Biomedical subjects

J Das

Publications and source records attributed to J Das.

At least 37 records · Page 2Linked to original sources

PubMed1999

Kinetic asymmetry as a key source of functional diversity in biochemical networks.

From the analysis of the dynamic properties of various symmetric and asymmetric kinetic schemes, the present report demonstrates that all kinetic schemes, which can be hypothetically divided into two equal halves about an axis of mirror symmetry, are endowed with structural metastability under mass-closed conditions. In mass-closed symmetric schemes, absolute symmetry in reaction conditions in two halves is essential for the occurrence of ordered dynamic behaviour. Even an infinitesimal deviation from the symmetry relations instantaneously drives such systems from limit-cycles to turbulence. Reaction schemes with no axes of symmetry may exhibit a large variety of complex, structurally stable temporal order for wide ranges of values of system parameters and variables. Kinetic asymmetry, therefore, may confer to biochemical networks the functional diversity as well as stability against environmental perturbations.

Journal Article↗

PubMed1999

Hepatoprotective activity of Ficus racemosa leaf extract on liver damage caused by carbon tetrachloride in rats.

An extract of the leaves of Ficus racemosa Linn. (Moraceae) was evaluated for hepatoprotective activity in rats by inducing chronic liver damage by subcutaneous injection of 50% v/v carbon tetrachloride in liquid paraffin at a dose of 3 mL/kg on alternate days for a period of 4 weeks. The biochemical parameters SGOT, SGPT, serum bilirubin and alkaline phosphatase were estimated to assess the liver function. The activity of extract was also comparable to a standard liver tonic (Neutrosec).

Alanine Transaminase↗

PubMed1999

Resurgent Vibrio cholerae O139: rearrangement of cholera toxin genetic elements and amplification of rrn operon.

The unprecedented genesis of a novel non-O1 Vibrio cholerae strain belonging to serogroup O139, which caused an epidemic in late 1992 in the Indian subcontinent, and its subsequent displacement by El Tor O1 vibrios after 18 months initiated a renewed investigation of the aspects of the organism that are related to pathogenesis. The reappearance of V. cholerae O139 with altered antibiotic sensitivity compared to O139 Bengal (O139B) in late 1996 has complicated the epidemiological scenario of V. cholerae and has necessitated an examination of possible rearrangements in the genome underlying such rapid changes in the phenotypic traits. With a view to investigating whether the phenotypic changes that have occurred are associated with alteration in the genome, the genome of the resurgent V. cholerae O139 (O139R) strains were examined. Pulsed-field gel electrophoresis analysis of NotI- and SfiI-digested genomic DNA of O139R isolates showed restriction fragment length polymorphism including in the cholera toxin (CTX) genetic element locus and with O139B isolates. Analyses of the organization of the CTX genetic elements in O139R strains showed that in contrast to two copies of the elements connected by two direct-repeat sequences (RS) in most of the genomes of O139B isolates, the genomes of all O139R strains examined, except strain AS192, have three such elements connected by a single RS. While the RS present in the upstream of the CTX genetic elements in the genome of O139R is of O139B origin, the RS connecting the cores of the elements has several new restriction sites and has lost the BglII site which is supposed to be conserved in all O1 strains and O139B. The endonuclease I-CeuI, which has sites only in the rrn operons in the genomes of all organisms examined so far, has 10 sites in the genomes of O139R strains, compared to 9 in the genomes of O139B strains. The recent isolates of V. cholerae O139 have thus gained one rrn operon. This variation in the number of rrn operons within a serogroup has not been reported for any other organism. The results presented in this report suggest that like the pathogenic El Tor O1 strains, the genomes of O139 strains are undergoing rapid alterations.

Cholera Toxin↗

PubMed1999

The mutK gene of Vibrio cholerae: a new gene involved in DNA mismatch repair.

