Assessment of phytodiversity and phytoremediation potential of plants in the vicinity of a thermal power plant.

A study was carried out to evaluate phytodiversity along with the metal accumulation potential of native plants growing in the vicinity of a thermal power plant (TPP). We documented 26 tree species, six shrubs, and 35 herbs. Importance value index (IVI), which measures the extent to which a species dominates in an area, was found highest for Senna siamea (95.7) followed by Tectona grandis (56.5), and Pithecellobium dulce (19.6). Soil was acidic (pH 5.4) in nature with higher concentrations of Al and Fe. The pH of ground water was found acidic while pH of nearby river was found slightly alkaline. Values of PM2.5 and PM10 were slightly higher than NAAQS standards for industrial areas. The concentration of metals was found higher in aquatic plants than in terrestrial plants. In general, herbs and shrubs showed more metal accumulation potential than trees. Our results suggest that Senna siamea could be used for revegetation purposes in FA landfills. Further, terrestrial and aquatic plants such as Ageratina adenophora and Stuckenia pectinata could be used for reclamation of Mn, Zn, Al, and Fe from contaminated soils. Hydrilla verticillata (Ni and Mn), Nelumbo nucifera, and Ipomoea aquatica (Cr) can be used for metal removal from contaminated water.

The study focuses on the assessment of phytodiversity, soil and water analysis, ambient air quality, and bioaccumulation of heavy metals in plants growing in and around a thermal power plant. The study assumes significance as more than 65% of India's electricity generation is still by coal-fired power plants, having major implications for air, soil, and water pollution. By selecting native plant species adapted to the region, we can enhance biodiversity, restore habitats, and contribute to the overall ecological health of the area surrounding the power plant.

Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach.

In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria). However, at the species level, we reported the presence of some representative pathogenic taxa, such as Acinetobacter baumannii and Moraxella osloensis. The functional annotation predicted at various levels based on SEED-based subsystem, KEGG ortholog identity (KO), Cluster of Orthologous Groups (COGs) database identified the predominance of genes associated with primary and secondary metabolism along with a crucial role in environmental and genetic signals, cellular communication, and cell signalling. Comparative Genome Analysis (CGA) using The Pathosystem Resource Integration Centre (PATRIC) tool based on genome annotation and assembly of the metagenomic libraries for representative taxon Acinetobacter baumannii (NCBI tax id:470) characterized the reads with a unique genome identifier of 470.20380 (A. baumannii DDLJ4) which is evolutionary closer to A. baumannii ATCC 470.17978 400667.7. In addition, the CARD database results about the presence of potential AMR pathotypes and the prevalence of adeABC, adeIJK, abeM gene-specific clusters that function as multidrug efflux pumps. Overall, the results provided a comprehensive insight into virulence and anti-microbial resistance mechanism and could be useful for developing potential drug targets against the possible AMR pathotypes.

[99mTc-BBPA]: A possible SPECT agent to understand the role of 18-kDa translocator protein (PBR/TSPO) during neuro-glial interaction.

The translocator protein (TSPO, 18 kDa) is one of the most promising biomarker to understand the role of neuroinflammation in human as well as in different animal species. Here we report a new TSPO-selective ligand 2-(5-(2-(bis(pyridin-2-yl methyl)amino)acetamido)-2-oxobenzo[d] oxazol-3(2H)-yl)-N-methyl-N-phenylacetamide, BBPA, which is supposed to be a potential probe to understand the role of TSPO in neuro-glial interaction through SPECT modality.

A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.).

Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.

Synthesis and evaluation of technetium-99m labelled 1-(2-methoxyphenyl)piperazine derivative for single photon emission computed tomography imaging for targeting 5-HT1A.

Quantitative changes in expression level of 5HT1A are somewhere related to common neurological disorders such as anxiety, major depression and schizophrenia. We have designed EDTA conjugated SPECT imaging probe for localization of 5HT1A receptor in brain. For designing SPECT probe we have employed the concept of bivalent approach and a homodimeric system with desirable pharmacokinetics of 5HT1A imaging. 99mTc-EDHT was also evaluated for its stability through serum stability assay and glutathione challenge experiment. Biodistribution study showed the highest accumulation of radioactivity in kidney which depicted the renal mode of excretion from the body. However in brain the uptake of 1.21% ID per gram was observed in initial 5 min of drug administration. On blocking the receptor this percent get decreased to 0.97% ID per gram. The regional distribution in brain was also performed which showed the accumulation of drug in cerebellum, cortex and hippocampus part, which are already known for 5HT1A expression. Dynamic study in rabbit is also in support of results derived from biodistribution and blood kinetics experiment. These finding suggest that 99mTc-EDHT holds promising place for further optimization before nuclear medicine applications in different animal species.

