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BIOGYAN VOLUME IV |
BIOINFORMATICS CENTRE NEWS LETTER Quarterly news letter |
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PREFACE With the advancement of modern techniques in biology, biotechnology has progressed exponentially in the last decade. Bioinformatics is practiced worldwide by biotechnologists to access various database for research and to exchange information for comparison, conformation, storage and analysis. Bioinformatics is a science typically associated with database in genomics, proteomics, structural and functional information for genes and proteins, of all forms of life on earth. Distributed Information Sub Centre (DISC) is a node of Bioinformatics network (BTIS net) established at Sikkim State Council of Science and Technology, Department of Science and Technology with the support of Department of Biotechnology (DBT), Government of India. The main objective of the project is to establish network in various biological researches. Sikkim being rich in biodiversity needs digitization of bio- resources and promotion and encouragement of the research activities for its proper management and sustenance. “BIOGYAN” a Scientific Informative news letter is being published periodically by the Sikkim Bioinformatics center with the aim of keeping the scientific fraternity abreast with the developments in the field of biotechnology and bioinformatics related to bio diversity and the latest advancements in science. The latest edition which is the forth edition of the news letter comprises of research papers, articles, news and latest events in biological sciences and the modern techniques. I Hope that the news letter will be of great use to the scholars and researchers.
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Contents
Page No.
Bioinformatics an overview Priya Darshini Gurung, Rabina Gurung, B.C. Basistha, Prakash Sharma and Laydong Lepcha
Antifungal activity of Cymbopogon citratus (DC) Stapf. against sour rot disease of tomato caused by Geotrichum candidum Link. Manjila Sharma
Know more about H1N1 Influenza virus Laydong Lepcha, Rabina Gurung, B.C. Basistha, Priyadarshini Gurung, Prakash Sharma
Status of Gloriosa superba L. in certain areas of Sikkim Safal Pradhan & Ashok K. Jain |
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Biogyan, Vol. IV. 2010 Bioinformatics- An overview 1*Priya Darshini Gurung, 1Rabina Gurung, 1B.C. Basistha, 1Prakash Sharma and 1Laydong Lepcha. 1Sikkim State Council of Science & Technology, Department of Science & Technology, Government of Sikkim, Gangtok - 737 101, Sikkim Abstract Information science has been applied to biology to produce the field called Bioinformatics. Bioinformatics is the analysis of biological information using computers and statistical techniques, the science of developing and utilizing computer databases and algorithms to accelerate and enhance biological research. This article provides an introduction to the field of Bioinformatics and an overview of the aims and applications with examples of the databases, tools, software and the methods being used. Definition An interdisciplinary field involving biology, computer science, mathematics, statistics to analyze biological sequence data, genome contents and arrangements to predict the functions and structures of macromolecules (David W. Mount, Bioinformatics Sequence and Genome Analysis, p.p. 534). Introduction The term “Bioinformatics” was first used in the mid 1980s in order to describe the application of information science and technology in the life science; it is actually “the application of information technology to the management of biological data”. The principle enunciated by Crick says that information flows from gene (DNA) to the protein, occupies such a key place in modern molecular biology that it is frequently referred to as the “central dogma”- DNA acts as a template to replicate itself, DNA is transcribed into RNA, and RNA is translated into protein |
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Biogyan, Vol. IV. 2010, In the last few decades, advancements in the field of molecular biology and the equipments available for research in this field have allowed the rapid sequencing of large portions of the genomes of several species. For example approximately 82,853,685 DNA sequences records were available in the GenBank genetic sequence database as on Jan 2008. The Human Genome Project (HGP), a 13 years project coordinated by the U.S. Department of Energy and the National Institutes of Health designed to sequence all 24 of the human chromosomes got completed by 2003 itself. The main goals of the project were to identify all the genes in human DNA, determine the sequences of the 3 billion chemical base pairs that make up human DNA. To help achieve these goals, researchers also studied the genetic makeup of several non-human organisms. These included the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. As a result of tremendous advancement in the biological and molecular sciences , biological data are increasing at a tremendously rate and hence more and more computational and Information technology power is needed for maintenance, digitization ,analysis and interpretation of these generated data. Aim of Bioinformatics Bioinformatician collects the wealth of biological information and uses it to improve the living standards of human beings and other living beings. Today Bioinformatics is being applied to various fields like human health, environment, agriculture, biotechnology and biomedical research and development. It is used in the field of molecular medicine to produce the customized medicines for the prevention or cure of the diseases. Bioinformatics is today rapidly growing field all over the world. The aims of Bioinformatics are of three fold. Its first aim is to organize data in a way that allows researchers to access existent information and to submit new entries as they are produced. For example Protein Data Bank (PDB) where three dimensional macromolecular structures can be submitted. It contains information about experimentally determined structures of protein, nucleic acids, and complex assemblies.
