I N S I D E

T H I S I S S U E :

B U S I N E S S N A M E

V O L U M E 1 ,

IN FOCUS: ASTHMA

FACE TO FACE

With Dr. G. B. Nair

NICED: An Overview

BIOLOGIX :

In –Sillico Drug Design

BURNING ISSUES

UNSOLVED ISSUES

WEST BENGAL UNIVERSITY OF TECHNOLOGY

FROM ALUMNI’S

DESK

WBUT –SBT POLLS

QUIZ AND CROSS-

WORD

FACE TO FACE

IN FOCUS

POLLUTION

P A G E 2

B I O V A R I A N C E

P AV O L U M E 1 , I S S U E

FROM THE TEACHERS’ DESK

Publication of Biovariance by the students of the School of

Biotechnology is an exciting effort. It will certainly con-

tribute towards the expression of their ideas and thinking

on the present scenario in Biotechnology in particular and

different aspects of Science and Technology in general. I

wish a great success for Biovariance.

Dr. Subroto Kumar Dey,Director,School Of Biotechnol-

Congratulations for successful launching of your magazine. I

believe your dedication towards the development of this maga-

zine would be essentially required at all stages. Keep up the

hard work. With all the best wishes and regards.

Dr Jaya Bandhopadhyay, Lecturer ,WBUT

Dr. Raja Banerjee,Reader,WBUT

After waiting for quite a few years we would finally have

our departmental magazine. I express my best wishes and

heartfelt thanks to the current batch of students for this

wonderful gift to the department.

Dr Shaon Ray Chaudhuri ,Lecturer,WBUT

It is very encouraging to have the magazine ―Biovariance‖. I wish

you success.

Dr Rabi Majumdar

Advisor, School Of Biotechnology,WBUT

Biovariance –the colours of life , gives me a terrific feeling not only

because it has the name that I opted for selection but also because the

long awaited child has been conceived and will be born soon.

Dr Soumali Basu

Lecturer,Dept. Of Bioinformatics,WBUT

Good effort,Wish you success…!!!!!!!!

Mr. Subhranshu Supakar,Project Officer, WBUT

B I O V A R I A N C E

Tomader subho budhhir uday hok.

P A G E 4

“In addition to

having a major

impact on poverty

and hunger,

biotechnology

has great

potential to

alleviate

environmental

degradation”. (2001)

Caption describing

picture or graphic.

ITS ALL IN A

GENE AND

ITS

TRANSCRIPT

B I O V A R I A N C E

.

Biovariance is an exciting concept. I really appreciate

the effort students have taken in bringing this out. I

wish them all the best and hope they continue this

good work.

Dr Anindita Seal, Associate Lecturer,WBUT

A magazine is also the name of the device that holds bul-

lets. I hope your magazine will also be loaded with stuff

that impacts its readers. Best wishes for your enterprise.

Dr. Indrani Roy,Lecturer,School Of Biotechnology,WBUT

A great effort by the students . I wish ― Biovariance‖

becomes one of the best magazines in near future.

Dr. Salil. C. Dutta,

Advisor,School Of Biotechnology,WBUT

Biovariance, is blooming for the first time by our beloved students from the De-

partment of Biotechnology of this University with all its essence and breaking all

the barriers to create the ultimate bonding between the students and teachers with a

view to open up new vistas accumulating the scientific and technological informa-

tions of present and past. Amit Chakraborty, Project Officer, WBUT

I am happy to know that the students of Biotechnology are going to publish a magazine. Hope this will contain your thoughts and inspiration, not only on the narrow field of your class room specialization but also on the general applicability of the knowledge on the benefit of human kind. It is important to inquire who we are on the planet and what we do to keep it safe and vi-able for all. Never stop asking questions. Keep the windows of mind open. My best wishes for the success in your life". N.P.Bhattacharya,HEAD,Bioinformatics Dept,SINP,Guest lecturer,WBUT

It gives me high pleasure that Students of School of Biotechnology, WBUT have

shown their courage to launch a magazine Biovariance-colours of life. I wish the

magazine would be colourful with knowledge based articles and surely will make

great impact on student - teacher community.

Hearty congratulations on the successful launch of the scientific magazine

―Biovariance‖. May this experience be a guiding light in your future en-

deavours Chabita Saha, Lecturer, WBUT.

The publication of Biovariance by students of the School of Biotechnology is

indeed a praiseworthy effort.As a faculty member I feel proud of this achieve-

ment.I hope that this magazine will continue to excel and leave a prominent

impression in the area of biotechnology.

CONTENTS

P A G E 5

B I O V A R I A N C E

PAGE NUMBER CONTENTS

EDITORIAL

IN FOCUS

NEW SCIENTIST

Face to face with one of the

pioneers in the field of science in

India, a Foreign Associate of

National Academy of Sciences,

USA and the winner of the prestigious Shanti Swarup Bhatnagar

Award for Medical Sciences for the discovery of globally known

as Vibrio cholerae O139 Bengal and his contributions on

describing a cell-rounding factor from strains of Vibrio cholerae.

POLLUTION AND ASTHMA

A novel approach in understanding asthma and its rele-

vance with the current air pollution problems faced by the

country.

OUR DEMOGRAPHIC DIVI-

DEND OR A NIGHTMARE..??

FROM THE CAMPUS

A sneak peak into one the most

prestigious enteric disease

research centers in eastern India.

8

9

12

14

P A G E 6

B I O V A R I A N C E

UNSOLVED ISSUES

ASBESTOS POLLUTION –

A serious health hazard

PLASTIC BAGS-

Reality check up

RARE DISEASE - PROGERIA

BURNING ISSUES

WHITE BIOTECHNOLOGY:

Microbial production of commercially important products

based on In-Vitro manipulation by recombinant DNA

technologies and its relevance with India in Poly Lactic Acid

production.

Can it make our lives sweeter in

reality…??

BIOLOGIX

How a bioinformatic In- Sillico

drug design aided

approach can be used to execute the

rehabilitation of drug addiction by production of target

18

22

24

P A G E 7

B I O V A R I A N C E

DISCOVERIES

MOSQUITOCIDAL

VACCINES

MALARIA: A DISEASE FOR THE

POOR A novel strategy to combat ma-

laria by

BIONFORMATICA

PROTEIN MODELLING

ISSUES ON CAMPUS

WBUT CAMPUS : A place

with immense scope and

the capacity for improvement

BIOTECH POUTPURRI

CURRENT BIOTECH NEWS

QUIZ

AND

CROSSWORD

CAREER ASCENT

ALL ABOUT GRE

CURRENT NOTIFICATIONS

FROM ALUMNI’S DESK

DRUG DESIGN MADE EASIER

21

26

31

40

36

33

32

28

P A G E 8

Our demographic dividend or nightmare? -Dr Joydeep Mitra <utechbiotech@gmail.com>

Nandan Nilekani (Infosys co-founder) in his best selling book ‗Imagining India‘ (Penguin

Press, 2008) raises the stirring possibility that India would demographically be the youngest

nation within a few decades. If millions of young peoples‘ energy is harnessed constructively, it

could be a boon to the people of India and the world and if not, it would be a nightmare. With a

population of ~1,160,000,000, only 3 – 5% Indians read, write or understand English -an indis-

pensable currency of acquiring higher education. Adult literacy rates vary state wise within In-

dia; however, we still have the largest number of illiterate people among all countries. Malnour-

ishment and undernourishment in India is one of the highest in the world. The supply of clean

drinking water reliably separated from effluents, professional quality sewage treatment systems

remain an urgent yet unmet need. Water borne diseases deprive India‘s masses of immense pro-

ductivity gains including usurping hospital expenditures, thus cost economic growth and impose

human suffering on the most vulnerable. Disease causing microorganisms do not discriminate -

the most deprived among us are ones with the least amenities of care and support.

Science has delivered –the infant mortality rate has fallen, vaccination (small pox, polio,

among others), advances in medical care, sanitation, have increased longevity. More needs re-

main, especially in inventing sustainable energy use coupled with high standard of living. These

have to be met by the current young generation and be our demographic dividend which could

serve as an example in world history as has been accomplished by the following examples, de-

spite the prevailing challenging infrastructure within India.

Dr. Verghese Kurien‘s community based efforts in Anand, Gujarat, contributed exempla-

rily (white revolution) to enable India become the largest annual producer of milk in the world.

Prof. M. S. Swaminathan and his co-workers‘ scientific research have empowered Indian farm-

ers with sustainably higher crop yields fostering the much empowering green revolution. Mr.

Satyen ‗Sam‘ Pitroda and his colleagues ushered in the telecommunications revolution in India

which has accentuated connectivity among all citizens. Mr. E. Sreedharan has consistently dem-

onstrated the professional completion of government projects (Konkan Railway and Delhi

Metro Rail) within budget and on time. Scientists and engineers at the Indian Space Research

Organization have accomplished some of the most cost effective payload liftoffs of satellites

into space. Tata Motors‘ engineers produced the world‘s lowest priced car (nano) in India.

This issue contains an interview with Dr. G. Balakrish Nair of National Institute of Chol-

era and Enteric Diseases in Kolkata. Learning and watching how successful scientists work

might inspire us and could pave the way for us to find newer, better ways of prosperous, sustain-

able and peaceful livelihood. Scientists and engineers must play an immense constructive role.

Innovation by young Indian minds could maximize our dividends and meet our immense

challenges with Indian solutions to an India aspired by Rabindranath Thakur (1861-1941, Nobel

Literature, 1913) as:

Where the mind is without fear and the head is held high;

Where knowledge is free;

Where the world has not been broken up into fragments by narrow domestic walls;

Where words come out from the depth of truth;

Where tireless striving stretches its arms towards perfection;

Where the clear stream of reason has not lost its way into the dreary desert sand of

dead habit;

Where the mind is led forward by thee into ever-widening thought and action--

Into that heaven of freedom, my Father, let my country awake.

-- Rabindranath Thakur (in Gitanjali, 1910).

B I O V A R I A N C E

EDITORIAL

“Biotechnology has

the potential to

bring tremendous

benefits …” (July

10, 2001).

P A G E 9

IN FOCUS - POLLUTION AND ASTHMA

What is Asthma? Asthma, in medical terms is

characterized by hyperre-

sponsiveness of tracheo-

bronchial smooth muscles

to a variety of stimuli, re-

sulting in narrowing of air

tubes, often accompanied

by increased secretion, mu-

cosal edema and mucosal

plugging.

Asthma is now

recognized to be a primarily

inflammatory condition:

inflammation underlying

hyperactivity.

What triggers Asthma?

Trigger factors (Infection,

irritants, pollutants, exer-

cise, exposure to cold air,

psychogenic)

Recruitment of mast cells

and inflammatory cells.

Production of multitude of

mediators:

1. Release of mediators

stored in granules

(immediate) : Histamine,

Protease enzymes, TNFα

2. Release of phospholipids

from membrane followed

by mediator synthesis

(within minutes) : Pros-

taglandins, Leukotrienes ,

Plasma activating factors.

3. Activation of genes fol-

lowed by protein synthesis

(over hours): Interleukins,

Tumor necrosis factor α.

B I O V A R I A N C E

International Food

Information Council

(IFIC):

“Revolutionary,

unprecedented,

unsurpassed. These

adjectives are being used

to describe the Human

Genome Project’s

potential to benefit

society. The

understanding of the

human genome that has

been gained, is almost

certain to lead to

breakthroughs in

medicine that may

ultimately eradicate many

of today’s diseases”.

(Food Insight, October

2001.)

www.journal.prous.com/.../images

Causes of Asthma:

Environmental tobacco smoke: maternal cigarette smoking, is associated with high risk of

asthma prevalence and asthma morbidity, wheeze, and respiratory infections.

Poor air quality from traffic pollution.

High ozone levels has been repeatedly associated with increased asthma morbidity .

Caesarean sections: They have been associated with asthma when compared with vaginal birth.

It was proposed that this is due to modified bacterial exposure during Caesarean section compared

with vaginal birth, which modifies the immune system .

Psychological stress: It was found out that stress modulates the immune system to increase the

magnitude of the airway inflammatory response to allergens and irritants.

Antibiotic : It was found that antibiotics make one susceptible to development of asthma

because they modify gut flora, and thus the immune system.

BY: Amit Rai, M.Tech (Biotechnology)

P A G E 1 0 V O L U M E 1 , I S S U E 1

What are the approaches to the treat-

ment?

