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

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Presentation on theme: "Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik."— Presentation transcript:

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–CP1-04 Introduction Programmes and Courses  SEP–SBI081– U01-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… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives After studying this module, you should be able to navigate Genomic databases for  Human,  Mouse,  Yeast and  Other model organisms © 2007, YCMOU. All Rights Reserved.

6 School of Science and Technology, Online Counseling Resource… What is Genome Projects?-1  The major tools and methods related to genomics are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function.  Genomics appeared in the 1980s and took off in the 1990s with the initiation of genome projects for several species.  Genome projects are scientific endeavors that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus). © 2007, YCMOU. All Rights Reserved.

7 School of Science and Technology, Online Counseling Resource… What is Genome Projects?-2  The genome sequence for any organism requires the DNA sequences for each of the chromosomes in an organism to be determined.  For bacteria, which usually have just one chromosome, a genome project will aim to map the sequence of that chromosome.  Humans, with 22 pairs of chromosomes and 2 sex chromosomes, will require 24 separate chromosome sequences in order to represent the completed genome. © 2007, YCMOU. All Rights Reserved.

8 School of Science and Technology, Online Counseling Resource… Human Genome Project-1  Human Genome Project (HGP) was an international scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA and to identify the approximately 25,000 genes of the human genome from both a physical and functional standpoint.  The project began in 1990 initially headed by James D. Watson at the U.S. National institutes of health.  A working draft of the genome was released in 2000 and a complete one in 2003, with further analysis still being published.  A parallel project was conducted by the private company Celera Genomics. © 2007, YCMOU. All Rights Reserved.

9 School of Science and Technology, Online Counseling Resource… Human Genome Project-2  Most of the sequencing was performed in universities and research centers from the United States, Canada and Britain.  The mapping of human genes is an important step in the development of medicines and other aspects of health care.  While the objective of the Human Genome Project is to understand the genetic makeup of the human species, the project also has focused on several other nonhuman organisms such as E.coil, the fruit fly, and the laboratory mouse.  It remains one of the largest single investigational projects in modern science © 2007, YCMOU. All Rights Reserved.

10 School of Science and Technology, Online Counseling Resource… Human Genome Project-3  The sequence of the human DNA is stored in database available to anyone on the internet.  The U.S. National centre for Bioinformatics information (and sister organizations in Europe and Japan) house the gene sequence in a database known as Genbank along with sequences of known and hypothetical genes and proteins.  Other organizations such as the University of California, Santa Cruz, and Ensembl present additional data and annotation and powerful tools for visualizing and searching it.  Computer programs have been developed to analyse the data, because the data themselves are difficult to interpret without such programs. © 2007, YCMOU. All Rights Reserved.

11 School of Science and Technology, Online Counseling Resource… Human Genome Project-4  The process of identifying the boundaries between genes and other features in raw DNA sequence is called genome annotation and is the domain of bioinformatics.  While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects.  The best current technologies for annotation make use of statistical models that take advantage of parallels between DNA sequences and human language, using concepts from computer science such as formal grammars. © 2007, YCMOU. All Rights Reserved.

12 School of Science and Technology, Online Counseling Resource… Human Genome Project-5  All humans have unique gene sequences. Therefore the data published by the HGP does not represent the exact sequence of each and every individual's genome.  It is the combined genome of a small number of anonymous donors.  The HGP genome is a scaffold for future work in identifying differences among individuals.  Most of the current effort in identifying differences among individuals involves Single nucleotide polymorphism and the HapMap. © 2007, YCMOU. All Rights Reserved.

13 School of Science and Technology, Online Counseling Resource… How it was accomplished?-1  The genome was broken into smaller pieces; approximately 150,000 base pairs in length.  These pieces were then spliced into a type of vector known as "bacterial artificial chromosomes”, or BACs, which are derived from bacterial chromosomes which have been genetically engineered.  The vectors containing the genes can be inserted into bacteria where they are copied by the bacterial DNA replication machinery.  Each of these pieces was then sequenced separately as a small "shotgun" project and then assembled. © 2007, YCMOU. All Rights Reserved.

