Radiation Induced DNA Double Strand Break Studies of a Metal Sensitive Novel Bacterial Isolate from East Calcutta Wetland
30 Jun 2009-American Journal of Environmental Sciences (Science Publications)-Vol. 5, Iss: 3, pp 398-405
TL;DR: The strain was one of the members of the group of uncultivated bacterium as evident from phylogenetic analysis, thus indicating the successful cultivation of an as yet uncultivable novel microbe and also the non-specific growth of microbes in prescribed medium.
Abstract: Problem statement: This study was an attempt to isolate anaerobic microbes with potential for DNA double strand break repair using methanogen specific medium (DSMZ 120) from East Calcutta Wetland in India. It also intended to verify the specificity of the medium for isolation of the desired family of microbe. Approach: Culture based technique was used to obtain the pure isolate that was further characterized in details. For double strand break repair studies, isolate was irradiated with different doses of 60Co gamma rays and its subsequent repair was observed using pulse field gel electrophoresis and asymmetric field inversion gel electrophoresis. Inhibitor was used to predict the mechanism of repair. Results: In this study we isolated and characterized a metal sensitive anaerobic microbial strain obtained using methanogen specific medium (DSMZ 120) from East Calcutta Wetland in India. The strain was one of the members of the group of uncultivated bacterium as evident from phylogenetic analysis, thus indicating the successful cultivation of an as yet uncultivable novel microbe (GenBank Acc. No. FJ 930097) and also the non-specific growth of microbes in prescribed medium. It was a Gram positive Bacilli, member of Fermicutes with optimum growth at 25°C and pH-7. The growth curve analysis showed a lag phase up to 24 h, log phase from 24-48 h, an early stationary phase from 96 h onwards. The strain could repair the DNA double strand break caused by irradiation with 60Co γ rays. The dose profile study revealed maximum repair at 60 Grays and thereafter a drop in repair ability with increase in irradiation dose. The time required for repair showed an essential incubation period of 4 h. The DNA polymerase inhibitor, Arabinose CTP inhibited the repair indicating the involvement of polymerase in the repair process and thus pointing towards homologous recombination as the underlying mechanism. Conclusion: In this study we were able to cultivate an as yet uncultivable anaerobic bacterial isolate and predict the growth conditions for the isolate. On irradiation with 60Co γ rays the isolate showed maximum repair following 60 Gray damage. DNA polymerase inhibitor arabinose CTP inhibited the repair mechanism completely. This indicated that DNA polymerase took active part in repair process and thus the mechanism was that of homologous recombination repair.
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TL;DR: In this paper, a review of the East Kolkata Wetland (EKW) ecosystem is presented, which is a unique example of a wetland ecosystem involved in both resource recover y and environmental protection and in the process providing a stable urban fringe to an expanding metropolis.
Abstract: Problem statement: In the megacity Kolkata, the need for space to acco modate the ever increasing population is increasing day by day. As a result the encoarchment of the large wetland on the eastern frindge of the city is increasing and s o is the threat of its loosing the status of Ramsar Status. Approach: Proper documentation of the existing traditional p ractice with sound scientific basis and the direct as well as indirect benefit that the city receives as a result of its existance could b e an approach towards its conservation. Results: East Kolkata Wetland (EKW) is a unique example of a wetland ecosystem involved in both resource recover y and environmental protection and in the process providing a stable urban fringe to an expanding met ropolis. It ensures economic benefit and employment generation because of resource recovery activities based on utilization of the city's sewage. It acts as a sink for city sewage and garba ge, even at times a little flow of industrial efflu ents with toxic heavy metals as well as hazardous contaminants like sulphate and nitrate to name a few. The purification process operating there depends to a l arge extent on the activity of the diverse microbia l population using liberal sunshine. On trying to und erstand the microbial flora, a rich diversity of th e bacterial domain was revealed with immense potential for commercial application. The extracellular enzymes from microbial origin of EKW were used for detergent formulation, dehairing of hide at neutral pH, silver recovery from exposed X-ray film s and so on. The microbes themselves could entrap metals inside them as nanoparticles, remove sulphat e from solution and prevent nitrate mediated eutrophication. The soluble waste from the megacity goes through various rounds of purification in the waste water fisheries, called Bheri in local parlance before being used for agricultur e. This in turn results in fish production and purification of the waste wa ter up to 99% in terms of faecal coliform count and to a large extent for other parameters. The metal conten t in the muscles of the surface feeder and bottom feeder fishes were comparable to that of the same v ariety from rain water fed ponds, indicating safe u se of the waste water. The agriculture using waste wat er mostly produces paddy and vegetables. The green leafy vegetables produced from EKW when compared with same variety from non-EKW were found to be healthy without any additional unwanted metal accumulation. The entire resource recovery process was relatively safe, ecofriendly as well as economi cal. Conclusion/Recommendations: Thus EKW purifies the waste of a large part of the city, gen erates edible resources, provides employment, houses diverse flora and fauna and also harbours a rich re pertoire of microbes with immense potential for application. The objective of the present review is to emphasize the need of its conservation and also intensify the research on the microbial diversity i n these wetlands.
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References
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TL;DR: An increased knowledge of DSB repair and of other DNA DSB responses may provide opportunities for developing more effective treatments for cancer, with particular emphasis on non-homologous end-joining and homologous recombination.
