INSIDE THIS ISSUE: BUSINESS NAME VOLUME 1, IN FOCUS: ASTHMA FACE TO FACE With Dr. G. B. Nair NICED: An Overview BIOLOGIX : In –Sillico Drug Design BURNING ISSUES UNSOLVED ISSUES WEST BENGAL UNIVERSITY OF TECHNOLOGY FROM ALUMNI’S DESK WBUT –SBT POLLS QUIZ AND CROSS- WORD FACE TO FACE IN FOCUS POLLUTION
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I N S I D E
T H I S I S S U E :
B U S I N E S S N A M E
V O L U M E 1 ,
IN FOCUS: ASTHMA
FACE TO FACE
With Dr. G. B. Nair
NICED: An Overview
BIOLOGIX :
In –Sillico Drug Design
BURNING ISSUES
UNSOLVED ISSUES
WEST BENGAL UNIVERSITY OF TECHNOLOGY
FROM ALUMNI’S
DESK
WBUT –SBT POLLS
QUIZ AND CROSS-
WORD
FACE TO FACE
IN FOCUS
POLLUTION
P A G E 2
B I O V A R I A N C E
P AV O L U M E 1 , I S S U E
FROM THE TEACHERS’ DESK
Publication of Biovariance by the students of the School of
Biotechnology is an exciting effort. It will certainly con-
tribute towards the expression of their ideas and thinking
on the present scenario in Biotechnology in particular and
different aspects of Science and Technology in general. I
wish a great success for Biovariance.
Dr. Subroto Kumar Dey,Director,School Of Biotechnol-
Congratulations for successful launching of your magazine. I
believe your dedication towards the development of this maga-
zine would be essentially required at all stages. Keep up the
hard work. With all the best wishes and regards.
Dr Jaya Bandhopadhyay, Lecturer ,WBUT
Dr. Raja Banerjee,Reader,WBUT
After waiting for quite a few years we would finally have
our departmental magazine. I express my best wishes and
heartfelt thanks to the current batch of students for this
wonderful gift to the department.
Dr Shaon Ray Chaudhuri ,Lecturer,WBUT
It is very encouraging to have the magazine ―Biovariance‖. I wish
you success.
Dr Rabi Majumdar
Advisor, School Of Biotechnology,WBUT
Biovariance –the colours of life , gives me a terrific feeling not only
because it has the name that I opted for selection but also because the
long awaited child has been conceived and will be born soon.
Dr Soumali Basu
Lecturer,Dept. Of Bioinformatics,WBUT
Good effort,Wish you success…!!!!!!!!
Mr. Subhranshu Supakar,Project Officer, WBUT
B I O V A R I A N C E
Tomader subho budhhir uday hok.
P A G E 4
“In addition to
having a major
impact on poverty
and hunger,
biotechnology
has great
potential to
alleviate
environmental
degradation”. (2001)
Caption describing
picture or graphic.
ITS ALL IN A
GENE AND
ITS
TRANSCRIPT
B I O V A R I A N C E
.
Biovariance is an exciting concept. I really appreciate
the effort students have taken in bringing this out. I
wish them all the best and hope they continue this
good work.
Dr Anindita Seal, Associate Lecturer,WBUT
A magazine is also the name of the device that holds bul-
lets. I hope your magazine will also be loaded with stuff
that impacts its readers. Best wishes for your enterprise.
Dr. Indrani Roy,Lecturer,School Of Biotechnology,WBUT
A great effort by the students . I wish ― Biovariance‖
becomes one of the best magazines in near future.
Dr. Salil. C. Dutta,
Advisor,School Of Biotechnology,WBUT
Biovariance, is blooming for the first time by our beloved students from the De-
partment of Biotechnology of this University with all its essence and breaking all
the barriers to create the ultimate bonding between the students and teachers with a
view to open up new vistas accumulating the scientific and technological informa-
tions of present and past. Amit Chakraborty, Project Officer, WBUT
I am happy to know that the students of Biotechnology are going to publish a magazine. Hope this will contain your thoughts and inspiration, not only on the narrow field of your class room specialization but also on the general applicability of the knowledge on the benefit of human kind. It is important to inquire who we are on the planet and what we do to keep it safe and vi-able for all. Never stop asking questions. Keep the windows of mind open. My best wishes for the success in your life". N.P.Bhattacharya,HEAD,Bioinformatics Dept,SINP,Guest lecturer,WBUT
It gives me high pleasure that Students of School of Biotechnology, WBUT have
shown their courage to launch a magazine Biovariance-colours of life. I wish the
magazine would be colourful with knowledge based articles and surely will make
great impact on student - teacher community.
