Differential sensitivity of Chironomus and human hemoglobin to gamma radiation.

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb. Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study.

Structural insights into the activation mechanism of phosphoinositide 3-kinase alpha.

Phosphoinositide 3-kinases (PI3Ks) are lipid kinases known to regulate important cellular functions by phosphorylating the inositol ring of inositol-phospholipids (PtdIns) at 3' position. The PI3Kα is a heterodimer and the activation of the catalytic subunit (p110α) is regulated by its regulatory subunit (p85α). The current work deals with studying the activation mechanism of the PI3Kα using multi micro-second molecular dynamic simulations. Structural changes involved in activation mechanism is studied by gradually releasing the inhibitory effects of different domains of regulatory subunit namely, n-terminal SH2 (nSH2) and inter SH2 (iSH2). The observation shows that even in the presence of n-terminal and inter SH2 domain (niSH2) of regulatory subunit, the catalytic domain has some intrinsic activation activity and the presence of c-terminal SH2 (cSH2) domain may be required for complete inhibition. The release of nSH2 domain leads to loss of interactions between iSH2 domain (regulatory subunit) and C2 and kinase domain (catalytic subunit). The study shows that early events in the activation mechanism involve the movement of the ABD domain of the catalytic subunit along with the linker region between ABD and RBD region which may lead to movement of ABD closer to the CLobe of the kinase domain. This movement is essentially as it triggers the rearrangement of CLobe especially the catalytic loop and activation loop which bring catalytic important residues closer to ATP and PIP2(phosphatidylinositol-4,5-bisphosphate). Water mediated interaction analysis reveal that water may be playing an important role in the transfer of phosphate from ATP to PIP2. The study shows that initial signal for release of inhibitory effect of the regulatory subunit might be propagated through the linker region between ABD and RBD through allosteric effect to different regions of the protein. These understanding of early events during the activation mechanism may help in the design of better therapeutic targeting PI3K.

iCEED: Integrated customized extraction of enzyme data.

Enzymes catalyze diverse biochemical reactions and are building blocks of cellular and metabolic pathways. Data and metadata of enzymes are distributed across databases and are archived in various formats. The enzyme databases provide utilities for efficient searches and downloading enzyme records in batch mode but do not support organism-specific extraction of subsets of data. Users are required to write scripts for parsing entries for customized data extraction prior to downstream analysis. Integrated Customized Extraction of Enzyme Data (iCEED) has been developed to provide organism-specific customized data extraction utilities for seven commonly used enzyme databases and brings these resources under an integrated portal. iCEED provides dropdown menus and search boxes using typehead utility for submission of queries as well as enzyme class-based browsing utility. A utility to facilitate mapping and visualization of functionally important features on the three-dimensional (3D) structures of enzymes is integrated. The customized data extraction utilities provided in iCEED are expected to be useful for biochemists, biotechnologists, computational biologists, and life science researchers to build curated datasets of their choice through an easy to navigate web-based interface. The integrated feature visualization system is useful for a fine-grained understanding of the enzyme structure-function relationship. Desired subsets of data, extracted and curated using iCEED can be subsequently used for downstream processing, analyses, and knowledge discovery. iCEED can also be used for training and teaching purposes.

Bioinformatics education in India.

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.

Utility of Body Mass Index Quick Screening Tool for Assessing Nutritional Category of Children.

Body mass index (BMI) quick screening tool was used on retrospective data of 415 boys and 428 girls (8-14 years). Sensitivity and specificity of the BMI tool were assessed by comparing with the Indian Academy of Pediatrics BMI charts. The BMI tool had high sensitivity and specificity to identify children with normal BMI and underweight. However, its sensitivity varied between 50-57.4% for overweight and obese children, respectively.

Antibody Class(es) Predictor for Epitopes (AbCPE): A Multi-Label Classification Algorithm.

