (2-yr mean) higher profitability with 80% subsidy on installing sub-surface drip irrigation system and similar profitability without subsidy scenario compared with their respective flood irrigated CA-based systems.

Fe-exchanged nano-bentonite outperforms Fe3O4 nanoparticles in removing nitrate and bicarbonate from wastewater

Nitrate (NO₃^-) and bicarbonate (HCO₃^-) are harmful for the water quality and can potentially create negative impacts to aquatic organisms, crops and humans. This study deals with the removal of NO₃^- and HCO₃^- from contaminated wastewater using Fe-exchanged nano-bentonite and Fe₃O₄ nanoparticles. X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, surface area measurement and particle size analysis revealed that the adsorbents fall under the nano-scale size range with high specific surface area, and Fe was successfully exchanged in the nano-bentonite clay. The kinetics of adsorption was well defined by pseudo-first order and pseudo-second order kinetic models for both NO₃^- and HCO₃^-. The Fe-exchanged nano-bentonite was a better performing adsorbent of the oxyanions than Fe₃O₄ nanoparticles. According to the Sips isothermal model, the Fe-exchanged nano-bentonite exhibited the highest NO₃^- and HCO₃^- adsorption potential of 64.76 mg g^-1 and 9.73 meq g^-1, respectively, while the respective values for Fe₃O₄ nanoparticles were 49.90 mg g^-1 and 3.07 meq g^-1. Thus, inexpensiveness and easy preparation process of Fe-exchanged nano-bentonite make it attractive for NO₃^- and HCO₃^- removal from contaminated wastewater with significant environmental and economic benefits.

Differential response of Indian mustard (Brassica juncea L., Czern and Coss) under salinity: photosynthetic traits and gene expression

To explore the effect of salt stress on photosynthetic traits and gene expression in Indian mustard, four genotypes CS 54 (national check for salinity), CS 52-SPS-1-2012 (salt tolerant mutant), CS 614-4-1-4-100-13 (salt sensitive mutant) and Pusa bold (high yielding variety) were evaluated under irrigation water salinity (ECiw 12, and 15 dS m-1). Results suggest genotype CS 52-SPS-1-2012 followed by CS 54 performed better under imposed salt stress due to differential regulation of Na+ accumulation in the roots and main stem, restriction of Na+ influx from root to shoot, maintaining higher net photosynthetic traits under saline stress compared to CS 614-4-1-4-100-13 and Pusa bold. Further, overexpression of antiporters (SOS1, SOS2, SOS3, ENH1 and NHX1) and antioxidant (APX1, APX4, DHAR1 and MDHAR) genes in salt tolerant genotypes CS 52-SPS-1-2012 and CS 54 demonstrated their significant role in imparting salt tolerance in Indian mustard.

Differential expression of salt-responsive genes to salinity stress in salt-tolerant and salt-sensitive rice (Oryza sativa L.) at seedling stage

The understanding of physio-biochemical and molecular attributes along with morphological traits contributing to the salinity tolerance is important for developing salt-tolerant rice (Oryza sativa L.) varieties. To explore these facts, rice genotypes CSR10 and MI48 with contrasting salt tolerance were characterized under salt stress (control, 75 and 150 mM NaCl) conditions. CSR10 expressed higher rate of physio-biochemical parameters, maintained lower Na/K ratio in shoots, and restricted Na translocation from roots to shoots than MI48. The higher expression of genes related to the osmotic module (DREB2A and LEA3) and ionic module (HKT2;1 and SOS1) in roots of CSR10 suppresses the stress, enhances electrolyte leakage, promotes the higher compatible solute accumulation, and maintains cellular ionic homeostasis leading to better salt stress tolerance than MI48. This study further adds on the importance of these genes in salt tolerance by comparing their behaviour in contrasting rice genotypes and utilizing specific marker to identify salinity-tolerant accessions/donors among germplasm; overexpression of these genes which accelerate the selection procedure precisely has been shown.

Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains

In Indo-Gangetic plains (IGP) of India, natural resources (soil, water, and environment) are degrading under the conventional-till (CT)-based management practices in rice-wheat cropping system. A long-term field experiment was conducted to understand the soil bacterial diversity and abundance under different sets of management scenarios (Sc). The study comprised of four scenarios, namely, -Sc.I CT-based rice-wheat system (farmers' practice); Sc.II, partial conservation agriculture (CA) based in which rice is under CT-wheat and mungbean under zero-tillage (ZT); Sc.III, full CA-based in which rice-wheat-mungbean are under ZT and Sc.IV, where maize-wheat-mungbean are under ZT. These scenarios varied in cropping system, tillage, and crop residue management practices. Using Illumina MiSeq sequencing technology, the variable regions V3-V4 of 16S rRNA were sequenced and the obtained reads were analyzed to study the diversity patterns in the scenarios. Results showed the presence of 53 bacterial phyla across scenarios. The predominant phyla in all scenarios were Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes which accounted for more than 70% of the identified phyla. However, the rice-based systems (Sc.I, Sc.II, and Sc.III) were dominated by phylum Proteobacteria; however, maize-based system (Sc.IV) was dominated by Acidobacteria. The class DA052 and Acidobacteriia of Acidobacteria and Bacteroidetes of Bacteroidia were exceptionally higher in Sc.IV. Shannon diversity index was 8.8% higher in Sc.I, 7.5% in Sc.II, and 2.7% in Sc.III compared to Sc.IV. The findings revealed that soil bacterial diversity and abundance are influenced by agricultural management practices as bacterial diversity under full CA-based management systems (Sc.III and Sc.IV) was lower when compared to farmer's practice (Sc.I) and partial CA (Sc.II) scenarios.