1.Prevention of AG:AB reaction

2.Suppression of inflammation and

bronchial hyper reactivity

3.Prevention of release of mediators

4.Antagonism of released mediators

5.Blockade of constrictor neurotrans-

mitter

6.Mimicking dilator neurotransmitter

7.Directly acting bronchodilators

of 9%, 10.5%,

18.5%, 24.5% and

29.5% respectively.

The increased preva-

lence correlated well

with demographic

changes of the city.

Further to the hospi-

tal study, a school

survey in 12 schools

on 6550 children in

the age group of 6 to 15 years was un-

dertaken for prevalence of asthma and

children were categorized into three

groups depending upon the geographical

POLLUTION AND ASTHMA:

Epidemiology of Asthma in India

1. Bangalore

Allergic respiratory disorders, in par-

ticular asthma are increasing in preva-

lence, which is a global phenomenon.

Genetic predisposition is one of the

common factors in children for the in-

creased prevalence - urbanization, air

pollution and environmental tobacco

smoke contribute more significantly. A

hospital based study on 20,000 children

under the age of 18 years from

1979,1984,1989,1994 and 1999 in the

city of Bangalore showed a prevalence

situation of the school in relation to

vehicular traffic and the socioeco-

nomic group of children. Group I-

Children from schools of heavy traffic

and cough are also common

symptoms associated with

use of inhaled steroids

Systemic side effects:

Treatment with corticoster

oids may cause hypotha

lamic-pituitary adrenal

(HPA) axis suppression by

reducing corticotrophin

(ACTH) production , which

in turn leads to reduced

cortisol secretion by

the adrenal gland.

Steroids can also induce

Osteoporosis by in-

creasing bone

resorption and

decreasing bone

formation.

Local side effects:

Local side effects of

inhaled steroids depend

on delivery system, dose

and frequency of adman

stration. The most common

local side effect is Dyspho

nia (Hoarseness) which is

reversible after discontinue

tion of therapy.

Orophayngeal candiasis

(Thrush) affect adults more

often children.

Sore throat, throat irritation

SAY NO TO

POLLUTION

Corticosteroids: The mainstay in

asthma therapy

The realization that asthma is pri-

marily an inflammatory disease

which accentuates with time, if

not controlled, and the availability

of inhaled steroids that produce

few adverse effects has led to an

early introduction and more ex-

tensive use of corticosteroids in

asthma.

How it works?

Glucocorticoids suppress

immunological competence.They

suppress all types of hypersensiti-

zation and allergic phenoena.The

clinical effect appears to be due

to suppression of recruitment of leuko-

cytes at the site of contact with antigen

and inflammatory response to immu-

nological injury.

They cause greater suppression of cell

mediated immunity in which T cells

are primarily involved.e.g. delayed

hypersensitivity and graft rejec-

tion.This is the basis of use in autoim-

mune diseases and organ transplanta-

tion. Factors involved may be inhibi-

tion of IL-1 release from macro-

phages ; inhibition of IL-2 formation

and action as a result of which T cell

proliferation is not stimulated; sup-

pression of natural killer cells etc.

Adverse effects of Corticosteroids:

www.soylabs.com/img/osteoporosis.jpg

P A G E 1 1 V O L U M E 1 , I S S U E 1

References:

Books:

1. Essentials of Medical Pharmacology, K.D.Tripathi, 5th Edition

2. Goodman & Gilman‘s Pharmacological basis of Therapeutics.

3. Bioorganic and Medicinal Chemistry, Gupta, Jindal & Kumar,Vol.12 Issue 24

Websites:

1. www.indiainfoline.com

2. www.pharmabiz.com

3. www.vhn.net

4. www.healthcare.com

5. www.druginfonet.com

6. www.journal.prous.com/.../images

7. www.soylabs.com/img/osteoporosis.jpg

8. www.nhlbi.nih.gov/guidelines/asthma/03_sec2_def.pdf

9. en.wikipedia.org/wiki/Asthma

dioxide (SO2), suspended particu-

late matter (SPM) and oxides of

nitrogen (NOX), emitted from trans-

port sector, during the years 1995–

2000 (without CNG) and the year

2001 (with CNG) has been made in

order to assess the impact of CNG

vehicles on ambient air quality in

Delhi. The annual average concen-

tration of SPM came down to 347

from 405 μg m−3, which is still be-

yond the permissible limits. The

concentration of annual averages of

CO, SO2 and NOX decreased to

4197 from 4681 μg m−3, 14

from 18 μg m−3 and 34 from

36 μg m−3, respectively, and are

well within the permissible lim-

its. An analysis of SO2/NOX and

CO/NOX concentrations, whose

correlation coefficient r2 has the

values 0.7613 and 0.7903, re-

spectively, indicates that point

sources are contributing to

SO2 and mobile sources are

contributing to NOX concentrations.

It has been found that concentration

contribution of above pollutants has

been reduced considerably.

Several initiatives were taken to

reduce extremely high levels of

pollutants present in the ambient

air of urban city. One of the

initiatives was to move public

transport to CNG, which has

been implemented in Delhi

since April 2001. Delhi boasts

CNG in nearly 2200 buses,

25,000 three wheelers, 6000

taxis and 10,000 cars. A relative

comparison of ambient air con-

centration of pollutants, e.g.

carbon monoxide (CO), sulphur

“In addition to

having a major

impact on

poverty and

hunger,

biotechnology

has great

potential to

alleviate

environmental

degradation”.

(2001)

and the socioeconomic group of children. Group I-

Children from schools of heavy traffic area showed

prevalence of 19.34%, Group II-Children from

heavy traffic region and low socioeconomic popula-

tion had 31.14% and Group III-Children from low

traffic area school had 11.15% respectively. (P: I &

II; II & III <0.001). A continuation of study in rural

areas showed 5.7% in children of 6-15 years. The

persistent asthma also showed an increase from

20% to 27.5% and persistent severe asthma 4% to

6.5% between 1994-99.

2. New Delhi

Delhi has seen a mind-boggling 500 per cent

in crease in industries in the last 30 years from

18,500 units in 1961 to around 93,000 in 2001.

In Delhi, as in most other cities, vehicular pollu-

tion is the main culprit for air pollution, account-

ing for 65 per cent of the city's total pollution.

Industry and thermal plants contribute 25 per

cent and the remaining 10 per cent is due to do-

mestic activity.

The Central Pollution Control Board

(CPCB) estimates that 2,000 metric tonnes of

poisonous gases and 300 million litres of waste

water and corrosive liquid by-products, are

pumped into New Delhi's environment each day.

Some industrial processes result in new, little-

known compounds, which endanger workers'

safety and health and persist in the environment

long after use.

The number of deaths reported due to

asthma was 7000 in year 2001.

P A G E 1 2

Dr Rob Adam, Director-

General: Arts, Culture,

Science and Technology:

“Government’s

Foresight Programme

has identified three

main drivers of future

economies;

information and

communications

technology, advanced

materials, and

biotechnology”.

JICA LANDMARK

NEW SCIENTIST:

G. Balakrish Nair is an eminent Indian mi-

crobiologist. Under the supervision of Dr.

Nair, 25 students have obtained their doc-

toral degrees. He is the author of over 400

research papers in the area of Clinical Mi-

crobiology, Molecular Epidemiology and

Molecular Pathogenesis of Enteric bacteria.

At present, he is the Director of National

Institute of Cholera & Enteric Diseases

(NICED), Kolkata, India. Before joining

NICED as director, he was the director of

Laboratory Sciences Division at the Interna-

tional Center for Diarrhoeal Diseases Re-

search, (ICDDR), Dhaka, Bangladesh.

In 1987-88, he did postdoctoral research on the heat-stable enter toxin of V. cholerae with Dr.

Tae Takeda in the Department of Infectious Diseases Research, National Children‘s Medical

Research Center, Tokyo, Japan and in 1994-95 he did his sabbatical research on molecular epi-

demiology of V. cholerae in the Department of Microbiology, Kyoto University, Japan with

Professor Yoshifumi Takeda. He was also a visiting scientist at the Department of International

Health, Johns Hopkins University, Baltimore, Maryland, USA in 1992 for 3 months where he

worked with Dr. David Sack and at the Laboratory Centre for Disease Control, Ottawa, Canada

He graduated from Loyola college, Madras University in 1975, gained his M.Sc (Title-A review

on L-asparaginase production in microorganisms and studies on L-asparaginase activity in estua-

rine fungi (Supervisor: Dr. D. Chandramohan) in Marine Biology in 1977 from Annamalai Uni-

versity and acquired the Degree of Ph.D (Title-Studies on ecology, serology and taxonomy of

Vibrio parahaemolyticus and allied vibrios from estuarine and neritic environs of Porto Novo

(Supervisor: Professor R. Natarajan) from Annamalai University in 1982. He joined the Depart-

ment of Microbiology,(NICED), Calcutta, a constituent Institute of the Indian Council of Medi-

cal Research and a WHO Collaborating Centre for Research and Training in Diarrhoeal Dis-

eases, in 1981 and worked there till April 5, 2000 after which he took up the current assignment.

He has been working on enteric pathogens with particular emphasis on Vibrio cholerae, the

causative agent of the disease cholera.

NICED

WITH

DR.DR G.B.NAIR, PhD, FNA, FNASC,

Suggestion to students:-

Think of what you can do and what

cannot be done there and it's relevant

to your needs.

Dr. Nair is an elected member of the Subcommittee on the Taxonomy of Vibrionaceae, Interna-

tional Committee on Systematic Bacteriology from 1986; in August 1996 at the Jerusalem IUMS

Congress; he was elected as the Secretary of this subcommittee. He was elected to the position of

Member-at-Large of the International Union of Microbiological Society (IUMS) at the Executive

Board Meeting held on July 7, 1994 at Prague, Czech Republic and held this position till August,

1999; he is the first Indian Microbiologist to be on the executive board of the IUMS. He was

elected as the Fellow of the National Academy of Sciences, India (FNASc) in 1995, as Member of

Guha Research Council (GRC) in 1997 and as Fellow of the Indian National Academy of Sci-

ences (FNA) in 2002. On April 30th, 2002, Dr. Nair was elected as a Foreign Associate of the

National Academy of Sciences, USA and on November 26th, 2004, he was elected as a Fellow of

the Third World Academy of Sciences, Trieste, Italy now renamed as the Academy of Sciences

for the Developing Nations, in November 2004.

BY: Chandan Gupta, M.Tech (Biotechnology

P A G E 1 3 V O L U M E 1 , I S S U E 1

Dr. Nair was awarded the Certificate of Merit by the Centers for Disease Control and Prevention (CDC), Atlanta, Georgia,

USA in recognition and appreciation for his outstanding contribution to Public Health Education for Vibrio cholerae and Chol-

era in March 1994. On January 5, 1998 he was awarded the Professor S.C. Mahalanobis Memorial Award from the Physiologi-

cal Society of India and delivered the Memorial Oration at the Indian Science Congress at Hyderabad. He was awarded the

prestigious Shanti Swarup Bhatnagar award for Medical Sciences in 1998 for his contributions, which lead to the discovery of

the new cholera causing serogroup now globally known as Vibrio cholerae O139 Bengal and for his contributions on describ-

ing a cell-rounding factor from strains of Vibrio cholerae.

Our Group at NICED on 20th April 09, From left to right: - Amit, Chandan, Santosh, Dr. G.B. Nair, Deblina and Abhinav

Dr. Nair is on the Editorial Board of several journals including Journal of Clinical Microbiology (Publication of the American

Society of Microbiology), Epidemiology and Infection (Cambridge University Press), Microbes and Environment, Indian

Journal of Medical Research, Indian Journal of Experimental Biology and the Indian Journal of Microbiology.

P A G E 1 4

“The first century of

the new Millennium

will belong … also to

biotechnology which

will bring

unprecedented

advances in human

and animal health,

agriculture and food

production,

manufacturing and

sustainable

environmental

management”.

(Foreword, National

Biotechnology Strategy

for South Africa).

From the Campus:

NICED today is engaged in research on diseases of national importance and bio-logical problems of global interest. It is the one of the major laboratories in India which initiated, right from its inception, multidisciplinary concerted efforts for conducting basic research on infectious diseases, specifically Amoebiasis and Cholera.