A new gene, mutK, of Vibrio cholerae, encoding a 19-kDa protein which is involved in repairing mismatches in DNA via a presumably methyl-independent pathway, has been identified. The product of the mutK gene cloned in either high- or low-copy-number vectors can reduce the spontaneous mutation frequency of Escherichia coli mutS, mutL, mutU, and dam mutants. The spontaneous mutation frequency of a chromosomal mutK knockout mutant was almost identical to that of wild-type V. cholerae cells, indicating that when the methyl-directed mismatch repair is blocked, the repair potential of MutK becomes apparent. The complete nucleotide sequence of the mutK gene has been determined, and the deduced amino acid sequence showed three open reading frames (ORFs), of which the ORF3 represents the mutK gene product. The mutK gene product has no significant homology with any of the proteins deposited in the EMBL data bank. ORF2, located upstream of mutK, encodes a 14-kDa protein which has more than 70% homology with a hypothetical protein found only downstream of the E. coli vsr gene. ORF1, located farther upstream of mutK, has more than 80% homology with a major cold shock protein found in several bacteria. Downstream of mutK, a partial ORF having 60% homology with an RNA methyltransferase has been identified. The mutK gene has recently been positioned in the ordered cloned DNA map of the genome of the V. cholerae strain from which the gene was isolated (10).

Amino Acid Sequence↗

PubMed1999

Studies on pyrylretinal analogues of bacteriorhodopsin.

The retinal analogues 3-methyl-5-(1-pyryl)-2E,4E-pentadienal (1) and 3,7-dimethyl-9-(1-pyryl)-2E,4E,6E,8E-nonatetr aenal (2), which contain the tetra aromatic pyryl system, have been synthesized and characterized in order to examine the effect of the extended ring system on the binding capabilities and the function of bacteriorhodopsin (bR). The two bR mutants, E194Q and E204Q, known to have distinct proton-pumping patterns, were also examined so that the effect of the bulky ring system on the proton-pumping mechanism could be studied. Both retinals formed pigments with all three bacterioopsins, and these pigments were found to have absorption maxima in the range 498-516 nm. All the analogue pigments showed activity as proton pumps. The pigment formed from wild-type apoprotein bR with 1 (with the shortened polyene side chain) showed an M intermediate at 400 nm and exhibited fast proton release followed by proton uptake. Extending the polyene side chain to the length identical with retinal, analogue 2 with wild-type apoprotein gave a pigment that shows M and O intermediates at 435 nm and 650 nm, respectively. This pigment shows both fast and slow proton release at pH 7, suggesting that the pKa of the proton release group (in the M-state) is higher in this pigment compared to native bR. Hydrogen azide ions were found to accelerate the rise and decay of the O intermediate at neutral pH in pyryl 2 pigment. The pigments formed between 2 and E194Q and E204Q showed proton-pumping behavior similar to pigments formed with the native retinal, suggesting that the size of the chromophore ring does not alter the protein conformation at these sites.

Bacteriorhodopsins↗

PubMed1998

Adsorption of Phosphate from Aqueous Solution Using Activated Red Mud.

Adsorption of phosphate (PO3-4) from aqueous solution on activated red mud (ARM) was studied as a function of time, pH, temperature, concentration of adsorbent and adsorbate in acetic acid-sodium acetate buffer medium. The adsorption of phosphate follows Langmuir as well as Freundlich adsorption isotherms. The process efficiency was found to be 80-90% at room temperature. This can be extended to the treatment of industrial effluents containing phosphates like that from phosphatic fertilizer plants. Copyright 1998 Academic Press.

Journal Article↗

PubMed1998

Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias.

