STUDIES ON THE BIOLOGY OF THE WEDGE CLAM DONAX INCARNATUS (GMELIN) FROM THE MALIPPURAM BEACH OF KERALA

The present investigations have considerably enhanced the existing knowledge on the biology and distribution/availability pattern of D.incarnatus in the Malippuram region. The species occurs in good concentration during October - March/April, and disappears from the area during late premonsoon and monsoon months. Recolonising the area in September, it grows fast in the subsequent months. The life span of the species is estimated to be about an year. Studies on the reproductive biology of the species have revealed that there are two spawning peaks, the major peak in February - March and minor peak, in December. The salinity regime of the area influences the reproductive activity. These observations form the original contribution in the thesis. The information on variation in water content, protein,glycogen and lipid levels in relation to reproductive cycle has helped to a better understanding of the gametogenic activity and spawning of the species. Similarly, the findings on salinity tolerance and filtration rate have shown that small sized clams exhibit greater tolerance range than larger clams, and grow at a faster rate with active metabolism. It is hoped that these information would considerably add to the present knowledge of the basic facts which are relevant to the improvement and management of the clam fishery of this region.

Biology of Flat Toadfish,Colletteichthys dussumieri(Valenciennes,1837) of Cochin Estuary

Dept.of Marine Biology,Microbiology and Biochemistry,Cochin University of Science and Technology

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Microalgae in the Southwest Coast of India

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology

Marine Yeasts from the Slope Sediments of Arabian Sea and Bay of Bengal

The present study provides an account of the occurrence and diversity of marine yeasts in the slope sediments of Arabian Sea and Bay of Bengal. It also gives a clear idea about the role of yeasts in the benthic realm of marine ecosystem. The lipolytic potential of the organisms indicate the presence of rich lipid moieties in the study area. The isolates, Candida sp. SD 302 and Pichia guilliermondii SD 337 were proved to have potential oil degrading property and can be employed as bioremediators of oil spill after further characterization. The black yeasts isolated during the study area were found to have high commercial value by virtue of the by-products obtained from them. The melanin and the melanin degrading enzyme extracted from these organisms are potential bioactive materials for application in cosmetology.

Haematological responses of green mussel Perna viridis (Linnaeus) to heavy metals copper and mercury

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology

INVESTIGATIONS ON THE STRESS EFFECTS OF PETROLEUM HYDROCARBONS ON METAPENAEUS DOBSON (MIERS)

The present investigation has addressed the effects of PHC contaminated culture medium on the morphology, physiology and behaviour of shrimps. The shrimp Metapenaeus dobsoni is an important member of the crustacean animal community abounding the oil contaminated benthic regions of Cochin backwater system. Since it is known that true pollutants can disrupt the sustainability of ecosystems by its effect on species, populations and communities,a representative species was used for the study. The results discussed in this work is bound to help in understanding the ecotoxicant resistance that the animal may display under toxic conditions compared to dynamic steady-state systems in nature.

Biochemical and Histopathological Effects of Aflatoxin on Oreochromis mossambicus ( Peters )

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology

Meiobenthos of the Shelf Waters of West Coast of India With Special Reference to Free-Living Marine Nematodes

Department of Marine Biology, Microbiology and Biotechnology, Cochin University of Science and Technology

Nutritional responses in Indian white shrimp Fenneropenaeus indicus to varying protein: energy combinations in compounded artificial feeds

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology

Biochemical Effects of Anionic, Cationic and Non Ionic Surfactants on a Tropical Teleost Oreochromis Mossambicus(Peters) and a Marine Cyanobacterium Synechocystis Salina Wislouch

The present work is a base line attempt to investigate and assess the toxicities of three surfactants viz. anionic sodium dodecyl sulfate (SDS), non ionic Triton X-1OO (TX-IOO) and cationic cetyl trimethyl ammonium bromide (CTAB). These compounds represent simple members of the often neglected group of aquatic pollutants i.e. the anionic alkyl sulfates, non ionics and the cationics. These compounds are widely used In plastic industry, pesticide/herbicide formulations, detergents, oil spill dispersants, molluscicides etc. The test organisms selected for the present study are the cyanobacterium Synechocystis salina Wislouch representing a primary producer in the marine environment and a fresh water adapted euryhaline teleost Oreochromis mossambicus (peters) at the consumer level of the ecological pyramid. The fish species, though not indigenous to our country, is now found ubiquitously in fresh water systems and estuaries. Also it is highly resistant to pollutants and has been suggested as an indicator of pollution in tropical region .

