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Background: Wild food plants (WFPs) play an important role in the traditional dietary habits of various indigenous communities worldwide, particularly in mountainous regions. To understand the dynamics of food preferences, cross-cultural studies on food plants should be conducted across diverse ethnic groups in a given area. In this context, the current study investigated the use of WFPs by seven different cultural groups in the Kashmir Himalayan Region. In this area, people gather wild plants and their parts for direct consumption, traditional foods, or sale in local markets. Despite this reliance, documentation of the food system, especially concerning WFPs, is notably lacking. Hence, our research aimed to document WFPs, along with associated traditional ecological knowledge, and identify major threats to their long-term sustainability in Division Muzaffarabad. Methods: Through a comprehensive approach involving questionnaires, interviews, focus groups, and market surveys, we gathered data from 321 respondents. PCA was performed to analyze threats and plant use using "factoextra" in R software. Origin Pro was used to create a chord diagram, while R software was used to generate a Polar heat map. Additionally, a Venn diagram was created using Bioinformatics software. Results: The study included 321 informants, of whom 75.38% were men and 24.61% were women. In total, 113 plant taxa from 74 genera and 41 botanical families were reported. Polygonaceae and Rosaceae accounted for the majority (17 species each), followed by Lamiaceae (7 species). Leaves were the most used part as food sources (41.04%), followed by fruits (33.33%). Most of the species are consumed as cooked (46.46%) and as raw snacks (37.80%). A total of 47 plant species were collected and cooked as wild vegetables, followed by 40 species used as fruits. This study is the first to describe the market potential and ecological distribution of WFPs in the study area. Cross-comparison showed that utilization of WFPs varies significantly across the region and communities, including their edible parts and mode of consumption. Jaccard index (JI) value ranged from 5.81 to 25. Furthermore, the current study describes 29 WFPs and 10 traditional food dishes that have rarely been documented in Pakistan's ethnobotanical literature. Climate change, invasive species, expansion of agriculture, and plant diseases are some of the most significant threats to WFPs in the study area. Conclusions: The older age group has more knowledge about WFPs compared to the younger generation, who are not interested in learning about the utilization of WFPs. This lack of interest in information about WFPs among the younger generation can be attributed to their limited access to markets and availability of food plants in the study area. Traditional gathering of food plants has been reduced in younger generations during recent years; therefore, it is crucial to develop effective conservation strategies. These efforts not only safeguard indigenous flora, food knowledge, and cultural heritage, but they also contribute to food security and public health by utilizing local wild foods in the examined area. [ABSTRACT FROM AUTHOR]

The Integrated Course Design (ICD), using Fink's taxonomy of significant learning, popularly known as ICD/SL, is a handy way to create a better learning environment for students. It is a learner-centered approach with the desired end-product, but at the same time, it upgrades the teaching by improving the instructors' delivery mechanism. Our goal of this study was to see whether ICD/SL affects students' class participation and academic performance in the "Introduction to Bioinformatics" course offered at the Department of Biological Science, BITS Pilani, Pilani campus, India. Three class groups were chosen for this purpose: 2019–2020 (51 students), 2020–2021 (77 students), and 2021–2022 (72 students). The control group, 2019–2020, received no ICD/SL instruction; the remaining two groups, 2020–2021 and 2021–2022, received ICD/SL instruction that included revised learning goals based on Fink's taxonomy and new teaching and evaluation activities. A Likert scale was utilized to assess students' academic feedback using the Kruskal–Wallis test to determine the P-value. The findings showed that the treatment groups had higher class participation and academic performance in the summative assessment of final grades. In the experimental groups, the class participation was 23 to 27% higher compared to the control group. The absenteeism rate on the course decreased from 14% in 2019–2020 to 9% in 2020–2021 and 4% in 2021–2022. Also, in the treatment groups, 83 to 90% of students were in the High to Excellent category, compared to 74% in the control group. The failure rate of the course decreased from nearly 18 to 10% in 2021–2022 and only 6% in 2020–2021. There were significant differences between the treatment and control groups in class participation and academic performance (P < 0.05). This study has shown that the use of ICD/SL has the potential to improve students' class participation and academic performance. [ABSTRACT FROM AUTHOR]

In India, drug-resistant tuberculosis (DR-TB) is a major public health issue and a significant challenge to stop TB program. An estimated 27% of new TB cases and 44% of previously treated TB cases are resistant to at least one anti-TB drug. The conventional methods for DR-TB diagnosis are time-consuming and have limitations, leading to delays in treatment initiation and the spread of the disease. Next-generation sequencing (NGS) based approaches have emerged as a promising tool for diagnosing DR-TB, simultaneously offering rapid and accurate detection of resistance mutations in multiple genes. NGS-based approaches generate a large amount of data, which requires efficient and reliable bioinformatics pipelines for data analysis. TBProfiler and Mykrobe are the bioinformatics pipelines that have been created to analyze NGS data for the diagnosis of DR-TB. These pipelines use reference-based and machine-learning approaches to detect resistance mutations and predict drug susceptibility, enabling clinicians to make informed treatment decisions. Implementing NGS-based approaches and bioinformatics pipelines for DR-TB diagnosis can potentially improve patient outcomes by facilitating early detection of drug resistance and guiding personalized treatment regimens. However, the widespread adoption of these approaches in India faces several challenges, including high costs, limited infrastructure, and a lack of trained personnel. Addressing these challenges requires concerted effort to ensure equitable access to and effective implementation of these innovative technologies. [ABSTRACT FROM AUTHOR]

The early detection and accurate diagnosis of liver fibrosis, a progressive and potentially serious liver condition, are crucial for effective medical intervention. Invasive methods like biopsies for diagnosis can be risky and expensive. This research presents a novel computer-aided diagnosis model for liver fibrosis using a hybrid approach of minimum redundancy maximum relevance (MRMR) feature selection, bidirectional long short-term memory (BiLSTM), and convolutional neural networks (CNN). The proposed model involves multiple stages, including image acquisition, preprocessing, feature representation, fibrous tissue identification, and classification. Notably, histogram equalization is employed to enhance image quality by addressing variations in brightness levels. Performance evaluation encompasses a range of metrics such as accuracy, precision, sensitivity, specificity, F1 score, and error rate. Comparative analyses with established methods like DCNN, ANN-FLI, LungNet22, and SDAE-GAN underscore the efficacy of the proposed model. The innovative integration of hybrid MRMR-BiLSTM-CNN architecture and the horse herd optimization algorithm significantly enhances accuracy and F1 score, even with small datasets. The model tackles the complexities of hyperparameter optimization through the IHO algorithm and reduces training time by leveraging MRMR feature selection. In practical application, the proposed hybrid MRMR-BiLSTM-CNN method demonstrates remarkable performance with a 97.8% accuracy rate in identifying liver fibrosis images. It exhibits high precision, sensitivity, specificity, and minimal error rate, showcasing its potential for accurate and non-invasive diagnosis. [ABSTRACT FROM AUTHOR]

