Biomedical subjects

Dibyendu Sarkar

Publications and source records attributed to Dibyendu Sarkar.

16 recordsLinked to original sources

PubMed2006

Arsenic biogeochemistry and human health risk assessment in organo-arsenical pesticide-applied acidic and alkaline soils: an incubation study.

Organo-arsenical compounds are considered non-carcinogenic, and hence, are still allowed by the regulatory agencies for use in agriculture as pesticides. Due to rapid encroachment of suburban areas into former agricultural lands, the potential for human exposure to soil-arsenic has increased tremendously in recent years. However, insufficient data is available on the stability of organo-arsenicals in soils; as to whether they remain in an organic form, or are converted over time to potentially carcinogenic inorganic forms. A static incubation study was conducted to estimate soil speciation and in-vitro bioavailability (i.e., bioaccessibility) of arsenic as a function of soil properties. Two chemically variant soil types were chosen, based on their potential differences with respect to arsenic reactivity: an acid sand with minimal arsenic retention capacity and an alkaline clay loam with relatively high concentrations of Fe/Al and Ca/Mg. The soils were amended with dimethylarsenic acid (DMA) at three rates, 45, 225 and 450 mg/kg, and incubated for 1 year. A sequential extraction scheme was employed to identify the geochemical forms of arsenic in soils, which were correlated with the in-vitro bioavailable fractions of arsenic. Human health risk calculated in terms of excess cancer risk (ECR) showed that risk assessment based on bioaccessible arsenic concentrations instead of the traditional total soil arsenic is a more realistic approach. Results showed that soil properties (such as pH, Fe/Al content and soil texture) of the two soils dictated the geochemical speciation, and hence, bioaccessibility of arsenic from DMA, indicating that the use of organic arsenicals as pesticides in mineral soils may not be a safe practice from a human health risk perspective.

Arsenic↗

PubMed2006

Transcriptional autoregulation by Mycobacterium tuberculosis PhoP involves recognition of novel direct repeat sequences in the regulatory region of the promoter.

The PhoP-PhoR two-component system is essential for virulence and intracellular growth of Mycobacterium tuberculosis (MTB) in human and mouse macrophages or in mice. Here, PhoP and truncated PhoR sensor proteins were shown to participate in phosphotransfer reactions using conserved residues characteristic of two-component signaling systems. beta-Galactosidase activity originating from phoP promoter-lacZ construct was inhibited in presence of PhoP, suggesting transcriptional auto-inhibition by the response regulator. In vitro binding of PhoP is consistent with the in vivo transcriptional repression, indicating phosphorylation-independent assembly of the transcription initiation complex at elevated concentrations of PhoP. DNaseI protection studies reveal a consensus recognition sequence within the phoP promoter that includes three 9-bp direct repeat units. Each repeat unit adjusts to the consensus (1)AC(T)/(G)(T)/(G)(T)/(G)P(y)AP(u)C(9). Alteration in the sequence of the newly-identified direct repeat units relieved phoP transcriptional repression in presence of PhoP, suggesting that PhoP represses its own expression by sequence-specific interaction(s) with the repeat units. Together, these results identify so far unknown PhoP-regulated genetic determinants in the regulatory region of the phoP promoter that are central to understanding of how PhoP may possibly function as a global regulator in MTB.

Animals↗

PubMed2006

Arsenic immobilization in soils amended with drinking-water treatment residuals.

Use of Fe/Al hydroxide-containing materials to remediate As-contaminated sites is based on the general notion that As adsorption in soils is primarily controlled by Fe/Al (hydr)oxides. A low-cost and potentially effective substitute for natural Fe/Al hydroxides could be the drinking-water treatment residuals (WTRs). Earlier work in our laboratory has shown that WTRs are effective sorbents for As in water. We hypothesized that land-applied WTRs would work equally well for As-contaminated soils. Results showed that WTRs significantly (p<0.001) increased the soil As sorption capacity. All WTR loads (2.5, 5, and 10%) significantly (p<0.001) increased the overall amount of As sorbed by both soils when compared with that of the unamended controls. The amount of As desorbed with phosphate (7500 mg kg(-1) load) was approximately 50%. The WTR effectiveness in increasing soil As sorption capacities was unaffected by differences in both soils' chemical properties.

