Computational identification of potential inhibitory compounds in Indian medicinal and aromatic plant species against major pathogenicity determinants of SARS-CoV-2

SARS-CoV-2 (COVID-19) viral pandemic has been reported across 223 countries and territories. Globalized vaccination programs alongside administration of repurposed drugs will assumingly confer a stronger and longer individual specific immune protection. However, considering possible recurrence of the disease via new variants, a conveniently deliverable phytopharmaceutical drug might be the best option for COVID-19 treatment. In the current study, the efforts have been made to identify potential leads for inhalation therapy as nasal swabs have been reported to transfer viral load prominently. In that direction, 2363 Essential oil (EOs) compounds from Indian medicinal and aromatic plants were screened through docking analysis and potential candidates were shortlisted that can interfere with viral pathogenicity. The main protease (M^pro) of SARS-CoV-2 interacted closely with jatamansin (JM), 6,7-dehydroferruginol (FG) and beta-sitosterol (BS), while Papain-like Protease (PL^pro) with friedelane-3-one (F3O) and lantadene D (LD) independently. Reduced Lantadene A (LAR) exhibited preferable interaction with RNA-dependent-RNA-polymerase (RdRp) whereas Lantadene A (LA) with RdRp and spike-glycoprotein (SG-pro) both target proteins. When compared against highest binding affinity conformations of well-known inhibitors of targets, these prioritized compounds conferred superior or comparable SARS-CoV-2 protein inhibition. Additionally, promising results were noted from pharmacokinetics prediction for all shortlisted compounds. Besides, molecular dynamics simulation for 100 ns in two replicates and binding free energy analysis revealed the stability of complexes with optimum compactness. To the best of our knowledge, the current investigation is a unique initial attempt whereby EO compounds have been computationally screened, irrespective of their known medicinal properties to fight COVID-19 infection.Communicated by Ramaswamy H. Sarma.

Comparative transcriptomics uncovers differences in photoautotrophic versus photoheterotrophic modes of nutrition in relation to secondary metabolites biosynthesis in Swertia chirayita

Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S. chirayita were generated to decipher the crucial molecular components associated with the secondary metabolites biosynthesis. Illumina HiSeq sequencing yielded 57,460 and 43,702 transcripts for green house grown (SCFG) and tissue cultured (SCTC) plants, respectively. Biological role analysis (GO and COG assignments) revealed major differences in SCFG and SCTC transcriptomes. KEGG orthology mapped 351 and 341 transcripts onto secondary metabolites biosynthesis pathways for SCFG and SCTC transcriptomes, respectively. Nineteen out of 30 genes from primary metabolism showed higher in silico expression (FPKM) in SCFG versus SCTC, possibly indicating their involvement in regulating the central carbon pool. In silico data were validated by RT-qPCR using a set of 16 genes, wherein 10 genes showed similar expression pattern across both the methods. Comparative transcriptomes identified differentially expressed transcription factors and ABC-type transporters putatively associated with secondary metabolism in S. chirayita. Additionally, functional classification was performed using NCBI Biosystems database. This study identified the molecular components implicated in differential modes of nutrition (photoautotrophic vs. photoheterotrophic) in relation to secondary metabolites production in S. chirayita.

Modular Design of Picroside-II Biosynthesis Deciphered through NGS Transcriptomes and Metabolic Intermediates Analysis in Naturally Variant Chemotypes of a Medicinal Herb, Picrorhiza kurroa

Picroside-II (P-II), an iridoid glycoside, is used as an active ingredient of various commercial herbal formulations available for the treatment of liver ailments. Despite this, the knowledge of P-II biosynthesis remains scarce owing to its negligence in Picrorhiza kurroa shoots which sets constant barrier for function validation experiments. In this study, we utilized natural variation for P-II content in stolon tissues of different P. kurroa accessions and deciphered its metabolic route by integrating metabolomics of intermediates with differential NGS transcriptomes. Upon navigating through high vs. low P-II content accessions (1.3-2.6%), we have established that P-II is biosynthesized via degradation of ferulic acid (FA) to produce vanillic acid (VA) which acts as its immediate biosynthetic precursor. Moreover, the FA treatment in vitro at 150 μM concentration provided further confirmation with 2-fold rise in VA content. Interestingly, the cross-talk between different compartments of P. kurroa, i.e., shoots and stolons, resolved spatial complexity of P-II biosynthesis and consequently speculated the burgeoning necessity to bridge gap between VA and P-II production in P. kurroa shoots. This work thus, offers a forward looking strategy to produce both P-I and P-II in shoot cultures, a step toward providing a sustainable production platform for these medicinal compounds via-à-vis relieving pressure from natural habitat of P. kurroa.

Comparative whole-transcriptome analysis in Podophyllum species identifies key transcription factors contributing to biosynthesis of podophyllotoxin in P. hexandrum

