Molecular Docking and Interaction Studies of Identified Abscisic Acid Receptors in Oryza sativa: An In-Silico Perspective on Comprehending Stress Tolerance Mechanisms.

Background: Abiotic stresses affect plants in several ways and as such, phytohormones such as abscisic acid (ABA) play an important role in conferring tolerance towards these stresses. Hence, to comprehend the role of ABA and its interaction with receptors of the plants, a thorough investigation is essential. Aim: The current study aimed to identify the ABA receptors in Oryza sativa, to find the receptor that binds best with ABA and to examine the mutations present to help predict better binding of the receptors with ABA. Methods: Protein sequences of twelve PYL (Pyrabactin resistance 1) and seven PP2C (type 2C protein phosphatase) receptors were retrieved from the Rice Annotation Project database and their 3D structures were predicted using RaptorX. Protein-ligand molecular docking studies between PYL and ABA were performed using AutoDock 1.5.6, followed by 100ns molecular dynamic simulation studies using Desmond to determine the acceptable conformational changes after docking via root mean square deviation RMSD plot analysis. Protein-protein docking was then carried out in three sets: PYL-PP2Cs, PYL-ABA-PP2C and PYL(mut)-ABA-PP2C to scrutinize changes in structural conformations and binding energies between complexes. The amino acids of interest were mapped at their respective genomic coordinates using SNP-seek database to ascertain if there were any naturally occurring single nucleotide polymorphisms (SNPs) responsible for triggering rice PYLs mutations. Results: Initial protein-ligand docking studies revealed good binding between the complexes, wherein PYL6-ABA complex showed the best energy of -8.15 kcal/mol. The 100ns simulation studies revealed changes in the RMSD values after docking, indicating acceptable conformational changes. Furthermore, mutagenesis study performed at specific PYL-ABA interacting residues followed by downstream PYL(mut)-ABA-PP2C protein-protein docking results after induction of mutations demonstrated binding energy of -8.17 kcal/mol for PP2C79-PYL11-ABA complex. No naturally occurring SNPs that were responsible for triggering rice PYL mutations were identified when specific amino acid coordinates were mapped at respective genomic coordinates. Conclusion: Thus, the present study provides valuable insights on the interactions of ABA receptors in rice and induced mutations in PYL11 that can enhance the downstream interaction with PP2C.

Impact of regulatory spin of pioglitazone on prescription of antidiabetic drugs among physicians in India: A multicentre questionnaire-based observational study.

Background & objectives: Pioglitazone was suspended for manufacture and sale by the Indian drug regulator in June 2013 due to its association with urinary bladder carcinoma, which was revoked within a short period (July 2013). The present questionnaire-based nationwide study was conducted to assess its impact on prescribing behaviour of physicians in India. Methods: Between December 2013 and March 2014, a validated questionnaire was administered to physicians practicing diabetes across 25 centres in India. Seven hundred and forty questionnaires fulfilling the minimum quality criteria were included in the final analysis. Results: Four hundred and sixteen (56.2%) physicians prescribed pioglitazone. Of these, 281 used it in less than the recommended dose of 15 mg/day. Most physicians (94.3%) were aware of recent regulatory events. However, only 333 (44.8%) changed their prescribing pattern. Seventeen of the 416 (4.1%) physicians who prescribed pioglitazone admitted having come across at least one type 2 diabetes mellitus patient (T2DM) who had urinary bladder carcinoma, and of these 13 said that it was in patients who took pioglitazone for a duration of more than two years. Only 7.8 per cent of physicians (n=58) categorically advocated banning pioglitazone, and the rest opined for its continuation or generating more evidence before decision could be taken regarding its use in T2DM. Interpretation & conclusions: Majority of the physicians though were aware of the regulatory changes with regard to pioglitazone, but their prescribing patterns were not changed for this drug. However, it was being used at lower than the recommended dose. There is a need for generating more evidence through improved pharmacovigilance activities and large-scale population-based prospective studies regarding the safety issues of pioglitazone, so as to make effectual risk-benefit analysis for its continual use in T2DM.

Simultaneous expression of regulatory genes associated with specific drought-adaptive traits improves drought adaptation in peanut.