Adsorption↗

PubMed2006

High uptake of 2,4,6-trinitrotoluene by vetiver grass--potential for phytoremediation?

2,4,6-Trinitrotoluene (TNT) is a potent mutagen, and a Group C human carcinogen that has been widely used to produce munitions and explosives. Vast areas that have been previously used as ranges, munition burning, and open detonation sites are heavily contaminated with TNT. Conventional remediation activities in such sites are expensive and damaging to the ecosystem. Phytoremediation offers a cost-effective, environment-friendly solution, utilizing plants to extract TNT from contaminated soil. We investigated the potential use of vetiver grass (Vetiveria zizanioides) to effectively remove TNT from contaminated solutions. Vetiver grass plants were grown in hydroponic systems containing 40 mg TNTL(-1) for 8d. Aqueous concentrations of TNT reached the method detection limit ( approximately 1 microg L(-1)) within the 8-d period, demonstrating high affinity of vetiver for TNT, without any visible toxic effects. Results from this preliminary hydroponic study are encouraging, but in need of verification using TNT-contaminated soils.

Biodegradation, Environmental↗

PubMed2006

Bioaccumulation and physiological effects of mercury in Sesbania drummondii.

The accumulation of mercury and its effect on growth, photosynthesis and antioxidative responses were studied in Sesbania drummondii seedlings. Mercury concentration in shoots as well as in the roots increased with increasing Hg concentrations in the growth solution. The accumulation of Hg was more in roots than shoots. At 100 mg l-1 Hg concentration, shoots accumulated 998 mg Hg kg -1 dry weight (dw) while roots accumulated 41,403 mg Hg kg-1 dw. Seedlings growth was not significantly affected at lower concentrations of Hg. A concentration of 100 mg l-1 Hg inhibited growth by 36.8%, with respect to control. Photosynthetic activity was assessed by measuring chlorophyll a fluorescence by determination of Fv/Fm and Fv/Fo values. Photosynthetic integrity was not affected up to 50 mg l-1 Hg concentration, however, concentrations higher than 50 mg l-1 affected photosynthetic integrity. Sesbania responded to Hg induced oxidative stress by modulating non-enzymatic antioxidants [glutathione (GSH) and non-protein thiols (NPSH)] and enzymatic antioxidants: superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione reductase (GR). Glutathione content and GSH/GSSG ratio increased up to a concentration of 50 mg l-1 while slight down at 100 mg l-1 Hg. The content of NPSH significantly increased with increasing Hg concentrations in the growth medium. The activities of antioxidative enzymes, SOD, APX and GR followed the same trends as antioxidants first increased up to a concentration of 50 mg l-1 Hg and then slight decreased. The results of present study suggest that Sesbania plants were able to accumulate and tolerate Hg induced stress using an effective antioxidative defense mechanisms.

Antioxidants↗

PubMed2006

Evaluating a drinking-water waste by-product as a novel sorbent for arsenic.

Arsenic (As) carcinogenicity to humans and other living organisms has promulgated extensive research on As treatment technologies with varying levels of success; generally, the most efficient methods come with a significantly higher cost burden and they usually perform better in removing As(V) than As(III) from solution. In the reported study, a novel sorbent, a waste by-product of the drinking-water treatment process, namely, drinking-water treatment residuals (WTRs) were evaluated for their ability to adsorb both As(V) and As(III). Drinking-WTRs can be obtained free-of-charge from drinking-water treatment plants, and they have been successfully used to reduce soluble phosphorus (P) concentrations in poorly P-sorbing soils. Phosphate and arsenate molecules have the same tetrahedral geometry, and they chemically behave in a similar manner. We hypothesized that the WTRs would be effective sorbents for both As(V) and As(III) species. Two WTRs (one Fe- and one Al-based) were used in batch experiments to optimize the maximum As(V) and As(III) sorption capacities, utilizing the effects of solid:solution ratios and reaction kinetics. Results showed that both WTRs exhibited high affinities for soluble As(V) and As(III), exhibiting Freundlich type adsorption with no obvious plateau after 2-d of reaction (15000 mg kg-1). The Al-WTR was highly effective in removing both As(V) and As(III), although As(III) removal was much slower. The Fe-WTR showed greater affinity for As(III) than for As(V) and reached As(III) sorption capacity levels similar to those obtained with the Al-WTR-As(V) system (15000 mg kg-1). Arsenic sorption kinetics were biphasic, similar to what has been observed with P sorption by the WTRs. Minimal (<3%) desorption of sorbed As(III) and As(V) was observed, using phosphate as the desorbing ligand. Dissolved Fe2+ concentrations measured during As(III) sorption were significantly correlated (r2=0.74, p<0.005) with the amount of As(III) sorbed by the Fe-WTR. Lack of correlation between Fe2+ in solution and sorbed As(V) (r2=0.2) suggests reductive dissolution of the Fe-WTR mediating As(III) sorption. Results show promising potential for the WTRs in irreversibly retaining As(V) and As(III) that should be further tested in field settings.