Hearty congratulations on the successful launch of the scientific magazine
―Biovariance‖. May this experience be a guiding light in your future en-
deavours Chabita Saha, Lecturer, WBUT.
The publication of Biovariance by students of the School of Biotechnology is
indeed a praiseworthy effort.As a faculty member I feel proud of this achieve-
ment.I hope that this magazine will continue to excel and leave a prominent
impression in the area of biotechnology.
CONTENTS
P A G E 5
B I O V A R I A N C E
PAGE NUMBER CONTENTS
EDITORIAL
IN FOCUS
NEW SCIENTIST
Face to face with one of the
pioneers in the field of science in
India, a Foreign Associate of
National Academy of Sciences,
USA and the winner of the prestigious Shanti Swarup Bhatnagar
Award for Medical Sciences for the discovery of globally known
as Vibrio cholerae O139 Bengal and his contributions on
describing a cell-rounding factor from strains of Vibrio cholerae.
POLLUTION AND ASTHMA
A novel approach in understanding asthma and its rele-
vance with the current air pollution problems faced by the
country.
OUR DEMOGRAPHIC DIVI-
DEND OR A NIGHTMARE..??
FROM THE CAMPUS
A sneak peak into one the most
prestigious enteric disease
research centers in eastern India.
8
9
12
14
P A G E 6
B I O V A R I A N C E
UNSOLVED ISSUES
ASBESTOS POLLUTION –
A serious health hazard
PLASTIC BAGS-
Reality check up
RARE DISEASE - PROGERIA
BURNING ISSUES
WHITE BIOTECHNOLOGY:
Microbial production of commercially important products
based on In-Vitro manipulation by recombinant DNA
technologies and its relevance with India in Poly Lactic Acid
production.
Can it make our lives sweeter in
reality…??
BIOLOGIX
How a bioinformatic In- Sillico
drug design aided
approach can be used to execute the
rehabilitation of drug addiction by production of target
18
22
24
P A G E 7
B I O V A R I A N C E
DISCOVERIES
MOSQUITOCIDAL
VACCINES
MALARIA: A DISEASE FOR THE
POOR A novel strategy to combat ma-
laria by
BIONFORMATICA
PROTEIN MODELLING
ISSUES ON CAMPUS
WBUT CAMPUS : A place
with immense scope and
the capacity for improvement
BIOTECH POUTPURRI
CURRENT BIOTECH NEWS
QUIZ
AND
CROSSWORD
CAREER ASCENT
ALL ABOUT GRE
CURRENT NOTIFICATIONS
FROM ALUMNI’S DESK
DRUG DESIGN MADE EASIER
21
26
31
40
36
33
32
28
P A G E 8
Our demographic dividend or nightmare? -Dr Joydeep Mitra <[email protected]>
Nandan Nilekani (Infosys co-founder) in his best selling book ‗Imagining India‘ (Penguin
Press, 2008) raises the stirring possibility that India would demographically be the youngest
nation within a few decades. If millions of young peoples‘ energy is harnessed constructively, it
could be a boon to the people of India and the world and if not, it would be a nightmare. With a
population of ~1,160,000,000, only 3 – 5% Indians read, write or understand English -an indis-
pensable currency of acquiring higher education. Adult literacy rates vary state wise within In-
dia; however, we still have the largest number of illiterate people among all countries. Malnour-
ishment and undernourishment in India is one of the highest in the world. The supply of clean
drinking water reliably separated from effluents, professional quality sewage treatment systems
remain an urgent yet unmet need. Water borne diseases deprive India‘s masses of immense pro-
ductivity gains including usurping hospital expenditures, thus cost economic growth and impose
human suffering on the most vulnerable. Disease causing microorganisms do not discriminate -
the most deprived among us are ones with the least amenities of care and support.