NICED also conducts research on acute diarrhoeal diseases of diverse eti-ologies as well as typhoid fever, infective hepatitis and HIV/AIDS related epidemi-ological research and screening. Institute also trains health professionals for better management and prevention of diarrheal diseases and for rapid and correct diag-nosis of etiological agents. Epidemiologi-cal investigations of diarrheal diseases are carried out in different parts of India. Antiserum of Vibrio cholerae is raised in the Institute and supplied to the national and international laboratories. Presently, specific monoclonal antiserum for detec-

tion of Vibrio cholerae O139 strains was developed which has been supplied to WHO (SEARO), New Delhi for distribu-tion to various national and interna-tional laboratories. The Institute has its basic science set up with well equipped, modern technological facilities in differ-ent disciplines such as bacteriology, virology, parasitology, biochemistry, pathophysiology, molecular biology, electron microscopy, immunology and vaccine development.

In order to fulfill the vision, National Institute of Cholera and Enteric Diseases (NICED) shall identify enteric infections of national health priority, Initiate appropriate multidisciplinary research to develop strategies for treat-ment, control and prevention of enteric infections of national health priority , Collaborate with other national and in-ternational scientists who are working for the same vision.

search. The WHO and UNICEF also pro-vide assistance on applied research. Sev-eral workshops on management and pre-ventive aspects of diarrheal diseases are sponsored by WHO, UNICEF and Ministry of Health and Family Welfare, Govt. of India. These national and international workshops are conducted at the Institute and also in different parts of India involv-ing doctors of State Health Services and international participants. Each year 4-5 post-graduate students of this Institute get Ph.D. degree from different Universi-ties in the state (Calcutta University, Jadavpur University, Kalyani University, Burdwan University, Viswa Bharati Uni-versity). Post-graduate medical students also attend courses at the Institute for training on diarrheal diseases and scien-tists act as co-guides for M.D. students for thesis work. WHO and JICA also send international fellows.

Though the Institute is principally financed by the Indian Council of Medical Research (ICMR), New Delhi, different national and international funding agencies extend sup-port to the Institute on specific research

projects. The Japanese International Co-operative Agencies (JICA) has financed a

technical collaborative research with the Institute to conduct re-search molecular aspects of differ-ent enteropathogens with special emphasis on Vibrios. Under the JICA-NICED exchange programme Japanese scientists are working in the Institute and scientists and technical persons of the Institute are also receiving training in ad-vance Japanese laboratories. De-partment of Biotechnology (DBT), Government of India DST, CSIR, Ministry of Environment, etc. sup-port several projects on basic re-

DEPT. OF

VIROLOGY,

NICED

B I O V A R I A N C E

NATIONAL INSTITUTE OF CHOLERA & ENTERIC DISEASES (NICED)

BY: Chandan Gupta, M.Tech(Biotechnology)

P A G E 1 5 V O L U M E 1 , I S S U E 1

Achievements of NICED

Scientists of NICED documented the efficacy of oral rehydration salts solution (ORS) in young children with dehydrating acute diarrhoea including cholera, which led to wide-spread acceptance of ORS particularly in children.

Documented the efficacy of doxycycline, norfloxacin and ciprofloxacin for cholera. Nalidixic acid, norfloxacin and ciprofloxacin are recommended nationally and interna-

tionally for the treatment of shigellosis. Identification of new serogroup Vibrio cholerae O139, Bengal from NICED, prompt re-

porting to the national and international scientific community and tracing the pathway of spread of this new serogroup. On the basis of research at NICED, WHO recommended that O139 cholera should be notified as cholera.

Documented the clinical characteristics, stool and blood biochemistry of patients in-fected with V.cholerae O139 which was indistinguishable from those of typical O1 chol-era.

Detection of Adult Diarrhoea Rotavirus (ADRV), belonging to Group B rotavirus from Calcutta, the first report of its occurrence outside China.

users (IDUs) in North-Eastern States of India, particularly Manipur. Development of oral recombinant cholera vaccineVA1.3 as a collaborative effort with

CSIR institutes (IM Tech & IICB). High prevalence of HIV infection among injecting drug users (IDUs) in Manipur,

Mizoram and Nagaland was documented by NICED scientists. High prevalence of HIV seropositivity among antenatal mothers was also detected. Reported first sattelite epidemic of Herpes zoster among IDUs from Asia. Association Herpes zoster infection and tuberculosis and

IMMUNOLOGY LAB

Photo:- Parasitology lab of NICED

MOLECULAR

MICROBIOLOGY LAB

B I O V A R I A N C E

BY: Chandan Gupta, M.Tech(Biotechnology)

P A G E 1 6

“Biotech is a

terrific industry,

but it's not like

having a big

chip-

manufacturing

industry.s”

FACE TO FACE:

B I O V A R I A N C E

An interview with Dr Dr G.B.Nair, Director ,NICED,Kolkata

1. What is the one thing that inspired you to be a

scientist?

Dr G.B.Nair: I always wanted to be a scientist. I

have a very diverse background. I did my Ph.D in

marine microbiology. Right from the beginning, I

wanted my work to be related to human health and

as a marine microbiologist, I thought I could do it

best.

2. What are the things that still motivate you and make you focused enough to attain newer heights?

Dr G B Nair: It is always related to my science being some help to people and this is the message

I would like to convey to the students. What is the mandate ? How you‘re guided by the interest

to help poor people. India is still a rapid emerging economy. 750 millions still comes under the

poorest strata. 750 millions out of 1.4 billion is a huge data. Most of my research is directed to

the community and poor people at large.

3.What virtues you realized in yourself which helped you choose research as a profession?

Dr G B Nair: My virtue which has helped me choosing my career is exceptionally hard work and tell

my students that there is absolutely no substitute for hard work. You might be intelligent but if you‘re

not hard working, it would not take you far.

4.Which is the toughest job: Doing research or working as an administrator ?

Dr G B Nair: The virtue which has helped me choosing my career is my exceptional hard work I also

tell my students that there is absolutely no substitute for hard work. You might be intelligent but if

you‘re not hard working, it would not take you far.

5.― Quality or Qualification‖ – Which matters more in life?

Dr G B Nair: Both. If you‘re not qualified, you cannot do anything of quality. If you don‘t

have the Ph.D , you cannot go beyond a certain stage. You should first establish yourself

and then pursue quality work.

6. What was your childhood dream? To what extent do you think that you have achieved

it when you look back ?

Dr G B Nair : I have achieved more than I had dreamed of. In Cholera, our work is interna-

tionally recognized. When I was doing my Ph.D , there was a time when I didn‘t know

where to go because as a marine microbiologist, there were no openings. I was very fortu-

nate that I got a job in this institute as an Assistant Research Officer in 1981 and follows.

BY: Abhinav.K.V,Ami Rai,Chandan Gupta, M.Tech (Biotechnology)

P A G E 1 7 V O L U M E 1 , I S S U E 1

“Science is the

organized way

of thinking

proved by

systematic

observations.”

2. What are the things that still motivate you and make you focused enough to attain newer heights?

7. Can you enlighten us on the technology transfer program under JICA and what implications does it have on

the development in science and technology for students of biotechnology ?

Dr G B Nair : JICA program was started as a post doctoral program in 1987. That was first time when I met

Dr. Takeda who is my mentor and then he offered me a post doctoral fellowship. I think collaboration is

more about human interaction and this JICA building is a standing monument of that. Dr. Takeda became

interested in Calcutta and he initiated JICA.

8. Is the current status of the research going on suitable enough to support the sustainable development of

the living standard of the underprivileged in India ?

Dr G B Nair :Science needs to be translated into public good and many of research organizations across

the country are taking up the challenge. I was away from here from 2000-2007 working in International

Centre of Diarrheal Diseases in Dhaka, Bangladesh. One issue that continuously bugged me was that

money was less here but when I came back I was amazed to see the amount of money available for re-

search here. Chinese have adopted a fascinating strategy to get back people from outside by giving them

huge salaries but the good thing is that India is still a democratic and that is a big difference.

9. What basic measures and policies would you suggest to promote basic science at the school

level ?

Dr G B Nair : I would try to change the way science is taught. When I was at the international

position, what I found in me was the inability of to communicate well during meetings which I

acquired quickly. Our system doesn‘t allow us to question. Our system doesn‘t propagate that.

I would like to make students more inquisitive and question more.

10.What qualities would you like to incorporate in younger generation in order to build a

good scientific temperament and the right attitude ?

Dr G B Nair : I would like to incorporate the ability to innovate. That is an outstanding re-

quirement. Students want access to the things which are easier. I would try to tell my stu-

dents that your creativeness is the most important. You may not have best of everything but

still you can do high quality research just by innovation.

11. What is ―Science‖ to you ?

Dr G B Nair : Science is an organized way of thinking, an organized way of experimenting

and an organized way to come at a logical conclusion is what my definition of ―Science‖.

12. What are the areas in which do you think the attitude of an Indian researcher is lacking ?

Dr G B Nair : Our education system should not be flawed. What is important is to harness this

massive brain power which is going all over the world .The need is to tap that brain power

and utilize it for the benefit of humanity.

13.What is your message to Gen-Y ?

Dr G B Nair : My message to Gen-Y is to do hard logical work. At the back of your mind,

you should think of the relevance of your work. Do the things only you and no else can do.

Focus your work that is helpful for the masses. Think of a thing

you can do, what can not be done and work on what is relevant. B I O V A R I A N C E

P A G E 1 8

“Biotechnology is a

key industry for the

future. Without

biotechnology India

can hardly ensure

wellbeing for its

future generation”.

(2001)

DARP 32 CIRCUITS

Physiological basis of drug addiction:-

BIOLOGIX

There are many health hazards and social

problems worldwide. The modern era of

science and technology have developed

efficient steps to sort out the problems. One

of such problems which is still to be eradi-

cated and is affecting the mankind is drug

addiction.

Every year thousands of people, specially among

the younger generation are getting killed by the

acute intake of drugs.

The ill effects of drug addiction on

human body are directly related to

the central nervous system. It gets

weakened and may even lead to

death. Excessive drug usage causes

the release and prolonged action of

dopamine and serotonin. Dopamine

binds to D1 receptor(DRD1,a hu-

man gene) which is present in cen-

tral nervous system. This G-protein

coupled receptor stimulates adenylyl

cyclase and activates cyclic AMP-

dependent protein kinases. D1 re-

ceptors regulate neural growth, neu-

ral transmission in the human

physiological system. So, in drug

addiction, DA binds to D1 receptor

triggering a signaling cascade within

the cell. cAMP dependent protein

kinase phosphorylates cAMP re-

sponse element binding (CREB)

factor, a transcription factor which

induces the synthesis of certain

genes including C-Fos.

B I O V A R I A N C E

Drug addiction has become one of the serious

worldwide problem with genetic and environmental

implications. It is still to be completely eradicated

from this world. It is the continuous usage of illegal

and over the counter drug which leads to the slowed

ability to respond to external stimuli.[5(b)]

These deadly drugs are generally classified as:

1.Stimulants (e.g-Caffeine, Cocaine, Nicotine)

2.Sedatives (e.g-Alcohol, Barbiturates)

3.Benzodiazepines (e.g-Flunitrazepam,Temazepam)

CAN BIOINFORMATICS HEAL DRUG ADDICTION ??

Fig2:- Dopamine [5c]

Fig 1: Graph showing mortality rates[5(a)]

Figure3:- D1 receptor[5d]

DARPP-32,a protein in the brain

facilitates addictive behaviors.

Silencing of DARP-32 protein with

some kinds of active ligand can in-

hibit the active site of DARPP-32, it

can inhibit production of this protein

and could help to prevent drug addic-

tion.

Figure4: CREB[5(b)]

BY: Devawati Dutta,Shaumabha Mazumdar, M.Tech (Bioinformatics)

Bioinformatics approach to solve this problem:-

P A G E 1 9 V O L U M E 1 , I S S U E 1

addiction related genes by using

the FASTA format.

The KOBAS server

have many distinctive tools to

find out the result if we give as

input the sequences of drug ad-

dicted genes. It analyzes the

data, taking in the input of

FASTA sequences of drug ad-

dicted genes and using all the

known genes in human genome

This database has a user inter-

face which supports browsing of

the genes by chromosome or

pathways, advanced text search

by gene ID, Organism, Type of

addictive substances, Technol-

ogy platform, Protein domain

and sequence search by BLAST

search. We can also find out the

DNA sequence or the amino

acid sequences of the human

as background and interprets the p-value and other

values .On the basis of the analysis, it gives a predic-

tion of the common molecular pathway of these drug

addicted genes.[1]

A recent research paper has published that there are

396 addiction related genes and identified five path-

ways that are common to addiction of four different

substance: cocaine, opium, nicotine and alcohol. Also,

there are 18 metabolic and signaling pathway common

to the addiction related genes[1]. All these pathways

were interlinked with each other through CAMII.

