Aerobic microbial manufacture of nanoscale selenium: exploiting nature’s bio-nanomineralization potential

The potential of the environment to yield organisms that can produce functional bionanominerals is demonstrated by selenium-tolerant, aerobic bacteria isolated from a seleniferous rhizosphere soil. An isolate, NS3, was identified as a Bacillus species (EU573774.1) based on morphological and 16S rRNA characterization. This strain reduced Se(IV) under aerobic conditions to produce amorphous α Se(0) nanospheres. A room-temperature washing treatment was then employed to remove the biomass and resulted in the production of clusters of hexagonal Se(0) nano-rods. The Se(0) nanominerals were analyzed using electron microscopy and X-ray diffraction techniques. This Bacillus isolate has the potential to be used both in the neutralizing of toxic Se(IV) anions in the environment and in the environmentally friendly manufacture of nanomaterials.     

Physicochemical and bioactivity of cross-linked chitosan–PVA film for food packaging applications

This work aimed to develop a novel antimicrobial coating based on chitosan and PVA to evaluate its effect on minimally processed tomato by means of microbiological analyses. In this report an antimicrobial film was prepared by blending chitosan (CS) and poly(vinyl alcohol) (PVA) with glutaraldehyde as the cross-linker. The miscibility and morphology of the film were investigated by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The thermal property of the chitosan–PVA film was examined by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The microbiological screening has demonstrated the antimicrobial activity of the film against food pathogenic bacteria viz. Escherichia coli, Staphylococcus aureus, and Bacillus subtilis. The obtained results indicate the film may be a promising material for food packaging applications.     

Up regulation of the GRP-78 and GADD-153 and down regulation of Bcl-2 proteins in primary glomerular diseases: a possible involvement of the ER stress pathway in glomerulonephritis

Alpha-lipoic acid (LA) has recently been reported to afford protection against neurodegenerative disorders in humans and experimental animals. However, the mechanisms underlying LA-mediated neuroprotection remain an enigma. Because peroxynitrite has been extensively implicated in the pathogenesis of various forms of neurodegenerative disorders, this study was undertaken to investigate the effects of LA in peroxynitrite-induced DNA strand breaks, a critical event leading to peroxynitrite-elicited cytotoxicity. Incubation of φX-174 plasmid DNA with the 3-morpholinosydnonimine (SIN-1), a peroxynitrite generator, led to the formation of both single- and double-stranded DNA breaks in a concentration- and time-dependent fashion. The presence of LA at 100–1,600 μM was found to significantly inhibit SIN-1-induced DNA strand breaks in a concentration-dependent manner. The consumption of oxygen induced by 250 μM SIN-1 was found to be decreased in the presence of high concentrations of LA (400–1,600 μM), indicating that LA at these concentrations may affect the generation of peroxynitrite from auto-oxidation of SIN-1. It is observed that incubation of the plasmid DNA with authentic peroxynitrite resulted in a significant formation of DNA strand breaks, which could also be dramatically inhibited by the presence of LA (100–1,600 μM). EPR spectroscopy in combination with spin-trapping experiments, using 5,5-dimethylpyrroline-N-oxide (DMPO) as spin trap, resulted in the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from authentic peroxynitrite and LA at 50–1,600 μM inhibited the adduct signal. Taken together, these studies demonstrate for the first time that LA can potently inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. In view of the critical involvement of peroxynitrite in the pathogenesis of various neurodegenerative diseases, the inhibition of peroxynitrite-mediated DNA damage by LA may be responsible, at least partially, for its neuroprotective activities.     

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background

The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better.

Results

Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions.Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family.

Conclusions

CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.     

Long-term daily access to alcohol alters dopamine-related synthesis and signaling proteins in the rat striatum

Chronic alcohol exposure can adversely affect neuronal morphology, synaptic architecture and associated neuroplasticity. However, the effects of moderate levels of long-term alcohol intake on the brain are a matter of debate. The current study used 2-DE (two-dimensional gel electrophoresis) proteomics to examine proteomic changes in the striatum of male Wistar rats after 8 months of continuous access to a standard off-the-shelf beer in their home cages. Alcohol intake under group-housed conditions during this time was around 3–4 g/kg/day, a level below that known to induce physical dependence in rats. After 8 months of access rats were euthanased and 2-DE proteomic analysis of the striatum was conducted. A total of 28 striatal proteins were significantly altered in the beer drinking rats relative to controls. Strikingly, many of these were dopamine (DA)-related proteins, including tyrosine hydroxylase (an enzyme of DA biosynthesis), pyridoxal phosphate phosphatase (a co-enzyme in DA biosynthesis), DA and cAMP regulating phosphoprotein (a regulator of DA receptors and transporters), protein phosphatase 1 (a signaling protein) and nitric oxide synthase (which modulates DA uptake). Selected protein expression changes were verified using Western blotting. We conclude that long-term moderate alcohol consumption is associated with substantial alterations in the rat striatal proteome, particularly with regard to dopaminergic signaling pathways. This provides potentially important evidence of major neuroadaptations in dopamine systems with daily alcohol consumption at relatively modest levels.     