Adsorption↗

PubMed2005

Aluminum-based drinking-water treatment residuals: a novel sorbent for perchlorate removal.

Perchlorate contamination of aquifers and drinking-water supplies has led to stringent regulations in several states to reduce perchlorate concentrations in water at acceptable levels for human consumption. Several perchlorate treatment technologies exist, but there is significant cost associated with their use, and the majority of them are unable to degrade perchlorate to innocuous chloride. We propose the use of a novel sorbent for perchlorate, i.e. an aluminum-based drinking-water treatment residual (Al-WTR), which is a by-product of the drinking-water treatment process. Perchlorate sorption isotherms (23+/-1 degrees C) showed that the greatest amount (65%) of perchlorate removed by the Al-WTR was observed with the lowest initial perchlorate load (10 mg L(-1)) after only 2 h of contact time. Increasing the contact time to 24 h, perchlorate removal increased from 65 to 76%. A significant correlation was observed between the amounts of perchlorate removed with evolved chloride in solution, suggesting degradation of perchlorate to chloride.

Adsorption↗

PubMed2005

Nucleotide-induced conformational change in the catalytic subunit of the phosphate-specific transporter from M. tuberculosis: implications for the ATPase structure.

The nucleotide binding subunit of the phosphate-specific transporter (PstB) from Mycobacterium tuberculosis is a member of the ABC family of permeases, which provides energy for transport through ATP hydrolysis. We utilized the intrinsic fluorescence of the single tryptophan containing protein to study the structural and conformational changes that occur upon nucleotide binding. ATP binding appeared to lead to a conformation in which the tryptophan residue had a higher degree of solvent exposure and fluorescence quenching. Substantial alteration in the proteolysis profile of PstB owing to nucleotide binding was used to decipher conformational change in the protein. In limited proteolysis experiments, we found that ATP or its nonhydrolyzable analog provided significant protection of the native protein, indicating that the effect of nucleotide on PstB conformation is directly associated with nucleotide binding. Taken together, these results indicate that nucleotide binding to PstB is accompanied by a global conformational change of the protein, which involves the helical domain from Arg137 to Trp150. Results reported here provide evidence that the putative movement of the alpha-helical sub-domain relative to the core sub-domain, until now only inferred from X-ray structures and modeling, is indeed a physiological phenomenon and is nucleotide dependent.

ATP-Binding Cassette Transporters↗

PubMed2005

Fate and bioavailability of arsenic in organo-arsenical pesticide-applied soils. Part-I: incubation study.

A laboratory incubation study was conducted to estimate geochemical speciation and in vitro bioavailability of arsenic as a function of soil properties. Two chemically-variant soil types were chosen, based on their potential differences with respect to arsenic reactivity: an acid sand with minimal arsenic retention capacity and a sandy loam with relatively high concentration of amorphous Fe/Al-oxides, considered a sink for arsenic. The soils were amended with dimethylarsenic acid (DMA) at three rates: 45, 225, and 450 mg/kg. A sequential extraction scheme was employed to identify the geochemical forms of arsenic in soils, which were correlated with the "in vitro" bioavailable fractions of arsenic to identify the most bioavailable species. Arsenic bioavailability and speciation studies were done at 0 time (immediately after spiking the soils with pesticide) and after four-months incubation. Results show that soil properties greatly impact geochemical speciation and bioavailability of DMA; soils with high concentrations of amorphous Fe/Al oxides retain more arsenic, thereby rendering them less bioavailable. Results also indicate that the use of organic arsenicals as pesticides in mineral soils may not be a safe practice from the viewpoint of human health risk.