Science has delivered –the infant mortality rate has fallen, vaccination (small pox, polio,
among others), advances in medical care, sanitation, have increased longevity. More needs re-
main, especially in inventing sustainable energy use coupled with high standard of living. These
have to be met by the current young generation and be our demographic dividend which could
serve as an example in world history as has been accomplished by the following examples, de-
spite the prevailing challenging infrastructure within India.
Dr. Verghese Kurien‘s community based efforts in Anand, Gujarat, contributed exempla-
rily (white revolution) to enable India become the largest annual producer of milk in the world.
Prof. M. S. Swaminathan and his co-workers‘ scientific research have empowered Indian farm-
ers with sustainably higher crop yields fostering the much empowering green revolution. Mr.
Satyen ‗Sam‘ Pitroda and his colleagues ushered in the telecommunications revolution in India
which has accentuated connectivity among all citizens. Mr. E. Sreedharan has consistently dem-
onstrated the professional completion of government projects (Konkan Railway and Delhi
Metro Rail) within budget and on time. Scientists and engineers at the Indian Space Research
Organization have accomplished some of the most cost effective payload liftoffs of satellites
into space. Tata Motors‘ engineers produced the world‘s lowest priced car (nano) in India.
This issue contains an interview with Dr. G. Balakrish Nair of National Institute of Chol-
era and Enteric Diseases in Kolkata. Learning and watching how successful scientists work
might inspire us and could pave the way for us to find newer, better ways of prosperous, sustain-
able and peaceful livelihood. Scientists and engineers must play an immense constructive role.
Innovation by young Indian minds could maximize our dividends and meet our immense
challenges with Indian solutions to an India aspired by Rabindranath Thakur (1861-1941, Nobel
Literature, 1913) as:
Where the mind is without fear and the head is held high;
Where knowledge is free;
Where the world has not been broken up into fragments by narrow domestic walls;
Where words come out from the depth of truth;
Where tireless striving stretches its arms towards perfection;
Where the clear stream of reason has not lost its way into the dreary desert sand of
dead habit;
Where the mind is led forward by thee into ever-widening thought and action--
Into that heaven of freedom, my Father, let my country awake.
NICED today is engaged in research on diseases of national importance and bio-logical problems of global interest. It is the one of the major laboratories in India which initiated, right from its inception, multidisciplinary concerted efforts for conducting basic research on infectious diseases, specifically Amoebiasis and Cholera.
NICED also conducts research on acute diarrhoeal diseases of diverse eti-ologies as well as typhoid fever, infective hepatitis and HIV/AIDS related epidemi-ological research and screening. Institute also trains health professionals for better management and prevention of diarrheal diseases and for rapid and correct diag-nosis of etiological agents. Epidemiologi-cal investigations of diarrheal diseases are carried out in different parts of India. Antiserum of Vibrio cholerae is raised in the Institute and supplied to the national and international laboratories. Presently, specific monoclonal antiserum for detec-
tion of Vibrio cholerae O139 strains was developed which has been supplied to WHO (SEARO), New Delhi for distribu-tion to various national and interna-tional laboratories. The Institute has its basic science set up with well equipped, modern technological facilities in differ-ent disciplines such as bacteriology, virology, parasitology, biochemistry, pathophysiology, molecular biology, electron microscopy, immunology and vaccine development.
In order to fulfill the vision, National Institute of Cholera and Enteric Diseases (NICED) shall identify enteric infections of national health priority, Initiate appropriate multidisciplinary research to develop strategies for treat-ment, control and prevention of enteric infections of national health priority , Collaborate with other national and in-ternational scientists who are working for the same vision.
search. The WHO and UNICEF also pro-vide assistance on applied research. Sev-eral workshops on management and pre-ventive aspects of diarrheal diseases are sponsored by WHO, UNICEF and Ministry of Health and Family Welfare, Govt. of India. These national and international workshops are conducted at the Institute and also in different parts of India involv-ing doctors of State Health Services and international participants. Each year 4-5 post-graduate students of this Institute get Ph.D. degree from different Universi-ties in the state (Calcutta University, Jadavpur University, Kalyani University, Burdwan University, Viswa Bharati Uni-versity). Post-graduate medical students also attend courses at the Institute for training on diarrheal diseases and scien-tists act as co-guides for M.D. students for thesis work. WHO and JICA also send international fellows.
