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

WEST BENGAL UNIVERSITY OF TECHNOLOGY

V O L U M E 1 ,

INSIDE
THIS ISSUE:

 IN FOCUS: ASTHMA

 FACE TO FACE

With Dr. G. B. Nair

 NICED: An Overview

 BIOLOGIX :

In –Sillico Drug Design

 BURNING ISSUES

 UNSOLVED ISSUES

 FROM ALUMNI’S
DESK

 WBUT –SBT POLLS

 QUIZ AND CROSS-

WORD

IN FOCUS

POLLUTION

FACE TO FACE
PAGE 2

BIOVARIANCE
 VOLUME 1, ISSUE PA

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-

Tomader subho budhhir uday hok.

Dr. Raja Banerjee,Reader,WBUT

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

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

BIOVARIANCE
 PAGE 4

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

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 great effort by the students . I wish ― Biovariance‖

becomes one of the best magazines in near future.
Caption describing
picture or graphic. 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
“In addition to the barriers to create the ultimate bonding between the students and teachers with a
having a major view to open up new vistas accumulating the scientific and technological informa-
impact on poverty tions of present and past. Amit Chakraborty, Project Officer, WBUT
and hunger,
biotechnology
has great I am happy to know that the students of Biotechnology are going to publish a magazine. Hope
potential to this will contain your thoughts and inspiration, not only on the narrow field of your class room
alleviate specialization but also on the general applicability of the knowledge on the benefit of human
environmental kind. It is important to inquire who we are on the planet and what we do to keep it safe and vi-
degradation”. able for all. Never stop asking questions. Keep the windows of mind open. My best wishes for
(2001) 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-
ITS ALL IN A deavours Chabita Saha, Lecturer, WBUT.
GENE AND
ITS
TRANSCRIPT
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.

BIOVARIANCE
 CONTENTS
PAGE 5

PAGE NUMBER CONTENTS

EDITORIAL

8 OUR DEMOGRAPHIC DIVI-

DEND OR A NIGHTMARE..??

9 IN FOCUS

POLLUTION AND ASTHMA

A novel approach in understanding asthma and its rele-

vance with the current air pollution problems faced by the
country.

NEW SCIENTIST
12

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.

14 FROM THE CAMPUS

A sneak peak into one the most

prestigious enteric disease

research centers in eastern India.

BIOVARIANCE
PAGE 6

18 BIOLOGIX

How a bioinformatic In- Sillico

drug design aided

approach can be used to execute the

rehabilitation of drug addiction by production of target

BURNING ISSUES
22
WHITE BIOTECHNOLOGY:
Can it make our lives sweeter in

reality…??

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.

24 UNSOLVED ISSUES

ASBESTOS POLLUTION –
A serious health hazard

PLASTIC BAGS-
Reality check up

RARE DISEASE - PROGERIA

BIOVARIANCE
PAGE 7

DISCOVERIES
26
MOSQUITOCIDAL
VACCINES

MALARIA: A DISEASE FOR THE

POOR A novel strategy to combat ma-
laria by

28 BIONFORMATICA
PROTEIN MODELLING

CAREER ASCENT

32 ALL ABOUT GRE

CURRENT NOTIFICATIONS

BIOTECH POUTPURRI
33
CURRENT BIOTECH NEWS

FROM ALUMNI’S DESK

36
DRUG DESIGN MADE EASIER

ISSUES ON CAMPUS
40 WBUT CAMPUS : A place

with immense scope and

the capacity for improvement

21 QUIZ

AND
31
CROSSWORD

BIOVARIANCE
 PAGE 8

EDITORIAL
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-
“Biotechnology has ers with sustainably higher crop yields fostering the much empowering green revolution. Mr.
the potential to Satyen ‗Sam‘ Pitroda and his colleagues ushered in the telecommunications revolution in India
bring tremendous which has accentuated connectivity among all citizens. Mr. E. Sreedharan has consistently dem-
benefits …” (July onstrated the professional completion of government projects (Konkan Railway and Delhi
10, 2001). 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).

