Quarterly e -Newsletter from Bioinformatics Centre
Volume IV, Issue I
The Bioinformatics Centre (DIC) at
KAU runs under the Biotechnology
Information System Network (BTISnet)
programme of DBT, Ministry of Science
& Technology, and Government of India.
The Centre was upgraded to Distributed
Information Centre during 2004 to
promote Bioinformatics research and
education. The Centre enhances access to
global information in life sciences
especially plant sciences and plant
biotechnology involving scientists and
students of the University and other S&T
institutions and acts as a support centre to
the Centre for Plant Biotechnology &
Molecular Biology. The Centre is
involved in a wide range of research
work on plant-pathogen interaction
studies, study of active compounds in
medicinal plants and in-silico analysis of
antifungal peptides in plants. In addition
to this, the Centre offers a credit course
in Bioinformatics to post graduate Plant
Biotechnology students, conducts routine
training programs in Bioinformatics and
maintains various databases relevant to
Proteomics & Genomics
Bioinformatics has become an integral part of research and
development in the biological sciences including health
care, agriculture, environmental management, and society.
It is panoptically acknowledged that the vista of biology is
in the midst of a ‘data explosion’. This data at the genomic,
transcriptomic and proteomic levels is obviously
substantial to advance our knowledge. Advances in
bioinformatics offer unprecedented opportunities for
biologists to rapidly collect and analyze enormous amounts
of data. These vast stores of information have a rich
potential to expedite scientific discovery and prevent
expensive duplication of experiments… Bioinformatics can
revolutionize not only the research sector but also its
judicious application can do wonders in transferring
knowledge to millions of marginal farmers of the country…
Biobits is a quarterly e- newsletter published by the
Bioinformatics Centre to promote overall concerns in
Bioinformatics applications in Agriculture.
Letters & Ideas
Largest-Ever Map of Plant Protein Interactions
First systematic network map of protein-protein interactions in the plant Arabidopsis
thaliana has been developed. Arabidopsis is a plant that has 27,000 proteins and serves
as a popular model organism for biological studies of plants, analogous to lab rats that
serve as popular model organisms for biological studies of animals.
The new Arabidopsis network map
defines 6,205 protein-to-protein
Arabidopsis interactions involving
2,774 individual proteins and it
known as an “Interactome”. By
itself, this map doubles the volume
of data on protein interactions in
plants that is currently available.
The production of the Arabidopsis network map was made possible, in part, by the
previous production of the genome sequence of Arabidopsis; this sequence is a veritable "parts
list" of the plant's genetic components. But more revealing than the genome sequence, the
network map provides insights on the functions of proteins, the compositions of protein
communities, and the evolutionary changes of proteins through time, among other things. This
work will help the researchers to get a system level picture of how Arabidopsis works, and guide
further research on other plant species, including those used in human agriculture and even
This work resulted in sorting of the protein interaction pairs found into functional groups,
revealing networks and "communities" of proteins that work together. And also it helped to find
the evidence that the Arabidopsis protein partnerships tend to change quickly after the
duplication event, then more slowly as the duplicated gene settles into its new function and is
held there by evolutionary pressure.
Possible Cure for Leukemia Found in Fish Oil
A newly produced compound from fish oil has targeted leukemia stem cells and
could lead to cure the disease. The compound - delta-12-protaglandin J3, or D12-PGJ3-
targets and kills the stem cells of chronic myelogenous leukemia (CML) in mice. This
compound is produced from EPA - Eicosapentaenoic Acid - an Omega-3 fatty acid found
in fish and in fish oil. It is found that this compound kills complete cancer causing stem
cells in the mice’s spleen and bone marrow by activating the gene p53and thus programs
the cell’s own death.
The available therapy for CML can only extends the patients life by keeping the
number of leukemia cells low, but the drugs fail to completely cure the disease because
they do not target leukemia stem cells and thus they are unable to kill them. In this
experiment, each mouse was injected about 600 nano grams of D12-PGJ3 each day for a
week and the test showed that the mice were completely cured of the disease and the
blood count was normal with a normal sized spleen.
Proteomics & Genomics
Genome of First Arachnid cracked
The genome of first arachnid –
spider mite is found. This brings new
insight into the evolution of
arthropods and offers new
opportunities to develop crop
protection against the spider mite.
Spider mites belong to the group of
the arachnids and are related to dust
mites and other parasitic mites such
as ticks that transmit serious
diseases to humans and animals.
Spider mites are colonial, invasive
mites that feed on plant juices.
The spider mite Tetranychus urticae likes over 1100 different plant species and is a
real plague in ornamental gardens and in greenhouse cultivation in our regions, among
which, tomatoes, peppers, cucumbers, strawberries, or complete corn and soybean fields.
But Spider mite pests lead to reduced harvests for farmers and are a threat to food
This genome contains unique genes that have not been identified in other
arthropods. These new genes play an important role in the development of spider mites
during evolution. This helped to identify numerous genes - involved in detoxification and
digestion - which help to explain the unsurpassed resistance of spider mites to pesticides
and its polyphagy and also identified the factors that are responsible for the production of
silk threads by the spider mite.
