Synergistic impact of nanomaterials and plant probiotics in agriculture: A tale of two-way strategy for long-term sustainability.

Modern agriculture is primarily focused on the massive production of cereals and other food-based crops in a sustainable manner in order to fulfill the food demands of an ever-increasing global population. However, intensive agricultural practices, rampant use of agrochemicals, and other environmental factors result in soil fertility degradation, environmental pollution, disruption of soil biodiversity, pest resistance, and a decline in crop yields. Thus, experts are shifting their focus to other eco-friendly and safer methods of fertilization in order to ensure agricultural sustainability. Indeed, the importance of plant growth-promoting microorganisms, also determined as "plant probiotics (PPs)," has gained widespread recognition, and their usage as biofertilizers is being actively promoted as a means of mitigating the harmful effects of agrochemicals. As bio-elicitors, PPs promote plant growth and colonize soil or plant tissues when administered in soil, seeds, or plant surface and are used as an alternative means to avoid heavy use of agrochemicals. In the past few years, the use of nanotechnology has also brought a revolution in agriculture due to the application of various nanomaterials (NMs) or nano-based fertilizers to increase crop productivity. Given the beneficial properties of PPs and NMs, these two can be used in tandem to maximize benefits. However, the use of combinations of NMs and PPs, or their synergistic use, is in its infancy but has exhibited better crop-modulating effects in terms of improvement in crop productivity, mitigation of environmental stress (drought, salinity, etc.), restoration of soil fertility, and strengthening of the bioeconomy. In addition, a proper assessment of nanomaterials is necessary before their application, and a safer dose of NMs should be applicable without showing any toxic impact on the environment and soil microbial communities. The combo of NMs and PPs can also be encapsulated within a suitable carrier, and this method aids in the controlled and targeted delivery of entrapped components and also increases the shelf life of PPs. However, this review highlights the functional annotation of the combined impact of NMs and PPs on sustainable agricultural production in an eco-friendly manner.

Cold-tolerant phosphate-solubilizing Pseudomonas strains promote wheat growth and yield by improving soil phosphorous (P) nutrition status.

It is well-known that phosphate-solubilizing bacteria (PSB) promote crop growth and yield. The information regarding characterization of PSB isolated from agroforestry systems and their impact on wheat crops under field conditions is rarely known. In the present study, we aim to develop psychrotroph-based P biofertilizers, and for that, four PSB strains (Pseudomonas sp. L3, Pseudomonas sp. P2, Streptomyces sp. T3, and Streptococcus sp. T4) previously isolated from three different agroforestry zones and already screened for wheat growth under pot trial conditions were evaluated on wheat crop under field conditions. Two field experiments were employed; set 1 includes PSB + recommended dose of fertilizers (RDF) and set 2 includes PSB - RDF. In both field experiments, the response of the PSB-treated wheat crop was significantly higher compared to the uninoculated control. In field set 1, an increase of 22% in grain yield (GY), 16% in biological yield (BY), and 10% in grain per spike (GPS) was observed in consortia (CNS, L3 + P2) treatment, followed by L3 and P2 treatments. Inoculation of PSB mitigates soil P deficiency as it positively influences soil alkaline phosphatase (AP) and soil acid phosphatase (AcP) activity which positively correlated with grain NPK %. The highest grain NPK % was reported in CNS-treated wheat with RDF (N-0.26%, P-0.18%, and K-1.66%) and without RDF (N-0.27, P-0.26, and K-1.46%), respectively. All parameters, including soil enzyme activities, plant agronomic data, and yield data were analyzed by principal component analysis (PCA), resulting in the selection of two PSB strains. The conditions for optimal P solubilization, in L3 (temperature-18.46, pH-5.2, and glucose concentration-0.8%) and P2 (temperature-17°C, pH-5.0, and glucose concentration-0.89%), were obtained through response surface methodology (RSM) modeling. The P solubilizing potential of selected strains at <20°C makes them a suitable candidate for the development of psychrotroph-based P biofertilizers. Low-temperature P solubilization of the PSB strains from agroforestry systems makes them potential biofertilizers for winter crops.

Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer.