Research analysis have revealed that the genetic factors contribute 40%-60% of the vulnerability to drug addiction .The

main question that comes to mind: what are the genes involved in acute drug usage? Is there a common molecular path-

way underlying addiction to different abusive substances? Whether computational biology can play some tricks to solve

this social problem? However, microarray analysis have found out the relative gene expression of drug addicted pa-

tients, but computational biology can play some part to the gene expression profiling and data mining of drug addicted

genes.

The bioinformatics analysis of the drug addicted genes have lead to the development of KARG database

(Knowledge of Addicted Related Genes) which is available at http://karg.cbi.pku.edu.cn.[1] A description of database

statistics is given in table 1.

Dr Florence

Wambugu,

Director, ISAAA,

East Africa:

“In addition to

having a major

impact on poverty

and hunger,

biotechnology

has great

potential to

alleviate

environmental

degradation”.

(2001)

Table 1:- Steps showing Collection of data and identification of common molecular networks for Drug addiction.[1]

B I O V A R I A N C E

binding/ active sites, generate candidate molecules,

check for their drug likeness, dock these molecules

with the target , rank them according to their binding

affinities, further optimize the molecules to improve

binding characteristics

Various research scientists have worked out to predict

the solutions of drug addiction problem in the field of

bioinformatics and papers have been published

Some UB research workers have find out that the nano

particles can be used to target the drug addicted pro-

teins[2]. With the latest development of science and

technology, if we can solve the drug addiction prob-

lem, then we can save millions of life .

How to cure drug affected people in the

world? No doubt several anti addictive

drugs are available in the market, but the

fact is that their efficacy is doubtful. We

can use high performance computational

including molecular dynamics simulations,

developing algorithm, computing clusters,

homology modeling and the most impor-

tant molecular docking. The latest re-

search work on pharmaceutical industry is

on structure based drug design.

.In-silico methods can help in identifying

drug targets via bioinformatics tools which

analyze the target structures for possible

P A G E 2 0 V O L U M E 1 , I S S U E 1

The main question that comes in our

mind how to eradicate this problem?

Special Offer

This is a good place to make a special offer for joining your

organization, purchasing a product, or requesting your service. You

can also transform the feedback into a sign-up or generic feedback

form.

FREE

OFFER

DOCKED POSE OF

A SMALL

MOLECULE

A diagrammatical representation of the bioinformatical approach to predict the cure of drug addiction problem is given below:-

Table 2:- Bioinformatical approach to the solve drug addiction prob-

1.C.-Y. Li, X. Mao, L. Wei, Genes and (common) pathways underlying

drug

2.Chen F, Li T, Fan SL, Dang YH, Chen T, Yan CX. [Gene expression profiling

in drug addicted brain ]2008 Jul;30(7):809-14. Review. Chinese. PMID:18779121 [PubMed - indexed for MEDLINE]

3.Drug Addiction: From Basic Research to Therapy - by Rao S. Rapaka, Wolfgang Sadée - 2008 - Medical - 782 pages.

References:-

B I O V A R I A N C E

P A G E 2 1

QUEST

1.What is the alternate name of the enzyme glutamate synthase?

2. Which vegetable on fermentation gives a product called Sauerkraut?

3. What is the name of the plant toxin that inhibits electron transfer in the NADH-Q

reductase complex and can be used as a fish and insect poison?

4. What is Virapap?

5. What is the term used for the process of producing pharmaceuticals using geneti

cally modified plants or animals?

6. Which is the fastest method of DNA sequencing?

7. What are ruderal sites?

8. Which is the most effective method for producing virus free plants?

9. Sonti is a beer prepared in India by fermentation of rice. Apart from yeasts ,a

particular mold is used for this fermentation. What is the name of the mold?

10. The colour and flavour of saffron are due to _____ and ­­_____ .

11. Flavr Savr tomato was developed by utilizing which technology?

12. What is the full form of GEMP?

13. What is the name of the plant glycoside that inhibits ATP-ADP translocase?

14. What is calpain-10?

15. Lewy bodies are associated with which neurodegenerative disease?

.

B I O V A R I A N C E

QUIZ :

CARTOON:

BY: Deblina Chakraborty,M.Tech (Biotechnology)

BY: Deblina Chakraborty,M.Tech (Biotechnology)

Identify the person in this picture

BURNING ISSUE :

P A G E 2 2 V O L U M E 1 , I S S U E 1

White biotechnology also

known as industrial biotechnol-

ogy is the glowing field of bio-

technology. The main aim of

white biotechnology is to reduce

the number of steps involved in

bioprocesses which lead to good

economic growth and make

the world better place to live.

White biotechnology uses the

natural tools in production of bio-

based chemicals, materials and

fuels. The economic growth associ-

ated with this field is estimated

about €11-12 billion per annum by

2010.

White biotechnology is

used mainly in fermentation tech-

nology, Biocatalysis and Pharma

industry. It is being used in these

fields for the production of bio-

chemicals, Biomaterials and Biofu-

els by using agricultural by-

products which are converted into

sugar by chemo/physical treatment

or enzyme1.

bleaching can be cut by 40%. So

adopting it for paper and pulp

industry would be both environ-

ment friendly and cost effective 2,3. Using white biotechnology

process in 'Paper and Pulp' in-

dustry involves the use of a

number of Xylanase producing

microorganism for the produc-

tion and bleaching of pulp for

paper.

White biotechnology

can also be used in paper and

pulp industry. It reduces the

amount of cholrine chemicals

necessary for bleaching by 10-

15% and also reduces chlorine

in water and air as well as chlo-

rine dioxide by a combined 75

tons per year and hence it also

lowers water toxicity. Using

this, energy requirement for

Benefits of producing PLA:-

1. PLA can replace petroleum

in the creation of polymers.

2. PLA can be used in the pro-

duction of plastic cups and pack-

ing materials. Main advantage is

that the plastic produced by PLA

is biodegradable and recyclable.

So it can potentially

contribute in the elimination of

pollution produced by plastic

materials and also save the pe-

troleum which if used in indus-

try can lead to more pollution.

Other use of having sugar is

that it can be used in produc-

tion of bioethanol. Bioethanol

from cellulose generates 8 to

10 times as much net energy as

is required for its production. It

is estimated that one gallon of

cellulosic ethanol can replace

30 gallons of imported oil.

Sugar availability is

high in India, our country being

the second largest sugar pro-

ducer in world. And it is more

than enough to serve the nation

so can be put to the secondary

use of a substrate for PLA (Poly

lactic acid)

MICROBIAL POPULATION

“Biotechnology

has the

potential to

bring

tremendous

benefits

…” (July 10,

2001).

WHITE BIOTECHNOLOGY AND ITS RELEVANCE IN INDIA

Agricultural by product (Biochemicals, Biomaterials, Biofuels etc)

A life cycle analysis shows net negative

greenhouse gas emissions when ethanol

in a fuel mix is higher than the standard

10%.

India has the raw materials to set up the

biotech industry, first being our surplus

sugar and second is the enzyme, which is

the major requirement in distilleries,

textile, leather processing industries. At

present various companies working in

this sector are : Advanced Biochemicals,

Biocon India, Maple Biotech, Bharat

Biotech, Novozymes, Artemis Biotech

and others. Indian enzyme products are

also supplied to Europe and other Asian

countries.

B I O V A R I A N C E

BY: Santosh Kumar Chaudhary,M.Tech (Biotechnology)

WHITE BIOTECHNOLOGY AND ITS RELEVANCE IN INDIA

Many researches are going on in India to maximize the production of xylanase from different microorganism.

Some are as follows-

1) A xylanase producing fungi has been isolated from soil and identified as

Trichoderma messesi-SAF3. Maximum growth of the microorganism is found

under submerged condition enriched medium, whereas highest enzyme produc-

tion was recorded at 72Hrs. Purified enzyme hydrolyzed xylan to xylopentose

and xylose. A number of xylanase producing microorganism were isolated

from different soils of district Paschim Medinipur, West Bengal, India as selec-

tive xylan agar medium by plate dilution technique4.

2) An experiment is conducted in university of Mumbai for the production of

xylanase by Immobilization of Aspergillus sp. on nylon bloting cloth whose

yield is 1.68 fold higher than that of freely suspended cells Aspergillus sp.5.

3) Amino acids such as DL-2-amino-n-butyric acid, DL-alanine, L-lysine

monohydrochloride, DL-valine and L-proline enhanced total xylanase produc-

tion from Staphylococcus sp. SG-13 up to 5.5-fold. The present study showed

that xylanase production has mainly been governed by the chemical structure of

amino acids and their analogues6.

4) IICB Kolkata has patented the process for the production containing xy-

lanase and carboxy methyl cellulose from termitomyces clypeatus having ac-

cession no IICB-411.

Biotechnology applied to pharmaceutical sector in the production of riboflavin (vitamin B2) which re-

duces the emission of carbon-dioxide by 80% and water emissions by 67%. The market share of the bio-

technology method of vitaminB2 production increased from 5% in 1990 to 75% in 2002 7 . Many re-

searches are going on in india to increase the production of riboflavin. Fermentation studies were carried

out for the bioproduction of riboflavin with an agro industrial byproduct, molasses as the carbon source

and lentils as the nitrogen source using E. ashbyii strain in Department of Chemical Engineering, S.V.

University, Tirupati 8.( G. Prabhakaret al 1992).

Many researches are going on for the production of industrially compatible micro-organism but

biotechnology as an industry is still at its infancy, there are very few industries that are using bioprocesses

for their productions. The reasons for this are many. One may be the lack of knowledge of important bio-

catalysts among the managerial staff at companies, they may not be familiar with the different bioproduc-

tion processes, existing potential microbes and lack of suppliers and advertising of biocatalysts in the

mills. Additional barrier is that Industries do not want to take risk with a new technology and still prefer

the tried and tested classical ways. Also, these new methods would require investments early on, in new

machines, training of personnel etc and not many are yet ready to make these investments when the

returns are not guaranteed and it is difficult to determine the long term benefits.

REFERENCE: 1.Europabio,―WhiteBiotech,‖(2004)availableathttp://www.europabio.org/pages/white_biotech.asp#what.

2.Bajpai, Pratima, ―Biotechnology for Environmental Protection in the Pulp and Paper Industry,‖Executive Summary (98)

3.Office of Compliance,―Toxic Releases Inventory (TRI) Releases for Pulp and PaperFacilities‖(2000) .

4.Sanjay Kar, Asish Mandal, Pradeep K. das Mohapatra, Keshab C. Mondal; Bikash R. Pati. Production of cellulose-free

xynalase by Trichoderma reesei SAF3.Brazilian Journal of Microbiology (2006) 37:462-464.

5.Purushottam V. Gawande and Madhusudan Y. Kamat. Immobilization of Aspergillus sp. on nylon bolting cloth for

production of xylanase. Journal of Fermentation and Bioengineering.Volume 86, Issue 2, 1998, Pages 243-246.

6.Saurabh Gupta, Bharat Bhushan and G.S. Hoondal1. Enhanced production of xylanase from Staphylococcus sp. SG-13

using amino acids. World Journal of Microbiology and Biotechnology. Volume 15, Number 4 / August, 1999. Vibrio cholerae

B I O V A R I A N C E

P A G E 2 4

“Biotechnology

has the potential to

bring tremendous

benefits …” (July

10, 2001).

OUR EARTH IN

TROUBLE..

UNSOLVED ISSUES

Asbestos is a serious health

hazard commonly found in

our environment today. The

name asbestos is given to a

group of minerals that occur

naturally in the environment

as bundles of fibres and can

be separated into thin, resil-

ient threads. These fibres

are resistant to heat, fire,

and chemicals and are bad

conductor of electricity.

Exposure to asbestos may

increase the risk of asbesto-

sis, lung cancer, meso-thelioma, other cancers,

and other nonmalignant lung and pleural disor-ders. Workplace, commu-

nities and the homes are the

common areas for the peo-

ple to get exposed to the

asbestos, which releases

asbestos fibres in the air

when disturbed. Asbestos

fibres are harmful because

they are extremely small

and sharp. Ordinary-sized

dust is caught and expelled

by the body's defences be-

fore it can be breathed in to

the lungs or swallowed into

the stomach but asbestos

fibres slips through and may

get trapped in the lungs and

remain there for a long time

and it is carcinogenic in

nature .

While white asbestos min-

ing is currently banned in

India, its import, export or

use in manufacturing is re-

stricted. But still some In-

dustries have asbestos plants

located even in Midnapore

in West Bengal though there

is a ban over asbestos. Re-

cently, a ship named Blue

Lady containing asbestos

has been permitted to anchor

at Alang, Gujarat. The ship

does not have the mandatory

Form 7 documents from

country of export required

for hazardous waste ship-

ments. Neither does it have

a complete inventory of

toxic wastes on board.

