Search

Abstract: Chicory, or ‘Cichorium intybus’, is an erect perennial herb that can be used to treat a variety of diseases, including enteric sickness, diabetes, haemorrhoids, malaria, allergies, digestive issues, and more. The enzyme, called 6G-FFT, uses 1-kestose as a substrate for the synthesis of the more complex and branched fructans. To understand the residues involved in this conjugation reaction between 6G-FFT and 1-kestose, molecular docking study was performed. The amino acids ASP157, ASP33, SER32, TRP57, GLU211, ASP244, and GLU117 of the 6G-FFT protein showed a good interaction with the ligand by SP (Standard Precision) docking studies. Results for XP (Extra Precision) docking studies also suggest the amino acids THR153, GLU117, ASP244, GLU211, TRP57, ASP33 and ASP157 interact with the docking score of -10.6 Kcal/mol. Among these interacting amino acids, GLU117, ASP244, GLU211, TRP57, ASP33, and ASP157 were found to be common in both methods. This in silico study will be beneficial for further exploring conjugation reactions in Cichorium intybus.

Abstract: Breast cancer is one of the most frequent invasive malignancies in women globally and the leading cause of mortality. The HER2 target is an important therapeutic option for treating breast cancer. In the present study, efforts have been made to virtually screen the natural kinase inhibitors through molecular docking. A total of 800 HER2 protein inhibitor compounds were selected to screen out the potential inhibitors of the HER2 protein. The docking study demonstrated that these HER2 protein inhibitors confirm the strong binding interaction with HER2 protein based on the docking score, indicating that kinase inhibitors can play a major role in preventing breast cancer. Among all the inhibitors, the flavanone compound named 6-C-(3-Hydroxyisopentyl) eriodictyol, IUPAC: 2-(3, 4- dihydroxyphenyl)-5, 7-dihydroxy-6-(3-hydroxy-3-methylbutyl)- 2, 3-dihydrochromen-4-one observed to have the maximum docking score value of (-8.717), indicating the highest binding affinity with HER2 protein which might serve as the promising compound for the development of a new class of drug to combat breast cancer.

The field of 3D cell culture and its applications is rooted in the understanding of cell biology, tissue engineering, tissue morphology, disease mechanisms, and drug action. For many years, traditional 2D cell culture systems have been widely used but have proven to be limited in their ability to accurately replicate the complex microenvironment of tissues. This often results in issues with cell proliferation, aggregation, and differentiation. 3D cell culture systems have emerged as a solution to this problem and have demonstrated a more accurate simulation of in vivo physiology. This has had a major impact on drug discovery and includes the use of spheroids, organoids, scaffolds, hydrogels, and organs. This review has addressed fundamental questions and exploited utility in 3D in vitro mode of cell culture in view of therapeutics.

Background: Cichorium intybus is a perennial herb in the Asteraceae family that has significant ethano-medical properties and is utilized in Ayurveda and Unani therapy. The enzyme costunolide synthase contributes in the biosynthesis pathway of sesquiterpene lactones, which is thought to give the plant antimalarial action. Methods: This work uses several in-silico techniques along with docking experiments to show the structural and physiochemical characteristics of the enzyme costunolide synthase. Costunolide synthase protein interacts with lactucin and lactucopicrin with lower energy interactions of -4.99 kcal/mol for total 3 hydrogen bonds and -6.55 kcal/mol for total 2 hydrogen bonds, respectively. One domain named CYP 450 has been found which catalyzes a variety of oxidative reactions of a large number of structurally different compounds that are both endogenous and exogenous from all major domains of life. The mitochondrial cellular localization of protein was revealed with a maximum score of 1.833. Results: The phylogenetic study revealed that the enzyme costunolide synthase from Cichorium intybus has a greater resemblance to Cichorium endivia and Lactuca sativa of costunolide synthase. Molecular docking findings of sesquiterpene lactones (lactucin and lactucopicrin) with Plasmepsin II protein of P. falciparum parasites after clinical trials with sesquiterpene lactones may give the more evidences and explanations for the active involvement of lactucin and lactucopicrin as an antimalarial compound. Conclusion: This research will be used in future wet lab studies to figure out how the costunolide synthase enzyme regulates sesquiterpene lactones and to investigate additional regulatory enzyme involved in the synthesis of sesquiterpene lactones.

Traditionally, intelligence was considered to be a mental skill that primarily consisted of two narrow spheres: mathematical / logical and oral / linguistic, or IQ. Howard Gardner expanded this little idea to include many intellectuals. Later, Daniel Goleman introduced a new type of ability, emotional intelligence (EI), the ability to understand personal and others' emotions. The construction of more intelligence, as well as emotional intelligence in particular, has received a lot of attention recently, especially in terms of leadership capacity. There is some evidence that EI traits (e.g., self-awareness, self-control, motivation, public awareness, and relationship management) may be better predictors of leadership performance and success than traditional “intelligence quotient,” or IQ.