A cautionary note on exact unconditional inference for a difference between two independent binomial proportions

Fisher's exact test for comparing response proportions in a randomized experiment can be overly conservative when the group sizes are small or when the response proportions are close to zero or one. This is primarily because the null distribution of the test statistic becomes too discrete, a partial consequence of the inference being conditional on the total number of responders. Accordingly, exact unconditional procedures have gained in popularity, on the premise that power will increase because the null distribution of the test statistic will presumably be less discrete. However, we caution researchers that a poor choice of test statistic for exact unconditional inference can actually result in a substantially less powerful analysis than Fisher's conditional test. To illustrate, we study a real example and provide exact test size and power results for several competing tests, for both balanced and unbalanced designs. Our results reveal that Fisher's test generally outperforms exact unconditional tests based on using as the test statistic either the observed difference in proportions, or the observed difference divided by its estimated standard error under the alternative hypothesis, the latter for unbalanced designs only. On the other hand, the exact unconditional test based on the observed difference divided by its estimated standard error under the null hypothesis (score statistic) outperforms Fisher's test, and is recommended. Boschloo's test, in which the p-value from Fisher's test is used as the test statistic in an exact unconditional test, is uniformly more powerful than Fisher's test, and is also recommended.     

Effect of helium-neon laser on wound healing

To estimate the biostimulatory effects of low intensity laser radiation on healing of skin wounds, two linear skin wounds were produced on either side of dorsal midline in rats and immediately sutured. Wounds on the left side were irradiated daily with helium neon laser at 4 Joules/sq.cm for 5 min., while those on right side were not exposed and served as controls. The mean time required for complete closure in control group was 7 days while irradiated test wounds took only 5 days to heal (P < 0.01). The mean breaking strength, as measured by the ability of the wound to resist rupture against force, was found to be significantly increased in the test group. Early epithelization, increased fibroblastic reaction, leucocytic infiltration and neovascularization were seen in the laser irradiated wounds. The results establish the biostimulatory effects of low intensity laser radiation on healing of skin wounds.     

Free radical scavenging potential of Picrorhiza kurrooa Royle ex Benth

For assessing free radical scavenging potential of P. kurrooa, the antioxidant activity of P. kurrooa extract was studied by lipid peroxidation assay using rat liver homogenate. The extract (1 mg/ml) showed marked protection (up to 66.68%) against peroxidation of liver phospholipids. Besides, reduced glutathione showed very encouraging activity. The extract also exhibited significant scavenging activity. Thus augmenting the wide use of plant in the indigenous system of medicine, which may partly be due to antioxidant and free radical scavening activity of the extract.     

Dynamics of Physical Interaction between HIV-1 Nef and ASK1: Identifying the Interacting Motif(S)

FasL mediated preferential apoptosis of bystander CTLs while protection of infected CD4⁺T cells remains one of the hallmarks of immune evasion during HIV infection. The property of infected host cells to evade cell-autonomous apoptosis emanates from ability of HIV-1Nef -protein to physically interact with ASK-1 and thereby inhibit its enzymatic activity. The specific domains of HIV-1Nef through which it may interact with ASK1 and thereby impair the ASK1 activity remain unidentified so far and represent a major challenge towards developing clear understanding about the dynamics of this interaction. Using mammalian two hybrid screen in association with site directed mutagenesis and competitive inhibitor peptides, we identified constituent minimal essential domain (152 DEVGEANN 159) through which HIV-1Nef interacts with ASK1 and inhibits its function. Furthermore our study also unravels a novel alternate mechanism underlying HIV-1 Nef mediated ASK1 functional modulation, wherein by potentiating the inhibitory ser⁹⁶⁷ phosphorylation of ASK1, HIV-1Nef negatively modulated ASK1function.