Benzothiazole derivative bearing amide moiety induces p53-mediated apoptosis in HPV16 positive cervical cancer cells.

In our previous study, we screened the anti-cancer properties of 10 benzothiazole derivatives in cervical cancer cell lines. In the present study, we aimed to delineate the mechanism of the apoptotic pathway (whether intrinsic or extrinsic) following the treatment of N-(4-(benzo[d]thiazol-2-yl)phenyl)-5-chloro-2-methoxybenzamide (named as A-07) on cervical cancer cell lines. Cellular stress by reactive oxygen species was measured using DCFDA dye by flowcytometry. Protein expression and localization was checked by immunofluorescence for γH2A.X, TP53, and CASP-3. Expression profiles of BAX and BCL-2 was done by semi-quantitative RT-PCR and PARP-1 (Poly(ADP-ribose) polymerase-1) by Western blot analysis. Bioinformatic studies were done using PDB websites, metaPocket 2.0 server, YASARA software and Discovery Studio 3.5 Visualizer. We demonstrate that the compound A-07 leads to ROS generation and double strand breaks in SiHa and C-33A cells. The induction of apoptosis in SiHa cells is associated with increased nuclear expression of the tumor suppressor protein, TP53. The shift in BAX/BCL-2 ratio, increased expression of Caspase-3 and cleaved Poly(ADP-ribose) polymerase-1 favour apoptotic signal in SiHa. In silico studies revealed that A-07 has inhibiting capabilities to the E6/E6AP/P53 complex. Our data suggest that treatment of A-07 causes p53 and caspase dependent apoptosis in HPV 16 infected SiHa cells.

Molecular docking of anti-inflammatory drug diclofenac with metabolic targets: Potential applications in cancer therapeutics.

Diclofenac is a potent NSAID of clinical choice, which is widely used for containing inflammation. Moreover, recent experimental evidences overwhelmingly substantiate its antineoplastic potential. However, the precise molecular mechanisms of diclofenac's anticancer activity remain poorly understood. Neoplastic cells display reprogrammed metabolic features, which are manifested and regulated by a complex networking of molecular pathways. However, the effect of diclofenac on tumor cell metabolism are not yet clearly deciphered. Hence, the present investigation was carried out to identify and characterize key diclofenac targets of tumor metabolism, cell survival and chemoresistance. The interactions of diclofenac with such targets was analysed by PatchDock and YASARA (Yet Another Scientific Artificial Reality Application). The docking ability of diclofenac with its targets was based on analysis of dissociation constant (Kd), geometric shape complementarity score (GSC score), approximate interface area (AI area) and binding energy. The findings of this investigation reveal that diclofenac is capable of interacting with all of the selected molecular targets. Prominent interactions were observed with GLUT1, MCT4, LDH A, COX1, COX2, BCRP/ABCG2, HDM2/MDM2 and MRP1 compared to other targets. Interactions were of noncovalent nature involving ionic, hydrophobic interactions, Van der Waals forces and H-bonds, which varied depending on targets. This study for the first time, characterizes the nature of molecular interactions of diclofenac with selected targets involved in cancer cell metabolism, pH homeostasis, chemosensitivity, cell signalling and inflammation. Hence, these findings will be highly beneficial in optimizing the utility of diclofenac in development of novel cancer therapeutics.

Nitric oxide (NO) stimulates steroidogenesis and folliculogenesis in fish.

