Locating probable genes using Fourier transform approach

FTG is a web server for analyzing nucleotide sequences to predict the genes using Fourier transform techniques. This server implements the existing Fourier transform algorithms for gene prediction and allows the rapid visualization of analysis by output in GIF format.     

Orthogonal potency analysis of mesenchymal stromal cell function during ex vivo expansion

Adult bone marrow mesenchymal stromal cells (MSCs) have cross-functional, intrinsic potency that is of therapeutic interest. Their ability to regenerate bone, fat, and cartilage, modulate the immune system, and nurture the growth and function of other bone marrow hematopoietic stem/progenitor cells have all been evaluated by transplant applications of MSCs. These applications require the isolation and expansion scaled cell production. To investigate biophysical properties of MSCs that can be feasibly utilized as predictors of bioactivity during biomanufacturing, we used a low-density seeding model to drive MSCs into proliferative stress and exhibit the hallmark characteristics of in vitro aging. A low-density seeding method was used to generate MSCs from passages 1–7 to simulate serial expansion of these cells to maximize yield from a single donor. MSCs were subjected to three bioactivity assays in parallel to ascertain whether patterns in MSC age, size, and shape were associated with the outcomes of the potency assays. MSC age was found to be a predictor of adipogenesis, while cell and nuclear shape was strongly associated to hematopoietic-supportive potency. Together, these data evaluate morphological changes associated with cell potency and highlight new strategies for purification or alternatives to assessing MSC quality.     

Strobilanthes kannanii – a new species of Acanthaceae from the Western Ghats,India

Strobilanthes kannanii, a new species of Acanthaceae from southern Western Ghats is described and illustrated. It shows similarity to S. sessilis in some vegetative, floral and palynological characters. Notes on the habitat, distribution, and affinities are also provided along with color images and line drawings.     

Constitutively Active MAVS Inhibits HIV-1 Replication via Type I Interferon Secretion and Induction of HIV-1 Restriction Factors

Type I interferon is known to inhibit HIV-1 replication through the induction of interferon stimulated genes (ISG), including a number of HIV-1 restriction factors. To better understand interferon-mediated HIV-1 restriction, we constructed a constitutively active form of the RIG-I adapter protein MAVS. Constitutive MAVS was generated by fusion of full length MAVS to a truncated form of the Epstein Barr virus protein LMP1 (ΔLMP1). Supernatant from ΔLMP1-MAVS-transfected 293T cells contained high levels of type I interferons and inhibited HIV replication in both TZM-bl and primary human CD4+ T cells. Supernatant from ΔLMP1-MAVS-transfected 293T cells also inhibited replication of VSV-G pseudotyped single cycle SIV in TZM-bl cells, suggesting restriction was post-entry and common to both HIV and SIV. Gene array analysis of ΔLMP1-MAVS-transfected 293T cells and trans-activated CD4+ T cells showed significant upregulation of ISG, including previously characterized HIV restriction factors Viperin, Tetherin, MxB, and ISG56. Interferon blockade studies implicated interferon-beta in this response. In addition to direct viral inhibition, ΔLMP1-MAVS markedly enhanced secretion of IFN-β and IL-12p70 by dendritic cells and the activation and maturation of dendritic cells. Based on this immunostimulatory activity, an adenoviral vector (Ad5) expressing ΔLMP1-MAVS was tested as a molecular adjuvant in an HIV vaccine mouse model. Ad5-Gag antigen combined with Ad5-ΔLMP1-MAVS enhanced control of vaccinia-gag replication in a mouse challenge model, with 4/5 animals showing undetectable virus following challenge. Overall, ΔLMP1-MAVS is a promising reagent to inhibit HIV-1 replication in infected tissues and enhance vaccine-mediated immune responses, while avoiding toxicity associated with systemic type I interferon administration.     

Bioconversion of brewer's spent grains to bioethanol

Spent grains (SG), the residue remaining after extraction of wort, are a major by-product of brewing. This lignocelluose-rich biomass may provide a source of sugars for fuel ethanol fermentations. Dilute acid and enzyme treatments were developed to convert the hemicellulose and cellulose fractions to glucose, xylose and arabinose. Pretreatment of dried, milled grains with 0.16 N HNO(3) at 121 degrees C for 15 min was chosen as the most suitable method for solubilizing grains before enzymatic digestion with cellulase and hemicellulase preparations. Solids loading concentrations (10%, 15% and 20% w/v) were compared and reducing sugar between 40 and 48 g (100 g SG)(-1) was extracted. Hydrolysate, prepared from 20% SG, pretreated with 0.16 N HNO(3), partially neutralized to pH 5-6 and digested with enzymes for 18 h, contained 27 g L(-1) glucose, 16.7 g L(-1) xylose and 11.9 g L(-1) arabinose. Fermentation of this hydrolysate for 48 h by Pichia stipitis and Kluyveromyces marxianus resulted in 8.3 and 5.9 g L(-1) ethanol corresponding to ethanol conversion yields of 0.32 and 0.23 g ethanol (g substrate)(-1), respectively. Substrate utilization efficiency was less when compared with glucose/xylose mixtures in synthetic media, suggesting that yeast inhibitory compounds derived from SG were present in the hydrolysate.     

