Microbial Research Commons Including Viruses

1
Microbial Research Commons Including Viruses

• Prof. A.S. Kolaskar
• Bioinformatics Center
• University of Pune
• Pune, India

2
Introduction

• Increasing research in life sciences and
  biotechnology in Indian Universities and national
  research institutions
• Increased need for microbial and genetic
  resources
• Establishment of microbial and other biological
  culture collections in universities and research
  institutions

3
Culture Collections In India

• Microbial Type Culture Collection and Gene Bank
  (MTCC), Chandigarh World Intellectual Property
  Organization (WIPO, recognized as International
  Depository Authority)
• National Collection of Industrial Microorganisms
  (NCIM), Pune Cultures are deposited for
  patenting
• Virus cultures at National Institute of Virology
  (NIV)
• National Facility for Animal Tissue and Cell
  Cuture, Pune

4
Culture Collections In India

• Anaerobic Bacterial Resource Center (ABRC),
  Hyderabad
• National Collection of Dairy Cultures, Karnal
• National Fungal Culture Collection of India, Pune
• University of Mumbai Food and Fermentation
  Technology Division

21 Culture Collections from India registered with
WDCM
5
Thailand Network of Culture Collections

• Biotech Culture Collection (BCC) 3430
• Department of Medical Sciences Thailand (DMST)
  442
• Department of Agriculture (DOA) 1163
• Thailand Institute of Scientific and
  Technological Research 515

6
Issues

• Limited characterization
• Very few cultures characterized at DNA finger
  printing level
• Data not fully computerized and information not
  available on the web
• Duplication of cultures in the repository
• Material Transfer Agreement similar to that in
  ATCC is followed by most repositories
• No systems in place to detect or prevent misuse
  of MTA
• Redistribution of cultures at informal level
• Very few scientists conversant with taxonomic
  classification even at the national culture
  collections
• Issues related to Biosafety and National security
  are not given due importance

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PUMP-E Salient Features

• Dynamic Representation of pathways
• Dynamically building the organism-specific
  pathways from genomic data
• Development of Software for
• Automated data updating (Perl scripts)
• Reformatting and organization of relevant
  information from different databases
• Drawing pathways diagrams
• Comparison of pathways
• Visualization of ligands, enzymes
• Prediction of enzyme-substrate interactions
• URL- http//202.41.70.51/mpe/

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Approaches

• Data acquisition Integration
• Dynamic Visualization of Metabolic Pathways
• Query Interface
• Molecular Visualization
• Structure Prediction of Proteins
• Simulation of 3D Structures of Enzymes and
  Metabolites

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PUMP-E
Compound
Homology models
Enzyme
Database
Organism
Gene
Reaction
Pathway
User-friendly Query interface
Search by keywords
Molecular viewer
Dynamic generation of queried pathway
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Source Databases for Data Acquisition 

• Sequence databases TIGR, NCBI, EBI
• Metabolite databases KEGG
• Metabolic pathway database KEGG
• 3D Structure database PDB
• Enzyme Database KEGG, EXPASY, IUBMB, BRENDA
• Kinetics Data NIST
• Organism List GOLD
• Motifs, patterns signatures PROSITE

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PUMP-E Front End and Query System

• Web-based query interface
• Supports complex advanced queries
• Developed using ASP, HTML and java
• Tested by various testing tools such as
• Winrunner, Test Director etc.

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PUMP-E Front End and Query System
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PUMP-E
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Total number of pathways in bacteria under study
as per BioCyc 9.1
Organism name Phylum Genome Size (Mbp) Total number of pathways
Agrobacterium tumefaciens Bacillus anthracis Bacillus subtilis Caulobacter crescentus Chlamydia trachomatis Escherichia coli Francisella tularensis Haemophilus influenzae Helicobacter pylori Mycoplasma pneumoniae Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv Shigella flexneri Treponema pallidum Vibrio cholerae Proteobacteria Firmicutes Firmicutes Proteobacteria Chlamydiae Proteobacteria Proteobacteria Proteobacteria Proteobacteria Firmicutes Actinobacteria Actinobacteria Proteobacteria Spirochaetes Proteobacteria 5.673462 5.22729 4.21463 4.01695 1.04252 4.63968 1.89282 1.83014 1.66787 0.816394 4.40384 4.41153 4.6072 1.13801 4.03346 207 254 145 176 61 198 184 127 123 48 186 184 179 56 207
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Hamming Distance Calculations

• Identical Pathways (0)
• Start and end products are identical
  intermediate steps are same.
• Similar Pathways (1)
• Start and end products are identical
  intermediate steps are different
• Pathways are absent (2)
• Start or end products are not same

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Metabolic pathway path profile
Columns represents n number of pathways and
rows represent 15 bacteria under study. Each
column corresponds to a particular type of
pathway. 2 denote pathway follows same path, 1
denotes pathway follows different path while 0
denotes absence of pathway. This represents a
part of the organism specific metabolic pathway
path profile.
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Metabolic pathway path profile based tree
19
Comparison of Pathways from Genus Bacillus with
E.Coli
198 Pathways of E.Coli are compared with pathways
data from Biocyc for each of these organisms
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Pathways absent in Genus Bacillus Present in
E.Coli

• Electron transport (aerobic and anaerobic)
• Phenyl ethyl amine degradation
• L-lyxose degradation
• Pyridoxal 5-phosphate salvage pathway
• Super pathway of pyridoxal 5-phosphate
  biosynthesis and salvage
• D-allose degradation
• Fructose lysine degradation
• Taurine degradation

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Effect of pathways absent in genus Bacillus

• Because of absence of L-lyxose degradation
  pathways in genus bacillus, it cannot utilize
  L-lyxose sugar as source of energy
• D-Allose cannot be utilized as a sole carbon
  source by bacteria of genus bacillus as D-allose
  degradation pathway is absent
• Under sulfate starvation conditions, bacteria
  from genus bacillus cannot utilizes taurine as a
  sulfur source owing to absence of Taurine
  degradation pathway.
• Bacillus cannot grow on fructoselysine or
  psicoselysine as the sole carbon source because
  of absence of Fructose lysine degradation.

