Absract Archive December 2008 Research article A Study of in silico Drug Docking for Triosephosphate Isomerase in Plasmodium falciparum Abstract Malaria is a disease caused by the protozoan Plasmodium falciparum. It affects both the adults and children equally. This parasite lacks in functional TCA cycle and solely dependent on glycolysis for its energy supply. One such enzyme is triose phosphate isomerase. This catalyses the isomerization of D-Glyceraldehyde 3 phosphate to dihyfroxy acetone phosphate. An attempt was made to identify the potential drug and inhibit the enzyme as well as to modify their side chain to impure the binding efficienty. Hence, an effort was taken to modify the active sites. (His 95, Glu 165, Lys 12) of the twose phosphate isomerase with docking technique. Using chemsketch the ligands (Phosphono acetic acid, triclofos and limnoids) were generated and it is used to dock it. The another ligand in which the methyl group of limnoid is replaced with phosphave and form limnoid phosphate is also used. The Quantitative-structure activity Relationships (QSAR) was done for this modified and unmodified ligand, limnoid to know about the physio-chemical properties using the softwasre dragon. It was noted that all the ligand shows better stability when complexed with Glu 165. Key words: malaria, binding, docking, QSAR, ligand. Introduction Malaria is a disease caused by the protozoan Plasmodium falciparum. It affects both the adults and the children equally. Globally around 300-400 million people are affected by this dreaded disease each year and have been found out to be fatal to 2-3 million among them. P. falciparum is more prevalent in the Asian subtropical zone. (Miller et al.,, 1994). A quick look at the life cycle of Plasmodium falciparum shows that it is a complex process as it involves 2 hosts from entirely different phyla, viz. invertebrates and vertebrates. Hence, it requires adaptations to two different host body systems. The invertebrate host is the female Anopheles mosquito. The vertebrate host (Human) is infected by the bite of this mosquito containing the sporozoite form of the parasite in its salivary glands. These enter the blood stream and invade the liver. Here, asexual reproduction occurs, resulting in the release of merozoites. These invade the erythrocytes. Within the erythrocytes the merozoites undergo a cycle of development involving the ring stage and the trophozoite stage. Some of these merozoites differentiate into sexual stages called gametocytes. When a female Anopheles mosquito bites a person at this stage, the mosquito ingests these gametocytes. Within the invertebrate the female and male gametocytes fuse to form oocytes, which give rise to the sporozoite stage. These eventually get lodged into the salivary glands of the mosquito and the cycle gets repeated. (Florens et al., 2002). It is during the erythrocytic invasion that the parasite needs a lot of energy. As the parasite lacks a functional TCA cycle, it is solely dependant on glycolysis for its energy supply.(Mehta et al., 2006). Thus the glycolytic enzymes provide a good drug targets. (Perie et al., 2002). One such enzyme taken for this study is Triosephosphate isomerase. Triosephosphate isomerase catalyzes the isomerization of D-glyceraldehyde-3-phosphate to dihydroxyacetone phosphate (DHAP). Through experimenting it has been concluded that Triosephosphate isomerase is an “evolutionarily perfect enzyme”. (Jain, 2006). PfTIM (Plasmodium falciparum Triosephosphate isomerase) is a dimeric glycolytic enzyme. It also plays an important role in gluconeogenesis, hexose monophosphate shunt and fatty acid biosynthesis. This enzyme has eight helices alternating with eight b strands along with the polypeptide chain. These are arranged antiparallel to each other, approximately. It might be argued that the same TIM is present in humans too and as to how a drug can be targeted such that it does not affect the host. The PfTIM when compared to Human TIM shows many important differences. A hydrophobic Leu183 in PfTIM replaces Glu183 residue in human TIM. Cys13 is present in PfTIM instead of Met13 in human TIM. Also there is replacement of the conserved residue Ser96 in the active site by Phe96 in the parasite enzyme. (Velankar et al, 1997).The residues Lys12, His95 and Glu165 form part of the PfTIM active sites. Hence, the drugs must be docked to these sites to inhibit the action of the enzyme. These residues are not rigid and the most flexible being the Glu165. Ligand binding has pronounced effect on the flexible loop 6 region constituted by residues165 178, which undergoes a large movement upon ligand binding. (Williams et al., 1995). Author : Maruthamuthu Rajadurai. in-silico prediction of structural and functional aspects of a hypothetical