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T Chakraborty

Publications and source records attributed to T Chakraborty.

At least 19 recordsLinked to original sources
PubMed2006

GECO--linear visualization for comparative genomics.

UNLABELLED: In order to understand and interpret phylogenetic and functional relationships between multiple prokaryotic species, qualitative and quantitative data must be correlated and displayed. GECO allows linear visualization of multiple genomes using a client/server based approach by dynamically creating .png- or .pdf-formatted images. It is able to display ortholog relations calculated using BLASTCLUST by color coding ortholog representations. Irregularities on the genomic level can be identified by anomalous G/C composition. Thus, this software will enable researchers to detect horizontally transferred genes, pseudogenes and insertions/deletions in related microbial genomes. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet

Algorithms↗
PubMed2006

Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.

UNLABELLED: The analysis of protein function is a challenge and a major bottleneck towards well-annotated and analysed microbial genomes. In particular, bacterial surface proteins present an opportunity for pharmacological intervention and vaccine development. We present Augur, an automatic prediction pipeline that integrates major surface prediction algorithms and enables comparative analysis, classification and visualization for gram-positive bacteria on a genomic scale. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/augur

Algorithms↗
PubMed2006

Origin of threefold symmetric torsional potential of methyl group in 4-methylstyrene.

To understand the effect of the para position vinyl group substitution in toluene on methyl torsion, we investigated 4-methylstyrene, a benchmark molecule with an extended pi conjugation. The assignment for a 33 cm(-1) band in the excitation spectrum to the 3a(2) torsional transition, in addition to the assignments suggested previously for the other bands in the excitation spectrum, leads to the model potentials for the ground as well as excited states with V(3) (")=19.6 cm(-1), V(6) (")=-16.4 cm(-1) and V(3) (')=25.6 cm(-1), V(6) (')=-30.1 cm(-1), respectively. These potentials reveal that both in ground and excited states, the methyl group conformations are staggered with a 60 degrees phase shift between them. MP2 ab initio calculations support the ground state conformations determined from experiments, whereas Hartree-Fock calculations fail to do so. The origin of the modified ground state potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis shows that the local delocalization (bond-antibond hyperconjugation) interactions of the methyl group with the parent molecule is sixfold symmetric. The threefold symmetric potential, on the other hand, stems from the interaction of the vinyl group and the adjacent ring pi bond. The threefold symmetric structural energy arising predominantly from the pi electron contribution is the barrier forming term that overwhelms the antibarrier contribution of the delocalization energy. The observed 60 degrees phase shift of the excited state potential is attributed to the pi(*)-sigma(*) hyperconjugation between out of plane hydrogens of the methyl group and the benzene ring.

Journal Article↗
PubMed2006

[Microarray-based transcriptome analyses in infectious diseases. A new diagnostic method].

The complex interaction between a pathogen and a host is the molecular basis of infectious diseases. Microarray technology is a powerful tool to investigate the crosstalk between pathogen and the host as it assesses whole genome expression profiles in response to disease. Deciphering the molecular details on both sides of the host-pathogen interaction will increase our understanding of the pathogenesis of infectious diseases and offer improvements in their diagnosis, treatment, prognosis, and prevention.

Biomarkers↗
PubMed2005

Origin of methyl torsional barrier in 1-methyl-2-(1H)-pyridone.

The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2(1h)-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V(3)=244 cm(-1) and V(6)=15 cm(-1) for the ground state and V(3)=164 cm(-1) and V(6)=40 cm(-1) for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bond-antibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CHsigma(*) and ring pi(*) observed in lowest unoccupied molecular orbital (LUMO) stabilizes the methyl group conformer that undergoes a 60 degrees rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.

Journal Article↗
PubMed2005

Salmonella-mediated oral DNA vaccination using stabilized eukaryotic expression plasmids.