The Ministry of Mines and

Minerals remarks that it may

lift the ban on asbestos min-

ing. It is ignoring the views

of exposure victims, in-

formed recommendations of

public sector medical ex-

perts, and mounting evi-

dence of an asbestos disease

epidemic emerging in devel-

oped countries. The fact

remains, that the govern-

ment is pity reluctant over

this issue. So general aware-

ness should be created about

substitutes such as the vari-

ous types of MMMF (man

made mineral fibre), that are

generally much less hazard-

ous although not completely

free from risk.

REFERENCES:

http://www.asmasiapacific.org/download_file.php?uid=81

http://www.medicinenet.com/asbestos-related_disorders/page4.htm

B I O V A R I A N C E

ASBESTOS POLLUTION – A serious health hazard

PLASTIC BAGS: A Reality check up

In today‘s world one of the greatest threats is the use of plastics

which is detrimental to our life. The government should come

forward and should try to resolve the issue as it has got several

negative impact in our daily life, as plastics are not biodegrad-

able. It deteriorates the fertility of the land and as a consequence af-

fects the agriculture, and if burnt, produces obnoxious smell and haz-

ardous gases which may in turn affect the human health.

On the other hand, the plastic bags are photo degraded and overtime they breakdown into

smaller, more toxic petro-polymers which eventually contaminate the air, waterways and soil. As a

consequence microscopic particles can enter the food chain, and the effect on the wildlife can be

catastrophic. Nearly 200 different species of sea life including whales, dolphins, seals and turtles die

due to plastic bags .They die after ingesting plastic bags which by mistake they intake as food. To

control this situation the government has already proposed some laws, in which if you carry a plastic

bag you may have to pay a lakh of rupees as fine or spend five years in prison.

BY: Shoumabha Mazumdar, M.Tech (Bioinformatics)

BY: Anindyo Roy, M.Tech (Biotechnology),Pallabi Pal ( Int PhD)

P A G E 2 5 V O L U M E 1 , I S S U E 1

with progeria usually develop

severe atherosclerosis. This is a

condition in which the walls of

their arteries, blood vessels that

carry nutrients and oxygen from

the heart to the rest of the body

stiffen and thicken, often re-

stricting blood flow to their

hearts or brains.

There is no

proven treatment and no clue in

sight. Though scientists have

identified exactly the location of

gene causing Progeria but there

is no treatment or prevention for

Progeria at this time. Finding a

cure for Progeria will not only

help these children, but may

provide keys for treating mil-

lions of adults with heart disease

and stroke associated with the

natural aging process. Number

of people infected is about 1 in

8 million [reported]. In dealing

with a disorder such as progeria,

support groups play a vital role

that includes health care profes-

sionals, family and friends. On

the other hand the government

should also encourage the scien-

tists by funding more on the

researches that is related to

progeria, as every new research

brings us closer to cure.

Progeria (Greek word: meaning

prematurely old) is a rare dis-

ease and peculiar combination

of dwarfism and premature ag-

ing. In this disease a person ages

physically 8 times as fast as a

normal person while their mind

ages normally. The disorder

may be hereditary or non-

hereditary.Progeria, in some

forms, is Autosomal Recessive

[mutation to LMNA (LaminA)].

Evidence suggests that the

Progeria gene is located on

chromosome 1. A child with

progeria will begin showing

symptoms around 18 to 24

months after birth. Facial ap-

pearances and body structure is

the main distinctive feature by

which one can recognize the

affected ones. The average life-

span of the affected child is

about 13 years and is most

likely to die of heart disease or

stroke. As because the children

PROGERIA : An Early Aging Disease

The law comes under Section V of the Environment Protection Act of 1986. According to the Act, usage, sale or storage of

any kind of plastic bags is forbidden. The Government of India have banned the manufacture and use of plastic carry-bags

of thickness below 20 microns and size 8‖ X 12‖. The use of recycled or coloured plastic bags for carrying food-stuff has

been prohibited for health reasons. But the law cannot be implemented as the traders complained that if they shift from plas-

tic bags, the cost will increase four to five times and ultimately the customers will have to bear the cost. So the government

should take up some alternative steps to minimize the pollution without burdening the common mass. The use of jute and

paper bags should be implemented, and if possible the government should also use the biopolymer to curtail the consump-

tion of plastic. Plastic bags can also be recycled but it rarely happens. If the government can minimize the use of plastic it

would not only decrease the pollution but it would also decrease the dependency on foreign oil as the plastics are made from

the oil (a non-renewable energy source).

REFERENCE: http://www.progeriaresearch.org/

about_progeria.html

http://www.progeriafamilycircle.de/eng/eng.html

“Are we doin

our part

towards

mother

nature…??”

A

Race

Against

Time

B I O V A R I A N C E

BY: Shoumabha Mazumdar, M.Tech (Bioinformatics)

BY: Shoumabha Mazumdar, M.Tech (Bioinformatics)

P A G E 2 6

MALARIA KILLS….

DISCOVERIES

In light of insecticide

resistance and environmental con-

cerns regarding the use of insecti-

cides1, control of vector borne

diseases using anti-vector vaccines

is particularly appealing. Malaria

is a disease that can be controlled

using this approach. Two general

characteristics of malaria transmis-

sion cycle may allow the disease

to be controlled through an anti

mosquito vaccine targeting ma-

laria vectors, First, mosquitoes and

man are the only two hosts of the

four species of human malaria

parasite, and second, malaria is

only transmitted laterally amongst

these two hosts.

The basic principle is that

blood feeding vectors ingest blood

for energy and egg production.

The bloodmeal contains red blood

cells, serum and immune factors

that are normally present in the

host bloodstream. If the host is

vaccinated with antigens from

vector tissue (e.g midgut proteins),

the host‘s immune response will

be directed towards these antigens

and the bloodstream will have

immune factors against these Ags

circulating in it. These

immune factors when ingested

with blood meal attack the native

antigen (e.g, the vector midgut),

this can lead to

death or impair-

ment of the vec-

tor. A spectrum

of immune fac-

tors are involved

in this namely,

antibodies,

lectins, complement, and immune

effector cells (cytotoxic T-

lymphocytes, NK cells, and

macrophages) are some of these

factors that may act separately

or synergistically to impair the

insect.

Past research has proven the

feasibility of killing blood feed-

ing vectors and reducing their

fecundity via immunological

factors ingested along with

blood from the host.

However successful

identification of molecular fac-

tors within vectors has been

rare. This may be said to be the

rate limiting step of this re-

search. The difficulty being that

the experimental animals when

immunized with a homogenized

vector tissue, a polyclonal and

multifactorial immune response

is produced against this homo-

geneous mix of vector antigens.

And it becomes difficult to

match an immune effecter like

antibody to a single antigen.

B I O V A R I A N C E

MOSQUITOCIDAL VACCINES FOR MALARIA—

A DISEASE OF THE POOR

Adapted from: Immunological targeting of critical insects antigens.

AMERICAN ENTOMOLOGIST • Volume 48 Number 3. Page no. 150-158.

(Brian D. Foy, Gerry F. Killeen, Tereza Magalhaes, and John C. Beier)

Fig. Possible molecular-immunological mechanisms of vector impairment and death. 3

(1) Enzyme/receptor inhibition or blockage of protein channels through antibody or

lectin binding (yellow shapes).(2) Cellular lysis by a complement membrane attack

complex (green circles). (3) Antibody-dependent cell-mediated cytotoxicity (ADCC), via cationic protein, hydrolases, reactive oxygen intermediates, cytokines, or other

released factors (red circles). Whether ADCC, or cytotoxic T-cells alone, can induce

apoptosis of vector cells is not known .

Immunodominance,

immune masking, and anti-

body cross-reactivity further

complicate the matter. Exten-

sive biochemical purification

of the vector tissue prior to

immunization is usually done

to preempt this, but such work

is extremely laborious and

impractical when dealing with

smaller vectors such as mos-

quitoes.2

Most of the ap-

proaches involved in discov-

ery of new and unique antivec-

tor antigens apply a reduction-

ist approach to sort and test

individual antigens or immune

factors. . In this way, the con-

fusion of multi- immune fac-

tors recognizing many anti-

gens does not conceal the

identification of critical anti-

gens.

BY: Meenu Maan, M.Tech (Biotechnology)

P A G E 2 7 V O L U M E 1 , I S S U E 1

One approach involves sorting of antigens on

basis of weights and charges4, techniques like

SDS-PAGE and Isoelectric focusing can be

used. Another reductionist approach involving

antigens is expression library immunization

technology and its derivatives5. This method is

being applied to vectors by immunizing mice

with a cDNA expression library derived from

midgets of bloodfed A.gambiae. A.gambiae were

fed on these mice and an increased mosquito

mortality was observed ( unpublished data).

A reductionist approach regarding immune ef-

fectors can also be a successful antivector im-

mune strategy. One method is to make mAbs

from immunized animals, and then feed these

mAbs individually via a membrane feeder to

assess their ability to reduce vector survivorship

or fecundity6.

MALARIA

LIFECYCLE

COUNTERING MALARIA

“Revolutionary,

unprecedented,

unsurpassed. These

adjectives are being used to

describe the Human

Genome Project’s potential

to benefit society. The

understanding of the

human genome that has

been gained, is almost

certain to lead to

breakthroughs in medicine

that may ultimately

eradicate many of today’s

diseases”. (Food Insight,

October 2001.)

Another novel approach use phage-displayed

antibodies and peptides. Bacteriophages can

display peptides or antibody fragments (scFv)

on their surface when the cDNA of these pro-

teins are cloned into the phagemid (phage

genes inserted into a plasmid) genome; in this

way, the protein‘s genotype is directly linked to

its phenotype. One can isolate binding-clones

of interest from a library of phage-displayed

peptides or proteins by panning the library on

almost any antigen. The selected clones and

their translated proteins can then be easily rep-

licated, mass-produced, and purified in the

laboratory by exploiting the life-cycle of bacte-

riophages within bacterial cells.

In conclusion, these anti-vector vac-

cines may prove to be the much needed impetus

in control of diseases like malaria, dengue,

Japanese encephalitis, chicken guinea etc and

may even be applied to control other ectopara-

sites like ticks and also plant pests.

References cited:

1.Casida, J. E., and G. B. Quistad. 1998.

Golden age of insecticide research: past, present, or future? Annu.Rev. Entomol. 43: 1-16.

2. Billingsley 1994.

Approaches to vector control: new and trusted. 2. Molecular targets in the insect midgut.

Trans. R. Soc. Trop. Med. Hyg. 88: 136- 140,Kay, B. H., and D. H. Kemp. 1994.

Vaccines against arthropods. Am. J. Trop. Med. Hyg. 50: 87-96,Jacobs-Lorena,

M., andF. J. A. Lemos. 1995. Immunologic strategies for control of insect disease vec-

tors: a critical assessment. Parasitol. Today 11: 144-147.,Wikel 1996,Immunologic control

of vectors, pp. 575-594. In B. J. Beaty and W. C. Marquardt [eds.], The biology of disease

vectors. University Press of Colorado, Niwot, CO

3. Brian D. Foy, Gerry F. Killeen, Tereza Magalhaes, and John C. Beier, 2002.

Immunological targeting of critical insect antigens.

4. Tellam, R. L., and C. H. Eisemann. 1998. Inhibition of growth of Lucilia cuprina larvae using serum from sheep vaccinated with

first-instar larva antigens. Int. J. Parasitol. 28: 439-450.

5.Barry et al. 1995.

Protection against mycoplasma infection using ex-

pression- library immunization. Nature 377: 632- 635.

MALARIAL PARASITE

B I O V A R I A N C E

P A G E 2 8

“BIOINFORMATICS

GIVES US AN

OPTION OF

NARROWING DOWN

THE DISCOVERY

PIPELINE…..”

PROTEIN

MODELLING

Protein Modeling: The ability of proteins to per-

form biological functions

depends on the formation of a

three-dimensional structure

(fold) that is stable in the

normal environment of the

protein. For example, en-

zymes often catalyze reac-

tions using an active site.

This is a cavity of three-

dimensional structure of the

enzyme. An understanding of

structure of a protein leads to

a function of a protein and

the mechanism of their ac-

tion. So the structural knowl-

edge is vital for understand-

ing the diverse function, rec-

ognition of molecules by

Transport proteins, protein-

protein interaction, interac-

tion between components of

signaling pathways, regula-

tion of gene expression (by

DNA binding protein), recog-

nize a molecular signal by

receptor proteins

etc at molecular level.