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Pathways present in Genus Bacillus Absent in
E.Coli

• 2 Nitro propane degradation
• Denitrification pathway
• Folate transformations
• Formaldehyde assimilation
• Methanogenesis from acetate
• Octane oxidation
• Spermine biosynthesis
• Xylulose monophosphate cycle

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Effect of pathways absent in E.coli

• Xylulose monophosphate cycle and Methanogenesis
  from acetate are characteristic pathways of
  methanogenic bacteria and E.coli is not a
  methanogenic bacteria. Hence these pathways are
  absent in E.coli
• E.coli cannot reduce nitrate to dinitrogen
  because of absence of Denitrification pathway
• Formaldehyde produced from the oxidation of
  methane and methanol by methanotrophic bacteria
  is assimilated by Formaldehyde assimilation
  pathway. This pathway is absent in E.coli as it
  is not methanogenic

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Issues

• Taxonomic classification as per NCBI and thus
  errors can creep in
• No standard system to represent metabolic
  pathways
• Errors in annotation at gene level translate into
  errors in metabolic pathways
• Usefulness of metabolic pathways for
  characterization of microbes is not exploited

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Animal Virus Information System
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Signature peptide sequences for animal virus
families
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Species specific peptides Family Flaviviridae
Protein Envelope glycoproteins
28
VirGen Comparative genomics data mining of
viral genomes
Browse VirGen at http//bioinfo.ernet.in/virgen/vi
rgen.html
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Salient Features of VirGen

• Organizes genomic data in a structured fashion
  navigating from the family to an isolate
• Full genomes of viruses
• Compilation of representative genome entries for
  every viral species (Virus Taxonomy, 7th report
  of ICTV)
• Complete annotation of every genomic entry 
• Graphical representation of genome organization
• Generation of alternative names of proteins
• On-the-fly genome comparisons using BLAST2
• Multiple Sequence Alignment (MSA) of genomes,
  proteomes and individual proteins
• Whole genome phylogeny
• Prediction of B-cell epitopes

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VirGen Home
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Genome Sample Record in VirGen
Tabular display of genome annotation
Alternate names of proteins
Retrieve sequence in FASTA format
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Browsing the Module of Whole Genome Phylogenetic
Trees
Most parsimonious tree of genus Flavivirus Input
data Whole genome Method DNA parsimony Bootstrap
ping 1000
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Case Study Insertions in Pestivirus 1
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Issues

• ICTV classification and information available in
  published literature do not always match
• No standard method to describe viral
  isolates/strains
• Electron micrograph and other image data are not
  readily available making identification difficult
  and inaccurate
• Recombination occurs much faster in viruses than
  in bacteria/other microbes
• Host/vector information needs to be described in
  standard language
• Minimal availability of Immunological properties
  and therapeutic options in the databases

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Suggestions

• Devise measures to build confidence amongst
  underdeveloped and developing nations that their
  resources will not be exploited
• Networking and consortia among scientists,
  curators of culture collections, policy makers
  from developed and developing countries
• Material transfer agreements should be
  standardized by taking into consideration
  national security and biosafety
• Create awareness about open access and open
  educational resources
• Lobbying to policy makers to make publicly
  available the outcomes of government funded
  research
• Encouraging scientists to publish in open access
  journals
• Organize training programs by international
  experts to improve quality of culture collections
  and databases
• Improve access to specialized culture collections

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National Knowledge Commission

• The National Knowledge Commission (NKC) was
  constituted in 2005 as a high-level advisory body
  to the Prime Minister of India. The Commission
  has been given a mandate to guide policy and
  direct reforms, focusing on certain key areas
  such as education, science and technology,
  agriculture, industry, e-governance etc. Easy
  access to knowledge, creation and preservation of
  knowledge systems, dissemination of knowledge and
  better knowledge services are core concerns of
  the commission.

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National Knowledge Commission
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NKC Working Model

• Identify focus areas/target groups
• Consultations formal and informal
• Background research and analysis
• Constitution of Working Groups
• Internal deliberations of NKC
• Finalization of recommendations
• Submission to PM
• Widespread dissemination
• Implementation

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Suggestions

• Devise measures to build confidence amongst
  underdeveloped and developing nations that their
  resources will not be exploited
• Networking and consortia among scientists,
  curators of culture collections, policy makers
  from developed and developing countries
• Material transfer agreements should be
  standardized by taking into consideration
  national security and biosafety
• Create awareness about open access and open
  educational resources
• Lobbying to policy makers to make publicly
  available the outcomes of government funded
  research
• Encouraging scientists to publish in open access
  journals
• Organize training programs by international
  experts to improve quality of culture collections
  and databases
• Improve access to specialized culture collections