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Swiftly increasing population and industrial developments of urban areas has accelerated the worsening of the water quality in recent years. Groundwater samples from different locations of the Doon valley, Garhwal Himalaya were analyzed to measure concentrations of six potential toxic elements (PTEs) viz. chromium (Cr), nickel (Ni), arsenic (As), molybdenum (Mo), cadmium (Cd), and lead (Pb) using Inductively Coupled Plasma Mass Spectrometer (ICP-MS) with the aim to study the spatial distribution and associated hazards. In addition, machine learning algorithms have been used for prediction of water quality and identification of influencing PTEs. The results inferred that the mean values (in the units of µg L -1 ) of analyzed PTEs were observed in the order of Mo (1.066) > Ni (0.744) > Pb (0.337) > As (0.186) > Cr (0.180) > Cd (0.026). The levels and computed risks of PTEs were found below the safe limits. The radial basis function neural network (RBF-NN) algorithms showed high level of accuracy in the predictions of heavy metal pollution index (HPI), heavy metal evaluation index (HEI), non-carcinogenic (N-CR) and carcinogenic (CR) parameters with determination coefficient values ranged from 0.912 to 0.976. However, the modified heavy metal pollution index (m-HPI) and contamination index (CI) predictions showed comparatively lower coefficient values as 0.753 and 0.657, respectively. The multilayer perceptron neural network (MLP-NN) demonstrated fluctuation in precision with determination coefficient between 0.167 and 0.954 for the prediction of computed indices (HPI, HEI, CI, m-HPI). In contrast, the proficiency in forecasting of non-carcinogenic and carcinogenic hazards for both sub-groups showcased coefficient values ranged from 0.887 to 0.995. As compared to each other, the radial basis function (RBF) model indicated closer alignments between predicted and actual values for pollution indices, while multilayer perceptron (MLP) model portrayed greater precision in prediction of health risk indices., (© 2024. The Author(s).)

Identifying cancer risk groups by multi-omics has attracted researchers in their quest to find biomarkers from diverse risk-related omics. Stratifying the patients into cancer risk groups using genomics is essential for clinicians for pre-prevention treatment to improve the survival time for patients and identify the appropriate therapy strategies. This study proposes a multi-omics framework that can extract the features from various omics simultaneously. The framework employs autoencoders to learn the non-linear representation of the data and applies tensor analysis for feature learning. Further, the clustering method is used to stratify the patients into multiple cancer risk groups. Several omics were included in the experiments, namely methylation, somatic copy-number variation (SCNV), micro RNA (miRNA) and RNA sequencing (RNAseq) from two cancer types, including Glioma and Breast Invasive Carcinoma from the TCGA dataset. The results of this study are promising, as evidenced by the survival analysis and classification models, which outperformed the state-of-the-art. The patients can be significantly (p-value<0.05) divided into risk groups using extracted latent variables from the fused multi-omics data. The pipeline is open source to help researchers and clinicians identify the patients' risk groups using genomics., (© 2024. The Author(s).)

The agroforestry system is the best option to achieve the net zero carbon emissions target for India. Keeping this view, carbon sequestration and credit potential of gamhar based agroforestry system has been assessed. The experiment was carried out in randomized block design in seven different treatments with five replications. Gamhar tree biomass accumulation was higher in gamhar based agroforestry system compared to sole gamhar. Among different tree components, stem contributed a maximum to total gamhar tree biomass followed by roots, leaves and branches. The average contributions of stems, roots, leaves and branches in total tree biomass in two annual cycles (2016-17 and 2017-18) varied between 50 and 60, 19.8 and 20, 19.2 and 20, and 10.7 and 12.7 percent, respectively. In case of crops, above ground, below ground and total biomass was significantly higher in sole intercrops than gamhar based agroforestry system. Total (Tree + interrops + Soil) carbon stock, carbon sequestration, carbon credit and carbon price were significantly affected by treatments, and was maximum in Sole Greengram-Mustard. Net carbon emission was also recorded lowest in Sole Greengram-Mustard for which the values were 811.55% and 725.24% and 760.69% lower than Sole Gamhar in 2016-17, 2017-18 and in pooled data, respectively., (© 2024. The Author(s).)