Marine yeasts as source of single cell protein and immunostimulant for application in penaeid prawn culture systems

The study revealed the potential of marine yeasts as a source of single cell protein and immunostimulant for prawns. Prawns fed with the selected marine yeasts were showing more growth compared to the control feed and commercial feed. Yeasts being rich with proteins, vitamins and carbohydrates serve as a growth promoter for prawns as being evidenced in this study. The better performance of marine yeasts, D. hansenii S8 and S100 and C. tropicalis S186 compared to S. cerevisiae S36 as a feed supplement is worth investigating. Besides being a rich nutritional source, yeasts act as immunostimulants by virtue of its high carbohydrate (Beta, 1-3 glucan) and RNA content. Beta, 1-3 glucan, a cell wall component of yeasts /fungi is the most commonly used immunostimulant in aquaculture. The present study shows that even the whole cell yeast could serve as a good immunostimulant when supplied through diet. Extraction of Beta-1,3 glucan results in the removal of nutrients like proteins, vitamins etc. from the cell biomass.Utilization of the yeast biomass as such in the diet would help perform a dual role as nutritional component and immunostimulant for aquaculture applications.

Process Optimization for Mass Production of Marine Yeast Candida sp. S 27 and its Nutritional Characterization

The main source of protein for human and animal consumption is from the agricultural sector, where the production is vulnerable to diseases, fluctuations in climatic conditions and deteriorating hydrological conditions due to water pollution. Therefore Single Cell Protein (SCP) production has evolved as an excellent alternative. Among all sources of microbial protein, yeast has attained global acceptability and has been preferred for SCP production. The screening and evaluation of nutritional and other culture variables of microorganisms are very important in the development of a bioprocess for SCP production. The application of statistical experimental design in bioprocess development can result in improved product yields, reduced process variability, closer confirmation of the output response to target requirements and reduced development time and overall cost.The present work was undertaken to develop a bioprocess technology for the mass production of a marine yeast, Candida sp.S27. Yeasts isolated from the offshore waters of the South west coast of India and maintained in the Microbiology Laboratory were subjected to various tests for the selection of a potent strain for biomass production. The selected marine yeast was identified based on ITS sequencing. Biochemical/nutritional characterization of Candida sp.S27 was carried out. Using Response Surface Methodology (RSM) the process parameters (pH, temperature and salinity) were optimized. For mass production of yeast biomass, a chemically defined medium (Barnett and Ingram, 1955) and a crude medium (Molasses-Yeast extract) were optimized using RSM. Scale up of biomass production was done in a Bench top Fermenter using these two optimized media. Comparative efficacy of the defined and crude media were estimated besides nutritional evaluation of the biomass developed using these two optimized media.

Production of Alkaline Protease by Free and Immobilised Cells of VIBRIO sp. Under Different Fermentation Systems and Its Application on Deproteinisation of Prawn Shell Waste for Chitin Recovery

This thesis presents a detailed account of a cost - effective approach towards enhanced production of alkaline protease at profitable levels using different fermentation designs employing cheap agro-industrial residues. It involves the optimisation of process parameters for the production of a thermostable alkaline protease by Vibrio sp. V26 under solid state, submerged and biphasic fermentations, production of the enzyme using cell immobilisation technology and the application of the crude enzyme on the deproteinisation of crustacean waste.The present investigation suggests an economic move towards Improved production of alkaline protease at gainful altitudes employing different fermentation designs utilising inexpensive agro-industrial residues. Moreover, the use of agro-industrial and other solid waste substrates for fermentation helps to provide a substitute in conserving the already dwindling global energy resources. Another alternative for accomplishing economically feasible production is by the use of immobilisation technique. This method avoids the wasteful expense of continually growing microorganisms. The high protease producing potential of the organism under study ascertains their exploitation in the utilisation and management of wastes. However, strain improvement studies for the production of high yielding variants using mutagens or by gene transfer are required before recommending them to Industries.Industries, all over the world, have made several attempts to exploit the microbial diversity of this planet. For sustainable development, it is essential to discover, develop and defend this natural prosperity. The Industrial development of any country is critically dependent on the intellectual and financial investment in this area. The need of the hour is to harness the beneficial uses of microbes for maximum utilisation of natural resources and technological yields. Owing to the multitude of applications in a variety of industrial sectors, there has always been an increasing demand for novel producers and resources of alkaline proteases as well as for innovative methods of production at a commercial altitude. This investigation forms a humble endeavour towards this perspective and bequeaths hope and inspiration for inventions to follow.

Meiobenthos of Cochin backwaters in relation to macrobenthos and environmental parameters

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology