Dry-reagent gold nanoparticle-based lateral flow biosensor for the simultaneous detection of Vibrio cholerae serogroups O1 and O139

Cholera is a communicable disease caused by consumption of contaminated food and water. This potentially fatal intestinal infection is characterised by profuse secretion of rice watery stool that can rapidly lead to severe dehydration and shock, thus requiring treatment to be given immediately. Epidemic and pandemic cholera are exclusively associated with Vibrio cholerae serogroups O1 and O139. In light of the need for rapid diagnosis of cholera and to prevent spread of outbreaks, we have developed and evaluated a direct one-step lateral flow biosensor for the simultaneous detection of both V. cholerae O1 and O139 serogroups using alkaline peptone water culture. Serogroup specific monoclonal antibodies raised against lipopolysaccharides (LPS) were used to functionalize the colloidal gold nanoparticles for dual detection in the biosensor. The assay is based on immunochromatographic principle where antigen-antibody reaction would result in the accumulation of gold nanoparticles and thus, the appearance of a red line on the strip. The dry-reagent dipstick format of the biosensor ensure user-friendly application, rapid result that can be read with the naked eyes and cold-chain free storage that is well-suited to be performed at resource-limited settings.     

Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray

We have developed an oligonucleotide microarray for the detection of biodegradative genes and bacterial diversity and tested it in five contaminated ecosystems. The array has 60-mer oligonucleotide probes comprising 14,327 unique probes derived from 1,057 biodegradative genes and 880 probes representing 110 phylogenetic genes from diverse bacterial communities, and we named it as BiodegPhyloChip. The biodegradative genes are involved in the transformation of 133 chemical pollutants. Validation of the microarray for its sensitivity specificity and quantitation were performed using DNA isolated from well-characterized mixed bacterial cultures also having non-target strains, pure degrader strains, and environmental DNA. Application of the developed array using DNA extracted from five different contaminated sites led to the detection of 186 genes, including 26 genes unique to the individual sites. Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well-characterized genera involved in biodegradation of various pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal), and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to the enzyme hydroxylases, monooxygenases, and dehydrogenases which were present in all the five samples. Thus, the array developed and validated here shall be useful in assessing not only the biodegradative potential but also the composition of environmentally useful bacteria, simultaneously, from hazardous ecosystems.     

Deciphering the key molecular and cellular events in neutrophil transmigration during acute inflammation

Recruitment of leukocytes circulating in our blood to the sites of infection or tissue damage is the key phenomenon in the acute inflammatory response(s). Among the leukocytes, neutrophils are primarily recruited into the areas of acute inflammation. When neutrophils interact with activated endothelium of the blood vessels, they become migratory and cross the endothelial layer of the blood vessel wall in a process called as leukocyte extravasation. Identifying and understanding the gene regulation of this extravasation phenomenon is one of the key objective of biomedical research aimed at ameliorating or alleviating the symptoms of various diseases, such as rheumatoid arthritis, asthma, anaphylaxis, atherosclerosis, ulcerative colitis etc., that are exacerbated by inappropriate inflammatory stimuli. Here, we decipher and discuss the key genes implicated in the leukocyte transmigration using the acute inflammation model called as the Dextran Sulphate Sodium (DSS) induced Colitis in mice as a classic paradigm.     

Optimized in vitro micro-tuber production for colchicine biosynthesis in Gloriosa superba L. and its anti-microbial activity against Candida albicans

Plant Cell, Tissue and Organ Culture (PCTOC) - Gloriosa superba L. tubers are a rich source of commercially important colchicine and due to overexploitation, the species has become vulnerable. In...     

Gelsemiaceae (Gentianales) expanded to include the enigmatic Asian genus Pteleocarpa

The enigmatic South‐East Asian monotypic genus Pteleocarpa has been considered as a genus incertae sedis among the eudicots for a long time. Molecular data (plastid and nuclear ribosomal regions) from 44 widely sampled species across Lamiidae and phylogenetic analyses have finally clarified its familial relationships, and it is here included in Gelsemiaceae (order Gentianales). Its morphological characteristics support a placement in this family and order as a result of the presence of potential synapomorphies, such as imbricate and commonly yellow corollas, latrorse anther dehiscence, divided styles and compressed seeds. Unique characters for Pteleocarpa in Gelsemiaceae are alternate leaves and indehiscent samaras. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 482–496.     