BACKGROUND AND OBJECTIVES: Discrepancy between forward and reverse ABO grouping could be due to several reasons including genetic mutations of the alleles encoding group specific transferase. The healthy donors found with weak A antigen were investigated to ascertain the allele responsible for variation. MATERIALS AND METHODS: Standard serological methods were employed using commercial antisera. The molecular sequencing was performed on DNA with enrichment library prep kit and a custom designed overlapping probe panel. Binary alignment mapping files, generated on board the Illumina MiSeq instrument and aligned to the GRCh37/Hg19 reference genome, were uploaded to the QIAGEN CLC genomics workbench software (version. 20) where variant call files were generated and analyzed. RESULTS: Red blood cells (RBCs) of six healthy donors, showing weak mix-field agglutination by anti-A and anti-A, B and plasma with absence or weakly reacting anti-A, were investigated serologically. The RBCs incubated with anti-A yield positive elution and their saliva lacked A but possessed H antigen thereby classifying as a historical known phenotype Aend. Family study on 4 probands showed inheritance of the trait. Molecular studies revealed presence of ABO*A allele carrying rare novel variant referred to as c.106delinsGG in line with HGVS recommendation that was thought to be responsible for the variant of A. CONCLUSION: Six cases serologically defined as A were found to be associated with novel weak allele ABO*A (c.106delinsGG). The Aweak phenotype with the novel allele has not been displayed on International Society of Blood Transfusion database, though c.106delinsGG is listed in the UCSC genome browser under rs782544248. [ABSTRACT FROM AUTHOR]

Objectives: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson's disease (PD). We sequenced microbial DNA using fecal samples collected from PD cases and healthy controls (HCs) to evaluate the role of gut microbiota. Methods: Full-length bacterial 16S rRNA gene sequencing of fecal samples was performed using amplified polymerase chain reaction (PCR) products on the GridION Nanopore sequencer. Sequenced data were analyzed using web-based tools BugSeq and MicrobiomeAnalyst. Results: We found that certain bacterial families like Clostridia UCG 014, Cristensenellaceae, and Oscillospiraceae are higher in abundance, and Lachinospiracea, Coriobacteriaceae and genera associated with short-chain fatty acid production, Faecalibacterium, Fusicatenibacter, Roseburia and Blautia, are lower in abundance among PD cases when compared with the HC. Genus Akkermansia, Dialister, Bacteroides, and Lachnospiraceae NK4A136 group positively correlated with constipation in PD. Conclusion: Observations from this study support the other global research on the PD gut microbiome background and provide fresh insight into the gut microbial composition of PD patients from a south Indian population. We report a higher abundance of Clostridia UCG 014 group, previously not linked to PD. [ABSTRACT FROM AUTHOR]

Aim: The aim of this study was to analyze the cross-presentation of allopeptides derived from donor major histocompatibility (MHC) molecules by recipient class I MHC molecules in the context of transplantation rejection. Materials and Methods: The MHC molecules were selected based on frequency distribution in the Kerala (India) population using the "allelefrequency. net" database. The most frequent alleles were chosen as donor and recipient alleles. Different immunoinformatics servers such as Netcytotoxic T lymphocyte, NetMHCpan, and Immune Epitope Database MHC I were used for predicting potential T-cell epitopes, and MHC class I epitopes, respectively, from the chosen donor MHC molecule. Three peptides with strong binding affinities in all three predictions were selected for further analysis. The binding of these peptides to the second MHC class I molecule, the recipient one, and transporter associated with antigen processing protein was confirmed by molecular docking using the "AutoDockVina" tool. The binding interactions were visualized using the "Discovery Studio Visualizer" platform. Results: The ability of the selected class I MHC molecule, human leukocyte antigens (HLAs)-A* 11:01, considered the donor allele, to act as an exogenous antigen and to get processed into peptides and presented on the second class I MHC molecule, HLA-A*02:01, considered the recipient allele was confirmed. This immunoinformatics approach could help us to identify potential epitopes from an HLA class I molecule and to measure its ability to get cross-presented on a second HLA class I molecule to trigger the process of cell-mediated rejection. Conclusion: This immunoinformatics approach could help us to identify potential epitopes from an HLA class I molecule and to measure its ability to get cross-presented on a second HLA class I molecule to trigger the process of cell-mediated rejection. Our study provides an easy in silico method for predicting the chances of cell mediated rejection in organ transplantations involving an unrelated donor. We hope that this computational analysis will pave the way for simplifying the process involved in organ rejection prediction. [ABSTRACT FROM AUTHOR]

Background: Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder. The aim of the present investigation was to identify gene signature specific to T2DM. Methods: The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes. Results: A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1 were screened out as the critical genes. ROC analysis provides prognostic value of hub genes. Conclusion: The potential crucial genes, especially APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1, might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets. [ABSTRACT FROM AUTHOR]

Aim: This study is an attempt to screen the key immune elements that participate during HBV infection and the related pathways that are modulated. Background: The pathogenesis of Hepatitis B virus and the corresponding clinical manifestations in the host are primarily immunemediated. Methods: This study utilizes a PCR array to screen immune-related genes that are differentially expressed in the presence of the virus in HBV replicating HepG2.2.15 cells as compared to control HepG2 cells. The significantly up-regulated genes were subjected to bioinformatic analysis utilizing GSEA and STRING. Additionally, ELISA was used to corroborate the levels of Alpha 1 antitrypsin (AAT) from patients' sera. Results: The expressions of 31% of the studied genes were significantly up-regulated (> 2-fold, p<0.05) in HepG2.2.15 cells compared to controls, and this included the SERPINA1, FN1, IL1R2, LBP, LY96, LYZ and PROC genes. When they were clustered based on biological processes, signaling pathways, and disease progression, the genes related to biotic stimulus, complement-coagulation cascades, and fibrosis, respectively, showed the highest (p<0.05) enrichment. Analysis of patients' sera by ELISA revealed that the serum AAT (SERPINA1) levels were significantly higher in asymptomatic carriers and in patients with chronic liver disease than in controls (p<0.05). Moreover, SERPINA1 levels were also positively correlated with the levels of serum ALT (r=0.4495, p<0.05) among HBV infected patients. Conclusion: The current study highlights the key immune elements and pathways that are modulated during HBV infection and proposes the possible use of AAT as a non-invasive immunological biomarker to follow the progression of liver disease. [ABSTRACT FROM AUTHOR]

