Web Resources for Metagenomics Studies

The development of next-generation sequencing(NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.     

Fracture resistance to treated teeth using known endodontics techniques in Indian patients

Teeth with crown structure less than 50% can be restored. Therefore, it is of interest to evaluate an in vitro efficacy of Zirconia post, Glass fiber post, polyethylene-woven fiber posts, and Quartz posts. Forty eight recently extracted mandibular first premolar teeth were randomly grouped in to 4 different groups with 12 samples in each group. After endodontic treatment samples in all groups underwent post preparation followed by restoration with respective posts. The mean fracture resistance (Newton) were 463.5 ± 14.3 (Group I) 425.2± 23.5 (group II), 410.4± 18.6 (Group 3) and 385.2 ± 14.2 (group 4). Data shows that Zirconia post had highest fracture resistance compared to other tested groups.     

Molecular and functional characterization of endophytic fungi from traditional medicinal plants

This study reports the isolation of 63 endophytic fungal isolates from two traditional medicinal plants, Ocimum sanctum and Sapindus detergens from different locations of Amritsar, India. The functional characterization of the fungi for their ability to produce anti bacterial and anti cancer agent was carried out. Sixteen strains were characterized at molecular level by sequencing the amplified ITSI-5.8-ITSII region of rDNA. The phylogenetic tree resolved the endophytic fungi into different clades. The fungal endophytes belonging to order Pleosporales (Alternaria sp., Phoma sojicola and Exserohilum sp.) were functionally versatile as they produced diverse biomolecules including antibacterial agent active against Mycobacterium smegmatis, as well as cytotoxic activity against different human cancer cell lines of lung, ovary, breast, prostrate, neuroblastoma and colon.     

Resistance to trophic neurite outgrowth of sensory neurons exposed to insulin

Insulin offers trophic support through receptors expressed widely on peripheral neurons. In this work, we studied whether peripheral sensory neurons demonstrate resistance to its trophic properties, a property relevant during type 2 diabetes mellitus or following supraphysiological therapy. Insulin receptors were not only localized to neuronal membranes and cytoplasm but also had a unique, previously unrecognized localization to neuronal nuclei. We confirmed that nanomolar doses increased neurite outgrowth of adult sensory neurons, but in response to micromolar doses of insulin, even following a brief 2-h exposure, survival and outgrowth of neurites were blunted. Neurons exposed to picomolar insulin concentrations in their media for 5 days had resistance to the impact of later nanomolar doses of insulin. Using a stripe assay seeded with insulin, neurites were more likely to reject higher doses of insulin. Insulin down-regulated mRNAs of the insulin receptor β subunit and up-regulated levels of GSK-3β, both potential mechanisms of insulin resistance, while down-regulating the protein expression of pAkt and pGSK-3β. Overall, these studies identify neuronal nuclear targeting of insulin and evidence for insulin-induced resistance to its trophic properties. The findings have implications for the understanding of the actions of insulin in the treatment of diabetes and neurological disorders.     

Genetic evidence of tiger population structure and migration within an isolated and fragmented landscape in Northwest India

Background

Majority of the tiger habitat in Indian subcontinent lies within high human density landscapes and is highly sensitive to surrounding pressures. These forests are unable to sustain healthy tiger populations within a tiger-hostile matrix, despite considerable conservation efforts. Ranthambore Tiger Reserve (RTR) in Northwest India is one such isolated forest which is rapidly losing its links with other tiger territories in the Central Indian landscape. Non-invasive genetic sampling for individual identification is a potent technique to understand the relationships between threatened tiger populations in degraded habitats. This study is an attempt to establish tiger movement across a fragmented landscape between RTR and its neighboring forests, Kuno-Palpur Wildlife Sanctuary (KPWLS) and Madhav National Park (MNP) based on non-invasively obtained genetic data.

Methods

Data from twelve microsatellite loci was used to define population structure and also to identify first generation migrants and admixed individuals in the above forests.