Background: Lactucine is related to the sesquiterpene lactone group of naturally occurring compounds and has a variety of pharmacological effects including anticancer properties found in Chicory, Wormwood, Laurus nobilis, Pyrethrum, Chamomile, etc. Lactucine has an anticancer effect which may induce apoptosis in cancerous cells and protect other cells from getting infected. Objective: In this study, Lactucine and its derivatives were screened, and performed their in-silico docking study with the proteins involved in the apoptosis-inducing effect in human leukemia cancer. Methods: The three-dimensional structure of lactucine and its derivatives were retrieved in the SDF format. Active sites of protein structures were determined by Sitemap. LigPrep module was used for geometrical refining of chemical structures of lactucine and its derivatives. The protein preparation wizard of Maestro (Schrodinger) was used for protein preparation. From the receptor-complex structure, the cocrystallized ligands were removed from the active site position of the receptor chain. All ligands were docked using default Glide settings for a grid centered on the ligand and structure. Flexible docking was performed using the extra precision (XP) feature of Glide module. The best docking poses for the lactucine and their derivatives were selected based on their docking score. The ADMET properties of lactucine 15-oxalate have been predicted by admetSAR software. Results: Proteins and ligands three-dimensional structures were retrieved from PDB and Pubchem databases, respectively. All lactucine derivatives suitably docked on the apoptosis-inducing proteins with ample Glide scores Lactucin 15-oxalate interacts with proteins which are responsible for apoptosis with a maximum of six H-bonds. Other types of interactions are also involved, like Pi-cation, Pi-Pi stacking, salt bridges, and halogen bonds. Protein CDK-4 has shown the highest number of H-bond (LYS142 salt bridges), ALA16, VAL14, ASP99, LYS35, TYR17, and ASN145) with the Lactucin 15-oxalate.. ADMET properties of lactucin 15-oxalate met with the criteria of being eligible to be a novel drug for the treatment of human leukemia cancer. The Dock score of both the Dasatinib drug and the lactucine-15-oxalate with the apoptosis-inducing protein stipulates that the selected ligand has equitable interaction with the target proteins. Conclusion: In this study, lactucine derivatives were docked with apoptosis-inducing proteins for the prediction of its anticancer effect. Lactucin15-oxalate has shown the highest binding affinity for the CDK-4 target and can be used as a lead compound for cancer treatment. Glide and Dock score for docking of lactucin 15-oxalate with CDK-4, well as the number of hydrogen bonding, is in agreement to use this ligand for study. These in-silico results are valuable to proceed with the in vitro and in vivo studies related to the anti-cancer role of lactucin 15-oxalate.

Researchers discovered that diets rich in anthocyanin-rich fruits and vegetables significantly impacted gut flora. To conclude, large-scale randomized controlled clinical trials are challenging to conduct; therefore, merging data from multiple small studies may aid. A systematic review collects and analyses all research on a particular subject and design. This comprehensive review and meta-analysis examined the influence of dietary anthocyanins on Firmicutes/Bacteroide (Fir/Bac) and short-chain fatty acids (SCFAs) content. The current meta-analysis followed the guidelines of PRISMA—the preferred reporting items for systematic reviews and meta-analyses. Diets high in anthocyanins substantially reduced the Fir/Bac ratio in the assessed trials. Among three SCFAs, the highest impact was observed on acetic acid, followed by propionic acid, and then butanoic acid. The meta-analysis results also obtained sufficient heterogeneity, as indicated by I2 values. There is strong evidence that anthocyanin supplementation improves rodent gut health biomarkers (Fir/Bac and SCFAs), reducing obesity-induced gut dysbiosis, as revealed in this systematic review/meta-analysis. Anthocyanin intervention duration and dosage significantly influenced the Fir/Bac ratio and SCFA. Anthocyanin-rich diets were more effective when consumed over an extended period and at a high dosage.

Colored wheat has gained enormous attention from the scientific community, but the information available on the anthocyanin biosynthetic genes is very minimal. The study involved their genome-wide identification, in silico characterization and differential expression analysis among purple, blue, black and white wheat lines. The recently released wheat genome mining putatively identified eight structural genes in the anthocyanin biosynthesis pathway with a total of 1194 isoforms. Genes showed distinct exon architecture, domain profile, regulatory elements, chromosome emplacement, tissue localization, phylogeny and synteny, indicative of their unique function. RNA sequencing of developing seeds from colored (black, blue and purple) and white wheats identified differential expressions in 97 isoforms. The F3H on group two chromosomes and F3′5′H on 1D chromosomes could be significant influencers in purple and blue color development, respectively. Apart from a role in anthocyanin biosynthesis, these putative structural genes also played an important role in light, drought, low temperature and other defense responses. The information can assist in targeted anthocyanin production in the wheat seed endosperm.

Drug discovery and optimization of lead compounds become complex when 3D structures of macromolecules are not available. The advancement in computer-aided drug designing and high-throughput virtual screening has opened new doors for significant therapeutic approaches in modern technology instead of conventional methods, which are found to be cost-effective and time-consuming. So, this carried to be striving area across the world. Because of this problem, the idea of ligand-based drug designing has thrown light on the similarity principle where similar molecules exhibit similar biological properties. The unification of these methodologies led to an expanding area in the chemical and biological data, along with the rise in the difficulty of the R&D process. Here, we discussed the methods used for pharmacophore modeling, hypothesis building and validation, and quantitative structure–activity relationship analysis.