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Biogyan, Vol. IV. 2010
Second aim is to develop tools, soft wares and resources that aid in the analysis of data. For example an unknown sequence can be identified or a homology between two sequences can be determined by using the tool BLAST (Basic Local Alignment Search Tool). Third aim is to use these tools and soft wares to analyze the data and interpret the result in a biologically meaningful manner. Data analysis is an important aspect of Bioinformatics as the data are useless until they are analyzed and interpreted in a proper way.. Major applications of Bioinformatics
2. Homology prediction
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Biogyan,
Vol. IV. 2010 3. Genome characterization Identification and characterization of occurrence of certain features in the genome of an organism, genome comparison and gene expression analysis. Example: Expression level in cancerous vs. non cancerous tissues. Conclusion Computational methods have become indispensable to biological investigations. Bioinformatics developed for the analysis of biological sequence data now encompasses a wide range of subject areas including genome and structure analysis, gene expression and SNP mapping, molecular modeling and drug designing etc. This article provides an introductory overview of the field -Bioinformatics. The article mainly focused the origin, aim and the major applications of Bioinformatics today. References
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Biogyan,
Vol. IV. 2010 Antifungal activity of Cymbopogon citratus (DC) Stapf. against sour rot disease of tomato caused by Geotrichum candidum Link. Manjila Sharma Sikkim State Council of Science and Technology Government of Sikkim Gangtok Abstract The sour rot disease of tomato is caused by the pathogen Geotrichum candidum Link. It was isolated from the infected tomato fruit. The antifungal activity of essential oil of Cymbopogon citratus was assessed in-vitro by poisoned food technique using eight different concentrations i.e.,0.625, 1.25, 2.5, 5.0, 10.0, 20.0, 40.0, 80.0(μl/ml) in 80% acetone. Fungi toxicity of essential oil was calculated in terms of mycelial growth inhibition percentage of the test fungus. Cymbopogon citrates was found to be very effective as it inhibited the mycelial growth of the test fungus completely with the Minimum Inhibitory Concentrations (MIC values) of 5 μl/ml. Introduction Among different useful plant species, medicinal and aromatic plants (MAPs) are the most popular and rich resources of the country. They possess the properties like antibacterial, antifungal, antiviral, anthelminthic, anticancer, sedative, laxative, cardio tonic, diuretic and others. The medicinal properties of plants are due to the presence of active components or secondary metabolites such as alkaloids, glycosides, saponins, essential oils, mucilage, tannins, bitter principles etc. Green aromatic and medicinal plants have been found to be less phytotoxic, more systemic, and easily biodegradable. Tomato: Tomato or Lycopersicon esculentum is a major vegetable crop of the world due to its high economical and nutritive value. Tomato production in large scale can vastly improve the annual income of farmers. It is well suited to processing and can provide huge employment opportunities in processing factories for people. The availability of tomato is almost throughout the year. Test fungus: Geotrichum candidum Link., the causal agent of sour rot disease of tomato can cause considerable damage to the stored tomato fruits in quality and quantity. The fungus was |
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Biogyan, Vol. IV. 2010 found to rot the tomato fruits by early ripening due to the evolution of C02. Sour rot first appears as a water-soaked lesion, yellowish white and slightly rose. The cuticle is easily removed from the epidermis around the lesions.
Fig.1 Diseased tomato
The fungus proceeds to disintegrate the fruit into a slimy and watery mass. The characteristic sour odour attracts fruit flies which can further spread the fungus into other injured fruit. Because of this sour odour, this disease is called sour rot. The microscopic feature reveals that the hyphae bear numerous anthroconidia which are unicellular, hyaline and found in chains. They result from the fragmentation of undifferentiated hyphae by fission through double septa and measure 6-12 x 3-6μm.