Wastewater malodour is the proverbial 'elephant in the room' notwithstanding its severe implications on sanitation, health, and hygiene. The predominant malodorous compounds associated with wastewater treatment plants and toilets are volatile organic compounds, such as hydrogen sulphide, ammonia, methanethiol, and organic acids. Among them, methanethiol warrants more attention owing to its relatively low olfactory threshold and associated cytotoxicity. This requires an efficient odour-abatement method since conventional techniques are either cost-prohibitive or leave recalcitrant byproducts. Bacteriophage-based methodology holds promise, and the described work explores the potential. In this study, a non-lysogenous Pseudomonas putida strain is used as a model organism that produces methanethiol in the presence of methionine. Two double-stranded DNA phages of genome sizes > 10 Kb were isolated from sewage. ɸPh&#95;PP01 and ɸPh&#95;PP02 were stable at suboptimal pH, temperature, and at 10% chloroform. Moreover, they showed adsorption efficiencies of 53% and 89% in 12 min and burst sizes of 507 ± 187 and 105 ± 7 virions per cell, respectively. In augmented synthetic wastewater, ɸPh&#95;PP01 and ɸPh&#95;PP02 reduced methanethiol production by 52% and 47%, respectively, with the concomitant reduction in P. putida by 3 logs in 6 h. On extension of the study in P. putida spiked-sewage sample, maximum reduction in methanethiol production was achieved in 3 h, with 49% and 48% for ɸPh&#95;PP01 and ɸPh&#95;PP02, respectively. But at 6 h, efficiency reduced to 36% with both the phages. The study clearly demonstrates the potential of phages as biocontrol agents in the reduction of malodour in wastewater., (© 2023. The Author(s).)

Tight unconventional rocks are characterized by the presence of laminations, preferentially oriented cracks, and an interconnected network of compliant minerals. Such anisotropic features can mechanically deform due to pressure depletion during production, leading to a human-induced change of elastic and fluid transport properties. Rock physics models allow us to better predict and assess stress- and direction-dependent elastic moduli of the rock, useful for horizontal stress estimates. However, elastic anisotropy can be challenging to measure and interpret. We have developed an anisotropy template that can be used to assess stress-dependent changes in elastic moduli and investigate rock textures. We present here the template construction using an effective medium model consisting of stiff and compliant layers and crack inclusions and evaluate the origin of stress-dependent stiffness changes in acoustic data from Berea, Bakken, Three Forks, and Mancos formations., (© 2023. Springer Nature Limited.)

High concentrations of potentially toxic elements (PTEs) in potable water can cause severe human health disorders. Present study examined the fitness of groundwater for drinking purpose based on the occurrence of nine PTEs in a heavy pilgrim and tourist influx region of the Garhwal Himalaya, India. The concentrations of analyzed PTEs in groundwater were observed in the order of Zn > Mn > As > Al > Cu > Cr > Se > Pb > Cd. Apart from Mn and As, other PTEs were within the corresponding guideline values. Spatial maps were produced to visualize the distribution of the PTEs in the area. Estimated water pollution indices and non-carcinogenic risk indicated that the investigated groundwater is safe for drinking purpose, as the hazard index was < 1 for all the water samples. Assessment of the cancer risk of Cr, As, Cd, and Pb also indicated low health risks associated with groundwater use, as the values were within the acceptable range of ≤ 1 × 10 -6 to 1 × 10 -4 . Multivariate statistical analyses were used to describe the various possible geogenic and anthropogenic sources of the PTEs in the groundwater resources although the contamination levels of the PTEs were found to pose no serious health risk. However, the present study recommends to stop the discharge of untreated wastewater and also to establish cost-effective as well as efficient water treatment facility nearby the study area. Present work's findings are vital as they may protect the health of the massive population from contaminated water consumption. Moreover, it can help the researchers, governing authorities and water supplying agencies to take prompt and appropriate decisions for water security., (© 2023. Springer Nature Limited.)

The occurrence of heavy metals (HMs) in drinking water has been a critical water quality concern for a long time and can compromise its aesthetic value to the larger extent. Chronic exposure of human beings to these toxic and non-toxic HMs through water ingestion can result in significant health risks. To assess these associated health risks, the present study was planned, designed and carried out for analyses of nine HMs namely, Al, Cr, Mn, Co, Ni, Cu, Zn, Cd and Pb in the potable water samples collected from different sources located across the Mandakini valley of Garhwal Himalaya, India using Inductively Coupled Plasma Mass Spectrometry. The measured values of Al, Cr, Mn, Co, Ni, Cu, Zn, Cd and Pb were found in the range of BDL-27.4 µg l -1 , 0.26-4.5 µg l -1 , BDL-139 µg l -1 , 0.02-0.9 µg l -1 , 0.4-5.5 µg l -1 , 0.07-9.2 µg l -1 , BDL-4164 µg l -1 , BDL-0.8 µg l -1 , and BDL-11.2 µg l -1 , respectively. The observed values of analyzed HMs except Zn and Pb were found below the reference values prescribed by the WHO, USEPA and BIS. In addition, Zn concentration exceeded its maximum permissible limit (4000 µg l -1 ) recommended by WHO for infants at one station only. The observed indices show that there are no health risks from HMs contamination via drinking water in the region. Moreover, the estimated hazard quotients for children and adults also revealed no potential health risks. The results of present study will be useful as baseline data for state and national regulatory agencies., (© 2022. The Author(s).)