Introduction: Viral infections of Central Nervous System (CNS) are associated with severe neurological sequelae and can lead to significant morbidity, if not adequately diagnosed and treated. An immunological assay detecting antibodies in the Cerebrospinal Fluid (CSF) of the patients is widely used for diagnosis of viral infections of the CNS. In the present study, diagnostic efficacy of in-house designed synthetic peptide based Enzyme Linked Immunosorbent Assay (ELISA) was evaluated for detection of antibodies against neurotropic viruses panel such as Cytomegalovirus (CMV), Epstein-Barr virus (EBV), Varicella Zoster Virus (VZV), Japanese Encephalitis Virus (JEV), Dengue (DENV), West Nile Virus (WNV) and Chandipura Virus (CHPV) in CSF of suspected cases. Aim: To determine the diagnostic efficacy of in-house developed synthetic peptide-based ELISA in viral infections of the CNS. Materials and Methods: A retrospective study was conducted in Central India Institute of Medical Science, Nagpur, Maharashtra, India. The suspected case of CNS viral infections of the patients were enrolled in this study from January 2013 to December 2015. Total 150 suspected cases of viral CNS infections and 135 control cases were recruited. Total 32 synthetic peptides of highly immunogenic proteins of respective seven neurotropic viruses were designed and synthesised. The designed peptides were evaluated in CSF samples of both the viral CNS infections and control cases for detection of Imunoglobulin G (IgG) and IgM antibodies using in-house developed antibody detection method. The developed tests were further compared with commercially available antibody detection ELISA kit. The sensitivity and specificity of peptide-ELISA were determined by Receiver Operating Curve (ROC) analysis and p-value was calculated by comparison of means by t-test. Results: Out of total 150 cases of CNS viral infections, a total of 31 CSF samples including 15 for CMV and 16 of JEV were positive by in-house peptide ELISA. The synthetic peptides STGDVVDISP, KQKSLVEL, RTLEVFKE, RSSNVED of CMV and ITYECPK, RRSVSVQT, GESSLVN of JEV showed a significant difference in mean absorbance value for IgM and IgG antibodies in CSF of suspected cases of viral CNS infection. Conclusion: The results demonstrated that the synthetic peptidebased ELISA is rapid, cost-effective, simple and efficient immunodiagnostic assay for initial screening of viral CNS infection. [ABSTRACT FROM AUTHOR]

Cancer statistics in 2020 reveals that breast cancer is the most common form of cancer among women in India. One in 28 women is likely to develop breast cancer during their lifetime. The mortality rate is 1.6 to 1.7 times higher than maternal mortality rates. According to the US statistics, about 42,170 women in the US are expected to die in 2020 from breast cancer. The chance of survival can be increased through early and accurate diagnosis of cancer. The pathologists manually analyze the histopathology images using high-resolution microscopes to detect the mitotic cells. This is a time-consuming process because there is a minute difference between the normal and mitotic cells. To overcome these challenges, an automatic analysis and detection of breast cancer by using histopathology images play a vital role in prognosis. Earlier researchers used conventional image processing techniques for the detection of mitotic cells. These methods were found to be producing results with low accuracy and time-consuming. Therefore, several deep learning techniques were adopted by researchers to increase the accuracy and minimize the time. The hybrid deep learning model is proposed for selecting abstract features from the histopathology images. In the proposed approach, we have concatenated two different CNN architectures into a single model for effective classification of mitotic cells. Convolution neural network (CNN) automatically detects efficient features without human intervention and classifies cancerous and non-cancerous images using a hybrid fully connected network. It is a computationally efficient, very powerful, and efficient model for performing automatic feature extraction. It detects different phenotypic signatures of nuclei. In order to enhance the accuracy and computational efficiency, the histopathology images are preprocessed, segmented, and feature extracted through CNN and fed into a hybrid CNN for classification. The hybrid CNN is obtained by concatenating two CNN models; together, this is called model leveraging. Model averaging can be improved by weighting the contributions of each sub-model to the combined prediction by the expected performance of the sub-model. The proposed hybrid CNN architecture with data preprocessing with median filter and Otsu-based segmentation technique is trained using 50,000 images and tested using 50,000 images. It provides an overall accuracy of 98.9%. [ABSTRACT FROM AUTHOR]

The clinical manifestations of FGFR3 sequence variations can vary from mild unnoticed short stature to neonatal lethal dwarfism and can be causative of phenotypes including achondroplasia, hypochondroplasia, and thanatophoric dysplasia. Clinical data describe an 11 month old girl with restricted growth and preserved intellect. She had rhizomelic short stature with peculiar facies but no Acanthosis nigricans. In view of the absence of the hotspot mutation c.1138 G>A/G>C (p.Gly380Arg), complete gene sequencing was done that revealed a rare sequence variation, NM_000142.4:c.1043C>G (p.Ser348Cys) in FGFR3. This sequence variation has not been reported from India so far. This report emphasizes the benefit of sequencing the whole gene in individuals who are negative for hotspot mutation of achondroplasia with strong clinical suspicion. [ABSTRACT FROM AUTHOR]

With the exponential spread of the coronavirus disease 2019 (COVID‐19) pandemic across the world within the 12 months, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains are continuously trying to adapt themselves to the host environment by random mutations. When doing so, some variants with evolutionary advantages such as better human to human transmissibility potential might get naturally selected. This short communication demonstrates how the mutation frequency patterns are evolving in 2457 SAR‐CoV‐2 strains isolated from COVID‐19 patients across diverse Indian states. We have identified 19 such variants showing contrasting mutational probabilities in the span of 7 months. Out of these, 14 variants are showing increasing mutational probabilities suggesting their propagation with time due to their unexplored evolutionary advantages. However, the mutational probabilities of five variants have significantly decreased in June onward as compared to March/April, suggesting their termination with time. Further in‐depth investigation of these identified variants will provide valuable knowledge about the evolution, infection strategies, transmission rates, and epidemiology of SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics /, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements. • FisOmics is a workbench of multi-objective vision in fish genomics. • System administrator manages workbench modules and all information about authenticated users to utilize workbench. • An integration of different fish genomic resources for exploring the information. • Implemented tools facilitate different kinds of analyses of DNA sequences. • Well-suited local search with embedded results by querying on different databases. [ABSTRACT FROM AUTHOR]

The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat. [ABSTRACT FROM AUTHOR]

Introduction: Malaria, a tropical disease, caused by Plasmodium is curable; still, the burden of malaria infection exists in third world countries. India, particularly among the South-East Asian region, has the maximum mortality rate. The parasites have developed resistance against antimalarial drugs. Alternatively, plants are the most important and ancient source of the drug and spices, in particular, are being used to treat various ailments. Aim: To identify the effect of common Indian spices in targeting malarial proteases. Materials and Methods: A bioinformatics approach was used to target malarial proteases which exhibit an important role in the erythrocytic cycle of the pathogen by degrading Haemoglobin. Proteases, in particular, Falcipain and Plasmepsin were used to perform docking studies to identify potent molecule for inhibition of malarial progression. Data were collected in the form of structural files from PDB (for protein) and PubChem (for ligands). The Protein structures and ligands were prepared and molecular docking had been done to predict interactions. Results: All the eighteen compounds used in study have shown quite a good affinity with target proteins in the terms of energy (negative binding energy). However, comparatively, interactions of falcipain 2 with thymol and gingerol were almost three times lower than other ligand. Except these, energy ranges were in between 30-40 kilo Joule in negative. Strongest interactions were found in between Plasmepsin 4-piperamide and plasmepsin 2-gingerol. Also, it was found that gingerol was most potent bioactive molecule interacting with almost all proteins as predicted by docking studies. Conclusion: Plasmepsin 2 and Plasmepsin 4 with gingerol and piperamide with highest cdocker energy might indicate the potential of molecules in targeting these proteases. Also, Gingerol was found to be most potent in interacting with malarial proteases. [ABSTRACT FROM AUTHOR]