The use of Salmonella for the delivery of plasmid-encoded heterologous antigens to eukaryotic host cells has proven successful in experimental systems, but its general applicability is still hampered by a severe instability of transformants carrying these expression plasmids. To overcome the problem of plasmid instability, new low copy number expression plasmids were constructed using different replicons. Comparative studies between transformants of the high copy number plasmid pCMVbeta and the different low copy number plasmids that contain the pMB1, p15A or pSC101 replicons on the pCMVbeta backbone, revealed a dramatic increase in plasmid stability both in vitro and in vivo. Analysis of the resulting immune responses against antigens encoded by these vectors indicated that the increased stability resulted in a strong and reproducible induction of both antigen-specific CD4(+) and CD8(+) T-cell and antibody responses even after a single application. In addition, protective immunity was induced against Listeria monocytogenes using listeriolysin as antigen, regardless of the copy number of the delivery plasmid employed. Finally, Salmonella expressing two independent antigens on compatible low copy number plasmids elicited robust responses to either antigen that is as effective as Salmonella transformed with each plasmid singly adding further versatility to this delivery system.

Administration, Oral↗
PubMed2005

Common human Toll-like receptor 9 polymorphisms and haplotypes: association with atopy and functional relevance.

BACKGROUND: Toll-like receptor 9 (TLR9) is a pattern-recognition receptor that detects unmethylated CpG motifs prevalent in bacterial and viral DNA. TLR9 stimulation is a key event after bacterial infection, triggering innate immunity and T-helper type 1 skewed adaptive immunity. Synthetic CpG-oligodeoxynucleotides (CpG-ODNs) represent a promising and novel class of immune adjuvants for allergy treatment, vaccination, and cancer therapy. However, common functional TLR9 gene variants could interfere with the clinical utilization of CpG-ODN in immunotherapy. Recently, a possible association of TLR9 polymorphism C-1237T with asthma has been reported. OBJECTIVE: The aim of the present study was to investigate whether TLR9 polymorphisms or haplotypes have functional relevance and are associated with atopy. METHODS: We genotyped five common TLR9 single-nucleotide polymorphisms (SNPs) in promoter, exon, and intron regions of the gene in 527 healthy blood donors, and estimated four common haplotypes. The total IgE and specific IgE levels against the most common aeroallergens were measured (n=303). IFN-alpha production by plasmacytoid dendritic cells (pDCs) was analysed after stimulation with TLR9 ligand CpG-ODN (n=220). RESULTS: No significant influence of common TLR9 polymorphisms and haplotypes on the total and specific IgE levels was found. Functional analysis of CpG-ODN-induced IFN-alpha did not indicate a significant role for common TLR9 gene polymorphisms in TLR9 function. CONCLUSION: We conclude that common genetic differences in the TLR9 gene exert no major influence on allergy susceptibility, and are unlikely to have on impact on clinical application of CpG-ODNs.

Genetic Predisposition to Disease↗
PubMed2004

A protective merozoite protein of Plasmodium falciparum shares an epitope with surface antigens of Paramecium.

A Plasmodium falciparum cDNA expression clone, lambdaPf9, had been identified earlier as a protective epitope, using anti-lambdaPf9 antibodies and combinatorial phagotopes. A segment of the Pf9 gene showed homology with Paramecium immobilization surface antigens such as 51B, 51A and 156G. A synthetic Pf9-peptide was designed from this region, and specific antibodies were raised. Each of these anti-Pf9 antibodies and combinatorial reagents, as well as anti-Paramecium 51B antibodies, recognized the Pf9-peptide on ELISA, and the same protein band in parasite immunoblots. The P. falciparum protein was released from the merozoite membrane fraction on treatment with PI-PLC, indicating the presence of a GPI anchor. Anti-Pf9-peptide antibodies specifically inhibited the growth of P. falciparum in culture. Immunofluorescence assays showed the reactivity of anti-Pf9-peptide sera with P. falciparum merozoites and gametocytes, as well as on the surface of Paramecium tetraurelia. The Pf9-peptide was able to induce proliferation of splenic lymphocytes obtained from mice infected with the rodent malarial parasites Plasmodium berghei and Plasmodium yoelii. These results point towards Plasmodium Pf9 as a conserved novel protective protein, sharing an epitope with Paramecium surface antigens.