BACKGROUND: Ovarian cancer is the world's dreaded disease and its prevalence is expanding globally. The study of integrated molecular networks is crucial for the basic mechanism of cancer cells and their progression. During the present investigation, we have examined different flavonoids that target protein kinases B (AKT1) protein which exerts their anticancer efficiency intriguing the role in cross-talk cell signalling, by metabolic processes through in-silico approaches. METHOD: Molecular dynamics simulation (MDS) was performed to analyze and evaluate the stability of the complexes under physiological conditions and the results were congruent with molecular docking. This investigation revealed the effect of a point mutation (W80R), considered based on their frequency of occurrence, with AKT1 protein. RESULTS: The ligand with high docking scores and favourable behaviour on dynamic simulations are proposed as potential W80R inhibitors. A virtual screening analysis was performed with 12,000 flavonoids satisfying Lipinski's rule of five according to which drug-likeness is predicted based on its pharmacological and biological properties to be active and taken orally. The pharmacokinetic ADME (adsorption, digestion, metabolism, and excretion) studies featured drug-likeness. Subsequently, a statistically significant 3D-QSAR model of high correlation coefficient (R2) with 0.822 and cross-validation coefficient (Q2) with 0.6132 at 4 component PLS (partial least square) were used to verify the accuracy of the models. Taxifolin holds good interactions with the binding domain of W80R, highest Glide score of - 9.63 kcal/mol with OH of GLU234 and H bond ASP274 and LEU156 amino acid residues and one pi-cation interaction and one hydrophobic bond with LYS276. CONCLUSION: Natural compounds have always been a richest source of active compounds with a wide variety of structures, therefore, these compounds showed a special inspiration for medical chemists. The present study has aimed molecular docking and molecular dynamics simulation studies on taxifolin targeting W80R mutant protein of protein kinase B/serine- threonine kinase/AKT1 (EC:2.7.11.1) protein of ovarian cancer for designing therapeutic intervention. The expected result supported the molecular cause in a mutant form which resulted in a gain of ovarian cancer. Here we discussed validations computationally and yet experimental evaluation or in vivo studies are endorsed for further study. Several of these compounds should become the next marvels for early detection of ovarian cancer.

In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species.

Alternaria brassicae and Alternaria brassicicola are two major phytopathogenic fungi which cause Alternaria blight, a recalcitrant disease on Brassica crops throughout the world, which is highly destructive and responsible for significant yield losses. Since no resistant source is available against Alternaria blight, therefore, efforts have been made in the present study to identify defense inducer molecules which can induce jasmonic acid (JA) mediated defense against the disease. It is believed that JA triggered defense response will prevent necrotrophic mode of colonization of Alternaria brassicae fungus. The JA receptor, COI1 is one of the potential targets for triggering JA mediated immunity through interaction with JA signal. In the present study, few mimicking compounds more efficient than naturally occurring JA in terms of interaction with COI1 were identified through virtual screening and molecular dynamics simulation studies. A high quality structural model of COI1 was developed using the protein sequence of Brassica rapa. This was followed by virtual screening of 767 analogs of JA from ZINC database for interaction with COI1. Two analogs viz. ZINC27640214 and ZINC43772052 showed more binding affinity with COI1 as compared to naturally occurring JA. Molecular dynamics simulation of COI1 and COI1-JA complex, as well as best screened interacting structural analogs of JA with COI1 was done for 50 ns to validate the stability of system. It was found that ZINC27640214 possesses efficient, stable, and good cell permeability properties. Based on the obtained results and its physicochemical properties, it is capable of mimicking JA signaling and may be used as defense inducers for triggering JA mediated resistance against Alternaria blight, only after further validation through field trials.

Identification and characterization of calcium transporter gene family in finger millet in relation to grain calcium content.

Calcium (Ca) is an essential mineral for proper growth and development of plants as well as animals. In plants including cereals, calcium is deposited in seed during its development which is mediated by specialized Ca transporters. Common cereal seeds contain very low amounts of Ca while the finger millet (Eleusine coracana) contains exceptionally high amounts of Ca in seed. In order to understand the role of Ca transporters in grain Ca accumulation, developing seed transcriptome of two finger millet genotypes (GP-1, low Ca and GP-45 high Ca) differing in seed Ca content was sequenced using Illumina paired-end sequencing technology and members of Ca transporter gene family were identified. Out of 109,218 and 120,130 contigs, 86 and 81 contigs encoding Ca transporters were identified in GP-1 and GP-45, respectively. After removal of redundant sequences, a total of 19 sequences were confirmed as Ca transporter genes, which includes 11 Ca(2+) ATPases, 07 Ca(2+)/cation exchangers and 01 Ca(2+) channel. The differential expressions of all genes were analyzed from transcriptome data and it was observed that 9 and 3 genes were highly expressed in GP-45 and GP-1 genotypes respectively. Validation of transcriptome expression data of selected Ca transporter genes was performed on different stages of developing spikes of both genotypes grown under different concentrations of exogenous Ca. In both genotypes, significant correlation was observed between the expression of these genes, especially EcCaX3, and on the amount of Ca accumulated in seed. The positive correlation of seed mass with the amount of Ca concentration was also observed. The efficient Ca transport property and responsiveness of EcCAX3 towards exogenous Ca could be utilized in future biofortification program.

Virtual screening of natural inhibitors to the predicted HBx protein structure of Hepatitis B Virus using molecular docking for identification of potential lead molecules for liver cancer.

The HBx protein in Hepatitis B Virus (HBV) is a potential target for anti-liver cancer molecules. Therefore, it is of interest to screen known natural compounds against the HBx protein using molecular docking. However, the structure of HBx is not yet known. Therefore, the predicted structure of HBx using threading in LOMET was used for docking against plant derived natural compounds (curcumin, oleanolic acid, resveratrol, bilobetin, luteoline, ellagic acid, betulinic acid and rutin) by Molegro Virtual Docker. The screening identified rutin with binding energy of -161.65 Kcal/mol. Thus, twenty derivatives of rutin were further designed and screened against HBx. These in silico experiments identified compounds rutin01 (-163.16 Kcal/mol) and rutin08 (- 165.76 Kcal/mol) for further consideration and downstream validation.

TRIPATH: A Biological Genetic and Genomic Database of Three Economically Important Fungal Pathogen of Wheat - Rust: Smut: Bunt.

UNLABELLED: Wheat, the major source of vegetable protein in human diet, provides staple food globally for a large proportion of the human population. With higher protein content than other major cereals, wheat has great socio- economic importance. Nonetheless for wheat, three important fungal pathogens i.e. rust, smut and bunt are major cause of significant yield losses throughout the world. Researchers are putting up a strong fight against devastating wheat pathogens, and have made progress in tracking and controlling disease outbreaks from East Africa to South Asia. The aim of the present work hence was to develop a fungal pathogens database dedicated to wheat, gathering information about different pathogen species and linking them to their biological classification, distribution and control. Towards this end, we developed an open access database Tripath: A biological, genetic and genomic database of economically important wheat fungal pathogens - rust: smut: bunt. Data collected from peer-reviewed publications and fungal pathogens were added to the customizable database through an extended relational design. The strength of this resource is in providing rapid retrieval of information from large volumes of text at a high degree of accuracy. Database TRIPATH is freely accessible. AVAILABILITY: http://www.gbpuat-cbsh.ac.in/departments/bi/database/tripath/

Transcriptional expression analysis of genes involved in regulation of calcium translocation and storage in finger millet (Eleusine coracana L. Gartn.).

Finger millet (Eleusine coracana) variably accumulates calcium in different tissues, due to differential expression of genes involved in uptake, translocation and accumulation of calcium. Ca(2+)/H(+) antiporter (CAX1), two pore channel (TPC1), CaM-stimulated type IIB Ca(2+) ATPase and two CaM dependent protein kinase (CaMK1 and 2) homologs were studied in finger millet. Two genotypes GP-45 and GP-1 (high and low calcium accumulating, respectively) were used to understand the role of these genes in differential calcium accumulation. For most of the genes higher expression was found in the high calcium accumulating genotype. CAX1 was strongly expressed in the late stages of spike development and could be responsible for accumulating high concentrations of calcium in seeds. TPC1 and Ca(2+) ATPase homologs recorded strong expression in the root, stem and developing spike and signify their role in calcium uptake and translocation, respectively. Calmodulin showed strong expression and a similar expression pattern to the type IIB ATPase in the developing spike only and indicating developing spike or even seed specific isoform of CaM affecting the activity of downstream target of calcium transportation. Interestingly, CaMK1 and CaMK2 had expression patterns similar to ATPase and TPC1 in various tissues raising a possibility of their respective regulation via CaM kinase. Expression pattern of 14-3-3 gene was observed to be similar to CAX1 gene in leaf and developing spike inferring a surprising possibility of CAX1 regulation through 14-3-3 protein. Our results provide a molecular insight for explaining the mechanism of calcium accumulation in finger millet.

In silico-prediction of downstream MYB interacting partners of MAPK3 in Arabidopsis.

Protein-Protein interactions (PPIs) are vital to most biological processes thus the identification of PPIs is of primary importance. Here, we endeavor to identify the downstream interacting partners of (AtMAPK3P) in Arabidopsis thaliana using the docking approach. Out of 131 members of MYB transcription factors 41 members are showing interactions with AtMAPK3P while the rest are showing non-interaction. Using minimal sequence motif search as well as through docking approach several novel MYB interacting proteins were also reported in the present study which need to be confirmed by in vitro kinase assay. Together, the results obtained essentially enhance our knowledge of the MAPK interacting protein network and provide a valuable research resource for developing a nearly important link between pathogen-activated MAPK signaling pathways and downstream transcriptional programming.

Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.

Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.

Phyto diab care: Phytoremedial database for antidiabetics.

UNLABELLED: Diabetes, a chronic disease debilitating to normal healthy lifestyle, onsets due to insufficient amount of insulin production or ineffective utilization of the amount produced. Although, pharmaceutical research has brought up remedial drugs and numerous candidates in various phases of clinical trials, off-target effects and unwanted physiological actions are a constant source of concern and contra indicatory in case of diabetic patients. Here we present a phytoremedial database, Phyto Diab Care, broadly applicable to any known anti-diabetic medicinal plant and phytochemicals sourced from them. Utilization of the traditional medicine knowledge for combating diabetes without creating unwanted physiological actions is our major emphasis. Data collected from peer-reviewed publications and phytochemicals were added to the customizable database by means of an extended relational design. The strength of this resource is in providing rapid retrieval of data from large volumes of text at a high degree of accuracy. Enhanced web interface allows multi-criteria based information filtering. Furthermore, the availability of 2D and 3D structures from molecular docking studies with any efficacy on the insulin signaling pathway makes the resource searchable and comparable in an intuitive manner. Phyto Diab Care compendium is publicly available and can be found in online. AVAILABILITY: http://www.gbpuat-cbsh.ac.in/departments/bi/database/phytodiabcare/HOME%20PAGE/Home%20page.html.

in silico-prediction of downstream WRKY interacting partners of MAPK3 in Brassica.

Protein-Protein interactions (PPIs) are vital to most biological processes thus the identification of PPIs is of primary importance. Here, we endeavor to identify the downstream interacting partners of (BjMPK3P) in Brassica juncea using the docking approach. Out of 63 and 37 members of BrWRKY and BnWRKY transcription factors, 50 and 29 members are showing interactions with BjMPK3P respectively while the rest are showing non-interaction. Twenty two WRKY members are common to both the species. Using minimal sequence motif search as well as through docking approach several novel WRKY interacting proteins were also reported in the present study which need to be confirmed by in vitro kinase assay. Together, the results obtained essentially enhance our knowledge of the MAPK interacting protein network and provide a valuable research resource for developing a nearly important link between pathogen-activated MAPK signaling pathways and downstream transcriptional programming.

Differential induction of two different cystatin genes during pathogenesis of Karnal bunt (Tilletia indica) in wheat under the influence of jasmonic acid.

In the present study, expression patterns of two different wheat cystatins (WCs) were studied under the influence of jasmonate signaling in triggering resistance against Karnal bunt (KB). Cystatins are cysteine proteinase inhibitors (CPI) constituting a multigene family which regulate the activity of endo- and/or exogenous cysteine proteinases (CP). Two wheat varieties HD-29 (resistant, R) and WH-542 (susceptible, S) were pre-conditioned with jasmonate and then artificially inoculated with sporidial suspension of Tilletia indica to study its influence in inducing defense by regulating cystatin genes. On the transcriptional level, WC4 and WC5 gave different temporal expression patterns. Expression of WC4 was higher in boot emergence stage which is most susceptible to KB and then slowly declined in both varieties. Expression of WC5 showed an entirely reverse pattern of expression, which kept on rising as the grains matured. Cystatin activity determination by inhibitor assay gave higher activity in resistant variety and under JA treatment. Estimation of specific activity of total cystatin at different days after inoculation (DAI) showed that JA positively induced cystatin expression in both varieties but R variety always registered a greater cystatin expression than the susceptible one (P<0.05). In plants inoculated with pathogen, initially there was a rise in cystatin activity which gradually decreased 7 DAI when compared with the un-inoculated plants. Based on these findings it is clearly demonstrated that jasmonate acts as a potential activator of induced resistance by up-regulating cystatin expression and provides the conditioning effect prior to infection through the maintenance of critical balance of CP/CPI interaction. However, different cystatin genes show different temporal expression patterns and may play different roles at various developmental stages of the grain.

Expression analysis of MAP2K9 and MAPK6 during pathogenesis of Alternaria blight in Arabidopsis thaliana ecotype Columbia.

Arabidopsis thaliana ecotype Columbia was used as a host in order to investigate the involvement of MAP kinase machinery in the pathogenesis of Alternaria blight. Semi-quantitative reverse transcriptase polymerase chain reaction and quantitative real time PCR based approaches were used to determine the change in transcript profile of MAP2K9 and MAPK6 in leaves of A. thaliana ecotpe Columbia at early, middle and late stages of Alternaria blight infection. It was observed that the expression of both MAP2K9 and MAPK6 simultaneously increased up to middle stage of disease progression. There was observed a positive correlation between the expression of MAPK6 and MAP2K9 as disease progressed from initial to middle stage of infection. Then, the expression of MAP2K9 decreased and that of MAPK6 increased as disease progressed towards late stage of infection. The increased levels of MAP2K9 and MAPK6, seem to be necessary for plant to defend the pathogen up to middle stage of infection. However, MAP2K9 may be down regulated at late stage of infection by pathogen to promote it's efficient colonization. Since MAPK6 expression remains unaltered till late stage, it suggests that it's expression is not only regulated by MAP2K9 but also by other MAP2K's. The above results are consistent with observations of earlier studies. In conclusion, the present study has suggested MAP2K9/MAPK6 module as possible target, which is influenced during pathogenesis of Alternaria blight in A. thaliana ecotype Columbia. Hence genetic modulation in expression levels of these components in Arabidopsis or Brassica could be a possible strategy for engineering defense against Alternaria blight disease.

Genome-wide comparative in silico analysis of calcium transporters of rice and sorghum.

The mechanism of calcium uptake, translocation and accumulation in Poaceae has not yet been fully understood. To address this issue, we conducted genome-wide comparative in silico analysis of the calcium (Ca(2+)) transporter gene family of two crop species, rice and sorghum. Gene annotation, identification of upstream cis-acting elements, phylogenetic tree construction and syntenic mapping of the gene family were performed using several bioinformatics tools. A total of 31 Ca(2+) transporters, distributed on 9 out of 12 chromosomes, were predicted from rice genome, while 28 Ca(2+) transporters predicted from sorghum are distributed on all the chromosomes except chromosome 10 (Chr 10). Interestingly, most of the genes on Chr 1 and Chr 3 show an inverse syntenic relationship between rice and sorghum. Multiple sequence alignment and motif analysis of these transporter proteins revealed high conservation between the two species. Phylogenetic tree could very well identify the subclasses of channels, ATPases and exchangers among the gene family. The in silico cis-regulatory element analysis suggested diverse functions associated with light, stress and hormone responsiveness as well as endosperm- and meristem-specific gene expression. Further experiments are warranted to validate the in silico analysis of the predicted transporter gene family and elucidate the functions of Ca(2+) transporters in various biological processes.

MAP Kinase analyser: A tool for plant kinase and substrate analysis.

MAPK (Mitogen Activated Protein Kinase) is a Ser/Thr kinase, which plays a crucial role in plant growth and development, transferring the extra cellular stimuli into intracellular response etc. Manual identification of these MAPK in the plant genome is tedious and time taking process. There are number of online servers which predict the P-site (phosphorylation site), find the motifs and domain but there is no specific tool which can identify all them together. In order to identify the P-Site, phosphorylation site consensus sequences and domain of the MAPK in plant genome, we developed a tool, MAP Kinase analyzer. MAP kinase analyzer take protein sequence as input in the fasta format and the output of tool includes: 1) The prediction of the phosphorylation site viz., Serine (S), Threonine (T), and Tyrosine (Y), Contex, Position, Score and phosphorylating kinase as well as the graphical output; 2) Phosphorylation site consensus sequence pattern for different kinases and 3) Domain information about the MAPK's. The MAP kinase analyser tool and supplementary files can be downloaded from http://www.bioinfogbpuat/mapk_OWN_1/.

MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways.

The mitogen-activated protein kinase (MAPK) cascades play diverse roles in intra- and extra-cellular signaling in plants. MAP kinases are the component of kinase modules which transfer information from sensors to responses in eukaryotes including plants. They play a pivotal role in transduction of diverse extracellular stimuli such as biotic and abiotic stresses as well as a range of developmental responses including differentiation, proliferation and death. Several cascades are induced by different biotic and abiotic stress stimuli such as pathogen infections, heavy metal, wounding, high and low temperatures, high salinity, UV radiation, ozone, reactive oxygen species, drought and high or low osmolarity. MAPK signaling has been implicated in biotic stresses and has also been associated with hormonal responses. The cascade is regulated by various mechanisms, including not only transcriptional and translational regulation but through post-transcriptional regulation such as protein-protein interactions. Recent detailed analysis of certain specific MAP kinase pathways have revealed the specificity of the kinases in the cascade, signal transduction patterns, identity of pathway targets and the complexity of the cascade. The latest insights and finding are discussed in this paper in relation to the role of MAPK pathway modules in plant stress signaling.