Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium

<p>Abstract</p> <p>Background</p> <p>Bacterial taxonomy and phylogeny based on <it>rrs </it>(16S rDNA) sequencing is being vigorously pursued. In fact, it has been stated that novel biological findings are driven by comparison and integration of massive data sets. In spite of a large reservoir of <it>rrs </it>sequencing data of 1,237,963 entries, this analysis invariably needs supplementation with other genes. The need is to divide the genetic variability within a taxa or genus at their <it>rrs </it>phylogenetic boundaries and to discover those fundamental features, which will enable the bacteria to naturally fall within them. Within the large bacterial community, <it>Clostridium </it>represents a large genus of around 110 species of significant biotechnological and medical importance. Certain <it>Clostridium </it>strains produce some of the deadliest toxins, which cause heavy economic losses. We have targeted this genus because of its high genetic diversity, which does not allow accurate typing with the available molecular methods.</p> <p>Results</p> <p>Seven hundred sixty five <it>rrs </it>sequences (> 1200 nucleotides, nts) belonging to 110 <it>Clostridium </it>species were analyzed. On the basis of 404 <it>rrs </it>sequences belonging to 15 <it>Clostridium </it>species, we have developed species specific: (i) phylogenetic framework, (ii) signatures (30 nts) and (iii) <it>in silico </it>restriction enzyme (14 Type II REs) digestion patterns. These tools allowed: (i) species level identification of 95 <it>Clostridium </it>sp. which are presently classified up to genus level, (ii) identification of 84 novel <it>Clostridium </it>spp. and (iii) potential reduction in the number of <it>Clostridium </it>species represented by small populations.</p> <p>Conclusions</p> <p>This integrated approach is quite sensitive and can be easily extended as a molecular tool for diagnostic and taxonomic identification of any microbe of importance to food industries and health services. Since rapid and correct identification allows quicker diagnosis and consequently treatment as well, it is likely to lead to reduction in economic losses and mortality rates.</p

Bulk-phase thermodynamic properties and dielectric constant of ethanol: an ab initio quantum mechanical approach combined with a statistical model

Ab initio theory at the HF/6-311G(d,p) level has been used to compute the hydrogen bonding thermodynamics in bulk liquid ethanol. Inter-cluster hydrogen bonding is assumed to mimic the H-bonding in bulk ethanol. Rotation of the clusters has been neglected, but translational and vibrational motions are taken into account for calculating bulk thermodynamic parameters. Results are well in agreement with an earlier report [J. Chem. Phys. 116, 4212 (2002)]. For a more accurate dipole moment of monomer, MP2/6-311++G(d,p) calculation was done. Use of the computed thermodynamic data in a statistical model yields the Kirkwood-Frohlich correlation factor and the dielectric constant of ethanol (21.0) close to the experimental value, 24.3 at 298 K

Characterization of the ATPase activity of topoisomerase II from Leishmania donovani and identification of residues conferring resistance to etoposide

We have cloned and expressed the 43 kDa N-terminal domain of Leishmania donovani topoisomerase II. This protein has an intrinsic ATPase activity and obeys Michaelis–Menten kinetics. Cross-linking studies indicate that the N-terminal domain exists as a dimer both in the presence and absence of nucleotides. Etoposide, an effective antitumour drug, traps eukaryotic DNA topoisomerase II in a covalent complex with DNA. In the present study, we report for the first time that etoposide inhibits the ATPase activity of the recombinant N-terminal domain of L. donovani topoisomerase II. We have modelled the structure of this 43 kDa protein and performed molecular docking analysis with the drug. Mutagenesis of critical amino acids in the vicinity of the ligand-binding pocket reveals less efficient inhibition of the ATPase activity of the enzyme by etoposide. Taken together, these results provide an insight for the development of newer therapeutic agents with specific selectivity

A novel ATP-binding cassette transporter, ABCG6 is involved in chemoresistance of Leishmania

ATP-binding cassette (ABC) transporters constitute the biggest family of membrane proteins involved in drug resistance and other biological activities. Resistance of leishmanial parasites to therapeutic drugs continues to escalate in developing countries and in many instances it is due to overexpressed ABC efflux pumps. Progressively adapted camptothecin (CPT)-resistant parasites show overexpression of a novel ABC transporter, which was classified as ABCG6. Transfection and overexpression of LdABCG6 in wild type parasites, shows its localization primarily in the plasma membrane and flagellar pocket region. Overexpressed LdABCG6 confers substantial CPT resistance to the parasites by rapid drug efflux. Various inhibitors have been tested for their ability to revert the CPT-resistant phenotype to specifically understand the inhibition of LdABCG6 transporter. Transport experiments using everted membrane vesicles were carried out to gain an insight into the kinetics of drug transport. This study provides further knowledge of specific membrane traffic ATPase and its involvement in the chemoresistance of Leishmania

Association of specific p53 polymorphisms with keratosis in individuals exposed to arsenic through drinking water in West Bengal, India

