Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.

BACKGROUND: Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS: We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS: In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS: In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.

Meta QTL analysis for dissecting abiotic stress tolerance in chickpea.

BACKGROUND: Chickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea. RESULTS: A meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc. CONCLUSION: The results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.

Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.).

The grain-filling stage in Triticum aestivum (wheat) is highly vulnerable to increasing temperature as terminal heat stress diminishes grain quality and yield. To examine the mechanism of terminal heat tolerance, we performed the biochemical and gene expression analyses using two heat-tolerant (WH730 and WH1218) and two heat-sensitive (WH711 and WH157) wheat genotypes. We observed a significant increase in total soluble sugar (25%-47%), proline (7%-15%), and glycine betaine (GB) (22%-34%) contents in flag leaf, whereas a decrease in grain-filling duration, 1000-kernel weight (8%-25%), and grain yield per plant (11%-23%) was observed under the late-sown compared to the timely sown. The maximum content of osmolytes, including total soluble sugar, proline, and GB, was observed in heat-tolerant genotypes compared to heat-sensitive genotypes. The expression of 10 heat-responsive genes associated with heat shock proteins (sHsp-1, Hsp17, and HsfA4), flavonoid biosynthesis (F3'-1 and PAL), ß-glucan synthesis (CslF6 and CslH), and xyloglucan metabolism (XTH1, XTH2, and XTH5) was studied in flag leaf exposed to different heat treatments (34, 36, 38, and 40°C) at 15 days after anthesis by quantitative real-time polymerase chain reaction. A significant increase in the relative fold expression of these genes with increasing temperature indicated their involvement in providing heat-stress tolerance. The high differential expression of most of the genes in heat-tolerant genotype "WH730" followed by "WH1218" indicates the high adaptability of these genotypes to heat stress compared to heat-sensitive wheat genotypes. Based on the previous results, "WH730" performed better in terms of maximum osmolyte accumulation, grain yield, and gene expression under heat stress.

Structural and functional characteristics and expression profile of the 20S proteasome gene family in Sorghum under abiotic stress.

The 26S proteasome is a molecular machine that catalyzes and degrades protein intracellularly with the help of its core complex called 20S proteasome. The 20S proteasomes degrade and cleave denatured, cytotoxic, damaged, and unwanted proteins via proteolysis and impart biotic and abiotic stress tolerance in model plants. This study identified 20 genes, namely, 10 SbPA and 10 SbPB that encode for α- and ß-subunits of the 20S proteasome in Sorghum bicolor (L.) Moench (2n= 20). These genes have been found distributed on the 1st, 2nd, 3rd, 4th, 5th, 7th, and 10th chromosomes. These sorghum genes were orthologous to corresponding rice. Phylogenetic analysis clustered these genes into seven clades, each with one of the seven α-subunits (1 to 7) and one of the seven ß-subunits (1 to 7). In silico gene expression analysis suggested that nine genes were involved in abiotic stress response (cold, drought, and abscisic acid hormone). The expression of these proteasomal genes was studied in shoots and roots exposed to different abiotic stresses (cold, drought, and abscisic acid) by quantitative real-time polymerase chain reaction. A significant increase in the relative fold expression of SbPBA1, SbPAA1, SbPBG1, SbPBE1, and SbPAG1 genes under ABA and drought stress provides an insight into its involvement in abiotic stress. No expression was observed for cold stress of these genes indicating their non-involvement. It is believed that additional investigation into the SbPA/SbPB genes would aid in the creation of S. bicolor cultivars that are resistant to climate change.

Nanoparticles as novel elicitors in plant tissue culture applications: Current status and future outlook.