Fig.2 Anthroconidia of the test fungus Test plant: Cymbopogon citratus (DC) Stapf. Distribution: Distributed in central and eastern Nepal at 500 to 1800m in open, rocky places, also in north western India. Local name: Lemongrass |
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Biogyan, Vol. IV. 2010 Family: Gramineae. Description: The plant is a tall tufted perennial with a short rhizome. It is cultigens which rarely flower, widely distributed all over the tropics of the hemisphere. The roots are fibrous and rhizomed; leaves are graminaceous with parallel venation. The leaves posses silica lining and is rough to touch. Many glands are present all over the body especially in leaves .The plant is lemon scented and have strong aroma. Uses: The essential oil of Lemongrass is an excellent anti-depressant and has a strengthening effect on the nervous system. Its leaves are used to make tea which can relieve stomach and gut problems and are also used in tea to overcome respiratory problems. Lemongrass oil can also be used in bath or massage oils for soothing muscular and nerve pain. Methodology The infected tomato was firstly surface sterilized by using HgCl2. With flame sterilized needle, infected portion of tomato was slightly scrapped and placed in the petri-dishes containing Potato Dextrose Agar (PDA) media. Then the plates were kept in incubator at 25+20C for the proper growth of fungus. Essential oil of the test fungus was diluted into different concentrations (80μl/ml, 40μl/ml, 20μl/ml, 10μl/ml, 5μl/ml, 2.5μl/ml, 1.25μl/ml, and 0.625μl/ml) for assaying fungi toxicity. Seven days old culture of the test fungus was used for the preparation of inoculums discs of 4mm in diameter. The fungi toxicities of the essential oils were assessed by Poisoned food technique (Grover and Moore, 1962). After one week of incubation, mean growth measurement was calculated from three replicates of each of the plant species. Growth inhibition of treatment against control was calculated by percentage. Result Fungitoxicity of essential oil of Cymbopogon citratus was assessed in different concentrations against the sour rot of tomato caused by Geotrichum candidum. The essential oil showed positive results in inhibiting the mycelial growth of Geotrichum candidum.
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Biogyan Vol. IV. 2010
Fig.3 Antifungal activity of different Concentrations of Cymbopogon citratus (Clockwise), Center -control set.
MIC (Minimum Inhibitory Concentration) of essential oil can be expressed as the minimum dose of the oil required for complete (100%) inhibition of mycelial growth of the test fungus. MIC of E. oil was obtained by employing different concentrations of oil till the minimum concentration of it was achieved for the complete inhibition of mycelial growth of the test fungus. Essential oil component in the test plant with antimicrobial activity was citral and the MIC value was found to be 5µl/ml. Discussion and Conclusion Among the tomato diseases, sour rot is one of the most destructive post harvest disease caused by the pathogen, Geotrichum candidum. It develops at injuries caused by insects, mechanical means or plucking during harvest. This study was carried out with isolation of the test fungus (G.candidum) and controls at different concentrations of essential oil of Cymbopogon citratus. Essential oil plant species showed different antifungal activities which varied with different concentrations of the oil. The percentage of mycelial growth inhibition was varied with different pathogens which might be due to differences in the virulence of the pathogens. The oil showed fungistatic nature at the MIC. It has the potency to withstand high inoculums density. The antifungal potency of oil was found to be greater in comparison to some prevalent synthetic fungicides. The test plants contain the chemical components which bear fungitoxic properties that inhibit the mycelial growth of the test fungus. This essential oil was found to be the most effective with the inhibition percentage of 100% even at a low concentration of 5.0μl/ml. So Cymbopogon oil could be used to manage aflatoxin formation and fungal growth of Geotrichum candidum in stored tomat
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Biogyan Vol. IV, 2010 Significance of study Currently, fungicides are not used to control fungal pests or mycotoxin production on stored tomato. Sikkim is declared as an organic state since synthetic chemical fungicides can cause adverse health effects to the consumers. Tomato treated with the essential oil of Cymbopogon could be used to manage fungal pests as well as the insect pests and it is also chemically safe and acceptable to consumers. References Beye, F.1978. Insecticide from vegetable kingdom. Plant Res. Devel.7:13-31. Brown, E., I. Mohamed and C. Clay, 1995. Fresh Fruit Research. Florida Department of Citrus scientific research. Couzon, S., C. Courioul., A. Amrane and Y.Prigent. 2003. Carbondioxide emission in relation to the growth of Geotrichum candidum in solid cultures. University de Remmes 1. France. Fawcett, C. H and D. M. Spencer. 1970. Plant chemotherapy with natural products. Ann. Rev.Phytopath.8:403-418. Kruger, B.1992. An illustrated guide to herbs their medicine and magic. Little brown and Company Ltd., Boston, London.
Parajuli, D. P., A. R. Gyawali and B. M. Shrestha. 1998. A manual of the important non-timber forest products in Nepal. Training and manpower development in C.F.M, Pokhara. 29 - 34.