The present study was undertaken to understand the physiological significance of the existence of nitric oxide synthase (NOS)/nitric oxide (NO) system in fish ovary. For this, two doses of NO donor, sodium nitroprusside (SNP, 25 µg and 50 µg) and NOS inhibitor, N-nitro-l-arginine methyl ester (l-NAME, 50 µg and 100 µg)/100 g body weight were administered during the two reproductive phases of reproductive cycle of the Clarias batrachus During the late-quiescence phase, high dose of l-NAME decreased the NO, testosterone, 17ß-estradiol, vitellogenin contents in serum and ovary and activities of 5-ene-3ß-hydroxysteroid dehydrogenases (3ß-HSD) and 17ß-hydroxysteroid dehydrogenases (17ß-HSD) in ovary, whereas higher dose of SNP increased these parameters. l-NAME also reduced oocytes-I but increased perinucleolar oocytes in the ovary, whereas SNP treatment increased the number of advanced oocytes (oocytes-I and II) than the perinucleolar oocytes when compared with control ovary. During the mid-recrudescence phase, both doses of SNP increased NO, testosterone, 17ß-estradiol and vitellogenin in serum and ovary; however, l-NAME treatment lowered their levels. The activities of ovarian 3ß-HSD and 17ß-HSD were also stimulated by SNP, but l-NAME suppressed their activities compared to the control. The SNP-treated ovaries were dominated by oocyte-II and III stages, whereas l-NAME-treated ovary revealed more perinucleolar oocytes and oocytes-I and practically no advanced oocytes. Expression of endothelial NOS (eNOS), inducible NOS (iNOS) and neuronal NOS (nNOS) was augmented by the SNP and declined by l-NAME treatments as compared to the control. This study, thus, provides distinct evidence of NO-stimulated steroidogenesis, vitellogenesis and folliculogenesis in fish.

Pro-steroidogenic and pro-spermatogenic actions of nitric oxide (NO) on the catfish, Clarias batrachus: An in vivo study.

In an earlier study we have demonstrated reproductive-stage dependent, cell specific existence of inducible nitric oxide synthase (iNOS) and neuronal nitric oxide synthase (nNOS)/NO system in testis of the catfish, Clarias batrachus. The present study is an extension to examine the role of NO in steroidogenesis and spermatogenesis through in vivo administration of a NO donor, sodium nitroprusside (SNP) and a NOS inhibitor, N-nitro-l-arginine methyl ester (l-NAME) during the quiescence and recrudescence phase of the reproductive cycle of the catfish. Effects of these chemicals were assessed on the gonadosomatic index (GSI), levels of circulating & testicular testosterone, NO, activities of 3ß-hydroxysteroid dehydrogenase (3ß-HSD), 17ß-hydroxysteroid dehydrogenase (17ß-HSD) in testis, expression of different NOS isoforms and testicular morphology in relation to spermatogenesis. SNP treatment increased the GSI, testicular and circulating testosterone & NO, activities of testicular 3ß-HSD & 17ß-HSD, and expression of NOS isoforms. It also increased the area and perimeters of interstitium and seminiferous tubules in the testis. It accelerated the spermatogenesis, as was evident from the large number of spermatids/spermatozoa in seminiferous tubules and very few spermatogonial cells/primary spermatocytes in comparison to the control testis. On the contrary, l-NAME significantly suppressed GSI, testosterone & NO levels in serum and testis, and activities of testicular 3ß-HSD & 17ß-HSD. It also suppressed the expression of NOSs in testis. Though l-NAME did not alter the spermatogonial mitotic proliferation with the advancement of testicular recrudescence, it halted the progression of spermatogenesis (meiotic division and spermatozoa formation) as was clear from the increase in spermatogonial cells and very few advanced germ cells in the seminiferous tubules in l-NAME treated testis, compared to the control testis. The above noted effects were highly pronounced in the recrudescing catfish. Their effects were very marginal and at a particular dose levels of SNP and l-NAME in the quiescent testis. This study distinctly provides evidence of pro-steroidogenic and pro-spermatogenic role of NO. This study also demonstrates the existence of eNOS in fish testis for the first time. The positive feedback control of expression of all isoform of NOS in testis by NO is also noteworthy.

Immunolocalization of nitric oxide synthase (NOS) isoforms in ovarian follicles of the catfish, Clarias batrachus and its relation with ovarian activity.

