Search PubMed⌕ Search

Biomedical subjects

A Sarkar

Publications and source records attributed to A Sarkar.

At least 19 recordsLinked to original sources
PubMed2006

Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation.

The effects of binding on the phosphorylation-dephosphorylation cycle (PDPC) - one of the key components of the signal transduction processes - is analyzed based on a mathematical model. The model shows that binding of proteins, forming a complex, diminishes the ultrasensitivity of the PDPC to the differences in activity between kinase and phosphatase in the cycle. It is also found that signal amplification depends upon the strength of the binding affinity of the protein (phosphorylated or dephosphorylated) to other proteins . It is also observed that the amplification of signal is not only dependent on phosphorylation potential but also on binding properties and resulting adjustments in binding energies.

Animals↗
PubMed2006

Molecular Biomarkers: their significance and application in marine pollution monitoring.

This paper presents an overview of the significance of the use of molecular biomarkers as diagnostic and prognostic tools for marine pollution monitoring. In order to assess the impact of highly persistent pollutants such as polychlorinated biphenyls (PCB), polychlorinated dibenzo-dioxins (PCDD), polychlorinated dibenzo-furans (PCDF), polynuclear aromatic hydrocarbons (PAH), tributyltin (TBT) and other toxic metals on the marine ecosystem a suite of biomarkers are being extensively used worldwide. Among the various types of biomarkers, the following have received special attention: cytochrome P4501A induction, DNA integrity, acetylcholinesterase activity and metallothionein induction. These biomarkers are being used to evaluate exposure of various species of sentinel marine organisms (e.g. mussels, clams, oysters, snails, fishes, etc.) to and the effect of various contaminants (organic xenobiotics and metals) using different molecular approaches [biochemical assays, enzyme linked immuno-sorbent assays (ELISA), spectrophotometric, fluorometric measurement, differential pulsed polarography, liquid chromatography, atomic absorption spectrometry]. The induction of the biotransformation enzyme, cytochrome P4501A in fishes (Callionymus lyra, Limanda limanda, Serranus sp., Mullus barbatus) and mussels (Dreissena polymorpha) by various xenobiotic contaminants such as PCBs, PAHs, PCDs is used as a biomarker of exposure to such organic pollutants. The induction of cytochrome P4501A is involved in chemical carcinogenesis through catalysis of the covalent bonding of organic contaminants to a DNA strand leading to formation of DNA adduct. Measurement of the induction of cytochrome P4501A in terms of EROD (7-ethoxy resorufin O-deethylase) activity is successfully used as a potential biomarker of exposure to xenobiotic contaminants in marine pollution monitoring. In order to assess the impact of neurotoxic compounds on marine environment the evaluation of acetylcholinesterase activity in marine organisms is used as a biomarker of exposure to neurotoxic agents such as organophosphorus, carbamate pesticides etc. Metallothioneins (MTs) are induced by toxic metals such as Cd, Hg, and Cu by chelation through cysteine residues and are used in both vertebrates and invertebrates as a biomarker of metal exposure. The measurement of the levels of DNA integrity in marine organisms such as Sea stars (Asterias rubens) from the North Sea and the marine snails (Planaxis sulcatus) from the Arabian Sea along the Goa coast exposed to environmental xenobiotic contaminants clearly indicated the extent and the nature of pollution at the sampling sites along coastal environment.

Acetylcholinesterase↗
PubMed2006

Acetylcholinesterase activities in marine snail (Cronia contracta) as a biomarker of neurotoxic contaminants along the Goa coast, West coast of India.