Background: Primate T-lymphotropic viruses type 1 (PTLV-1) are complex retroviruses infecting both human (HTLV-1) and simian (STLV-1) hosts. They share common epidemiological, clinical and molecular features. In addition to the canonical gag, pol, env retroviral genes, PTLV-1 purportedly encodes regulatory (i.e. Tax, Rex, and HBZ) and accessory proteins (i.e. P12/8, P13, P30). The latter have been found essential for viral persistence in vivo. Methodology/Principal findings: We have isolated a STLV-1 virus from a bonnet macaque (Macaca radiata–Mra18C9), a monkey from India. The complete sequence was obtained and phylogenetic analyses were performed. The Mra18C9 strain is highly divergent from the known PTLV-1 strains. Intriguingly, the Mra18C9 lacks the 3 accessory open reading frames. In order to determine if the absence of accessory proteins is specific to this particular strain, a comprehensive analysis of the complete PTLV-1 genomes available in Genbank was performed and found that the lack of one or many accessory ORF is common among PTLV-1. Conclusion: This study raises many questions regarding the actual nature, role and importance of accessory proteins in the PTLV-1 biology. [ABSTRACT FROM AUTHOR]

The role of foot-and-mouth disease virus (FMDV) persistently infected ruminants in initiating new outbreaks remains controversial, and the perceived threat posed by such animals hinders international trade in FMD-endemic countries. In this study we report longitudinal analyses of genetic and antigenic variations of FMDV serotype O/ME-SA/Ind2001d sublineage during naturally occurring, persistent infection in cattle and buffalo at an organised dairy farm in India. The proportion of animals from which FMDV RNA was recovered was not significantly different between convalescent (post-clinical) and sub-clinically infected animals or between cattle and buffalo across the sampling period. However, infectious virus was isolated from a higher proportion of buffalo samples and for a longer duration compared to cattle. Analysis of the P1 sequences from recovered viruses indicated fixation of mutations at the rate of 1.816 x 10-2substitution/site/year (s/s/y) (95% CI 1.362–2.31 x 10−2 s/s/y). However, the majority of point mutations were transitional substitutions. Within individual animals, the mean dN/dS (ω) value for the P1 region varied from 0.076 to 0.357, suggesting the selection pressure acting on viral genomes differed substantially across individual animals. Statistical parsimony analysis indicated that all of the virus isolates from carrier animals originated from the outbreak virus. The antigenic relationship value as determined by 2D-VNT assay revealed fluctuation of antigenic variants within and between carrier animals during the carrier state which suggested that some carrier viruses had diverged substantially from the protection provided by the vaccine strain. This study contributes to understanding the extent of within-host and within-herd evolution that occurs during the carrier state of FMDV. [ABSTRACT FROM AUTHOR]

Accurate and timely diagnosis is very critical for management, control and elimination of the malaria. Malaria rapid diagnostic tests (RDTs) have improved the diagnosis and management of malaria in remote areas, community and places where microscopy is not available for diagnosis. According to WHO report 2018, Plasmodium falciparum malaria constitutes more than 50% of malaria cases in India. Most of the RDTs used for diagnosis of falciparum malaria today employ HRP2 as a target antigen. However, low density parasitemia and deletion of hrp-2 gene in P. falciparum leads to false negative results and necessitates the development of alternative/ new or improved RDT for malaria diagnosis. We have analysed the genetic diversity and homology modelling of Pfgdh (glutamate dehydrogenase), ldh (lactate dehydrogenase) and aldolase genes in P. falciparum isolates from the eight endemic states of India to assess their potential as antigen for RDT development. We observed negligible sequence diversity in Pfgdh in comparison to the low level of diversity in ldh and aldolase gene. No structural or functional changes were observed in modelling studies and all three genes were under negative purifying selection pressure. The highly conserved nature of pfgdh gene suggests that GDH could be a potential target molecule for Pan/Pf diagnostic test for malaria. [ABSTRACT FROM AUTHOR]

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0–5.3% while congeneric distances varied from 2.8–23.2%. Excepting one species pair (Oxyopes azhari–Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance happens when microorganisms mutates in manners that render the drugs like antibacterial, antiviral, antiparasitic and antifungal, ineffective. The normal mutation process is encouraged by the improper use of antibiotics. Mutations leading to quinolone resistance occur in a highly conserved region of the quinolone resistance-determining region (QRDR) of DNA gyrAse and topoisomerase IV gene. We analyzed antibiotic resistant genes and single nucleotide polymorphism (SNP) in gyrA and parC genes in QRDR in 120 E. coli isolates (both diarrheagenic and non-pathogenic) recovered from fresh stool samples collected from children aged less than 5 years from Delhi, India. Antibiotic susceptibility testing was performed according to standard clinical and laboratory standards institute (CLSI) guidelines. Phylogenetic analysis showed the clonal diversity and phylogenetic relationships among the E. coli isolates. The SNP analysis depicted mutations in gyrA and parC genes in QRDR. The sul1 gene, responsible for sulfonamide resistance, was present in almost half (47.5%) of the isolates across the diseased and healthy samples. The presence of antibiotic resistance genes in E. coli isolates from healthy children indicate the development, dissemination and carriage of antibiotic resistance in their gut. Our observations suggest the implementation of active surveillance and stewardship programs to promote appropriate antibiotic use and minimizing further danger. [ABSTRACT FROM AUTHOR]

Background: Leprosy is a slow, chronic disorder caused by Mycobacterium leprae. India has achieved elimination of leprosy in December 2005 but new cases are being detected and continue to occur in some endemic pockets. The possible ways of transmission of leprosy is not fully understood and is believed that leprosy is transmitted from person to person in long term contact. Studying the transmission dynamics is further complicated by inability to grow M. leprae in culture medium and lack of animal models. More than one family members were found to be affected by leprosy in some highly endemic pockets. This study reported the transmission pattern of leprosy in a family having 4 patients. Methodology/Principal findings: We investigated the transmission of leprosy in a single family having 4 patients using microsatellite typing. DNA was isolated from slit skin smear samples taken from the patients and the isolated DNA were amplified using microsatellite loci TA11CA3. The amplified products were sequenced using Sanger’s sequencing methods and the copy number variation in the microsatellite loci between strains were elucidated by multiple sequence alignment. The result showed that all the 4 members of the family acquired infection from 3 different strains of M. leprae from 3 different sources. The elder and middle daughters were infected by same types of strains having the repeat unit TA13CA3 and could have acquired the infection from social contacts of leprosy cases while the father and younger daughter were infected by strains with the repeat unit TA12CA3 and TA11CA3 and could have acquired infection from social contacts. Conclusions/Significance: The study suggested that three family members viz, elder daughter, father and younger daughter could be infected by M. leprae from 3 different sources and the history of the disease and genetic analysis showed that the middle daughter acquired infection from her elder sister in due course of contact. This study implies that the transmission of leprosy not only occurred amongst the house hold members but also has been transmitted from social and neighborhood contacts in long term association with the them. [ABSTRACT FROM AUTHOR]