Proteins are very flexible biomolecules. The accurate knowledge of protein structure is very important from its functional point of view. In protein structure prediction, the three-dimensional structure of a protein is modeled from its amino acid sequence using knowledge-based approaches. Computational algorithms and tools have made significant improvements in the field of structural modeling. Protein structure prediction methods include comparative modeling (homology modeling), threading, and ab initio approach. Several tools and software have been developed for the 3D modeling of proteins. Each protein modeling methods have certain limitations that should be kept in mind while selecting a tool for structure modeling. The structural details of X-ray crystallography and nuclear magnetic resonance spectroscopy-verified protein structures guide the development of modeling software and also useful in assessing the accuracy of the protein model.

Finger millet (Eleusine coracana L.) is climate resilient minor millet of Asia and Africa with wide adaptation and unparallel nutritional profile. To date, genomic resources available in finger millet are scanty and genetic control of agronomic traits remains elusive. Here, a collection of eco-geographically diverse 186 genotypes was quantified for variation in 13 agronomic traits and reaction to blast to identify marker-trait associations (MTAs) using genotyping-by-sequencing (GBS) and genome-wide association study (GWAS). GBS generated 2977 high quality single nucleotide polymorphism (SNPs) markers and identified three subpopulations with varying admixture levels. General linear and mixed model approaches of GWAS to correct for population structure and genetic relatedness identified 132 common MTAs for agronomic traits across the years. The phenotypic variance explained by the makers varied from 4.8% (TP692389-flag leaf width) to 20% (TP714446-green fodder weight). Of these, 26 MTAs showed homology with candidate genes having role in plant growth, development and photosynthesis in the genomes of foxtail millet, rice, maize, wheat and barley. We also found 4 common MTAs for neck blast resistance, which explained 5.9-15.1% phenotypic variance. Three MTAs for neck blast resistance showed orthologues in related genera having putative functions in pathogen defense in plants. The results of this work lay a foundation for understanding the genetic architecture of agronomic traits and blast resistance in finger millet and provide a framework for genomics assisted breeding.

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 the present computational study, we found that lactucin 15-oxalate a chemical component present in the cichorium intybus (chicory) has a potential apoptosis inducing effect in human leukemia cancer cell and may acts as an anticancer agent. Lactucine and its derivatives were used as ligand molecules to trace out its binding interactions with proteins involved in apoptosis and these ligands were docked with different apoptosis inducing protein such as caspases, cytochrome C, apaf-1, CDKs, etc involved in cell cycle regulation. Among lactucine derivatives, the lactucin 15-oxalate showed virtuous affinity for the apoptosis inducing protein. In addition to this, the number of the hydrogen bonding was higher with lactucin 15-oxalate as compare to other derivatives which indicates its suitability as an anticancer agent. An apoptosis inducing agent if implemented for the treatment of leukemia cancer, then it can reduce the use of multidrug dose therapy and chemotherapeutic drugs. However, different in vitro as well as clinical trials are needed for further validation of the lactucin 15-oxalate.

Cichorium intybus, commonly known as Chicory, is a perennial herb with immense ethanomedical activity and being used in folklore medicine. Due to the presence of ample lactone, this plant has anti-malarial activity. The biosynthesis pathway of sequiterpene lactone (lactucin), which is considered to provide antimalarial activity to the plant, has Germacrene A Synthase as novel rate-limiting enzyme. This study demonstrates the structural and physiochemical properties of the enzyme Germacrene A Synthase through various bioinformatics approaches along with the docking studies. Through the in silico studies it was found that Germacrene A synthase protein interact with the lactucin with the lower energy − 7.3 kcal/mol and total 3 hydrogen bonds were formed by the Germacrene A Synthase at Gly45, Leu46, Tyr246 respectively while Leu41, Glu47, Tyr49, Asn43, Asp42, Ala50, Gln250, Leu249 amino acid residues act together through hydrophobic interactions. It was also found that the Hsp 90 protein of malaria parasite bound with lactucin with lower binding energy i.e. -5.5 kcal/mol. Two domain named terpene synthase has been determined which were found actively participate in the lactucin formation. Through CELLO, cellular localization of protein has been determined in the cytoplasm with maximum score of 2.829. The phylogenetic analysis showed that Germacrene A Synthase enzyme of chicory showing higher similarity with the Germacrene A synthase of Chichorium endivia and Lactuca sativa. Molecular docking results of lactucin and Hsp 90 protein of malarial parasites proceeding clinical trials with lactucin may give the more clue and justification for the active participation of lactucin as antimalarial compound. This study is progressively useful for further wet lab experiments and more in silico analysis to discover the mechanism of lactucin regulation by Germacrene A Synthase enzyme and also to analyze another regulating enzyme or the last enzyme involved in lactucin biosynthesis.

