1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. OC_SEP –SBI081– CP1_05 Introduction Programmes and Courses  SEP-SBI081– U1-CP1

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com © 2007, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved. How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… Learning Objectives  After studying this module, you should be able to browse Genomic databases for:  Plant,  Microbial,  Parasite and  Viral genomes © 2007, YCMOU. All Rights Reserved.

6. School of Science and Technology, Online Counseling Resource… Plant Genome-1  P lants are organisms belonging to the kingdom Planate.  They include familiar organisms such as trees, herbs, bushes, grasses, vines, fern, mosses and green algae.  About 350,000 species of plants, defined as seed plants, bryophytes, ferns and fern allies, are estimated to exist currently.  Green plants, sometimes called metaphytes or viridiplantae, obtain most of their energy from sunlight via a process called photosythesis.  The whole world is dependent plant for nutrition and other resources, so it is necessary to study plants in details for their improvement. © 2007, YCMOU. All Rights Reserved.

7. School of Science and Technology, Online Counseling Resource… Plant Genome-2  Eukaryotic genomes are much more complex than prokaryotic genomes. Plant genomes are more complex than other eukaryotic genomes.  Prior to the development of recombinant DNA technology genomes, were analysed by reassociation kinetics techniques.  Reassociation kinetic experiments are performed by melting DNA and allowing it to reanneal upon itself or with another population of either DNA or RNA molecules.  The kinetics of the reassociation provide data that can be used to analyze the overall structure, evolution and expression of genomes. © 2007, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… Plant Genome-3  The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.) genome.  Rice is an experimental model for the cereal crops research and an agriculturally important plant, providing food for more than half of the world population.  The estimated rice genome size is about 430 Mb, which is the smallest among all the cereal crops and about one seventh of human and 3.5 times of Arapdopsis genomes.  The goal at MOsDB is to provide all available data about rice genes and genomics, including (in the future) mutant information and expression profiles. © 2007, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Plant Genome-4  The MOsDB database includes current (updated on daily basis) published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica..  The International Rice Genome Sequencing Project deploys a chromosome by chromosome, clone by clone approach, and deposits BAC/PAC-sized contigs to the public databases.  Monsanto and Syngenta, two US-operating companies, have also announced the establishment of working drafts of the rice genome at different coverage in April of 2000 and February of 2001, respectively © 2007, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Plant Genome-5 © 2007, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource… Plant Genome-6  The genome sequence of O.s. spp indica was obtained by a "whole genome shotgun".  The project was initiated in May, 2000 at Beijing Genomics Institute and the working draft was done in Oct. 2001.  The release covers the draft sequence assembly of the rice genome from 93-11, a cultivar of domesticated rice subspecies (indica), the major rice subspecies cultivated in China and many other Asian-pacific regions.  Functional coverage of the assembled sequence, based on STSs, ESTs, and full-length cDNAs, is estimated to be 92%. © 2007, YCMOU. All Rights Reserved.

12. School of Science and Technology, Online Counseling Resource… Microbial Genome Projects  Microbes are the organisms which are not visual to naked eye and studied with help of microscope.  Microbial genome projects offers a timely summary of the principles, approaches, and applications.  It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome- wide functional analysis, applied functional genomics, and future directions. © 2007, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… Microbial Genome-1  Encyclopedia of Escherichia coli K-12 Genes and Metabolism  EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655.  The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.  "Multidimensional annotation of the Escherichia coli K-12 Genome," Nucleic Acids Research.  The EcoCyc web site is updated quarterly. © 2007, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… Microbial Genome-2  E. coli Wiki it integrates a number of existing E. coli databases, and it will capture E. coli functional genomics data and sequence data for non-pathogenic E. coli strains.  Our vision is for these two resources to form a seamless information infrastructure for E. coli. Both projects are funded by NIH/NIGMS. © 2007, YCMOU. All Rights Reserved.

15. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-1  The parasites are the organisms which can not synthesis their own food, they are dependent on other organisms for food.  Their association with host may be benefical to host or may be harmful, hence their study is very important.  The parasites genome projects revealed important metabolic pathways which can be targeted to develop antiparasite drugs and antigens for potentialvaccines.  However, many other fruitful results can be obtained using comparative genomics in this field, for example regulation of transcription is still quite unknown in these organisms. © 2007, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-2  The Trypanosoma cruzi Genome Project  Trypanosoma brucei Genome Project  Trypanosoma brucei genome sequencing at Sanger  Trypanosoma brucei genome sequencing at TIGR  LGN- Leishmania Genome Network  Leishmania Genome sequencing in Seattle  Leishmania Genome sequencing at Sanger Leishmania network. © 2007, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-3  Plasmodium Gene Identification program P.falciparum.  Plasmodium falciparum Gene Sequence Tag project.  Plasmodium falciparum Genome Sequencing (Sanger Centre)  Malaria Network WWW site (Australia)  Malaria Genome site (Australia)  Malaria-WHO, Malaria database (from WHO) Malaria Antigen Database © 2007, YCMOU. All Rights Reserved.

18. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-4 © 2007, YCMOU. All Rights Reserved.

19. School of Science and Technology, Online Counseling Resource…  PlasmoDB.org hosts genomic and proteomic data (and more) for different species of the parasitic eukaryote Plasmodium, the cause of Malaria.  It brings together data provided by numerous laboratories worldwide, and adds its own data analysis.  Publications relying on PlasmoDB should acknowledge the database developers and the scientists who have made their data available.  PlasmoDB is part of an NIH/NIAID funded Bioinformatics Resource centre to provide Apicomplexan Database Resources. Parasite Genome Projects-5 © 2007, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-6 © 2007, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… Parasite Genome Projects-7 © 2007, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… Viral Genome Project  A virus (from the latin virus meaning "toxin" or "poison"), is a sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell.  All living things are susceptible to viral infections... plants, animals, or bacteria can all be infected by a virus specific for that type of organism.  The difficulty in developing antiviral therapies stems from the large number of variant viruses that can cause the same disease, as well as the inability of drugs to disable a virus without disabling healthy cells © 2007, YCMOU. All Rights Reserved.

23. School of Science and Technology, Online Counseling Resource… Viral Genomes-1  VIDA contains a complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes.  For each family you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures.  "VirOligo" is derived from Virus Oligonucleotide. The VirOligo database collects virus-specific oligonucleotides for virus detection from published literature. © 2007, YCMOU. All Rights Reserved.

24. School of Science and Technology, Online Counseling Resource… Viral Genomes-2 Homologous protein family search Search by: homologous protein family number virus name (choose from list) protein function (keyword/functional class) GenBank protein number free text Search by sequence similarity Search profiles © 2007, YCMOU. All Rights Reserved.

25. School of Science and Technology, Online Counseling Resource… Viral Genomes-3 Sample List of Viruses  SARS Coronavirus  Foot-and-Mouth disease virus  Variola (Small pox) virus  Influenza A virus  Bovine herpesvirus  Bovine viral diarrhea virus  Bovine respiratory syncytial viru  Alcelaphine herpesvirus  Bovine adenovirus © 2007, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… Viral Genomes-4 Data available on homologous protein families from the following virus families:  Arteriviridae  Coronaviridae  Herpesviridae  Papillomaviridae  Poxviridae © 2007, YCMOU. All Rights Reserved.

27. School of Science and Technology, Online Counseling Resource… Viral Genomes-5  Links to complete genome sequences : Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae.  Analyse virus sequences with Virus Genome Annotator.  Gene Ontology herpes simplex virus 1 GO_HSV-1. © 2007, YCMOU. All Rights Reserved.

28. School of Science and Technology, Online Counseling Resource… What You Learn-1…  Plants are source of energy for whole world, so it is very important to study plant genome in details.  The genome databases creation is in progress for maize, rice, tomato.  The model organisms for plant genome is Arabidopsis thaliana.  The parasite and microbes are model organisms for one or the other purpose, so their study and genome database creation will be helpful in understand diseases and developing drugs.  Viruses are very important, as they are on the boundary line of living and non-living organisms. © 2007, YCMOU. All Rights Reserved.

29. School of Science and Technology, Online Counseling Resource… What You Learn-2…  Viruses are utilize in biotechnology work as vector and for other some many purposes, so virus genome database creation will be a mile stone. © 2007, YCMOU. All Rights Reserved.

30. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Write a short note on plant genome project and its outcome. 2.Write a short note on parasite and microbial genome project and its outcome. 3.Write a short note on virus genome project and its outcome. © 2007, YCMOU. All Rights Reserved.

31. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.What are plants, their importance and outcome of the project. 2.What are parasites and microbes, their importance and outcome of the project. 3.What is virus, its importance and outcome of the project. © 2007, YCMOU. All Rights Reserved.31 © 2007, YCMOU. All Rights Reserved.

32. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Principles of Genome Analysis And Genomics Author: Primrose, S.B. & Twyman, R.M. Publisher: Blackwell Publishing Company.  Book2 Title: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins Author: Andreqas D. Baxevanis, B. F. Francis Ouellette Publisher: John Wiley and Sons, New York © 2007, YCMOU. All Rights Reserved.

33. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Bioinformatics Sequence and Genome Analysis Author:David W. Mount. Publisher: Cold Spring Harborlaboratory Press.  Book4 Title: Bionformatics Concepts, Skills and Application Author: Rastogi, S.C., Mendiratta N, Rastogi, Publisher: CBS Publishers & Distributors © 2007, YCMOU. All Rights Reserved.

34. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia © 2007, YCMOU. All Rights Reserved.

35. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You © 2007, YCMOU. All Rights Reserved.