Although, more than six million people are endemically exposed to inorganic arsenic in West Bengal, India by drinking heavily contaminated groundwater, only about 300,000 people show arsenic induced skin lesions. This suggests that genetic variability plays an important role in arsenic induced skin lesions and skin cancers. Arsenic induced keratosis is considered as a possible precancerous state of in situ carcinoma. Several reports have suggested the role of p53 polymorphisms as potential marker for risk assessment of different types of cancers. This prompted us to study the association of three p53 polymorphisms with arsenic induced keratosis in a population exposed to arsenic through drinking water. A total of 366 unrelated individuals (177 individuals with arsenic induced keratosis and 189 individuals with no arsenic induced skin lesions) were recruited from North 24 Parganas, Nadia and Murshidabad districts between January 2003 and February 2005 for the study of the genotypic distribution of three p53 polymorphisms (16 bp duplication at intron 3, codon 72 Arg/Pro and G &#x003E; A at intron 6 [nt 13,494]) by PCR-RFLP. The arginine homozygous genotype at codon 72, and homozygous genotype of no duplication polymorphism at intron 3 were over represented in the individuals with keratosis compared with individuals with no skin lesions (OR = 2.086; 95% CI = 1.318–3.299 and OR = 2.086; 95% CI = 1.257–3.457, respectively). This study indicates that individuals carrying the arginine homozygous genotype at codon 72, and/or no duplication homozygous genotype at intron 3 are at risk for the development of arsenic induced keratosis

Investigation on the structure and thermoelectric properties of CuxTe binary compounds

Cu2Te is a superionic conductor that belongs to the Phonon Liquid Electron Crystal class of thermoelectric (TE) materials. Despite the simple chemical formula, the crystal structures and phases in the Cu2Te system have not been understood properly. In this work, we study the structural and TE properties of Cu2Te (CT2), Cu1.6Te (CT1.6) and Cu1.25Te (CT1.25). The samples were synthesized via a solid-state reaction method. Powder X-ray diffraction analysis revealed that the samples have different crystal structures depending upon the Cu : Te stoichiometry. The elemental compositional analysis showed that all the samples are copper deficient. This is due to the precipitation of metallic copper on the surface of the ingot arising from the thermal dissociation of Cu2Te. The transport properties were measured in the temperature range 300 K-600 K. The electrical conductivity (sigma) decreases with an increase in temperature indicating a metal-like behaviour for all the samples. The positive Seebeck coefficients (S) for all the samples indicates that majority charge carriers are holes. The sample CT2 has a higher S (29.5 mu V K (1) at 573 K) and a lower sigma (2513 S cm(-1) at 573 K) due to a lower carrier (hole) concentration compared to the other two samples. With the increase in Cu deficiency, the hole concentration increases, and this leads to higher electronic thermal conductivity in the samples CT1.6 and CT1.25. The maximum thermoelectric figure of merit of 0.03 at 524 K is achieved for the sample CT2 owing to its higher power factor (0.24 mW m(-1) K-2) and lower thermal conductivity (3.8 W m(-1) K-1). The present study bridges the gap between the theoretical predictions and experimental observations involving the various possible structures in this system. Furthermore, we have shown that the Cu vacancies are detrimental to the thermoelectric performance of Cu2Te

Comparison of health effects between individuals with and without skin lesions in the population exposed to arsenic through drinking water in West Bengal, India

A study was conducted to explore the effect of arsenic causing conjunctivitis, neuropathy and respiratory illness in individuals, with or without skin lesions, as a result of exposure through drinking water, contaminated with arsenic to similar extent. Exposed study population belongs to the districts of North 24 Parganas and Nadia, West Bengal, India. A total of 725 exposed (373 with skin lesions and 352 without skin lesions) and 389 unexposed individuals were recruited as study participants. Participants were clinically examined and interviewed. Arsenic content in drinking water, urine, nail and hair was estimated. Individuals with skin lesion showed significant retention of arsenic in nail and hair and lower amount of urinary arsenic compared to the group without any skin lesion. Individuals with skin lesion also showed higher risk for conjunctivitis ((odd’s ratio) OR: 7.33, 95% CI: 5.05–10.59), peripheral neuropathy (OR: 3.95, 95% CI: 2.61–5.93) and respiratory illness (OR: 4.86, 95% CI: 3.16–7.48) compared to the group without any skin lesion. The trend test for OR of the three diseases in three groups was found to be statistically significant. Again, individuals without skin lesion in the exposed group showed higher risk for conjunctivitis (OR: 4.66, 95% CI: 2.45–8.85), neuropathy (OR: 3.99, 95% CI: 1.95–8.09), and respiratory illness (OR: 3.21, 95% CI: 1.65–6.26) when compared to arsenic unexposed individuals. Although individuals with skin lesions were more susceptible to arsenicinduced toxicity, individuals without skin lesions were also subclinically affected and are also susceptible to arsenic-induced toxicity and carcinogenicity when compared to individuals not exposed to arsenic

Hopping-Mediated Anion Transport through a Mannitol-Based Rosette Ion Channel

Artificial anion selective ion channels with single-file multiple anion-recognition sites are rare. Here, we have designed, by hypothesis, a small molecule that self-organizes to form a barrel rosette ion channel in the lipid membrane environment. Being amphiphilic in nature, this molecule forms nanotubes through intermolecular hydrogen bond formation, while its hydrophobic counterpart is stabilized by hydrophobic interactions in the membrane. The anion selectivity of the channel was investigated by fluorescence-based vesicle assay and planar bilayer conductance measurements. The ion transport by a modified hopping mechanism was demonstrated by molecular dynamics simulation studies