Though the Institute is principally financed by the Indian Council of Medical Research (ICMR), New Delhi, different national and international funding agencies extend sup-port to the Institute on specific research
projects. The Japanese International Co-operative Agencies (JICA) has financed a
technical collaborative research with the Institute to conduct re-search molecular aspects of differ-ent enteropathogens with special emphasis on Vibrios. Under the JICA-NICED exchange programme Japanese scientists are working in the Institute and scientists and technical persons of the Institute are also receiving training in ad-vance Japanese laboratories. De-partment of Biotechnology (DBT), Government of India DST, CSIR, Ministry of Environment, etc. sup-port several projects on basic re-
DEPT. OF
VIROLOGY,
NICED
B I O V A R I A N C E
NATIONAL INSTITUTE OF CHOLERA & ENTERIC DISEASES (NICED)
BY: Chandan Gupta, M.Tech(Biotechnology)
P A G E 1 5 V O L U M E 1 , I S S U E 1
Achievements of NICED
Scientists of NICED documented the efficacy of oral rehydration salts solution (ORS) in young children with dehydrating acute diarrhoea including cholera, which led to wide-spread acceptance of ORS particularly in children.
Documented the efficacy of doxycycline, norfloxacin and ciprofloxacin for cholera. Nalidixic acid, norfloxacin and ciprofloxacin are recommended nationally and interna-
tionally for the treatment of shigellosis. Identification of new serogroup Vibrio cholerae O139, Bengal from NICED, prompt re-
porting to the national and international scientific community and tracing the pathway of spread of this new serogroup. On the basis of research at NICED, WHO recommended that O139 cholera should be notified as cholera.
Documented the clinical characteristics, stool and blood biochemistry of patients in-fected with V.cholerae O139 which was indistinguishable from those of typical O1 chol-era.
Detection of Adult Diarrhoea Rotavirus (ADRV), belonging to Group B rotavirus from Calcutta, the first report of its occurrence outside China.
users (IDUs) in North-Eastern States of India, particularly Manipur. Development of oral recombinant cholera vaccineVA1.3 as a collaborative effort with
CSIR institutes (IM Tech & IICB). High prevalence of HIV infection among injecting drug users (IDUs) in Manipur,
Mizoram and Nagaland was documented by NICED scientists. High prevalence of HIV seropositivity among antenatal mothers was also detected. Reported first sattelite epidemic of Herpes zoster among IDUs from Asia. Association Herpes zoster infection and tuberculosis and
IMMUNOLOGY LAB
Photo:- Parasitology lab of NICED
MOLECULAR
MICROBIOLOGY LAB
B I O V A R I A N C E
BY: Chandan Gupta, M.Tech(Biotechnology)
P A G E 1 6
“Biotech is a
terrific industry,
but it's not like
having a big
chip-
manufacturing
industry.s”
FACE TO FACE:
B I O V A R I A N C E
An interview with Dr Dr G.B.Nair, Director ,NICED,Kolkata
1. What is the one thing that inspired you to be a
scientist?
Dr G.B.Nair: I always wanted to be a scientist. I
have a very diverse background. I did my Ph.D in
marine microbiology. Right from the beginning, I
wanted my work to be related to human health and
as a marine microbiologist, I thought I could do it
best.
2. What are the things that still motivate you and make you focused enough to attain newer heights?
Dr G B Nair: It is always related to my science being some help to people and this is the message
I would like to convey to the students. What is the mandate ? How you‘re guided by the interest
to help poor people. India is still a rapid emerging economy. 750 millions still comes under the
poorest strata. 750 millions out of 1.4 billion is a huge data. Most of my research is directed to
the community and poor people at large.
3.What virtues you realized in yourself which helped you choose research as a profession?