Adaptation of crops to drought-prone rain-fed conditions can be achieved by improving plant traits such as efficient water mining (by superior root characters) and cellular-level tolerance mechanisms. Pyramiding these drought-adaptive traits by simultaneous expression of genes regulating drought-adaptive mechanisms has phenomenal relevance in improving stress tolerance. In this study, we provide evidence that peanut transgenic plants expressing Alfalfa zinc finger 1 (Alfin1), a root growth-associated transcription factor gene, Pennisetum glaucum heat-shock factor (PgHSF4) and Pea DNA helicase (PDH45) involved in protein turnover and protection showed improved tolerance, higher growth and productivity under drought stress conditions. Stable integration of all the transgenes was noticed in transgenic lines. The transgenic lines showed higher root growth, cooler crop canopy air temperature difference (less CCATD) and higher relative water content (RWC) under drought stress. Low proline levels in transgenic lines substantiate the maintenance of higher water status. The survival and recovery of transgenic lines was significantly higher under gradual moisture stress conditions with higher biomass. Transgenic lines also showed significant tolerance to ethrel-induced senescence and methyl viologen-induced oxidative stress. Several stress-responsive genes such as heat-shock proteins (HSPs), RING box protein-1 (RBX1), Aldose reductase, late embryogenesis abundant-5 (LEA5) and proline-rich protein-2 (PRP2), a gene involved in root growth, showed enhanced expression under stress in transgenic lines. Thus, the simultaneous expression of regulatory genes contributing for drought-adaptive traits can improve crop adaptation and productivity under water-limited conditions.

Liposome encapsulated anticancer drugs on autophagy in cancer cells - Current and future perspective.

Autophagy act as a double-edged sword in cancer with both tumor promoting and inhibiting roles. Under normal conditions of autophagy, the damaged cell organelles and other debris degrade inside the lysosome to provide energy and macromolecular precursors. However, enhanced autophagy can lead to apoptosis and programmed cell death highlighting its significance in cancer therapy. Liposome-based drug delivery systems for treating cancer patients have significant advantages over their non-formulated or free drug counterparts which could be effectively used to manipulate autophagy pathway in cancer patients. In the current review, drug uptake by the cells and its role in autophagy-mediated cancer cell death are discussed. Besides, the challenges and translational difficulties associated with the use of liposome-based chemotherapeutic drugs in clinical trials and in biomedical applications are also discussed.

Decision Support System and Web-Application Using Supervised Machine Learning Algorithms for Easy Cancer Classifications.

Using a decision support system (DSS) that classifies various cancers provides support to the clinicians/researchers to make better decisions that can aid in early cancer diagnosis, thereby reducing chances of incorrect disease diagnosis. Thus, this work aimed at designing a classification model that can predict accurately for 5 different cancer types comprising of 20 cancer exomes, using the mutations identified from whole exome cancer analysis. Initially, a basic model was designed using supervised machine learning classification algorithms such as K-nearest neighbor (KNN), support vector machine (SVM), decision tree, naïve bayes and random forest (RF), among which decision tree and random forest performed better in terms of preliminary model accuracy. However, output predictions were incorrect due to less training scores. Thus, 16 essential features were then selected for model improvement using 2 approaches. All imbalanced datasets were balanced using SMOTE. In the first approach, all features from 20 cancer exome datasets were trained and models were designed using decision tree and random forest. Balanced datasets for decision tree model showed an accuracy of 77%, while with the RF model, the accuracy improved to 82% where all 5 cancer types were predicted correctly. Area under the curve for RF model was closer to 1, than decision tree model. In the second approach, all 15 datasets were trained, while 5 were tested. However, only 2 cancer types were predicted correctly. To cross validate RF model, Matthew's correlation co-efficient (MCC) test was performed. For method 1, the MCC test and MCC cross validation was found to be 0.7796 and 0.9356 respectively. Likewise, for second approach, MCC was observed to be 0.9365, corroborating the accuracy of the designed model. The model was successfully deployed using Streamlit as a web application for easy use. This study presents insights for allowing easy cancer classifications.

Development of AtMYB12-expressing transgenic tobacco callus culture for production of rutin with biopesticidal potential.