The measurement of acetylcholinesterase (AChE) activity is used worldwide as a biomarker of environmental contamination due to neurotoxic substances. In the present study the AChE activities was measured in marine snails (Cronia contracta) collected seasonally from six sampling sites (viz. Arambol, Anjuna, Dona Paula, Vasco, Velsao and Palolem) along the Goa coast during the pre-monsoon (April, 2004), monsoon (September, 2004) and post-monsoon (November, 2004) periods. The AChE activities in C. contracta showed wide variation along the Goa coast. It was found to be quite high at the reference site, Palolem (23.97, 21.72 and 24.85) throughout the sampling period (April-November, 2004). The AChE activities in C. contracta decreased significantly at Vasco (44.6-52.4% reduction) followed by Dona Paula (24.9-36.2% reduction), Velasao (10.8-35.9% reduction), Arambol (12.6-37.3% reduction) and Anjuna (0-12.7% reduction). Such a significant variation of AChE activities in the marine snail along the Goa coast can be attributed to neurotoxic substances prevalent in those regions. The high concentration of different neurotoxic metals (lead, cadmium, copper, manganese and iron) and petroleum hydrocarbons in the tissues of the marine snails at Dona Paula, Vasco and Velsao clearly substantiate reduction of AChE activities in C. contracta. The in vitro studies on the inhibition of AChE by different metals and PHC indicated that lead, cadmium and copper are the most predominant inhibitor. Based on the AChE activities in C. contracta the sampling sites along the Goa coast can be classified into three major clusters such as highly contaminated sites (Dona Paula, Vasco and Velsao), moderately contaminated sites (Arambol, Anjuna) and least contaminated site (Palolem).

Acetylcholinesterase↗
PubMed2006

Bioremediation of toxic substances by mercury resistant marine bacteria.

Bioremediation of toxic substances includes microbe-mediated enzymatic transformation of toxicants to non-toxic, often assimilable, forms. Mercury-resistant marine bacteria are found to be very promising in dealing with mercury, and a host of other highly toxic heavy metals and xenobiotics. In the present studies we have shown that the Pseudomonas aeruginosa CH07 (NRRL B-30604) has been able to degrade a variety of PCB congeners including a complete degradation of CB-126 and CB-181. The culture was able to remove over 70% Cd from growth medium when supplemented with 100 ppm Cd. The same bacterium rapidly biotransformed/removed toxic mercury from wastewater in a bioreactor system.

Bacteria↗
PubMed2006

Inhibition of RelA phosphorylation sensitizes apoptosis in constitutive NF-kappaB-expressing and chemoresistant cells.

The compound 5-(4-methoxyarylimino)-2-N-(3,4-dichlorophenyl)-3-oxo-1,2,4-thiadiazolidine (P(3)-25) is known to possess anti-bacterial, anti-fungal, anti-tubercular, and local anesthetic activities. We studied the anti-tumorigenic activity of P(3)-25 and the role of nuclear transcription factor kappaB (NF-kappaB) in this process. In constitutive NF-kappaB-expressing cells, treatment with P(3)-25 inhibited the expression of NF-kappaB-dependent reporter gene, adhesion molecules, and cyclooxygenase. It downregulated phosphorylation of p65 by inhibiting upstream kinases, such as protein kinase A and casein kinase II, but did not alter NF-kappaB DNA-binding activity. Alone, P(3)-25 induced apoptosis in NF-kappaB-expressing and doxorubicin-resistant breast cancer cells, and in the presence of other chemotherapeutic agents, it potentiated apoptosis. Overall, our results suggest that P(3)-25 exerts antitumorigenic activity by inhibiting phosphorylation of p65, the transcriptionally active subunit of NF-kappaB by inhibiting its upstream kinases, and potentiates apoptosis mediated by chemotherapeutic agents. These results suggest novel approaches for designing of anticancer drugs for combination chemotherapy.

Antineoplastic Agents↗
PubMed2005

Influence of air-sea fluxes on chlorine isotopic composition of ocean water: implications for constancy in delta37Cl--a statistical inference.

The behaviors of chlorine isotopes in relation to air-sea flux variables have been investigated through multivariate statistical analyses (MSA). The MSA technique provides an approach to reduce the data set and was applied to a set of 7 air-sea flux variables to supplement and describe the variation in chlorine isotopic compositions (delta37Cl) of ocean water. The variation in delta37Cl values of surface ocean water from 51 stations in 4 major world oceans--the Pacific, Atlantic, Indian and the Southern Ocean has been observed from -0.76 to +0.74 per thousand (av. 0.039+/-0.04 per thousand). The observed delta37Cl values show basic homogeneity and indicate that the air-sea fluxes act differently in different oceanic regions and help to maintain the balance between delta37Cl values of the world oceans. The study showed that it is possible to model the behavior of chlorine isotopes to the extent of 38-73% for different geographical regions. The models offered here are purely statistical in nature; however, the relationships uncovered by these models extend our understanding of the constancy in delta37Cl of ocean water in relation to air-sea flux variables.