Can productivity and profitability be enhanced in intensively managed cereal systems while reducing the environmental footprint of production? Assessing sustainable intensification options in the breadbasket of India

In the most productive area of the Indo-Gangetic Plains in Northwest India where high yields of rice and wheat are commonplace, a medium-term cropping system trial was conducted in Haryana State. The goal of the study was to identify integrated management options for further improving productivity and profitability while rationalizing resource use and reducing environmental externalities (i.e., "sustainable intensification", SI) by drawing on the principles of diversification, precision management, and conservation agriculture. Four scenarios were evaluated: Scenario 1 - "business-as-usual" [conventional puddled transplanted rice (PTR) followed by (fb) conventional-till wheat]; Scenario 2 - reduced tillage with opportunistic diversification and precision resource management [PTR fb zero-till (ZT) wheat fb ZT mungbean]; Scenario 3 - ZT for all crops with opportunistic diversification and precision resource management [ZT direct-seeded rice (ZT-DSR) fb ZT wheat fb ZT mungbean]; and Scenario 4 - ZT for all crops with strategic diversification and precision resource management [ZT maize fb ZT wheat fb ZT mungbean]. Results of this five-year study strongly suggest that, compared with business-as-usual practices, SI strategies that incorporate multi-objective yield, economic, and environmental criteria can be more productive when used in these production environments. For Scenarios 2, 3, and 4, system-level increases in productivity (10-17%) and profitability (24-50%) were observed while using less irrigation water (15-71% reduction) and energy (17-47% reduction), leading to 15-30% lower global warming potential (GWP), with the ranges reflecting the implications of specific innovations. Scenario 3, where early wheat sowing was combined with ZT along with no puddling during the rice phase, resulted in a 13% gain in wheat yield compared with Scenario 2. A similar gain in wheat yield was observed in Scenario 4 vis-à-vis Scenario 2. Compared to Scenario 1, wheat yields in Scenarios 3 and 4 were 15-17% higher, whereas, in Scenario 2, yield was either similar in normal years or higher in warmer years. During the rainy (kharif) season, ZT-DSR provided yields similar to or higher than those of PTR in the first three years and lower (11-30%) in Years 4 and 5, a result that provides a note of caution for interpreting technology performance through short-term trials or simply averaging results over several years. The resource use and economic and environmental advantages of DSR were more stable through time, including reductions in irrigation water (22-40%), production cost (11-17%), energy inputs (13-34%), and total GWP (14-32%). The integration of "best practices" in PTR in Scenario 2 resulted in reductions of 24% in irrigation water and 21% in GWP, with a positive impact on yield (0.9 t/ha) and profitability compared to conventional PTR, demonstrating the power of simple management changes to generate improved SI outcomes. When ZT maize was used as a diversification option instead of rice in Scenario 4, reductions in resource use jumped to 82-89% for irrigation water and 49-66% for energy inputs, with 13-40% lower GWP, similar or higher rice equivalent yield, and higher profitability (27-73%) in comparison to the rice-based scenarios. Despite these advantages, maize value chains are not robust in this part of India and public procurement is absent. Results do demonstrate that transformative opportunities exist to break the cycle of stagnating yields and inefficient resource use in the most productive cereal-based cropping systems of South Asia. However, these SI entry points need to be placed in the context of the major drivers of change in the region, including market conditions, risks, and declining labor availability, and matching with the needs and interests of different types of farmers.

Constitutive expression of Brassica juncea annexin, AnnBj2 confers salt tolerance and glucose and ABA insensitivity in mustard transgenic plants

Annexins belong to a plasma membrane binding (in a calcium dependent manner), multi-gene family of proteins, which play ameliorating roles in biotic and abiotic stresses. The expression of annexin AnnBj2 of Indian mustard is tissue specific with higher expression in roots and under treatments with sodium chloride and abscisic acid (ABA) at seedling stage. The effect of constitutive expression of AnnBj2 in mustard was analyzed in detail. AnnBj2 OE (over expression) plants exhibited insensitivity to ABA, glucose and sodium chloride. The insensitivity/tolerance of the transgenic plants was associated with enhanced total chlorophylls, relative water content, proline, calcium and potassium with reduced thiobarbituric acid reactive substances and sodium ion accumulation. The altered ABA insensitivity of AnnBj2 OE lines is linked to downregulation of ABI4 and ABI5 transcription factors and upregulation of ABA catabolic gene CYP707A2. Furthermore, we found that overexpression of AnnBj2 upregulated the expression of ABA-dependent RAB18 and ABA-independent DREB2B stress marker genes suggesting that the tolerance phenotype exhibited by AnnBj2 OE lines is probably controlled by both ABA-dependent and -independent mechanisms.

Identification of mega-environments and rice genotypes for general and specific adaptation to saline and alkaline stresses in India

In the present study, a total of 53 promising salt-tolerant genotypes were tested across 18 salt-affected diverse locations for three years. An attempt was made to identify ideal test locations and mega-environments using GGE biplot analysis. The CSSRI sodic environment was the most discriminating location in individual years as well as over the years and could be used to screen out unstable and salt-sensitive genotypes. Genotypes CSR36, CSR-2K-219, and CSR-2K-262 were found ideal across years. Overall, Genotypes CSR-2K-219, CSR-2K-262, and CSR-2K-242 were found superior and stable among all genotypes with higher mean yields. Different sets of genotypes emerged as winners in saline soils but not in sodic soils; however, Genotype CSR-2K-262 was the only genotype that was best under both saline and alkaline environments over the years. The lack of repeatable associations among locations and repeatable mega-environment groupings indicated the complexity of soil salinity. Hence, a multi-location and multi-year evaluation is indispensable for evaluating the test sites as well as identifying genotypes with consistently specific and wider adaptation to particular agro-climatic zones. The genotypes identified in the present study could be used for commercial cultivation across edaphically challenged areas for sustainable production.