Podophyllum species (Podophyllum hexandrum Royle and Podophyllum peltatum) are a major source of deriving anticancer drugs from their major chemical constituent, podophyllotoxin. However, information lacks on regulatory components of podophyllotoxin biosynthesis; therefore, different classes of transcription factors were identified through mining transcriptomes of Podophyllum species and validated through qRT-PCR analysis vis-à-vis podophyllotoxin contents in different tissues/organs of Podophyllum hexandrum. A total of 82, 278, 70, and 90 transcripts were identified in shoots and 89, 273, 72, and 91 transcripts in rhizomes of P. hexandrum transcriptome; 70, 268, 48, and 92 transcripts were in shoots and 58, 245, 41, and 85 transcripts in rhizomes of P. peltatum transcriptome corresponding to bZIP, MYB, WRKY, and bHLH families of transcription factors, which have been shown in regulating biosynthesis of secondary metabolites. Two unique transcripts encoding bHLH and MYB/SANT TFs in shoots of P. peltatum (medp_podpe_41091 and medp_podpe_2547) and bZIP and MYB TFs in rhizomes of P. hexandrum (medp_podhe_163581 and medp_podhe_147614) correlated with podophyllotoxin content. Quantification of podophyllotoxin and comparative expression analysis between high (2.51 %) versus low (0.59) podophyllotoxin content accessions revealed 0.04 to ~16-folds increase in transcripts of transcription factors, thereby further supporting the association of identified transcription factors with podophyllotoxin content. bZIP TF showed the highest transcript abundance (19.60-folds) in P. hexandrum rhizomes (2.51 % podophyllotoxin) compared to shoots (0.01 %). In silico analysis of putative promoter regions of pathway genes in other plant species revealed the presence of sequence elements for MYB and WRKY transcription factors, thereby suggesting their role in controlling the production of podophyllotoxin. A repertoire of additional transcription factors has been provided, which can be functionally validated and used in designing a suitable genetic intervention strategy towards enhanced production of podophyllotoxin.

Immunostimulatory and growth promoting potential of Tinospora cordifolia (Thunb.) Miers on fingerlings of Amur Carp

The enhancement of immunity of fish through application of natural immunostimulants would help in minimizing the risk of occurrence of diseases in aquaculture. The present study was designed to evaluate the growth promoting and immunostimulatory effect of Guduchi, Tinospora cordifolia (Thunb.) Miers ex Hook F. leaf powder in fingerlings of Amur carp (Cyprinus carpio haeYnatopterus Martens). The fingerlings were divided into four treatment groups, Ti, T2, T₃ and T₄. Experimental diets were prepared by mixing rice bran, deoiled mustard cake, soybean meal and vitamin mineral mixture. The leaf powder of T. cordifolia was incorporated into diets D₂, D₃, and D₄ @ 0.25%, 0.5% and 0.75%, respectively. In control diet D₁, leaf powder of T. cordifolia was not incorporated. T₁ group fishes were fed with D, diet, T2 with D₂, T₃ with D₃ and T₄ with D₄ @ 5% body weight per day for 90 days. Fingerlings fed with diet D₄ achieved significantly improved Specific Growth Rate (1), Feed Conversion Ratio (2.76), and Gross Conversion Efficiency (0.361) as compared .to the control and all other treatments (P <0.05). Hematological and biochemical parameters, total leuckocyte count (53.849x103/[L), total erythrocyte count (3.50x106/iL), hemoglobin concentration (17.17%), total serum protein, albumin and globulin (12.35, 1.56 and 10.78 g/dL) in D₄ diet fed fishes showed increase as compared to the control and all other treatments (P <0.05). The above research revealed that Tinospora cordifolia leaf powder has significant growth promoting and immunostimulatory potential in Amur carp raising.

NGS Transcriptomes and Enzyme Inhibitors Unravel Complexity of Picrosides Biosynthesis in Picrorhiza kurroa Royle ex. Benth

Picrorhiza kurroa is an important medicinal herb valued for iridoid glycosides, Picroside-I (P-I) and Picroside-II (P-II), which have several pharmacological activities. Genetic interventions for developing a picroside production platform would require knowledge on biosynthetic pathway and key control points, which does not exist as of today. The current study reports that geranyl pyrophosphate (GPP) moiety is mainly contributed by the non-mevalonate (MEP) route, which is further modified to P-I and P-II through phenylpropanoid and iridoid pathways, in total consisting of 41 and 35 enzymatic steps, respectively. The role of the MEP pathway was ascertained through enzyme inhibitors fosmidomycin and mevinolin along with importance of other integrating pathways using glyphosate, aminooxy acetic acid (AOA) and actinomycin D, which overall resulted in 17%-92% inhibition of P-I accumulation. Retrieval of gene sequences for enzymatic steps from NGS transcriptomes and their expression analysis vis-à-vis picrosides content in different tissues/organs showed elevated transcripts for twenty genes, which were further shortlisted to seven key genes, ISPD, DXPS, ISPE, PMK, 2HFD, EPSPS and SK, on the basis of expression analysis between high versus low picrosides content strains of P. kurroa so as to eliminate tissue type/ developmental variations in picrosides contents. The higher expression of the majority of the MEP pathway genes (ISPD, DXPS and ISPE), coupled with higher inhibition of DXPR enzyme by fosmidomycin, suggested that the MEP route contributed to the biosynthesis of P-I in P. kurroa. The outcome of the study is expected to be useful in designing a suitable genetic intervention strategy towards enhanced production of picrosides. Possible key genes contributing to picroside biosynthesis have been identified with potential implications in molecular breeding and metabolic engineering of P. kurroa.

Expression analysis of biosynthetic pathway genes vis-à-vis podophyllotoxin content in Podophyllum hexandrum Royle

Podophyllum hexandrum Royle is known for its vast medicinal properties, particularly anticancer. It contains higher amount of podophyllotoxin (4.3 %), compared to Podophyllum peltatum (0.025 %) and other plant species; as a result, it has been used worldwide in the preparation of various drugs including anticancer, antimalarial, antiviral, antioxidant, antifungal, and so on. Currently, Etoposide (VP-16-213), Vumon® (Teniposide; VM-26), Etopophos®, Pod-Ben- 25, Condofil, Verrusol, and Warticon are available in the market. Due to highly complex synthesis and low cell culture yields of podophyllotoxin (0.3 %), the supply of raw material cannot be met due to increasing industrial demands. The knowledge on podophyllotoxin biosynthetic pathway vis-à-vis expression status of genes is fragmentary. Quantitative expression analysis of 21 pathway genes has revealed 9 genes, namely SD, PD, PCH, CM, CMT, CAD, CCR, C4H, and ADH, that showed increase in transcript abundance up to 1.4 to 23.05 folds, respectively, vis-à-vis podophyllotoxin content in roots (1.37 %) and rhizomes (3.05 %) of P. hexandrum. In silico analysis of putative cis-regulatory elements in promoter regions of overexpressed genes showed the presence of common Skn-1 motif and MBS elements in CMT, CAD, CCR, C4H, and ADH genes, thereby, suggesting their common regulation. The outcome of the study has resulted in the identification of suitable candidate genes which might be contributing to podophyllotoxin biosynthesis that can act as potential targets for any genetic intervention strategies aimed at its enhanced production.