Development of vaccines and therapeutic antibodies to deal with infectious and other diseases are the most perceptible scientific interventions that have had huge impact on public health including that in the current Covid-19 pandemic. From inactivation methodologies to reverse vaccinology, vaccine development strategies of 21st century have undergone several transformations and are moving towards rational design approaches. These developments are driven by data as the combinatorials involved in antigenic diversity of pathogens and immune repertoire of hosts are enormous. The computational prediction of epitopes is central to these developments and numerous B-cell epitope prediction methods developed over the years in the field of immunoinformatics have contributed enormously. Most of these methods predict epitopes that could potentially bind to an antibody regardless of its type and only a few account for antibody class specific epitope prediction. Recent studies have provided evidence of more than one class of antibodies being associated with a particular disease. Therefore, it is desirable to predict and prioritize 'peptidome' representing B-cell epitopes that can potentially bind to multiple classes of antibodies, as an open problem in immunoinformatics. To address this, AbCPE, a novel algorithm based on multi-label classification approach has been developed for prediction of antibody class(es) to which an epitope can potentially bind. The epitopes binding to one or more antibody classes (IgG, IgE, IgA and IgM) have been used as a knowledgebase to derive features for prediction. Multi-label algorithms, Binary Relevance and Label Powerset were applied along with Random Forest and AdaBoost. Classifier performance was assessed using evaluation measures like Hamming Loss, Precision, Recall and F1 score. The Binary Relevance model based on dipeptide composition, Random Forest and AdaBoost achieved the best results with Hamming Loss of 0.1121 and 0.1074 on training and test sets respectively. The results obtained by AbCPE are promising. To the best of our knowledge, this is the first multi-label method developed for prediction of antibody class(es) for sequential B-cell epitopes and is expected to bring a paradigm shift in the field of immunoinformatics and immunotherapeutic developments in synthetic biology. The AbCPE web server is available at http://bioinfo.unipune.ac.in/AbCPE/Home.html.

Insights into the Inhibition Mechanism of Human Pancreatic α-Amylase, a Type 2 Diabetes Target, by Dehydrodieugenol B Isolated from Ocimum tenuiflorum.

Use of human pancreatic α-amylase (HPA) inhibitors is one of the effective antidiabetic strategies to lower postprandial hyperglycemia via reduction in the dietary starch hydrolysis rate. Many natural products from plants are being studied for their HPA inhibitory activity. The present study describes isolation of dehydrodieugenol B (DDEB) from Ocimum tenuiflorum leaves using sequential solvent extraction, structure determination by one-dimensional (1D) and two-dimensional (2D) NMR analyses, and characterization as an HPA inhibitor using kinetics, binding thermodynamics, and molecular docking. DDEB uncompetitively inhibited HPA with an IC50 value of 29.6 µM for starch and apparent K i ' of 2.49 and Ki of 47.6 µM for starch and maltopentaose as substrates, respectively. The circular dichroism (CD) study indicated structural changes in HPA on inhibitor binding. Isothermal titration calorimetry (ITC) revealed thermodynamically favorable binding (ΔG of -7.79 kcal mol-1) with a dissociation constant (K d) of 1.97 µM and calculated association constant (K a) of 0.507 µM. Molecular docking showed stable HPA-inhibitor binding involving H-bonds and Pi-alkyl, alkyl-alkyl, and van der Waals (vDW) interactions. The computational docking results support the noncompetitive nature of DDEB binding. The present study could be helpful for exploration of the molecule as a potential antidiabetic drug candidate to control postprandial hyperglycemia.

SWATH-MS based quantitative proteomics analysis to evaluate the antileishmanial effect of Commiphora wightii- Guggul and amphotericin B on a clinical isolate of Leishmania donovani.

Drug resistance and relapse after treatment of visceral leishmaniasis (VL) with the chemotherapeutic drugs has impeded the VL elimination programme especially, in the endemic region of Bihar, India. Currently, Antimonials (Sbv) have been rendered obsolete (Bihar) as frequent treatment failure and relapse in Sbv treated patient's warrants greater vigilance and attention to the limited drugs. A clinical isolate of L.donovani obtained from an Amphotericin B (AmB) relapse patient was evaluated for its susceptibility to AmB and a hyperlipidemic drug Guggul. The evaluation of susceptibility or resistance to any drug still relies on in vitro assay on promastigote and amastigote stages of Leishmania spp. as there are no validated markers which can ascertain drug resistance in Leishmania. The anti-promastigote effect of AmB and Guggul were demonstrated by significant cellular and morphological changes exhibiting apoptosis-mediated cell death. To further illustrate the molecular mechanism of the parasite's response upon exposure to either AmB and Guggul, sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for quantitative proteomics analysis was performed along with computational data analysis; revealing considerable differences in the proteome profiles which could be regarded as putative markers for resistance or drug targets for development of therapeutic antileishmanials.

CD40 signaling is impaired in L. major-infected macrophages and is rescued by a p38MAPK activator establishing a host-protective memory T cell response.