BIOVARIANCE
 IN FOCUS - POLLUTION AND ASTHMA
PAGE 9

BY: Amit Rai, M.Tech (Biotechnology)

inflammation underlying 2. Release of phospholipids

What is Asthma? hyperactivity. from membrane followed
Asthma, in medical terms is by mediator synthesis
characterized by hyperre- What triggers Asthma? (within minutes) : Pros-
sponsiveness of tracheo- Trigger factors (Infection, taglandins, Leukotrienes ,
bronchial smooth muscles irritants, pollutants, exer- Plasma activating factors.
to a variety of stimuli, re- cise, exposure to cold air, 3. Activation of genes fol-
sulting in narrowing of air psychogenic) lowed by protein synthesis
tubes, often accompanied Recruitment of mast cells (over hours): Interleukins,
by increased secretion, mu- and inflammatory cells.
cosal edema and mucosal Tumor necrosis factor α.
Production of multitude of
plugging. mediators:
Asthma is now 1. Release of mediators
recognized to be a primarily stored in granules
inflammatory condition: (immediate) : Histamine,
Protease enzymes, TNFα
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”. www.journal.prous.com/.../images
(Food Insight, October
2001.)

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.

BIOVARIANCE
 VOLUME 1, ISSUE 1 PAGE
SAY NO TO
POLLUTION
What are the approaches to the treat- early introduction and more ex-
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 zation and allergic phenoena.The
7.Directly acting bronchodilators
Adverse effects of Corticosteroids:
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
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
10
Corticosteroids: The mainstay in to suppression of recruitment of leuko-
asthma therapy cytes at the site of contact with antigen
The realization that asthma is pri- and inflammatory response to immu-
nological injury.
marily an inflammatory disease
They cause greater suppression of cell
which accentuates with time, if
not controlled, and the availability mediated immunity in which T cells
of inhaled steroids that produce are primarily involved.e.g. delayed
few adverse effects has led to an hypersensitivity and graft rejec-
tion.This is the basis of use in autoim-
tensive use of corticosteroids in mune diseases and organ transplanta-
asthma. tion. Factors involved may be inhibi-
tion of IL-1 release from macro-
How it works? phages ; inhibition of IL-2 formation
Glucocorticoids suppress and action as a result of which T cell
immunological competence.They proliferation is not stimulated; sup-
suppress all types of hypersensiti- pression of natural killer cells etc.
clinical effect appears to be due
and cough are also common Osteoporosis by in-
symptoms associated with creasing bone
use of inhaled steroids resorption and
Systemic side effects: decreasing bone
Treatment with corticoster formation.
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
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 www.soylabs.com/img/osteoporosis.jpg
on 6550 children in
situation of the school in relation to
the age group of 6 to 15 years was un-
vehicular traffic and the socioeco-
dertaken for prevalence of asthma and
nomic group of children. Group I-
children were categorized into three
Children from schools of heavy traffic
groups depending upon the geographical
VOLUME 1, ISSUE 1 PAGE 11

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

and the socioeconomic group of children. Group I- tion is the main culprit for air pollution, account-
Children from schools of heavy traffic area showed ing for 65 per cent of the city's total pollution.
prevalence of 19.34%, Group II-Children from Industry and thermal plants contribute 25 per
cent and the remaining 10 per cent is due to do-
heavy traffic region and low socioeconomic popula-
mestic activity.
tion had 31.14% and Group III-Children from low The Central Pollution Control Board
traffic area school had 11.15% respectively. (P: I & (CPCB) estimates that 2,000 metric tonnes of
II; II & III <0.001). A continuation of study in rural poisonous gases and 300 million litres of waste
areas showed 5.7% in children of 6-15 years. The water and corrosive liquid by-products, are
persistent asthma also showed an increase from pumped into New Delhi's environment each day.
20% to 27.5% and persistent severe asthma 4% to Some industrial processes result in new, little-
known compounds, which endanger workers'
6.5% between 1994-99.
safety and health and persist in the environment
long after use.
2. New Delhi
The number of deaths reported due to
Delhi has seen a mind-boggling 500 per cent
asthma was 7000 in year 2001.
in crease in industries in the last 30 years from
18,500 units in 1961 to around 93,000 in 2001.
“In addition to
having a major
impact on
Several initiatives were taken to dioxide (SO2), suspended particu- 4197 from 4681 μg m−3, 14
poverty and
reduce extremely high levels of late matter (SPM) and oxides of from 18 μg m−3 and 34 from
hunger,
pollutants present in the ambient nitrogen (NOX), emitted from trans- 36 μg m−3, respectively, and are
biotechnology
air of urban city. One of the port sector, during the years 1995– well within the permissible lim-
has great
initiatives was to move public 2000 (without CNG) and the year its. An analysis of SO2/NOX and
potential to
transport to CNG, which has 2001 (with CNG) has been made in CO/NOX concentrations, whose
alleviate
been implemented in Delhi order to assess the impact of CNG correlation coefficient r2 has the
environmental
since April 2001. Delhi boasts vehicles on ambient air quality in values 0.7613 and 0.7903, re-
degradation”.
CNG in nearly 2200 buses, Delhi. The annual average concen- spectively, indicates that point
(2001)
25,000 three wheelers, 6000 sources are contributing to
tration of SPM came down to 347
taxis and 10,000 cars. A relative SO2 and mobile sources are
from 405 μg m−3, which is still be-
comparison of ambient air con- contributing to NOX concentrations.
yond the permissible limits. The
centration of pollutants, e.g. It has been found that concentration
concentration of annual averages of
carbon monoxide (CO), sulphur contribution of above pollutants has
CO, SO2 and NOX decreased to
been reduced considerably.