Dr G B Nair: My virtue which has helped me choosing my career is exceptionally hard work and tell
my students that there is absolutely no substitute for hard work. You might be intelligent but if you‘re
not hard working, it would not take you far.
4.Which is the toughest job: Doing research or working as an administrator ?
Dr G B Nair: The virtue which has helped me choosing my career is my exceptional hard work I also
tell my students that there is absolutely no substitute for hard work. You might be intelligent but if
you‘re not hard working, it would not take you far.
5.― Quality or Qualification‖ – Which matters more in life?
Dr G B Nair: Both. If you‘re not qualified, you cannot do anything of quality. If you don‘t
have the Ph.D , you cannot go beyond a certain stage. You should first establish yourself
and then pursue quality work.
6. What was your childhood dream? To what extent do you think that you have achieved
it when you look back ?
Dr G B Nair : I have achieved more than I had dreamed of. In Cholera, our work is interna-
tionally recognized. When I was doing my Ph.D , there was a time when I didn‘t know
where to go because as a marine microbiologist, there were no openings. I was very fortu-
nate that I got a job in this institute as an Assistant Research Officer in 1981 and follows.
that a proteins fold spontaneously to their native
conformations to attain the most stable structure
in minimum thermodynamic free energy. So if the
total free energy of a protein could be minimized
through thermodynamic approach, one can pre-
dict the three dimensional structure of a particular
protein. But the progress of this approach to pre-
dict the 3-D structure of a protein is less compare
to others because it is a difficult job to achieve
this. This is a biggest challenge for the scientists.
B I O V A R I A N C E
BY: Arnab Nayek, M.Tech(Bioinformatics)
P A G E 2 9 V O L U M E 1 , I S S U E 1
Bioinformatics has taken the ma-
jor role to solve this problem in the
field of protein modeling. We have
solved a three-dimensional struc-
ture of a small plant hormone pro-
tein Systemin from its amino acid
sequence (which was known)
through simulated annealing
method by a software TINKER.
The given protein sequence is:
1 ALA VAL GLN SER LYS
PRO PRO SER LYS ARG ASP
PRO PRO LYS MET
16 GLN THR ASP
It is established that the mini-
mized energy values from the
given guess structure (initial
structure) through iterated simu-
lated annealing method (400
times) by the help of a Software
TINKER. The TINKER molecu-
lar modeling software is a com-
plete and general package for mo-
lecular mechanics and dynamics,
with some special features for
biopolymers. TINKER is de-
signed to be an easily used and
flexible system of programs and
routines for molecular mechanics
and dynamics as well as other
energy-based and structural ma-
nipulation calculations. It is in-
tended to be modular enough to
enable development of new com-
putational methods and efficient
enough to meet most production
calculation needs. Rather than
incorporating all the functionality
in one monolithic program,
TINKER provides a set of rela-
tively small programs that inter-
operate to perform complex com-
putations, from which ANNEAL
and NEWTON programs are
selected. The series of major pro-
grams included in this project
described below and perform the
following core tasks.
This steps is required iteratively upto 400
times for producing lowest energy mini-
mized values from each run directory
output file (newton.run.o*).
After producing the 400 output files
(newton.run.o*) from each run directory,
it is required to filter out the lowest en-
ergy minimized value output files among
400 files. And hence we sorted the Final
Function Value (lowest energy value)
from each output file
newton.run.o.* among 400.
The program file anneal.run and newton.run are
submitted to the job queue, connection to the jobs
running on a remote server, facilitated and imple-
mented by the software TINKER. After submitting
the jobs, the running started following the simulated
annealing procedure of anneal.xyz, the given guess
structure of predefined sequence. After producing the
files anneal.001 to anneal.032 (the time required is 2
and ½ hours), the program Newton, started to run,
which converts the minimized structure anneal.032 to
newton.xyz and more stable Newton truncated new-
ton.xyz_2 respectively and produces the output files
(newton.run.o*) of energy minimization values, also
containing the calculated lowest energy minimized
final function value, which is required for sorting.
of the guess initial structure, we
use the following command for
MD run from UNIX platform,
where the specified software
TINKER is installed.