Leishmania, a protozoan parasite, lives and multiplies as amastigote within macrophages. It is proposed that the macrophage expressed CD40 interacts with CD40 ligand on T cells to induce IFN-gamma, a Th1-type cytokine that restricts the amastigote growth. Here, we demonstrate that CD40 cross-linking early after infection resulted in inducible nitric oxide synthetase type-2 (iNOS2) induction and iNOS2-dependent amastigote elimination. Although CD40 expression remained unaltered on L. major-infected macrophages, delay in the treatment of macrophages or of mice with anti-CD40 antibody resulted in significant reduction in iNOS2 expression and leishmanicidal function suggesting impaired CD40 signaling in Leishmania infection. The inhibition of CD40-induced iNOS2 expression by SB203580, a p38-mitogen activated protein kinase (p38MAPK)-specific inhibitor, and the reversal of the inhibition by anisomycin, a p38MAPK activator, suggested a crucial role of p38MAPK in CD40 signaling. Indeed, the CD40-induced p38MAPK phosphorylation, iNOS2 expression and anti-leishmanial function were impaired in Leishmania-infected macrophages but were restored by anisomycin. Anisomycin's effects were reversed by SB203580 emphasizing the role of p38MAPK in CD40-induced iNOS2-dependent leishmanicidal function. Anisomycin administration in L. major-infected BALB/c mice resulted in significant reduction in the parasite load and established a host-protective Th1-type memory response. Also implicated in these findings is a scientific rationale to define novel anti-parasite drug targets and to bypass the problem of drug resistance.

SWATH-MS based quantitative proteomics analysis to evaluate the antileishmanial effect of Commiphora wightii- Guggul and Amphotericin B on a clinical isolate of Leishmania donovani.

The present study provides comprehensive proteomics analyses of the response of L. donovani parasite to pharamacological stress in vitro. Identification of differentially expressed proteins with associated molecular functions and metabolic pathways, clearly provides an insight into the potential mechanism of the antileishmanial effects as well as a comparative response of the parasite to Guggul and AmB. Treatment of parasite with AmB results in an enhanced modulatory mechanism to counteract the drug induced stress which may have contributed to relapse. In the case of Guggul treatment, an effective antipromastigote activity was observed, which is being reported for the first time. Thus, a deeper understanding of the molecular pathways in the Leishmania parasite in response to pharmacological stress would help in designing novel and effective strategies in targeting the key molecules essential for parasite survival. It will also help in screening of new lead molecules targeting these vital pathways which could be used as an adjunct therapy along with the limited repertoire of antileishmanial drugs.

Use of Continuous Metabolic Syndrome Score in Overweight and Obese Children.

OBJECTIVE: To assess the utility of continuous metabolic syndrome score (cMetS) for predicting metabolic syndrome (MS) and determine the cut-off values in overweight and obese children. METHODS: This study was conducted among 104 children (7-14 y) attending obesity clinics of a tertiary care hospital in Mumbai, India. The cMetS was computed by standardizing the residuals of waist circumference (WC), mean arterial blood pressure (MAP), high density lipoprotein cholesterol (HDL-C), triglycerides (TG), and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) by regressing them according to age and sex and aggregating them. The optimal cut-off of cMetS for predicting MS was determined by the receiver operation characteristic (ROC) curve analysis. RESULTS: The cMetS increased significantly with increase in the number of MS risk factors. It was significantly high in children with MS than those without it (boys: 1.070 + 1.834 vs. -1.478 + 2.262; girls: 2.092 + 1.963 vs. -2.253 + 2.140; combined children group: 1.572 + 1.950 vs. -1.907+ 2.374; p < 0.001). The score predicted MS with high accuracy in girls; (AUC of 0.95, 95% CI: 0.90-1.00), moderate accuracy in boys (AUC of 0.79, 95% CI: 0.65-0.92) and in the combined group (AUC of 0.87, 95% CI 0.80-0.94) respectively. The cut-off of cMetS yielding maximal sensitivity and specificity for predicting the MS was -1.009 in boys (sensitivity 93% and specificity 62%); -0.652 in girls (sensitivity 96.4% and specificity 77%) and - 0.6881 in the combined group (sensitivity 91.2% and specificity 70.2%). CONCLUSIONS: cMetS predicted MS with moderate to high accuracy. It had high sensitivity and specificity in predicting MS in overweight and obese children.

AllerBase: a comprehensive allergen knowledgebase.

Database URL: http://bioinfo.net.in/AllerBase/Home.html.

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis.

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

Erratum to: BioDB extractor: customized data extraction system for commonly used bioinformatics databases.

[This corrects the article DOI: 10.1186/s13040-015-0067-z.].

