microbial research commons including viruses
Download
Skip this Video
Download Presentation
Microbial Research Commons Including Viruses

Loading in 2 Seconds...

play fullscreen
1 / 39

Microbial Research Commons Including Viruses - PowerPoint PPT Presentation


  • 78 Views
  • Uploaded on

Microbial Research Commons Including Viruses. Prof. A.S. Kolaskar Bioinformatics Center University of Pune Pune, India. Introduction. Increasing research in life sciences and biotechnology in Indian Universities and national research institutions

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Microbial Research Commons Including Viruses ' - zoe


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
microbial research commons including viruses

Microbial Research Commons Including Viruses

Prof. A.S. Kolaskar

Bioinformatics Center

University of Pune

Pune, India

introduction
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
culture collections in india
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
culture collections in india1
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

thailand network of culture collections
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
issues
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
pump e salient features
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/
approaches
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
slide9

PUMP-E

Homologymodels

Compound

Enzyme

Database

Organism

Gene

Reaction

Pathway

User-friendly

Query interface

Search by keywords

Molecular viewer

Dynamic generation of queried pathway

source databases for data acquisition
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
pump e front end and query system
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.
hamming distance calculations
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
metabolic pathway path profile
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.

comparison of pathways from genus bacillus with e coli

Bacillus anthracis

Bacillus cereus 10987

Bacillus subtilis

Bacillus cereus Zk

Bacillus anthracis Sterne

Bacillus halodurans C-125

Bacillus anthracis strain A2012

Bacillus licheniformis ATCC 14580

Bacillus cereus ATCC14579

Bacillus anthracis Ames Ancestor

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

pathways absent in genus bacillus present in e coli
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
effect of pathways absent in genus bacillus
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.
pathways present in genus bacillus absent in e coli
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
effect of pathways absent in e coli
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 ofDenitrification 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
issues1
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
signature peptide sequences for animal virus families

Family

Genus

Protein

Peptide

Togaviridae

Alphavirus

Structural polyprotein

AYEHXXV/TXPN

Filoviridae

Filovirus

Nucleocapsid protein

PQLSAIALGVAT

AHGSTLAGVNV

GEQYQQLREAA

Iridoviridae

Lymphocystivirus

Iridovirus

Capsid protein

TSXFIDXAT

IEKXXYGG

SRXGDYXL

Papovaviridae

Papillomavirus

L1 protein

CKYPDF/Y

GHPLF/YNKV/L

Polyomavirus

Coat protein VP1

PDPXXNEN

GVGPLCK

QVEEVR

Coat protein VP2

WXLPLXLGLYG

Arenaviridae

Arenavirus

Surface glycoprotein

MLXKEYXXRQXXTP

PTHXHIXGXXCPXPHR

LXLXGRSC

Flaviviridae

Flavivirus

Non structural protein 1

CWYXMEIRP

Envelope glycoprotein

DRGWGNXCGXFGKG

Adenoviridae

Hexon protein

FKPYSGTA

GVLAGQ

PNYCFPL ,NPFNHHRN

Signature peptide sequences for animal virus families
species specific peptides family flaviviridae protein envelope glycoproteins

Virus

Peptide

Unique upto -

number of

mismatches

St. Louis encephalitis virus

VNPFISTGGAN

3

EGRPAT

0

Murray valley encephalitis virus

VTANPYVASSTA

3

Japanese encephalitis virus

LDVRMINIEA[S/V]Q

3

West Nile virus

TTKATGWIIQK

3

Kunjin virus

STKATGRTILKE

3

Langat virus

DGAEAWNEAGR

3

FTCEDKK

0

VGFSGTRP

0

Yellow fever virus

MRVTKDTN[D/G][N/S]NL

3

Powassan virus

KDNQDWNSVE

3

Dengue type 1 virus

GTVLVQV

0

Dengue type 2 virus

GTIVIRV

0

Dengue type 3 virus

TEATQL

0

GTILIKV

0

Dengue type 4 virus

TTAKEVA

0

GTTVVKV

0

Tick borne encephalitis virus

GFLTSVGKA

0

Louping ill virus

NPHWNNVER

0

Species specific peptidesFamily – Flaviviridae Protein – Envelope glycoproteins
slide28

VirGen

Comparative genomics & data mining of viral genomes

Browse VirGen at

http://bioinfo.ernet.in/virgen/virgen.html

salient features of virgen
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
virgen home

Genome analysis &

Comparative genomics resources

Menu to browse viral families

Search using Keywords & Motifs

Guided tour & Help

Navigation bar

VirGen Home
slide31

Genome Sample Record in VirGen

Tabular display of genome annotation

‘Alternate names’ of proteins

Retrieve sequence in FASTA format

browsing the module of whole genome phylogenetic trees

Most parsimonious tree of genus Flavivirus

Input data: Whole genome

Method: DNA parsimony

Bootstrapping: 1000

Browsing the Module of Whole Genome Phylogenetic Trees

Most parsimonious tree of genus Flavivirus

Input data: Whole genome

Method: DNA parsimony

Bootstrapping: 1000

slide33

891-1787 bp region remains

unannotated using

representative strain

What is the origin of the insert ???

BLAST with VirGen confirmed the non-viral origin of the insert

BLAST with GenBank produced significant

match with Bos taurus J-domain protein

Case Study: Insertions in Pestivirus 1

issues2
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
suggestions
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
national knowledge commission
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.
national knowledge commission1

Access

Creation

Concepts

Services

Applications

National Knowledge Commission
nkc working model
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
suggestions1
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
ad