Groundwater spring potential zonation using AHP and fuzzy-AHP in Eastern Himalayan region: Papum Pare district, Arunachal Pradesh, India.

In the present study, the groundwater spring potential zone (GSPZ) was identified using an integrated approach of remote sensing (RS) and geographic information system (GIS), analytic hierarchy process (AHP), and fuzzy-AHP based on multicriteria decision-making (MCDM). Thus, ten associated factors with groundwater springs have been considered: slope, drainage density, lineament density, geomorphology, lithology, soil texture, land use and land cover, rainfall, groundwater level, and spring discharge. The analysis output was categorized into low, moderate, and high. The result of the AHP model shows the area under the high potential zone (16.61%), the moderate potential zone (60.42%), and the low potential zone (22.61%). The result of the fuzzy-AHP model shows that the area falls under the high potential zone (30.40%), moderate potential zone (41.29%), and low potential zone (22.61%). The validation results showed fuzzy-AHP with the area under the curve 0.806, which is slightly better than 0.779 of AHP. So, the resulting GSPZ map confirms that the thematic layers used in the study have a significant role in groundwater spring occurrence and distribution. It was recommended that any groundwater spring rejuvenation or protection activities must be implemented in medium to very high potential zones.

Influence of short- and long-term persistence on identification of rainfall temporal trends using different versions of the Mann-Kendall test in Mizoram, Northeast India.

Investigating the temporal dynamics of rainfall in a changing climate, especially in rainfed agriculture regions, is crucial for analyzing climate-induced changes and offering adaptation options. Since Mizoram experiences unfavorable impacts of rain nearly every year, the region rainfall has been altering over the years, and vital climatic activity is becoming uncontrollable. The current study is primarily concerned with the changing trend of rainfall over Mizoram, which includes both short-term persistence (STP) and long-term persistence (LTP) of rainfall in seasonal and annual time series of rainfall overseeing for the period of 25 years of daily average rainfall from 1996 to 2020 collected collectively from the seven stations over the study area of Mizoram. Four different Mann-Kendall method iterations were used to analyze rainfall trends: the original or conventional method (without autocorrelation) (MnKn1), removing lag-1 autocorrelation (trend-free pre-whitening), considering multiple lag autocorrelation (more than lag-1 autocorrelation) (MnKn3), and Hurst coefficient or LTP (MnKn4). In the analysis, the study found that during monsoon, station Lawngtlai (LT) observed the highest rainfall having a Z value of 1.986, increased by 0.466 cm/year, while station Serchhip (SC) observed the lowest rainfall having Z value of -2.282, decreased by -0.163 cm/year. After applying modified MnKn4, we observed LTP of rainfall in winter at station Lawngtlai (LT) with an increasing trend and other stations observing STP in almost all seasons either increasing or decreasing trend. Therefore, possible climate change adaptation measures should be made to optimize rainfall use for various applications for the states of Mizoram.

CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops.

Cereals are the most important food crops and are considered key contributors to global food security. Loss due to abiotic stresses in cereal crops is limiting potential productivity in a significant manner. The primary reasons for abiotic stresses are abrupt temperature, variable rainfall, and declining nutrient status of the soil. Varietal development is the key to sustaining productivity under influence of multiple abiotic stresses and must be studied in context with genomics and molecular breeding. Recently, advances in a plethora of Next Generation Sequencing (NGS) based methods have accelerated the enormous genomic data generation associated with stress-induced transcripts such as microarray, RNAseq, Expressed Sequenced Tag (ESTs), etc. Many databases related to microarray and RNA-seq based transcripts have been developed and profusely utilized. However, an abundant amount of transcripts related to abiotic stresses in various cereal crops arising from EST technology are available but still remain underutilized in absence of a consolidated database. In this study, an attempt has been made with a primary goal to integrate, analyse, and characterise the available resources of ESTs responsive to abiotic stresses in major cereals. The developed CerealESTdb presents a customisable search in two different ways in the form of searchable content for easy access and potential use. This database comprises ESTs from four major cereal crops, namely rice (Oryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolour L.), and maize (Zea mays L.), under a set of abiotic stresses. The current statistics of this cohesive database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1,746 associated metabolic pathways. We anticipate that developed CerealESTdb will be helpful in deciphering the knowledge of complex biological phenomena under abiotic stresses to accelerate the molecular breeding programs towards the development of crop cultivars resilient to abiotic stresses. The CerealESTdb is publically available with the URL http://cabgrid.res.in/CerealESTDb.

The burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population: Results from a statewide sentinel-based population survey in Karnataka, India.