Bacteriophages are generally specific, and a cocktail of phages is needed to combat different bacterial targets. Their production usually requires pathogenic isolation hosts. We identified a novel strain, Escherichia coli ST155, that could serve as a production host for three different polyvalent phages (ϕPh&#95;SE03, ϕPh&#95;SD01, and ϕPh&#95;EC01), thus superseding the use of individual isolation hosts. Upon propagation in E. coli ST155, the phages demonstrated differential intergeneric infectivity against Salmonella enterica, E. coli OP50, Shigella dysenteriae, E. coli MDR, and Acinetobacter baumannii. Phages were characterised based on morphology, latent period, burst size, the efficiency of plating, and restriction enzyme profile. Survival assay on Caenorhabditis elegans, the absence of Shiga toxin, and enterotoxigenic E. coli virulence genes indicated that E. coli ST155 could be non-pathogenic. Lack of antibiotic resistance and absence of functional prophages rendered the host suitable for environmental applications. As a proof-of-concept, phage ϕPh&#95;SE03 was produced in ST155 by employing a unique Bacteriophage Amplification Reactor-Lytics Broadcasting System and was simultaneously disseminated into S. enterica augmented wastewater, which resulted in a 3-log reduction in 24 h. The study establishes the potential of E. coli ST155 as a phage production host thereby minimising the possibility of accidental release of pathogenic hosts into wastewater., (© 2022. The Author(s).)

For the extraction of spatially important regions from mass spectrometry imaging (MSI) data, different clustering methods have been proposed. These clustering methods are based on certain assumptions and use different criteria to assign pixels into different classes. For high-dimensional MSI data, the curse of dimensionality also limits the performance of clustering methods which are usually overcome by pre-processing the data using dimension reduction techniques. In summary, the extraction of spatial patterns from MSI data can be done using different unsupervised methods, but the robust evaluation of clustering results is what is still missing. In this study, we have performed multiple simulations on synthetic and real MSI data to validate the performance of unsupervised methods. The synthetic data were simulated mimicking important spatial and statistical properties of real MSI data. Our simulation results confirmed that K-means clustering with correlation distance and Gaussian Mixture Modeling clustering methods give optimal performance in most of the scenarios. The clustering methods give efficient results together with dimension reduction techniques. From all the dimension techniques considered here, the best results were obtained with the minimum noise fraction (MNF) transform. The results were confirmed on both synthetic and real MSI data. However, for successful implementation of MNF transform the MSI data requires to be of limited dimensions., (© 2022. The Author(s).)

Effects of dissolved paramagnetic oxygen (O 2 ) in water on 1 H nuclear magnetic resonance (NMR) Carr-Purcell-Meiboom-Gill (CPMG) experiments is evaluated at a 1 H Larmor frequency of 2 MHz. Dissolution of O 2 into water significantly reduces the 1 H transverse relaxation coefficient (T 2 ). For deoxygenated water, T 2 is 3388 ms, water at ambient atmospheric conditions (7.4 mg/L O 2 ) exhibits a T 2 of 2465 ms, and dissolution of 2710 mg/L O 2 further reduces T 2 to 36 ms. The results were fit with an empirical model to facilitate prediction of T 2 times for bulk water as a function of paramagnetic oxygen concentrations in solution. Dissolved O 2 also greatly influences 1 H NMR CPMG experiments of confined water in a model system composed of Berea sandstone. For this system, 90 mg/L O 2 in H 2 O enhances T 2 relaxation of bulk water such that the relaxation time is comparable to physically confined water in the sandstone pores. Given the sensitivity of NMR T 2 coefficients to paramagnetic oxygen, low-field NMR-based characterization of fluid and porous media structure requires control of dissolved oxygen, as geospatial variation in the partial pressure of O 2 alone is expected to perturb fluid and pore relaxation times by up to 60 and 36%, respectively.

