Subhasis Sarkar

Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups

Gingivo-buccal oral squamous cell carcinoma (OSCC-GB), an anatomical and clinical subtype of head and neck squamous cell carcinoma (HNSCC), is prevalent in regions where tobacco-chewing is common. Exome sequencing (n=50) and recurrence testing (n=60) reveals that some significantly and frequently altered genes are specific to OSCC-GB (USP9X, MLL4, ARID2, UNC13C and TRPM3), while some others are shared with HNSCC (for example, TP53, FAT1, CASP8, HRAS and NOTCH1). We also find new genes with recurrent amplifications (for example, DROSHA, YAP1) or homozygous deletions (for example, DDX3X) in OSCC-GB. We find a high proportion of C>G transversions among tobacco users with high numbers of mutations. Many pathways that are enriched for genomic alterations are specific to OSCC-GB. Our work reveals molecular subtypes with distinctive mutational profiles such as patients predominantly harbouring mutations in CASP8 with or without mutations in FAT1. Mean duration of disease-free survival is significantly elevated in some molecular subgroups. These findings open new avenues for biological characterization and exploration of therapies.

Metal concentrations in water and sediments from tourist beaches of Acapulco, Mexico.

A survey on the metal concentrations (As, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, V, Zn) in beach water and sediments is reported from the tourist destination of Acapulco city on the Pacific coast of Mexico. The concentration of dissolved trace metals (DTMs) in beach water and acid leachable trace metals (ALTMs) in sediments indicated that they are anthropogenic in nature due to the increased tourist activities in the crowded beach locations. The statistical analysis indicates Fe and Mn play a major role as metal scavengers in both the medium (water and sediment) and the higher value of other metals is site specific in the study area, indicating that they are transported from the local area. Comparison results suggest that the beach water quality has deteriorated more than the sediments and special care needs to be taken to restore the beach quality.

Total mercury content in marine organisms of the hooghly estuary, West Bengal, India

This paper reports concentrations of total Hg (both organic and inorganic) in different selected biota (seagrass, gastropods, bivalves and fishes) collected from the coastal regions of deltaic Sundarbans, West Bengal, India. Species-dependent variability is very much distinct where high level of Hg was found in carnivorous species. A high degree of organ specificity was pronounced in case of bivalves where gill and mantle exhibited higher Hg accumulation due to the ion exchange activity of the mucous in these organs. The available data demonstrates the potentiality of the shellfishes as sentinel accumulators of this element and they can be successfully used as sensitive index of pollution. The data also reveals that this coastal zone is getting polluted and necessary preventive measures must be adopted to make the best possible use of the available marine resources.

The suitability of tropical marine bivalves as biomonitors of heavy metals in deltaic sundarbans, North-East India

Abstract The determination of Fe, Cu, Zn, Mn, Co, Ni and Cd was carried out in the soft tissues of two bivalves, Crassostrea cucullata (Born) and Anadara granosa (Linnaeus) from coastal regions of deltaic Sundarbans, West Bengal, India. Both species - dependent variability and regional variations of metal concentrations in these molluscs were observed. Gill and mantle showed a higher bioaccumulation in the majority of the cases. The correlation coefficient between the concentrations of metal in the soft tissues was determined. Month-wise distribution of metals was significant as revealed by analysis of variance (ANOVA). C . cucullata has shown to be a potentially useful species for monitoring environmental pollution in this estuarine system.

Detection of Rib Shadows in Digital Chest Radiographs

We propose a method for detection of rib shadows in chest radiographs that uses the knowledge of human anatomy of the thorax. Information present in the radiograph is then suitably extracted to enable the detection procedure. The method is simple but heuristic in nature and the implementation is quite fast. Details of the proposed method and the results are presented.

Sewage treatment in a single pond system at East Kolkata Wetland, India

East Kolkata Wetland (EKW), a Ramsar site, greatly contributes towards purification of city sewage employing single pond system. However, the underlying mechanism remains unknown. Therefore to gain an insight, in this study efforts have been made to understand the rate of biodegradation and the time dependent changes of different physicochemical factors and their interactions that are involved in the process. For this purpose, different parameters such as BOD, COD, faecal coliforms etc. have been measured at different time intervals during the purification process. The results reveal that biodegradation rate at EKW pond is very high and wastewater gets stabilized within 10 days of retention. The higher rate of biodegradation in pond system at EKW (k = 0.7 day(-1)) than in laboratory based in vitro experiment (k = 0.12 day(-1)) reveals the important contribution from other environmental components that are unique for this system. The results also demonstrate the significant influence (P< or =0.01) of temperature, pH and dissolved oxygen on the purification of waste water. Thus the current study provides an insight about the optimal pathway of gradual improvement of wastewater quality in the single pond system at EKW and may serve to explore the inherent mechanism to a great extent.