Nitric oxide, a gaseous molecule, is produced during the conversion of arginine to citrulline by the action of NOS isoforms (eNOS, iNOS or nNOS). Role of NO in regulation of mammalian reproduction is well established; however, practically no report is available on fishes. Hence, in the present study, expression of all three isoforms of NOS was worked out in the ovary of Clarias batrachus immunohistochemically during different phases of its reproductive cycle and its relation with ovarian activities. No immunoreactivity of eNOS was observed in the ovary of C. batrachus during the late-quiescence and early-recrudescence phases. While during the recrudescence phase (April and May) it expressed intensely in thecal and granulosa cells of the oocyte-II and III, but immune-intensity decreased in the late-recrudescence and spawning phases (June and July). Similar pattern of immunoprecipitation was also observed in case of iNOS. However, the immunoreactivity pattern of nNOS was quite varied, it expressed moderately only in the nucleus and cytoplasm of perinuclear and oocyte-I stages during late-quiescence phase. While during the early recrudescence phase, the expression of nNOS disappeared completely from the nucleus and cytoplasm, rather it expressed intensely in the thecal and granulosa cells, which declined in the late-recrudescence and spawning phases. Moderate immunoreactivity of iNOS could also be localized in the zona radiata of ovulated oocyte. The intense NOS immunoreactivity in the thecal and granulosa cells coincided with increased levels of ovarian NO and 17ß-estradiol content. They exhibited statistically significant positive correlation amongst themselves, suggesting the involvement of ovarian NOS/NO system in oogenesis and steroidogenesis in the catfish.

Laboratory Assessment of Molluscicidal Activities of Cannabis sativa, Acacia nilotica, and Tinospora cordifolia Against Snail Host of Fasciola spp.

Background: The potential molluscicidal extracts, obtained from indigenous plants Cannabis sativa, Acacia nilotica, and Tinospora cordifolia, were tested for toxicity against freshwater pulmonate snail Lymnaea acuminata, an intermediate host of Fasciola hepatica. The organic extracts had a significant effect on young snails. Materials and Methods: All organic extracts and column-purified fractions gave median lethal concentrations (19-100.05 mg/L; 24 h) that fell well within the threshold level of 100 mg/L, set for a potential molluscicide by the World Health Organization. Results: The toxicity of T. cordifolia stem acetone extract (96 h LC50: 16.08 mg/L) was more pronounced compared with C. sativa leaf ethanol extract (96 h LC50: 16.32 mg/L) and A. nilotica leaf ethanol extract (96 h LC50: 24.78 mg/L). ß-caryophyllene, gallic acid, and berberine were characterized and identified as active molluscicidal components. Co-migration of ß-caryophyllene (retardation factor [Rf] 0.95), gallic acid (Rf 0.30), and berberine (Rf 0.23) with column-purified parts of Cannabis sativa, Acacia nilotica, and Tinospora cordifolia on thin-layer chromatography demonstrates same Rf value, that is, 0.95, 0.30, and 0.23, respectively. Conclusion: This study indicates that these extracts thus represent potential plant-derived molluscicides that are worthy of further investigations.

In Silico Structural and Functional Insight into the Binding Interactions of the Modeled Structure of Watermelon Urease with Urea.

Urease (EC 3.5.1.5) is an amidohydrolase. This nickel-dependent metalloenzyme converts urea into NH3 and CO2. Despite their vital role in plants, the structure and function of watermelon (Citrullus lanatus) urease are unknown. We used third- and fourth-generation gene prediction algorithms to annotate the C. lanatus urease sequence in this investigation. The solved urease structure from Canavalia ensiformis (PDB ID: 4GY7) was utilized as a template model to identify the target 3-D model structure of the unknown C. lanatus urease for the first time. Cluretox, the C. lanatus urease intrinsic disordered area identical to Jaburetox, was also found. The C. lanatus urease structure was docked with urea to study atom interaction, amino acid interactions, and binding analyses in the urease-urea complex at 3.5 Å. This study found that amino acids His517, Gly548, Asp631, Ala634, Thr569, His543, Met635, His407, His490, and Ala438 of C. lanatus urease bind urea. To study the molecular basis and mode of action of C. lanatus urease, molecular dynamics simulation was performed and RMSD, RMSF, Rg, SAS, and H-bond analyses were done. The calculated binding free energy (ΔG) for the urea-urease complex at 100 ns using the MM/PBSA method is -7.61 kJ/mol. Understanding its catalytic principles helps scientists construct more efficient enzymes, tailor fertilization to boost agricultural output, and create sustainable waste management solutions.