Effect of salinity and use of stress indices of morphological and physiological traits at the seedling stage in rice

Rice (Oryza sativa L.) is the most important cereal crop and a major staple food for majority of the human populations worldwide. Rice crop is sensitive to salinity. In spite of large number of studies on salinity tolerance of rice, our knowledge on the overall effect of salinity on rice seedling growth is limited. Improvement in salt tolerance of crop plants remains indescribable, largely due to the fact that salinity is a complex trait which affects almost every aspect of the physiology, biochemistry and genomics of plants. The present investigation was conducted to establish the relationship between various morphological, physiological traits and stress indices. A set of 131 rice accessions was evaluated in two levels namely, non-stress (EC ~ 1.2 dS/m) and saline stress (EC ~ 10 dS/m) in hydroponics at seedling stage. Root length and shoot lengths were reduced by 52 and 50%, respectively in saline stress compared to non-stress conditions. There was a significant correlation between various morphological and physiological parameters in non-saline in addition to saline stress as well as non-stress. The effect of the increased Na+ concentration in the medium is detrimental to root length and shoot length as observed by reduction in root length and a concomitant reduction in shoot length. Increased concentration of Na+ led to augmented Na+/K+ ratio with increased stress in the medium and decreased expression of traits. A significant positive correlation (r=0.60) was noticed between stress tolerance index (STI) of root and shoot length. The stress susceptibility index (SSI) for root length was expressed significant positive correlation with SSI for shoot length (r=0.43). SSI for K+ content was registered significant negative correlation with STI for Na+ content (r=-0.43). The three accessions namely, IC 545004, IC 545486 and IC 545215 were found to be the best performers adjudged on the morphological and physiological criteria in saline stress situation. These three rice accessions could be used as a donor parent or for genotypic studies in future breeding programs.

Determination of minimum inhibitory concentrations of itraconazole, terbinafine and ketoconazole against dermatophyte species by broth microdilution method

PURPOSE

Various antifungal agents both topical and systemic have been introduced into clinical practice for effectively treating dermatophytic conditions. Dermatophytosis is the infection of keratinised tissues caused by fungal species of genera Trichophyton, Epidermophyton and Microsporum, commonly known as dermatophytes affecting 20-25% of the world's population. The present study aims at determining the susceptibility patterns of dermatophyte species recovered from superficial mycoses of human patients in Himachal Pradesh to antifungal agents; itraconazole, terbinafine and ketoconazole. The study also aims at determining the minimum inhibitory concentrations (MICs) of these agents following the recommended protocol of Clinical and Laboratory Standards Institute (CLSI) (M38-A2).

METHODOLOGY

A total of 53 isolates of dermatophytes (T. mentagrophyte-34 in no., T. rubrum-18 and M. gypseum-1) recovered from the superficial mycoses were examined. Broth microdilution method M38-A2 approved protocol of CLSI (2008) for filamentous fungi was followed for determining the susceptibility of dermatophyte species.

RESULTS

T. mentagrophyte isolates were found more susceptible to both itraconazole and ketoconazole as compared to terbinafine (MIC50: 0.125 µg/ml for itraconazole, 0.0625 µg/ml for ketoconazole and 0.5 µg/ml for terbinafine). Three isolates of T. mentagrophytes (VBS-5, VBSo-3 and VBSo-73) and one isolate of T. rubrum (VBPo-9) had higher MIC values of itraconazole (1 µg/ml). Similarly, the higher MIC values of ketoconazole were observed in case of only three isolates of T. mentagrophyte (VBSo-30 = 2 µg/ml; VBSo-44, VBM-2 = 1 µg/ml). The comparative analysis of the three antifungal drugs based on t-test revealed that 'itraconazole and terbinafine' and 'terbinafine and ketoconazole' were found independent based on the P < 0.005 in case of T. mentagrophyte isolates. In case of T. rubrum, the similarity existed between MIC values of 'itraconazole and ketoconazole' and 'terbinafine and ketoconazole'.

CONCLUSION

The MIC values observed in the present study based on standard protocol M38-A2 of CLSI 2008 might serve as reference for further studies covering large number of isolates from different geographic regions of the state. Such studies might reflect on the acquisition of drug resistance among isolates of dermatophyte species based on MIC values.

Degradation kinetics of bioactive components, antioxidant activity, colour and textural properties of selected vegetables during blanching

Bioactive components of fruit and vegetables play an important role in scavenging free radicals and protect the body from degenerative diseases. A kinetic study was conducted to quantify the losses occurring in bioactive components, antioxidant activity and changes in colour and firmness of four commonly used vegetables (beetroot, green pea, eggplant and green pepper) during heat treatment (70-90 °C). The study revealed that logistic model can predict the variation in bioactive components and antioxidant activity with higher R² and lower root mean square error (RMSE) as compared to first order model due to logarithmic reduction in these properties in the beginning of the process itself. However zero and first order kinetic models were found suitable to predict the changes occurring in colour and firmness respectively during blanching. D, z value, activation energy (E_a), activation enthalpy and entropy were calculated for all measured parameters for selected vegetables in the temperature range of 70-90 °C. These finding would be useful in designing thermal processes and related calculations for these vegetables.

Agronomic improvements can make future cereal systems in South Asia far more productive and result in a lower environmental footprint

South Asian countries will have to double their food production by 2050 while using resources more efficiently and minimizing environmental problems. Transformative management approaches and technology solutions will be required in the major grain-producing areas that provide the basis for future food and nutrition security. This study was conducted in four locations representing major food production systems of densely populated regions of South Asia. Novel production-scale research platforms were established to assess and optimize three futuristic cropping systems and management scenarios (S2, S3, S4) in comparison with current management (S1). With best agronomic management practices (BMPs), including conservation agriculture (CA) and cropping system diversification, the productivity of rice- and wheat-based cropping systems of South Asia increased substantially, whereas the global warming potential intensity (GWPi) decreased. Positive economic returns and less use of water, labor, nitrogen, and fossil fuel energy per unit food produced were achieved. In comparison with S1, S4, in which BMPs, CA and crop diversification were implemented in the most integrated manner, achieved 54% higher grain energy yield with a 104% increase in economic returns, 35% lower total water input, and a 43% lower GWPi. Conservation agriculture practices were most suitable for intensifying as well as diversifying wheat-rice rotations, but less so for rice-rice systems. This finding also highlights the need for characterizing areas suitable for CA and subsequent technology targeting. A comprehensive baseline dataset generated in this study will allow the prediction of extending benefits to a larger scale.