The most interest-

ing and exiting motivation to

know the three-dimensional

structure of a protein is for

designing a drug molecule,

because a specific drug can

target a specific protein by

selectively binding its sur-

face. Unfortunately, struc-

tural knowledge is still

rather limited, because the

experimental process of

structure determination is

slow for most of the proteins

and not possible for many.

The database of known

structures currently contains

more than 18000 protein

structures, but the databases

of sequences contain hun-

dreds of thousands of se-

quences. This gap between

sequence and structure

knowledge is often termed

the sequence structure gap;

from a practical point of

view, it is the main factor

influenced the scientist for

prediction of protein three-

dimensional structure.With

the development of tech-

niques in molecular biology

that allow rapid identifica-

tion, isolation, and sequenc-

ing of genes, we are now

able to infer the sequences

of many proteins. However,

it is still a time-consuming

task to obtain the three-

dimensional structures of

these proteins. A major goal

of structural biology is to

predict the three-

dimensional structure from

the sequence, a pursuit that

has not yet been realized.

Thus, alternative strategies

are being applied to develop

models of protein structure

when the constraints from

X-ray diffraction or NMR

has the homolog structure in the data-

base i.e. if we align the query sequence

with the homolog sequence found in the

database by sequence similarity search-

ing and if it shows at least 25% identity

upon alignment on 80 or more residues.

So it is not 100% sure that all times dur-

ing the alignment one can find the ho-

molog sequence in the database by data-

base similarity search. The other meth-

ods of structure prediction except homol-

ogy modeling which is a smart approach

THREE MAIN APPROACHES FOR

SRTUCTURE PREDICTION:

HOMOLOGY MODELLING

FOLD RECOGNITION

SECONDARY STRUCTURE

PREDICTION

AB-INITIO MODELLING

So from the chart we can predict

that Homology modeling is the

best among the all if only the tar-

get sequence or query sequence

in the field of molecular modeling is the Ab-

initio structure prediction. This strategy tells

that a proteins fold spontaneously to their native

conformations to attain the most stable structure

in minimum thermodynamic free energy. So if the

total free energy of a protein could be minimized

through thermodynamic approach, one can pre-

dict the three dimensional structure of a particular

protein. But the progress of this approach to pre-

dict the 3-D structure of a protein is less compare

to others because it is a difficult job to achieve

this. This is a biggest challenge for the scientists.

B I O V A R I A N C E

BY: Arnab Nayek, M.Tech(Bioinformatics)

P A G E 2 9 V O L U M E 1 , I S S U E 1

Bioinformatics has taken the ma-

jor role to solve this problem in the

field of protein modeling. We have

solved a three-dimensional struc-

ture of a small plant hormone pro-

tein Systemin from its amino acid

sequence (which was known)

through simulated annealing

method by a software TINKER.

The given protein sequence is:

1 ALA VAL GLN SER LYS

PRO PRO SER LYS ARG ASP

PRO PRO LYS MET

16 GLN THR ASP

It is established that the mini-

mized energy values from the

given guess structure (initial

structure) through iterated simu-

lated annealing method (400

times) by the help of a Software

TINKER. The TINKER molecu-

lar modeling software is a com-

plete and general package for mo-

lecular mechanics and dynamics,

with some special features for

biopolymers. TINKER is de-

signed to be an easily used and

flexible system of programs and

routines for molecular mechanics

and dynamics as well as other

energy-based and structural ma-

nipulation calculations. It is in-

tended to be modular enough to

enable development of new com-

putational methods and efficient

enough to meet most production

calculation needs. Rather than

incorporating all the functionality

in one monolithic program,

TINKER provides a set of rela-

tively small programs that inter-

operate to perform complex com-

putations, from which ANNEAL

and NEWTON programs are

selected. The series of major pro-

grams included in this project

described below and perform the

following core tasks.

This steps is required iteratively upto 400

times for producing lowest energy mini-

mized values from each run directory

output file (newton.run.o*).

After producing the 400 output files

(newton.run.o*) from each run directory,

it is required to filter out the lowest en-

ergy minimized value output files among

400 files. And hence we sorted the Final

Function Value (lowest energy value)

from each output file

newton.run.o.* among 400.

The program file anneal.run and newton.run are

submitted to the job queue, connection to the jobs

running on a remote server, facilitated and imple-

mented by the software TINKER. After submitting

the jobs, the running started following the simulated

annealing procedure of anneal.xyz, the given guess

structure of predefined sequence. After producing the

files anneal.001 to anneal.032 (the time required is 2

and ½ hours), the program Newton, started to run,

which converts the minimized structure anneal.032 to

newton.xyz and more stable Newton truncated new-

ton.xyz_2 respectively and produces the output files

(newton.run.o*) of energy minimization values, also

containing the calculated lowest energy minimized

final function value, which is required for sorting.

of the guess initial structure, we

use the following command for

MD run from UNIX platform,

where the specified software

TINKER is installed.

$ nohup anneal.run &

It converts the initial structure

into final structure – anneal.032

through iterative simulated an-

nealing method, which is the

energy minimized structure. This

structure is then converted into

newton.xyz and newton.xyz_2

respectively through the Newton

minimization method.

The file newton.xyz_2, which

is produced by Newton mini-

mization method, and which

is the coordinate file of that

given structure (guess struc-

ture) is copying into a file

name anneal.xyz and which is

again copying into a directory

name as run1(which was pre-

viously created). The files

anneal.key,

anneal.run, newton.key,

newton.run are also copy into

the directory run1.

To obtain minimized structure

values, 400 times of iterative

steps of energy minimization

was carried out.

Here, we started with the 5 ma-

jor files which are required for

the initialization of the Molecu-

lar Dynamics run.

The files are – Anneal.key – MD parameters

Anneal.run – MD scripts

Anneal.xyz – Initial guess struc-

ture

Newton.key – MD Parameters

For starting the initialization

process of energy minimization

“In addition to

having a major

impact on

poverty and

hunger,

biotechnology

has great

potential to

alleviate

environmental

degradation”.

(2001)

B I O V A R I A N C E

P A G E 3 0

So for producing pdb file it

requires two input files –

one is .xyz Cartesians coor-

dinate file and the other is .seq

file. .seq file is the extended

sequence file which was known

previously and .xyz is the new-

ton.xyz_2 file which has pro-

duced. For converting the .xyz

coordinate file to .pdb file one

program xyzpdb is there which

is built in the software TINKER.

So now we have reached to our

exact destination i.e. the pdb file

formation, from which we can

predict the three-dimensional

structure of a protein and which

structure was also submitted to

the PDB database.

B I O V A R I A N C E

For establishing the re-

quired pdb file (.pdb for-

mat) which tells the three-

dimensional structure of a

protein is the ultimate

goal of this work.

The 3-D structure of the protein SYSTEMIN: RASMOL view

Acknowledgments: Dr. Ansuman Lahiri (Lecturer in the dept. of BMBG, University of Calcutta)

References: Introduction to BIOINFORMATICS (Arthur M.Lesk)

Protein visualization in PYMOL

CROSSWORD

P A G E 3 1 V O L U M E 1 , I S S U E 1

1. Sequence format that begins with a single-line description

followed by lines of sequence data ,can be used as

query input when searching tools like BLAST or Clustal W.

4. Proteinaceous compound of which the spicules in

Demospongiae are composed.

6. A space introduced into an alignment to compensate for

insertions or deletions in one sequence relative to another.

8. Compound whose activated form emits light.

10. Complex sulfated polysaccharide, extracted from red algae

and used as a solidifying agent in culture media.

11. _______ is used as a high level disinfectant in hospitals to

disinfect surfaces.

12. Heme protein that carries electrons, usually as member

of electron transport chains.

15. A complex, branched polysaccharide made of-

many glucose molecules joined into chains of varying lengths.

17. Increased risk of atherosclerosis is associated with de

creased serum levels of ______.

The 3-D structure of the protein SYSTEMIN: RASMOL view

Can you solve it the

fastest..?????

DOWN ACROSS

1. Primary protein component of prokaryotic flagella.

2. Homologous sequences ina single species that are the result of

gene duplication.

3. An inactive form of the repressor protein, which becomes the

active repressor when the corepressor binds to it.

5.Group of cloned pieces of DNA representing overlapping regions

of a particular chromosome.

7.The ratio of _______ to cytokinin in certain plant tissues

determines initiation of root versus shoot buds.

9. Associations between actinomycetes and plant roots

.

11. A small molecule which can elicit an immune response only

when attached to a large carrier such as a protein.

12. Class of biochemical compounds like sugars, starch, chitin etc.

13. A measure of the amount of dissolved oxygen needed by

microbes to degrade organic matter in a water body.

14. Continuous-mode fermentor in which fresh medium is

introduced to keep turbidity constant.

16. The number of different alignments with a score equal to

or better than that can be expected to occur simply by chance.

B I O V A R I A N C E

BY: Deblina Chakraborty,M.Tech (Biotechnology)

P A G E 3 2

GRE–

ASPIRING HIGH..

CAREER ASCENT

Aiming to study abroad in foreign universities

and aspiring for quality education?

Requirement : “The candidate should have a

good score in GRE/TOEFL or both.

Challenge 1:Scoring a high score in GRE

Here is the solution to all your problems.

Something which provides you with a de-

tailed approach on systematic preparation on

GRE.

The GRE is an aptitude test. Like all

aptitude tests, it must choose a medium

in which to measure intellectual

ability. The GRE has chosen math and

English.

OK, the GRE is an aptitude test. The

question is—does it measure apti-

tude for graduate school? The

GRE‘s ability to predict perform-

ance in school is as poor as the

SAT's. This is to be expected

since the tests

are written by the same company

(ETS) and are similar. The GRE‘s

verbal section, however, is signifi-

cantly

harder (more big words), and,

surprisingly, the GRE‘s math sec-

tion is slightly easier. The GRE

also

includes a writing section that the SAT

does not. The GRE is approximately

three hours long. Only two-hours-and-

thirty-minutes of the test count toward

your score—the experimental section is

not scored.

B I O V A R I A N C E

ALL ABOUT GRE:

There are two types of GRE-one is the general

GRE and the other is subject GRE.The sub-

jects include Biochemistry,cell and molecular

biology,biology,chemistry,computer sci-

ence,literature in eng-

lish,mathematics,physics,psychology. Test is

composed of verbal reasoning (V), quantita-

tive reasoning (Q), and analytical writing

(AW) sections .Registration is necessary for

appearing in the GRE exam.Registration can

be made through online,telephone and

mail.Test centers fill up quickly,so early regis-

tration is recommended to get prefered test

locations and date selection.For cancellation

or rescheduling test information should be

conveyed not later than three full days.

Comparative percentile section wise scores

On the test, you cannot skip questions; each

question must be answered before moving to

the next question.

However, if you can eliminate even one of the

answer-choices, guessing can be advantageous.

It is significantly harder to create a good but incorrect answer-choice than it is to produce the

correct answer. For this reason usually only two attractive answer-choices are offered. One

correct; the other either

intentionally misleading or only partially correct. The other three answer-choices are usually

fluff. This makes educated guessing on the GRE immensely effective.

BY: Priyanka Biswas ,Int Phd (Microbiology)

P A G E 3 3 V O L U M E 1 , I S S U E 1

loid related disease. Natto kinase an anticlotting serine protease

present in Natto is the principle component that dissolves the fi-

brous protein aggregates .Thus Natto may provide an effective

treatment for Alzheimer‘s disease as well as presenting some deli-

cious dishes.

Reference:

Hsu et al. amyloid-Degrading Ability of Natto kinase from Ba-

cillus subtilis Natto.

Journal of Agricultural and Food Chemisty,2009;57.

Amyloids aggregates of fibrous

proteins, the major component of

amyloid plaques accumulated in

many neurodegenerative disease

like Alzheimer‘s disease can be tar-

geted by popular fermented food

(Bacillus subtilis) in South-East

Asia called Natto. According to

scientists in Taiwan, Natto which is

made from boiled soybean can be

effectively used to treat such amy-

Natto

BIOTECH POUTPURRI

“To catch the

reader's

attention,

place an

interesting

sentence or

quote from the

story here.”