14 School of Science and Technology, Online Counseling Resource… How it was accomplished?-2  The larger, 150,000 base pairs go together to create chromosomes.  This is known as the "hierarchical shotgun" approach, because the genome is first broken into relatively large chunks, which are then mapped to chromosomes before being selected for sequencing. © 2007, YCMOU. All Rights Reserved.

15 School of Science and Technology, Online Counseling Resource… Potential Benefits of Human Genome Project Research -1  Rapid progress in genome science and a glimpse into its potential applications have spurred observers to predict that biology will be the foremost science of the 21st century.  Technology and resources generated by the Human Genome Project and other genomics research are already having a major impact on research across the life sciences.  The potential for commercial development of genomics research presents U.S. industry with a wealth of opportunities, and sales of DNA-based products and technologies in the biotechnology industry are projected to exceed $45 billion by 2009. © 2007, YCMOU. All Rights Reserved.

16 School of Science and Technology, Online Counseling Resource… Potential Benefits of Human Genome Project Research -2  sequence and analysis of the human genome provide a map for gaining a better understanding of the genetic basis of human diversity.  An exciting application of genome variability comes from the fact that SNPs in genes encoding drug targets or drug metabolism pathways can determine the therapeutic utility of pharmacologic agents, a concept known as pharmacogenetics.  Although the potential for individualized therapy— based on a patient's genetic information—has been accelerated by the availability of the human genome sequence, the polymorphisms associated with drug responsiveness still need to be identified. © 2007, YCMOU. All Rights Reserved.

17 School of Science and Technology, Online Counseling Resource… Potential Benefits of Human Genome Project Research -3  The work on interpretation of genome data is still in its initial stages. It is anticipated that detailed knowledge of the human genome will provide new avenues for advances in medicine and biotechnology.  Clear practical results of the project emerged even before the work was finished. For example, a number of companies, such as Myriad Genetics started offering easy ways to administer genetic tests that can show predisposition to a variety of illnesses, including breast cancer,disorder of hemostasis, cystic fibrosis, liver diseases and many others. © 2007, YCMOU. All Rights Reserved.

18 School of Science and Technology, Online Counseling Resource… Potential Benefits of Human Genome Project Research - 4  The etiologiese for cancer, Alzheimer's disease and other areas of clinical interest are considered likely to benefit from genome information and may lead in the long term to significant advances in their management.  sequences from different organisms is also opening new avenues in the study of the theory of evolution.  In many cases, evolutionary questions can now be framed in terms of molecular biology; indeed, many major evolutionary milestones (the emergence of the ribosome and organelles, the development of embryos with body plans, the vertebrate immune syste) can be related to the molecular level. © 2007, YCMOU. All Rights Reserved.

19 School of Science and Technology, Online Counseling Resource… Potential Benefits of Human Genome Project Research - 5  Many questions about the similarities and differences between humans and our closest relatives (the primates, and indeed the other mammala) are expected to be illuminated by the data from this project.  Serves an an integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use these data in their research efforts. © 2007, YCMOU. All Rights Reserved.

20 School of Science and Technology, Online Counseling Resource…  Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi, with about 1,500 species.  The yeast species Saccharomyces cerevisiae been used in baking and fermenting alcoholic beverages for thousands of years.  It is also extremely important as a model organism in modern cell biology research, and is the most thoroughly researched eukaryotic microorganism.  Researchers have used it to gather information into the biology of the eukaryotic cell and ultimately human biology. Yeast Functional Genomics Database-1 © 2007, YCMOU. All Rights Reserved.