From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network

Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.

Studies on Osmo-air dehydration of different Indian apricot (Prunus armeniaca L.) cultivars

Suitability of seven cultivars of apricot viz. New Castle, Kaisha, Royal, Suffaida, Nari, Kullu (Local) and Chulli (wild apricot) was evaluated for dehydration. Osmotic dehydration of fruits consisting of dipping prepared fruits in 70° Brix sucrose syrup containing 2,000 ppm potassium metabisulphite (KMS) for 24 h followed by cabinet air drying (55 °C) to desired moisture (20 ± 0.5 %) gave better dried product with good colour and appeal. Dried whole or halved fruits after removal of stones were preferred over whole fruits with stones with respect to appearance, texture and overall acceptability. Among different cultivars of apricot; cv. Kaisha followed by New Castle were found better with respect to yield as well as quality of dried product. Further, the quality of the osmo-air dried wild apricot fruits was found statistically at par with the quality of the osmo-air dried product obtained from cultivated apricots. Therefore, wild apricot fruits can also be utilized for preparation of acceptable quality of dried product.

Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.

A structural insight into hydroxamic acid based histone deacetylase inhibitors for the presence of anticancer activity

Histone deacetylase inhibitors (HDACi) have been actively explored as anti-cancer agents due to their ability to prevent deacetylation of histones, resulting in uncoiling of chromatin and stimulation of a range of genes associated in the regulation of cell survival, proliferation, differentiation and apoptosis. During the past several years, many HDACi have entered pre-clinical or clinical research as anti-cancer agents with satisfying results. Out of these, more than 8 novel hydroxamic acid based HDACi i.e., belinostat, abexinostat, SB939, resminostat, givinostat, quisinostat, pentobinostat, CUDC-101 are in clinical trials and one of the drug vorinostat (SAHA) has been approved by US FDA for cutaneous T-cell lymphoma (CTCL). It is clear from the plethora of new molecules and the encouraging results from clinical trials that this class of HDAC inhibitors hold a great deal of promise for the treatment of a variety of cancers. In this review, we classified the hydroxamic acid based HDACi on the basis of their structural features into saturated, unsaturated, branched, un-branched and 5, 6-membered cyclic ring linker present between zinc binding group and connecting unit. The present article enlists reports on hydroxamic acid based HDACi designed and developed using concepts of medicinal chemistry, demonstrating that hydroxamate derivatives represent a versatile class of compounds leading to novel imaging and therapeutic agents. This article will also provide a complete insight into various structural modifications required for optimum anticancer activity.

Development and use of molecular markers: past and present

Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.

Further evidence that a terminal drought tolerance QTL of pearl millet is associated with reduced salt uptake

Earlier, we established that a major drought tolerance QTL on linkage group 2 of pearl millet is also associated with reduced salt uptake and enhanced growth under salt stress. Present study was undertaken to re-assess the performance of drought tolerant (PRLT 2/89-33) and drought sensitive (H 77/833-2) parents along with two QTL-NILs (ICMR 01029 and ICMR 01040), under salinity stress specifically imposed during post-flowering growth stages when plants had developed their ion sinks in full. Time course changes in ionic accumulation and their compartmentalization in different plant parts was studied, specifically to monitor and capture changes conferred by the two alleles at this QTL, at small intervals. Amongst different plant parts, higher accumulation of toxic ion Na+ was recorded in roots. Further, the Na+ concentration in roots of the testcross hybrid of the drought-sensitive parent (H 77/833-2) reached its maximum at ECiw 15 dS m-1 within 24 h after salinity imposition, whereas it continued to increase with time in the testcross hybrids of the drought tolerant parent PRLT 2/89-33 as well as those of its QTL-NILs (ICMR 01029 and ICMR 01004) and reached at its maximum at 120 h stage. Comparison of differential distribution of toxic ions in individual leaves revealed that Na+ ions were not uniformly distributed in the leaves of the drought-tolerant parent and drought-tolerant QTL-NILs; but accumulated preferentially in the older leaves, whereas the hybrid of the drought-sensitive parent showed significantly higher Na+ concentration in all main stem leaves irrespective of their age. Dynamics of chlorophyll and proline concentration variation studied under salt stress at late flowering stages revealed a greater reduction, almost twice, in both leaf chlorophyll and proline concentrations in younger leaves in the hybrids of the sensitive parent as compared to the tolerant parent and QTL NILs. Imposition of salinity stress even at flowering stage affected the yield performance in pearl millet, wherein higher yield was recorded in drought tolerant parent and the two QTL-NILs compared to drought sensitive parent.