Rao, G. P. and A. K. Srivastava. 1994. Toxicity of essential oils of higher plants against fungal pathogens of Sugarcane. Current trends on sugarcane pathology: International book and periodical supply service, Pitampura, Delhi. 347-365. |
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Biogyan Vol. IV, 2010
Know more about H1N1 INFLUENZA VIRUS Laydong Lepcha1, Rabina Gurung1, , B.C. Basistha1 Priyadarshini Gurung1, Prakash Sharma1 1 Sikkim Bioinformatics Centre, Sikkim State Council of Science & Technology
Fig. Virus structure The term “Influenza” was first coined in the early 16 century by the Italians which means influence as they believed that the disease was caused by a bad influence from the Heaven. The recent outbreak of contagious Swine Flu disease is caused by H1N1 Influenza virus. H1N1 Influenza virus is a Group A type virus. It exhibits a capacity to create acute contagious viral infection characterized by inflammation of the respiratory tract , fever, chills, muscular pain, and prostration. The virus consists of tightly fitted Protein coat known as Capsid. The surface Protein which forms the whole capsid exhibits two sorts of virus strains, Hemagglutinin and Neuraminidase. The discovery of these virus strains and protein classification have become a part of the name H1N1 virus, H for Hemagglutinin and N for Neuraminidase. The Influenza A Virus consists of one of sixteen possible Hemagglutinin surface Proteins and one of nine possible Neuraminidase surface Proteins. The function of Hemagglutinin Protein is to support attachment of virus and invade cells while Neuraminidase Protein support for the |
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Biogyan Vol. IV.2010 release of viral particles to the cells. They also acts as antigens and exhibit immune system responses that helps to prevent viral infection or reduce viral imitation independently, that’s why they are recognized as foreign matters by human body and other host cells. These surface Proteins undergo changes in series of genetic mutation over a period of time and result in the gradual evolution of viruses and collapse of its natural immune property due to these changes it is also called antigenic drift. This changes enable the viruses to attack new host cell or in new ways in the same hosts. The changes are less common but more injurious that’s why it is known as antigenic shifts as well.
Fig. Neuraminidase Fig. Hemagglutinin The attention of Virus materialize with the cleave of Sialic acid (C11H10NO9) residues in cellular receptor by Neuraminidase protein which bind the newly formed virions to the cell and to one another, which enables infections to spread further to the new host cell. In case of Swine Flu from the mucoproteins Sialic acid (C11H10NO9) residues are sliced down immensely by Neuraminidase protein which results infection to spread enormously to the host cells. Such an event restrain the normal functional activity of cell.
Sialic acid The Neuraminidase retarders imitates Neuraminidase’s natural substrate and bind to the active site, preventing the enzyme from cleaving host-cell receptors, thereby preventing infection of new host cells and halting the spread of infection. Though two approved Neuraminidase’s inhibitors such as Zanamivir (Relenza) and Oseltamivir (Tamiflu) have toxicity but shows |
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Biogyan Vol. IV.2010 effectiveness against all Neuraminidase subtypes and against all strains of Influenza virus but it has also shown its resistance to antiviral such as Oseltamivir (Tamilflu) and are found spreading. Hemagglutinin an antibody helps for the agglutination of RBC (Red Blood Corpuscles). This led to the congestion of Red blood vessel which consequently stops the circulation of blood to various parts of body. This makes hemoglobin contents toxic and fatal. Such viral metabolism has made H1N1 influenza a serious and dominant strains. Though investigations have found some inhibitors such as Zanamivir (Relenza) and Oseltamivir (Tamiflu) which are effective in restraining the viruses the case of virus’s resistant character is already been notified. High precaution, keeping self awareness, maintaining distance from the H1N1 influenza infected patients are the ways to prevent the disease from spreading.