Plant tissue culture is the primary, fundamental, and applied aspect of plant biology. It is an indispensable and valuable technique for investigating morphogenesis, embryogenesis, clonal propagation, crop improvements, generation of pathogen-free plants, gene transfer and expression, and the production of secondary metabolites. The extensive use of various nanoparticles (NPs) in fields such as cosmetics, energy, medicine, pharmaceuticals, electronics, agriculture, and biotechnology have demonstrated positive impacts in microbial decontamination, callus differentiation, organogenesis, somatic variations, biotransformation, cryopreservation, and enhanced synthesis of bioactive compounds. This review summarizes the current state of knowledge with regard to the use of nanoparticles in plant tissue culture, with a particular focus on the beneficial outcomes. The positive (beneficial) and negative (toxic) effects of engineered NPs in tissue culture medium, delivery of transgenes, NPs toxicity concerns, safety issues, and potential hazards arising from utilization of nanomaterials in agriculture through plant tissue culture are discussed in detail, along with the future prospects for these applications. In addition, the potential use of novel nanomaterials such as graphene, graphite, dendrimers, quantum dots, and carbon nanotubes as well as unique metal or metalloid NPs are proposed. Further, the potential mechanisms underlying NPs elicitation of tissue culture response in different applications are critically evaluated. The potential of these approaches in plant nanobiotechnology is only now becoming understood and it is clear that the role of these strategies in sustainably increasing crop production to combat global food security and safety in a changing climate will be significant.

Measurement of radon concentration in soil gas and radon exhalation rate from soil samples along and across the Main Central Thrust of Garhwal Himalaya, India.

The present study focuses on measuring radon concentrations in soil gas at various depths, radon exhalation rate (surface and mass) from soil samples, and gamma dose rate along and across the Main Central Thrust of Garhwal Himalaya, India. Radon concentration in soil gas, surface, and mass exhalation rates was measured using a portable SMART radon monitor (RnDuo). Furthermore, the gamma dose rate was measured using a pocket radiation monitor. The soil gas radon concentration varied from 15 ± 4 to 579 ± 82 Bq m-3 at a depth of 25 cm, 10 ± 2 to 533 ± 75 Bq m-3 at a depth of 30 cm, and 9 ± 1 to 680 ± 95 Bq m-3 at a depth of 35 cm. The surface and mass exhalation rates were found 3 ± 0.7 to 98 ± 3 Bq m-2 h-1 (with AM ± SD = 36 ± 28 Bq m-2 h-1) and 1 ± 0.2 to 95 ± 2 mBq kg-1 h-1 (with AM ± SD = 30 ± 22 mBq kg-1 h-1), respectively. The gamma dose rate for the present study area varies from 0.11 ± 0.05 to 0.28 ± 0.05 µSv h-1 with a mean value of 0.17 ± 0.05 µSv h-1. The correlation analysis between the exhalation rates (mass and surface) and radon concentration of soil gas at various depths was carried out in the current study.

Physiological traits and expression profile of genes associated with nitrogen and phosphorous use efficiency in wheat.

BACKGROUND: Nitrogen (N) and phosphorous (P) play a very important role in the growth and development of wheat as well as major constituents of biological membranes. To meet the plant's nutritional demand these nutrients are applied in the form of fertilizers. But the plant can utilize only half of the applied fertilizer whereas the rest is lost through surface runoff, leaching and volatilization. Thus, to overcome the N/P loss we need to elucidate the molecular mechanism behind the N/P uptake. METHODS: In our study, we used DBW16 (low NUE), and WH147 (high NUE) wheat genotypes under different doses of N, whereas HD2967 (low PUE) and WH1100 (high PUE) genotypes were studied under different doses of P. To check the effect of different doses of N/P, the physiological parameters like total chlorophyll content, net photosynthetic rate, N/P content, and N/PUE of these genotypes were calculated. In addition, gene expression of various genes involved in N uptake, utilization, and acquisition such as Nitrite reductase (NiR), Nitrate transporter 1/Peptide transporter family (NPF2.4/2.5), Nitrate transporter (NRT1) and NIN Like Protein (NLP) and induced phosphate starvation (IPS), Phosphate Transporter (PHT1.7) and Phosphate 2 (PHO2) acquisition was studied by quantitative real-time PCR. RESULTS: Statistical analysis revealed a lower percent reduction in TCC, NPR, and N/P content in N/P efficient wheat genotypes (WH147 & WH1100). A significant increase in relative fold expression of genes under low N/P concentration was observed in N/P efficient genotypes as compared to N/P deficient genotypes. CONCLUSION: Significant differences in physiological data and gene expression among N/ P efficient and deficient wheat genotypes could be useful for future improvement of N/P use efficiency.