Assessing the performance of the photo-acoustic infrared gas monitor for measuring CO(2), N(2)O, and CH(4) fluxes in two major cereal rotations

Rapid, precise, and globally comparable methods for monitoring greenhouse gas (GHG) fluxes are required for accurate GHG inventories from different cropping systems and management practices. Manual gas sampling followed by gas chromatography (GC) is widely used for measuring GHG fluxes in agricultural fields, but is laborious and time-consuming. The photo-acoustic infrared gas monitoring system (PAS) with on-line gas sampling is an attractive option, although it has not been evaluated for measuring GHG fluxes in cereals in general and rice in particular. We compared N2 O, CO2 , and CH4 fluxes measured by GC and PAS from agricultural fields under the rice-wheat and maize-wheat systems during the wheat (winter), and maize/rice (monsoon) seasons in Haryana, India. All the PAS readings were corrected for baseline drifts over time and PAS-CH4 (PCH4 ) readings in flooded rice were corrected for water vapor interferences. The PCH4 readings in ambient air increased by 2.3 ppm for every 1000 mg cm(-3) increase in water vapor. The daily CO2 , N2 O, and CH4 fluxes measured by GC and PAS from the same chamber were not different in 93-98% of all the measurements made but the PAS exhibited greater precision for estimates of CO2 and N2 O fluxes in wheat and maize, and lower precision for CH4 flux in rice, than GC. The seasonal GC- and PAS-N2 O (PN2 O) fluxes in wheat and maize were not different but the PAS-CO2 (PCO2 ) flux in wheat was 14-39% higher than that of GC. In flooded rice, the seasonal PCH4 and PN2 O fluxes across N levels were higher than those of GC-CH4 and GC-N2 O fluxes by about 2- and 4fold, respectively. The PAS (i) proved to be a suitable alternative to GC for N2 O and CO2 flux measurements in wheat, and (ii) showed potential for obtaining accurate measurements of CH4 fluxes in flooded rice after making correction for changes in humidity.

New insights into chemistry and anti-infective potential of triazole scaffold

Research and development for novel substances possessing anti-infective activity have attracted considerable attention due to the escalating resistance towards conventional antibiotics. Therefore, the discovery and development of effective antimicrobial drugs with novel mechanism of action have become an insistent task for infectious diseases research programs. Triazole scaffold has been consistently rewarded as a promising versatile lead molecule with a pivotal position in modern medicinal chemistry. The literature reveals that this heterocyclic moiety has drawn attention of the chemists, pharmacologists, microbiologists and other researchers owing to its indomitable biological potential as anti-infective agents. The present communication is a cogent attempt to review the chemistry and antimicrobial activities of triazole derivatives reported in recent scientific literature. The biological profiles of these new triazole derivatives represent a fruitful matrix for further development as promising and superior anti-infective medicinal agents.

Formulation and acceptability of foam mat dried seabuckthorn (Hippophae salicifolia) leather

Technology for utilization of seabuckthorn berries for preparation of fruit leather/bar was optimized by modifying the foam mat drying technique. The conversion of seabuckthorn juice/pulp into foam was standardized by whipping the pulp after addition of CMC @ 0-3% at 5 °C and drying the resultant foam in dehydrator (55 ± 2 °C) to a moisture content of about 12-14%. The fruit bar prepared from sulphited juice/pulp wrapped in a butter paper followed by packing in polyethylene pouches (20 g) and stored at ambient temperature (14.6-26.1 °C) experienced least changes in quality attributes like ascorbic acid (1045.7 mg/100 g vs 997.5 mg/100 g) and carotenoids (80.4 mg/100 g vs 72.3 mg/100 g) as compared to the leather made from the unsulphited pulp. Storage studies indicate that fruit bars are mildly hygroscopic (0.46-0.65) and can be stored within the RH of 46-65% at room temperature.

Voriconazole-refractory fungal infection of phacoemulsification tunnel

A 44-year-old man presented 28 days after cataract surgery (phacoemulsification) in right eye with multiple pinpoint infiltrates in posterior stroma at cataract surgery wound site. Visual acuity was 20/60. Corneal scraping from the floor of the corneal tunnel revealed fungus which was later identified to be Aspergillus flavus. The patient was started on oral voriconazole 200 mg twice daily and topical voriconazole 1% every hour. Two intracameral injections of voriconazole (50 micrograms/ 0.1 ml) were given 72 h apart, five days after starting initial therapy. Infiltrates increased in size and density in spite of 20 days of voriconazole therapy. Full-thickness patch graft was done to arrest progressive necrosis. Four months after surgery, patient had 20/60 best-corrected visual acuity. There was no recurrence in one-year follow-up. Present case illustrates the therapeutic challenge in fungal tunnel infections and possibility of voriconazole-resistant Aspergillus species.

Utilization of wild apricot kernel press cake for extraction of protein isolate

The kernels of apricot (Prunus armeniaca) stones are utilized for extraction of oil. The press cake left after extraction of oil was evaluated for preparation of protein isolate for its use in food supplementation. The apricot kernels contained 45-50% oil, 23.6-26.2% protein, 4.2% ash, 5.42% crude fibre, 8.2% carbohydrates and 90 mg HCN/100 g kernels, while press cake obtained after oil extraction contained 34.5% crude protein, which can be utilized for preparation of protein isolates. The method standardized for extraction of protein isolate broadly consisted of boiling the press cake with water in 1:20 (w/v) ratio for 1 h, raising pH to 8 and stirring for a few min followed by filtration, coagulation at pH 4 prior to sieving and pressing of coagulant for overnight and drying followed by grinding which resulted in extraction of about 71.3% of the protein contained in the press cake. The protein isolate contained 68.8% protein, 6.4% crude fat, 0.8% ash, 2.2% crude fibre and 12.7% carbohydrates. Thus the apricot kernel press cake can be utilized for preparation of protein isolate to improve the nutritional status of many food formulations.

Bioefficacy of insecticides against Leucinodes orbonalis on brinjal

Studies on bioefficacy of insecticides against brinjal shoot and fruit borer, Leucinodes orbonalis Guenee on brinjal were carried out during 2007 and 2008. The results on bioefficacy of insecticides showed that in terms of shoot infestation, emamectin benzoate (0.002%), endosulfan (0.05%), novaluron (0.01%) and lambda-cyhalothrin (0.004%) were found superior. The total number of drooping shoots was minimum (4.17) in emamectin benzoate followed by endosulfan (6.83) and novaluron (7.00), as compared to spinosad (9.17), deltamethrin (11.67) and Bacillus thuringiensis (13.17). In terms of reduction in fruit infestation, emamectin benzoate (0.002%) was highly effective followed by endosulfan (0.05%), agrospray oil T (0.2%) and spinosad (0.0024%). However, cost benefit ratio was highest in agrospray oil T (0.2%) followed by lambda-cyhalothrin (0.004%), endosulfan (0.05%) and deltamethrin (0.0028%).