UNLABELLED: Flavonoids synthesized by the phenylpropanoid pathway participate in a number of physiological and biochemical processes in plants. Flavonols, among flavonoids, are considered as health-protective components in functional foods and they protect plants against certain insect pests. There have been efforts to develop strategies for the enhanced production of flavonols in plants, but limited success was achieved due to complex regulation and poor substrate availability. In the present study, we have developed and optimized method for callus cultures for transgenic tobacco line expressing a flavonol-specific transcription factor, AtMYB12, with an objective to use callus as an alternative source of rutin. Transgenic callus displayed enhanced expression of genes related to biosynthetic pathway leading to increased accumulation of flavonols, especially rutin. At each time point of callus growth, the rutin content of transgenic callus was several folds higher than that of wild-type tobacco callus. Supplementation of semi-synthetic diet with extract from transgenic callus as well as purified rutin led to mortality and growth reduction in the Spodoptera litura and Helicoverpa armigera larvae. This study suggests the biotechnological potential of AtMYB12-expressing callus cultures for the production of rutin, which can be used for biopesticide formulations against insect pests. KEY MESSAGE: Tobacco callus cultures expressing AtMYB12 accumulate enhanced content of rutin and can be used as a potential alternative source of rutin as well as biopesticides against insect pests.

Autophagy and cancer: Can tetrandrine be a potent anticancer drug in the near future?

Autophagy is an essential catabolic process in mammalian cells to maintain cellular integrity and viability by degrading the old and damaged cell organelles and other contents with the help of lysosomes. Deregulation in autophagy can be one of the major contributors leading to the continuous cell proliferation and development of tumors. Tetrandrine, a bisbenzylisoquinoline alkaloid known to have potent bioactivities such as anticancer, antimicrobial, anti-inflammatory, antidiabetic, antioxidant, immunosuppressive, cardiovascular, and calcium channel blocking effects. The present review evaluated the effectiveness of tetrandrine in targeting key proteins in the autophagy pathway to induce anticancer effect based on the available literature. An attempt is also made to understand the influence of tetrandrine in regulating autophagy by mTOR dependant and mTOR-independent pathways. In addition, the review also highlights the limitations involved and future perspectives in developing tetrandrine as a chemotherapeutic drug to treat cancer.

MutaXome: A Novel Database for Identified Somatic Variations of In silico Analyzed Cancer Exome Datasets.

Advancements in the field of cancer research have enabled researchers and clinicians to access a massive amount of data to aid cancer patients and to add to the existing knowledge of research. However, despite the existence of reliable sources for extricating this data, it remains a challenge to accurately comprehend and draw conclusions based on the entirety of available information. Therefore, the current study aimed to design and develop a database for the identified variants of 5 different cancer types using 20 different cancer exomes. The exome data were retrieved from NCBI SRA and an NGS data clean-up protocol was implemented to obtain the best quality reads. The reads which passed the quality checks were then used for calling the variants which were then processed and filtered. This data was used to normalize and the normalized data generated was used for developing the database. MutaXome, which stands for mutations in cancer exome was designed in SQL, with the front end in bootstrap and HTML, and backend in PHP. The normalized data containing the variants inclusive of Single Nucleotide Polymorphisms (SNPs), were added into MutaXome, which contains detailed information regarding each type of identified variant. This database, available online via http://www.vidyalab.rf.gd/, serves as a knowledge base for cancer exome variations and holds much potential for enriching it by linking it to a decision support system as prospective studies.

Modulation of transcriptome and metabolome of tobacco by Arabidopsis transcription factor, AtMYB12, leads to insect resistance.

Flavonoids synthesized by the phenylpropanoid pathway participate in myriad physiological and biochemical processes in plants. Due to the diversity of secondary transformations and the complexity of the regulation of branched pathways, single gene strategies have not been very successful in enhancing the accumulation of targeted molecules. We have expressed an Arabidopsis (Arabidopsis thaliana) transcription factor, AtMYB12, in tobacco (Nicotiana tabacum), which resulted in enhanced expression of genes involved in the phenylpropanoid pathway, leading to severalfold higher accumulation of flavonols. Global gene expression and limited metabolite profiling of leaves in the transgenic lines of tobacco revealed that AtMYB12 regulated a number of pathways, leading to flux availability for the phenylpropanoid pathway in general and flavonol biosynthesis in particular. The tobacco transgenic lines developed resistance against the insect pests Spodoptera litura and Helicoverpa armigera due to enhanced accumulation of rutin. Suppression of flavonol biosynthesis by artificial microRNA reversed insect resistance of the AtMYB12-expressing tobacco plants. Our study suggests that AtMYB12 can be strategically used for developing safer insect pest-resistant transgenic plants.

