Biomedical subjects

Debarati Paul

Publications and source records attributed to Debarati Paul.

11 recordsLinked to original sources

PubMed2006

Biofilms: implications in bioremediation.

Biofilms are assemblages of single or multiple populations that are attached to abiotic or biotic surfaces through extracellular polymeric substances. Gene expression in biofilm cells differs from planktonic stage expression and these differentially expressed genes regulate biofilm formation and development. Biofilm systems are especially suitable for the treatment of recalcitrant compounds because of their high microbial biomass and ability to immobilize compounds. Bioremediation is also facilitated by enhanced gene transfer among biofilm organisms and by the increased bioavailability of pollutants for degradation as a result of bacterial chemotaxis. Strategies for improving bioremediation efficiency include genetic engineering to improve strains and chemotactic ability, the use of mixed population biofilms and optimization of physico-chemical conditions. Here, we review the formation and regulation of biofilms, the importance of gene transfer and discuss applications of biofilm-mediated bioremediation processes.

Bacteria↗

PubMed2006

Genetically modified crops: success, safety assessment, and public concern.

With the emergence of transgenic technologies, new ways to improve the agronomic performance of crops for food, feed, and processing applications have been devised. In addition, ability to express foreign genes using transgenic technologies has opened up options for producing large quantities of commercially important industrial or pharmaceutical products in plants. Despite this high adoption rate and future promises, there is a multitude of concerns about the impact of genetically modified (GM) crops on the environment. Potential contamination of the environment and food chains has prompted detailed consideration of how such crops and the molecules that they produce can be effectively isolated and contained. One of the reasonable steps after creating a transgenic plant is to evaluate its potential benefits and risks to the environment and these should be compared to those generated by traditional agricultural practices. The precautionary approach in risk management of GM plants may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Effective risk assessment and monitoring mechanisms are the basic prerequisites of any legal framework to adequately address the risks and watch out for new risks. Several agencies in different countries monitor the release of GM organisms or frame guidelines for the appropriate application of recombinant organisms in agro-industries so as to assure the safe use of recombinant organisms and to achieve sound overall development. We feel that it is important to establish an internationally harmonized framework for the safe handling of recombinant DNA organisms within a few years.

Animals↗

PubMed2006

Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete.

A Gram-positive actinobacterium, strain RKJ300(T), capable of utilizing p-nitrophenol and 2,4-dinitrophenol, was isolated from a pesticide-contaminated site in India. The morphological and chemotaxonomic properties of the isolate were typical of members of the genus Rhodococcus. The DNA G+C content was 72 mol%. Strain RKJ300(T) exhibited the highest level of sequence similarity with Rhodococcus wratislaviensis NCIMB 13082(T) (99.3 %), followed by Rhodococcus opacus DSM 43205(T) (98.8 %), Rhodococcus percolatus MBS1(T) (98.6 %) and Rhodococcus koreensis DNP505(T) (98.1 %). The low levels of DNA-DNA relatedness (49-58 %) with the above micro-organisms, and the differences in the biochemical and physiological properties, suggest that strain RKJ300(T) should be classified within a novel species of the genus Rhodococcus, for which the name Rhodococcus imtechensis sp. nov. is proposed. The type strain is RKJ300(T) (=MTCC 7085(T)=JCM 13270(T)).

Base Composition↗

PubMed2006

Chemotaxis of Ralstonia sp. SJ98 towards p-nitrophenol in soil.

Bioremediation of contaminated sites has been accepted as an efficient and cheaper alternative to physicochemical means of remediation in several cases. Although chemotactic behaviour of many bacteria has been studied earlier and assays have been developed to study bacterial chemotaxis in semi-solid media, this phenomenon has never been demonstrated in soil. For bioremediation application it is important to know whether bacteria actually migrate through the heterogenous soil medium towards a gradient of a particular chemoattractant. In the present study we have successfully demonstrated bacterial chemotaxis of a Ralstonia sp. SJ98 in soil microcosm using qualitative and quantitative plate and tray assays. The migration of bacteria has been established using several methods such as plate counting, vital staining and flow cytometry and slot blot hybridization. A non-chemotactic p-nitrophenol utilizing strain Burkholderia cepacia RKJ200 has been used as negative control. Our work clearly substantiates the hypothesis that chemotactic bacteria may enhance in situ bioremediation of toxic pollutants from soils and sediments.

Biodegradation, Environmental↗

PubMed2006

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Arthrobacter↗

PubMed2005

Enhanced biodegradation of beta- and delta-hexachlorocyclohexane in the presence of alpha- and gamma-isomers in contaminated soils.