References:
Books:
1. Essentials of Medical Pharmacology, K.D.Tripathi, 5 th 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
 PAGE 12

NEW SCIENTIST: BY: Chandan Gupta, M.Tech (Biotechnology

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

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
JICA LANDMARK
Institute of Cholera & Enteric Diseases
(NICED), Kolkata, India. Before joining Suggestion to students:-
NICED as director, he was the director of
Dr Rob Adam, Director- Laboratory Sciences Division at the Interna- Think of what you can do and what
General: Arts, Culture,
tional Center for Diarrhoeal Diseases Re- cannot be done there and it's relevant
Science and Technology:
“Government’s search, (ICDDR), Dhaka, Bangladesh.
to your needs.
Foresight Programme

has identified three

main drivers of future 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-
economies;
rine fungi (Supervisor: Dr. D. Chandramohan) in Marine Biology in 1977 from Annamalai Uni-
information and versity and acquired the Degree of Ph.D (Title-Studies on ecology, serology and taxonomy of
communications
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-
technology, advanced ment of Microbiology,(NICED), Calcutta, a constituent Institute of the Indian Council of Medi-
materials, and 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.
biotechnology”. He has been working on enteric pathogens with particular emphasis on Vibrio cholerae, the
causative agent of the disease cholera.

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

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
NICED 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.
VOLUME 1, ISSUE 1 PAGE 13

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.
 PAGE 14
From the Campus:
BY: Chandan Gupta, M.Tech(Biotechnology)
NATIONAL INSTITUTE OF CHOLERA & ENTERIC DISEASES (NICED)
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-
“The first century of ological research and screening. Institute
the new Millennium also trains health professionals for better
will belong … also to management and prevention of diarrheal
diseases and for rapid and correct diag-
biotechnology which
nosis of etiological agents. Epidemiologi-
will bring cal investigations of diarrheal diseases
unprecedented are carried out in different parts of India.
advances in human Antiserum of Vibrio cholerae is raised in
and animal health, the Institute and supplied to the national
agriculture and food and international laboratories. Presently,
production, specific monoclonal antiserum for detec-
manufacturing and
sustainable Though the Institute is principally financed
environmental by the Indian Council of Medical Research
management”. (ICMR), New Delhi, different national and
(Foreword, National international funding agencies extend sup-
port to the Institute on specific research
Biotechnology Strategy
projects. The Japanese International Co-
for South Africa).
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
DEPT. OF JICA-NICED exchange programme
VIROLOGY, Japanese scientists are working in
NICED 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-
BIOVARIANCE
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.
VOLUME 1, ISSUE 1 PAGE 15

Photo:- Parasitology lab of NICED

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

MOLECULAR
MICROBIOLOGY LAB

IMMUNOLOGY LAB

BIOVARIANCE
 PAGE 16

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

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.

“Biotech is a
3.What virtues you realized in yourself which helped you choose research as a profession?
terrific industry,
but it's not like Dr G B Nair: My virtue which has helped me choosing my career is exceptionally hard work and tell
having a big 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.
chip-
manufacturing
industry.s”
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.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 17

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

of thinking

proved by
9. What basic measures and policies would you suggest to promote basic science at the school
level ? systematic
Dr G B Nair : I would try to change the way science is taught. When I was at the international
observations.”
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.
BIOVARIANCE
 PAGE 18

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

CAN BIOINFORMATICS HEAL DRUG ADDICTION ??