OBJECTIVE: To estimate the burden of active infection and anti-SARS-CoV-2 IgG antibodies in Karnataka, India, and to assess variation across geographical regions and risk groups. METHODS: A cross-sectional survey of 16,416 people covering three risk groups was conducted between 3-16 September 2020 using the state of Karnataka's infrastructure of 290 healthcare facilities across all 30 districts. Participants were further classified into risk subgroups and sampled using stratified sampling. All participants were subjected to simultaneous detection of SARS-CoV-2 IgG using a commercial ELISA kit, SARS-CoV-2 antigen using a rapid antigen detection test (RAT) and reverse transcription-polymerase chain reaction (RT-PCR) for RNA detection. Maximum-likelihood estimation was used for joint estimation of the adjusted IgG, active and total prevalence (either IgG or active or both), while multinomial regression identified predictors. RESULTS: The overall adjusted total prevalence of COVID-19 in Karnataka was 27.7% (95% CI 26.1-29.3), IgG 16.8% (15.5-18.1) and active infection fraction 12.6% (11.5-13.8). The case-to-infection ratio was 1:40 and the infection fatality rate was 0.05%. Influenza-like symptoms or contact with a COVID-19-positive patient were good predictors of active infection. RAT kits had higher sensitivity (68%) in symptomatic people compared with 47% in asymptomatic people. CONCLUSION: This sentinel-based population survey was the first comprehensive survey in India to provide accurate estimates of the COVID-19 burden. The findings provide a reasonable approximation of the population immunity threshold levels. Using existing surveillance platforms coupled with a syndromic approach and sampling framework enabled this model to be replicable.

Multifunctional, fluorescent DNA-derived carbon dots for biomedical applications: bioimaging, luminescent DNA hydrogels, and dopamine detection.

Here, we describe the synthesis of 2-3 nm, hydrophilic, blue fluorescence-emitting carbon dots (C-Dots, made using a DNA precursor) by the hydrothermal route from the gelling concentration of 2% (w/v) DNA. These dots exhibited highly efficient internalization in pathogenic fungal cells, negligible cytotoxicity, good PL stability, and high biocompatibility, thus demonstrating their potential as nanotrackers in microbial studies. Bioimaging was performed using Candida albicans as the representative for microbial pathogens. The novelty of these dots is that they formed fluorescent nanocomposite hydrogels with the same DNA much below the gelation concentration (1% w/v) and the tunable gels possessed strength between 20 and 80 Pa with the corresponding gelation temperature Tgel between 40 to 50 °C. The network density and gelation free energy data supported the superior crosslinking ability of these dots. The as-prepared hydrogels can replace the existing toxic quantum dot-based hydrogels for drug delivery. We also demonstrated the use of a DNA hydrogel-fabricated working electrode (DNA-C-Dot/ITO electrode) for the biosensing of dopamine. Our electrochemical biosensor had a detection limit of 5 × 10-3 mM for dopamine. These multifunctional, fluorescent C-Dots and hydrogel after suitable conjugation or loading with molecules and drugs hold promising potential for further exploitation in bioimaging, targeted drug delivery, wound healing, and biosensing applications.

Effect of organic and inorganic salt environment on the complex coacervation of in situ formed protein nanoparticles and DNA.

Complex coacervation was noticed between in situ formed protein (a primarily hydrophobic Zein protein with pI = 6.2) nanoparticles (size 80-120 nm) and ds-DNA (a high charge density polyanion), in the ionic liquid (IL) solutions of 1-ethyl-3-methyl imidazolium chloride [C2mim][Cl], and 1-octyl-3-methyl imidazolium chloride [C8mim][Cl], in the studied ionic strength range of I = 10-4 to 6 × 10-1 M, which was extended to strong monovalent 1:1 electrolyte (NaCl) to explore the commonality between the organic and inorganic salt (ionic) environment on coacervation. The salt dependent coacervation profile was monitored from the measured turbidity of the interacting solution, and zeta potential, (ζ) and apparent hydrodynamic radius (Rh) of interpolymer complexes, which depicted the following three discernible interaction regimes common to all the salts: (i) Region-I: I = 0.0001-0.01 M, primary binding, (ii) Region-II, I = 0.01-0.1 M, secondary binding, and (iii) Region-III, I = 0.1-0.6 M, saturation binding. The free-energy and the network density calculations favored preferential coacervation in [C2mim][Cl] samples. Nonetheless, commonality in the overall ionic strength dependent coacervation profiles could still be observed.