$ nohup anneal.run &
It converts the initial structure
into final structure – anneal.032
through iterative simulated an-
nealing method, which is the
energy minimized structure. This
structure is then converted into
newton.xyz and newton.xyz_2
respectively through the Newton
minimization method.
The file newton.xyz_2, which
is produced by Newton mini-
mization method, and which
is the coordinate file of that
given structure (guess struc-
ture) is copying into a file
name anneal.xyz and which is
again copying into a directory
name as run1(which was pre-
viously created). The files
anneal.key,
anneal.run, newton.key,
newton.run are also copy into
the directory run1.
To obtain minimized structure
values, 400 times of iterative
steps of energy minimization
was carried out.
Here, we started with the 5 ma-
jor files which are required for
the initialization of the Molecu-
lar Dynamics run.
The files are – Anneal.key – MD parameters
Anneal.run – MD scripts
Anneal.xyz – Initial guess struc-
ture
Newton.key – MD Parameters
For starting the initialization
process of energy minimization
“In addition to
having a major
impact on
poverty and
hunger,
biotechnology
has great
potential to
alleviate
environmental
degradation”.
(2001)
B I O V A R I A N C E
P A G E 3 0
So for producing pdb file it
requires two input files –
one is .xyz Cartesians coor-
dinate file and the other is .seq
file. .seq file is the extended
sequence file which was known
previously and .xyz is the new-
ton.xyz_2 file which has pro-
duced. For converting the .xyz
coordinate file to .pdb file one
program xyzpdb is there which
is built in the software TINKER.
So now we have reached to our
exact destination i.e. the pdb file
formation, from which we can
predict the three-dimensional
structure of a protein and which
structure was also submitted to
the PDB database.
B I O V A R I A N C E
For establishing the re-
quired pdb file (.pdb for-
mat) which tells the three-
dimensional structure of a
protein is the ultimate
goal of this work.
The 3-D structure of the protein SYSTEMIN: RASMOL view
Acknowledgments: Dr. Ansuman Lahiri (Lecturer in the dept. of BMBG, University of Calcutta)
References: Introduction to BIOINFORMATICS (Arthur M.Lesk)
Protein visualization in PYMOL
CROSSWORD
P A G E 3 1 V O L U M E 1 , I S S U E 1
1. Sequence format that begins with a single-line description
followed by lines of sequence data ,can be used as
query input when searching tools like BLAST or Clustal W.
4. Proteinaceous compound of which the spicules in
Demospongiae are composed.
6. A space introduced into an alignment to compensate for
insertions or deletions in one sequence relative to another.
8. Compound whose activated form emits light.
10. Complex sulfated polysaccharide, extracted from red algae
and used as a solidifying agent in culture media.
11. _______ is used as a high level disinfectant in hospitals to
disinfect surfaces.
12. Heme protein that carries electrons, usually as member
of electron transport chains.
15. A complex, branched polysaccharide made of-
many glucose molecules joined into chains of varying lengths.
17. Increased risk of atherosclerosis is associated with de
creased serum levels of ______.
The 3-D structure of the protein SYSTEMIN: RASMOL view
Can you solve it the
fastest..?????
DOWN ACROSS
1. Primary protein component of prokaryotic flagella.
2. Homologous sequences ina single species that are the result of
gene duplication.
3. An inactive form of the repressor protein, which becomes the
active repressor when the corepressor binds to it.
5.Group of cloned pieces of DNA representing overlapping regions
of a particular chromosome.
7.The ratio of _______ to cytokinin in certain plant tissues
determines initiation of root versus shoot buds.
9. Associations between actinomycetes and plant roots
.
11. A small molecule which can elicit an immune response only
when attached to a large carrier such as a protein.
12. Class of biochemical compounds like sugars, starch, chitin etc.
13. A measure of the amount of dissolved oxygen needed by
microbes to degrade organic matter in a water body.
14. Continuous-mode fermentor in which fresh medium is
introduced to keep turbidity constant.
16. The number of different alignments with a score equal to
or better than that can be expected to occur simply by chance.
B I O V A R I A N C E
BY: Deblina Chakraborty,M.Tech (Biotechnology)
P A G E 3 2
GRE–
ASPIRING HIGH..
