January 2012, Volume IV, Issue I - Bioinformatics Centre, Kerala ...

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January 2012, Volume IV, Issue I - Bioinformatics Centre, Kerala ...

Biobits

Quarterly e -Newsletter from Bioinformatics Centre

Volume IV, Issue I

January 2012

About Us

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

agriculture.

Contents

Cover Story

Agricultural Bioinformatics

Drug Discovery

Proteomics & Genomics

News Archive

Discovery Today

Cover Story

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.

Cutting Edge

Our Focus

Letters & Ideas


Agricultural Bioinformatics

Contents

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

pharmaceuticals.

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.

Source: http://www.sciencedaily.com/releases/2011/07/110728144936.htm

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Drug Discovery

Contents

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.

Source: http://www.sciencedaily.com/releases/2011/12/111222103112.htm

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Proteomics & Genomics

Contents

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

production.

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.

Source: http://www.vib.be/en/news/Pages/Genetic-code-of-first-arachnid-cracked.aspx

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News Archive

Contents

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

intestines.

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

brain.

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

structure.

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.

Source: http://www.sciencedaily.com/releases/2011/12/111229091638.htm

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Discovery Today

Contents

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

recovery.

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

disease.

Source: http://www.sciencedaily.com/releases/2011/12/111209105746.htm

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Cutting Edge

Contents

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.

Source: http://www.sciencedaily.com/releases/2011/12/111222142452.htm

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Our Focus

Contents

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

pathogens.

Modeled structure of chitinase from

cowpea (Vigna unguiculata)

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Letters & Ideas

Contents

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

senior scientists.

So post your comments and suggestions to mail bic@kau.in or kaubioinfo@gmail.com.

Training

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,

2011.

For more details visit our website: www.kauhort.in/CPBMB.htm

About The Team:

Dr.R.Keshavachandran (Coordinator)

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,

Thrissur, Kerala-680656.

www.kaubic.in, email: kaubioinfo@gmail.com,

kauniv.btisnet@nic.in or bic@kau.in

Ph: 0487-2371994, Fax: 91487-2371994.

Click here for our BioBits Archives

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