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.
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)

DARP 32 CIRCUITS

“Biotechnology is a
Fig 1: Graph showing mortality rates[5(a)]
key industry for the
future. Without Physiological basis of drug addiction:-
DARPP-32,a protein in the brain
biotechnology India The ill effects of drug addiction on facilitates addictive behaviors.
can hardly ensure human body are directly related to Silencing of DARP-32 protein with
wellbeing for its the central nervous system. It gets some kinds of active ligand can in-
weakened and may even lead to hibit the active site of DARPP-32, it
future generation”.
death. Excessive drug usage causes can inhibit production of this protein
(2001) the release and prolonged action of and could help to prevent drug addic-
dopamine and serotonin. Dopamine tion.
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 Fig2:- Dopamine [5c]
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 Figure3:- D1 receptor[5d] Figure4: CREB[5(b)]
genes including C-Fos.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 19

Bioinformatics approach to solve this problem:-

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]

This database has a user inter- addiction related genes by using as background and interprets the p-value and other
face which supports browsing of the FASTA format. values .On the basis of the analysis, it gives a predic-
the genes by chromosome or The KOBAS server tion of the common molecular pathway of these drug
pathways, advanced text search have many distinctive tools to addicted genes.[1]
by gene ID, Organism, Type of find out the result if we give as A recent research paper has published that there are
addictive substances, Technol- input the sequences of drug ad- 396 addiction related genes and identified five path-
ogy platform, Protein domain dicted genes. It analyzes the ways that are common to addiction of four different
and sequence search by BLAST data, taking in the input of substance: cocaine, opium, nicotine and alcohol. Also,
search. We can also find out the FASTA sequences of drug ad- there are 18 metabolic and signaling pathway common
DNA sequence or the amino dicted genes and using all the to the addiction related genes[1]. All these pathways
acid sequences of the human known genes in human genome were interlinked with each other through CAMII.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 20

The main question that comes in our

mind how to eradicate this problem?
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
A diagrammatical representation of the bioinformatical approach to predict the cure of drug addiction problem is given below:-
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- DOCKED POSE OF
lem, then we can save millions of life . A SMALL
MOLECULE

FREE
OFFER

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.

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

References:-

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.

BIOVARIANCE
 QUEST
PAGE 21

BY: Deblina Chakraborty,M.Tech (Biotechnology)

QUIZ :
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?
.
Identify the person in this picture

CARTOON: BY: Deblina Chakraborty,M.Tech (Biotechnology)

BIOVARIANCE
 VOLUME 1, ISSUE 1 PAGE 22

BURNING ISSUE :
WHITE BIOTECHNOLOGY AND ITS RELEVANCE IN INDIA
BY: Santosh Kumar Chaudhary,M.Tech (Biotechnology)

natural tools in production of bio-

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. Agricultural by product
White biotechnology uses the
based chemicals, materials and
fuels. The economic growth associ-
ated with this field is estimated
“Biotechnology
about €11-12 billion per annum by
2010. has the
White biotechnology is potential to
used mainly in fermentation tech- bring
nology, Biocatalysis and Pharma tremendous
industry. It is being used in these benefits
fields for the production of bio- …” (July 10,
chemicals, Biomaterials and Biofu-
2001).
els by using agricultural by-
products which are converted into
sugar by chemo/physical treatment
or enzyme1.
(Biochemicals, Biomaterials, Biofuels etc)

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)
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.
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.

White biotechnology bleaching can be cut by 40%. So

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
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 MICROBIAL POPULATION
paper.

BIOVARIANCE
 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

BIOVARIANCE
 UNSOLVED ISSUES
PAGE 24

ASBESTOS POLLUTION – A serious health hazard

BY: Shoumabha Mazumdar, M.Tech (Bioinformatics)

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
OUR EARTH IN conductor of electricity.
TROUBLE.. 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
“Biotechnology asbestos fibres in the air
has the potential to when disturbed. Asbestos
bring tremendous fibres are harmful because
benefits …” (July they are extremely small
10, 2001). 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

PLASTIC BAGS: A Reality check up

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

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.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 25

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).