Abstract: The DNA double-strand break (DSB) is the principle cytotoxic lesion for ionizing radiation and radio-mimetic chemicals but can also be caused by mechanical stress on chromosomes or when a replicative DNA polymerase encounters a DNA single-strand break or other type of DNA lesion. DSBs also occur as intermediates in various biological events, such as V(D)J recombination in developing lymphoid cells. Inaccurate repair or lack of repair of a DSB can lead to mutations or to larger-scale genomic instability through the generation of dicentric or acentric chromosomal fragments. Such genome changes may have tumourigenic potential. In other instances, DSBs can be sufficient to induce apoptosis. Because of the threats posed by DSBs, eukaryotic cells have evolved complex and highly conserved systems to rapidly and efficiently detect these lesions, signal their presence and bring about their repair. Here, I provide an overview of these systems, with particular emphasis on the two major pathways of DSB repair: non-homologous end-joining and homologous recombination. Inherited or acquired defects in these pathways may lead to cancer or to other human diseases, and may affect the sensitivity of patients or tumour cells to radiotherapy and certain chemotherapies. An increased knowledge of DSB repair and of other DNA DSB responses may therefore provide opportunities for developing more effective treatments for cancer.
1,159 citations
TL;DR: The presence of methanogenic bacteria was assessed in peat and soil cores taken from upland moors and formed two clusters on the end of long branches within the methanogen radiation that are distinct from each other.
Abstract: The presence of methanogenic bacteria was assessed in peat and soil cores taken from upland moors. The sampling area was largely covered by blanket bog peat together with small areas of red-brown limestone and peaty gley. A 30-cm-deep core of each soil type was taken, and DNA was extracted from 5-cm transverse sections. Purified DNA was subjected to PCR amplification with primers IAf and 1100Ar, which specifically amplify 1.1 kb of the archaeal 16S rRNA gene, and ME1 and ME2, which were designed to amplify a 0.75-kb region of the alpha-subunit gene for methyl coenzyme M reductase (MCR). Amplification with both primer pairs was obtained only with DNA extracted from the two deepest sections of the blanket bog peat core. This is consistent with the notion that anaerobiosis is required for activity and survival of the methanogen population. PCR products from both amplifications were cloned, and the resulting transformants were screened with specific oligonucleotide probes internal to the MCR or archaeal 16S rRNA PCR product. Plasmid DNA was extracted from probe-positive clones of both types and the insert was sequenced. The DNA sequences of 8 MCR clones were identical, as were those of 16 of the 17 16S rRNA clones. One clone showed marked variation from the remainder in specific regions of the sequence. From a comparison of these two different 16S rRNA sequences, an oligonucleotide was synthesized that was 100% homologous to a sequence region of the first 16 clones but had six mismatches with the variant. This probe was used to screen primary populations of PCR clones, and all of those that were probe negative were checked for the presence of inserts, which were then sequenced. By using this strategy, further novel methanogen 16S rRNA variants were identified and analyzed. The sequences recovered from the peat formed two clusters on the end of long branches within the methanogen radiation that are distinct from each other. These cannot be placed directly with sequences from any cultured taxa for which sequence information is available.
490 citations
TL;DR: Inhibition of H2-dependent methanogenesis was explained by successful competition by sulfate reducers for H2, as the H2 partial pressures decreased upon addition of sulfate, but acetate concentrations did not decrease, and a conceivable explanation is sulfate-dependent interspecies H2 transfer between acetate-utilizing methanogens and H2
105 citations
"Radiation Induced DNA Double Strand..." refers background in this paper
...They also play an important role in interspecies H2 transfer in anaerobic ecosystem ([4])....
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TL;DR: Three bacterial isolates from different sites of East Calcutta Wetland show tolerance to heavy metals and were found to be efficient metal accumulators as evident from Energy Dispersive X Ray Fluorescence analysis and Transmission Electron Microscopy (TEM).
Abstract: The present paper put forth the isolation and complete characterization of three bacterial isolates from different sites of East Calcutta Wetland (ECW). These isolates show tolerance to heavy metals like Ag, Al, Cu, Cr, Co, Ni, Pb and were found to be efficient metal accumulators as evident from Energy Dispersive X Ray Fluorescence (EDXRF) analysis and Transmission Electron Microscopy (TEM). Beyond intracellular accumulation, these isolates also show metal deposition in form of particles inside the cells which can further open up the area of microbe fabricated nanoparticle generation. The heavy metal accumulation in the cell can trigger different response mechanism such as change in cell morphology which was observed by scanning electron microscopy (SEM). The metal uptake property of these isolates can be applied for the heavy metal removal and recovery from industrial effluents.
60 citations
"Radiation Induced DNA Double Strand..." refers background or methods in this paper
...The detailed protocols f r the different areas of characterization were as rep ort d by Adarsh et al.([8])....
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...It is well known for its integrated resource recovery ([7-14])....
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...The detailed protocols f r the different areas of characterization were as report d by Adarsh et al.[8]....
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TL;DR: In this paper, the authors investigated the reason for the markedly greater efficiency of the Bheris in fish production compared to other water bodies like rain water ponds or sewage fed fish ponds elsewhere.
Abstract: Waste water fed fisheries are a common feature in different parts of the world. Yet not all work as efficiently as those operating at East Calcutta Wetland for more than 70 years now. The objective of this study is to unravel the reason for the markedly greater efficiency of the Bheris in fish production compared to other water bodies like rain water ponds or sewage fed fish ponds elsewhere. The study indicates that plankton growth could be an important factor responsible for greater fish production in the Bheris. The architecture of the Bheri itself acts as a facilitator in the process. It is proposed that planktons can act as biomarker for water quality assessment in fish production.
47 citations
"Radiation Induced DNA Double Strand..." refers background in this paper
...It is well known for its integrated resource recovery ([7-14])....
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