Air↗
PubMed2005

Ecotoxicological effect of grounded MV River Princess on the intertidal benthic organisms off Goa.

The ecotoxicological effects of oil spill from the grounded vessel MV River Princess on the intertidal benthic organisms of Sinquerim-Candolim beach at Goa were investigated. An intertidal expanse of 1 km on either side of the grounded vessel was selected to evaluate the concentration of total petroleum hydrocarbon (TPH) in the sediment and its effects on the composition, abundance and diversity of micro-, meio- and macrobenthos. TPH in the intertidal sediment ranged from 7.8 to 89 microg g(-1) (mean 35.44+/-26.35 SD). Microbenthos comprised of microalgae, protozoans and juvenile forms of meiobenthos. Apart from juvenile nematodes, which were abundant, Coscinodiscus spp., Navicula spp., and Nitzschia spp. representing microalgae were also observed in microbenthic samples. Meiobenthos was represented by 13 taxa and their total density ranged between 92 and 1057 nos. 10 cm(-2). Maximum meiobenthic abundance of 1057 nos. 10 cm(-2) was observed at Sinquerim. Nematodes were the dominant meiobenthic taxa followed by turbellarians and harpacticoid copepods. The macrobenthos was numerically dominated by polychaetes, followed by crustaceans whereas bivalve molluscs were less represented. There was substantial increase in the petroleum concentration in the beach sediment compared to the previously reported values and highest TPH (89 microg g(-1) sediment) values were in the vicinity of the grounded vessel. The polychaete/amphipod ratio and cumulative and partial dominance abundance-biomass curves showed significant negative impact of TPH on macrofauna. The benthic community structure also showed measurable changes, as there was significant decrease (60%) in the number of species. Given that the microalgal counts were low in sediment, it is assumed that the intertidal meiofauna was possibly using oil-degrading bacteria as alternate food source. In conclusion, the results reported here suggest that the grounded ore carrier is not only detrimental to the beach community, that may take longer time for recovery, but also affects the beach morphology which may have long-term impact on local fishery.

Accidents↗
PubMed2005

Preparation and characterization of ultrafine co and ni particles in a polymer matrix.

A facile route for in situ synthesis of Co and Ni nanoparticles in a preorganized polyacrylamide gel is reported. Metal-polymer composites were prepared by gamma-irradiation at room temperature. The Co nanoparticles were roughly 3-5 nm in size and were stable in the polymer matrix in the presence of air. The presence of Co and Ni nanoparticles was established by their ability to transfer an electron to methyl viologen {paraquat: 1,1'-dimethyl 4,4'-dipyridinium dichloride; MV(2+) (Cl(-))(2)}. The Co and Ni nanoparticles were probed for their magnetic characteristics by a superconducting quantum interferometer device (SQUID) magnetometer and display a low superparamagnetic blocking temperature T(B) of about 13 and 10 K, respectively. The field-dependent magnetic behavior below T(B) displays the standard features corresponding to superparamagnetism, as expected for very small Co and Ni crystallites. This also suggests that particles are polycrystalline in nature.

Journal Article↗
PubMed2005

Scaling behavior of the Portevin-Le Chatelier effect in an Al-2.5%Mg alloy.

The scaling behavior of the Portevin-Le Chatelier (PLC) effect was studied by deforming an Al-2.5%Mg alloy for a wide range of strain rates. To reveal the exact scaling nature, the time series data of true stress versus time, obtained during deformation, were analyzed by two complementary methods: the finite variance scaling method and the diffusion entropy analysis. From these analyses we could establish that, in the entire span of strain rates, the PLC effect showed the Levy-walk property.

Journal Article↗
PubMed2005

Eruption disturbances: an aetiological-cum-management perspective.

Failure of permanent teeth to erupt without any known cause is a rare incident. We report a case of multiple unerupted permanent teeth and make an effort to predict all possible causes of non-eruption of permanent teeth clinically and radiographically. It is essential to diagnose and treat eruption disturbances as early as possible because treatment at a later stage is usually more complicated due to the tendency of malocclusion to increase with time and reduced ability of remaining dentition to adjust.