PROGERIA : An Early Aging Disease BY: Shoumabha Mazumdar, M.Tech (Bioinformatics)

Progeria (Greek word: meaning with progeria usually develop

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
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 A
hearts or brains. Race “Are we doin
There is no Against
proven treatment and no clue in Time our part
sight. Though scientists have
towards
identified exactly the location of
gene causing Progeria but there that includes health care profes- mother
is no treatment or prevention for sionals, family and friends. On
Progeria at this time. Finding a the other hand the government nature…??”
cure for Progeria will not only should also encourage the scien-
help these children, but may tists by funding more on the
provide keys for treating mil- researches that is related to
lions of adults with heart disease progeria, as every new research
and stroke associated with the brings us closer to cure.
natural aging process. Number
of people infected is about 1 in REFERENCE:
http://www.progeriaresearch.org/
8 million [reported]. In dealing about_progeria.html
with a disorder such as progeria, http://www.progeriafamilycircle.de/eng/eng.html
support groups play a vital role

BIOVARIANCE
 PAGE 26
DISCOVERIES
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)
In light of insecticide
resistance and environmental con-
cerns regarding the use of insecti-
cides1, control of vector borne
diseases using anti-vector vaccines
MALARIA KILLS…. 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
BIOVARIANCE
BY: Meenu Maan, M.Tech (Biotechnology)
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 .
effector cells (cytotoxic T- Immunodominance,
lymphocytes, NK cells, and immune masking, and anti-
macrophages) are some of these body cross-reactivity further
factors that may act separately complicate the matter. Exten-
or synergistically to impair the sive biochemical purification
insect. of the vector tissue prior to
Past research has proven the immunization is usually done
feasibility of killing blood feed- to preempt this, but such work
ing vectors and reducing their is extremely laborious and
fecundity via immunological impractical when dealing with
factors ingested along with smaller vectors such as mos-
blood from the host. quitoes.2
However successful Most of the ap-
identification of molecular fac- proaches involved in discov-
tors within vectors has been ery of new and unique antivec-
rare. This may be said to be the tor antigens apply a reduction-
rate limiting step of this re- ist approach to sort and test
search. The difficulty being that individual antigens or immune
the experimental animals when factors. . In this way, the con-
immunized with a homogenized fusion of multi- immune fac-
vector tissue, a polyclonal and tors recognizing many anti-
multifactorial immune response gens does not conceal the
is produced against this homo- identification of critical anti-
geneous mix of vector antigens. gens.
And it becomes difficult to
match an immune effecter like
antibody to a single antigen.
VOLUME 1, ISSUE 1 PAGE 27

Another novel approach use phage-displayed

antibodies and peptides. Bacteriophages can
display peptides or antibody fragments (scFv)
MALARIA on their surface when the cDNA of these pro-
LIFECYCLE 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
One approach involves sorting of antigens on peptides or proteins by panning the library on
basis of weights and charges4, techniques like almost any antigen. The selected clones and
SDS-PAGE and Isoelectric focusing can be their translated proteins can then be easily rep-
used. Another reductionist approach involving licated, mass-produced, and purified in the
antigens is expression library immunization laboratory by exploiting the life-cycle of bacte-
technology and its derivatives5. This method is riophages within bacterial cells. “Revolutionary,
being applied to vectors by immunizing mice In conclusion, these anti-vector vac- unprecedented,
with a cDNA expression library derived from cines may prove to be the much needed impetus unsurpassed. These
midgets of bloodfed A.gambiae. A.gambiae were in control of diseases like malaria, dengue, adjectives are being used to
fed on these mice and an increased mosquito Japanese encephalitis, chicken guinea etc and describe the Human
mortality was observed ( unpublished data). may even be applied to control other ectopara- Genome Project’s potential
A reductionist approach regarding immune ef- sites like ticks and also plant pests. to benefit society. The
fectors can also be a successful antivector im- understanding of the
mune strategy. One method is to make mAbs human genome that has
from immunized animals, and then feed these been gained, is almost
mAbs individually via a membrane feeder to certain to lead to
assess their ability to reduce vector survivorship breakthroughs in medicine
or fecundity6. that may ultimately
eradicate many of today’s
References cited: diseases”. (Food Insight,
1.Casida, J. E., and G. B. Quistad. 1998. October 2001.)
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. MALARIAL PARASITE
5.Barry et al. 1995.
Protection against mycoplasma infection using ex-
pression- library immunization. Nature 377: 632- 635.