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment.

Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure.

Persistent Organic Pollutants (POPs) in Sediments and Biota in Coastal Environments of India

Persistent organic pollutants (POPs) are semivolatile organic compounds of special concern because of their toxicity, persistence, long-range transport and bioaccumulation potential. They are present in the marine environment, notably in coastal areas affected by municipal sewage, agricultural and aquaculture effluents, industry and shipping traffic. The 7,555 km-length coastal region of India is the most vulnerable zone facing frequent geohazards, e.g. tsunami and flooding. It is contaminated from direct discharge of wastes from the densely populated coastal areas, runoff of fertilizers, dumping by vessels, oil spills, deforestation and ill-planned river basin developments. This chapter summarizes the knowlegde on residues of 5 classes of persistent organic pollutants (POPs) such as dichlorodiphenyltrichloroethane and its metabolites (DDTs), hexachlorocyclohexane and its isomers (HCHs), polycyclic aromatic hydrocarbon and its congeners (PAHs), polychorinated biphenyl and its congeners (PCBs) and polybrominated diphenyl ether and its congeners (PBDEs) in the sediments and in selective biota: bivalve mollusks, fishes and marine mammals. Their potential ecotoxicological impacts on biota have also been assessed based on the sediment quality guidelines (SQG) specified by USEPA (The incidence and severity of sediment contamination in surface waters of the United States, vol 1, National sediment quality survey. EPA 823-R-97-006, Washington, DC, 1997a: Environmental protection agency, National Sediment Quality Survey, App D, Washington DC, 1997b) and by Canadian Council of Ministers of the Environment (CCME, Canadian quality guidelines for the protection of aquatic life-summary tables. Available from. http://www.ccme.ca/assets/pdf/sed summary_table.pdf, 2002).

Nitrogen dynamics of the aquatic system is an important driving force for efficient sewage purification in single pond natural treatment wetlands at East Kolkata Wetland

At East Kolkata Wetlands, though the domestic city sewage is purified very rapidly, the mechanisms of treatment remains inadequately explored. In this context, the present study investigated nitrogen dynamics of the single pond treatment systems during purification and explored its potential role in sewage treatment. For this purpose the concentrations of different forms of nitrogen present both in water and soil at different time points of purification were measured. The organic nitrogen content decreased sharply, in the early phase, with an increase in ammonium concentration. Notably the reduction in organic nitrogen was significantly higher than the increase in NH4+ which can be attributed to the volatilization of NH4+ under alkaline pH. This volatilization results in reduced oxygen demand. The nitrate-N concentration decreased sharply from soil with a concomitant increase in water column. However the reduction of nitrate in soil was significantly higher than the increase in water column. It indicated the occurrence of denitrification under anoxic condition wherein nitrate serves as terminal electron acceptor. Additionally a part of the nitrate supported planktonic growth. Thus it describes another mechanism of reducing oxygen demand. The initial NH4+-N concentration in the soil was very low and it increased gradually during purification due to increasing soil cation exchange capacity. Thus by trapping NH4+ ion soil contributes towards preventing contamination of water. Thus at EKW, the cumulative activities in water and soil involved in nitrogen dynamics lead to overall reduction of the oxygen demand and contribute towards efficient sewage purification.

Impingement of marine organisms in a tropical atomic power plant cooling water system

A one-year impingement monitoring was conducted at Madras Atomic Power Station (MAPS), Kalpakkam, southeastern coast of India and identified a total of 67 species of marine organisms in the cooling water system. Estimates of total annual impingement contributed about 1.47×106 individuals and 142.5t of biomass. Jellyfish contributed about 6.8×105 individuals and 135.6t of biomass. Crabs, shrimps and fish were the most vulnerable organisms contributing about 4.29×105 individuals, 1.39×105 individuals and 2.16×105 individuals respectively. Commercially important species namely Trichiurus lepturus, Sardinella longiceps and Portunus pelagicus were found to be impinged 1.88% and 0.29% by number and weight of the total biomass respectively. Out of ~327 fish species recorded at Kalpakkam, only about 9.4% of species were impinged at MAPS. Multispecies impingement at MAPS poses the problem of finding the best mitigation options for tropical conditions.