Larvicidal activities of Knema attenuata (Hook. f. & Thomson) Warb. (Myristicaceae) extracts against Aedes albopictus Skuse and Anopheles stephensi Liston.

In recent years, uses of environment friendly and biodegradable natural insecticides of plant origin have received renewed attention as agents for vector control. The present study was undertaken to investigate the effect of aril and kernel extracts of Knema attenuata (Hook. f. & Thomson) Warb. (Myristicaceae) on larvae of Aedes albopictus Skuse and Anopheles stephensi Liston under laboratory conditions. The aril was extracted with chloroform and ethanol; the kernel was extracted with ethanol and hexane. The extracts were tested against the 3rd-4th instar larvae collected from Bunder area, Mangalore, India, which is a well-known fishing harbour, where several mosquito-borne diseases were reported. All the graded concentrations (100, 200, 300, 400 and 500 ppm) showed significant larval mortality after 24 h of observation. Chloroform extracts of aril showed 100% mortality against both larval forms of A. albopictus and A. stephensi at the concentration of 500 ppm. Among the extracts tested, chloroform extracts of aril and ethanol extracts of kernel exhibited higher toxicity against both A. albopictus (LC(50), 141 ppm and 159 ppm; LC(90), 290 ppm and 342 ppm) and A. stephensi (LC(50), 160 ppm and 162 ppm; LC90, 445 ppm and 458 ppm). Hexane extracts of kernel exhibited least toxicity against A. albopictus (LC50, 239 ppm; LC(90), 484 ppm), whereas ethanol extracts of aril showed the least toxicity against A. stephensi (LC(50), 290; LC(90), 498). A preliminary phytochemical assay revealed the presence of phenolics, tannins, steroids, terpenes, resins, and glycolipids in all the extracts. Alkaloids, flavonoids and saponins were absent. The lower LC(50) value of the chloroform extracts of K. attenuata aril indicates its potentiality as a larvicide against A. albopictus and A. stephensi mosquito larvae.

Picobirnavirus detection in bovine and buffalo calves from foothills of Himalaya and Central India.

The present study describes detection of picobirnavirus (PBV) in faecal samples from bovine and buffalo calves employing the polyacrylamide gel electrophoresis (PAGE). A total of 136 faecal samples from buffalo (n = 122) and cow calves (n = 14) exhibiting clinical signs of diarrhoea and from healthy calves were collected during 2007-2010 from subtropical (central India) and tarai area of western temperate Himalayan foothills (Uttarakhand). The dsRNA nature of the virus was confirmed by nuclease treatment (RNase A, RNaseT1 and DNase 1). PAGE results confirmed 3.67% (5/136) positivity for PBV, showing a typical genomic migration pattern with two discrete bands with size of approximately 2.4 and 1.7 kbps for the larger and smaller segments, respectively. Among the five PBV samples identified, three were from buffalo calves and one from cow calf exhibiting clinical signs of acute diarrhoea, while one sample from non-diarrhoeic buffalo calf also showed the presence of PBV. None of the samples showed dual infection of rotavirus and PBV. The preliminary findings indicate sporadic incidences of PBV in bovine calves and emphasize the need for the development of better diagnostics for early detection and genetic characterization of these emerging isolates of farm animals of economic significance.

ABO phenotype and SARS-CoV-2 infection: Is there any correlation?

COVID-19 is the currently evolving viral disease worldwide. It mainly targets the respiratory organs, tissues and causes illness. A plethora of studies has been performing to bring proper treatment and prevent people from the infection. Likewise, susceptibility to some infectious diseases has been associated with blood group phenotypes. The co-relationship of blood group with the occurrence of SARS-CoV-2 infection and death has been examined in numerous studies. This review explained the described studies regarding the correlation of blood group and the other essential factors with COVID-19.

D-Aspartic acid induced oxidative stress and mitochondrial dysfunctions in testis of prepubertal rats.