Sequestration of industrial carbon dioxide (CO 2 ) in deep geological saline aquifers is needed to mitigate global greenhouse gas emissions; monitoring the mechanical integrity of reservoir formations is essential for effective and safe operations. Clogging of fluid transport pathways in rocks from CO 2 -induced salt precipitation reduces injectivity and potentially compromises the reservoir storage integrity through pore fluid pressure build-up. Here, we show that early warning of salt precipitation can be achieved through geophysical remote sensing. From elastic P- and S-wave velocity and electrical resistivity monitoring during controlled laboratory CO 2 injection experiments into brine-saturated quartz-sandstone of high porosity (29%) and permeability (1660 mD), and X-ray CT imaging of pore-scale salt precipitation, we were able to observe, for the first time, how CO 2 -induced salt precipitation leads to detectable geophysical signatures. We inferred salt-induced rock changes from (i) strain changes, (ii) a permanent ~ 1.5% decrease in wave velocities, linking the geophysical signatures to salt volume fraction through geophysical models, and (iii) increases of porosity (by ~ 6%) and permeability (~ 7%). Despite over 10% salt saturation, no clogging effects were observed, which suggests salt precipitation could extend to large sub-surface regions without loss of CO 2 injectivity into high porosity and permeability saline sandstone aquifers.

Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.

This study summarizes the seasonal experimental data on the activity concentrations of indoor 222 Rn (Radon), 220 Rn (Thoron) and their progeny in Mansa and Muktsar districts of Punjab (India) using LR-115 solid state nuclear track detector based time integrated pin-hole cup dosimeters and deposition based progeny sensors for the assessment of radiological dose. The indoor 222 Rn concentration was observed higher in the rainy and winter seasons while 220 Rn concentration was observed higher in the winter season. However, Equilibrium Equivalent Concentrations (EECs) of 222 Rn and 220 Rn exhibited distinct seasonal behaviour unlike their parent nuclides. The average equilibrium factors for 222 Rn (F Rn ) and 220 Rn (F Tn ) were found 0.47 ± 0.1 and 0.05 ± 0.01, respectively. The annual arithmetic means of unattached fractions of 222 Rn ([Formula: see text]) and 220 Rn ([Formula: see text]) were found to be 0.09 ± 0.02 and 0.10 ± 0.02, respectively. The attachment rate (X Rn ) and attachment rate coefficients (β) of 222 Rn progeny were also calculated to understand the proper behaviour of progeny species in the region. A new alpha flux based technique has been proposed and used for the assessment of absorbed dose rate and annual effective dose rate for radiation protection purpose.

Jatropha curcas L. (Family - Euphorbiaceae) is a perennial tree of special interest due to its potential as a biofuel plant with high carbon sequestration. In this study, physiological investigations coupled with transcriptomics in relation to photosynthesis were evaluated in Jatropha grown under ambient (395 ppm) and elevated (550 ppm) CO 2 atmosphere. Morphophysiological analysis revealed that Jatropha sustained enhanced photosynthesis during its growth under elevated CO 2 for one year which might be linked to improved CO 2 assimilation physiology and enhanced sink activity. We sequenced and analyzed the leaf transcriptome of Jatropha after one year of growth in both conditions using Illumina HiSeq platform. After optimized assembly, a total of 69,581 unigenes were generated. The differential gene expression (DGE) analysis revealed 3013 transcripts differentially regulated in elevated CO 2 conditions. The photosynthesis regulatory genes were analysed for temporal expression patterns at four different growth phases which highlighted probable events contributing to enhanced growth and photosynthetic capacity including increased reducing power, starch synthesis and sucrose mobilization under elevated CO 2 . Overall, our data on physiological and transcriptomic analyses suggest an optimal resource allocation to the available and developing sink organs thereby sustaining improved photosynthetic rates during long-term growth of Jatropha under CO 2 enriched environment.

Inflammatory bowel disease (IBD) is difficult to diagnose due to nonspecific and variable symptoms, and lack of reliable diagnostic tests. Current methods are invasive, non-sensitive, non-predictive, and do not easily discriminate between its two main forms. Consequently, there remains a great need for reliable serum markers for IBD. Here, using a longitudinal study of various mouse models of colitis, we identified a serum miRNA signature that indicated the development of colitis and discriminated between inflammations of various origins (colitis from arthritis). Unlike the existing biomarkers, the newly identified signature also serves to distinguish individuals at risk, predict the type of inflammation, and evaluate the response to therapeutics. Moreover, the miRNA signature identified in mice predicted ulcerative colitis with 83.3% accuracy. In future, the signature identified herein could play a central role in monitoring inflammatory disorders and therapeutic responses in patients, thereby paving the way for personalized medicine.

