Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300

We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from pesticide-contaminated soil in Punjab, India. The genome sequence of the strain RKJ300 will be helpful in exploring the molecular pathways involved in the degradation of nitrophenols.     

A molecular machine biosensor: construction, predictive models and experimental studies

This paper describes the construction, operation and predictive modeling of a molecular machine, functioning as a high sensitivity biosensor. Embedded gramicidin A (gA) ionchannels in a self-assembled tethered lipid bilayer act as biological switches in response to target molecules and provide a signal amplification mechanism that results in high sensitivity molecular detection. The biosensor can be used as a rapid and sensitive point of care diagnostic device in different media such as human serum, plasma and whole blood without the need for pre and post processing steps required in an enzyme-linked immunosorbent assay. The electrical reader of the device provides the added advantage of objective measurement. Novel ideas in the construction of the molecular machine, including fabrication of biochip arrays, and experimental studies of its ability to detect analyte molecules over a wide range of concentrations are presented. Remarkably, despite the complexity of the device, it is shown that the response can be predicted by modeling the analyte fluid flow and surface chemical reactions. The derived predictive models for the sensing dynamics also facilitate determining important variables in the design of a molecular machine such as the ion channel lifetime and diffusion dynamics within the bilayer lipid membrane as well as the bio-molecular interaction rate constants.     

Molecular analysis of gut microbiota in obesity among Indian individuals

Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR (P less than 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.     

Metabolic fingerprinting to discriminate diseases of stored carrots

Volatile metabolites from headspace gas of carrot cv. Vita‐treat inoculated with water or four different pathogens Botrytis cinerea, Erwinia carotovora subsp. carotovora, Aspergillus niger and Fusarium avenaceum were profiled using gas chromatography and mass spectrometry to develop a technology to discriminate diseases. The inoculation of carrot roots with water or different pathogens released a total of 137 different volatile metabolites. Among them, 39 compounds were relatively consistent and 11 were specific to one or more diseases/inoculations. E. carotovora subsp. carotovora produced seven disease‐specific metabolites: 1‐butanol, 3‐methyl; 1‐pentanol; 1‐propanol, 2‐methyl; 2,3‐butanedione; boronic acid, ethyl; butane, 1‐methoxy‐3‐methyl; and ethane, ethoxy. Some metabolites were disease/inoculation discriminatory and were not detected in all treatments: 1,2‐dimethoxy‐ethene was common in carrots inoculated with E. carotovora subsp. carotovora and B. cinerea, while 2‐butanone, 3‐chloro‐4‐hydroxy‐1,4‐diphenyl was common in carrots inoculated with E. carotovora subsp. carotovora, F. avenaceum and water‐inoculated control. The significant mass ions, based on univariate analysis, from a total of 150 (46–195 m/z) and compounds from a total of 32 were further subjected to stepwise discriminant analysis and discriminant analysis. The models for 3 days after inoculation (DAI) were better than those for 6 DAI and 3 + 6 DAI, where up to 90% of the observations were correctly classified into respective inoculations. The disease‐discriminatory compounds from different diseases/inoculations and discriminant analysis models developed here have the potential for the early detection and discrimination of postharvest diseases of carrot cv. Vita‐treat, after validation under commercial conditions.     

Glyphosate Resistance as a Versatile Selection Marker for <Emphasis Type="Italic">Arabidopsis</Emphasis> Transformation

Molecular genetic studies on the model plant Arabidopsis thaliana often involve multiple rounds of Agrobacterium-mediated transformation. Such procedures require multiple marker genes that would allow for efficient selection of transgenic plants in each cycle of transformation. Here, we report on a selection marker cassette based on a codon-modified glyphosate N-acetyltransferase (GAT) gene whose expression is driven by a powerful EL2Ω promoter. After introduction of the GAT expression cassette into A. thaliana via Agrobacterium-mediated transformation, glyphosate-resistant primary transformants are efficiently selected by glyphosate, either added to the culture medium or by spraying a glyphosate solution onto seedlings grown in soil. Robust glyphosate-resistant phenotypes are always associated with the presence of the GAT cassette. In addition, RT-PCR analysis of T₂ transformants has demonstrated that resistance to glyphosate is associated with higher levels of GAT expression. Resistance conferred by GAT is specific to glyphosate and not to other commonly used selection chemical compounds. These results demonstrate the versatility of the GAT cassette suitable for both large-scale, soil-based selection system of transgenic plants as well as their characterization in vitro.     

Isolation and characterization of nine microsatellite loci in an ant-tended treehopper Publilia concava

Publilia concava is an eastern North American membracid commonly occurring in large but spatially patchy aggregations, primarily on the host plant Solidago altissima. Like other myrmecophiles, P. concava provides sugary excretions to ants in return for the various protective, competitive or even sanitary benefits that ants provide. We developed nine microsatellite loci from P. concava. Mean per locus allele number was 6.78, and observed heterozygosities ranged from 0.03 to 0.850. One locus exhibited significant heterozygote deficit, possibly due to the presence of null alleles. These markers provide important tools for future spatial ecological studies in this model system for the study of mutualism.