Previously we demonstrated the potential of D-aspartic acid (D-Asp), an acidic amino acid to induce oxidative response in prepubertal rat testis in vitro. In the present study, we determined the extent of oxidative stress in the testis of prepubertal rats that were administered D-Asp (100 and 500 mg/kg bw/d, i.p. 7 days). D-Asp treatment significantly elevated the levels of reactive oxygen species, malondialdehyde and hydroperoxide in cytosol and mitochondria of testis, which were accompanied by enhanced glutathione levels, elevated activities of glutathione-dependent enzymes and catalase suggesting a state of oxidative stress. Further, the activities of D-aspartate oxidase and 3beta-hydroxy steroid dehydrogenase were elevated in the testis. The testis mitochondria of D-Asp-treated rats showed altered citric acid and complex enzyme activities, reduction in membrane potential, increased permeability and intracellular Ca(2+) levels. Collectively, these findings suggest the potential of D-Asp to induce oxidative perturbations in the testis of prepubertal rats and this mechanism may in part be responsible for the observed physiological effects.

Aleurothrixus trachoides (Back) can transmit begomovirus from Duranta to potato, tomato and bell pepper.

Solanum whitefly, Aleurothrixus trachoides (Back). (Hemiptera: Aleyrodidae) was considered as a non-virus vector by European and Mediterranean Plant Protection Organization (EPPO) reports. However, in the present study it was found to transmit Duranta leaf curl virus (DLCV) to tomato, bell pepper and potato. A. trachoides infested field samples of Duranta sp (100%) and tomato (20%) tested positive for begomovirus by PCR using begomovirus degenerate primers and primers specific to Tomato leaf curl New Delhi virus showing amplicon of 520 bp and 2.7 Kb respectively. The DNA samples of A. trachoides collected from virus positive duranta and tomato plants also tested positive for the virus. Virulent whiteflies from duranta could successfully transmit DLCV to bell pepper (26%) and tomato (13 %) plants as confirmed by Rolling Circle Amplification. The rate of virus transmission by A. trachoides from DLCV inoculated tomato to bell pepper and tomato to potato was 100% and tomato to tomato was 80%. The results suggest whitefly A. trachoides as the vector for DLCVand to the best of our knowledge, this is the first report for A. trachoides as vector of begomovirus. These findings suggest need for reconsideration of A. trachoides as a virus-vector. This will have great impact on solanaceous vegetable cultivation in India and other parts of the world.

Tetrandrine isolated from Cyclea peltata induces cytotoxicity and apoptosis through ROS and caspase pathways in breast and pancreatic cancer cells.

Tetrandrine is a bisbenzylisoquinoline alkaloid known to exhibit anticancer activity against different cancers. In the present study, the cytotoxic effect of tetrandrine isolated from Cyclea peltata on pancreatic (PANC-1) and breast (MDA-MB-231) cancer cells was evaluated in vitro with an attempt to understand the role of tetrandrine on the generation of reactive oxygen species (ROS) and caspase activation. Results demonstrate the dose- and time-dependant cytotoxic effect of tetradrine on both MDA-MB-231 and PANC-1 cells with IC50 values ranging between 51 and 54 µM and 22 and 27 µM for 24 h and 48 h of incubation respectively. In addition, treatment of MDA-MB-231 and PANC-1 cells with tetrandrine showed the shrunken cytoplasm and damaged cell membrane in a dose- and time-dependant manner under the microscope. Also, tetrandrine treatment revealed an elevated levels of reactive oxygen species and increased activities of caspase-8, -9 and -3 confirming the apoptosis of cells through both extrinsic death receptor and intrinsic caspase activation. Therefore, the present study suggests the apoptosis of cells with the activation of caspase pathways mainly intrinsic pathway as a downstream event of tetrandrine-induced ROS generation. Hence, reactive oxygen species-mediated caspase activation pathway may be potentially targeted with the use of tetrandrine to treat breast and pancreatic cancers.

Oxidative alterations induced by D-aspartic acid in prepubertal rat testis in vitro: a mechanistic study.