Holy basil (Ocimum sanctum L.) and sweet basil (Ocimum basilicum L.) are the most commonly grown basil species in India for essential oil production and biosynthesis of potentially volatile and non-volatile phytomolecules with commercial significance. The aroma, flavor and pharmaceutical value of Ocimum species is a significance of its essential oil, which contains most of the monoterpenes and sesquiterpenes. A large number of plants have been studied for characterization and identification of terpene synthase genes, involved in terpenoids biosynthesis. The goal of this study is to discover and identify the putative functional terpene synthase genes in O. sanctum. HMMER search was performed by using a set of 13 well sequenced and annotated plant genomes including the newly sequenced genome of O. sanctum with Pfam-A database locally, using HMMER 3.0 hmmsearch for the two Pfam domains (PF01397 and PF03936). Using this search method 81 putative terpene synthases genes (OsaTPS) were identified in O. sanctum; the study further reveals 47 OsaTPS were putatively functional genes, 19 partial OsaTPS, and 15 OsaTPS as probably pseudogenes. All these identified OsaTPS genes were compared with other plant species, and phylogenetic analysis reveals the subfamily classification of OsaTPS in TPS-a, -b, -c, -e, -f and TPS-g subfamilies clusters. This genome-wide identification of OsaTPS genes, their phylogenetic analysis and secondary metabolite pathway mapping predictions together provide a comprehensive understanding of the TPS gene family in Ocimum sanctum and offer opportunities for the characterization and functional validation of numbers of terpene synthase genes. [ABSTRACT FROM AUTHOR]

Agricultural bioinformatics is one of the recent and the fastest emerging disciplines of the science exploiting computational approaches to biology and life sciences. It is facilitated through mathematical algorithms and statistical techniques essential for the development of a required labyrinthine algorithm that can interpret biological data and configure assumptions from biological shreds of evidences. The discipline comprises many quantitative examinations of the knowledge relating to the biological macromolecules, seeking aid from high-end computing systems and progresses further to computer science and communication technology solving arduous conundrums in the respective fields of life science and more precisely in the field of agriculture. India has mainly focused on the technological upgradation but lacks effective policy measures to have shifts from the traditional technologies. The National System of Innovation framework presents the current landscape of agriculture bioinformatics, and can be mapped for research purpose. The framework requires a variety of expertise stakeholders' networks for productive results, which can cater to the present and the future food demands, and can pinpoint needed solutions. This paper discusses the growth of agricultural bioinformatics in India and the challenges in that field. [ABSTRACT FROM AUTHOR]

Objectives: Burkholderia pseudomallei, the causative agent for melioidosis, has become a public health problem in India and across the world. Melioidosis can be difficult to diagnose because of the inconsistent clinical presentations of the disease. This study aims to determine the genetic diversity among the clinical isolates of B. pseudomaelli from India in order to establish a molecular epidemiology and elucidate the Southeast Asian association. Methods: Molecular typing using multi locus sequence typing was performed on thirty one archived B. pseudomallei clinical isolates, previously characterised from specimens obtained from patients admitted to the Christian Medical College & Hospital, Vellore from 2015 to 2016. Further investigations into the genetic heterogeneity and evolution at a regional and global level were performed using insilico tools. Results: Multi locus sequence typing (MLST) of the isolates from systemic and localized forms of melioidosis, including blood, pus, tissue, and urine specimens, revealed twenty isolates with novel sequence types and eleven with previously reported sequence types. High genetic diversity was observed using MLST with a strong association within the Southeast Asian region. Conclusions: Molecular typing of B. pseudomallei clinical isolates using MLST revealed high genetic diversity and provided a baseline molecular epidemiology of the disease in India with a strong Southeast Asian association of the strains. Future studies should focus on whole genome based Single-Nucleotide-Polymorphism (SNP) which has the advantage of a high discriminatory power, to further understand the novel sequence types reported in this study. [ABSTRACT FROM AUTHOR]

Pearl millet [Pennisetum glaucum (L.) R. Br.] is an important “orphan” cereal and the most widely grown of all the millet species worldwide. It is also the sixth most important cereal in the world after wheat, rice, maize, barley, and sorghum, being largely grown and used in West Africa as well as in India and Pakistan. The present study was carried out in the frame of a program designed to increase benefits and reduce potential health problems deriving from the consumption of pearl millet. The specific goal was to provide a database of information on the variability existing in pearl millet germplasm as to the amounts of phytate, the most relevant antinutrient compound, and the goitrogenic compounds C-glycosylflavones (C-GFs) accumulated in the grain.Results we obtained clearly show that, as indicated by the range in values, a substantial variability subsists across the investigated pearl millet inbred lines as regards the grain level of phytic acid phosphate, while the amount of C-GFs shows a very high variation. Suitable potential parents to be used in breeding programs can be therefore chosen from the surveyed material in order to create new germplasm with increased nutritional quality and food safety. Moreover, we report novel molecular data showing which genes are more relevant for phytic acid biosynthesis in the seeds as well as a preliminary analysis of a pearl millet orthologous gene for C-GFs biosynthesis. These results open the way to dissect the genetic determinants controlling key seed nutritional phenotypes and to the characterization of their impact on grain nutritional value in pearl millet. [ABSTRACT FROM AUTHOR]

Orientia tsutsugamushi (Ots) is an obligate, intracellular, mite-transmitted human pathogen which causes scrub typhus. Understanding the diversity of Ots antigens is essential for designing specific diagnostic assays and efficient vaccines. The protective immunodominant type-specific 56 kDa antigen (TSA) of Ots varies locally and across its geographic distribution. TSA contains four hypervariable domains. We bioinformatically analyzed 345 partial sequences of TSA available from India, most of which contain only the three variable domains (VDI-III) and three spacer conserved domains (SVDI, SVDII/III, SVDIII). The total number (152) of antigenic types (amino acid variants) varied from 14–36 in the six domains of TSA that we studied. Notably, 55% (787/1435) of the predicted CD4 T-cell epitopes (TCEs) from all the six domains had high binding affinities (HBA) to at least one of the prevalent Indian human leukocyte antigen (HLA) alleles. A surprisingly high proportion (61%) of such TCEs were from spacer domains; indeed 100% of the CD4 TCEs in the SVDI were HBA. TSA sequences from India had more antigenic types (AT) than TSA from Korea. Overall, >90% of predicted CD4 TCEs from spacer domains were predicted to have HBA against one or more prevalent HLA types from Indian, Korean, Asia-Pacific region or global population data sets, while only <50% of CD4 TCEs in variable domains exhibited such HBA. The phylogenetically and immunologically important amino acids in the conserved spacer domains were identified. Our results suggest that the conserved spacer domains are predicted to be functionally more important than previously appreciated in immune responses to Ots infections. Changes occurring at the TCE level of TSA may contribute to the wide range of pathogenicity of Ots in humans and mouse models. CD4 T-cell functional experiments are needed to assess the immunological significance of these HBA spacer domains and their role in clearance of Ots from Indian patients. [ABSTRACT FROM AUTHOR]