BioDB extractor: customized data extraction system for commonly used bioinformatics databases.

BACKGROUND: Diverse types of biological data, primary as well as derived, are available in various formats and are stored in heterogeneous resources. Database-specific as well as integrated search engines are available for carrying out efficient searches of databases. These search engines however, do not support extraction of subsets of data with the same level of granularity that exists in typical database entries. In order to extract fine grained subsets of data, users are required to download complete or partial database entries and write scripts for parsing and extraction. RESULTS: BioDBExtractor (BDE) has been developed to provide 26 customized data extraction utilities for some of the commonly used databases such as ENA (EMBL-Bank), UniprotKB, PDB, and KEGG. BDE eliminates the need for downloading entries and writing scripts. BDE has a simple web interface that enables input of query in the form of accession numbers/ID codes, choice of utilities and selection of fields/subfields of data by the users. CONCLUSIONS: BDE thus provides a common data extraction platform for multiple databases and is useful to both, novice and expert users. BDE, however, is not a substitute to basic keyword-based database searches. Desired subsets of data, compiled using BDE can be subsequently used for downstream processing, analyses and knowledge discovery. AVAILABILITY: BDE can be accessed from http://bioinfo.net.in/BioDB/Home.html.

Inflammatory myofibroblastic tumor.

Inflammatory myofibroblastic tumors are well described in lung and upper respiratory tract of young adults and children. Intra-abdominal forms of the disease are reported to occur most frequently in the liver, followed by stomach, bowel and spleen. A 13-year-old girl who had intermittent fever ranging from 99-101 degrees F of three months period and significant weight loss was referred as a case of pyrexia of unknown origin. The patient was subjected to laparotomy. A solid mass was found arising from the mesentery, four feet from the iliocaecal junction and was adherent to the wall of ileum. The patient became afebrile after the removal of the mass and has gained weight and remained well during the ten months since discharge.

Prevalence, pattern and outcome of congenital heart disease in Bhabha Atomic Research Centre Hospital, Mumbai.

OBJECTIVE: To assess the prevalence, pattern and outcome of congenital heart disease (CHD) among the babies born in Bhabha Atomic Research Centre (BARC) Hospital, Mumbai and to compare the pattern of CHD with the study done in the same hospital in year 1999. METHODS: A prospective, longitudinal study was conducted from January 2006 through December 2011. Babies presenting with murmur were closely followed up till the diagnosis and further to assess the outcome. 2-D Echocardiography was used as a diagnostic tool. RESULTS: The overall prevalence of CHD was 13.28 per 1,000 live births. Ventricular septal defect (VSD) was the commonest CHD (42.86 %) followed by Atrial septal defect (ASD) (25.71 %) giving the prevalence of 5.69 and 3.41 per 1,000 live births respectively. Tetrology of Fallot's (TOF) was the main cyanotic CHD (8.57 %) with the prevalence of 1.13 per 1,000 live births. VSD and TOF were prevalent in males. ASD was prevalent in females. Associated structural anomalies were detected in 22.86 % cases; Down's syndrome being the commonest.Spontaneous closure rate of 71.4 % in muscular VSD and 50 % in perimembranous VSD was observed. All small sized VSD's closed spontaneously and all large sized VSD's required surgical intervention. Spontaneous closure was observed in 44.44 % of ASD cases. Overall, device closure was required in 17.14 % and 25.71 % underwent open heart surgery. CONCLUSIONS: The pattern of CHD has remained almost the same compared to the previous study. The outcome was excellent due to early diagnosis, regular follow up and timely intervention.

Sodium valproate - Induced skeletal myopathy.

The authors report a case of skeletal myopathy in a four-year-old boy on long-term sodium valproate therapy for secondary epilepsy due to neurocysticercosis. He presented with clinical features of limb girdle weakness. EMG revealed features of myopathy. Carnitine deficiency due to sodium valproate was suspected and plasma carnitine levels were found to be low. Sodium valproate was withdrawn. L-carnitine supplementation resulted in marked clinical recovery as well as rise in plasma carnitine levels.

Sodium valproate -- induced skeletal myopathy.

The authors report a case of skeletal myopathy in a four-year-old boy on long-term sodium valproate therapy for secondary epilepsy due to neurocysticercosis. He presented with clinical features of limb girdle weakness. EMG revealed features of myopathy. Carnitine deficiency due to sodium valproate was suspected and plasma carnitine levels were found to be low. Sodium valproate was withdrawn. L-carnitine supplementation resulted in marked clinical recovery as well as rise in plasma carnitine levels.