The chlorinated insecticide hexachlorocyclohexane (HCH) has been used extensively in the past, and contaminated sites are present throughout the world. Toward their bioremediation, we isolated a bacterium Pseudomonas aeruginosa ITRC-5 that mediates the degradation of all the four major isomers of HCH under aerobic conditions, both in liquid-culture and contaminated soils. In liquid-culture, the degradation of alpha- and gamma-HCH is rapid and is accompanied with the release of 5.6 micromole chloride ions and 4.1 micromole CO2 micromole(-1) HCH-isomer. The degradation of beta- and delta-isomers is slow, accompanied with the release of 0.9 micromole chloride ions micromole(-1) HCH-isomer, and results in a transient metabolite 2,3,4,5,6-pentachlorocyclohexan-1-ol. The strain ITRC-5 also mediates the degradation of alpha-, beta-, gamma-, and delta-isomers in contaminated soils, where degradation of otherwise persistent beta- and delta-HCH is enhanced severalfold in the presence of alpha- or gamma-HCH. The degradation of soil-applied beta- and delta-HCH under aerobic conditions has not been reported earlier. The isolate ITRC-5 therefore demonstrates potential for the bioremediation of HCH-wastes and contaminated soils.

Aerobiosis↗

PubMed2005

Pot and field studies on bioremediation of p-nitrophenol contaminated soil using Arthrobacter protophormiae RKJ100.

Biodegradation of p-nitrophenol (PNP), a priority pollutant, was studied as a model system for bioremediation of sites contaminated with nitroaromatic/organic compounds. Bioremediation of PNP-containing soil was first carried out in pots using immobilized and free cells of Arthrobacter protophormiae RKJ100 in order to ascertain the role of a suitable carrier material. Results showed that stability of the introduced strain was enhanced upon immobilization and that the rate of PNP depletion decreased with increasing depth of soil. Small-scale field studies (in one square meter plots) were then conducted in which PNP-contaminated soil from an agricultural field was bioaugmented with strain RKJ100 under natural environmental conditions. PNP was totally depleted in 5 days by immobilized cells, whereas free cells were able to deplete 75% of PNP in the same time period. The fate of the released strain as monitored by plate counts, hybridization studies, and real-time polymerase chain reaction revealed fairly stable population of the cells upon immobilization on corncob powder throughout the period of study.

Arthrobacter↗

PubMed2005

Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications.

Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s).

Bacteria↗

PubMed2005

Suicidal genetically engineered microorganisms for bioremediation: need and perspectives.

In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their development. In order to address the anticipated risks due to the uncontrolled survival/dispersal of GEMs or recombinant plasmids into the environment, some attempts have been made to construct systems that would contain the released organisms. This article discusses the designing of safer genetically engineered organisms for environmental release with specific emphasis on the use of bacterial plasmid addiction systems to limit their survival thus minimizing the anticipated risk. We also conceptualize a novel strategy to construct "Suicidal Genetically Engineered Microorganisms (SGEMs)" by exploring/combining the knowledge of different plasmid addiction systems (such as antisense RNA-regulated plasmid addiction, proteic plasmid addiction etc.) and inducible degradative operons of bacteria.

Bacteria↗

PubMed2005

Accessing microbial diversity for bioremediation and environmental restoration.

Biological methods for decontamination promise an improved substitute for ineffective and costly physico-chemical remediation methods, although so far only a fraction of the total microbial diversity (i.e. the culturable fraction with metabolic potential) has been harnessed for this purpose. Exploring and exploiting the "overlooked" genetic resource might ameliorate concerns associated with the degradation of recalcitrant and xenobiotic pollutants that are not degraded or only poorly degraded by known culturable bacteria. Recent advances in the molecular genetics of biodegradation and in knowledge-based methods of rational protein modification provide insight into the development of "designer biocatalysts" for environmental restoration. The application of such genetically engineered microorganisms (GEMs) in the environment has been limited, however, owing to the risks associated with uncontrolled growth and proliferation of the introduced biocatalyst and horizontal gene transfer. Programming rapid death of the biocatalyst soon after the depletion of the pollutant could minimize the risks in developing these technologies for successful bioremediation.

Bacteria↗

PubMed2003

Branching of o-nitrobenzoate degradation pathway in Arthrobacter protophormiae RKJ100: identification of new intermediates.

We have earlier reported a novel reductive pathway for o-nitrobenzoate (ONB) degradation (at 0.5 mM) in Arthrobacter protophormiae RKJ100, which proceeds via the formation of o-hydroxylaminobenzoate (HABA) and anthranilate (AA). During growth of this organism at 40 times higher concentration (20 mM) of ONB, 3-hydroxyanthranilate (HAA) was identified as an intermediate by thin layer chromatography, gas chromatography and high performance liquid chromatography studies. Crude cell extracts of ONB-grown cells showed HAA 3,4-dioxygenase activity suggesting HAA as a terminal aromatic intermediate of the catabolic energy-yielding pathway as shown before in Pseudomonas fluorescens strain KU-7. HAA is further cleaved to 2-amino-3-carboxymuconic-6-semialdehyde by the action of HAA 3,4-dioxygenase. In this report we propose that ONB degradation occurs via the formation of HABA and the pathway branches at this point to form the two different aromatic intermediates AA and HAA by the action of a reductase and a mutase, respectively.

3-Hydroxyanthranilic Acid↗