Contents of therapeutic metabolites in Swertia chirayita correlate with the expression profiles of multiple genes in corresponding biosynthesis pathways

Swertia chirayita, an endangered medicinal herb, contains three major secondary metabolites swertiamarin, amarogentin and mangiferin, exhibiting valuable therapeutic traits. No information exists as of today on the biosynthesis of these metabolites in S. chirayita. The current study reports the expression profiling of swertiamarin, amarogentin and mangiferin biosynthesis pathway genes and their correlation with the respective metabolites content in different tissues of S. chirayita. Root tissues of greenhouse grown plants contained the maximum amount of secoiridoids (swertiamarin, 2.8% of fr. wt and amarogentin, 0.1% of fr. wt), whereas maximum accumulation of mangiferin (1.0% of fr. wt) was observed in floral organs. Differential gene expression analysis and their subsequent principal component analysis unveiled ten genes (encoding HMGR, PMK, MVK, ISPD, ISPE, GES, G10H, 8HGO, IS and 7DLGT) of the secoiridoids biosynthesis pathway and five genes (encoding EPSPS, PAL, ADT, CM and CS) of mangiferin biosynthesis with elevated transcript amounts in relation to corresponding metabolite contents. Three genes of the secoiridoids biosynthesis pathway (encoding PMK, ISPD and IS) showed elevated levels (∼57-104 fold increase in roots), and EPSPS of mangiferin biosynthesis showed an about 117 fold increase in transcripts in leaf tissues of the greenhouse grown plants. The study does provide leads on potential candidate genes correlating with the metabolites biosynthesis in S. chirayita as an initiative towards its genetic improvement.

Sex-Biased Temporal Gene Expression in Male and Female Floral Buds of Seabuckthorn (Hippophae rhamnoides)

Seabuckthorn is an economically important dioecious plant in which mechanism of sex determination is unknown. The study was conducted to identify seabuckthorn homologous genes involved in floral development which may have role in sex determination. Forty four putative Genes involved in sex determination (GISD) reported in model plants were shortlisted from literature survey, and twenty nine seabuckthorn homologous sequences were identified from available seabuckthorn genomic resources. Of these, 21 genes were found to differentially express in either male or female flower bud stages. HrCRY2 was significantly expressed in female flower buds only while HrCO had significant expression in male flowers only. Among the three male and female floral development stages (FDS), male stage II had significant expression of most of the GISD. Information on these sex-specific expressed genes will help in elucidating sex determination mechanism in seabuckthorn.

Investigation of an outbreak of infectious pustular balanoposthitis in cattle breeding bulls at a frozen semen bank

Infectious pustular balanoposthitis (IPB) is one of the reproductive disorders caused by bovine herpesvirus 1 (BoHV1) that can be transmitted through artificial insemination. A herd of 63 breeding bulls at a frozen semen bank in Odisha state in India experienced a suspected outbreak of IPB, with 11 bulls showing clinical signs of the infection. Clinical signs were noticed in two bulls initially and a few days after in the other nine animals. Serum samples from 53 bulls were examined for anti-BoHV1 antibodies using a virus neutralisation test (VNT) and a competitive enzyme-linked immunosorbent assay (cELISA); the remaining ten bulls were not included in the study because it was difficult to restrain them at that time. Paired serum samples were collected 21 days apart from ten clinically affected bulls (the eleventh clinically affected bull was not included in the study for the reason stated above). In the neutralisation test, the paired serum samples showed a two- to fourfold increase in anti-BoHV1 antibody titre; in the cELISA, the paired samples were also found positive for anti-BoHV1 antibodies. Serum samples from 43 in-contact bulls were collected about day 22 after the first observation of clinical infection in the herd. Among these serum samples, a total of 30 were found positive for anti-BoHV1 antibodies in the VNT and a total of 30 were found positive in cELISA. Ten samples were positive in one test but not the other and 25 tested positive in both tests. In all, 35 serum samples from in-contact bulls tested positive in either one or both of the two types of test. An overall agreement of 76.74% was found in detection of anti-BoHV1 antibodies in the two tests. Sensitivity was higher than specificity in detection of anti-BoHV1 antibodies in the serum samples. The glycoprotein C region of the genomic DNA of BoHV1 was amplified from semen samples by polymerase chain reaction. The findings from the outbreak indicate that continuous monitoring of breeding bulls at frozen semen banks is warranted to avoid the risks associated with artificial insemination.