Genetic and in silico analysis of Indian sporadic young onset patient with amyotrophic lateral sclerosis.

Background: Amyotrophic lateral sclerosis (ALS) is an old onset devastating neurodegenerative disorder. Young-onset ALS cases especially sporadic ones who are between 25 and 45 years are rarely affected by the disease. Despite the identification of numerous candidate genes associated with ALS, the etiology of the disease remains elusive due to extreme genetic and phenotypic variability. The advent of affordable whole exome sequencing (WES) has opened new avenues for unraveling the disease's pathophysiology better. Methods and results: We aimed to determine the genetic basis of an Indian-origin, young onset sporadic ALS patient with very rapid deterioration of the disease course without any cognitive decline who was screened for mutations in major ALS candidate genes by WES. Variants detected were reconfirmed by Sanger sequencing. The clinicopathological features were investigated and two heterozygous missense variants were identified: R452W, not previously associated with ALS, present in one of the four conserved C terminal domains in ANXA11 and R208W in SIGMAR1, respectively. Both of these variants were predicted to be damaging by pathogenicity prediction tools and various in silico methods. Conclusion: Our study revealed two potentially pathogenic variants in two ALS candidate genes. The genetic makeup of ALS patients from India has been the subject of a few prior studies, but none of them examined ANXA11 and SIGMAR1 genes so far. These results establish the framework for additional research into the pathogenic processes behind these variations that result in sporadic ALS disease and further our understanding of the genetic makeup of Indian ALS patients.

Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate.

This study focuses a bioinformatics-based prediction of arsC gene product arsenate reductase (ArsC) protein in Cronobacter sakazakii BAA-894 strain. A protein structure-based study encloses three-dimensional structural modeling of target ArsC protein, was carried out by homology modeling method. Ultimately, the detection of active binding regions was carried out for characterization of functional sites in protein. The ten probable ligand binding sites were predicted for target protein structure and highlighted the common binding residues between target and template protein. It has been first time identified that modeled ArsC protein structure in C. sakazakii was structurally and functionally similar to well-characterized ArsC protein of Escherichia coli because of having same structural motifs and fold with similar protein topology and function. Investigation revealed that ArsC from C. sakazakii can play significant role during arsenic resistance and potential microorganism for bioremediation of arsenic toxicity.

Ankle block in forefoot reconstruction before or after inflation of tourniquet--Does timing matter?

BACKGROUND: Forefoot surgery causes postoperative pain frequently requiring strong painkillers. Regional blocks are now increasingly used in order to control postoperative pain especially in the first 24h when the pain is at its worst. We conducted a prospective study to see if timing of ankle block i.e. before or after inflation of tourniquet showed any difference in efficacy in postoperative pain control in first 24h. METHODS: A prospective randomised study was conducted between September 2010 and August 2011 involving 60 patients. Group A (n=30) had the ankle block administered after and Group B (n=30) had a block before inflation of a thigh tourniquet. Patients were given assessment forms to chart their pain on visual analogue scale (VAS) score at 4h and 24h postoperatively. RESULTS: Both groups demonstrated good postoperative pain control. Average VAS pain score at four and twenty fours after surgery was 2.5 and 4.5 in Group A and 3.9 and 6.3 in Group B respectively. Pain control, both at 4 and 24h surgery was better in Group A but this was statistically significant only at 24h. CONCLUSIONS: A regional anaesthetic ankle block should be routinely used in forefoot surgery to control postoperative pain. The ankle block should be applied after the inflation of tourniquet as this appears to provide better pain control.

The diagnostic value of single photon-emission computed tomography bone scans combined with CT (SPECT-CT) in diseases of the foot and ankle.