As exemplified by the growing interest in the quantum anomalous Hall effect, the research on topology as an organizing principle of quantum matter is greatly enriched from the interplay with magnetism. In this vein, we present a combined electrical and thermoelectrical transport study on the magnetic Weyl semimetal ${\mathrm{EuCd}}_{2}{\mathrm{As}}_{2}$. Unconventional contribution to the anomalous Hall and anomalous Nernst effects were observed both above and below the magnetic transition temperature of ${\mathrm{EuCd}}_{2}{\mathrm{As}}_{2}$, indicating the existence of significant Berry curvature. ${\mathrm{EuCd}}_{2}{\mathrm{As}}_{2}$ represents a rare case in which this unconventional transverse transport emerges both above and below the magnetic transition temperature in the same material. The transport properties evolve with temperature and field in the antiferromagnetic phase in a different manner than in the paramagnetic phase, suggesting different mechanisms to their origin. Our results indicate ${\mathrm{EuCd}}_{2}{\mathrm{As}}_{2}$ is a fertile playground for investigating the interplay between magnetism and topology, and potentially a plethora of topologically nontrivial phases rooted in this interplay.

Millets and pseudocereals are ancient domesticated food grains and continue to be staple foods for a large segment of Asian, African and Andean population. They are nutritionally superior to major cereals in terms of slow digestible carbohydrates, non-allergenic proteins, dietary fibre and micronutrients. They contain 55–75% starch, 7–15% protein, 2–5% lipid, 2–4% minerals, and 7–15% dietary fibre. The unique nutritional features of these food grains lay in the health beneficial nutraceutical contents. The nutritional and health benefits of millets and pseudocereals have been very well documented and they are recommended to minimize the intensity as well as management of non-communicable diseases such as diabetes, cardiovascular diseases, and obesity. The nutritional and health benefits of these grains have been receiving increased attention and efforts are being made to provide them to the non-traditional consumers worldwide in convenience ready-to-cook and ready-to-eat forms. In the present scenario of sedentary life style, prevention of life style related diseases and to lead healthy life, regular consumption of millets, and pseudocereals is highly desirable.

Although the food systems in developing countries have changed dramatically since the green revolution, malnutrition still remains a challenge and is now known to include the concurrent dimensions of under-nourishment and micronutrient deficiency as a serious issue in developing as well as developed countries. An average cereal protein value of 10% will give us the total cereal protein production of approximately 17 million tons annually. The accumulation of seed protein is a complicated characteristic and seed storage proteins are proteins that considerably accumulate in developing seed, whose principal role is to behave as the nitrogen, carbon, and sulfur storage reserve. These proteins are mobilized quickly during the germination of seeds and are the principal cause of nitrogen reduction to increasing plantings. In particular, the enzymatic functions of seed storage proteins are not known although proteins are structurally distinct in storage from various crops, they all have certain prevalent features. Plant storage proteins may be categorized into two categories; proteins from seed storage (SSPs) and plant storage (VSPs). SSPs are a group of proteins that accumulate in seeds at high concentrations in the late stages of seed development, whereas VSPs are protein accumulation in vegetative tissues, such as roots and tubers, based on plant species. SSPs are depleted during germination, and the subsequent amino acids are used as a food source by the growing seedlings. The most popular proteins in crops are the SSPs and the most commonly consumed plant proteins by human beings are crop proteins. Millets are considered as an enriched source of many essential amino acids derived from many quality proteins. According to World Health Organization, the proteins harboring more than 40% essential amino acids are called quality proteins and upon digestion and hydrolytic cleavage, several bioactive peptides having multiple health attributes are generated. In this chapter, we have briefly described about the proteins and peptides and their role in nutritional improvement present in millet.

We prove two Lieb-Schultz-Mattis type theorems that apply to any translationally invariant and local fermionic $d$-dimensional lattice Hamiltonian for which fermion-number conservation is broken down to the conservation of fermion parity. We show that when the internal symmetry group $G^{\,}_{f}$ is realized locally (in a repeat unit cell of the lattice) by a nontrivial projective representation, then the ground state cannot be simultaneously nondegenerate, symmetric (with respect to lattice translations and $G^{\,}_{f}$), and gapped. We also show that when the repeat unit cell hosts an odd number of Majorana degrees of freedom and the cardinality of the lattice is even, then the ground state cannot be simultaneously nondegenerate, gapped, and translation symmetric., Comment: 51 pages with 2 figures

The spin-1/2 Heisenberg model on the pyrochlore lattice is an iconic frustrated three-dimensional spin system with a rich phase diagram. Besides hosting several ordered phases, the model is debated to possess a spin-liquid ground state when only nearest-neighbor antiferromagnetic interactions are present. Here, we contest this hypothesis with an extensive numerical investigation using both exact diagonalization and complementary variational techniques. Specifically, we employ a RVB-like many-variable Monte Carlo ansatz and convolutional neural network quantum states for (variational) calculations with up to $4\times 4^3$ and $4 \times 3^3$ spins, respectively. We demonstrate that these techniques yield consistent results, allowing for reliable extrapolations to the thermodynamic limit. Our main results are (1) the determination of the phase transition between the putative spin-liquid phase and the neighboring magnetically ordered phase and (2) a careful characterization of the ground state in terms of symmetry-breaking tendencies. We find clear indications of spontaneously broken inversion and rotational symmetry, calling the scenario of a featureless quantum spin-liquid into question. Our work showcases how many-variable variational techniques can be used to make progress in answering challenging questions about three-dimensional frustrated quantum magnets., Comment: 9 pages, 5 figures