Aluminum Oxide↗

PubMed2005

Bioremediation of petroleum hydrocarbons in contaminated soils: comparison of biosolids addition, carbon supplementation, and monitored natural attenuation.

Two methods of biostimulation were compared in a laboratory incubation study with monitored natural attenuation (MNA) for total petroleum hydrocarbon (TPH) degradation in diesel-contaminated Tarpley clay soil with low carbon content. One method utilized rapid-release inorganic fertilizers rich in N and P, and the other used sterilized, slow-release biosolids, which added C in addition to N and P. After 8 weeks of incubation, both biostimulation methods degraded approximately 96% of TPH compared to MNA, which degraded 93.8%. However, in the first week of incubation, biosolids-amended soils showed a linear two orders of magnitude increase in microbial population compared to MNA, whereas, in the fertilizer-amended soils, only a one order of magnitude increase was noted. In the following weeks, microbial population in the fertilizer-amended soils dropped appreciably, suggesting a toxic effect owing to fertilizer-induced acidity and/or NH(3) overdosing. Results suggest that biosolids addition is a more effective soil amendment method for biostimulation than the commonly practiced inorganic fertilizer application, because of the abilities of biosolids to supplement carbon. No statistically significant difference was observed between the biostimulation methods and MNA, suggesting that MNA can be a viable remediation strategy in certain soils with high native microbial population.

Bacteria↗

PubMed2005

Consideration of soil properties in assessment of human health risk from exposure to arsenic-enriched soils.

Encroachment of residential development on agricultural lands in the United States where arsenical pesticides were extensively used prior to the 1990s has increased the potential for human exposure to arsenic (As), a group A carcinogen. Soil ingestion by children is a critical issue in assessing health risks from exposure to As-enriched soils. In the absence of a universal "soil model" on As bioavailability, many baseline risk assessment studies use the assumption that all (100%) As present in soil is bioavailable. However, As exists in many geochemical forms as dictated by soil chemical properties. Because As bioavailability is a function of soil speciation, using total soil arsenic values potentially overestimates human health risk, thereby increasing site cleanup expenses. A laboratory incubation study was conducted to estimate in vitro As bioavailability as a function of soil properties in four chemically variant soil types contaminated with sodium arsenite pesticide. Results demonstrate that As speciation in certain soils translates to significant lowering of As bioavailability and hence potential cancer risk.

Arsenic↗

PubMed2004

Human health risks from arsenic in soils: does one model fit all?

In the absence of a "soil model" on arsenic bioavailability, many investigators conducting baseline risk assessments of arsenic-enriched sites have assumed that all arsenic present in the soil is bioavailable. This assumption overestimates actual human health risk because various geochemical forms of arsenic are stable, or insoluble, in human digestive juices. The authors conducted a laboratory incubation study to analyze the in vitro bioavailability of arsenic in soils as a function of soil properties. Four different soil types were selected on the basis of their potential differences with respect to arsenic reactivity. Each soil was amended with sodium arsenite at a rate representative of a routine 1-yr application of arsenical pesticide in an agricultural system. The soils were incubated for 1 yr, after which the authors measured soil-specific total and bioavailable arsenic concentrations. Results demonstrated that soil physicochemical properties significantly affect arsenic bioavailability, and hence estimates of cancer risk, which in turn affect site cleanup cost projections.

Agriculture↗

PubMed2003

Identification of the lambda integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation.

Lambda integrase (Int) is a heterobivalent DNA-binding protein that together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA complexes that execute integrative and excisive recombination at specific loci on the chromosomes of phage lambda and its Escherichia coli host. The large carboxyl-terminal domain of Int is responsible for binding to core-type DNA sites and catalysis of DNA cleavage and ligation reactions. The small amino-terminal domain (residues 1-70), which specifies binding to arm-type DNA sites distant from the regions of strand exchange, consists of a three-stranded beta-sheet, proposed to recognize the cognate DNA site, and an alpha-helix. We report here that a site on this alpha-helix is critical for both homomeric interactions between Int protomers and heteromeric interactions with Xis. The mutant E47A, which was identified by alanine-scanning mutagenesis, abolishes interactions between Int and Xis bound at adjacent binding sites and reduces interactions between Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is essential for excisive recombination and contributes to the efficiency of the integrative reaction. NMR titration data with a peptide corresponding to Xis residues 57-69 strongly suggest that the carboxyl-terminal tail of Xis and the alpha-helix of the aminoterminal domain of Int comprise the primary interaction surface for these two proteins. The use of a common site on lambda Int for both homotypic and heterotypic interactions fits well with the complex regulatory patterns associated with this site-specific recombination reaction.