21 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-2  Other species of yeast, such as Candida albicans, are opportunistic pathogens and can cause infection in humans.  Yeasts have recently been used to generate electricity in microbial fuel cells,, and produce ethanol for the biofuel industry.  One of the milestones of genome research was the determination of the sequence of the whole genome of the well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae.  Goal of this project was the sequencing of the entire nuclear genome of the commonly used laboratory strain S288C. © 2007, YCMOU. All Rights Reserved.

22 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-3  MIPS Comprehensive Yeast Genome Database aims to present information on the genomic structure of Saccharomyces cerevisiae.  CYGD presents itself as a knowledge base organized according to the genomic structure.  The data are shown for different abstraction levels of the genome.  Update reports, graphical displays, and summary tables are provided for the entire genome, or alternatively, for one of the nuclear chromosomes or the mitochondrial genome (tabular,graphically).  The Comprehensive Yeast Genome Database project is also been supported by the European Commission. © 2007, YCMOU. All Rights Reserved.

23 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-4  A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL] provide complementary material.  In addition information and links to related ascomycetous species are added as far as genomic information is available.  The project generate a new quality of a genome resource beyond the sequence, integrating distributed database components and data acquisition sources. © 2007, YCMOU. All Rights Reserved.

24 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-5  The project aims to create a unique resource for the genome of Saccharomyces cerevisiae and other related organisms.  It will develop a novel state of the art type of information infrastructure, combining data generated by high-throughput methods in the laboratory with information from the public literature, results from bioinformatics analysis, and expert knowledge.  The project is coordinated by MIPS, partners are the Biomax Informatics GmbH, Martinsried; Institut Pasteur, Paris; Universite Louis-Pasteur, Strasbourg; INRA, Thiverval-Grignon; GBF, Braunschweig; Unveristat de Valencia, Valencia; Universite Libre de Bruxelles, Brussels © 2007, YCMOU. All Rights Reserved.

25 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-6  Systematic physical mapping with cosmids, and creation of the AAtDB database in the Goodman Laboratory, was a landmark commitment to physical mapping, and the later widespread adoption of YACs as substrates for mapping.  Several factors converged to catalyse a large-scale sequencing program.  These included the availability of a physical map of YACs, constant improvements in the efficiency of sequencing, the manifest value to the scientific community demonstrated by the yeast and C. elegans genome sequence, and initial data revealing a gene- rich genome emerging from a pilot-scale sequencing. © 2007, YCMOU. All Rights Reserved.

26 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-7  In particular, MIPS offers detailed genetic, biochemical, and cell biological information for all individual elements of the genomic structure, such as open reading frames (access ORFs via search tools using gene name aliases or text strings, or ORF listings regarding chromosome structure, or common attributes, such as function).  Just as well, genetic, biochemical, and cell biological data are supplied for RNA genes and various DNA elements (e.g. centromers, or upstream activation sequences).  Another means of data retrieval is available via browsing tables and graphics, reviews, or catalogues regarding a particular yeast topic. © 2007, YCMOU. All Rights Reserved.

27 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-8  YFGdb/SGD Lite Gbrowse: view yeast genome annotation, including GO annotation, SNP data, and transcription factor binding sites  The project started in 1989 and finished in spring 1996. More than 100 laboratories from Europe, USA, Canada and Japan took part of the joined effort.  The long term goal of the YFGdb project is to collect, curate, and freely disseminate all available yeast functional genomics data, along with requisite analysis tools.  The SGD Lite database is now part of YFGdb. Tools currently available include: © 2007, YCMOU. All Rights Reserved.

28 School of Science and Technology, Online Counseling Resource… Yeast Functional Genomics Database-9  YFGdb/SGD Lite Gbrowse: view yeast genome annotation, including GO annotation, SNP data, and transcription factor binding sites  Yeast SNPs Browser (YSB) Gbrowse: view comprehensive SNP data from Schacherer et al. (2007) Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. PLoS ONE 2(3): e322. © 2007, YCMOU. All Rights Reserved.