Biases in the codon usage and base compositions at three codon sites in different genes of A+T-rich Gram-negative bacterium Haemophillus influenzae and G+C-rich Gram-positive bacterium Mycobacterium tuberculosis have been examined to address the following questions: (1) whether the synonymous codon usage in organisms having highly skewed base compositions is totally dictated by the mutational bias as reported previously (Sharp, P.M., Devine, K.M., 1989. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17, 5029-5039), or is also controlled by translational selection; (2) whether preference of G in the first codon positions by highly expressed genes, as reported in Escherichia coli (Gutierrez, G., Marquez, L., Marin, A., 1996. Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucleic Acids Res. 24, 2525-2527), is true in other bacteria; and (3) whether the usage of bases in three codon positions is species-specific. Result presented here show that even in organisms with high mutational bias, translational selection plays an important role in dictating the synonymous codon usage, though the set of optimal codons is chosen in accordance with the mutational pressure. The frequencies of G-starting codons are positively correlated to the level of expression of genes, as estimated by their Codon Adaptation Index (CAI) values, in M. tuberculosis as well as in H. influenzae in spite of having an A+T-rich genome. The present study on the codon preferences of two organisms with oppositely skewed base compositions thus suggests that the preference of G-starting codons by highly expressed genes might be a general feature of bacteria, irrespective of their overall G+C contents. The ranges of variations in the frequencies of individual bases at the first and second codon positions of genes of both H. influenzae and M. tuberculosis are similar to those of E. coli, implying that though the composition of all three codon positions is governed by a selection-mutation balance, the mutational pressure has little influence in the choice of bases at the first two codon positions, even in organisms with highly biased base compositions.

Animals↗

PubMed1998

Liposome encapsulated vitamin A compounds exhibit greater stability and diminished toxicity.

Absorption and fluorescence studies of retinol (vitamin A alcohol) and retinol palmitate (vitamin A palmitate) intercalated in phosphatidylcholine (PC) liposomes show that these compounds are bound to the lipid bilayer. It is further found that retinol binds liposomes with greater affinity as compared to retinol palmitate. In addition, the delivery of liposome-incorporated retinoids to the blood has also been studied and it is found that these systems reduce blood viscosity and cause less lysis of red blood cells than retinoid compounds not complexed in liposomes.

Anticarcinogenic Agents↗

PubMed1998

Vibrio cholerae O139 Bengal: combined physical and genetic map and comparative analysis with the genome of V. cholerae O1.

A combined physical and genetic map of the genome of strain SG24 of Vibrio cholerae O139 Bengal, a novel non-O1 strain having epidemic potential, has been constructed by using the enzymes NotI, SfiI, and CeuI. The genome of SG24 is circular, and the genome size is about 3. 57 Mb. The linkages between 47 NotI and 32 SfiI fragments of V. cholerae SG24 genomic DNA were determined by combining two approaches: (i) identification of fragments produced by enzyme I in fragments produced by enzyme II by the method of fragment excision, redigestion, and end labeling and (ii) use of the linking clone libraries generated from the genome of classical O1 strain 569B. The linkages between nine CeuI fragments were determined primarily by analyses of partial fragments of the CeuI-digested genome. More than 80 cloned homologous and heterologous genes, including several operons, have been positioned on the physical map. The map of the SG24 genome represents the second map of a V. cholerae genome, and a comparison of this map with that of classical O1 strain 569B revealed considerable diversity in DNA restriction sites and allowed identification of hypervariable regions. Several genetic markers, including virulence determinant genes, are in different positions in the SG24 and 569B genomes.

Chromosome Mapping↗

PubMed1998

Ordered cloned DNA map of the genome of Vibrio cholerae 569B and localization of genetic markers.

By using a low-resolution macrorestriction map as the foundation (R. Majumder et al., J. Bacteriol. 176:1105-1112, 1996), an ordered cloned DNA map of the 3.2-Mb chromosome of the hypertoxinogenic strain 569B of Vibrio cholerae has been constructed. A cosmid library the size of about 4,000 clones containing more than 120 Mb of V. cholerae genomic DNA (40-genome equivalent) was generated. By combining landmark analysis and chromosome walking, the cosmid clones were assembled into 13 contigs covering about 90% of the V. cholerae genome. A total of 92 cosmid clones were assigned to the genome and to regions defined by NotI, SfiI, and CeuI macrorestriction maps. Twenty-seven cloned genes, 9 rrn operons, and 10 copies of a repetitive DNA sequence (IS1004) have been positioned on the ordered cloned DNA map.