Rice bean [Vigna umbellate (Thumb.) Ohwi and Ohashi] is an underutilized crop believed to be domesticated in the Myanmar-Thailand region of Asia. In India, rice bean is mainly cultivated in the North-Eastern Hills, which is a hotspot for biological diversity. A 5' anchored PCR was used to develop microsatellite markers in rice bean. Twenty-eight specific primer pairs were designed and employed to characterize sixty five ricebean accessions collected from North East India. A total of 179 alleles were amplified with an average of 6.393 alleles per locus. The gene diversity was high (mean 0.534) in the accessions collected from Darjeeling, Nagaland and Manipur, which are bordering areas with East Nepal and Myanmar, respectively. Exceptionally high outcrossing rate was observed in the entire population. Population structure analysis identified three distinct clusters in which accessions collected from areas bordering Myanmar and East Nepal grouped separately. Using a combination of STRUCTURE and Principal Coordinate Analysis, relative affinity of the intermediate accessions could be established. However, differences in allelic counts among populations were non-significant. The results showed that there is a high level of genetic diversity within the accessions, with high outcrossing rate. [ABSTRACT FROM AUTHOR]

The interaction of previously reported 656 phytocompound ligands with four well-characterized diabetic target proteins were studied in 20 plant species throughin silicoscreening techniques. The binding energy, number of hydrogen bonds, and hydrogen binding residues with the receptor molecules were analyzed using the CDOCKER protocol of the software Discovery Studio 4.0. A total 23 molecules were found to have interaction with the four target proteins. Among these compounds, based on the ADME/toxicity profile, three promising drug candidates, namely, methyl gallate, ferulic acid, and anthranilic acid, were recommended as potential lead molecule for the treatment of type 2 diabetes mellitus. [ABSTRACT FROM PUBLISHER]

Background: Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes Japanese Encephalitis (JE) and Acute Encephalitis Syndrome (AES) in humans. Genotype-I (as co-circulating cases with Genotype-III) was isolated in 2010 (JEV28, JEV21) and then in 2011 (JEV45) from Midnapur district, West Bengal (WB) for the first time from clinical patients who were previously been vaccinated with live attenuated SA14-14-2 strain. We apply bioinformatics and immunoinformatics on sequence and structure of E protein for analysis of crucial substitutions that might cause the genotypic transition, affecting protein-function and altering specificity of epitopes. Results: Although frequency of substitutions in E glycoprotein of JEV28, JEV21 and JEV45 isolates vary, its homologous patterns remain exactly similar as earlier Japan isolate (Ishikawa). Sequence and 3D model-structure based analyses of E protein show that only four of all substitutions are critical for genotype-I specific effect of which N103K is common among all isolates indicating its role in the transition of genotype-III to genotype-I. Predicted B-cell and T-cell epitopes are seen to harbor these critical substitutions that affect overall conformational stability of the protein. These epitopes were subjected to conservation analyses using a large set of the protein from Asian continent. Conclusions: The study identifies crucial substitutions that contribute to the emergence of genotype-I. Predicted epitopes harboring these substitutions may alter specificity which might be the reason of reported failure of vaccine. Conservation analysis of these epitopes would be useful for design of genotype-I specific vaccine. [ABSTRACT FROM AUTHOR]

Processing cow ghee (clarified butterfat) with therapeutic herbs, i.e. ghrita, is recognized for augmenting the therapeutic efficacy of plant materials. Ashwagandha ghrita (AG) is an effective Ayurvedic formulation consisting of Indian ginseng, i.e., Withania somnifera (L.) Dunal, the main constituent used to treat infertility, weakness, gynaecological disorders, and general debility. The present investigation was undertaken to corroborate the ethnopharmacological claim of AG as ' Vajikarana Rasayana' for its aphrodisiac potential using bioinformatics (in-silico) and experimental (in-vitro and in-vivo) approaches. AG was formulated as per the methods reported in Ayurved sarsangraha. AG was further subjected to HPLC, GCMS analysis, and biological (acute toxicity and aphrodisiac) assessment per the standard procedures. Thirty-eight bioactives of Indian ginseng were subjected to computational studies (molecular docking and network pharmacology) to confirm the plausible mechanism. AG was found to be safe up to 2000 mg/kg body wt., and it showed dose-dependent upsurge (p < 0.01 and p < 0.05, wherever necessary) in mount and intromission frequency, genital grooming, and anogenital sniffing at 150 and 300 mg/kg body weight suggesting aphrodisiac activity. In-vitro studies demonstrated significant relaxation of the Corpus Cavernosal Smooth Muscle at all concentrations in a dose-dependent manner. Furthermore, the results of molecular modelling studies were in agreement with the biological activity and showed interaction with phosphodiesterase-5 as a possible target. AG exhibited an aphrodisiac effect and substantiated the traditional claim of Indian ginseng-based ghrita formulation as 'Vajikarana Rasayana'. [Display omitted] • In Ayurveda , Withania somnifera (L.) Dunal (Ashwagandha) is revered as Rasayana. • The medicinal efficacy of plant components is known to be increased when processed with ghee. • Ashwagandha ghrita is a cow ghee-based traditional herbal preparation used to treat infertility. • It is the first scientific confirmation of the aphrodisiac claims made for Ashwagandha ghrita. [ABSTRACT FROM AUTHOR]

In 2015, the swine derived A(H1N1)pdm09 pandemic strain outbreak became widespread throughout the different states of India. The reported cases and deaths in 2015 surpassed the previous years with more than 39000 laboratory confirmed cases and a death toll of more than 2500 people. There are relatively limited complete genetic sequences available for this virus from Asian countries. In this study, we describe the full genome analysis of influenza 2015 A(H1N1)pdm09 viruses isolated from West Bengal between January through December 2015. The phylogenetic analysis of the haemagglutinin sequence revealed clustering with globally circulating strains of genogroup 6B. This was further confirmed by the constructed concatenated tree using all eight complete gene segments of Kolkata A(H1N1)pdm09 isolates with the other strains from different timeline and lineages. A study from Massachusetts Institute of Technology (MIT) in 2015 reported novel mutations T200A and D225N in haemagglutinin gene of a 2014 Indian strain (A/India/6427/2014). However, in all the pandemic strains of 2014–2015 reported from India, so far including A(H1N1)pdm09 strains from Kolkata, D225N mutation was not observed, though the T200A mutation was found to be conserved. Neuraminidase gene of the analyzed strains did not show any oseltamivir resistant mutation H275Y suggesting continuation of Tamiflu® as drug of choice. The amino acid sequences of the all gene segments from 2015 A(H1N1)pdm09 isolates identified several new mutations compared to the 2009 A(H1N1)pdm09 strains, which may have contributed towards enhanced virulence, compared to 2009 A(H1N1)pdm09 strains. [ABSTRACT FROM AUTHOR]