Common antigens prediction in bacterial bioweapons: a perspective for vaccine design

Bioweapons (BWs) are a serious threat to mankind and the lack of efficient vaccines against bacterial bioweapons (BBWs) further worsens the situation in face of BW attack. Experts believe that difficulties in detection and ease in dissemination of deadly pathogens make BW a better option for attack compared to nuclear weapons. Molecular biology techniques facilitate the use of genetically modified BBWs thus creating uncertainty on which bacteria will be used for BW attack. In the present work, available resources such as proteomic sequences of BBWs, protective antigenic proteins (PAPs) reported in Protegen database and VaxiJen dataset, and immunogenic epitopes in immune epitope database (IEDB) were used to predict potential broad-specific vaccine candidates against BBWs. Comparison of proteomes sequences of BBWs and their analyses using in-house PERL scripts identified 44 conserved proteins and many of them were known to be immunogenic. Comparison of conserved proteins against PAPs identified six either as PAPs or their homologues with a potential of providing protection against multiple pathogens. Similarly, mapping of conserved proteins against experimentally known IEDB epitopes identified six epitopes which had exact epitope match in four proteins including three from earlier predicted six PAPs. These epitopes were also reported to provide protection against several pathogens. In the backdrop of conserved heat shock GroEL protein from Salmonella enterica providing protection against five diverse bacterial pathogens involved in different diseases, and synthetic proteins produced by combination of epitopes from Mycobacterium tuberculosis and 4 viruses providing protection against both bacterium and viruses, the identified putative immunogenic conserved proteins and immune-protective epitopes can further be explored for their potential as broad-specific vaccine candidates against BBWs.

Can mycobacterial genomics generate novel targets as speed-breakers against the race for drug resistance

The rise of multi-drug resistant and extensively drug resistant M. tuberculosis around the world poses a great threat to human health, and necessitates development of new, effective and inexpensive anti-tubercular agents. The availability of knowledge on molecular biology of M. tuberculosis infection coupled with whole genome sequences, transcriptomic, proteomic and metabolomic data sets have provided insights on the genes/proteins indispensable for initiation and maintenance of persistence, cross-talk with and/or sensing the host immune response, and finally the reactivation of persistent M. tuberculosis to a growing state. The review will focus on analysis of current state of M. tuberculosis genomic resources, host-pathogen interaction studies in the context of pathogen persistence, and the efforts made or required in the development and utilization of computational tools, models and metabolic network analyses to speed up the process of drug target discovery, particularly eradicating the dormant infections.

EpiCombFlu: exploring known influenza epitopes and their combination to design a universal influenza vaccine

MOTIVATION

Influenza is responsible for half a million deaths annually, and vaccination is the best preventive measure against this pervasive health problem. Influenza vaccines developed from surveillance data of each season are strain-specific, and therefore, are unable to provide protection against pandemic strains arising from antigenic shift and drift. Seasonal epidemics and occasional pandemics of influenza have created a need for a universal influenza vaccine (UIV). Researchers have shown that a combination of conserved epitopes has the potential to be used as a UIV.

RESULT

In the present work, available data on strains, proteins, epitopes and their associated information were used to develop a Web resource, 'EpiCombFlu', which can explore different influenza epitopes and their combinations for conservation among different strains, population coverage and immune response for vaccine design. Forward selection algorithm was implemented in EpiCombFlu to select optimum combination of epitopes that may be expressed and evaluated as potential UIV.

AVAILABILITY

The Web resource is freely available at http://117.211.115.67/influenza/home.html.

CONTACT

chittaranjan.rout@juit.ac.in

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

Background

Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs.

Results

A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset.

Conclusions

Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html

Chemometric profile of root extracts of Rhodiola imbricata Edgew. with hyphenated gas chromatography mass spectrometric technique

Rhodiola imbricata Edgew. (Rose root or Arctic root or Golden root or Shrolo), belonging to the family Crassulaceae, is an important food crop and medicinal plant in the Indian trans-Himalayan cold desert. Chemometric profile of the n-hexane, chloroform, dichloroethane, ethyl acetate, methanol, and 60% ethanol root extracts of R. imbricata were performed by hyphenated gas chromatography mass spectrometry (GC/MS) technique. GC/MS analysis was carried out using Thermo Finnigan PolarisQ Ion Trap GC/MS MS system comprising of an AS2000 liquid autosampler. Interpretation on mass spectrum of GC/MS was done using the NIST/EPA/NIH Mass Spectral Database, with NIST MS search program v.2.0g. Chemometric profile of root extracts revealed the presence of 63 phyto-chemotypes, among them, 1-pentacosanol; stigmast-5-en-3-ol, (3β,24S); 1-teracosanol; 1-henteracontanol; 17-pentatriacontene; 13-tetradecen-1-ol acetate; methyl tri-butyl ammonium chloride; bis(2-ethylhexyl) phthalate; 7,8-dimethylbenzocyclooctene; ethyl linoleate; 3-methoxy-5-methylphenol; hexadecanoic acid; camphor; 1,3-dimethoxybenzene; thujone; 1,3-benzenediol, 5-pentadecyl; benzenemethanol, 3-hydroxy, 5-methoxy; cholest-4-ene-3,6-dione; dodecanoic acid, 3-hydroxy; octadecane, 1-chloro; ethanone, 1-(4-hydroxyphenyl); α-tocopherol; ascaridole; campesterol; 1-dotriacontane; heptadecane, 9-hexyl were found to be present in major amount. Eventually, in the present study we have found phytosterols, terpenoids, fatty acids, fatty acid esters, alkyl halides, phenols, alcohols, ethers, alkanes, and alkenes as the major group of phyto-chemotypes in the different root extracts of R. imbricata. All these compounds identified by GC/MS analysis were further investigated for their biological activities and it was found that they possess a diverse range of positive pharmacological actions. In future, isolation of individual phyto-chemotypes and subjecting them to biological activity will definitely prove fruitful results in designing a novel drug.