Solvent hydrophobicity induced complex coacervation of dsDNA and in situ formed zein nanoparticles.

Zein, a predominantly hydrophobic protein, was sustained as a stable dispersion in ethanol-water (80 : 20, % (v/v)) binary solvent at room temperature (25 °C). Addition of aqueous dsDNA solution (1% (w/v)) to the above dispersion prepared with the protein concentration of Czein = 0.01-0.5% (w/v) caused a concomitant change in ethanol content from 14-35% (v/v), which in turn generated zein nanoparticles in situ of size 80-120 nm increasing with water content. The subsequent associative interaction between DNA (polyanion; 2000 bps) and the positively charged zein nanoparticles, (at pH = 4) was driven by Coulombic forces, and by the solvent hydrophobicity due to the ethanol content of the binary solvent. Experimentally, two interesting regions of interaction were observed from turbidity, zeta potential, particle sizing, and viscosity data: (i) for Czein < 0.2% (w/v), zein nanoparticles of size 80 nm bind to dsDNA (primary complex) causing its condensation (apparent hydrodynamic size decreased from ≈2100 to 560 nm), and (ii) for 0.2% < Czein < 0.5% (w/v) larger nanoparticles (>80 nm) were selectively bound to primary complexes to form partially charge neutralized interpolymer soluble complexes (secondary complexes), followed by complex coacervation. During this process, there was depletion of water in the vicinity of the nucleic acid, which was replaced by hydration provided by the ethanol-water binary solvent. Equilibrium coacervate samples were probed for their microstructure by small angle neutron scattering, and for their viscoelastic properties by rheology. The interplay of solvent hydrophobicity, electrostatic interaction, and zein nanoparticle size dependent charge neutralization had a commensurate effect on this hitherto unexplored coacervation phenomenon.

DNA ionogel: Structure and self-assembly.

DNA dissolved in ionic liquid (IL) solution (1-ethyl-3-methylimidazolium chloride, [C2mim][Cl]) showed a transition to the gel phase ([DNA] ≥ 1% (w/v)). The gelation time was 400 s for the 1% [IL] sample which reduced to 260 s for 5% [IL] concentration. Gelation times, obtained from the viscosity and ergodicity breaking from the dynamic structure factor data, were remarkably identical to each other. Correspondingly, the gelation temperature which was ∼60 °C increased to 67 °C with [IL] content. The small angle neutron scattering (SANS) structure factor profile revealed the presence of the following three distinct length scales: (a) mesh size, ξ ≈ 3 ± 0.5 nm for ionogels, and ≈0.73 ± 0.06 nm, for sol; (b) cross-sectional radius of DNA strand, Rc ≈ 1.6 ± 0.1 nm; and (c) the characteristic inter-cluster distance ≈33 ± 5 nm. Physical conformation of the DNA-IL complexes remained close to the Gaussian coil definition. It was observed that without IL, in the sol phase, the system was completely ergodic and did not gel, while on addition of IL a sudden transition to the non-ergodic (arrested) gel phase occurred. This was due to the formation of an amorphous network of DNA-IL complexes preceding gelation. In summary, it is shown that the DNA ionogels can be prepared with a tunable gel strength (27-70 Pa) and gelation temperature (60-67 °C). Further, the relaxation dynamics was found to be hierarchical in IL content of the gel, revealing considerable self-organization.

Design and development of portal for biological database in agriculture.

UNLABELLED: The application of novel and modern techniques in genetic engineering and genomics has resulted in information explosion in genomics. Three major genome databases under International Nucleotide Sequence Database collaboration NCBI, DDBJ and EMBL have been providing a convenient platform for submission of sequences which they share among themselves. Many institutes in India under Indian Council of Agricultural Research have scientists working on biotechnology and bioinformatics research. The various studies conducted by them, generate massive data related to biological information of plants, animals, insects, microbes and fisheries. These scientists are dependent on NCBI, EMBL, DDBJ and other portals for their sequence submissions, analysis and other data mining tasks. Due to various limitations imposed on these sites and the poor connectivity problem prevents them to conduct their studies on these open domain databases. The valued information generated by them needs to be shared by the scientific communities to eliminate the duplication of efforts and expedite their knowledge extended towards new findings. A secured common submission portal system with user-friendly interfaces, integrated help and error checking facilities has been developed in such a way that the database at the backend consists of a union of the items available on the above mentioned databases. Standard database management concepts have been employed for their systematic storage management. Extensive hardware resources in the form of high performance computing facility are being installed for deployment of this portal. AVAILABILITY: http://cabindb.iasri.res.in:8080/sequence_portal/