RepEx: A web server to extract sequence repeats from protein and DNA sequences

Evolution builds up new genetic material from existing ones, not in random, but in highly ordered and eloquent patterns. Most of these sequence repeats are revelatory of valuable information contributing to areas of disease research and function of macromolecules, to name a few. In the age of next generation genome sequencing, rapid and efficient extraction of all unbiased sequence repeats from macromolecules is the need of the hour. In view of this reckoning, an online web-based computing server, RepEx, has been developed to extract and display all possible repeats for DNA and protein sequences. Apart from exact or identical repeats, the server has been designed adeptly to identify and extract degenerate, inverted, everted and mirror repeats from both DNA and protein sequences. The server has striking output displays, featuring interactive graphs and comprehensive output files. In addition, RepEx has been accoutered with an easy-to-use interface and search filters to facilitate a user-defined query or search and is freely available and accessible via the World Wide Web at http://bioserver2.physics.iisc.ac.in/RepEx/.     

Synthesis of a series of ethylene glycol modified water-soluble tetrameric TPE-amphiphiles with pyridinium polar heads: Towards applications as light-up bioprobes in protein and DNA assay,and wash-free imaging of bacteria

Available online Development of water soluble AIE-active “light-up” bioprobes for the detection of biomacromolecules has drawn huge research interests in recent past. In this study, a series of ethylene glycol modified water soluble tetrameric tetraphenylethylene amphiphiles with pyridinium polar heads (TPE-xEG-Py, x = 3, 4, 6 or 1a-c) have been synthesized by varying the ethylene glycol spacer. Their unique structure allows them to form vesicles and other nanoaggregates in aqueous solutions. These amphiphiles were successfully utilized for fluorimetric detection and quantitation of BSA and DNA based on the electrostatic interactions to trigger AIE-emission from the TPE moiety. The electrostatic interaction was also proved very effective in wash-free imaging of both Gram-negative (E. coli) and Gram-positive (S. aureus) bacteria with up to 92 folds increase in fluorescence response within bacterial concentration 0–12 × 10⁸ CFU mL^?1. The strategy is advantageous due to cost-effective and easy synthesis, high water solubility, and fast response.     

A new simple,low-cost approach for generation of the PM10 fraction from soil and related materials: Application to human health risk assessment

A new simple, robust and low-cost wet laboratory method for the generation of the <10 μm (PM₁₀) particle size fraction is reported. A sedimentation method is directly compared with a centrifugation method for generation of the PM₁₀ fraction. Both approaches are based on an integrated form of Stokes’ law. Subsequently the sedimentation method was adopted. The results from the sedimentation method were corroborated using particle size distribution measurements. This approach for the generation of the PM₁₀ fraction was applied to soil and mine waste samples from Mitrovica, Kosovo as part of an investigation in to the human risk assessment from inhalation of the PM₁₀ fraction containing potentially harmful elements (PHEs). The average daily dose for Cd from the inhalation of suspended soil particles was calculated to be 0.021 and 0.010 μg kg⁻¹_BW d⁻¹ for a child and an adult, respectively. This corresponded to an inhalation dose of 0.50 and 0.70 μg Cd d⁻¹ for a child (20 kg) and an adult (70 kg), respectively.