protein of Arabidopsis thaliana (L) Heynh. Abstract Arabidopsis thaliana is a model plant for scientific research due to the presence of many desirable characteristics like rapid development, small plant size, mutable seeds, mutations quickly becoming homozygous etc. An in-silico technique was initiated to characterize a hypothetical protein to deduce its structural and functional information. The hypothetical protein analysed in the present study showed domain characteristics of ankyrin repeats family with beta-hairpin-alpha-hairpin repeat {multiple repeats of beta (2) - alpha (2) motif}. The protein showed five domains of 32 amino acid repeat units. The modelled protein revealed the presence of maximum number of random coils as its secondary structural elements. The existence of ankyrin repeats indicates its role in protein-protein interaction essential for various metabolic processes in organism. Keywords: Arabidopsis thaliana; hypothetical protein, ankyrin repeats, protein-protein interaction. Introduction Arabidopsis thaliana (L) Heynh. is a small flowering plant that is widely used as a model organism [1] in plant biology. It has a small genome of about 125 Mb organized into five chromosomes and contains an estimated 25,500 genes. More than 30 megabases of annotated genomic sequence has already been deposited in GenBank by a consortium of laboratories in Europe, Japan, and the United States. The entire genome has been sequenced which has enhanced the importance of Arabidopsis as a model for plant biology. Its genome was sequenced in the year 2000. Most of the DNA encodes 25,498 genes and very little junk DNA is present. Many characters of this unique plant such as prolific seed production, rapid development, small plant size, mutable seeds, normally self pollinated thereby making mutations quickly becoming homozygous and its expression, make it an ideal model organism for scientific research. The large scale genome sequencing project has generated a plethora of information both in terms of genes and proteins. There are however, a vast amount of proteins whose function and structure has not been unearthed yet. There is, therefore, an urgent need to characterize these hypothetical proteins whose only primary information in the form of sequence is available. The results generated will be helpful in gaining insight into the various metabolic, gene regulatory mechanism and the functional aspects of this unique model organism. Therefore, the present work involves the extensive use of tools and graphical software for a complete annotation of the hypothetical protein (Acc. No. gi|4206201|gb|AAD11589.1|). Short communication Investigation on The Bacteriological Quality of Drinking Water from two different sources Abstract The bacteriological quality of water samples collected from two different water sources viz. treated water supplied through taps and water from purification filter system, fitted with reverse osmosis processing assembly, was examined for its potability. The results indicated a Coliform MPN index of 1800 in samples collected from Tap water and none from samples examined after collection from Water Purification System. The presence of E.coli was found prominent in the tap water samples, as evidenced by IMViC test results. Proper disinfection of water samples through chlorination is suggested for making it potable for consumption. Creating awareness among the community through Health Education is also recommended for avoiding the outbreak of diseases transmitted through water. Key words: Coliforms, MPN index Water Purification System Introduction Water, an essential requirement for all forms of life, needs protection from pollution which otherwise pose a threat to human life. Different sources of water are available to meet the drinking needs of the community. However, the outbreak of different water-borne diseases like Cholera, Typhoid etc takes the life of many in alarming proportions in rural areas. Hence there is a need to study the hygienic and microbiological safety of various types of drinking water sources available in the rural areas. With this in mind, a study was undertaken to establish how safe the drinking water, which is now available to meet the drinking water needs of the society. It has already been indicated by earlier research that effectiveness of protected water system in controlling water- borne diseases among infants and pre- school children depends on (a) Purity and wholesomeness (b) Water is delivered within the dwellings or outside (c) Quantity supplied (d) Whether supply is continuous, thus avoiding storage of water. Hence there is a need to formulate principles that might govern the design of water supply systems in order to avoid water borne infections. E.coli is a type of fecal coliform