Enhanced production of isoflavones by elicitation in hairy root cultures of Soybean

A combined treatment of sonication (2 min) and vacuum infiltration (2 min) stimulated isoflavones production of 75.26 mg g^?1 DW which was 15.11-fold higher than control hairy root line at optimal harvest time of 40 days. Addition of MeJ at 100 μM concentration with 72 h exposure time on 30 day-old hairy root culture further enhanced total isoflavones production of 53.16 mg g^?1 DW (10.67-fold) and SA at 200 μM concentration with 96 h exposure period enhanced the production of isoflavones (28.79 mg g^?1 DW; 5.78-fold). MeJ-treated hairy roots reduced biomass accumulation whereas sonication, vacuum infiltration and SA did not exhibit a negative effect on biomass growth.     

Bacillus mesophilum sp. nov., strain IITR-54T,a novel 4-chlorobiphenyl dechlorinating bacterium

The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54^T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01 % yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54^T differs from all other species of Bacillus by at least 2.1 % at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9 %) followed by Bacillus infantis (97.7 %), Bacillus firmus (97.4 %), Bacillus drentensis (97.3 %), Bacillus circulans (97.2 %), Bacillus soli (97.1 %), Bacillus horneckiae (97.1 %), Bacillus pocheonensis (97.1 %) and Bacillus bataviensis (97.1 %), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C_15:0 (32.4 %) and anteiso-C_15:0 (27.4 %). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54^T with its phylogenetic relatives and suggest that the strain IITR-54^T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54^T (= MTCC 11060^T = JCM 19208^T).     

Antagonistic potential of native strain Streptomyces aurantiogriseus VSMGT1014 against sheath blight of rice disease

A total of 132 actinomycetes was isolated from different rice rhizosphere soils of Tamil Nadu, India, among which 57 showed antagonistic activity towards Rhizoctonia solani, which is sheath blight (ShB) pathogen of rice and other fungal pathogens such as Macrophomina phaseolina, Fusarium oxysporum, Fusarium udum and Alternaria alternata with a variable zone of inhibition. Potential actinomycete strain VSMGT1014 was identified as Streptomyces aurantiogriseus VSMGT1014 based on the morphological, physiological, biochemical and 16S rRNA sequence analysis. The strain VSMGT1014 produced lytic enzymes, secondary metabolites, siderophore, volatile substance and indole acetic acid. Crude metabolites of VSMGT1014 showed activity against R. solani at 5 µg ml^?1; however, the prominent inhibition zone was observed from 40 to 100 µg ml^?1. Reduced lesion heights observed in culture, cells-free filtrate, crude metabolites and carbendazim on challenge with pathogen in the detached leaf assay. The high content screening test clearly indicated denucleation of R. solani at 5 µg ml^?1 treatment of crude metabolite and carbendazim respectively. The results conclude that strain VSMGT1014 was found to be a potential candidate for the control of ShB of rice as a bio fungicide.     

PPS: A computing engine to find Palindromes in all Protein sequences

The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.

Availability

URL http://pranag.physics.iisc.ernet.in/pps/     

4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence

The nonproteinogenic amino acid 4-hydroxyphenylglycine (HPG) arises from the diversion of the tyrosine degradation pathway into secondary metabolism, and its biosynthesis requires a set of three enzymes. The gene cassette for HPG biosynthesis is widely spread in actinomycete bacteria, which incorporate the amino acid as a building block into various peptide antibiotics, but it has never been reported from another taxonomic group of eubacteria. A genome mining study has now revealed a putative HPG pathway in the predatory bacterium Herpetosiphon aurantiacus, which is phylogenetically distinct from Actinomycetes. Anomalies in the active center of one annotated key enzyme raised questions about the true product of this pathway, prompting an in vitro reconstitution attempt. This study confirmed the capability of H. aurantiacus for HPG production. Sequence analysis of the aberrant 4-hydroxymandelate synthase refines the existing model on the catalytic differentiation of iron(II)-dependent dioxygenases. Furthermore, we report a comprehensive analysis on the phylogeny of these enzymes, which sheds light on the evolution of paralogous gene sets and the ensuing metabolic diversity in a barely studied bacterium.