Results

Population structure was consistent with the Central Indian landscape and we could determine significant gene flow between RTR and MNP. We could identify individuals of admixed ancestry in both these forests, as well as first generation migrants from RTR to KPWLS and MNP.

Conclusions

Our results indicate reproductive mixing between animals of RTR and MNP in the recent past and migration of animals even today, despite fragmentation and poaching risk, from RTR towards MNP. Substantial conservation efforts should be made to maintain connectivity between these two subpopulations and also higher protection status should be conferred on Madhav National Park.     

Pulse wave analysis as an experimental tool to clinical application: past and present (review)

Pulse examination by palpation of a peripheral artery against a bony prominence is the most commonly used and widely accepted method. However this is subjective and thus prone to errors. Although pulse waveform was recorded in the 19th century, it did not gain popularity because of inconvenience in using the recording instruments and the absence of a sound theory to explain the wave forms recorded. Sphygmomanometry for recording blood pressure gained popularity as it was easy to record and had a sound theoretical background. Sphygmomanometry provides two extreme values of blood pressure but does not give a true representation of the blood pressure changes occurring in the entire cardiac cycle. Recently there has been resurgence in the analysis of the graphical recording of the pulse wave. Photoplethysmography is becoming a widely accepted technique in assessing the volume pulse. The whole review is about historical background, non-invasive methods of pulse recording, relation of the digital volume pulse to the pressure pulse and the advantages of recording the pressure pulse.     

Cytogenetic evaluation of malathion-induced toxicity in Sprague-Dawley rats

Malathion is a well known pesticide and is commonly used in many agricultural and non-agricultural settings. Its toxicity has been attributed primarily to the accumulation of acetylcholine (Ach) at nerve junctions, due to the inhibition of acetylcholinesterase (AChE), and consequently overstimulation of the nicotinic and muscarinic receptors. However, the genotoxicity of malathion has not been adequately studied; published studies suggest a weak interaction with the genetic material. In the present study, we investigated the genotoxic potential of malathion in bone marrow cells and peripheral blood obtained from Sprague-Dawley rats using chromosomal aberrations (CAs), mitotic index (MI), and DNA damage as toxicological endpoints. Four groups of four male rats, each weighing approximately 60 ± 2g, were injected intraperitoneally (i.p.) once a day for five days with doses of 2.5, 5, 10, and 20mg/kg body weight (BW) of malathion dissolved in 1% DMSO. The control group was made up of four animals injected with 1% DMSO. All the animals were sacrificed 24h after the fifth day treatment. Chromosome preparations were obtained from bone marrow cells following standard protocols. DNA damage in peripheral blood leukocytes was determined using alkaline single-cell gel electrophoresis (comet assay). Malathion exposure significantly increased the number of structural chromosomal aberrations (CAs) and the percentages of DNA damage, and decreased the mitotic index (MI) in treated groups when compared with the control group. Our results demonstrate that malathion has a clastogenic/genotoxic potential as measured by the bone marrow CA and comet assay in Sprague-Dawley rats.     

Study of photophysical properties of different metal complexes of Alq3

Different metal complexes of Alq₃ (K⁺, Sr²⁺, Ca²⁺ and Mg²⁺) were synthesized by the precipitation method. The characterization of photoluminescence showed that presence of Mg²⁺ ion enhances photoluminescence of Alq₃ phosphor. The emission spectra are observed at 560 nm when excited at a wavelength of 440 nm. The phosphor is excited at a longer wavelength in the blue region of small energy, so that it could be used as lamp phosphor. It is observed that the prepared phosphor AlMgq₅ is more suitable than Alq_3. The ionic radii of K⁺, Sr²⁺, Ca²⁺ and Mg²⁺ ions are in decreasing order. Therefore, the remarkable properties of AlMgq₅ could be considered as promising materials as opto‐ or optoelectronic materials. Copyright © 2012 John Wiley & Sons, Ltd.