Vitamin D receptor gene polymorphism(s) and breast cancer risk in north Indians

BACKGROUND

Vitamin D (1,25-dihydroxyVitamin D3) has shown experimentally anticarcinogenic effects and is thought to protect against breast cancer. The actions of Vitamin D are mediated via the Vitamin D receptor (VDR), and the polymorphisms at 3'UTR region of this gene are associated with the risk and progression of breast carcinoma. The current study is an attempt to examine the association of these variations with breast cancer risk in north Indians.

METHODS

A total of 160 cases and 140 control subjects were studied for the polymorphisms at 3' end of the VDR gene. A polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method and fragment analysis was performed to determine ApaI and TaqI polymorphisms and variable length poly-A microsatellite repeats. Linkage disequilibrium (LD) was calculated for each pair of polymorphisms. Unadjusted and adjusted odds ratios for breast cancer with genotypes comprising the polymorphic sites were calculated to understand their role towards breast cancer susceptibility.

RESULTS

Patient's with long poly-A repeat showed a significant association with disease (chi 2 = 9.52, df = 2, P <or= 0.01). Compared to subjects having two S alleles (SS), odds ratios (and 95% CI) were 0.75 (0.45-1.23) and 2.49 (1.18-5.27) for subjects having genotypes SL and LL, respectively. Among matched pairs (age), the poly-A LL genotype was found significantly associated with increased risk of breast cancer among early-onset cases (P = 0.02). The unconditional logistic regression analysis demonstrated a significant association between grade and LL genotype [(unadjusted odds ratio (95% CI): 4.45 (1.87, 10.63); adjusted odds ratio: 4.66 (1.88, 11.53)]. No significant association was observed for the VDR ApaI (chi 2 = 1.00, df = 2, P = 0.60) and TaqI polymorphism (chi 2 = 0.35, df = 2, P = 0.83). Although, strong LD was not observed among these polymorphic sites, it denies the total equilibrium at the same time. Based on haplotype distribution, the most common one observed among cases and controls was ATS while, genotype AATTLL had shown a significant association with the breast cancer risk (P = 0.02).

CONCLUSIONS

The results indicate that the VDR poly-A polymorphism is significantly associated with breast cancer risk in north Indians especially with early onset disease. Although, ApaI and TaqI did not show any significant association with the disease when analyzed in isolation, but TaqI might modulate the risk associated with L alleles. Further, understanding the functional role of these variants residing on the VDR haplotype associated with disease susceptibility may suggest novel approaches for breast cancer prevention and therapy.

3D-QSAR CoMFA study of some Heteroarylpyrroles as Possible Anticandida Agents

A three dimensional quantitative structure-activity relationship study using the comparative molecular field analysis method was performed on a series of 3-aryl-4-[α-(1H-imidazol-1-yl) aryl methyl] pyrroles for their anticandida activity. This study was performed using 40 compounds, for which comparative molecular field analysis models were developed using a training set of 33 compounds. Database alignment of all 33 compounds was carried out by root-mean-square fit of atoms and field fit of the steric and electrostatic molecular fields. The resulting database was analyzed by partial least squares analysis with cross-validation; leave one out and no validation to extract optimum number of components. The analysis was then repeated with bootstrapping to generate the quantitative structure-activity relationship models. The predictive ability of comparative molecular field analysis model was evaluated by using a test set of 7 compounds. The 3D- quantitative structure-activity relationship model demonstrated a good fit, having r² value of 0.964 and a cross validated coefficient r² value as 0.598. Further comparison of the coefficient contour maps with the steric and electrostatic properties of the receptor has shown a high level of compatibility and good predictive capability.

UgMicroSatdb: database for mining microsatellites from unigenes

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.

Biased distribution of microsatellite motifs in the rice genome

Microsatellites are useful tools to study the extent of divergence between two taxonomic groups that show high sequence similarity. We have compared microsatellite distribution to illustrate genetic variation between the two rice genomes, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. Microsatellite distribution proved to be non random as certain regions of very high microsatellite density have been identified. Microsatellite density in the subspecies japonica was computed marginally higher than in the subspecies indica in the genomic regions compared between the two subspecies. Unexpectedly high microsatellite densities were observed in 5'-untranslated regions of genes. These regions also displayed a clear motif bias. Some of the longest microsatellite repeats were found in intron sequences. Frequency, as well as motif bias was also noted with respect to the association of microsatellites with transposable elements. Microsatellite mutability values were exemplarily estimated for 90 loci by aligning the microsatellite containing regions between the two genomes. Poor rates of finding an orthologue corresponded with high microsatellite mutability in rice. These insights are likely to play a significant role in selecting microsatellite loci to be used in molecular breeding and studying evolutionary dynamics of the two subspecies.