COUNTERING MALARIA

BIOVARIANCE
 Protein Modeling:
PAGE 28

BY: Arnab Nayek, M.Tech(Bioinformatics)

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-
PROTEIN edge is vital for understand-
MODELLING
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
“BIOINFORMATICS DNA binding protein), recog-
GIVES US AN nize a molecular signal by
OPTION OF
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

NARROWING DOWN
THREE MAIN APPROACHES FOR
THE DISCOVERY SRTUCTURE PREDICTION:
HOMOLOGY MODELLING
PIPELINE…..” 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

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
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.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 29

1 ALA VAL GLN SER LYS and dynamics as well as other

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:
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
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
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.
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.
“In addition to
having a major
The file newton.xyz_2, which impact on
is produced by Newton mini- poverty and
mization method, and which hunger,
is the coordinate file of that biotechnology
given structure (guess struc-
has great
ture) is copying into a file
name anneal.xyz and which is potential to
again copying into a directory alleviate
name as run1(which was pre- environmental
viously created). The files degradation”.
anneal.key, (2001)
anneal.run, newton.key,
newton.run are also copy into
the directory run1.

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.
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.
BIOVARIANCE
 PAGE 30
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.
Protein visualization in PYMOL
BIOVARIANCE
So for producing pdb file it
requires two input files – The 3-D structure of the protein SYSTEMIN: RASMOL view
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.
Acknowledgments:
Dr. Ansuman Lahiri (Lecturer in the dept. of BMBG, University of Calcutta)
References: Introduction to BIOINFORMATICS (Arthur M.Lesk)
VOLUME 1, ISSUE 1 PAGE
CROSSWORD
DOWN
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 ______.
31
BY: Deblina Chakraborty,M.Tech (Biotechnology)
Can you solve it the
fastest..?????
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.
BIOVARIANCE
 CAREER ASCENT
PAGE 32

BY: Priyanka Biswas ,Int Phd (Microbiology)

ALL ABOUT GRE:

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.
GRE– The GRE is an aptitude test. Like all
ASPIRING HIGH.. 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
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.
not scored.
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.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 33

BIOTECH POUTPURRI
CURRENT BIOTECH NEWS BY: Anindyo Roy (M.Tech (Biotechnology)

Soyabean against Alzheimer

“To catch the

Natto reader's

attention,
Amyloids aggregates of fibrous
proteins, the major component of place an
amyloid plaques accumulated in loid related disease. Natto kinase an anticlotting serine protease
many neurodegenerative disease
present in Natto is the principle component that dissolves the fi- interesting
brous protein aggregates .Thus Natto may provide an effective
like Alzheimer‘s disease can be tar- sentence or
treatment for Alzheimer‘s disease as well as presenting some deli-
geted by popular fermented food
cious dishes.
(Bacillus subtilis) in South-East quote from the
Asia called Natto. According to Reference:
scientists in Taiwan, Natto which is Hsu et al. amyloid-Degrading Ability of Natto kinase from Ba- story here.”
made from boiled soybean can be cillus subtilis Natto.
effectively used to treat such amy- Journal of Agricultural and Food Chemisty,2009;57.

Granulomatous arthritis

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- Arthiritis— An acute problem
nized with proteoglycan. Two group of mice were in old age
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 . Reference:
The normal mice display more severe Rosenzweig et al.
inflammation as compared to knocked out mice . Activation of nucleotide oligomerization domain
The development of arthritis also in NOD-2 deac- 2 exacerbates a murine model of proteoglycan-
tivated mice demonstrates that the NOD-2 is not induced arthritis.
primary factor for developing inflammatory ar- Journal of Leukocyte Biology,2009; 85 (4): 711-
thritis in absence of MDP. This study will open 718
up new directions for treatment of arthritis.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 34

FLU CHIP:

Scientists at the University of ning. This method is useful

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-
A MICROARRAY– DNA ON CHIP
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 MICROARRAY”
breakthroughs in Science,
American Institute of Physics. An
interdisciplinary

New horizon in bioremediation: science”