AFLP fingerprinting of tartary buckwheat accessions (Fagopyrum tataricum) displaying rutin content variation

In light of the economic importance of buckwheat as well as existence of enormous accessions of Fagopyrum species in the Himalayan regions of India, the characterization of tartary buckwheat for rutin content variation vis-à-vis DNA fingerprinting was undertaken so as to identify fingerprint profiles unique to high rutin content accessions. Rutin content analysis in mature seeds of 195 accessions of Fagopyrum tataricum showed a wide range of variation (6 μg/mg to 30 μg/mg D.W.) with most of the accessions (81%) containing 10-16 μg/mg of rutin followed by 14% accessions with significantly higher rutin content (17 μg/mg to 30 μg/mg) and 5% accessions with low rutin content (≤10 μg/mg). AFLP fingerprinting of 18 accessions having high (≥17 μg/mg) and low rutin content (≤10 μg/mg) with 19 EcoRI/MseI primer combinations yielded 136 polymorphic fragments out of total 907. The hierarchical and model-based cluster analyses of AFLP data strongly suggested that the 18 populations of F. tataricum were clustered into two separate groups. The high and low rutin content accessions were clustered into two separate groups based on AFLP fingerprinting. The AFLP fingerprints associated with high rutin content accessions of F. tataricum are expected to be useful for evaluation, conservation and genetic improvement of buckwheat.

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria

Background

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed.

Methods

A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein's critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed.

Results

The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets.

Conclusions/Significance

UniDrug-Target is expected to accelerate pathogen-specific drug targets identification which will increase their success and durability as drugs developed against them have less chance to develop resistances and adverse impact on environment. The server is freely available at http://117.211.115.67/UDT/main.html. The standalone application (source codes) is available at http://www.bioinformatics.org/ftp/pub/bioinfojuit/UDT.rar.

Expression of flavonoid biosynthesis genes vis-à-vis rutin content variation in different growth stages of Fagopyrum species

Buckwheat is one of the field crops with the highest concentration of rutin, an important flavonoid of medicinal value. Two species of buckwheat, Fagopyrum esculentum and Fagopyrum tataricum, are the major sources of rutin. Seeds of latter contain 40-50× higher rutin compared to the former. The physiological and molecular bases of rutin content variation between Fagopyrum species are not known. The current study investigated the differences in rutin content in seeds and in other tissues and growth stages of two Fagopyrum species, and also correlated those differences with the expression of flavonoid pathway genes. The analysis of rutin content dynamics at different growth stages, S1-S9 (from seed germination to mature seed formation) of Fagopyrum species revealed that rutin content was higher during seedling stages of F. tataricum (3.5 to 4.6-fold) compared to F. esculentum and then increased exponentially from stages S3 to S6 (different leaf maturing stages and inflorescence) of F. esculentum, whereas it fluctuated in F. tataricum. The rutin content was highest in the inflorescence stage (S6) of both species, with a relatively higher biosynthesis and accumulation during post-flowering stages of F. tataricum compared to F. esculentum. The expression of flavonoid pathway genes, through qRT-PCR, in different growth stages vis-à-vis rutin content variation showed differential expression for four genes, PAL, CHS, CHI and FLS with the amounts of transcripts relatively higher in F. tataricum compared to F. esculentum, thereby, correlating these genes with the biosynthesis and accumulation of rutin. The expression of PAL was highest, 7.69 and 8.96-fold in Stages 2 (seedling stage) and 9 (fully developed seeds) of F. tataricum compared to F. esculentum, respectively. The expression of the CHS gene correlated with the rutin content because it was highest in the flowers (S6) and fully developed seeds (S9) of both Fagopyrum species, with relatively higher transcript amounts (2.13 and 3.19-fold, respectively) in F. tataricum (IC-329457) compared to F. esculentum (IC-540858). This study provides useful information on molecular and physiological dynamics of rutin biosynthesis and accumulation in Fagopyrum species and the correlation of expression of flavonoid biosynthesis genes with the rutin content can be useful in planning for genetic improvement.

A method for content uniformity determination of atenolol and losartan potassium in combined tablet dosage form

A simple, accurate, rapid, specific and reproducible UV spectrophotometric method was developed for estimation of content uniformity of atenolol and losartan potassium in its combined tablet dosage form. The method involves formation and solving the simultaneous equation using 226.4 and 254 nm as two wavelengths for atenolol and losartan, respectively. Developed method was employed to determine the atenolol and losartan content in ten individual tablet units of five market formulations. Methanol was used as solvent. The method was validated. From the results, it was concluded that all brands are within the content uniformity limit, 85-115%.

Newcastle disease virus as an oncolytic agent

Cancer is a major cause of deaths in humans. Though there has been significant progress in cancer therapy, the limited efficacy and toxicities of current chemo- and radiotherapies have provided an impetus for the search of new therapeutics. A therapeutic approach, which uses viruses for the treatment of cancer termed, oncolytic virotherapy has recently emerged. Newcastle disease virus (NDV) is one such virus with an inherent oncolytic property. NDV causes a highly infectious disease in poultry worldwide. In humans it is reported to have oncolytic and immuno-stimulatory effects. It specifically replicates in tumour cells while sparing normal cells and cause oncolysis. For many years different strains of the NDV have been investigated for treatment of various human cancers. Recent advances in reverse genetics provided investigators the tools to produce recombinant NDV with improved oncolytic property.

Venous air embolism during microelectrode recording in deep brain stimulation surgery in an awake supine patient

Venous air embolism (VAE) is a potentially serious complication in neurosurgery. It occurs most commonly during craniotomy in the sitting position. Diagnosis is difficult in awake patients on spontaneous ventilation due to different clinical manifestations. Prompt diagnosis and treatment are essential. We report venous air embolism in an awake patient undergoing deep brain stimulation for Parkinson's disease and discuss the pathogenesis, prevention and management of VAE.

