Analysis and prediction of antibacterial peptides

<p>Abstract</p> <p>Background</p> <p>Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacterial peptides, obtained from antimicrobial peptide database APD, in order to understand the preference of amino acid residues at specific positions in these peptides.</p> <p>Results</p> <p>It was observed that certain types of residues are preferred over others in antibacterial peptides, particularly at the N and C terminus. These observations encouraged us to develop a method for predicting antibacterial peptides in proteins from their amino acid sequence. First, the N-terminal residues were used for predicting antibacterial peptides using Artificial Neural Network (ANN), Quantitative Matrices (QM) and Support Vector Machine (SVM), which resulted in an accuracy of 83.63%, 84.78% and 87.85%, respectively. Then, the C-terminal residues were used for developing prediction methods, which resulted in an accuracy of 77.34%, 82.03% and 85.16% using ANN, QM and SVM, respectively. Finally, ANN, QM and SVM models were developed using N and C terminal residues, which achieved an accuracy of 88.17%, 90.37% and 92.11%, respectively. All the models developed in this study were evaluated using five-fold cross validation technique. These models were also tested on an independent or blind dataset.</p> <p>Conclusion</p> <p>Among antibacterial peptides, there is preference for certain residues at N and C termini, which helps to demarcate them from non-antibacterial peptides. Both the termini play a crucial role in imparting the antibacterial property to these peptides. Among the methods developed, SVM shows the best performance in predicting antibacterial peptides followed by QM and ANN, in that order. AntiBP (Antibacterial peptides) will help in discovering efficacious antibacterial peptides, which we hope will prove to be a boon to combat the dreadful antibiotic resistant bacteria. A user friendly web server has also been developed to help the biological community, which is accessible at <url>http://www.imtech.res.in/raghava/antibp/</url>.</p

Assessment of the Time Management and Stress among Nursing Staff in Selected Wards of Tertiary Care Hospital, Chandigarh (2017- 2018): A Descriptive Study

Nursing by its nature is an occupation which is prone to high degree of stress level and busy schedule. This study was done to assess the time management and stress among nursing staff and to assess the correlation between time management and stress among nurses. This was a descriptive study conducted in the selected wards of tertiary care hospital (Psychiatry Ward, Advance Trauma Centre, Advance Eye Centre, Maternity Ward, Communicable Disease Ward, Advance Pediatrics Centre). Data was collected by using socio-demographic profile, Nurses Time management Inventory for Personal life, Nurses Time Management Inventory for Professional life, Nursing Stress Inventory. The data was analyzed using SPSS (Version 20.0). The study revealed that about 60% of the subjects were having moderate personal time management while 55% of subjects were having moderate time management in professional life. 79% of the subjects were often stressed at working place and 38% of the subjects stated that they were very stressful. This study revealed the correlation between the time management and nursing stress which is significant at the 0,01 level. This showed that the time management and stress are inversely proportional to each other i.e. the low will be the time management; the greater will be the stress

Conduction Mechanism and Dielectric Properties in Polyaniline/Titanium Dioxide Composites

The conductivity and dielectric properties of polyaniline (PANI) and PANI/TiO2 composites have been studied over a temperature range (313-393 K) and frequency range (25 Hz- 50 MHz). The nature of temperature and frequency-dependent conductivity can be explained by Jonscher’s universal power law and used to find the related parameters such as frequency exponent (s), dc conductivity (σdc), and crossover frequency (ωH). Besides, the frequency exponent analysis through a distinct model suggests that the conduction occurred through small polaron tunnelling in all compositions and at different temperatures. On the other hand, the enthalpy of migration (Hm), dissociation enthalpy of cation from its indigenous location alongside a compensating center (Hf), and the activation energy were also calculated using the Arrhenius relation. The temperature-dependent dc conductivity was examined in the framework of the theoretical model; Mott’s variable range hopping model (VRH) and experimental results were in good agreement with the 3-dimensional VRH model. As a function of temperature, dielectric constants (ε’ and ε”) increase while decreasing with an increasing dopant. Being such a high dielectric constant value, these composites can be used as frequency converters, modulators, and dielectric amplifiers

Polyaniline Chromium Nitrate Composites: Influence of Chromium Nitrate on Conductivity and Thermal Stability of Polyaniline

Thermal stability and electrical conductivity are the key to the technological feasibility and sustainability of conductingpolymers (CPs) and their composites in real-time applications. Notably, the impact of filler loading on above mentionedparameters of CPs needs to be examined and addressed with facile and easily accessible techniques. In the present study,Polyaniline (PANI) /chromium nitrate composites have been prepared via in situ polymerization of aniline through thechemical oxidative polymerization route. After that, the conductivity and thermal stability of PANI have been investigated atdifferent weight percentage loadings of chromium nitrate viz 5, 10, 20, and 40 % in the composite materials.The morphological and structural analysis of the pristine and composite samples were executed with Scanning electronmicroscopy (SEM), Fourier transforms infrared (FTIR) spectroscopy, and X-ray diffraction (XRD) techniques. Thermalanalysis of proposed composites is carried out using the thermogravimetric analysis (TGA) method to evaluate variouskinetic parameters. The TGA thermogram and different calculated parameters revealed that the composites were morethermally stable than pristine PANI and that the composite having 20 wt % of chromium nitrate is thermally the most stable.The DC electrical conductivity data shows that PANI loaded with 20% chromium nitrate has the highest conductivity. Thisincrement in conductivity and thermal stability of the composites opens the path for many applications, such as sensors andelectronics