A relatively cheap and easy available According to the research team

material, chicken manure has been Bacillus species and Pseudomonas
found to degrade crude oil in contami- aeruginosa were the best oil-
nated soil as described by scientists at degrader.Proteus, Enterobacter, and
the University of Wuhan, China. The Micrococcus species were also
manure raises soil pH upto 6.3-7.4 found to be able to degrade crude
which is optimal for oil degrading oil.
bacteria..It was added to soil contami- Reference:
nated on a pollution basis of 10%(v/w Bello M. Yakubu, Huiwen Ma, and
crude to soil).75% of oil has been ChuYu Zhang.
found to be degraded in soil with ma- Biodegradation of crude oil in
nure after 2 weeks as compared to soil using chicken manure.
International Journal of Environment
manure free soil exhibited 50%natural
and Pollution, 2009, Volume
remediation. 36,Issue 4

ANTIBIOTIC REVOLUTION:

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
BIOVARIANCE
different from the naturally oc- leading to safe and healthy food for us.
curring protein..According to Reference :Society for General Mi-
Dr. Field a researcher involved crobiology , New, More Effective Hey…
in this study ,different Nisin Nisin Anti- nothing
variants can now be used spe- biotics of mine
cifically to target specific patho- Combat is use-
gen .Another benefit is that Superbugs less!!!
Nisin variants can now lagely And Food
replace the commercial food Diseases.
preservatives such as sug-
ars,salts and other chemicals in
combating bacterial growth ulti-
mately
 VOLUME 1, ISSUE
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
BIOVARIANCE
1 PAGE 35
BY: Anindyo Roy (M.Tech (Biotechnology)), Pallabi Pal (Int PhD Mol Bio)
hydrogen.According to re-
searchers at the Penn State
archeal biofilm could use the Reference:
Shaoan Cheng, Defeng Xing,
current to convert carbon di-
Douglas F. Call and Bruce E.
oxide and water to methane in Logan.
absence of any organic mate- Direct Biological Conver-
rial, usually found in micro- sion of Electrical Current
bial electrolysis cells.The into Methane by Electro-
cells has about 80 percent methanogenesis.
conversion efficiency of elec- Environ. Sci. Technol.,
tricity into meth- 2009 ,Pensylvenia State Uni- MCROBES-
ane.According to Bruce E. versity.
Logan, Kappe Professor of “A boon or a
Environmental Engineering,
Penn State that the electro- bane…???”
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.
 From the Alumni’s Desk
PAGE 36
DRUG DESIGN – Made Easier
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
DOCKING 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
IN-Sillico Drug structure and biological activity. This new un-
derstanding that a quantitative relationship ex-
Design need a isted ushered in the beginnings of computer-
aided drug design.
novel
ComputationL Computer-aided drug design is no longer merely
a promising technique. It is a practical and real-
biology istic way of helping the medicinal chemist. On
its own it is unlikely to lead to pharmaceutical
knowledge..
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
BIOVARIANCE
Md.Ataul Islam, Alumni WBUT SBT
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-
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
VOLUME 1, ISSUE 1 PAGE
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.
LIGAND DOCKING
USING GOLD
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.
BIOVARIANCE
37
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.
 PAGE 38

# 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.

# 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
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.

# Time-to-Market. The pre- # Insight.

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.
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.

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE
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.
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,
BIOVARIANCE
39
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.
BIOTECH-
“A technology
allowing the chemist to focus, synthesize, and for the
test only the most promising ligands. Thus, util-
izing computer aided drug design software to aid future.”
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.
 PAGE 40

ISSUES ON CAMPUS
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:

Caption describing General scientific scenario in India

picture or graphic.

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

“Democratic
B. What basic measures and policies should be there to promote
basic science at the school level?
sophistication is 1.Stress on practical oriented teaching
2.Quality of teachers should be improved
3.Stress on understanding concepts
the ultimate 4. No changes to be made
5.Others
sophistication…”
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

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 41

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

BIOVARIANCE
VOLUME 1, ISSUE 1 PAGE 42

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. NOTIFICATIONS

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 - 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:

Biotech Wing : Santosh Chaudhary M.Tech (Biotech)

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

Bioinformatics Wing : Devawati Dutta,Shaumabha Majumbar M.Tech (Bioinfo) Printed At :
Scientist and Interview Wing: Chandan Gupta 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.
DESIGN AND LAYOUT: Abhinav.K.V, M.Tech (Biotech)
BIOVARIANCE