CURRENT BIOTECH NEWS

Muramyldipeptide(MDP), a component of pepti-

doglycan found in both gram positive and gram

negative bacterial cell wall has been found to pro-

mote inflammatory arthritis by activating a spe-

cific gene called NOD-2(nucleotide binding oli-

gomerization domain containing two) located at

chromosome 16 in human. Group of researchers

from USA and Netherland has carried out an ex-

periment to demonstrate the potency of MDP to

promote inflammatory arthritis in mice immu-

nized with proteoglycan. Two group of mice were

employed, one with normal NOD-2 gene and an-

other with deactived NOD-2 gene. MDP was in-

jected to joints of each group of mice .

The normal mice display more severe

inflammation as compared to knocked out mice .

The development of arthritis also in NOD-2 deac-

tivated mice demonstrates that the NOD-2 is not

primary factor for developing inflammatory ar-

thritis in absence of MDP. This study will open

up new directions for treatment of arthritis.

Arthiritis— An acute problem

in old age

Granulomatous arthritis

Reference:

Rosenzweig et al.

Activation of nucleotide oligomerization domain

2 exacerbates a murine model of proteoglycan-

induced arthritis.

Journal of Leukocyte Biology,2009; 85 (4): 711-

718

Soyabean against Alzheimer

B I O V A R I A N C E

BY: Priyanka Biswas ,Int Phd (Microbiology)

BY: Anindyo Roy (M.Tech (Biotechnology)

P A G E 3 4 V O L U M E 1 , I S S U E 1

Scientists at the University of

Colorado, Boulder have devel-

oped a new technique for detect-

ing genetic information of Influ-

enza virus within a relatively

short period of time, just eleven

hour. The technique is based on

the microarray technology and

utilizes the specific binding of

viral RNA on the DNA chip.

The samples were collected

from patients throat and nasal

swap. The detection was done

by using a secondary DNA

probe tagged with fluorescent

dye with light up during scan-

ning. This method is useful

for identification of spe-

cific strains for Influenza

as well as SARS, measles,

HIV and hepatitis C also.

The advantange of this

method is that it can help

to combat epidemic and

pandemic by making sure

the identity of the invading

pathogenic strain and

speeding up the development of

vaccines against them.

Reference: Discoveries and

breakthroughs in Science,

American Institute of Physics.

different from the naturally oc-

curring protein..According to

Dr. Field a researcher involved

in this study ,different Nisin

variants can now be used spe-

cifically to target specific patho-

gen .Another benefit is that

Nisin variants can now lagely

replace the commercial food

preservatives such as sug-

ars,salts and other chemicals in

combating bacterial growth ulti-

mately

Researchers at the University of

Cork has engineered the antibi-

otic Nisin (an antimicrobial pro-

tein produced by a bacterium

Lactococcus lactis), to prevent

methicillin resistant Staphylo-

coccus aureus (MRSA)and Lys-

teria monocytogenes a food

borne pathogen by altering dif-

ferent amino acids.

These bioengineered

family of variants, are slightly

leading to safe and healthy food for us.

Reference :Society for General Mi-

crobiology , New, More Effective

Nisin Anti-

biotics

Combat

Superbugs

And Food

Diseases.

According to the research team

Bacillus species and Pseudomonas

aeruginosa were the best oil-

degrader.Proteus, Enterobacter, and

Micrococcus species were also

found to be able to degrade crude

oil.

Reference: Bello M. Yakubu, Huiwen Ma, and ChuYu Zhang. Biodegradation of crude oil in soil using chicken manure. International Journal of Environment and Pollution, 2009, Volume 36,Issue 4

A relatively cheap and easy available

material, chicken manure has been

found to degrade crude oil in contami-

nated soil as described by scientists at

the University of Wuhan, China. The

manure raises soil pH upto 6.3-7.4

which is optimal for oil degrading

bacteria..It was added to soil contami-

nated on a pollution basis of 10%(v/w

crude to soil).75% of oil has been

found to be degraded in soil with ma-

nure after 2 weeks as compared to

manure free soil exhibited 50%natural

remediation.

A MICROARRAY– DNA ON CHIP

FLU CHIP:

New horizon in bioremediation:

MICROARRAY”

An

interdisciplinary

science”

Hey…

nothing

of mine

is use-

less!!!

ANTIBIOTIC REVOLUTION:

B I O V A R I A N C E

P A G E 3 5 V O L U M E 1 , I S S U E 1

hydrogen.According to re-

searchers at the Penn State

archeal biofilm could use the

current to convert carbon di-

oxide and water to methane in

absence of any organic mate-

rial, usually found in micro-

bial electrolysis cells.The

cells has about 80 percent

conversion efficiency of elec-

tricity into meth-

ane.According to Bruce E.

Logan, Kappe Professor of

Environmental Engineering,

Penn State that the electro-

chemical reaction occurs

without the presence of any

metal catalysts and requires

less energy as compared to

conventional chemical indus-

trial methods for conversion

of carbon did oxide to meth-

ane.

Reference: Shaoan Cheng, Defeng Xing, Douglas F. Call and Bruce E. Logan. Direct Biological Conver-sion of Electrical Current into Methane by Electro-methanogenesis. Environ. Sci. Technol., 2009 ,Pensylvenia State Uni-

versity. MCROBES-

“A boon or a

bane…???”

New aspects of renewable energy:

Don‘t

worry.. I

am here

just feel

free to eat

Microbe can use electricicity to

convert carbon dioxide and water

into methane a renewable energy

source.Microbial electrolysis re-

quires an electrical voltage in

addition to that is produced by

bacteria using organic materials to

produce current that releases

B I O V A R I A N C E

BY: Anindyo Roy (M.Tech (Biotechnology)), Pallabi Pal (Int PhD Mol Bio)

P A G E 3 6

IN-Sillico Drug

Design need a

novel

ComputationL

biology

knowledge..

DOCKING

From the Alumni’s Desk

Introduction:

Evidence of the use of medicines and drugs can

be found as far back in time as the first Egyp-

tian dynasty, 3100 B.C. The drug discovery and

development process is scientifically complex

and full of risk, and is therefore, expensive and

time-consuming. Typically, a new chemical

entity (NCE) is promoted from discovery into

preclinical development and if it succeeds in

passing all hurdles, it is submitted for an inves-

tigational new drug (IND) application and

eventually enters phase I, II and III clinical

development. If the compound passes all clini-

cal trials, it is submitted for a new drug applica-

tion (NDA) and eventually enters the market

place. For the majority of the time drugs have

been used, discovering them has been a trial-

and-error process. It was not until the 1960's

that some understanding began to develop

about the quantitative relationship between

structure and biological activity. This new un-

derstanding that a quantitative relationship ex-

isted ushered in the beginnings of computer-

aided drug design.

significantly advance the discovery process.

Computer-aided molecular modeling helps

determine which molecules should be synthe-

sized and tested. Special computational tech-

niques are also available to discover biological

targets (proteins, nucleic acids) of a drug.

There has been a manifold increase in the

amount of experimental data because of the

burgeoning progress in high-throughput instru-

mentation and techniques. Accompanying this

progress has been a growing reliance of ex-

perimental researchers on computer-aided

drug design (CADD). CADD, or "rational drug

discovery," helps make it possible to select a

more manageable number of candidates that

can then be tested experimentally. Thus, both

intuition and rational analysis of databases can

be used to generate effective therapeutic com-

pounds. Besides the heavy emphasis on com-

puters, CADD relies extensively on various

Computer-aided drug design is no longer merely

a promising technique. It is a practical and real-

istic way of helping the medicinal chemist. On

its own it is unlikely to lead to pharmaceutical

novelties but it has become a significant tool, an

aid to thought and a guide to synthesis. Still

drugs must be synthesized and tested by the

computational techniques can contribute a clear

molecular rationale and above all provide a spur

to the imagination.

Advances in biomedical and pharmacological

research have continued to benefit

humanity by producing drugs that

either alleviate symptoms of disease

or provide a cure. Exploring the re-

lation between chemical structure

and function of compounds and in

finding a cure for diseases. This re-

cent success demonstrates that with

good experimental backing, the syn-

ergy between experimental and

computational approaches to drug design can

B I O V A R I A N C E

Although no single drug has been designed

solely by computer techniques, the contribu-

tion of these methods to drug discovery is no

longer a matter of dispute. All the world‘s

major pharmaceutical and biotechnology

companies use computational design tools.

At their lowest level the contributions repre-

sent the replacement of crude mechanical

models by display of structure which are a

much more accurate reflection of molecular

reality, capable of demonstrating motion and

solvent effects. Beyond this, theoretical cal-

culations permit the computation of binding

free energies and other relevant molecular

properties.

Two distinct categories of research are

clearly distinguishable:

a) A detailed molecular structure of the target

macromolecule, the drug receptor, is known

from x-ray crystallography, NMR or homol-

ogy modeling.

b) The target receptor-binding site has prop-

erties, which can only be inferred from a

knowledge of the variable activity of other-

Md.Ataul Islam, Alumni WBUT SBT

DRUG DESIGN – Made Easier

P A G E 3 7 V O L U M E 1 , I S S U E 1

Computational scientists need to understand physical

and organic chemistry, biochemistry, biophysics, mo-

lecular biology, statistics, data mining, and mathemat-

ics. They need to be able to study data sets for trends,

categorize and judge the validity of data and the meth-

odology of data collection, and have a drive to under-

stand the problems behind the development of models to

test hypotheses. This broad and diverse field offers tre-

mendous opportunities for scientists who have a variety

of skills such as programming and three-dimensional

visualization. The link between CADD and biology and

chemistry harnesses the tremendous progress in genom-

ics and proteomics that has led to the discovery of new

genes and proteins. Out of 5000 to 10,000 targets, only

about 500 targets have been characterized. This demon-

strates the numerous opportunities for data mining, de-

signing drug candidates, developing models to predict

biological activity, and studying interactions between

cellular targets and synthetic molecules.

In-silico screening of compound databases is presently the

most popular and useful cheminformatics applications in phar-

maceutical discovery. At the moment, virtual screening tech-

niques are roughly segregated into target structure and ligand-

based applications leading to heartening outcomes for novel

drug development. Besides protein-ligand docking, structure-

based approaches include the development of pharmacophore

features from active or binding site. Alternatively, methods

starting from hits or leads range from pharmacophores or

multi-dimensional Quantitative Structure-Activity Relation-

ship (QSAR) models and binary fingerprints to compound

clustering or partitioning methods and statistical techniques

capable of analyzing screening datasets and deriving predic-

tive models of bio-activity. Today SAR is a fundamental tool

for developing safer and potent drugs. The importance is on

management of time and minimization of animal sacrifice and

expenditure. Modern Pharmaceutical research with its drift

towards high-throughput systems demands swift and accurate

characterization of large number of compounds for potential

target proteins. As a matter of fact, these collections of com-

pounds must be scored for predictive bioactivity to prioritize

their suitability for chemical synthesis.

LIGAND DOCKING

USING GOLD

DNA as Target:

The sequencing of the human genome represents one of the major

scientific endeavors of this century. A major aspect of the utiliza-

tion of this information will be the provision of small molecules

which will recognize selected sequences, perhaps with the goal of

switching off particular genes as in cancer chemotherapy.

PROTEIN AS TARGET

If an enzyme structure is known then designing inhibitors which

will block activity in the test-tube should be a relatively straight-

forward problem. More spice to such a challenge is added if we at

the same time attempt to make the ligand bioreductive.

TRANSlTION-STATE MIMETICS:

Where no knowledge about the macromolecular target in atomic

detail exists, then it is still possible to utilize computer-aided de-

sign techniques. A popular idealized approach would be to com-

pute the energy profile of a biochemical transformation which

would be desirable to inhibit; locate the transition state or inter-

mediate and then create a stable mimic of these unstable tran-

sients recognized by the enzyme responsible for catalyzing the

reaction and would hence act as an inhibitor. Only two logical

steps are necessary: find the transient structure and secondly de-

sign a stable mimic. The former task is probably best achieved by

using a combination of quantum and molecular mechanics. The

second stage of the process invokes the introduction of the idea of

molecular similarity, a quantitative measure of just how similar

one molecule is to another. Perhaps the most important aspect of

similarity is similarity of shape and secondly similarity of mo-

lecular electrostatic potential.

There are several key areas where bioinformatics sup-

ports CADD research

# Virtual High-Throughput Screening (vHTS). Pharma-

ceutical companies are always searching for new leads

to develop into drug compounds. One search method is

virtual high-throughput screening. In vHTS, protein tar-

gets are screened against databases of small-molecule

compounds to see which molecules bind strongly to the

target. If there is a ―hit‖ with a particular compound, it

can be extracted from the database for further testing.