Bacteriophage lambda↗

PubMed2003

A modified in-vitro method to assess bioavailable arsenic in pesticide-applied soils.

An incubation study was designed to modify the existing in vitro methods to increase the accuracy in estimation of bioavailable arsenic in pesticide-applied soils. In addition to simulating arsenic dissolution in gastric and intestinal solutions, absorbtion by the intestinal membrane was also mimicked using iron-oxide coated filter paper strips inserted in nylon bags. The in vitro experiments were sequentially performed in two phases, namely, the stomach phase and the absorbed-intestinal phase. Arsenic extraction in the in vitro absorbed intestinal phase increased, thereby making it more comparable to the potential in vivo arsenic pool. While animal studies are needed to verify the in vitro results, preliminary data indicate that this modified method may be able to improve site-specific bioavailability predictions in arsenic-contaminated soils.

Arsenic↗

PubMed2002

Differential affinity and cooperativity functions of the amino-terminal 70 residues of lambda integrase.

The site-specific recombinase (Int) of bacteriophage lambda is a heterobivalent DNA-binding protein that binds two different classes of DNA-binding sites within its recombination target sites. The several functions of Int are apportioned between a large carboxy-terminal domain that cleaves and ligates DNA at each of its four "core-type" DNA-binding sites and a small amino-terminal domain, whose primary function is binding to each of its five "arm-type" DNA sites, which are distant from the core region. Int bridges between the two classes of binding sites are facilitated by accessory DNA-bending proteins that along with Int comprise higher-order recombinogenic complexes. We show here that although the 64 amino-terminal residues of Int bind efficiently to a single arm site, this protein cannot form doubly bound complexes on adjacent arm sites. However, 1-70 Int does show the same cooperative binding to adjacent arm sites as the full length protein. We also found that 1-70 Int specifies cooperative interactions with the accessory protein Xis when the two are bound to their adjacent cognate sites P2 and X1, respectively. To complement the finding that these two amino-terminal domain functions (along with arm DNA binding) are all specified by residues 1-70, we determined that Thr75 is the first residue of the minimal carboxy-terminal domain, thereby identifying a specific interdomain linker region. We have measured the affinity constants for Int binding to each of the five arm sites and the cooperativity factors for Int binding to the two pairs of adjacent arm sites, and we have identified several DNA structural features that contribute to the observed patterns of Int binding to arm sites. Taken together, the results highlight several interesting features of arm DNA binding that invite speculation about additional levels of complexity in the regulation of lambda site-specific recombination.

Amino Acid Sequence↗

PubMed2002

Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.

The integrase protein (Int) from bacteriophage lambda catalyzes the insertion and excision of the viral genome into and out of Escherichia coli. It is a member of the lambda-Int family of site-specific recombinases that catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria, and yeast and belongs to the subset of this family that possesses two autonomous DNA-binding domains. The heterobivalent properties of Int can be decomposed into a carboxyl-terminal domain that executes the DNA cleavage and ligation reactions and a smaller amino-terminal domain that binds to an array of conserved DNA sites within the phage arms, thereby arranging Int protomers within the higher-order recombinogenic complex. We have determined that residues Met-1 to Leu-64 of Int constitute the minimal arm-type DNA-binding domain (INT-DBD(1-64)) and solved the solution structure by using NMR. We show that the INT-DBD(1-64) is a novel member of the growing family of three-stranded beta-sheet DNA-binding proteins, because it supplements this motif with a disordered amino-terminal basic tail that is important for arm-site binding. A model of the arm-DNA-binding domain recognizing its cognate DNA site is proposed on the basis of similarities with the analogous domain of Tn916 Int and is discussed in relation to other features of the protein.

Arginine↗