Cholera Toxin↗

PubMed1997

Complex dynamics of mass-closed coupled autocatalytic systems in response to minute asymmetric perturbations.

The role of kinetic coupling in catering to a remote-control mechanism for the onset and regulation of self-organization phenomena in a multicompartmental biochemical system has been examined. Using two cyclic autocatalytic reaction networks operating in two chambers separated by a membrane and coupled through a common cofactor, it has been demonstrated that (i) in response to asymmetric perturbations, the coupled reaction networks exhibit a variety of temporal self-organization phenomena such as bistability, multiple periodicity, hard excitation and coexistence of aperiodic oscillation with limit cycle even in mass-closed conditions; (ii) without disturbing a network directly, its dynamic behaviour can be regulated by perturbing some other network kinetically coupled to it and (iii) the dynamics of two coupled networks can be made to flip-flop between oscillatory and steady-states simply by modulating the time of application of external perturbations. The extreme sensitivity of this model to minute asymmetric fluctuations in the environment can predict how the impact of local changes in physico-chemical conditions can be transmitted from one compartment to another through coupled biochemical pathways in a living cell.

Journal Article↗

PubMed1997

The secY gene of V. cholerae: identification, cloning and characterization.

The secY gene of Vibrio cholerae has been cloned and the complete nt sequence determined. It codes for a protein of 438 aa residues which functions as a translocator through which proteins cross the inner membrane. It can substitute for the Escherichia coli SecY protein and can suppress the phenotypic traits associated with E. coli secY mutants. The V. cholerae secY gene has about 71 and 83% similarity at the nt and aa levels respectively with the E. coli secY gene. Vibrio cholerae secY, similarly to the E. coli secY, is flanked by the genes encoding the ribosomal large subunit proteins L15 and L36. When expressed from the lac promoter, V. cholerae secY partially complements E. coli secY mutation even in absence of IPTG, while the E. coli secY gene complements only when IPTG is present. Presence of multiple SD sequences and a putative downstream (DS) box imply that the V. cholerae secY gene might have high translational efficiency. A V. cholerae mutant unable to translocate CTB through the inner membrane has been isolated. The secretion deficient phenotype of the mutant can be reversed by introducing the cloned V. cholerae secY gene.

Amino Acid Sequence↗

PubMed1997

The rpoH gene encoding sigma 32 homolog of Vibrio cholerae.

The Vibrio cholerae rpoH gene coding for the heat-shock sigma factor, sigma 32, has been cloned and shown to functionally complement Escherichia coli rpoH mutants. The nt sequence of the gene has been determined and the deduced aa sequence is more than 80% homologous to the E. coli rpoH gene product. Downstream of the V. cholerae rpoH gene, an unidentified dehydrogenase gene (udhA) is present on the opposite strand facing rpoH. The predicted secondary structure of the 5'-proximal region of V. cholerae rpoH mRNA is apparently different from the conserved secondary structures of the rpoH mRNA reported for several bacterial species. The 'RpoH box', a stretch of 9 aa (QRKLFFNLR) unique to sigma 32 factors, and the 'downstream box' sequence complementary to a part of the 16S rRNA, have been detected.

Amino Acid Sequence↗

PubMed1997

Wound healing activity of Leucas lavandulaefolia Rees.

Leucas lavandulaefolia Rees (Labiatae), commonly known as Halkusha, is a well-known plant in Indian traditional medicine. On the basis of its traditional use and literature references, this plant was selected for evaluation of its wound healing potential. A methanol extract of L. lavandulaefolia was examined for its wound healing activity both in the form of an ointment as well as an injection in two types of wound model in rats: (i) the excision wound model and (ii) the incision wound model. Both the injection and the ointment of the methanol extract of the plant material produced a significant response in both of the wound types tested. The results were also comparable to those of a standard drug, nitrofurazone, in terms of wound contracting ability, wound closure time, tensile strength and regeneration of tissues at the wound site.