Prion Protein and Its Interaction with the Immune System
The neurodegenerative disease Scrapie functions as a model for other diseases
caused by the accumulation of proteins resulting in tissue malformations (proteinpathies),
such as Alzheimer's and Parkinson's disease. A new doctoral study has uncovered a
number of factors relating to the uptake of the prion protein (PrP Sc ) associated with the
development of this disease and how this protein interacts with the immune cells in the
Scrapie in sheep belongs to a group of
diseases called "Transmissible spongiform
encephalopathies"(TSE) because they are
transmitted between individual animals and
produce sponge-like, degenerative changes in the
Prion diseases may be infectious,
hereditary or occur sporadically/spontaneously.
Disease arises when the normal prion protein
mutates to the diseased variant, which differs
from the healthy prion proteins by its change in
The studies revealed that the prion protein makes use of the normal physiological
uptake channel for macromolecules in the intestines and that this may have a significant
effect on the body's immunological surveillance system.
Future studies which can reveal how immunological cells are transported and how
the prion protein is processed in the body will be of great interest, not only in order to
provide more knowledge about scrapie, but also about other neurodegenerative
proteinpathies, both in humans and animals.
Antibody Design - Simple Method to Target Harmful Proteins
Antibodies are large proteins produced by the immune system to combat infection
and disease. They are comprised of a large Y-shaped protein topped with small peptide
loops. These loops bind to harmful invaders in the body, such as a viruses or bacteria.
Once an antibody is bound to its target, the immune system sends cells to destroy the
invader. Finding the right antibody can determine the difference between death and
To design an antibody, the
arrangement and sequence of the
antibody loops is of utmost importance.
Only a very specific combination of
antibody loops will bind to and neutralize
each target. With billions of different
possible loop arrangements and
sequences, it is seemingly impossible to
predict which antibody loops will bind to
a specific target molecule.
The new antibody design process was used to create antibodies that target the
Alzheimer’s protein. This work is based by exploiting the same protein interactions that
cause the disease in the brain to mediate binding of antibodies to toxic Alzheimer’s
protein particles. Alzheimer’s disease is due to Alzheimer’s protein, which sticks together
to form protein particles. These particles then damage the normal, healthy functions of
the brain. By binding to specific portions of the toxic protein, we could test hypotheses
about how to prevent or reverse cellular toxicity linked to Alzheimer’s disease.
The new Alzheimer’s antibodies developed only latched on to the harmful clumped
proteins and not the harmless monomers or single peptides that are not associated with
Computer Assisted Design (CAD) for RNA
Researchers have developed CAD-type models and simulations for RNA molecules
that make it possible to engineer biological components or “RNA devices” for controlling
genetic expression in microbes. This holds enormous potential for microbial-based
sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs
and a host of other goods now derived from petrochemicals.
This work establishes a
foundation for developing CAD
platforms to engineer complex RNAbased
control systems that can
process cellular information and
program the expression of very large
numbers of genes. Perhaps even
more importantly, we have provided
a framework for studying RNA
functions and demonstrated the
potential of using biochemical and
biophysical modeling to develop
rigorous design-driven engineering
strategies for biology.
Since biological systems exhibit functional complexity at multiple scales, there
arises a question of whether effective design tools can be created to increase the sizes
and complexities of the microbial systems. This work establishes a foundation for
developing CAD platforms to engineer complex RNA-based control systems that can
process cellular information and program the expression of very large number of genes.
Most importantly by using a generalized engineering strategies it provided a framework
for studying RNA functions and demonstrated the potential of using biochemical and
biophysical modeling to develop rigorous design-driven engineering strategies for biology.
Homology Modeling and Molecular Dynamics Study of
Chitinases from cowpea (Vigna unguiculata)
During infection, plant cells produce a
group of proteins, coded by non-homologous
genes, named Pathogenesis Related (PR)
Proteins. Seventeen PR-proteins families have
been identified based on biological activity,
which can range from cell-wall/membrane
degrading enzymes, to protease inhibitors, and
proteins related to oxidative metabolism.
Chitinase and ß-1-3-glucanase are believed to
be important pathogenesis-related proteins in
defending plants against pathogens.
Chitinase has been speculated to play a
crucial role in plant defense against
fungal pathogens because of its ability to
digest chitin, a major constituent of the
cell walls of a number of fungal
Modeled structure of chitinase from
cowpea (Vigna unguiculata)
Letters & Ideas
This particular column is especially for readers and those who are interested in the field of
Bioinformatics. Here we are creating a new opportunity to share your valuable ideas with
So post your comments and suggestions to mail email@example.com or firstname.lastname@example.org.
A 21 days Winter School on “Advances in Micropropagation of Horticulture Crops”
was conducted at the Centre for Plant Biotechnology and Molecular Biology, Kerala
Agricultural University, Vellanikkara, Thrissur for 25 participants from December 1-21,
For more details visit our website: www.kauhort.in/CPBMB.htm
About The Team:
Priyanka James, Parvathi Sudha K.K,
Nandana M, Mekha Mohan, Vipin A.M
How to Reach Us
Bioinformatics Centre (DIC),
ITBT Complex, Kerala Agricultural University, KAU P.O,
www.kaubic.in, email: email@example.com,
firstname.lastname@example.org or email@example.com
Ph: 0487-2371994, Fax: 91487-2371994.
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