29 School of Science and Technology, Online Counseling Resource… Mouse Genome © 2007, YCMOU. All Rights Reserved.

30 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-1  Mouse Genome Database (MGD) is an integrated data resource for mouse genetic, genomic, and biological information.  MGD includes a variety of data, ranging from gene characterization and genomic structures, to orthologous relationships between mouse genes and those of other mammalian species, to maps (genetic, cytogenetic, physical), to descriptions of mutant phenotypes, to characteristics of inbred strains, to information about biological reagents such as clones and primers.  Data are accessed via search/retrieval Web forms and displayed as tables, text, and graphical maps, with supporting primary data. © 2007, YCMOU. All Rights Reserved.

31 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-2  A rich set of hypertext links is provided, such as those from gene and clone information to DNA and protein sequence databases (GenBank, EMBL, DDBJ, SWISS-PROT), from bibliographic data to PubMed, from phenotypes to OMIM (Online Mendelian Inheritance in Man), and from gene homology records to the genomic databases of other species. © 2007, YCMOU. All Rights Reserved.

32 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-3  MGD's data integration process places disparate data in contextual relationship, bringing together information from electronic downloads, the mouse Chromosome Committees, submissions from individual researchers, and actively curated data from the published literature.  MGD encourages community participation via contributions of data and the development of consensus representations of the mouse genome.  Electronic bulletin boards are maintained to facilitate communication and collaboration among interested scientists. © 2007, YCMOU. All Rights Reserved.

33 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-4  MGD encourages community participation via contributions of data and the development of consensus representations of the mouse genome  URL: http://www.informatics.jax.orghttp://www.informatics.jax.org  User Support: E-mail: mgi-help @informatics.jax.orgmgi-help @informatics.jax.org  Electronic bulletin board: http://webmaster@informatics.jax.org/ http://webmaster@informatics.jax.org/  Data submissions: http://www.informatics.jax.org/mgihome/su bmissions/submissions_menu.shtml http://www.informatics.jax.org/mgihome/su bmissions/submissions_menu.shtml  or send e-mail to submissions@informatics.jax.org submissions@informatics.jax.org © 2007, YCMOU. All Rights Reserved.

34 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-5 This server provides data extracted and compiled from 1.The 2000–2001 Mouse Chromosome Committee Reports 2.Release 15 of the MIT microsatellite map (Oct 1997) 3.The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001) 4.Map Manager and text format chromosome maps (Apr 2001) © 2007, YCMOU. All Rights Reserved.

35 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-6 © 2007, YCMOU. All Rights Reserved.

36 School of Science and Technology, Online Counseling Resource… Mouse Genome Database-7 © 2007, YCMOU. All Rights Reserved.

37 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-1  Arabidopsis thaliana (cress, mouse-ear cress or Arabidopsis), is small flowering plant native to Europe, Asia, and north western Africa.  A spring annual with a relatively short life cycle, Arabidopsis is popular as a Model organism in plant biology and genetics.  Its genome is one of the smallest plant genomes and was the first plant genome to be sequenced.  Arabidopsis is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.  Arabidopsis has one of the smallest genomes among plants. © 2007, YCMOU. All Rights Reserved.

38 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-2  The small size of its genome make Arabidopsis thaliana useful for genetic mapping and sequencing — with about 157 million base pairand five chromosomes.  It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.  Much work has been done to assign functions to its 27,000genes and the 35,000 proteins they encode.  In the 1980s Arabidopsis started to become widely used in plant research laboratories around the world. © 2007, YCMOU. All Rights Reserved.

39 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-3  Arabidopsis is widely used as one of the model organisms for studying plant sciences including genetics and plant development.  It plays the role for agricultural sciences that mice and fruit flies Drosophila play in animal biology.  Although Arabidopsis thaliana has little direct significance for agriculture, it has several traits that make it a useful model for understanding the genetic, cellular, and molecular biology of flowering plants.  Plant transformation in Arabidopsis is routine, using Agrobacterium tumerfaciens to transfer DNA to the plant genome. © 2007, YCMOU. All Rights Reserved.