Time course of Newcastle disease virus-induced apoptotic pathways

Newcastle disease virus (NDV) causes economically significant Newcastle disease (ND) in almost all birds worldwide. Previous studies have shown that NDV induces caspase dependent apoptotic pathways in infected cells. In the present study, time course induction of apoptotic pathways in Vero cells is described. In NDV-infected cells, caspase-8 activity, percentage of cells showing TRAIL expression was higher at 24h p.i. (post-infection) compared to 48 h p.i. In contrast, caspase-9 activity, efflux of cytochrome c, loss of mitochondrial membrane potential was higher at 48 h compared to 24h p.i. The caspase-3 activity was high both times. Based on these results, it was concluded that at 24h p.i., NDV induces apoptosis through extrinsic apoptotic pathway while at 48 h p.i. predominantly through intrinsic apoptotic pathway.

Newcastle disease virus-induced cytopathic effect in infected cells is caused by apoptosis

The velogenic Newcastle disease virus (NDV) causes highly infectious and economically significant Newcastle disease (ND) in birds of various species. In cell culture NDV induces cytopathic effect (CPE) characterized by rounding, vacuolation, syncytia formation and cell death. Aside from cell to cell fusion caused by the F and HN glycoprotein of the virus molecular events leading to cell death are not known. In the current study, NDV-infected Vero cells, at 48 h p.i., showed nuclear condensation, cytoplasm blebbing, DNA fragmentation, and phosphatidylserine translocation to the cell surface. In addition, virus-infected cells demonstrated decreased DNA content and an increased Bax to Bcl-2 ratio, p53 level and caspase 3, 8, 9 expression compared to mock-infected cells. Based on these results, it was concluded that CPE in NDV-infected cells was caused by to the induction of apoptosis with the involvement of p53 and the Bax, dependent apoptotic pathways.

Rotavirus diarrhea in bovines and other domestic animals

Rotavirus diarrhea is the major cause of death of millions of children in developing countries besides causing economically significant malady in neonates of many domestic animals. In neonates, the infection is non-viremic, have very short incubation period, and manifests profuse diarrhea and severe dehydration. Concurrent infection with secondary pathogens may augment the disease severity. Diarrhea occurs due to virus-mediated destruction of absorption efficient enterocytes, activation of enteric nervous system, or due to a rotavirus enterotoxin. Diagnosis of the infection relies on conventional techniques like isolation in MA 104 cell lines, electron microscopy, electro-pherotyping, and various serological tests. Presently, diagnosis and molecular typing is performed using serotype specific RT-PCR, sequencing or genomic hybridization techniques. As the rotaviruses are known to exhibit extreme genetic diversity and outplay disinfection procedures, eradication of the pathogen is often difficult. Hence, for prevention, good management practices coupled with vaccination of dam for protecting young ones, has to be practiced. Recently, new generation prophylactic strategies including DNA vaccines, subunit vaccines, virus-like particles (VLPs) and edible vaccines have been found to induce sufficient levels of passive immunity. Aside to the infection in animals, zoonotic significance of the animal rotaviruses has to be further unearthed. In this review, efforts have been made to highlight the importance and prevalence of the disease in bovines, its pathogenesis along with preventive measures, salient features of rotaviruses and their inter-species transmission abilities, zoonotic implications, and a concise account of the infection in various domestic animals and poultry.

Thermal decomposition of expanded polystyrene in a pebble bed reactor to get higher liquid fraction yield at low temperatures

Expanded polystyrene is one of the polymers produced in large quantities due to its versatile application in different fields. This polymer is one of the most intractable components in municipal solid waste. Disposal of polymeric material by pyrolysis or catalytic cracking yields valuable hydrocarbon fuels or monomers. Literature reports different types of reactors and arrangements that have uniform temperatures during pyrolysis and catalytic cracking. The present study focuses on reducing the temperature to maximize the quantity of styrene monomer in the liquid product. A bench scale reactor has been developed to recover the styrene monomer and other valuable chemicals. Experiments were carried under partial oxidation and vacuum conditions in the temperature range of 300-500 degrees C. In the pyrolysis optimization studies, the best atmospheric condition was determined to be vacuum, the pyrolysis temperature should be 500 degrees C, yield of liquid product obtained was 91.7% and yield of styrene obtained was 85.5%. In the characterization studies, distillation and IR spectroscopy experiments were carried out. The remaining of the liquid product comprises of benzene, ethyl benzene, and styrene dimers and trimers.

Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation

Newcastle disease virus causes (NDV) apoptotic death of infected cells. In the present study, the stimulus that provoked the induction of apoptosis in infected cells was examined. Vero cells infected with NDV developed apoptosis as characterized by DNA fragmentation and decreased DNA content. In presence of ammonium chloride, infected cells did not show reduced DNA content indicating the requirement of virus entry for the induction of apoptosis. UV-inactivated NDV did not induce apoptosis in cells suggesting the need of virus replication. Although cycloheximide blocked NDV-induced apoptosis, actinomycin-D did not, suggesting that de-novo viral protein synthesis was critical for the induction of apoptosis. In addition, activation of caspases was also detected by flowcytometry, indirect fluorescent and colorimetric assays. Based on the results, it was concluded that NDV-induced apoptosis in Vero cells required virus replication, de-novo protein synthesis and caspase activation.

HN protein of Newcastle disease virus causes apoptosis in chicken embryo fibroblast cells

Newcastle disease virus (NDV), an avian paramyxovirus, induces apoptosis in chicken embryo fibroblast (CEF) cells. In the present investigation, the ability of haemagglutinin-neuraminidase (HN) protein of NDV to cause apoptosis in CEF cells was examined. The results revealed that cells expressing the HN protein demonstrated decreased DNA content, phosphatidylserine exposure and increased cytoplasmic vacuolation. Up-regulation of caspase-1, -9, -8, -3, loss of mitochondrial transmembrane potential and an increase in oxidative stress were also observed in cells expressing the HN protein. Based on the above results it can be concluded that HN protein of NDV causes apoptosis in CEF cells.