Introduction: Early Onset Parkinson's Disease (EOPD) is genetically heterogeneous. PARK2 mutations are the commonest cause of autosomal recessive EOPD followed by PINK1.DJ1 mutations is rare and there is scarce literature on its phenotype and long term outcome.Objectives: We undertook a retrospective study to determine the prevalence of DJ1 mutation(s) in an Indian population and describe the clinical features and long term outcome of EOPD patients with these mutations.Methods: One hundred EOPD patients and 114 controls were evaluated. All the seven coding exons of DJ1 gene were screened for novel and reported mutations by PCR- Sanger sequencing.Results: A novel homozygous missense mutation (c.313 A > T, p. Ile105Phe) in exon 5 was seen in one patient and four unrelated patients had a homozygous missense single nucleotide variant rs71653619 (c.293 G > A, p.Arg98Gln). The clinical phenotype comprised of asymmetrical onset, slowly progressive Parkinsonism with levodopa induced motor restlessness in a patient with the novel mutation (c.313 A > T, p. Ile105Phe) while subjects with c.293 G > A, p.Arg98Gln had early onset levodopa responsive symmetrical Parkinsonism.Conclusion: DJ1 mutations account for ∼5% of EOPD patients from the Indian population. This study further adds to the clinical spectrum of EOPD with DJ1 mutations. [ABSTRACT FROM AUTHOR]

Familial juvenile hyperuricemic nephropathy (FJHN), characterized by early-onset hyperuricemia, reduced fractional excretion of uric acid, and chronic renal failure is caused due to mutation in uromodulin (UMOD) gene. We identified a novel mutation in a family with multiple members affected with FJHN. Ten coding exons of UMOD gene in three family members with clinical and biochemical features of FJHN and one unaffected family member were sequenced, and sequence variants were analyzed for the pathogenicity by bioinformatics studies. A heterozygous novel missense mutation (c. 949 T >G) in exon 5 leading to the replacement of cysteine by glycine at position 317 was identified in all three affected family members. This mutation has not been reported earlier in Human Gene Mutation Database, Human Genome Variation, Clinvar, and 1000 Genome. The mutation lies in the cysteine-rich 2 domain of the protein, and the affected residue is evolutionary conserved in other species. To our knowledge, this is the first report of the identification of UMOD mutation in an Indian family. [ABSTRACT FROM AUTHOR]

India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges. [ABSTRACT FROM AUTHOR]

The present paper deals with the study of resources and services provided by Bioinformatics Centre libraries to their users. For the present study 15 libraries have been selected. Out of the fifteen questionnaires distributed to the librarian, fourteen returned the questionnaire (14/15). The response rate is ninety three percent (93%). The basic purpose of this study to identify the resources and services provided by these libraries to their users. The study reveals that UGC financed the maximum number of libraries i.e. ten libraries followed by DBT which financed nine libraries. Major databases users preferred are NCBI, GenBank, Entrez Swiss-Prot, MEDLINE, PDB and EDI. All the major library services are being provided by theses library to support the use of bioinformatics resources. Training programmes are conducted by the library to support the users' information need. [ABSTRACT FROM AUTHOR]

Bovine theileriosis is a serious threat to livestock worldwide. Uncertainty around species prevalence, antigenic diversity and genotypes of strains make it difficult to assess the impact of this parasite and to provide necessary treatment. We aimed to characterize genotypic diversity, phylogeny and prevalence of Theileria orientalis parasites from the states of Telangana and Andhra Pradesh, India by collecting bovine blood samples from the major districts of the two states. Bioinformatic analysis identified antigenic diversity among the prevalent parasite strains using major piroplasm surface protein (MPSP) gene. Our study revealed a prevalence rate of 4.8% (n = 41/862) of T. orientalis parasites in bovine animals and a new genotype of T. orientalis parasite which was not previously reported in India. The emergence of these new genotypes could be an explanation for the frequent outbreaks of bovine theileriosis. Further, whole genome sequencing of T. orientalis strains will help to elucidate the genetic factors relevant for transmissibility and virulence as well as vaccine and new drug development. [ABSTRACT FROM AUTHOR]

Objective: This paper shall first investigate the informatics areas and applications of the four Traditional Medicine systems - Traditional Chinese Medicine (TCM), Ayurveda, Traditional Arabic and Islamic Medicine and Traditional Malay Medicine. Then, this paper shall examine the national informatics infrastructure initiatives in the four respective countries that support the Traditional Medicine systems. Challenges of implementing informatics in Traditional Medicine Systems shall also be discussed.Methods: The literature was sourced from four databases: Ebsco Host, IEEE Explore, Proquest and Google scholar. The search term used was "Traditional Medicine", "informatics", "informatics infrastructure", "traditional Chinese medicine", "Ayurveda", "traditional Arabic and Islamic medicine", and "traditional malay medicine". A combination of the search terms above was also executed to enhance the searching process. A search was also conducted in Google to identify miscellaneous books, publications, and organization websites using the same terms.Results: Amongst major advancements in TCM and Ayurveda are bioinformatics, development of Traditional Medicine databases for decision system support, data mining and image processing. Traditional Chinese Medicine differentiates itself from other Traditional Medicine systems with documented ISO Standards to support the standardization of TCM. Informatics applications in Traditional Arabic and Islamic Medicine are mostly ehealth applications that focus more on spiritual healing, Islamic obligations and prophetic traditions. Literature regarding development of health informatics to support Traditional Malay Medicine is still insufficient. Major informatics infrastructure that is common in China and India are automated insurance payment systems for Traditional Medicine treatment. National informatics infrastructure in Middle East and Malaysia mainly cater for modern medicine. Other infrastructure such as telemedicine and hospital information systems focus its implementation in modern medicine or are not implemented and strategized at a national level to support Traditional Medicine.Conclusion: Informatics may not be able to address all the emerging areas of Traditional Medicine because the concepts in Traditional Medicine system of medicine are different from modern system, though the aim may be same, i.e., to give relief to the patient. Thus, there is a need to synthesize Traditional Medicine systems and informatics with involvements from modern system of medicine. Future research works may include filling the gaps of informatics areas and integrate national informatics infrastructure with established Traditional Medicine systems. [ABSTRACT FROM AUTHOR]

Examines quantitatively the growth and development of bioinformatics research in India in terms of the publication output as reflected in Web of Science (WoS) database for the period 2006-2010.The bibliographic details of 577bioinformatics data obtained from the WoS database were studied and it was found that among the total bioinformatics contributions, nearly half are from India. Majority of the contributions were multi- authored and the degree of collaboration was 0.93 and most of the publications were in the form of journal articles. BMC Bioinformatics published by Bio Med Central ranks first position with 28 publications followed by In Silico Biology (IOP press) with 24 publications. IISc, Bengaluru is the most productive bioinformatics research institute in the country followed by ISI, Kolkata. Delhi is the leading state with 6.41% of the total Indian contribution in bioinformatics followed by West Bengal with 5.37% publications. The data set has been found to be not a perfect fit for the Bradford's law of scattering. [ABSTRACT FROM AUTHOR]

