Identification of Escherichia coli through analysis of 16S rRNA and 16S-23S rRNA internal transcribed spacer region sequences

A bacterial strain, designated BzDS03 was isolated from water sample, collected from Dal Lake Srinagar. The strain was characterized by using 16S ribosomal RNA gene and 16S-23S rRNA internal transcribed spacer region sequences. Phylogenetic analysis showed that 16S rRNA sequence of the isolate formed a monophyletic clade with genera Escherichia. The closest phylogenetic relative was Escherichia coli with 99% 16S rRNA gene sequence similarity. The result of Ribosomal database project's classifier tool revealed that the strain BzDS03 belongs to genera Escherichia.16S rRNA sequence of isolate was deposited in GenBank with accession number FJ961336. Further analysis of 16S-23S rRNA sequence of isolate confirms that the identified strain BzDS03 be assigned as the type strain of Escherichia coli with 98% 16S-23S rRNA sequence similarity. The GenBank accession number allotted for 16S-23S rRNA intergenic spacer sequence of isolate is FJ961337.     

Estimation of mental effort in learning visual search by measuring pupil response

Perceptual learning refers to the improvement of perceptual sensitivity and performance with training. In this study, we examined whether learning is accompanied by a release from mental effort on the task, leading to automatization of the learned task. For this purpose, we had subjects conduct a visual search for a target, defined by a combination of orientation and spatial frequency, while we monitored their pupil size. It is well known that pupil size reflects the strength of mental effort invested in a task. We found that pupil size increased rapidly as the learning proceeded in the early phase of training and decreased at the later phase to a level half of its maximum value. This result does not support the simple automatization hypothesis. Instead, it suggests that the mental effort and behavioral performance reflect different aspects of perceptual learning. Further, mental effort would be continued to be invested to maintain good performance at a later stage of training.     

Ion-specific aggregation of gold-DNA nanoparticles using the dG quartet hairpin 5'-d(G4T4G4)

Ion-selective self-assembly of Au nanoparticles is described. The Oxytricha telomere DNA hairpin 5'-d(G4T4G4) immobilized on 13-nm Au nanoparticles forms a supramolecular assembly via dG-quartets, as determined by the color change and by scanning electron microscopy (SEM). The aggregation is ion-dependent and selective for Na+ ions. K+ is less efficient, while Li+ and Cs+ do not drive the aggregation. This work is the first effort to explore the use of secondary structures of DNA (quadruplexes) for producing self-assemblies of Au nanoparticles. It can be utilized to generate novel devices and materials, potentially useful for sensing and other applications in medicinal or engineering science.     

Synthesis of 2,3-unsaturated C-glycosides by HClO4-SiO2 catalyzed Ferrier rearrangement of glycals

Alkyl 2,3-unsaturated C-glycopyranosides have been prepared by Ferrier rearrangement of acyl or alkyl protected glycals catalyzed by HClO(4)-SiO(2).     

Direct one-pot conversion of acylated carbohydrates into their alkylated derivatives under heterogeneous reaction conditions using solid NaOH and a phase transfer catalyst

A convenient one-pot protocol for the direct conversion of acyl-protected carbohydrates into their alkylated counterparts has been developed by using alkyl halides in the presence of solid sodium hydroxide and a phase transfer catalyst. These economically convenient, mild, two-phase reaction conditions allow the preparation of a variety of monosaccharide intermediates for use in the synthesis of complex oligosaccharides.     

Retinoid metabolism during development of liver cirrhosis

The changes in retinoid metabolism have been documented in liver cirrhosis. However, the dynamic alterations in levels of this vitamin between circulation and liver during development of the liver cirrhosis are not well understood. The aim of this study was to measure retinoids in the liver and circulation in parallel, during and after development of cirrhosis induced by carbon tetrachloride and thioacetamide. Retinoid levels were measured by HPLC. A decrease in retinaldehyde and total retinol, together with an increase in retinoic acid was evident in liver from both carbon tetrachloride or thioacetamide treated rats within a month after initiation of treatment. Activity of enzymes involved in retinoid metabolism such as retinaldehyde oxidase, retinaldehyde dehydrogenase, and retinaldehyde reductase were decreased in the liver. In parallel, levels of retinol and retinaldehyde in the serum were increased while retinoic acid was decreased. This study indicates that during development of cirrhosis, there is reciprocal transfer of retinoid metabolites between the circulation and the liver.     

Word organization in coding DNA: A mathematical model

This article deals with the relationship between vocabulary (total number of distinct oligomers or “words”) and text-length (total number of oligomers or “words”) for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this relationship for CDSs. Here we develop a mathematical model to establish the relationship between the number of type of words (vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based on the parameters of the model, we formulate a mathematical equation, known as “equation of word organization”, whose parameters essentially indicate that nucleotide organization of coding sequences are different from one another. We also compare the word organization of CDSs with the random word distribution and conclude that a CDS is neither similar to a natural human language nor to a random one. Moreover, these sequences have their unique nucleotide organization and it is completely structured for specific biological functioning. IM and AS contributed equally to this work.     

Differential Alterations in Metabolic Pattern of the Spliceosomal UsnRNAs during Pre-Malignant Lung Lesions Induced by Benzo(a)pyrene: Modulation by Tea Polyphenols

The differential alterations of the spliceosomal UsnRNAs (U1, U2, U4, U5, and U6) were reported to be associated with cellular proliferation and development. The attempt was made in this study to analyze the metabolic pattern of the spliceosomal UsnRNAs during the development of pre-malignant lung lesions induced in experimental mice model system by benzo(a)pyrene (BP) and also to see how tea polyphenols, epigallocatechin gallate (EGCG) and epicatechin gallate (ECG), modulate the metabolism of these UsnRNAs during the lung carcinogenesis. No significant changes in the level of the UsnRNAs were seen in the inflammatory lung lesions at 9th week due to treatment of BP. However, there was significant increase in the level of U1 (∼2.5 fold) and U5 (∼47%) in the hyperplastic lung lesions at 17th week. But in the mild dysplastic lung lesions at 26th week, the level of UsnRNAs did not change significantly. Whereas, in the dysplastic lung lesions at 36th week there was significant increase in the level of the U2 (∼2 fold), U4 (∼2.5 fold) and U5 (∼2 fold). Due to the EGCG and ECG treatment the lung lesions at 9th week appeared normal and in the 17th, 26th, and 36th week it appeared as hyperplasia. The level of the UsnRNAs was significantly low in the lung lesions at 9th week (only U2 and U4 by EGCG), at 17th week (only U1 by EGCG/ECG), at 26th week (U1 by ECG; U2, U4 and U5 by EGCG/ECG) and at 36th week (U1 by ECG, U2 and U4 by EGCG/ECG). Whereas, there was significant increase in the level of U5 (by EGCG/ECG) and U6 (by EGCG only) in the lung lesions at 36th and 26th week respectively. This indicates that the metabolism of the spliceosomal UsnRNAs differentially altered during the development of pre-malignant lung lesions by BP as well as during the modulation of the lung lesions by the tea polyphenols.