BACKGROUND: A radionuclide bone scan with single photon-emission computed tomography and CT (SPECT-CT) is a new imaging modality which combines highly detailed CT with the functional information from a triple phase radionuclide bone scan. Little has been published about its diagnostic accuracy and usefulness in foot and ankle pathology. The aim of this study is to evaluate whether bone scans with SPECT-CT provide a useful contribution to the management of patients with foot and ankle pain, and whether it results in changes to clinical management. METHODS: A retrospective study involving 50 patients was conducted between March 2010 and April 2011. SPECT-CT was requested in cases where definitive clinical diagnosis could not be achieved after clinical examination and plain radiography. Pathology as highlighted on SPECT-CT was taken as the definitive diagnosis in these patients and was treated accordingly. Patients were subsequently seen in the follow up clinic to evaluate the outcome of their treatment. RESULTS: In 11 patients (22%), the provisional clinical diagnosis matched with the findings of the SPECT-CT and no change in treatment was necessary. In 39 patients (78%) the findings of the SPECT-CT did not correlate exactly with the initial clinical diagnosis and led to a modified treatment plan. The accuracy, sensitivity, specificity, positive predictive and negative predictive value of SPECT-CT in this series was 94%, 95.45%, 83.3%, 97.6% and 71.43% respectively. CONCLUSIONS: SPECT-CT is a useful investigation tool in foot and ankle pathologies. The present study shows a high diagnostic accuracy and we recommend its use in cases with diagnostic uncertainty.

Molecular modeling, docking and dynamics studies of fenugreek (Trigonella foenum-graecum) α-amylase.

α-Amylase catalyses the hydrolysis of glucosidic bonds in polysaccharides such as starch, glycogen and their degradation products. In the present study, the three-dimensional structure of fenugreek (Trigonella foenum-graecum) α-amylase was determined using a homology modeling-based technique. The best predicted model was deposited in PMDB server with PMDB ID PM0084364. The phylogenetic tree was created using the UPGMA method with 8 homologous protein sequences, Trigonella foenum-graecum was utilized as the target protein. Alignment of the phylogenetic tree identified two primary functional groupings (A and B). α-Amylase from the target genome Trigonella foenum-graecum (Acc. No: GHNA01022531.1) was clustered with Medicago truncatula (Acc. No: XP003589186.1), Cicer arietinum (Acc. No: XP004499059.1), Cajanus cajan (Acc. No: XP020231823.1), Vigna angularis (Acc. No: NP001316768.1) and Vigna mungo (Acc. No: P17859.1), in group A cluster, while Hordeum vulgare (Acc. No: Q40015) and Oryza sativa (PDB ID: 3WN6) were in cluster B. The molecular dynamics simulations were performed to understand the molecular basis and mode of action of Trigonella foenum-graecum α-amylase. Additionally, a geometry-based molecular docking technique was used to evaluate potential binding interactions between the modeled structure of α-amylase and maltose. The results show that Trp228, Glu226, Arg199, His308, Tyr165, Asp309, Phe202 and Asp201 from Trigonella foenum-graecum α-amylase enzyme is involved in the binding to the substrate maltose. Our study provides a 3D model of Trigonella foenum-graecum α-amylase and aids in understanding the atomic level molecular underpinnings of the mechanism of α-amylase interaction with substrate maltose. Ca2+ are essential for the stability of domain B since they are connected to it. Ca2+ site ligands are Asp139, Glu130, Thr133, Asp135 and Gly131 residues. HIGHLIGHTSIn silico analysis, gene prediction of α-amylase was carried from Trigonella foenum-graecum.Analysis of the structure of α-amylase was carried out using homology modelling.Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019.The molecular interaction between Trigonella foenum-graecum α-amylase and maltose was studied in silico using a molecular docking-based method.To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019.[Figure: see text]Communicated by Ramaswamy H. Sarma.

Ab initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1).

Transcription Termination Factor 1 (TTF1) is an essential mammalian protein that regulates transcription, replication fork arrest, DNA damage repair, chromatin remodelling etc. TTF1 interacts with numerous cellular proteins to regulate various cellular phenomena which play a crucial role in maintaining normal cellular physiology, and dysregulation of this protein has been reported to induce oncogenic transformation of the cells. However, despite its key role in many cellular processes, the complete structure of human TTF1 has not been elucidated to date, neither experimentally nor computationally. Therefore, understanding the structure of human TTF1 is crucial for studying its functions and interactions with other cellular factors. The aim of this study was to construct the complete structure of human TTF1 protein, using molecular modelling approaches. Owing to the lack of suitable homologues in the Protein Data Bank (PDB), the complete structure of human TTF1 was constructed by ab initio modelling. The structural stability was determined with molecular dynamics (MD) simulations in explicit solvent, and trajectory analyses. The frequently occurring conformation of human TTF1 was selected by trajectory clustering, and the central residues of this conformation were determined by centrality analyses of the Residue Interaction Network (RIN) of TTF1. Two residue clusters, one in the oligomerization domain and other in the C-terminal domain, were found to be central to the structural stability of human TTF1. To the best of our knowledge, this study is the first to report the complete structure of this essential mammalian protein, and the results obtained herein will provide structural insights for future research including that in cancer biology and related studies.Communicated by Ramaswamy H. Sarma.

Evolutionary aspects of mutation in functional motif and post-translational modifications in SARS-CoV-2 3CLpro (Mpro): an in-silico study.

SARS CoV-2 is the virus that caused the COVID-19 pandemic. The main protease is one of the most prominent pharmacological targets for developing anti-COVID-19 therapeutic drugs (Mpro); SARS-CoV-2 replication is dependent on this component. SARS CoV-2's Mpro/cysteine protease is quite identical to SARS CoV-1's Mpro/cysteine protease. However, there is limited information on its structural and conformational properties. The present study aims to perform a complete in silico evaluation of Mpro protein's physicochemical properties. The motif prediction, post-translational modifications, effect of point mutation, and phylogenetic links were studied with other homologs to understand the molecular and evolutionary mechanisms of these proteins. The Mpro protein sequence was obtained in FASTA format from the RCSB Protein Data Bank. The structure of this protein was further characterized and analyzed using standard bioinformatics methods. According to Mpro's in-silico characterization, the protein is a basic, non-polar, and thermally stable globular protein. The outcomes of the phylogenetic and synteny study showed that the protein's functional domain amino acid sequence is substantially conserved. Furthermore, it has undergone many changes at the motif level over time from porcine epidemic diarrhoea virus to SARS-CoV 2, possibly to achieve various functions. Several post-translational modifications (PTMs) were also observed, and the possibilities of changes in Mpro protein exhibit additional orders of peptidase function regulation. During heatmap development, the effect of a point mutation on the Mpro protein was seen. This protein's structural characterization will aid in a better understanding of its function and mechanism of action. Supplementary Information: The online version contains supplementary material available at 10.1007/s42485-023-00105-9.

Evaluation of Pleurotus Mushroom Effects on Histopathological Changes in Organs of Diabetic Rats.

Diabetes mellitus (DM) is a metabolic disorder that can be categorized mainly into type 1 and type 2. Diabetes type 1 is caused due to ß-cell destruction, whereas type 2 is caused by the resistance of cell receptors. Many therapies are available for the management of diabetes, but they have some side effects, and as a result of this, people are attracted to natural treatments. Pleurotus mushrooms are well documented for their medicinal attributes and their role in the treatment of diseases like cancer, infectious disease, neurodiseases, and inflammatory disease. The protective mechanism of the Pleurotus fossulatus (P. fossulatus) mushroom and its detailed histological study on kidneys and the liver in diabetic conditions were unexplored. The present study evaluated the effects of P. fossulatus aqueous extract on histological changes in the diabetic rat model. Male Wistar albino rats were used to create the diabetic model by using streptozotocin (STZ) intraperitoneal (IP) injection. The animals were separated into five different groups, with six animals in each. Only group I, animals that did not receive STZ, was considered a normal control. Group II was a diabetic control and received normal saline, and group III was a drug control and received metformin as a standard drug. Groups IV and V were dosing groups, which received the aqueous extract of P. fossulatus in 250 mg/kg and 500 mg/kg of body weight concentrations, labeled as T1 and T2 groups, respectively. The T1 and T2 groups clearly showed their potential to reverse the histopathological changes in the kidney and liver. However, the T2 group was more effective than the T1 group, as results indicate that functions of the glomerulus and its structural deformity were restored to their near-natural form in the T2 group. In the case of the liver, the histological changes like the dilatation of sinusoids, more numbers of the Kupffer cell formation, and necrosis were restored in the T2 group. All these results proved the potential of P. fossulatus against the side effects of diabetes. It could protect the organs from developing diabetic nephropathy (DN) and liver-related diseases like cirrhosis and nonalcoholic fatty liver disease (NAFLD).