The future of food and sustainability of the staple food crops are of utmost importance in the 21st century. Micronutrient deficiency, for example, in iron and zinc, is a common cause of human diseases. Mineral content of the staple food crops has therefore crosscutting importance for food engineering and planetary health. Finger millet, a staple food of agricultural importance worldwide, is rich in iron and zinc, and an ideal model to study the prospects of biofortified foods in times of climate change. We report here a multiomics study of the iron and zinc homeostasis in the finger millet. We identified and characterized 15 candidate genes potentially involved in iron and zinc homeostasis pathways in the finger millet. Structural and functional annotation of the candidate genes revealed a high similarity index with their respective homologs (Oryza sativa, Triticum aestivum, Zea mays, Hordeum vulgare, and Setaria italica). Transcriptome-wide expression analysis showed that genes involved in uptake and translocation of iron and zinc are highly expressed in the GP-1 genotype, while those involved in bioavailability of iron and zinc are expressed more in the GP-45 genotype of the finger millet. In conclusion, finger millet, being a stress-resilient crop, utilizes a combination of strategies in iron and zinc homeostasis pathway, which appear to play an important role in food crop acquisition of iron and zinc, despite environmentally limiting conditions. These data offer molecular insights on iron and zinc accumulation and paves the way for new strategies toward staple food crop with mineral biofortification.

Finger millet is a calcium-rich cereal crop of the grass family. The transcriptome data for finger millet is available at NCBI. It is of interest to annotate and characterize starch synthase enzyme from finger millet transcriptome data. Starch synthase plays an important role in the elongation of glucan chains during the formation of starch. The starch synthase enzyme is characterized using three domains (Glyco_transf_5, Glycos_transf_1 and Glyco_trans_1_4). Binding sites for GLC (alpha-d-glucose), PLP (Pyridoxal-5'- phosphate), AMP (Adenosine monophosphate) and GOL (Glycerol) are found. The phylogenetic analysis showed that the finger millet starch synthase is similar to the granule-bound starch synthase of Oryza sativa and Concrete amaricanus. We report the sequence (GenBank accession number KY648917) and the structural model of finger millet starch synthase (PMDB ID: PM0081600).

Phytoalexins are small antimicrobial molecules synthesized and accumulated by plants upon exposure to pathogens. Camalexin is an indole-derived phytoalexin, which is accumulated in plants including Arabidopsis thaliana, and other Brassicaceae, which plays a major role in disease resistance against fungal pathogens. The productivity of Brassica crops is adversely affected by Alternaria blight disease, which is caused by Alternaria brassicae. In Arabidopsis thaliana, MAP kinase signalling cascade is known to be involved in synthesis of camalexin, which contributes to disease resistance against a necrtrophic fungal pathogen, Botrytis cinerea. In the present study, MAPK signalling cascade leading to biosynthesis of camalexin that triggers defense responses in B. rapa upon exposure to the most devastating nectrophic fungus, Alternaria brassicae has been elucidated with the help of previously reported MAPK cascade in Arabidopsis thaliana, Molecular modelling, docking, and protein-protein interaction analysis of MAP kinases retrieved from Brassica rapa genome have been carried out to reveal the above cascade. The tertiary structure prediction of MAPKs obtained through molecular modelling revealed that all the protein models fulfil the criteria of being the stable structures. The molecular docking of predicted models for elucidating potential partners of MAPKs revealed strong interactions between MKK1, MKK4, MKK5, MAPK3 and MAPK6 with MKK9. The MAPK signalling cascade also shows different genes that express and play major role in camalexin biosynthesis in B. rapa during defense response to A. brassicae. The understanding of MAPK defense signaling pathway in B. rapa against devastating fungal pathogen Alternaria brassicae would help in devising strategies to develop disease resistance in Brassica crops.

Salmonella Typhimurium is an important pathogen having broad host range . Several genes contribute in virulence of Salmonella. Stn is an important virulent gene which code for Salmonellatoxin, increases the level of c-AMP in the host, and ultimately results into diarrhoea and vomiting. In present study stn gene was cloned, sequenced and on basis of sequence information of stn gene,phylogenetic relation was deduced between different serovars of Salmonella Typhimurium. Genomic DNA was isolated from field isolate of Salmonella Typhimurium (isolate No-A201) and stn gene was amplified using gene specific primer and cloned in pJET vector by the positive selection system. Amplification of stn gene yielded a product of approximately 750 bp. Subsequently gene was sequenced and a complete ORF of 750 bp was obtained. The sequence was submitted to NCBI Genbank and allotted the Accession No KF032246 was allocated.Sequence was further used for bioinformatics analysis of Stnprotein, which exhibited two major domains and one amino acid substitution at 609residue. On phylogenetic analysis, S.Typhimurium exhibited 99% similarity with Salmonella enterica subsp. entericaserovar Newport.Our findings indicate that stn is an important toxin gene, which is conserved among many serovars of Salmonella. Therefore, it may be proven as a suitable candidate for development of sub-unit vaccine against Salmonella.

Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. In this study it was try to find out the gene sequence of starch branching enzyme and annotate the sequence and submit the sequence for further use. Rice SBE sequence was taken as reference and for characterization of the sequence different in silico tools were used. Four domains were found in the finger millet Starch branching enzyme like alpha amylase catalytic domain from 925 to2172 with E value 0, N-terminal Early set domain from 634 to 915 with E value 1.62 e-42, Alpha amylase, C-terminal all-beta domain from 2224 to 2511 with E value 5.80e-24 and 1,4-alpha-glucan-branching enzyme from 421 to 2517 with E value 0. Major binding interactions with the GLC (alpha-d-glucose), CA (calcium ion), GOL (glycerol), TRS (2-amino-2-hydroxymethylpropane- 1, 3-diol), MG (magnesium ion) and FLC (citrate anion) are fond with different residues. It was found in the phylogenetic study of the finger millet SBE with the 6 species of grass family that two clusters were form A and B. In cluster A, finger millet showed closeness with Oryzasativa and Setariaitalica, Sorghum bicolour and Zea mays while cluster B was formed with Triticumaestivum and Brachypodium distachyon. The nucleotide sequence of Finger millet SBE was submitted to NCBI with the accession no KY648913 and protein structure of SBE of finger millet was also submitted in PMDB with the PMDB id - PM0080938. This research presents a comparative overview of Finger millet SBE and includes their properties, structural and functional characteristics, and recent developments on their post-translational regulation.

The three-dimensional modeling of protein structure is a reliable approach for understanding the biochemical functions along with the dynamics of protein interactions, which provides useful applications in developing drug molecules for curing diseases as well as certain other applications in biological and agricultural sciences. The conventional laboratory methods such as NMR and X-ray crystallography which are standard approaches for analysis of different proteins of interest are labor-intensive, expensive, and time-consuming. To address these challenges, the bioinformatics tools and approaches may open up new avenues for investigating the protein structures and functions. In the recent past, molecular modeling has been successfully used in various projects for 3D structure prediction of some therapeutically important proteins having applications ranging from medicine to agriculture. The approach of molecular modeling is based on the understanding of algorithms of protein structure prediction. This chapter illustrates the salient features of molecular modeling methods for a reliable and accurate structure prediction of the proteins in the field of drug designing.

The farmers of hill regions are mostly trivial farmers, practicing little external effort based production system. Agriculture, livestock, horticulture, and forestry collectively with animal husbandry provide opportunities for best possible consumption of the resources available in the system. Microorganisms are fundamental components to maintain the ecological integrity of any ecosystem, and the identification of native microorganisms as potent bioinoculants for plant growth promotion will definitely increase the production of agriculture products. Omics tools are capable to enhancing the nutritional quality of crops; growing agricultural production with a significant function in microbial-plant association by understanding the genomic secrets of microbes which significantly affecting the growth of agricultural economics. Genomics, transcriptomics, proteomics, and metabolomics, the major branches of omics, along with the microbiology are widely used to understand the complexities of microbial genomes, and these combined approaches are explored for high altitude regions also to produce resistant and improved quality crops but still reveal a high nutritional worth. Systems biology approach of omics enables to understand the multifarious interactions between genes, proteins, and metabolites within the expected phenotype. These approaches are a set of bioinformatics and computational analysis as well as chemical analytical methods including many more disciplines of biology for betterment of higher-altitude socioeconomic condition by producing quality agriproducts. Omics can allow advanced development of agricultural research for food, well-being, energy, feedstock, and chemicals while helping to protect, improve, and remediate the environment of high altitude regions.

Since green revolution, the food systems in most of the countries have dramatically changed but undernourishment still remains an inflammable problem. This alarming condition is even increasing due to the marginal supply of nutri-enriched food to eat. Under such chronically undernourished condition, dietary deficiencies of iron and zinc lead to compromised planetary health and economic losses. Given the micronutrient deficiency, there is an urgent call to devise or innovative a strategy for providing the requisite amount of iron and zinc in their daily intake to counter this issue. Thus being a high iron and zinc accumulating crop, finger millet can be efficiently used as an intricate model system to explore the prospects of genetic and molecular mechanisms which are responsible for nutrient enrichment in grains. We report here a promising role of nanotechnology in terms of their iron and zinc biofortification potentials in the finger millet. Comparative in vitro evaluation using lower concentration of Fe3O4 (100 ppm) and ZnO (5 ppm) nanoparticles (NPs) display a significant promotory effect on both mineral assimilation and growth parameters whereas higher concentrations of NPs, FeSO4.7H2O and ZnSO4.7H2O bulk salts marked inhibitory effects. The molecular modelling and docking interaction analysis infers that these nano-minerals may bind to significantly influence the modulation of regulatory genes. The result was further validated using real time PCR profiling. The differential expression profiling resulted in higher transcriptional modulation of iron and zinc transporters particularly EcFER1, EcIRT2, EcYSL2, EcZIP1 and EcZTP29 in nano-primed genotypes compared to controls. Thus in conclusion, being a nutrient by default and stress-resilient crop, nanoparticle formulations in finger millet triggers the epigenetic regulation of potential key regulatory genes involved in iron and zinc homeostasis. The study also indicates innovative role of nano-seed priming for biofortification which triggers differential modulation of iron and zinc acquisition and enrichment in grains despite nutrient limiting conditions.