Immunotoxicity of carbaryl in chicken

Effect of methyl carbonate pesticide, carbonyl, was studied on macrophage functions, lymphocyte proliferation and delayed type hypersensitivity response. Sixteen adult chicken, vaccinated against Newcaslte disease, were procured and randomly divided in two experimental groups. Chicken of group I served as control, while group II birds were given carbaryl at 20 ppm (No observable effect level, NOEL) in feed for 3 months. To measure the functional activity of phagocytic cells, nitroblue tetrazolium (NBT) reduction test was performed on peripheral blood leucocytes. Concanvalin A (Con-A) and lipopolysaccharide stimulated proliferation of T and B lymphocytes was assessed using MTT dye method. At the end of experiment, the phagocytic capacities of macrophages were significantly reduced in carbaryl treated group. Lymphocyte proliferation responses to Con-A and LPS were (23 and 28%, respectively lower) in chicken fed with carbaryl. Delayed hypersensitivity reaction to tuberculin was reduced to 77% of control values indicating inhibition of cell mediated immune response. The present study suggested of immunosuppressive effect of (NOEL dose carbaryl) in chicken.

Efficacy and safety of hydroxychloroquine sulphate in rheumatoid arthritis: a randomized, double-blind, placebo controlled clinical trial--an Indian experience

OBJECTIVE

Hydroxychloroquine (HCQ) has been used for a long time worldwide as a therapy for rheumatoid arthritis (RA). This trial was designed to determine whether HCQ was efficacious and safe in Indian patients with RA.

RESEARCH DESIGN AND METHODS

The trial was a multicentre, placebo controlled, randomized and double-blind study. One hundred and twenty-two patients with RA were enrolled in 3 different centres for the trial (26 males and 96 females in the age group of 18-60 years). Patients were randomized to receive either hydroxychloroquine tablets (n = 61) two tablets of 200 mg daily or placebo (n = 61) two tablets daily. After 8 weeks all patients received one tablet of hydroxychloroquine 200 mg daily for 4 weeks. Every patient also received one tablet of Nimesulide 100 mg twice daily.

MAIN OUTCOME MEASURES

Assessment of response at 12 weeks using modified ACR 20 (American College of Rheumatology 20) criteria where Health Assessment Questionnaire (HAQ) was replaced by ARA (American Rheumatology Association) functional class.

RESULTS

40.4% of patients on hydroxychloroquine showed improvement by modified ACR response criteria whereas only 20.7% (p = 0.02) showed improvement in the placebo group. No significant side effects were observed in any of the patients. There were no ocular toxicities.

CONCLUSIONS

Hydroxychloroquine was found to be an effective and well-tolerated drug in rheumatoid arthritis in Indian patients.

Down regulation of humoral immunity in chickens due to carbendazim

This study was planned to investigate the effect of very low dose of carbendazim on the humoral immune response in the chicken. Sixteen adult chickens, earlier vaccinated against New Castle Disease were divided in two experimental groups. Chickens of group I served as control, while group II birds were given a feed containing 200 ppm of carbendazim, which is considered no observable effect level (NOEL) dose, for a period of 6 months. The Humoral immune response was measured by the B-lymphocyte blastogenesis assay using lipopolysaccharide as mitogen and the quantitation of IgG, IgA, IgM levels by using respective antichicken conjugates, through an ELISA method. Total serum proteins, serum gamma-globulins and globulins were measured using commercially available kits. Carbendazim significantly (P< or =0.05) reduced both the B-lymphocyte proliferation and serum IgG, IgM and IgA levels, leading to decreased immunocompetence. At the end of experiment percent decrease in B-lymphocyte proliferation was 20.5% and that in serum IgG, IgM and IgA were 11.2, 22.9 and 28.8%, respectively. The percent decrease in total serum protein, serum gamma-globulins and serum globulins were 14.6, 18.5 and 9.7%, respectively. Results clearly indicated down regulation of humoral immunity by carbendazim at NOEL dose.

Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea

We have identified, genetically mapped and physically delineated the chromosomal location of a new rice blast resistance locus, designated Pi-CO39(t). This locus confers resistance to Magnaporthe grisea isolates carrying the AVR1-CO39 avirulence locus. The AVR1-CO39 locus is conserved in non-rice (cereals and grasses)-infecting isolates of M. grisea, making Pi-CO39(t) useful for engineering M. grisea resistance in rice and other cereals. The resistance in the rice line CO39 was inherited as a single dominant locus in segregating populations derived from F(2) and F(3) crosses between disease-resistant (CO39) and susceptible (51583) rice genotypes. Microsatellite, RFLP and resistance gene analog (RGA) markers were used to map the Pi-CO39(t) locus to a 1.2-cM interval between the probenazole-responsive ( RPR1) gene (0.2 cM) and RFLP marker S2712 (1.0 cM) on the short arm of rice chromosome 11. RFLP markers G320 and F5003, and resistance gene analogs RGA8, RGA38 and RGACO39 were tightly linked to the Pi-CO39(t) locus (no recombination detected in a sample of ~2400 gametes). A large-insert genomic library of CO39 was constructed in the binary plant transformation vector pCLD04541. A library screen using RGA8, RGA38 and probes derived from the ends of CO39 clones, as well as BAC end probes from the corresponding locus in the rice cv. Nipponbare, resulted in the assembly of three CO39 contigs of 180 kb, 110 kb and 145 kb linked to the Pi-CO39(t) locus. A 650-kb contig was also constructed representing the susceptible locus, pi-CO39(t), in the Nipponbare genome. The two genomes are highly divergent with respect to additions, deletions and translocations at the Pi-CO39(t) locus, as revealed by the presence or absence of mapping markers.