References: http://wiki.answers.com/Q/What_is_the_meaning_of_H1N1 http://www.rkm.com.au/VIRUS/Influenza/ http://nobelprize.org/educational_games/medicine/landsteiner/readmore.ht encarta.msn.com/text_761557270_3/influenza.html
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3H6J |
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Biogyan Vol. IV.2010 Status of Gloriosa superba L. in certain areas of Sikkim Safal Pradhan1* and Ashok K. Jain1 1* Sikkim State Council of Science & Technology,DST 1 School of Studies in Botany, Jiwaji University, Gwalior Sikkim is geographically diverse state and shelters rich and varied flora and fauna. The total forest cover comprises nearly 46% of the total land of the state, having about 7096 sq. kms. of the area. Out of a large number of species grown in various parts of the state Gloriosa superba has been gaining attention of the people of the state because of its medicinal importance and economic value. A good amount of tubers are being sold exported the state. Gloriosa superba is a striking tuberous climbing plant with brilliant wavy-edged yellow and red flowers whose tubers are grown commercially for Colchicine and has both medicinal as well as toxic properties. It is anthelminthic, laxative, alexiteric and abortifacient and used in treatment of ulcers, leprosy, piles, intestinal and skin ailments. It is mostly cultivated in the places of south district namely Sumbuk, Jorethang, Soreng, Daramdin, Sombaria etc. The present paper deals with the economic, medicinal and cultivation aspects of the species in some parts of the state. It has become the need of the hour to come forward and rescue this important glorious herb. Introduction Gloriosa superba has been gaining attention in the state because of its medicinal importance and economic value. Gloriosa superba is a striking tuberous climbing plant whose tubers are grown commercially for Colchicine. It is mostly cultivated in the places of south district of Sikkim. Uncontrolled exploitation and trading of the species requires immediate attention for its conservation. Its huge export from the state has caused an acute shortage of raw material for local drug industries. |
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Biogyan Vol. IV.2010 Materials and methodology The present work was carried out in tribal localities, government and private institutes of South district of Sikkim where Gloriosa superba is cultivated. The study was done from December 2007 upto May 2008. The study sites and the cultivators were surveyed during the time for following information: · Cultivation Requirements · Medicinal Use · Economic Gai
Fig. Gloriosa superba L Fig. Original Linnaeus herbarium sheet of Gloriosa superba
Observations Cultivation in Sikkim Gloriosa superba has the maximum occurrence in the south district of Sikkim.The main cultivated places are Sumbuk, Jorethang, Soreng, Daramdin, Sombaria. Sumbuk was the main place for Gloriosa superba cultivation in Sikkim many years back, from where the farmers supplied the tubers to the traders of Kalimpong which was eventually send for the manufacturing of medicines towards South India or abroad. But now Government of Sikkim has been taking initiative for the higher production of the plant and its parts, mainly tubers and |
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Biogyan Vol. IV.2010
‘cut’ flowers, through various projects and schemes. Due to the attractiveness of the flower, it is one of the main decorative plants all over the globe. SIRD (State Institute of Rural Development), Karfectar, South Sikkim also offers vital training and cultivation of the plant and its distribution. Cultivation Requirement
Propagatory part: It is commercially propagated from its underground rhizomes or is also sexually propagated by seeds. The plants raised from seeds take nearly three to four years to flower. Hence, except for experimental purposes, the growers do not favour seed propagation. Gloriosa sp. produces a biforked tuber during the growing season and each of these forks has only one growing bud |
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Biogyan Vol. IV.2010
Fig. Tuber of Gloriosa sp Fig. Seeds of Gloriosa Fig. Bed Preparation Fig. Support by plastic ropes Medicinal Importance Tribals of Patalkot use powder of rhizome with coconut oil in skin related diseases & in snake and scorpion bites. Crushed roots with water are used for curing baldness. Gonds and Bharias of Patalkot use rhizome for pregnancy related problems. In traditional medicine system, tuber is used for the treatment of bruises and sprains colic, chronic ulcers, hemorrhoids, cancer, impotency, nocturnal seminal emissions and leprosy. Many cultures believe the species to have various magical properties. The plump roots are used in parasitic skin infections, leprosy and internal worms. However, ingestion of any of the parts of the plants is extremely poisonous and can be fatal. |
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Biogyan Vol. IV.2010 Economic gain People involved in the cultivation are mostly the farmers. Realizing the economic gain now, Government Research Institutes and Private growers are also cultivating the plant. Government and Private Institutes also collect and export the tubers and seeds to National & International companies & factories for the production of medicine. Seeds are sold at around Rs. 800/- per kg on the basis of its condition and its length. The best size of the tubers for medicinal purpose is 3-4” and in good condition. Each such tuber can fetch upto Rs. 3-5.
Fig. Collection of Tubers Apart from collecting and exporting tubers and seeds, the research institutes also provide opportunity for growing Gloriosa superba to the new and old growers by distributing the propagatory parts of the plant. Conclusion Gloriosa superba is one of the most important medicinal plants of Sikkim. Its cultivation and trading can be of large gain due to its diversified medicinal properties .The roots are of great medicinal value and have an immense scope in cultivating and trading of G. superba. Economically it is in initial stage but still the producer and the traders are reaping large benefit through the cultivation and trade. Greater economic gain is possible by better management of the resources and greater information. Cultivation and trading of Gloriosa superba is extremely important to an over populated and predominantly agricultural country like India. Thousands of people in India die due to various ailments and diseases. This wonder plant can save life of thousands of people through its diversified medicinal properties. Though if taken in larger doses, |
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Biogyan Vol. IV.2010
its toxicity is equally dangerous. But a better knowledge of this plant
can lead to greater benefits. The authors are grateful towards executives and workers at State Institute for Rural Development (SIRD), Karfectar, Sikkim especially Mr. Gajendra whose inputs were valuable. |
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