CYP17 gene polymorphism and its association with high-risk north Indian breast cancer patients

A single T > C change at the 5' promoter region of the CYP17 gene is reported to be associated with increased risk of breast cancer. This study evaluates the influence of genetic polymorphism of CYP17 on breast cancer susceptibility. Two hundred and forty-two patients with histopathologically confirmed breast cancer and 212 age-matched controls were included in the present study. Information relating to age at onset of the disease, family history and estrogen receptor status was elicited. Investigation for CYP17 polymorphism was carried out in 106 early onset, 80 late onset and 56 familial cases. The frequencies of two CYP17 alleles were also analyzed in 116 (47.9%) cases with known estrogen receptor (ER) status confirmed immunohistochemically. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to detect the polymorphism, and the genotypes identified were assigned as homozygous wild type (A1A1), heterozygous variant (A1A2), and homozygous variant (A2A2). Associations between the various genotypes in patients and controls were investigated with Fisher's exact test. All the tests were two tailed. The results showed that the frequency of heterozygous and homozygous CYP17 genotype was higher in early onset breast cancer patients (94.3%) than in controls (80.3%), and the difference was significant (P = 0.001). A highly statistically significant increased risk in carriers of homozygous A2 allele was found in young patients (P < or = 0.001) in comparison with patients having late onset condition (P = 0.260). However, no significant association between the genotype and breast cancer risk was observed among women with strong family history. Further, data had showed that patients (80.6%) with at least one A2 allele tended to exhibit ER-independent cell proliferation, although statistical significance could not be established (P = 0.160). The present findings suggest that CYP17 A2 allele gene polymorphism might play a significant role in breast cancer development in young Indian women.

Identification of AFLP markers linked to the male fertility restorer gene of CMS (Moricandia arvensis) Brassica juncea and conversion to SCAR marker

We have developed a cytoplasmic male sterile (CMS) line of Brassica juncea through somatic hybridization with Moricandia arvensis and introgressed the fertility restorer gene into B. juncea. This fertility restorer locus is unique in that it is capable of restoring male fertility to two other alloplasmic CMS systems of B. juncea. As a first step toward cloning of this restorer gene we attempted molecular tagging of the Rf locus using the amplified fragment length polymorphism (AFLP) technique. A BC(1)F(1) population segregating for male sterility/fertility was used for tagging using the bulk segregant analysis method. Out of 64 primer combinations tested in the bulks, 5 combinations gave polymorphic amplification patterns. Further testing of these primers in individual plants showed four amplicons associated with the male fertility trait. Polymorphic amplicons were cloned and used for designing SCAR primers. One of the SCAR primers generated amplicons mostly in the fertile plants. Linkage analysis using MAPMAKER showed two AFLP and one SCAR markers linked to the male fertility gene with a map distance ranging from 0.6 to 2.9 cM. All the markers are located on one side of the Rf locus.

Isolation and characterization of a green tissue-specific promoter from pigeonpea [Cajanus cajan (L.) Millsp.]

Expression of rbcS genes encoding small subunit of rubisco, most abundant protein in green tissue, is regulated by at least three parameters--tissue type, light conditions and stage of development. One of the green tissue-specific promoters of rbcS gene family was isolated from pigeonpea by PCR. Expression of uidA gene encoding beta-glucuronidase in the transgenic tobacco plants under the control of pigeonpea rbcS promoter, clearly showed that this promoter was as strong as pea rbcS3A promoter characterized earlier. Study of the sequence similarity with pea rbcS3A promoter, especially the region (boxes I and III) that is required for rbcS3A expression, showed more than 50% divergence. In contrast, pigeonpea promoter sequence isolated in the present study was more similar to that of spinach and rice rbcS promoters.

Virus-induced silencing of WIPK and SIPK genes reduces resistance to a bacterial pathogen, but has no effect on the INF1-induced hypersensitive response (HR) in Nicotiana benthamiana

Activation of two mitogen-activated protein kinases (MAPKs), wound-induced protein kinase (WIPK) and salicylic acid-induced protein kinase (SIPK), is one of the earliest responses that occur in tobacco plants that have been wounded, treated with pathogen-derived elicitors or challenged with avirulent pathogens. We isolated cDNAs for these MAPKs (NbWIPKand NbSIPK) from Nicotiana benthamiana. The function of NbWIPK and NbSIPK in mediating the hypersensitive response (HR) triggered by infiltration with INF1 protein (the major elicitin secreted by Phytophthora infestans), and the defense response to an incompatible bacterial pathogen (Pseudomonas cichorii), was investigated by employing virus-induced gene silencing (VIGS) to inhibit expression of the WIPK and SIPK genes in N. benthamiana. Silencing of WIPK or SIPK, or both genes simultaneously, resulted in reduced resistance to P. cichorii, but no change was observed in the timing or extent of HR development after treatment with INF1.

Anaerobiosis induced virulence of Salmonella typhi

BACKGROUND & OBJECTIVES

Anaerobic conditions are frequently encountered by pathogens invading the gastrointestinal tract due to low/limiting oxygen conditions prevalent in the small intestine. This anaerobic stress has been suggested to enhance the virulence of gut pathogens. In the present study, we examined the effect of anaerobiosis on the virulence of Salmonella Typhi, a Gram negative bacteria which invades through the gut mucosa and is responsible for typhoid fever.

METHODS

Salmonella Typhi (ty2) was cultured in aerobic and anaerobic conditions to compare its virulence by rabbit ileal loop assay, hydrophobicity assay, expression of outer membrane proteins (OMPs) and antioxidant enzymes assay.

RESULTS

Anaerobically grown S. Typhi showed significantly higher cell surface hydrophobicity as compared to aerobic bacteria. In vivo toxin production by rabbit ileal loop assay also showed significantly higher fluid accumulation with anaerobic S. Typhi. Expression of OMPs in anaerobic S. Typhi showed a distinct induction of five outer membrane proteins. We observed that exposure of anaerobic S. Typhi to aerobic conditions induced significantly higher level of antioxidant enzymes like superoxide dismutase (SOD) and catalase.

INTERPRETATION & CONCLUSION

Our results suggest that exposure of S. Typhi to anaerobic conditions enhances its virulence.