Meso 2,3-dimercaptosuccinic acid (DMSA) and monoisoamyl DMSA effect on gallium arsenide induced pathological liver injury in rats

The effect of meso 2,3-dimercaptosuccinic acid (DMSA) and monoisoamyl DMSA (MiADMSA) on gallium arsenide (GaAs) induced liver damage was studied. The oral feeding rat model was used in this study. The animals were exposed to 10 mg/kg GaAs, orally, once daily, 5 days a week for 24 weeks and treated thereafter with single oral daily dose of either 0.3 mmol/kg DMSA or MiADMSA for two course of 5 days treatment. The animals were sacrificed thereafter. Lipid peroxidation was assessed by measuring liver thiobarbituric acid reactive substance (TBARS). Liver damage was assessed by number of biochemical variables and by light microscopy. The activity of superoxide dismutase (SOD) and delta-aminolevulinic acid dehydratase (ALAD) beside reduced glutathione (GSH) concentration was measured in blood. Exposure to GaAs produced a significant reduction in GSH while, increased the oxidized glutathione (GSSG) concentration. Hepatic glutathione peroxidase (GPx) and catalase activity increased significantly while level of serum transaminase increased moderately. Gallium arsenide exposure also produced marked hepatic histopathological lesions. Overall, treatment with MiADMSA proved to be better than DMSA in the mobilization of arsenic and in the turnover of some of the above mentioned GaAs sensitive biochemical alterations. Histopathological lesions also, responded more favorably to chelation treatment with MiADMSA than DMSA.

Effect of topically applied sulphur mustard on guinea pig liver

The study revealed that topically applied sulphur mustard, which is a potent blistering agent with mutagenic and carcinogenic properties, is also hepatotoxic. It produces severe steatosis and other pathological alterations, accompanied by biochemical changes. There is a significant rise in the levels of glutamic oxaloacetic transaminase (GOT) and glutamic pyruvate transaminase (GPT) after exposure. The liver injury appeared to peak on the third day. Recovery at the ultrastructural level could be noticed on the sixth day but was far from complete because the gross pathological changes were still severe.

Structural changes induced by sulphur mustard in rabbit skin

Sulphur mustard (SM) is a bifunctional alkylating agent which can react with a wide variety of molecules of biological interest. The interaction of SM with animal skin elicits a varied histopathological response in cellular components on a temporal scale. The extracellular matrix (ECM) undergoes tremendous structural changes as a result of SM exposure. Sulphur mustard induces oedema, infiltration of polymorphonuclear cells and destruction of cells. Injury appeared to be most severe on the third day after exposure, when the thickness of the skin registered the maximum change from the control. The initiation of recovery could be noticed on the 6th day, when the intercellular gap in the ECM began to reduce significantly, indicating reformation of damaged skin. Simultaneous reformation was also noticed in the epidermis and other cellular components. However, recovery was far from complete and continued beyond the 6th day.

Production of disease-free encapsulated buds of Zingiber officinale Rosc

Shoot buds of ginger were successfully encapsulated in 4% sodium alginate gel. Encapsulated buds were germinated in vitro to form roots and shoots. In vitro germination (emergence of sprouts) of encapsulated buds ranged from 16.7% to 81.8% on different media after 5 weeks of incubation. Normal plantlets with an average shoot length of 2.3 cm and 1.7 cm root length were successfully transplanted into unsterilized soil without any hardening process. These plantlets showed no symptoms of ginger yellows disease and the causal fungal pathogen failed to grow out on culture media (used as a diagnostic test).

Cell-mediated immune response in rotavirus-infected calves: leucocyte migration inhibition assay

The cell-mediated immune (CMI) response was determined in rotavirus-infected calves by leucocyte migration inhibition assay with blood, spleen, mesenteric lymph node and intestinal lymphocytes. The inhibition of migration was more prominent in intestinal and mesenteric lymph node lymphocytes than in spleen and blood. In rotavirus-infected calves, the assay indicated the presence of CMI response which was more prominent at the local site of infection.

Pyometra in camels: case report

Pyometra was recorded in five camels and Actinomyces pyogenes (Corynebacterium pyogenes) was isolated from pus of the affected camels.

Isolation of enterotoxigenic Escherichia coli from camels with diarrhoea

E. coli serogroups 02, 08, 083, 0103 and 0120 were isolated from seven camels with diarrhoea of which 02, 08, and 083 were found to be enterotoxigenic on rabbit ligated ileal loop test. Out of 125 apparently healthy camels, 75 strains of E. coli were isolated. The majority of isolates were susceptible to gentamycin, nitrofurantoin, trimethoprim plus sulphonamide, neomycin, kanamycin and chloramphenicol.

Comparison of the dot-immunobinding assay with the complement fixation test for the detection of Brucella antibodies in sheep

A dot-immunobinding assay (DIA), using as antigen a sonic extract of Brucella abortus dotted on nitrocellulose bound to a plastic strip, was employed for the detection of Brucella antibodies in 666 sheep sera. The results were compared with the complement fixation test (CFT). All the 242 sera belonging to two flocks were found to be negative by DIA. CFT was negative in 239 cases, whereas three samples showed anti-complementary activity. Of the 424 sera from the remaining three flocks, 98 were positive by both tests and six were positive in DIA, but negative in CFT. In addition, 14 of the 19 anti-complementary sera were also positive by DIA.

Separation of some antihistamines on impregnated TLC silica plates

Different metal salts have been tried as impregnating reagents for developing TLC separation schemes for some antihistamines on silica gel 'G' plates, using a new solvent system benzene + dimethyl formamide + acetic acid (30:10:7). Spots were visualized by spraying with a solution of Dragendroff's reagent.

Traumatic oesophageal perforation treated with Mousseau Barbin tube

A traumatic perforation of the oesophagus during endoscopy was managed successfully by the use of a Mousseau Barbin tube instead of by a thoractomy repair.