SET domain-containing genes catalyse histone lysine methylation, which alters chromatin structure and regulates the transcription of genes that are involved in various developmental and physiological processes. The present study identified 53 SET domain-containing genes in C4 panicoid model, foxtail millet (Setaria italica) and the genes were physically mapped onto nine chromosomes. Phylogenetic and structural analyses classified SiSET proteins into five classes (I-V). RNA-seq derived expression profiling showed that SiSET genes were differentially expressed in four tissues namely, leaf, root, stem and spica. Expression analyses using qRT-PCR was performed for 21 SiSET genes under different abiotic stress and hormonal treatments, which showed differential expression of these genes during late phase of stress and hormonal treatments. Significant upregulation of SiSET gene was observed during cold stress, which has been confirmed by over-expressing a candidate gene, SiSET14 in yeast. Interestingly, hypermethylation was observed in gene body of highly differentially expressed genes, whereas methylation event was completely absent in their transcription start sites. This suggested the occurrence of demethylation events during various abiotic stresses, which enhance the gene expression. Altogether, the present study would serve as a base for further functional characterization of SiSET genes towards understanding their molecular roles in conferring stress tolerance.

Heat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.

The annual exposure to indoor radon, thoron and their progeny imparts a major contribution to inhalation doses received by the public. In this study, we report results of time integrated passive measurements of indoor radon, thoron and their progeny concentrations that were carried out in Garhwal Himalaya with the aim of investigating significant health risk to the dwellers in the region. The measurements were performed using recently developed LR-115 detector based techniques. The experimentally determined values of radon, thoron and their progeny concentrations were used to estimate total annual inhalation dose and annual effective doses. The equilibrium factors for radon and thoron were also determined from the observed data. The estimated value of total annual inhalation dose was found to be 1.8 ± 0.7 mSv/y. The estimated values of the annual effective dose were found to be 1.2 ± 0.5 mSv/y and 0.5 ± 0.3 mSv/y, respectively. The estimated values of radiation doses suggest no important health risk due to exposure of radon, thoron and progeny in the study area. The contribution of indoor thoron and its progeny to total inhalation dose ranges between 13-52% with mean value of 30%. Thus thoron cannot be neglected when assessing radiation doses.

Involvement of 26S proteasomal subunits in plant pathogen-interactions, and the roles of each subunit in independently modulating the activity of many intra- and inter-cellular regulators controlling physiological and defense responses of a plant were well reported. In this regard, we aimed to functionally characterize a Solanum lycopersicum 26S proteasomal subunit RPT4a (SlRPT4) gene, which was differentially expressed after Tomato leaf curl New Delhi virus (ToLCNDV) infection in tolerant cultivar H-88-78-1. Molecular analysis revealed that SlRPT4 protein has an active ATPase activity. SlRPT4 could specifically bind to the stem-loop structure of intergenic region (IR), present in both DNA-A and DNA-B molecule of the bipartite viral genome. Lack of secondary structure in replication-associated gene fragment prevented formation of DNA-protein complex suggesting that binding of SlRPT4 with DNA is secondary structure specific. Interestingly, binding of SlRPT4 to IR inhibited the function of RNA Pol-II and subsequently reduced the bi-directional transcription of ToLCNDV genome. Virus-induced gene silencing of SlRPT4 gene incited conversion of tolerant attributes of cultivar H-88-78-1 into susceptibility. Furthermore, transient overexpression of SlRPT4 resulted in activation of programmed cell death and antioxidant enzymes system. Overall, present study highlights non-proteolytic function of SlRPT4 and their participation in defense pathway against virus infection in tomato.

ADP-ribosylation factors (ARFs) have been reported to function in diverse physiological and molecular activities. Recent evidences also demonstrate the involvement of ARFs in conferring tolerance to biotic and abiotic stresses in plant species. In the present study, 23 and 25 ARF proteins were identified in C3 model- rice and C4 model- foxtail millet, respectively. These proteins are classified into four classes (I-IV) based on phylogenetic analysis, with ARFs in classes I-III and ARF-like proteins (ARLs) in class IV. Sequence alignment and domain analysis revealed the presence of conserved and additional motifs, which may contribute to neo- and sub-functionalization of these proteins. Promoter analysis showed the presence of several cis-regulatory elements related to stress and hormone response, indicating their role in stress regulatory network. Expression analysis of rice ARFs and ARLs in different tissues, stresses and abscisic acid treatment highlighted temporal and spatial diversification of gene expression. Five rice cultivars screened for allelic variations in OsARF genes showed the presence of allelic polymorphisms in few gene loci. Altogether, the study provides insights on characteristics of ARF/ARL genes in rice and foxtail millet, which could be deployed for further functional analysis to extrapolate their precise roles in abiotic stress responses.