Physico-chemical properties reflect the functional and structural characteristics of a protein. The comparative study of the physicochemical properties is important to know role of a protein in exploring its molecular evolution. A number of online and offline tools are available for calculating the physico-chemical properties of a single protein sequence. However, a tool is not available for a comparative study with graphical visualization of Multi-FASTA sequences. Hence, we describe the development and utility of MFPPI V.1.0 (a web interface developed in JAVA platform) to input each FASTA sequence from Multi-FASTA file into the ProtParam web server for the calculation of physico-chemical properties. MFPPI V.1.0 calculates different physico-chemical properties for a given set of proteins in a single run and saves the data in the MSExcel sheet. Furthermore, it provides a graphical representation of protein physico-chemical properties for analysis and visualization of data in a user-friendly manner. Therefore, the output from the analysis helps to understand compositional changes and functional relationship in evolution among organisms. We have demonstrated the utility of MFPPI V.1.0 using 17 mtATP6 protein sequences from different mammalian species. It is available for free at http://insilicogenomics.in/mfpcalc/mfppi.html.

We explore various aspects of 2-form topological gauge theories in (3+1)d. These theories can be constructed as sigma models with target space the second classifying space $B^2G$ of the symmetry group $G$, and they are classified by cohomology classes of $B^2G$. Discrete topological gauge theories can typically be embedded into continuous quantum field theories. In the 2-form case, the continuous theory is shown to be a strict 2-group gauge theory. This embedding is studied by carefully constructing the space of $q$-form connections using the technology of Deligne-Beilinson cohomology. The same techniques can then be used to study more general models built from Postnikov towers. For finite symmetry groups, 2-form topological theories have a natural lattice interpretation, which we use to construct a lattice Hamiltonian model in (3+1)d that is exactly solvable. This construction relies on the introduction of a cohomology, dubbed 2-form cohomology, of algebraic cocycles that are identified with the simplicial cocycles of $B^2G$ as provided by the so-called $W$-construction of Eilenberg-MacLane spaces. We show algebraically and geometrically how a 2-form 4-cocycle reduces to the associator and the braiding isomorphisms of a premodular category of $G$-graded vector spaces. This is used to show the correspondence between our 2-form gauge model and the Walker-Wang model., 78 pages

We analyze $2+1d$ and $3+1d$ bosonic symmetry protected topological (SPT) phases of matter protected by onsite symmetry group $G$ by using dual bulk and boundary approaches. In the bulk, we study an effective field theory, which upon coupling to a background flat $G$ gauge field furnishes a purely topological response theory. The response action evaluated on certain manifolds, with appropriate choice of background gauge field, defines a set of SPT topological invariants. Further, SPTs can be gauged by summing over all isomorphism classes of flat $G$ gauge fields to obtain Dijkgraaf-Witten topological $G$ gauge theories. These topological gauge theories can be ungauged by first introducing and then proliferating defects that spoil the gauge symmetry. This mechanism is related to anyon condensation in $2+1d$ and condensing bosonic gauge charges in $3+1d$. In the dual boundary approach, we study $1+1d$ and $2+1d$ quantum field theories that have $G$ 't-Hooft anomalies that can be precisely canceled by (the response theory of) the corresponding bulk SPT. We show how to construct/compute topological invariants for the bulk SPTs directly from the boundary theories. Further, we sum over boundary partition functions with different background gauge fields to construct $G$ characters that generate topological data for the bulk topological gauge theory. Finally, we study a $2+1d$ quantum field theory with a mixed ${\mathbb{Z}}_{2}^{T/R}\ifmmode\times\else\texttimes\fi{}\text{U}(1)$ anomaly where ${\mathbb{Z}}_{2}^{T/R}$ is time-reversal/reflection symmetry, and the $\text{U}(1)$ could be a 0-form or 1-form symmetry depending on the choice of time reversal/reflection action. We briefly discuss the bulk effective action and topological response for a theory in $3+1d$ that cancels this anomaly. This signals the existence of SPTs in $3+1d$ protected by 0,1-form $\text{U}(1)\ifmmode\times\else\texttimes\fi{}{\mathbb{Z}}_{2}^{T,R}$.

Excitations in (3+1)D topologically ordered phases have very rich structures. (3+1)D topological phases support both point-like and string-like excitations, and in particular the loop (closed string) excitations may admit knotted and linked structures. In this work, we ask the question how different types of topological excitations contribute to the entanglement entropy, or alternatively, can we use the entanglement entropy to detect the structure of excitations, and further obtain the information of the underlying topological orders? We are mainly interested in (3+1)D topological orders that can be realized in Dijkgraaf-Witten gauge theories, which are labeled by a finite group $G$ and its group 4-cocycle $\omega\in\mathcal{H}^4[G;U(1)]$ up to group automorphisms. We find that each topological excitation contributes a universal constant $\ln d_i$ to the entanglement entropy, where $d_i$ is the quantum dimension that depends on both the structure of the excitation and the data $(G,\,\omega)$. The entanglement entropy of the excitations of the linked/unlinked topology can capture different information of the DW theory $(G,\,\omega)$. In particular, the entanglement entropy introduced by Hopf-link loop excitations can distinguish certain group 4-cocycles $\omega$ from the others.