Graphite furnace-atomic absorption spectrophotometric determination of palladium in soil

A new and sensitive procedure for the graphite furnace-atomic absorption spectrophotometric (GF-AAS) determination of Pd in soil at nanogram level is described. The method is based on prior separation and enrichment of the metal as Pd(II)-SnCl3- -N-butylacetamide (BAA) complex into 1-pentanol (PN) by solvent extraction method. The value of the molar absorptivity of the complex in three solvents, i.e. ethyl acetate, 1-pentanol, chloroform, lie in the range of (0.70-2.75) x 10(4) L mol(-1) cm(-1) at lambda(max) 360-440 nm. The metal could be enriched into organic solvent, i.e. PN, up to 10-folds. The sensitivity (A = 0.0044) of the method in the term of the peak height was 0.5 ng Pd/mL of the aqueous solution at an enrichment factor (EF) of 5. Optimization of analytical variables during enrichment and GF-AAS determination of the metal are discussed. The method has been applied for the analysis of Pd to soil samples derived from roads and highways in Germany.

ECOLOGY OF COMBAT FATIGUE AMONG TROOPS ENGAGED IN COUNTERINSURGENCY OPERATIONS

A two staged study design combining features of cohort and cross sectional methods, was used to ascertain incidence of combat fatigue in troops deployed in counterinsurgency operations and study their living conditions as compared to troops deployed in similar terrain and climate but not taking part in counterinsurgency operations. Psychiatric morbidity both outdoor and indoor which was used as a surrogate measure for combat fatigue was almost three times higher for troops deployed in counterinsurgency operations (RR=3.21 and 3.11 respectively). Troops deployed in counterinsurgency operations also had significantly higher levels of dissatisfaction regarding medical and physical facilities like accommodation, food, water, clothing and recreational facilities as compared to troops not deployed. However there were no significant differences in posting and leave policies between the two groups. Troops in counterinsurgency however, did feel more often than other troops that their work was not appreciated. They also showed higher and significant signs of stress indicators such as use of alcohol, unfavourable response to task, diminished efficiency, frustration, maladjustment, tension, isolation, etc. In view of the study findings better interpersonal communications particularly task appreciation and improvement of medical and physical facilities for troops in CI Ops have been recommended.

Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome

A size-selected genomic library comprising 280,000 colonies and representing approximately 18% of the chickpea genome, was screened for (GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (approximately 75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%-9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P > or = 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome.

The potential of microsatellites for hybridization- and polymerase chain reaction-based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species

The genetic variability in agronomically important chickpea accessions (Cicer arietinum L.) as detected by single-locus restriction fragment length polymorphism (RFLP) probes, random amplified polymorphic DNA (RAPD) and isoenzyme markers, is rather low. Recently, highly polymorphic microsatellites became the markers of choice for linkage mapping and population studies. We are currently following two main strategies to exploit the variability of microsatellites and adjacent sequences for genetic studies in chickpea. (i) In an approach referred to as oligonucleotide fingerprinting, microsatellite-complementary oligonucleotides were employed as multilocus probes for in-gel hybridization. A total of 38 different probes representing di-, tri- and tetranucleotide repeats were used to analyze variability between and within four accessions of C. arietinum. Hybridization signals were obtained with 35 probes. While the abundance and level of polymorphism of different target sequences varied considerably, distinct, intraspecifically informative banding patterns were obtained with the majority of probes and all restriction enzymes tested. No obvious correlation existed between abundance, fingerprint quality, and sequence characteristics of a particular motif. (ii) In a recently developed strategy called microsatellite primed polymerase chain reaction (MP-PCR), microsatellite-complementary oligonucleotides serve as single PCR primers for genomic DNA templates. We tested the general applicability of MP-PCR by amplifying DNA samples from tomato, chickpea and two related annual Cicer species with a variety of di-, tri- and tetranucleotide repeat primers. Most but not all primers generated distinct fingerprint-like banding patterns after agarose gel electrophoresis and ethidium bromide staining of the amplification products. Since the method proved to be sensitive to reaction conditions in a way similar to RAPD analysis, we increased the PCR specificity by the introduction of a modified "touch-down" protocol. In chickpea, touch-down MP-PCR generated highly reproducible banding patterns which predominantly revealed interspecific polymorphisms. The potential of different microsatellite-based strategies for genome analysis in chickpea is discussed.

Abundance and polymorphism of di-, tri-and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.)

The abundance and polymorphism of 38 different simple-sequence repeat motifs was studied in four accessions of cultivated chickpea (Cicer arietinum L.) by in-gel hybridization of synthetic oligonucleotides to genomic DNA digested with 14 different restriction enzymes. Among 38 probes tested, 35 yielded detectable hybridization signals. The abundance and level of polymorphism of the target sequences varied considerably. The probes fell into three broad categories: (1) probes yielding distinct, polymorphic banding patterns; (2) probes yielding distinct, monomorphic banding patterns, and (3) probes yielding blurred patterns, or diffused bands superimposed on a high in lane background. No obvious correlation existed between abundance, fingerprint quality, and the sequence characteristics of a particular motif. Digestion with methyl-sensitive enzymes revealed that simple-sequence motifs are enriched in highly methylated genomic regions. The high level of intraspecific polymorphism detected by oligonucleotide fingerprinting suggests the suitability of simple-sequence repeat probes as molecular markers for genome mapping.

Diagnosis of equid herpesviruses -1 and -4 by polymerase chain reaction

The polymerase chain reaction (PCR) is a sensitive technique used to detect DNA of viral pathogens. We have applied the technique to the detection of Equid herpesviruses-1 and -4 (EHV-1 and EHV-4) DNA within nasopharyngeal swab samples from horses. Ninety-eight samples from suspected field cases and in-contact horses were analysed. The assays were conducted blind and later decoded and compared with virus isolation data. Our results indicate that PCR is a sensitive and rapid technique for the diagnosis of EHV-1 and EHV-4 infection.

Bilateral spontaneous regression of retinoblastoma with dominant transmission

A young man with three patches of regressed retinoblastoma with good visual acuity is described. The other eye was phthisical. Circumstantial evidence suggests that this eye also has a regressed retinoblastoma. The patient's daughter showed histopathologically confirmed well-differentiated retinoblastoma.