Adult↗
PubMed2004

A logical analysis of the process of T cell activation: different consequences depending on the state of CD28 engagement.

The adaptive immune system is a complex organized action of several immune cell types like, T cells, B cells, dendritic cells, mast cells, and their ability to recognize self and foreign molecular information. Based on logical analysis, a model has been developed that describes TCR-ligand association coupled to intracellular signaling events that result in a proliferation signal. The model demonstrates that after TCR-ligand binding, the activation of tyrosine kinases in one of the paths leads to oscillations between the subsequent states of activation and deactivation of Ca(2+) initiation. In our studies the effect of costimulation on the primary signal has also been explored. Analysis reveals that costimulation increases by more than 2.5 fold the number of paths rendering a cell proliferation signal compared to the outcome when costimulation is blocked. Traversal of 97% of these paths attains a costimulation threshold of activation. We also examined a hypothesis that couples the primary signal and costimulation by modeling costimulation to act as an inhibitor on the Inhibitor proteins. Using this hypothesis our analysis showed a 25% increase in the number of paths leading to cell proliferation in comparison to when costimulation is blocked. Our model also reveals that this hypothesis actually decrease by approximately 50% the number of paths attaining cell proliferation compared to the number of available paths leading to cell proliferation when costimulation does not act as an inhibitor on Inhibitor proteins. This suggests that costimulation influences cell proliferation by providing a greater diversity of paths that converge to this state. However, costimulation should be thought independent of its regulatory interaction with the inhibitor proteins.

CD28 Antigens↗
PubMed2003

Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences.

piggyBac is a short inverted-repeat-type DNA transposable element originally isolated from the genome of the moth Trichoplusia ni. It is currently the gene vector of choice for the transformation of various insect species. A few sequences with similarity to piggyBac have previously been identified from organisms such as humans ( Looper), the pufferfish Takifugu rubripes ( Pigibaku), Xenopus ( Tx), Daphnia ( Pokey), and the Oriental fruit fly Bactrocera dorsalis. We have now identified 50 piggyBac-like sequences from publicly available genome sequences and expressed sequence tags (ESTs). This survey allows the first comparative examination of the distinctive piggyBac transposase, suggesting that it might contain a highly divergent DDD domain, comparable to the widespread DDE domain found in many DNA transposases and retroviral integrases which consists of two absolutely conserved aspartic acids separated by about 70 amino acids with a highly conserved glutamic acid about 35 amino acids further away. Many piggyBac-like sequences were found in the genomes of a phylogenetically diverse range of organisms including fungi, plants, insects, crustaceans, urochordates, amphibians, fishes and mammals. Also, several instances of "domestication" of the piggyBac transposase sequence by the host genome for cellular functions were identified. Novel members of the piggyBac family may be useful in genetic engineering of many organisms.

Animals↗
PubMed2003

Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae.

A Bacterial Artificial Chromosome (BAC) genomic DNA library of Anopheles gambiae, the major human malaria vector in sub-Saharan Africa, was constructed and characterized. This library (ND-TAM) is composed of 30,720 BAC clones in eighty 384-well plates. The estimated average insert size of the library is 133 kb, with an overall genome coverage of approximately 14-fold. The ends of approximately two-thirds of the clones in the library were sequenced, yielding 32,340 pair-mate ends. A statistical analysis (G-test) of the results of PCR screening of the library indicated a random distribution of BACs in the genome, although one gap encompassing the white locus on the X-chromosome was identified. Furthermore, combined with another previously constructed BAC library (ND-1), ~2,000 BACs have been physically mapped by polytene chromosomal in situ hybridization. These BAC end pair mates and physically mapped BACs have been useful for both the assembly of a fully sequenced A. gambiae genome and for linking the assembled sequence to the three polytene chromosomes. This ND-TAM library is now publicly available at both http://www.malaria.mr4.org/mr4pages/index.html/ and http://hbz.tamu.edu/, providing a valuable resource to the mosquito research community.

Animals↗
PubMed2003

P elements are found in the genomes of nematoceran insects of the genus Anopheles.