bacteria. Fecal coliforms are bacteria that are associated with human or animal wastes. They usually live in human or animal intestinal tracts, and their presence in drinking water is a strong indication of recent sewage or animal waste contamination. Thus, the purpose of this study was to investigate the bacteriological quality of water samples collected from Tap Water and Water Purification System. Authors:A .Bhattacharjee, S. R. Joshi,H .Choudhury, U. Maheswari. Review Microbial biotechnology Rapid Advances in an area of massive impact Abstract For thousands of years, microorganisms have been used to supply products such as bread, beer and wine. A second phase of traditional microbial biotechnology began during World War I and resulted in the development of the acetone-butanol and glycerol fermentations, followed by processes yielding, for example, citric acid, vitamins and antibiotics. In the early 1970s, traditional industrial microbiology was merged with molecular biology to yield more than 40 biopharmaceutical products, such as erythropoietin, human growth hormone and interferons. Today, microbiology is a major participant in global industry, especially in the pharmaceutical, food and chemical industries. Key words: Primary metabolites, Secondary metabolites, Recombinant DNA technology. Introduction Microorganisms are important for many reasons, particularly because they produce things that are of value to us (Demain, 1990). These can be very large materials (e.g. proteins, nucleic acids, carbohydrate polymers, even cells) or smaller molecules and are usually divided into metabolites that are essential for vegetative growth (primary) and those that are nessential (secondary). Microbial technology has made significant advances in recent years with an overwhelming impact on the society. The developments are very fast and new dimensions are being added every day. Microbial technology explores and exploits the microbial wealth for human requirement like production of microbial metabolites and products such as enzymes, organic acids, antibiotics, drugs and pharmaceuticals, in processes like recombinant protein expression, fermentation and downstream processing and in bioremediation, bioleaching, soil and waste management etc. On the other hand, there is a great deal of microbe-based biotechnological development and micro-organisms have become indispensable tools in molecular biology, genetic engineering and DNA technology research. Many of these advances are revolutionising medicine and paradoxically several pathogenic microbes. The twenty-first century belongs to the gene era. The illuminating ideas of genetic fundamentals are making modern biology the fastest growing and most exciting area of science and technology. The isolation of genes and their sequencing are now a routine phenomenon. The isolated genes can be multiplied and mutated at will. The altered gene can be introduced into host cells to investigate its effect on phenotype or to assign specific function. It is also now possible to synthesize genes based on their known nucleotide sequences. The landmark break has been the determination of the human genome sequence, which has given impetus to the disciplines of genomics, proteomics, pharmacogenomics, structural biology and bioinformatics. Of the vast range of exciting research areas, priorities for concerted attention would naturally be those with practicable objectives either realizable immediately or in the near future which could contribute to the economic growth of the country and to the protection and improvement of human health. From this point of view, some of the promising areas of research and development are outlined below ... Authors:R. Rajasekaran,R. Chandrasekaran,M. Muthuselvam. YING YANG Effect of IL-10 in the incidence of Cervical Cancer Abstract The cytokine family of protein has been shown to have a vital role in the control of normal cellular differentiation, mitosis and motility. These are important immunological mediators of cell mediated immunity against tumor. The family of cytokines includes variety of Interleukins (IL-1, IL-12, IL-10, IL-3 etc.), TNFs, IFNs, M-CSF, GM-CSF etc., each one having their specific source and target. The role of cytokine on the tumor cell is necessary to have a differentiation therapy which favor a unique and potentially effective, less toxic treatment paradigm for cancer. The most important of all cytokines is Interleukine-10 which has a dual biological role anti-inflammatory and anti-angiogenic effect. These IL 10 molecules are produced by T cells, Monocytes, Macrophages, B cells, Natural killer cells, Eosinophils, Mast cells and Keratinocytes. TH1 cells are their main target. In cervical cancer patients the incidence of IL-10 is found to increase with the severity