Animals↗

PubMed1997

Chaos game representation of proteins.

The present report proposes a new method for the chaos game representation (CGR) of different families of proteins. Using concatenated amino acid sequences of proteins belonging to a particular family and a 12-sided regular polygon, each vertex of which represents a group of amino acid residues leading to conservative substitutions, the method can generate the CGR of the family and allows pictorial representation of the pattern characterizing the family. An estimation of the percentages of points plotted in different segments of the CGR (grid points) allows quantification of the nonrandomness of the CGR patterns generated. The CGRs of different protein families exhibited distinct visually identifiable patterns. This implies that different functional classes of proteins follow specific statistical biases in the distribution of different mono-, di-, tri-, or higher order peptides along their primary sequences. The potential of grid counts as the discriminative and diagnostic signature of a family of proteins is discussed.

Algorithms↗

PubMed1997

Studies on the anti-inflammatory activity of rhizomes of Nelumbo nucifera.

The anti-inflammatory activity of the methanol extract of Nelumbo nucifera rhizome as well as of betulinic acid, a steroidal triterpenoid isolated from it, were evaluated on carrageenin and serotonin induced rat paw edema. Methanol extract at doses of 200 and 400 mg/kg and betulinic acid at doses of 50 mg/kg and 100 mg/kg p.o., showed significant anti-inflammatory activity in both the models of inflammation in rats. The effects produced were comparable to that of phenylbutazone and dexamethasone, two prototype anti-inflammatory drugs.

Animals↗

PubMed1997

Rearrangements in the genomes of Vibrio cholerae strains belonging to different serovars and biovars.

The intron-encoded enzyme I-CeuI provides an excellent tool for rapidly examining the organization of genomes of related species of bacteria. Vibrio cholerae strains belonging to serovars O1 and O139 have 9 I-ceuI sites in their genomes, and V. cholerae strains belonging to serovars non-O1 and non-O139 have 10 I-ceuI sites in their genomes. This information can be used as a criterion to differentiate O1 strains from non-O1 and non-O139 strains. To our knowledge, intraspecies variation in the number of rrn operons has not been reported in any other organism. Our data revealed extensive restriction fragment length polymorphism based on a comparison of the I-ceuI digestion profiles of strains belonging to different serovars and biovars. From the analysis of partial digestion products, I-CeuI macrorestriction maps of several classical, El Tor, and O139 strains were constructed. While the linkage maps are conserved within biovars, linkage maps vary substantially between biovars.

Cholera↗

PubMed1997

Biofilm susceptibility to antimicrobials.

Microbial biofilms, where organisms are intimately associated with each other and a solid substratum through binding and inclusion within an exopolymer matrix, are widely distributed in nature and disease. In the mouth, multispecies biofilms are associated not only with dental plaque and tooth decay but also with soft tissues of the buccal cavity and with most forms of periodontal disease. Organization of micro-organisms within biofilms confers, on the component species, properties which are not evident with the individual species grown independently or as planktonic populations in liquid media. While many of these properties relate to the establishment of functional, mixed-species consortia within the exopolymeric matrices, others relate to the establishment of physico-chemical gradients, within the biofilm, that modify the metabolism of the component cells. A consequence of biofilm growth that has profound implications for their control in the environment and in medicine is a markedly enhanced resistance to chemical antimicrobial agents and antibiotics. Mechanisms associated with such resistance in biofilms will form the substance of the present review. While some aspects of biofilm resistance are yet only poorly understood, the dominant mechanisms are thought to be related to: (i) modified nutrient environments and suppression of growth rate within the biofilm; (ii) direct interactions between the exopolymer matrices, and their constituents, and antimicrobials, affecting diffusion and availability; and (iii) the development of biofilm/attachment-specific phenotypes.

Anti-Bacterial Agents↗