CAREER ASCENT
Aiming to study abroad in foreign universities
and aspiring for quality education?
Requirement : “The candidate should have a
good score in GRE/TOEFL or both.
Challenge 1:Scoring a high score in GRE
Here is the solution to all your problems.
Something which provides you with a de-
tailed approach on systematic preparation on
GRE.
The GRE is an aptitude test. Like all
aptitude tests, it must choose a medium
in which to measure intellectual
ability. The GRE has chosen math and
English.
OK, the GRE is an aptitude test. The
question is—does it measure apti-
tude for graduate school? The
GRE‘s ability to predict perform-
ance in school is as poor as the
SAT's. This is to be expected
since the tests
are written by the same company
(ETS) and are similar. The GRE‘s
verbal section, however, is signifi-
cantly
harder (more big words), and,
surprisingly, the GRE‘s math sec-
tion is slightly easier. The GRE
also
includes a writing section that the SAT
does not. The GRE is approximately
three hours long. Only two-hours-and-
thirty-minutes of the test count toward
your score—the experimental section is
not scored.
B I O V A R I A N C E
ALL ABOUT GRE:
There are two types of GRE-one is the general
GRE and the other is subject GRE.The sub-
jects include Biochemistry,cell and molecular
biology,biology,chemistry,computer sci-
ence,literature in eng-
lish,mathematics,physics,psychology. Test is
composed of verbal reasoning (V), quantita-
tive reasoning (Q), and analytical writing
(AW) sections .Registration is necessary for
appearing in the GRE exam.Registration can
be made through online,telephone and
mail.Test centers fill up quickly,so early regis-
tration is recommended to get prefered test
locations and date selection.For cancellation
or rescheduling test information should be
conveyed not later than three full days.
Comparative percentile section wise scores
On the test, you cannot skip questions; each
question must be answered before moving to
the next question.
However, if you can eliminate even one of the
answer-choices, guessing can be advantageous.
It is significantly harder to create a good but incorrect answer-choice than it is to produce the
correct answer. For this reason usually only two attractive answer-choices are offered. One
correct; the other either
intentionally misleading or only partially correct. The other three answer-choices are usually
fluff. This makes educated guessing on the GRE immensely effective.
BY: Priyanka Biswas ,Int Phd (Microbiology)
P A G E 3 3 V O L U M E 1 , I S S U E 1
loid related disease. Natto kinase an anticlotting serine protease
present in Natto is the principle component that dissolves the fi-
brous protein aggregates .Thus Natto may provide an effective
treatment for Alzheimer‘s disease as well as presenting some deli-
cious dishes.
Reference:
Hsu et al. amyloid-Degrading Ability of Natto kinase from Ba-
cillus subtilis Natto.
Journal of Agricultural and Food Chemisty,2009;57.
Amyloids aggregates of fibrous
proteins, the major component of
amyloid plaques accumulated in
many neurodegenerative disease
like Alzheimer‘s disease can be tar-
geted by popular fermented food
(Bacillus subtilis) in South-East
Asia called Natto. According to
scientists in Taiwan, Natto which is
made from boiled soybean can be
effectively used to treat such amy-
Natto
BIOTECH POUTPURRI
“To catch the
reader's
attention,
place an
interesting
sentence or
quote from the
story here.”
CURRENT BIOTECH NEWS
Muramyldipeptide(MDP), a component of pepti-
doglycan found in both gram positive and gram
negative bacterial cell wall has been found to pro-
mote inflammatory arthritis by activating a spe-
cific gene called NOD-2(nucleotide binding oli-
gomerization domain containing two) located at
chromosome 16 in human. Group of researchers
from USA and Netherland has carried out an ex-
periment to demonstrate the potency of MDP to
promote inflammatory arthritis in mice immu-
nized with proteoglycan. Two group of mice were
employed, one with normal NOD-2 gene and an-
other with deactived NOD-2 gene. MDP was in-
jected to joints of each group of mice .
The normal mice display more severe
inflammation as compared to knocked out mice .