The objective of the present study was to investigate the oxidative induction response following in vitro treatment with D-aspartic acid (DA) in prepubertal rat testis (homogenates, explants, and cell suspensions). In all three preparations, DA enhanced (P<0.001) lipid peroxidation, manifest as increased reactive oxygen species (ROS) and malondialdehyde (MDA). Further, DA-induced oxidative induction was potentiated (P<0.001) in the presence of iron (5 microM) and 3-amino triazole and mercaptosuccinate (P<0.001), known inhibitors of the peroxide metabolizing enzymes, catalase and glutathione peroxidase, respectively. Testis homogenates exposed to L-arginine (LA) per se had reduced (P<0.001) endogenous levels of ROS and MDA; furthermore, pre-incubation with L-arginine markedly suppressed (P<0.001) DA-induced oxidative induction, suggesting an antagonistic action, perhaps due to LA-derived nitric oxide. In conclusion, DA caused significant oxidative induction in prepubertal rat testis, but this action was abrogated by L-arginine. The relevance of this phenomenon in vivo merits further study, as both of these molecules have specific physiological functions in the testis.

Genetic homogeneity in South American tomato pinworm, Tuta absoluta: a new invasive pest to oriental region.

South American tomato leaf miner, Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae), is an important invasive pest of Tomato which invaded India and Nepal in 2014 and 2016, respectively. In the present study, samples from five localities of India and one from Nepal were used for the investigation of genetic diversity of T. absoluta by employing a fragment in the mtDNA gene-encoding cytochrome oxidase I (COI). Based on the partial COI gene, high genetic homogeneity was detected in T. absoluta populations of India and Nepal with rest of the world. Less nucleotide diversity (π 0.00137) was also detected in the populations of T. absoluta from different countries. This is first attempt to analyze molecular data for this new invasive species from India and Nepal.

Hepatoprotective activity of the Leucas lavandulaefolia on D(+)galactosamine-induced hepatic injury in rats.

The chloroform extract of Leucas lavandulaefolia at an oral dose of 200 mg/kg and 400 mg/kg exhibited a significant protection on D(+)galactosamine induced liver damage in rats. Silymarin (25 mg/kg), a known hepatoprotective drug used as a standard also exhibited a significant activity.

Clinical evaluation of an ionic tooth brush on oral hygiene status, gingival status, and microbial parameter.

It has long been recognised that the presence of dental plaque leads to gingivitis and periodontal disease, as well as dental caries. Today tooth brushing is the most widely accepted method of removing plaque. Hence this present clinical study was undertaken to evaluate the effectiveness of an ionic toothbrush on oral hygiene status. For this study, 20 dental students in the age group of 18-20 years were included. All the subjects after undergoing dental prophylaxis were then provided with ionic toothbrushes, either active (equipped with lithium battery) or inactive (without lithium battery). Plaque index and gingival bleeding index were examined at 7th, 14th, and 21st day. Microbial assessment was done for detection of colony forming units (CFU) from the plaque samples which were collected on 0 day and 21st day, both before brushing and after brushing. Results shown a significant reduction in all the parameters and the reduction was more significant in active and inactive ionic toothbrush users. It was concluded that both active and inactive ionic toothbrushes reduced the plaque index and gingival bleeding index scores significantly and active ionic tooth brushes were more effective as compared to inactive ionic toothbrushes. There was no soft tissue trauma following the use of both type of toothbrushes, which showed that ionic toothbrushes were equally safe for regular long-term use.

Tetrandrine--A molecule of wide bioactivity.

Stephania tetrandra and other related species of Menispermaceae form the major source of the bisbenzylisoquinoline alkaloid - tetrandrine. The plant is extensively referenced in the Chinese Pharmacopoeia for its use in the Chinese medicinal system as an analgesic and diuretic agent and also in the treatment of hypertension and various other ailments, including asthma, tuberculosis, dysentery, hyperglycemia, malaria, cancer and fever. Tetrandrine, well-known to act as a calcium channel blocker, has been tested in clinical trials and found effective against silicosis, hypertension, inflammation and lung cancer without any toxicity. Recently, the efficacy of tetrandrine was tested against Mycobaterium tuberculosis, Candida albicans, Plasmodium falciparum and Ebola virus. Tetrandrine's pharmacological property has been proved to be through its action on different signalling pathways like reactive oxygen species, enhanced autophagic flux, reversal of multi drug resistance, caspase pathway, cell cycle arrest and by modification of calcium channels. The present review summarises current knowledge on the synthesis, distribution, extraction, structural elucidation, pharmacological properties and the mechanism of action of tetrandrine. Future perspectives in the clinical use of tetrandrine as a drug are also considered.