Chlorambucil-Loaded Graphene-Oxide-Based Nano-Vesicles for Cancer Therapy.

In this study, the authors have designed biocompatible nano-vesicles using graphene oxide (GO) for the release of chlorambucil (CHL) drugs targeting cancerous cells. The GO sheets were first sulfonated and conjugated with folic acid (FA) molecules for controlled release and high loading efficiency of CHL. The chlorambucil (CHL) drug loading onto the functionalized GO surface was performed through π-π stacking and hydrophobic interactions with the aromatic planes of GO. The drug loading and "in vitro" release from the nano-vesicles at different pH were studied. The average particle size, absorption, and loading efficiency (%) of FA-conjugated GO sheets (CHL-GO) were observed to be 300 nm, 58%, and 77%, respectively. The drug release study at different pH (i.e., 7.4 and 5.5) showed a slight deceleration at pH 7.4 over pH 5.5. The amount of drug released was very small at pH 7.4 in the first hour which progressively increased to 24% after 8 h. The rate of drug release was faster at pH 5.5; initially, 16% to 27% in the first 3 h, and finally it reached 73% after 9 h. These observations indicate that the drug is released more rapidly at acidic pH with a larger amount of drug-loading ability. The rate of drug release from the CHL-loaded GO was 25% and 75% after 24 h. The biotoxicity study in terms of % cell viability of CHL-free and CHL-loaded GO against human cervical adenocarcinoma cell line was found to have lower cytotoxicity of CHL-loaded nano-vesicles (IC50 = 18 µM) as compared to CHL-free (IC50 = 8 µM). It is concluded that a high drug-loading efficiency and controlled release with excellent biotoxicity of CHL-GO offers an excellent application in the biomedical field.

Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: Current understanding and future scope.

Bacteria emit a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Some bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect expression of genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be further explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOCs application under greenhouse and open field conditions are warranted.

3D Modeling of Non-coding RNA Interactions.

Non-coding RNAs (ncRNAs) are a growing class of transcripts, with lengths ranging from tens to several thousand of bases, involved in the regulation of a large number of biological processes and diseases. Many of these ncRNAs have emerged as the molecules of interest for prognostic, diagnostic, and therapeutic purposes in many diseases including cancer. Although ncRNAs do not encode proteins, they fold into complex structures to interact with target proteins, DNA, or other RNAs. In contrast to microRNAs (miRNAs) where researchers mainly focused on the nucleotide sequence for target prediction in the past, folding and structural conservation seems to be important to encode functions and interactions of long non-coding RNA (lncRNA). In this chapter, we discuss methods and tools available for the structural modeling of ncRNAs together with various examples from the literature where structural modeling helped decipher the function of ncRNAs. We also provide a step-by-step procedure to design 3D structures of ncRNAs combining state-of-the-art tools available toward the design of novel RNA therapeutics.

Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.).

The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding α- and ß-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for α- (PA) and ß-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (α1-7) and BnPB (ß1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus, and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.

Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum L.).

Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.

Nanotechnology-enabled biofortification strategies for micronutrients enrichment of food crops: Current understanding and future scope.

Nutrient deficiency in food crops severely compromises human health, particularly in under privileged communities. Globally, billions of people, particularly in developing nations, have limited access to nutritional supplements and fortified foods, subsequently suffering from micronutrient deficiency leading to a range of health issues. The green revolution enhanced crop production and provided food to billions of people but often falls short with respect to the nutritional quality of that food. Plants may assimilate nutrients from synthetic chemical fertilizers, but this approach generally has low nutrient delivery and use efficiency. Further, the overexposure of chemical fertilizers may increase the risk of neoplastic diseases, render food crops unfit for consumption and cause environmental degradation. Therefore, to address these challenges, more research is needed for sustainable crop yield and quality enhancement with minimum use of chemical fertilizers. Complex nutritional disorders and 'hidden hunger' can be addressed through biofortification of food crops. Nanotechnology may help to improve food quality via biofortification as plants may readily acquire nanoparticle-based nutrients. Nanofertilizers are target specific, possess controlled release, and can be retained for relatively long time periods, thus prevent leaching or run-off from soil. This review evaluates the recent literature on the development and use of nanofertilizers, their effects on the environment, and benefits to food quality. Further, the review highlights the potential of nanomaterials on plant genetics in biofortification, as well as issues of affordability, sustainability, and toxicity.