In vivo ROS production and use of oxidative stress-derived biomarkers to detect the onset of diseases such as Alzheimer’s disease,Parkinson’s disease,and diabetes

Breakthroughs in biochemistry have furthered our understanding of the onset and progression of various diseases, and have advanced the development of new therapeutics. Oxidative stress and reactive oxygen species (ROS) are ubiquitous in biological systems. ROS can be formed non-enzymatically by chemical, photochemical and electron transfer reactions, or as the byproducts of endogenous enzymatic reactions, phagocytosis, and inflammation. Imbalances in ROS homeostasis, caused by impairments in antioxidant enzymes or non-enzymatic antioxidant networks, increase oxidative stress, leading to the deleterious oxidation and chemical modification of biomacromolecules such as lipids, DNA, and proteins. While many ROS are intracellular signaling messengers and most products of oxidative metabolisms are beneficial for normal cellular function, the elevation of ROS levels by light, hyperglycemia, peroxisomes, and certain enzymes causes oxidative stress-sensitive signaling, toxicity, oncogenesis, neurodegenerative diseases, and diabetes. Although the underlying mechanisms of these diseases are manifold, oxidative stress caused by ROS is a major contributing factor in their onset. This review summarizes the relationship between ROS and oxidative stress, with special reference to recent advancements in the detection of biomarkers related to oxidative stress. Further, we will introduce biomarkers for the early detection of neurodegenerative diseases and diabetes, with a focus on our recent work.     

Significance of Microsclerotia in the Epidemiology of Black Pepper Anthracnose and an Approach for Disease Management in Nurseries

Anthracnose incited by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is a wide spread and economically important disease of black pepper. In the present study, role of microsclerotia (MS) in the trans‐seasonal perpetuation of C. gloeosporioides was investigated. Microscopical examination of the runner shoots exhibiting necrotic lesions revealed the presence of dark, melanized structures which resembled MS. The excised necrotic regions when subjected to high humidity produced acervulus with setae. Under in vitro conditions, C. gloeosporioides produced MS predominantly on the aerial surface as inseparable congregations, enmeshed in the mycelial mats in potato dextrose broth and as individual units 7–8 days after incubation on glass slides. Sequential events in the formation of MS included germination of conidia, formation of conidial anastomosis tubes, aggregation of hyphae, and the formation of melanized microsclerotial bodies. Three types of microsclerotial germination were observed under in vitro conditions viz., sporogenic, myceliogenic and both. PCR confirmation with CgInt species‐specific primer and ITS4 resulted in 450‐bp amplification. Since, runner shoots are predominantly used as propagating material in black pepper, an approach was devised to manage anthracnose under nursery conditions by treating the 2‐ to 3‐node cuttings (nursery planting material) with carbendazim (12%)—mancozeb (63%) @ 0.1% for 30 min. The results of the study suggests a new facet in the disease cycle of black pepper anthracnose, indicating that the pathogen survives as microsclerotia in planta and could act as a potential source of inoculum.     

Unearthing the Fossorial Tadpoles of the Indian Dancing Frog Family Micrixalidae

Tadpoles of the monotypic Indian dancing frog family Micrixalidae have remained obscure for over 125 years. Here we report the discovery of the elusive tadpoles of Micrixalus herrei from the sand beds of a forested stream in southern Western Ghats, and confirm their identity through DNA barcoding. These actively burrowing tadpoles lead an entirely fossorial life from eggs to late metamorphic stages. We describe their internal and external morphological characters while highlighting the following features: eel-like appearance, extensively muscularized body and tail, reduced tail fins, skin-covered eyes, delayed development of eye pigmentation in early pre-metamorphic stages (Gosner stages 25–29), prominent tubular sinistral spiracle, large transverse processes on vertebrae II and III, ankylosed ribs on transverse processes of vertebra II, notochord terminating before the atlantal cotyle-occipital condyle junction, absence of keratodonts, serrated well-formed jaw sheaths, and extensive calcified endolymphatic sacs reaching sacrum posteriorly. The tadpole gut contains mostly fine sediments and sand. We discuss the eel-like morphology and feeding habits of M. herrei in the context of convergence with other well-known fossorial tadpoles. This discovery builds the knowledge base for further comparative analyses and conservation of Micrixalus, an ancient and endemic lineage of Indian frogs.     

Diversity and distribution of molluscan fauna of Asthamudi estuary,Kerala, India

The survey of molluscan fauna of Ashtamudi estuary of the southwest coast of India recorded the presence of 119 species classified under 3 classes (Polyplacophora, Gastropoda and Bivalvia), 57 families and 96 genera. The species diversity was dominated by the Gastropoda (69 species), followed by the Bivalvia (49 species) and the Polyplacophora (1 species). The report includes four species recorded for the first time from India: Desmaulus edgarianus (Melvill, 1898), Pilosabia trigona (Gmelin, 1791), Nassarius javanus (Schepman, 1891) and Jorunna labialis (Eliot, 1908). The true diversity of the mangrove region was as good as that of a community with 31.380 (=?31) equally common species; the respective values for the bar mouth and lake regions were 15.516 and 8.997, respectively, indicating that the molluscan species assemblage of the mangrove was the most diverse and of the lake, the least. True β-diversity across this gradient registered 1.792, which means that though there were three communities, they were equivalent to only 1.792 (=?2) effective communities, i.e., the three actual communities were as different from each other as 2 with equal weights and no species in common.