We report the identification of genomic sequences in various anopheline mosquitoes (family Culicidae: suborder Nematocera: order Diptera) showing homology to the class II, short inverted-terminal-repeat (ITR) transposable element P from Drosophila melanogaster (family Drosophilidae; suborder Brachycera: order Diptera). Anopheles gambiae appears to have at least six distinct P elements. Other anopheline species, including four additional members of the An. gambiae species complex (An. arabiensis, An. merus, An. melas and An. quadriannulatus), Anopheles stephensi (all subgenus Cellia), An. quadrimaculatus (subgenus Anopheles) and Anopheles albimanus (subgenus Nyssorhynchus) also possess P elements similar to those found in An. gambiae. Ten distinct P element types were identified in the genus Anopheles. At least two of the An. gambiae elements appears to be intact and potentially functional. Phylogenetic analysis of the anopheline P elements reveals them to belong to a distinctly different clade from the brachyceran P elements.

Amino Acid Sequence↗
PubMed2003

Force-extension behavior of folding polymers.

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy epsilon associated with maintaining the folded state is comparable to k(B) T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA.

Journal Article↗
PubMed2002

Tropic failure of Phyllactinia corylea contributes to the mildew resistance of mulberry genotypes.

Different mulberry genotypes show great variation in their resistance to the powdery mildew Phyllactinia corylea. Conidial germination and hyphal growth of P. corylea on the leaf surface of two susceptible mulberry genotypes, viz., Kanva 2 (K2) and Victory 1 (V1) varieties of Morus indica, and on two resistant species, viz,, M. laevigata and M. serrata were studied by scanning electron microscopy. Conidial germination and growth of germ tubes were normal on all the leaves. The hyphae of P. corylea identify stomata on host leaves by their topographical features to produce the stomatopodia precisely over them. The holes and/or the grooves of stomata appear to provide the signals for the initiation of stomatopodia and similar structures are erratically developed over many local depressions or grooves on leaf surface. The abaxial surface of K2 leaf is smooth without prominent undulations of epidermal cell surface, and the stomata are flush with the leaf surface. Although successful penetration is also achieved on V1 leaf, its slightly undulated surface occasionally provides inaccurate tropic signals to the hyphae, inducing the development of stomatopodia away from the stomata. The leaf surfaces of M. laevigata and M. serrata are very rough with highly sculptured cuticle and abundant epidermal outgrowths. Stomata mostly remain sunken or hidden amidst the cuticular ornamentations and the hyphae fail to recognise the precise signals from them. As the surface architecture of the leaves provides many immense sources of tropic signals, stomatopodia are often produced over local depressions or grooves. In these cases the fungus fails to penetrate the leaf, does not develop beyond 24 h and penetration is rarely achieved on the leaves of the resistant plants. The study indicates that the stimulatory effect of the leaf surface topography of resistant varieties misleads the pathogen from successful penetration, thus contributing to the plant's resistance.

Ascomycota↗
PubMed2002

Breast-feeding counselling and its effect on the prevalence of exclusive breast-feeding.

This prospective intervention study was undertaken to assess the impact of repeated breast-feeding counselling on the rate of exclusive breast-feeding up to five months. The study was carried out in two breast-feeding counselling sub-centres, established at the community level in the vicinity of two maternity facilities and one main centre established in an urban children hospital. Eighty-four pregnant mothers who attended the maternity facilities for delivery of babies were randomly selected and repeatedly counselled regarding breast-feeding--once just before delivery and subsequently at the completion of 1, 2, 3, 4, 5, 6, 9, and 12 month(s) of age of the child. These child-mother pairs comprised the intervention group. Another group of 90 child-mother pairs was selected from the maternity facilities. Mothers in this group (comparison group) received a single session of breast-feeding counselling just before delivery of babies. Fifty-nine and 55 child-mother pairs in the intervention and the comparison groups respectively completed the one-year follow-up. In the intervention group, 54.2% and in the comparison group 36.4% of the babies were exclusively breastfed up to five months of age. Forty-two (88%) children in the intervention group and 29 (53%) in the comparison group were given complementary foods at the optimum time, e.g. after completion of five months, and 81% of the children in the intervention group and 100% of the children in the comparison group were given complementary foods in the first year of life. It was observed that repeated organized breast-feeding counselling significantly improved the prevalence of exclusive breast-feeding to 54% which is much above the existing national prevalence (12.7%) in Bangladesh.

Adult↗