Substrate-Free Untagged Detection of miR393a Using an Ultrasensitive Electrochemical Biosensor.

Rapid and sensitive detection of numerous regulatory pathways in growth and development processes and defensive responses in plant-pathogen interactions caused by miRNA has been the current interest of agricultural scientists. Herein, an uncomplicated ultrasensitive electrochemical biosensor was fabricated to detect miR393a, as its detection is of vital importance for plant diseases. A streptavidin-coated screen-printed carbon electrode (SPCE) was fabricated and characterized by scanning electrochemical microscopy, scanning electron microscopy, surface plasmon resonance, and cyclic voltammetry. The two-dimensional (2D) structure and chemical functionality of the streptavidin-coated SPCE render it a superior platform for loading a modified probe via a 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide-N-hydroxysuccinimide linker. This biorecognition platform is capable of efficiently using its excellent conductivity, greater surface area, and effective electrochemical execution due to its synergistic effect between streptavidin and carbon electrodes. The biosensor showed a good linear response (R 2 = 0.96) to miR393a concentrations ranging from 100 nM to 100 fM. This streptavidin-based biosensor is highly sensitive to the minimum concentration of miR393a, lowest detection limit, and ultrasensitivity under optimized conditions, i.e., 100 fM, 0.33 fM, and 33.72 µA fM-1 cm-2, respectively. In addition, remarkable recoveries could be obtained to confirm the feasibility of this assay in plant disease samples. The fabricated technology could offer a selective, adaptable, and farmer-friendly strategy for the timely detection of miRNA of plant samples.

ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features.

MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational method for prediction of miRNAs associated with abiotic stresses. Three types of datasets were used for prediction, i.e., miRNA, Pre-miRNA, and Pre-miRNA + miRNA. The pseudo K-tuple nucleotide compositional features were generated for each sequence to transform the sequence data into numeric feature vectors. Support vector machine (SVM) was employed for prediction. The area under receiver operating characteristics curve (auROC) of 70.21, 69.71, 77.94 and area under precision-recall curve (auPRC) of 69.96, 65.64, 77.32 percentages were obtained for miRNA, Pre-miRNA, and Pre-miRNA + miRNA datasets, respectively. Overall prediction accuracies for the independent test set were 62.33, 64.85, 69.21 percentages, respectively, for the three datasets. The SVM also achieved higher accuracy than other learning methods such as random forest, extreme gradient boosting, and adaptive boosting. To implement our method with ease, an online prediction server "ASRmiRNA" has been developed. The proposed approach is believed to supplement the existing effort for identification of abiotic stress-responsive miRNAs and Pre-miRNAs.

Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat.

The SPX gene family, ubiquitous in all vascular plants, plays a critical role in plant development and growth as well as in response to phosphorus stress. Based on genomic census, 46 TaSPX genes were identified in the wheat genome. All of them are evenly distributed on 13 of the 21 wheat chromosomes and chromosome 7A contains the largest members. As many as 57 gene specific SSRs were discovered among genomic sequences of identified TaSPXs. MicroRNA target analysis revealed that TaSPX genes were targeted by 9 different miRNAs including tae-miR1120a, tae-miR1120b-3p, tae-miR1120c-5p, tae-miR1122b-3p, tae-miR1122c-3p, tae-miR1130a, tae-miR1130b-3p, tae-miR1137a, and tae-miR1137b-5p. Expression profiles derived from transcriptome data and real-time quantitative PCR revealed that TaSPX genes were significantly induced by Pi starvation. The modeled 3D structure of wheat SPX proteins shared high level of homology with template structures, providing information to understand their functions at proteomic level. We have also refined the modeled 3D structures on 10 ns using molecular dynamics simulations for conformational stability. The discovered members of SPX gene family and their targeting miRNAs may provide resource for genetic improvement and promote P use efficiency in cereals.