Amino Acid Sequence↗
PubMed2004

Aeromonas hydrophila beta-hemolysin induces active chloride secretion in colon epithelial cells (HT-29/B6).

The diarrheal mechanisms in Aeromonas enteritis are not completely understood. In this study we investigated the effect of aeromonads and of their secretory products on ion secretion and barrier function of monolayers of human intestinal cells (HT-29/B6). Ion secretion was determined as a short-circuit current (I(SC)) of HT-29/B6 monolayers mounted in Ussing-type chambers. Transepithelial resistance (R(t)) served as a measure of permeability. A diarrheal strain of Aeromonas hydrophila (strain Sb) added to the mucosal side of HT-29/B6 monolayers induced a significant I(SC) (39 +/- 3 microA/cm(2)) and decreased the R(t) to approximately 10% of the initial value. A qualitatively identical response was obtained with sterile supernatant of strain Sb, and Aeromonas supernatant also induced a significant I(SC) in totally stripped human colon. Tracer flux and ion replacement studies revealed the I(SC) to be mainly accounted for by electrogenic Cl(-) secretion. Supernatant applied serosally completely abolished basal I(SC). The supernatant-induced I(SC) was inhibited by the protein kinase C inhibitor chelerythrine, whereas a protein kinase A inhibitor (H8) and a Ca(2+) chelator (BAPTA-AM) had no effect. Physicochemical properties indicated that the supernatant's active compound was an aerolysin-related Aeromonas beta-hemolysin. Accordingly, identical I(SC) and R(t) responses were obtained with Escherichia coli lysates harboring the cloned beta-hemolysin gene from strain SB or the aerA gene encoding for aerolysin. Sequence comparison revealed a 64% homology between aerolysin and the beta-hemolysin cloned from Aeromonas sp. strain Sb. In conclusion, beta-hemolysin secreted by pathogenic aeromonads induces active Cl(-) secretion in the intestinal epithelium, possibly by channel insertion into the apical membrane and by activation of protein kinase C.

Aeromonas hydrophila↗
PubMed2003

Clonal identity of Candida albicans in the oral cavity and the gastrointestinal tract of pre-school children.

The clonal relationship between oral and fecal Candida albicans isolated from children of pre-school age was examined using RAPD analysis. Significantly higher levels of C. albicans were found in saliva, dental plaque, carious specimens and stools of 56 patients with severe caries as compared to 52 healthy control subjects. The highest prevalence was found in carious specimens and a strong correlation was observed between its presence in saliva, dental plaque, carious specimen and feces. RAPD analysis of isolates from 23 patients with simultaneous oral and fecal C. albicans revealed clonal counterparts present in both oral and stool samples in 15 cases; five patients harbored closely related strains; and three patients harbored unrelated strains. Our results demonstrate a strong correlation between oral and gastrointestinal C. albicans colonization. We assume that carious teeth may constitute an ecologic niche for C. albicans potentially responsible for recurrent oral and non-oral candidiasis.

Abscess↗
PubMed2003

Effect of vanadium on colonic aberrant crypt foci induced in rats by 1,2 dimethyl hydrazine.

AIM: To investigate the chemo preventive effects of vanadium on rat colorectal carcinogenesis induced by 1,2-dimethylhydrazine (DMH). METHODS: Male Sprague-Dawley Rats were randomly divided into four groups. Rats in Group A received saline vehicle alone for 16 weeks. Rats in Group B were given DMH injection once a week intraperitoneally for 16 weeks; rats in Group C, with the same DMH treatment as in the Group B, but received 0.5-ppm vanadium in the form ammonium monovanadate ad libitum in drinking water. Rats in the Group D received vanadium alone as in the Group C without DMH injection. RESULTS: Aberrant crypt foci (ACF) were formed in animals in DMH-treated groups at the end of week 16. Compared to DMH group, vanadium treated group had less ACF (P<0.001). At the end of week 32, all rats in DMH group developed large intestinal tumors. Rats treated with vanadium contained significantly few colonic adenomas and carcinomas (P<0.05) compared to rats administered DMH only. In addition, a significant reduction (P<0.05) in colon tumor burden (sum of tumor sizes per animal) was also evident in animals of Group C when compared to those in rats of carcinogen control Group B. The results also showed that vanadium significantly lowered PCNA index in ACF (P<0.005). Furthermore, vanadium supplementation also elevated liver GST and Cyt P-450 activities (P<0.001 and P<0.02, respectively). CONCLUSION: Vanadium in the form of ammonium monovanadate supplemented in drinking water ad libitum has been found to be highly effective in reducing tumor incidence and preneoplastic foci on DMH-induced colorectal carcinogenesis. These findings suggest that vanadium administration can suppress colon carcinogenesis in rats.

1,2-Dimethylhydrazine↗
PubMed2002

Vibrational spectra of CCl4: isotopic components and hot bands. Part I.

Room temperature (295 degrees K) infrared spectra of CCl4 have been measured covering the 4000-200 cm(-1) region. Bands ascribable to the isotopic components in the first overtone of the asymmetric deformation (2v4) mode and the combination of the symmetric and the asymmetric deformation (v2 + v4) mode regions are observed in agreement with the percentage distribution of various isotopes. From these observations, the first ever estimate of the isotopic band positions in the regions of the v4 and v2 modes at room temperature are obtained. Successful assignment of the isotopic bands in the asymmetric stretching (v3) and combination of the symmetric stretching and asymmetric deformation (v1 + v4) mode regions has been achieved and realistic values of all the v3/(v1 + v4) mode Fermi resonance parameters are obtained. The experimental results suggest that the transitions, where the initial levels are not the ground state, contribute significantly and give rise to a very complicated vibrational spectrum for CCl4 vapour.

Carbon Tetrachloride↗
PubMed2001

Comparative genomics of Listeria species.

Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also emerged as a paradigm for intracellular parasitism. We present and compare the genome sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua (3,011,209 base pairs). We found a large number of predicted genes encoding surface and secreted proteins, transporters, and transcriptional regulators, consistent with the ability of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149 L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that virulence in Listeria results from multiple gene acquisition and deletion events.

Adaptation, Physiological↗
PubMed2001

Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain.

Listeria monocytogenes is an opportunistic, food-borne human and animal pathogen. Host cell invasion requires the action of the internalins A (InlA) and B (InlB), which are members of a family of listerial cell-surface proteins. Common to these proteins are three distinctive N-terminal domains that have been shown to direct host cell-specific invasion for InlA and InlB. Here, we present the high-resolution crystal structures of these domains present in InlB and InlH, and show that they constitute a single "internalin domain". In this internalin domain, a central LRR region is flanked contiguously by a truncated EF-hand-like cap and an immunoglobulin (Ig)-like fold. The extended beta-sheet, resulting from the distinctive fusion of the LRR and the Ig-like folds, constitutes an adaptable concave interaction surface, which we propose is responsible for the specific recognition of the host cellular binding partners during infection.

Amino Acid Motifs↗
PubMed2001

Half-polarized quantum hall states.

We report a theoretical analysis of the half-polarized quantum Hall states observed in a recent experiment. Our numerical results indicate that the ground state energy of the quantum Hall nu = 2 / 3 and nu = 2 / 5 states versus spin polarization has a downward cusp at half the maximal spin polarization. We map the two-component fermion system onto a system of excitons and describe the ground state as a liquid state of excitons with nonzero values of exciton angular momentum.

Journal Article↗
PubMed2001

Transfer of eukaryotic expression plasmids to mammalian host cells by bacterial carriers.

The concept of transkingom transfer of DNA from bacteria to other organisms has recently been extended to include eukaryotic host cells. Intracellular bacteria have been shown to transfer eukaryotic expression plasmids to mammalian host cells in vitro and in vivo. This can be used to induce immune responses towards protein antigens encoded by the plasmid, to complement genetic defects or even to direct the production of proteins in appropriate organs. The ease of generating such vehicles makes this a highly attractive area for further research.

Animals↗