of the disease. Key words: IL-10, IFN-y, TFN-a Introduction Globally cervical cancer is the second most common cause of cancer death in women (Tindle and Frazer, 1995). The chronic infection of keratinocytes of the uterine cervix by the Human Papilloma Virus (HPV) is associated with the development of cervical cancer (Giannini et al., 1998). HPV codes for six early proteins (E1, E2, E3, E4, E5, E6, E7) and two late proteins ( L1 and L2). E6 and E7 are oncoproteins (Maria et al., 2002). HPV infection alone is not sufficient for cancer development because majority of women with HPV infection do not develop cervical cancer (Tindle and Frazer, 1995 & Ho et al., 1998). The role of immune system in viral clearance is not clear, but there is clear evidence that cellular mediated immune response is important in the control of HPV infection (Stephen, 1988). The occurrence and progression of tumor is due to the loss of tumor antigenicity and suppression of immune system. Cytokines contribute to this phenomenon. Tumor associated suppression of immune system may be mediated by IL-10 (Germain et al., 1998). The role of IL-10 in cervical cancer is not clear. Thus, it is necessary to analyze the biological role of IL-10. Authors:Vinuselvi. P, AbiramiVeena, RVani, V.Sanjay Prasad. Mini Review Quorum Sensing- Let Bacteria Talk Abstract Quorum Sensing (QS), a wonderful natural method to regulate gene expressions in response to the fluctuation in the cell density of a given bacterial population and provides the key mechanism through which bacteria communicate. QS bacteria release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. Lots of bacterial physiological activities including symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation are being maintained by QS circuit. This method of QS bestows upon bacteria some of the essential qualities as that of higher organisms. The evolution of quorum sensing systems in bacteria could, probably, have been one of the early steps in the development of multicellularity. Apart from bacteria, social insects also communicate through QS. Key words : Quorum sensing, bacterial communication, inducers, computing & robotics Introduction Communication- the strongest and most important gesture ever evolved by nature for every living creation. Mankind wouldn't have progressed in absence of communication. With advancement of civilization, the various means of communications have also improved tremendously and will be so in future. And the most wonderful part is, it's not only us but even the smallest living creatures- Bacteria do communicate with each other! No, they don't use any language for that. Instead the bacterial communication is carried out by different signaling molecules which are released time to time in the environment. Upon releasing the signaling molecules, bacteria are capable of measuring the exact number of molecules i.e. the concentration of the molecules in a given population. What is quorum sensing? 'Quorum Sensing' (QS) can be described as a process through which the accumulation of signaling molecules enable a single cell to sense the number of bacteria (cell density). In nature, many different bacteria which live together and use various classes of signaling molecules. As they employ different languages they can not talk to other bacteria present in the environment. Today, several quorum sensing systems are intensively studied in various organisms such as marine bacteria and several pathogenic bacteria. QS helps bacteria to co-ordinate their behaviors. As environmental conditions often change rapidly, bacteria need to respond very fast in order to survive. These responses can be of different types including adaptation, nutrients availability, and defense against other microorganisms which offer competitive resistance and to get rid of the potentially dangerous toxic compounds. It is very important for pathogenic bacteria during infection of a host (e.g. humans, other animals or plants) to co-ordinate their virulence so that they can escape the host's immune responses for successful establishment of the infection. Many species of bacteria use quorum sensing to coordinate their gene expression based on the density of their respective population. Similarly, some insects also use quorum sensing to make collective decisions about where to nest. Apart from its specialized functions in biology, quorum sensing has many other useful applications for computing and robotics. Quorum sensing occusr within a single bacterial species as well as between diverse species, and regulate a lot of different processes, essentially serving as a simple communication network. A variety of different molecules could be used as signals for the entire process of QS. Authors:Indrani Bhattacharyya, Mayukh Choudhury.