We discuss several bosonic topological phases in (3+1) dimensions enriched by a global $\mathbb{Z}_2$ symmetry, and gauging the $\mathbb{Z}_2$ symmetry. More specifically, following the spirit of the bulk-boundary correspondence, expected to hold in topological phases of matter in general, we consider boundary (surface) field theories and their orbifold. From the surface partition functions, we extract the modular $\mathcal{S}$ and $\mathcal{T}$ matrices and compare them with $(2+1)$d toplogical phase after dimensional reduction. As a specific example, we discuss topologically ordered phases in $(3+1)$ dimensions described by the BF topological quantum field theories, with abelian exchange statistics between point-like and loop-like quasiparticles. Once the $\mathbb{Z}_2$ charge conjugation symmetry is gauged, the $\mathbb{Z}_2$ flux becomes non-abelian excitation. The gauged topological phases we are considering here belong to the quantum double model with non-abelian group in $(3+1)$ dimensions., 14 pages, 5 figures

In the present study, we identified seven major genes of oxalic acid biosynthesis pathway (SGAT, GGAT, ICL, GLO, MHAR, APO and OXO) from developing spike transcriptome of finger millet using rice as a reference. Sequence alignment of identified genes showed high similarity with their respective homolog in rice except for OXO and GLO. Transcript abundance (FPKM) reflects the higher accumulation of identified genes in GP-1 (low calcium genotype) as compared to GP-45 (high calcium genotype) which was further confirmed by qRT-PCR analysis, indicating differential oxalate formation in both genotypes. Determination of oxalic acid and tartaric acid content in developing spikes explain that higher oxalic acid content in GP-1 however, tartaric acid content was more in GP-45. Higher calcium content in GP-45 and lower oxalate accumulation may be due to the diversion of more ascorbic acid into tartaric acid and may correspond to less formation of calcium oxalate. Our results suggest that more than one pathway for oxalic acid biosynthesis might be present in finger millet with probable predominance of ascorbate-tartarate pathway rather than glyoxalate-oxalate conversion. Thus, finger millet can be use as an excellent model system for understanding more specific role of nutrients-antinutrients interactions, as evident from the present study.

The multi-flavor $BF$ theories in (3+1) dimensions with cubic or quartic coupling are the simplest topological quantum field theories that can describe fractional braiding statistics between loop-like topological excitations (three-loop or four-loop braiding statistics). In this paper, by canonically quantizing these theories, we study the algebra of Wilson loop and Wilson surface operators, and multiplets of ground states on three torus. In particular, by quantizing these coupled $BF$ theories on the three-torus, we explicitly calculate the $\mathcal{S}$- and $\mathcal{T}$-matrices, which encode fractional braiding statistics and topological spin of loop-like excitations, respectively. In the coupled $BF$ theories with cubic and quartic coupling, the Hopf link and Borromean ring of loop excitations, together with point-like excitations, form composite particles., 20 pages, 3 figures

Finger millet is a nutritious cereal and marker assisted breeding is essential for the identification of genes/alleles governing quality traits in finger millet. This study used an integrated breeding strategy supported by genomics, where selective genotyping of 113 diverse finger millet genotypes was carried out for understanding the complex genetic architecture of SPC (seed protein content) and related traits like DM (days to maturity) and GY (grain yield) in two geographically different locations in India i.e. Almora (E1) and Pantnagar (E2). Significant differences among genotypes were observed for SPC, DM and GY in both the locations. A set of 2977 genome-wide SNPs identified through genotyping by sequencing were used for MTA analysis. GLM resulted in 7, 10 and 9, while MLM found 4, 9 and 7 MTA's for SPC, DM and GY, respectively across the locations using TASSEL pipeline. Among GLM and MLM 4, 7 and 6 MTA's were found common for SPC, DM and GY, respectively. Another pipeline, GAPIT identified 12 MTA's each for SPC, DM and 11 MTA's for GY across the locations. NCBI blast of common SNP markers for all three traits resulted in 5, 3 and 5 most effective genome regions associated with SPC, DM and GY. Among them, the SNP responsible for gene encoding aspartyl protease exhibited strong SPC association and was found to be the most promising candidate for protein content variation in finger millet. For GY and DM, ATP synthase gene which catalyses the addition of a phosphate to ADP, capturing energy from the proton gradient as ATP was found prominent gene. Expression results for five genes associated with SPC showed higher transcript accumulation in high protein containing genotype in comparison to low protein containing genotype.

Finger millet [Eleusine coracana (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.

We discuss (2+1)-dimensional gapless surface theories of bulk (3+1)-dimensional topological phases, such as the BF theory at level $\mathrm{K}$, and its generalization. In particular, we put these theories on a flat (2+1) dimensional torus $T^3$ parameterized by its modular parameters, and compute the partition functions obeying various twisted boundary conditions. We show the partition functions are transformed into each other under $SL(3,\mathbb{Z})$ modular transformations, and furthermore establish the bulk-boundary correspondence in (3+1) dimensions by matching the modular $\mathcal{S}$ and $\mathcal{T}$ matrices computed from the boundary field theories with those computed in the bulk. We also propose the three-loop braiding statistics can be studied by constructing the modular $\mathcal{S}$ and $\mathcal{T}$ matrices from an appropriate boundary field theory., Comment: 25 pages, 1 figures