Abstract: Ethnopharmacological relevance: Herbal medicine value chains have generally been overlooked compared with food commodities. Not surprisingly, revenue generation tends to be weighted towards the end of the chain and consequently the farmers and producers are the lowest paid beneficiaries. Value chains have an impact both on the livelihood of producers and on the composition and quality of products commonly sold locally and globally and consequently on the consumers. In order to understand the impact of value chains on the composition of products, we studied the production conditions for turmeric (Curcuma longa) and the metabolomic composition of products derived from it. We aimed at integrating these two components in order to gain a better understanding of the effect of different value chains on the livelihoods of some producers. Materials and methods: This interdisciplinary project uses a mixed methods approach. Case studies were undertaken on two separate sites in India. Data was initially gathered on herbal medicine value chains by means of semi-structured interviews and non-participant observations. Samples were collected from locations in India, Europe and the USA and analysed using 1H NMR spectroscopy coupled with multivariate analysis software and with high performance thin layer chromatography (HPTLC). Results: We investigate medicinal plant value chains and interpret the impact different value chains have on some aspects of the livelihoods of producers in India and, for the first time, analytically assess the chemical variability and quality implications that different value chains may have on the products available to end users in Europe. There are benefits to farmers that belonged to an integrated chain and the resulting products were subject to a higher standard of processing and storage. By using analytical methods, including HPTLC and 1H NMR spectroscopy, it has been possible to correlate some variations in product composition for selected producers and identify strengths and weaknesses of some types of value chains. The two analytical techniques provide different and complementary data and together they can be used to effectively differentiate between a wide variety of crude drug powders and herbal medicinal products. Conclusions: This project demonstrates that there is a need to study the links between producers and consumers of commodities produced in so-called ‘provider countries’ and that metabolomics offer a novel way of assessing the chemical variability along a value chain. This also has implications for understanding the impact this has on the livelihood of those along the value chain. [Copyright &y& Elsevier]

Introduction: The present communication deals with tribe Anthemideae comprising of 47 species belonging to 1 1 genera based on the collections from Jammu and Kashmir State. Many of these species are mostly confined to the alpine zones of Kashmir Himalayas. The relevant data, number of species in Jammu and Kashmir, key to the species, diversity of the tribe anthemideae is indicated under enumeration in each genus. Material and Methods: The collections were made from the area under study to identify the different genera and species. Results: The present communication of tribe Anthemideae is first report of its kind from Jammu and Kashmir State comprising of 1 1 genera and 47 species of the tribe. [ABSTRACT FROM AUTHOR]

Abstract: The ever-increasing significance of biodiversity conservation and advancements in computer technology for digitization and management of data have catapulted biodiversity informatics into limelight. Biodiversity informatics enhances the efficiency of biodiversity management by researchers, policy makers, and funding agencies. Plant genetic resources (PGR) are a key component of biodiversity as they have a direct bearing on food and nutritional security. As a result, PGR informatics that specifically deals with agro-biodiversity needs greater patronage. This overview describes the state of biodiversity informatics with special reference to PGR informatics. The aim of this review is to generate awareness about the existing biodiversity information systems and to stimulate initiatives from all the concerned to frame a comprehensive action plan for developing biodiversity informatics in gene-rich countries with a special reference to India. [Copyright &y& Elsevier]

Abstract: This paper explores a trend in the development of innovation in emerging economies: exaptive technological capabilities. A growing proportion of innovation is originating in emerging economies that, being resource-constrained in a dynamic and uncertain environment, requires leveraging existing capabilities and recombining with new knowledge resources. An evolutionary biology model is applied to a process model whereby initial technological capabilities are renewed by the firm given an external selection event. Using a detailed case study across 6years, this paper investigates the exaptation process of Information Technology (IT) capabilities into bioinformatics by an Indian IT firm, Tata Consultancy Services (TCS). Findings suggest that just leveraging existing technological capabilities alone is a model set for failure. Such a tactic ignores the environment of the new technology application area. By investing in the needed complementary resources, TCS corrected its initial path to open source their software and offer consulting services on how to utilize the software and, thus, create intellectual property. These insights are valuable not only for the innovation management of traditional IT services to life sciences, but more broadly for firms in emerging economies that hope to renew and build exaptive technological capabilities to enter unforeseen new application areas by leveraging existing technological capabilities. [Copyright &y& Elsevier]

This study discusses some of the important aspects of laws/regulations formulated for the protection of plant varieties in Union for the Protection of New Varieties of Plants (UPOV) member states, European Community countries and India. The study also provides an insight into some of the unique features of Indian sui generis system for the protection of plant varieties. During this study, the registration of crop notified in India and in some selected UPOV member countries has been examined. Since India is not an UPOV member state, the system of plant variety protection (PVP) is independent of international scenario but aims for similar standards. The study provides useful information in order to analyse the implementation of PVP laws in UPOV member states and India. Some important features were selected for carrying out a comparative analysis. These include Intellectual Property Rights protection (patent/breeder's right), types of varieties protected, methods of testing, criteria for protection, duration of protection, exemptions (researcher/farmer's exemption), infringement and penalty and compulsory license. [ABSTRACT FROM AUTHOR]

Abstract: The novel proteins introduced into the genetically modified (GM) crops need to be evaluated for the potential allergenicity before their introduction into the food chain to address the safety concerns of consumers. At present, there is no single definitive test that can be relied upon to predict allergic response in humans to a new protein; hence a composite approach to allergic response prediction is described in this study. The present study reports on the evaluation of the Cry proteins, encoded by cry1Ac, cry1Ab, cry2Ab, cry1Ca, cry1Fa/cry1Ca hybrid, being expressed in Bt food crops that are under field trials in India, for potential allergenic cross-reactivity using bioinformatics search tools. The sequence identity of amino acids was analyzed using FASTA3 of AllergenOnline version 10.0 and BLASTX of NCBI Entrez to identify any potential sequence matches to allergen proteins. As a step further in the detection of allergens, an independent database of domains in the allergens available in the AllergenOnline database was also developed. The results indicated no significant alignment and similarity of Cry proteins at domain level with any of the known allergens revealing that there is no potential risk of allergenic cross-reactivity. [ABSTRACT FROM AUTHOR]

An account of bioinformatics education in India is presented along with future prospects. Establishment of BTIS network by Department of Biotechnology (DBT), Government of India in the 1980s had been a systematic effort in the development of bioinformatics infrastructure in India to provide services to scientific community. Advances in the field of bioinformatics underpinned the need for well-trained professionals with skills in information technology and biotechnology. As a result, programmes for capacity building in terms of human resource development were initiated. Educational programmes gradually evolved from the organisation of short-term workshops to the institution of formal diploma/degree programmes. A case study of the Master’s degree course offered at the Bioinformatics Centre, University of Pune is discussed. Currently, many universities and institutes are offering bioinformatics courses at different levels with variations in the course contents and degree of detailing. BioInformatics National Certification (BINC) examination initiated in 2005 by DBT provides a common yardstick to assess the knowledge and skill sets of students passing out of various institutions. The potential for broadening the scope of bioinformatics to transform it into a data intensive discovery discipline is discussed. This necessitates introduction of amendments in the existing curricula to accommodate the upcoming developments. [ABSTRACT FROM PUBLISHER]