40 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-4  The formal origins of the AGI can be traced to meetings held in June 1994 and August 1996 where a concrete strategy and goals to sequence the Arabidopsis genome were formulated.  Earlier the Arabidopsis Multinational Steering Committee had established a general framework of goals and aspirations for the Arabidopsis community, including obtaining a complete gene sequence.  The breakthrough year for Arabidopsis as the preferred model plant came in 1986 when T-DNA mediated transformation was first published and this coincided with the first gene to be clones and published. © 2007, YCMOU. All Rights Reserved.

41 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-5 © 2007, YCMOU. All Rights Reserved.

42 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-6  ABRC: Arabidopsis biological resource center  AGI: Arabidopsis genome initiative  AREX: Arabidopsis gene expression database  Arabinet: Arabidopsis information on the www  AtGDB: An Arabidopsis thalina plant genome database  AtGI: TIGR Arabidopsis thaliana gene index  ATGC: Genome sequencing at ATGC  ATIDB: Arabidopsis insertion database  CSHL: Arabidopsis genome analysis at Cold Spring  ESSA: Arabidopsis thalina project at MIPS © 2007, YCMOU. All Rights Reserved.

43 School of Science and Technology, Online Counseling Resource… Arabidopsis Thaliana-7  Genoscop:AGI in France  Kazusa:Arabidopsis thaliana genome info Japan  MPSS:Massively parallel signature sequencing  NASC: Nottingham Arabidopsis stock center  Stanford:Sequencing of the Arabidopsis genome at Stanford  TAIR: Arabidopsis information resource  TIGR: TIGR Arabidopsis genome annotation database  Wustl: Arabidopsis genome at Washington university  Trees: A forest tree genome database © 2007, YCMOU. All Rights Reserved.

44 School of Science and Technology, Online Counseling Resource… What You Learn-1…  Genome projects are scientific endeavors that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus).  Human Genome Project (HGP) was an international scientific research project with a primary goal to determine the sequence of the approximately 25,000 genes of the human genome from both a physical and functional standpoint.  The HGP genome is a scaffold for future work in identifying differences among individuals. © 2007, YCMOU. All Rights Reserved.

45 School of Science and Technology, Online Counseling Resource… What You Learn-2…  Yeasts are the model organism in modern cell biology research, and is the most thoroughly researched eukaryotic microorganism.  Yeast genomw project provided a novel state of the art type of information infrastructure, combining data generated by high-throughput methods in the laboratory with information from the public literature, results from bioinformatics analysis, and expert knowledge.  Mouse Genome Database (MGD) is an integrated data resource for mouse genetic, genomic, and biological information.  Arabidopsis is widely used model organisms for studying plant sciences including genetics and plant development. © 2007, YCMOU. All Rights Reserved.

46 School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Write a short note on human genome project and its outcome. 2.Write a short note on Yeast genome project and its outcome. 3.Write a short note on mouse genome project and its outcome. © 2007, YCMOU. All Rights Reserved.46 © 2007, YCMOU. All Rights Reserved.

47 School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Human genome, HGP, how it accomplish, benfits of human genome project. 2.What is yeast, its importance and outcome of the project. 3.What is mouse, its importance and outcome of the project. © 2007, YCMOU. All Rights Reserved.47 © 2007, YCMOU. All Rights Reserved.

48 School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Biophysical Chemistry (principles and techniques ) Author: Upadhay. Upadhay.Nath Publisher: Himalaya publishing House  Book2 Title: Physical Biochemistry (application to Biochemistry and molecular biology) Author: Freifelder Publisher: W. H. Freeman and Company © 2007, YCMOU. All Rights Reserved.

49 School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Essentials of Biophysics Author: Narayanan Publisher: New Age Int. Pub. New Delhi.  Book4 Title: A Text Book of Biophysics Author: Roy R.N. Publisher:New Central Book Agency © 2007, YCMOU. All Rights Reserved.

50 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.

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


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