With today‘s computational resources, several million

compounds can be screened in a few days on sufficiently

large clustered computers. Pursuing a handful of promis-

ing leads for further development can save researchers

considerable time and expense. # Sequence Analysis. In CADD research, one often

knows the genetic sequence of multiple organisms or the

amino acid sequence of proteins from several species. It

is very useful to determine how similar or dissimilar the

organisms are based on gene or protein sequences. With

this information one can infer the evolutionary relation-

ships of the organisms, search for similar sequences in

bioinformatics databases and find related species to

those under investigation.

There are several key areas where bioinformatics sup-

ports CADD research

# Virtual High-Throughput Screening (vHTS). Pharma-

ceutical companies are always searching for new leads

to develop into drug compounds. One search method is

virtual high-throughput screening. In vHTS, protein tar-

gets are screened against databases of small-molecule

compounds to see which molecules bind strongly to the

target. If there is a ―hit‖ with a particular compound, it

can be extracted from the database for further testing.

With today‘s computational resources, several million

compounds can be screened in a few days on sufficiently

large clustered computers. Pursuing a handful of promis-

ing leads for further development can save researchers

considerable time and expense. # Sequence Analysis. In CADD research, one often

knows the genetic sequence of multiple organisms or the

amino acid sequence of proteins from several species. It

is very useful to determine how similar or dissimilar the

organisms are based on gene or protein sequences. With

this information one can infer the evolutionary relation-

ships of the organisms, search for similar sequences in

bioinformatics databases and find related species to

those under investigation.

B I O V A R I A N C E

P A G E 3 8

# Homology Modeling. Another common challenge

in CADD research is determining the 3-D structure

of proteins. Most drug targets are proteins, so it‘s

important to know their 3-D structure in detail. It‘s

estimated that the human body has 500,000 to 1

million proteins. However, the 3-D structure is

known for only a small fraction of these. Homology

modeling is one method used to predict 3-D struc-

ture. In homology modeling, the amino acid se-

quence of a specific protein (target) is known, and

the 3-D structures of proteins related to the target

(templates) are known. Bioinformatics software

tools are then used to predict the 3-D structure of

the target based on the known 3-D structures of the

templates. # Similarity Searches. A common activity in bio-

pharmaceutical companies is the search for drug

analogues. Starting with a promising drug molecule,

one can search for chemical compounds

with similar structure or properties to a

known compound. There are a variety of

methods used in these searches, includ-

ing sequence similarity, 2D and 3D

shape similarity, substructure similarity,

electrostatic similarity and others.

# Drug Lead Optimization. When a

promising lead candidate has been found

in a drug discovery program, the next

step (a very long and expensive step!) is

to optimize the structure and properties

of the potential drug. This usually involves

a series of modifications to the primary

structure (scaffold) and secondary struc-

ture (moieties) of the compound.

# Time-to-Market. The pre-

dictive power of CADD can

help drug research pro-

grams choose only the most

promising drug candidates.

By focusing drug research

on specific lead candidates

and avoiding potential “dead

-end” compounds, biophar-

maceutical companies can

get drugs to market more

quickly.

# Physicochemical Modeling. Drug-receptor inter-

actions occur on atomic scales. To form a deep un-

derstanding of how and why drug compounds bind

to protein targets, we must consider the biochemical

and biophysical properties of both the drug itself

and its target at an atomic level. # Drug Bioavailability and Bioactivity. Most drug

candidates fail in Phase III clinical trials after many

years of research and millions of dollars have been

spent on them. And most fail because of toxicity or

problems with metabolism. The key characteristics

for drugs are Absorption, Distribution, Metabolism,

Excretion, Toxicity (ADMET) and efficacy—in

other words bioavailability and bioactivity. Al-

though these properties are usually measured in

the lab, they can also be predicted in advance with

bioinformatics software

B I O V A R I A N C E

Benefits of CADD

CADD methods and bioinformatics tools offer

significant benefits for drug discovery pro-

grams.

# Cost Savings. The Tufts Report suggests that

the cost of drug discovery and development

has reached $800 million for each drug suc-

cessfully brought to market. Many biopharma-

ceutical companies now use computational

methods and bioinformatics tools to reduce

this cost burden. Virtual screening, lead opti-

mization and predictions of bioavailability and

bioactivity can help guide experimental re-

search. Only the most promising experimental

lines of inquiry can be followed and experi-

mental dead-ends can be avoided early based

on the results of CADD simulations.

# Insight.

One of the non-quantifiable benefits of CADD and

the use of bioinformatics tools is the deep insight that

researchers acquire about drug-receptor interactions.

Molecular models of drug compounds can reveal

intricate, atomic scale binding properties that are

difficult to envision in any other way. When we show

researchers new molecular models of their putative

drug compounds, their protein targets and how the

two bind together, they often come up with new ideas

on how to modify the drug compounds for improved

fit. This is an intangible benefit that can help design

research programs.

P A G E 3 9 V O L U M E 1 , I S S U E 1

In the early 1990‘s there was a great deal of opti-

mism that computer aided drug design would revo-

lutionize the way in which drugs could be devel-

oped. The enduring exponential increase in com-

puting power had progressed to the point that rudi-

mentary estimations of ligand receptor comple-

mentarity could be performed. Furthermore, com-

puter graphics technology had achieved the ability

to generate vector models of chemical structures

and manipulate them in real-time. This offered,

for the first time, the ability to interactively study

computer models of ligand structures and their

binding interactions with a receptor. The use of

mass screening and combinatorial chemistry al-

lowed researchers to discover lead compounds in a

rapid and efficient manner. As such, denovo de-

sign tools and their associated problems were no

longer needed to generate lead structures. One

would surmise that computer-aided drug design

technology would have soon ceased to exist.

On the contrary, it soon became apparent that

computational tools were needed that could opti-

mize these lead compounds into potent drugs. The

concept of drug optimization versus denovo de-

sign is an important one. The difficulty with de-

novo ligand generation is that an entire structure

is being created from scratch. The confidence

one has of accurately predicting how this struc-

ture will interact and bind within a target receptor

is shaky at best. In drug optimization, we begin

with a lead compound whose bound structure

within the receptor has been characterized, most

likely through x-ray crystallography. Subtle

modifications are then performed to generate de-

rivative compounds using structure based drug

design to improve binding affinity. Because we

are making much smaller changes, our faith in the

validity of the resulting structures is far

greater.These derivatives then undergo testing to

determine which modifications improve binding.

allowing the chemist to focus, synthesize, and

test only the most promising ligands. Thus, util-

izing computer aided drug design software to aid

in the refinement of weak binding lead com-

pounds is the most effective manner in which

these tools can be employed. The use of com-

puter modeling to refine structures has become

standard practice in modern drug design. There-

fore, CADD and bioinformatics together are a

powerful combination in drug research and devel-

opment. An important challenge for us going for-

ward is finding skilled, experienced people to man-

age all the bioinformatics tools available to us.

The structures of the best ligands can then be eluci-

dated to verify the accuracy of the modifica-

tions. This refinement process continues iteratively

until optimal binding ligands are produced.

In addition, the act of generating chemical

derivatives is highly amenable to computerized auto-

mation. Consider the application of targeted structure

based combinatorial chemistry as discussed

above. Libraries of derivative components are assem-

bled based upon the analysis of the active site. Be-

cause of the combinatorial nature of this method, an

extremely large number of candidate structures may

be possible. A computer can rapidly generate and

predict the binding of all potential derivatives, creat-

ing a list of the best potential candidates. In essence,

the computer filters all weak-binding compounds,

BIOTECH-

“A technology

for the

future.”

B I O V A R I A N C E

P A G E 4 0

“Democratic

sophistication is

the ultimate

sophistication…”

Caption describing

picture or graphic.

ISSUES ON CAMPUS

B I O V A R I A N C E

WBUT-SCHOOL OF BIOTECH POLLS

As it is said, the first step in solving a problem is to first realize that there is a

problem and polls are generally conducted to create awareness about the pros

and cons of the situation prevailing in any system. The response obtained by the

organizers from all the members of the School Of Biotechnology was amazing and

we would like to thank them for their kind consideration and support for making

this attempt a grand success. In future also, we hope each and every individual

will help us in creating awareness about the common issues and get them sorted

out positively for making WBUT - SBT a better place to live and work in.

What WBUT-SBT thinks about these issues:

General scientific scenario in India

A. What improvements can be done in our methodology so that the

society can be benefited with science? 1. Ability to think out of the box 2.Improvement in policy making 3.Lack of high impact factor research 4.Lack of applied research and innovate 5.Others

B. What basic measures and policies should be there to promote

basic science at the school level? 1.Stress on practical oriented teaching 2.Quality of teachers should be improved 3.Stress on understanding concepts 4. No changes to be made 5.Others

C. What do you think is better in this scenario to achieve your goals in

science? 1.Smart work

2.Hard work

3.Basic understanding

4.Common sense

5.Others

D. What could be done to improve the research quality

among the Students?

1.Improvement of financial incentives

2.Providing the freedom of thought 3. Improve on basic knowledge 4.Encouraging logical approach

5.Others

P A G E 4 1 V O L U M E 1 , I S S U E 1

E. The faculties in the department:

1.Sufficient and has good technical knowledge

2.Efficient in making students understand concepts

3.Faculties for interdisciplinary fields is needed

4.none of the above 5.Others

F. What could be done to maintain the equipments and chemicals in the lab

in a good and working state

1.Annual maintenance contracts

2.Lab technicians should be appointed 3. Students should be made responsible 4.Instruments should work at least once in a month

5.Others

G. Is our University clean enough to be called as the 'Center Of Excellence’?

To what extent is the college and classroom infrastructure suitable enough to

create a good atmosphere for creative sustainable learning?

1.It‘s in our reach

2.Still a long way to go

3.If drastic changes in the system are made 4. Do not wish to comment

5.Others

H. Regarding the campus placements:

1.The efforts taken are sufficient 2.Higher studies should be encouraged instead 3.Training and awareness should be given to enhance industry compatibility 4.There is ample scope for improvement for us to be competent and suitable

enough for companies to recognize. 5.Others

I. E journals:

1.Subscription should be at par with other IITs 2.Only free abstracts would suffice my research 3.I do not have any idea about it.

4.Consumes a lot of time in obtaining paid papers

B I O V A R I A N C E

P A G E 4 2 V O L U M E 1 , I S S U E 1

What you need for Biotech career?

Big question isn‘t it. Well, most of the forums on internet, biotech aspirants always

ask or looking for good answer. Mostly it is frustrating you don‘t get right answer.

Somethings that are useful are:

#1 PLANNING :

If you are looking for a career in BIOTECHNOLOGY, you definitely need to plan

ahead. Most of the biotech aspirants are not truly opted for BIOTECHNOLOGY.

Reason is simple, before coming to BIOTECHNOLOGY, they might have tried their

luck in Medicine entrance exams.

It is not because we don‘t have jobs, it‘s just planning and finding information

start ahead and plan at least one year before what you want to do.

#2 Mentor:

Everybody needs a mentor in life. It is true for BIOTECHNOLOGY as well. Find a

lecturer in your college or research institute, whom you believe successful/active

interested in what you want to do and take help from him/her. He/She will guide you

not only in project/future work; moreover you get a good reference letter.

#3 Field :

Best thing is find a subject you really like during your course.

Choose your field according to the opportunities

#4 Internet:

Now a days with internet, we are flooded with information. Please

spend some time on web find out which sites are offering admis-

“BIOVARIANCE”-The Team

CHIEF EDITOR -

NOTIFICATIONS

Dr. Joydeep Mitra, Reader ,WBUT

CONVEENER - Abhinav.K.V, M.Tech (Biotech)

MAGAZINE WING GENERAL SECRETARY– Amit Rai,M.Tech (Biotech)

Members Of Magazine wing:

Bioinformatics Wing : Devawati Dutta,Shaumabha Majumbar M.Tech (Bioinfo)

Quiz and Crosswords Wing: Deblina Chakraborty M.Tech (Biotech)

Scientist and Interview Wing: Chandan Gupta M.Tech (Biotech)

Biotech Wing : Santosh Chaudhary M.Tech (Biotech)

Discoveries Wing : Meenu Maan M.Tech (Biotech)

Biotech Potpurri Wing : Anindyo Roy,M.Tech (Biotech), Arnab Nayek,M.Tech(Bionfo)

And all those individuals that helped us achieve this challenge with perfection.

Printed At :

DESIGN AND LAYOUT: Abhinav.K.V, M.Tech (Biotech) B I O V A R I A N C E