Preoperative characterization of indeterminate large adrenal masses with dual tracer PET-CT using fluorine-18 fluorodeoxyglucose and gallium-68-DOTANOC: initial results

PURPOSEWe aimed to evaluate the usefulness of dual tracer positron emission tomography-computed tomography (PET-CT) with flourine-18 fluorodeoxyglucose (18F-FDG) and gallium-68 [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid]-1-NaI3-octreotide (68Ga-DOTANOC) in preoperative characterization of large indeterminate adrenal masses.MATERIALS AND METHODSTen patients (four males, six females; median age, 35 years) with indeterminate, large (≥4 cm) adrenal masses were included in this prospective study. All patients underwent both 18F-FDG PET-CT and 68Ga-DOTANOC PET-CT within one week. Images were evaluated both visually and semi-quantitatively, with standardized uptake value (SUVmax) and SUVratio (SUVmax) of tumor/SUVmax) of mediastinum). Based on differential uptake pattern on 18F-FDG and 68Ga-DOTANOC, lesions were classified as cortical (18F-FDG>68Ga-DOTANOC), medullary (68Ga-DOTANOC>18F-FDG), or indeterminate (18F-FDG=68Ga-DOTANOC). Histopathology was taken as reference standard. Receiver operating characteristic (ROC) analysis was performed to find a cut-off of SUVmax) and SUVratio to differentiate cortical and medullary lesions.RESULTSOn histopathology, eight lesions were adrenocortical carcinomas, one was benign pheochromocytoma, and one was malignant pheochromocytoma. Visually, 18F-FDG PET-CT was positive in all ten lesions, while 68Ga-DOTANOC PET-CT was positive in two, both of which were pheochromocytomas. On SUVmax) based analysis, nine lesions were cortical and one was medullary. On ROC analysis, a SUVmax) cut-off of > 2.3 was obtained for 18F-FDG PET-CT and 3.6 for 68Ga-DOTANOC PET-CT for differentiating adrenal cortical and medullary lesions. The cut-off for SUVratio was 4.5 on 18F-FDG PET-CT and 11.1 on 68Ga-DOTANOC PET-CT.CONCLUSIONThese preliminary results demonstrate that dual tracer PET-CT using 18F-FDG and 68Ga-DOTANOC could be informative in the preoperative characterization of large indeterminate adrenal masses

Pre-main sequence variable stars in young open cluster NGC 1893

We present results of multi-epoch (fourteen nights during 2007-2010) $V$-band photometry of the cluster NGC 1893 region to identify photometric variable stars in the cluster. The study identified a total of 53 stars showing photometric variability. The members associated with the region are identified on the basis of spectral energy distribution, $J-H/H-K$ two colour diagram and $V/V-I$ colour-magnitude diagram. The ages and masses of the majority of pre-main-sequence sources are found to be $\lesssim$ 5 Myr and in the range 0.5 $\lesssim$ $M/M_{\odot}$ $\lesssim$ 4, respectively. These pre-main-sequence sources hence could be T Tauri stars. We also determined the physical parameters like disk mass and accretion rate from the spectral energy distribution of these T Tauri stars. The periods of majority of the T Tauri stars range from 0.1 to 20 day. The brightness of Classical T Tauri stars is found to vary with larger amplitude in comparison to Weak line T Tauri stars. It is found that the amplitude decreases with increase in mass, which could be due to the dispersal of disks of massive stars.Comment: 15pages, 16 figures and 5 tables, Accepted for publication in MNRA

Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

Background: Multi-drug resistance and severe/ complicated cases are the emerging phenotypes of vivax malaria, which may deteriorate current anti-malarial control measures. The emergence of these phenotypes could be associated with either of the two Plasmodium vivax lineages. The two lineages had been categorized as Old World and New World, based on geographical sub-division and genetic and phenotypical markers. This study revisited the lineage hypothesis of P. vivax by typing the distribution of lineages among global isolates and evaluated their genetic relatedness using a panel of new mini-satellite markers. Methods: 18S SSU rRNA S-type gene was amplified from 420 Plasmodium vivax field isolates collected from different geographical regions of India, Thailand and Colombia as well as four strains each of P. vivax originating from Nicaragua, Panama, Thailand (Pak Chang), and Vietnam (ONG). A mini-satellite marker panel was then developed to understand the population genetic parameters and tested on a sample subset of both lineages. Results: 18S SSU rRNA S-type gene typing revealed the distribution of both lineages (Old World and New World) in all geographical regions. However, distribution of Plasmodium vivax lineages was highly variable in every geographical region. The lack of geographical sub-division between lineages suggests that both lineages are globally distributed. Ten mini-satellites were scanned from the P. vivax genome sequence; these tandem repeats were located in eight of the chromosomes. Mini-satellites revealed substantial allelic diversity (7-21, AE = 14.6 +/- 2.0) and heterozygosity (He = 0.697-0.924, AE = 0.857 +/- 0.033) per locus. Mini-satellite comparison between the two lineages revealed high but similar pattern of genetic diversity, allele frequency, and high degree of allele sharing. A Neighbour-Joining phylogenetic tree derived from genetic distance data obtained from ten mini-satellites also placed both lineages together in every cluster. Conclusions: The global lineage distribution, lack of genetic distance, similar pattern of genetic diversity, and allele sharing strongly suggested that both lineages are a single species and thus new emerging phenotypes associated with vivax malaria could not be clearly classified as belonging to a particular lineage on basis of their geographical origin