Effect of Magnetized Water on Urea-Loading Efficiency of Mesoporous Nano-Silica: A Seed Germination Study on Wheat Crop.

Efficiently-loaded, controlled-release nanofertilizer systems improve fertilizer use efficiency, germination percentage, root and shoot length, seedling growth, and can overcome the problem of the ever-increasing cost of agrochemicals and their inherent post-application losses, which lead to severe soil, water, and eatable commodity pollution. In this study, magnetized distilled waters (MDWs) with various physicochemical characteristics have been used to enhance the urea loading efficiency into mesoporous nano silica (mNS). The mNS was in-house synthesized by a sol-gel method and characterized by UV-visible spectrophotometer (UV-Vis), Fourier Transform Infrared Spectroscopy (FTIR), Energy-dispersive X-ray (EDX) spectroscopy, X-ray powder diffractometer (XRD), and thermogravimetric (TGA)/differential thermal analyzer (DTA) and Field Emission Scanning Electron Microscope (FESEM). We then compared the effects of magnetized and normal water, mNS, urea-loaded mNS, and bare urea on the germination of wheat seeds under laboratory conditions. Comparing to mNS in DW, we detected an increase in root (4-fold) and shoot (1.85-fold) lengths when using mNS in MDW. The root and shoot length in case of urea loaded mNS in normal DW and MDW were 2.05 and 1.77 times more, respectively. The germination percentage and root and shoot length increased significantly in accordance to the exposure to 0.5% (w/v) mNS in magnetized water (mNS-MDW) and urea loaded mNS in magnetized water (mNSU-MDW) as compared to same treatment with mNS in distilled water (mNS-DW). Our findings show that the unfavorable effects of urea fertilizer on seed germination, seedling growth, and early plant growth on paper towels can be ameliorated, at least partially, by supplementation with mNSU-MDW. We conclude that mNS-MDW and mNSU-MDW might be effective alternatives for sustained and effective means of fertilizer use efficiency during wheat seed germination.

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.).

RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2-3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway.

---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants.

Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a web-resource containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat ( Triticum aestivum), rice ( Oryza sativa), maize ( Zea mays), barley ( Hordeum vulgare)), two alien species related to wheat ( Triticum urartu and Aegilops tauschii), and two model species ( Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.

Functional and structural insights into candidate genes associated with nitrogen and phosphorus nutrition in wheat (Triticum aestivum L.).

An extensive bioinformatics based study has been performed to gain insight into the structural and functional aspects of candidate genes involved in Nitrogen and Phosphorus nutrition in wheat. Based on our study, 37 N and P nutrition candidate genes were identified (24 NUE and 13 inorganic phosphate transporters) in wheat genome. 23 gene specific novel microsatellites were discovered using genomic sequences of identified N and P nutrition genes. We also identified the microRNAs that target ten candidate genes including TaAS1-3A, TaAS1-3D, TaASN2-1A, TaASN2-1B, TaANR1-6A, TaANR1-6B, TaNRT2.4-6A, TaNRT2.6-6A, TaNRT2.6-6B and TaPHT1.5-5B. Expression profiling of identified genes showed altered expression under N and P starvation. The proposed 3D structure of wheat N and P nutrition proteins shared high level homology with known experimental structures providing information to understand their functions at the biochemical level. Molecular dynamics simulations of refined modeled structures of wheat N and P nutrition proteins show conformational stability. The identified N and P nutrition candidate genes and their targeting miRNAs may provide resources for the genetic improvement and promote N and P use efficiency. Our study provides first-hand structural prospective of N and P nutrition candidate genes towards development of wheat varieties resilient to N and P stress.