Molecular diagnostics - TBGRI

austrianceilBiotechnology

Oct 1, 2013 (4 years and 10 days ago)

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Bioinformatics


a KAU perspective


Keshavachandran,R, Ajitha T.K, Lavina C.V, Deepthy P.S, Nazeem P.A and Girija D

Bioinformatics Centre, College of Horticulture, KAU, Vellanikkara, Thrissur, 680656

e
-
mail id. rkcs@rediffmail.com


The Distributed Inform
ation Sub Center at Kerala Agricultural University, Thrissur
was set up in May 1995 as the 23
rd

center of the BTISNet of DBT, Government of India.
The area of specilisation of the Centre is Agricultural Biotechnology. The Centre passed
through several phas
es involving Internet connectivity through the ordinary C band
connectivity, then the Ku band connectivity etc. Now the communication facilities of the
Centre have been strengthened by procuring an ISDN Internet connection and a connection
through ASIANET.

The Center caters to the needs of the students (UG, M Sc & Ph D) and
faculty of all departments of the Colleges in the main campus as well as of the other nearby
academic and research centers of the University. Over the years, DISC has come to occupy
a p
osition in the KAU in the area of Information Technology , information sources and
services based on Internet, CD
-
ROMs etc. The Centre has procured databases in the field
of Biotechnology and developed several databases in the field of Agriculture and
related
fields. The center regularly conducts training programmes in Bioinformatics. The research
activities in the field of Bioinformatics have been enhanced. The Centre has now been
upgraded to DIC to facilitate intensive research on Bioinformatics in

an effective manner.
During the year 2004, the Centre has also started offering a course on Bioinformatics for
the M.Sc Biotechnology students of the College of Horticulture.


Biotechnology research in KAU spread over various research stations and campuse
s
includes Plant Biotechnology, Animal Biotechnology and Fisheries Biotechnology. Thrust
areas for Plant Biotechnology include developing
in

vitro

protocols for mass multiplication
of elite types of fruit plants, ornamentals, medicinal plants, spices, plan
tation crops and
forest species. The other thrust areas include checking clonal stability and genetic fidelity
of
in vitro

derived plants using molecular markers, DNA finger printing and
characterisation of germplasm with molecular markers, imparting bioti
c and abiotic stress
tolerance in otherwise accepted crop varieties, genetic transformation for imparting/
improving expression of desired traits, i
n vitro

germplasm conservation, enhancement of
secondary metabolites production etc.


The crops identified f
or biotechnology research at KAU include spice crops like
black pepper, ginger, turmeric, vanilla, cardamom; plantation crops like cashew, coconut
and medicinal & aromatic plants such as
Kaempferia, Trichopus, Gymnema, Holostemma
and Coscinium.

For impro
vement of such crops through molecular breeding, it is highly
essential to identify/design specific probes/primers, micro
-
satellites, etc. By combining the
research results generated at the Biotechnology Centre and information retrieved from the
Bioinform
atics Centre, suitable probes, primers are being designed for characterization and
improvement of these unique crops through molecular breeding.



Molecular diagnostics for diseases



Molecular diagnostics include newer techniques for sensitive agents of d
isease in
biological materials. Modern diagnostic methods are based on high affinity biomolecular
interaction between ligand binders. These include DNA
-
DNA hybridization, DNA
-
RNA
hybridization, PCR techniques like BIO
-
PCR, RT
-
PCR, nested PCR, immuno
-
PCR,

RFLP,
RAPD, AFLP, etc. Information retrieved from available databases are being utilized for
detecting the conserved sequences for molecular diagnostics in crops like coconut (root
-
wilt), black pepper (little leaf), cardamom (kokke kandu, katte) and in a
nimals like cattle,
duck and buffaloes.


Apart from KAU research projects of the scientists, the Centre for Plant
Biotechnology and Molecular Biology, College of Horticulture also executes several PG
projects, externally aided projects etc. for which the c
enter has rendered facilities for
regular CD ROM database search,

Internet search, BLAST & FASTA searches, primer
designing, multiple sequence alignment with ClustalX, ClustalW, phylogenetic analysis
using PHYLIP, NTSYS etc. and usage of other Bioinformat
ics software.


Primer designing

The cDNA and amino acid sequences for

-
1,3 glucanase and hydroxy methyl
glutaryl CoA reductase (hmgr) genes from various plant species available with NCBI were
used to locate conserved regions and three sets of degenerate p
rimers were designed based
on conserved boxes among different genera and species of plants. Software available from
the public domain (Primer 3, Clustal W and BCM search launcher) were used for
designing.


Deposition of sequence in database

The amplicons

o
btained through RT PCR using the above primers were cloned and
sequenced. Sequence homology search revealed similarity of sequence with hmgr genes
already available in database.The sequences deposited in NCBI are those with Accession
No.
Bankit

488538

is
olated from the plant
Datura

and with Accession No. AY 228453
isolated from the plant
S.xanthocarpum




Molecular diagnostics

An RAPD band unique for race 3 of
Ralstonia solanacearum

causing bacterial wilt
in vegetables
and ginger
, was sequenced. S
equence homology search revealed similarity
with capsular protein in
Haemophilus influenzae.
The sequence is with Acc. No. AF
472594 and organism :
Ralstonia

solanacearum


Detection of genetic diversity in
Piper

species using RAPD and AFLP markers

The rela
tedness of disease genome of
Piper

is studied using dominant markers such
as Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length
Polymorphism (AFLP). Nine
Piper
species were included in the study. The study revealed
the genetic relation
ship /diversity among the related species. The results obtained are well
correlated with the conventional taxonomical interrelationships of these species.


The Centre’s website has been developed and made available through the Internet.
The URL of the si
te is http://www.bickau.org.


The topics handled in the training programmes conducted by the Centre were Basics
of Networking, Unix operating system, Internet browsing, Basics of Databse management,
Statistical tools in Agricultural research, Bioinformatic
s tools and sources, sequence
analysis of proteins and nuceic acids etc.

For all the trainings , course materials also have
been prepared and given to the trainees.


The Centre has procured databases such as Biotechnology Abstracts, Biological and
Agricul
tural Index, Agricola and Agrisearch.


The Databases Developed by the Centre include
Improved varieties of crops released
by KAU which provides d
etailed information on the cultural aspects, varietal description
etc. about the crop varieties released by KA
U,
Research highlights of Biotechnology in
KAU which provides abstracts of research results of different projects in Biotechnology at
KAU,
Database on β
-
1,3 glucanase, hydroxy methyl glutaryl CoA reductase and chitinase
from plant species which contains nucleotide and amino acid sequences, name of authors,


accession number and other relevant information, Colleges and research stations
of K
AU,


Tissue culture protocols,
Directory of KAU research projects.


The Software available in the Centre are
Macromedia Director 7, Omiga, Genedoc ,
Isisdraw, Spectrum,

NTSYS pc 2.1,

Rasmol, Qmol, Swiss pdb viewer,
Pymol,
Clustal X,
Treeview, Bioedit, Mo
lphy.


The other information resources of the Centre include Bioinformatics books, Journals
and Directories.


The ongoing research projects in the Centre are Genome analysis of
Trichoderma
viride
, Comparative analysis of opines produced by
Agrobacterium

sp
. and
Rhizobium

sp.
etc.


The Centre proposes to develop databases on Biofertilizer and Biocontrol agents
developed at KAU and another database on Characterisation and digitization of germ
plasm conserved at KAU.