The development of arthritis also in NOD-2 deac-
tivated mice demonstrates that the NOD-2 is not
primary factor for developing inflammatory ar-
thritis in absence of MDP. This study will open
up new directions for treatment of arthritis.
Arthiritis— An acute problem
in old age
Granulomatous arthritis
Reference:
Rosenzweig et al.
Activation of nucleotide oligomerization domain
2 exacerbates a murine model of proteoglycan-
induced arthritis.
Journal of Leukocyte Biology,2009; 85 (4): 711-
718
Soyabean against Alzheimer
B I O V A R I A N C E
BY: Priyanka Biswas ,Int Phd (Microbiology)
BY: Anindyo Roy (M.Tech (Biotechnology)
P A G E 3 4 V O L U M E 1 , I S S U E 1
Scientists at the University of
Colorado, Boulder have devel-
oped a new technique for detect-
ing genetic information of Influ-
enza virus within a relatively
short period of time, just eleven
hour. The technique is based on
the microarray technology and
utilizes the specific binding of
viral RNA on the DNA chip.
The samples were collected
from patients throat and nasal
swap. The detection was done
by using a secondary DNA
probe tagged with fluorescent
dye with light up during scan-
ning. This method is useful
for identification of spe-
cific strains for Influenza
as well as SARS, measles,
HIV and hepatitis C also.
The advantange of this
method is that it can help
to combat epidemic and
pandemic by making sure
the identity of the invading
pathogenic strain and
speeding up the development of
vaccines against them.
Reference: Discoveries and
breakthroughs in Science,
American Institute of Physics.
different from the naturally oc-
curring protein..According to
Dr. Field a researcher involved
in this study ,different Nisin
variants can now be used spe-
cifically to target specific patho-
gen .Another benefit is that
Nisin variants can now lagely
replace the commercial food
preservatives such as sug-
ars,salts and other chemicals in
combating bacterial growth ulti-
mately
Researchers at the University of
Cork has engineered the antibi-
otic Nisin (an antimicrobial pro-
tein produced by a bacterium
Lactococcus lactis), to prevent
methicillin resistant Staphylo-
coccus aureus (MRSA)and Lys-
teria monocytogenes a food
borne pathogen by altering dif-
ferent amino acids.
These bioengineered
family of variants, are slightly
leading to safe and healthy food for us.
Reference :Society for General Mi-
crobiology , New, More Effective
Nisin Anti-
biotics
Combat
Superbugs
And Food
Diseases.
According to the research team
Bacillus species and Pseudomonas
aeruginosa were the best oil-
degrader.Proteus, Enterobacter, and
Micrococcus species were also
found to be able to degrade crude
oil.
Reference: Bello M. Yakubu, Huiwen Ma, and ChuYu Zhang. Biodegradation of crude oil in soil using chicken manure. International Journal of Environment and Pollution, 2009, Volume 36,Issue 4
A relatively cheap and easy available
material, chicken manure has been
found to degrade crude oil in contami-
nated soil as described by scientists at
the University of Wuhan, China. The
manure raises soil pH upto 6.3-7.4
which is optimal for oil degrading
bacteria..It was added to soil contami-
nated on a pollution basis of 10%(v/w
crude to soil).75% of oil has been
found to be degraded in soil with ma-
nure after 2 weeks as compared to
manure free soil exhibited 50%natural
remediation.
A MICROARRAY– DNA ON CHIP
FLU CHIP:
New horizon in bioremediation:
MICROARRAY”
An
interdisciplinary
science”
Hey…
nothing
of mine
is use-
less!!!
ANTIBIOTIC REVOLUTION:
B I O V A R I A N C E
P A G E 3 5 V O L U M E 1 , I S S U E 1
hydrogen.According to re-
searchers at the Penn State
archeal biofilm could use the
current to convert carbon di-
oxide and water to methane in
absence of any organic mate-
rial, usually found in micro-
bial electrolysis cells.The
cells has about 80 percent
conversion efficiency of elec-
tricity into meth-
ane.According to Bruce E.
Logan, Kappe Professor of
Environmental Engineering,
Penn State that the electro-
chemical reaction occurs
without the presence of any
metal catalysts and requires
less energy as compared to
conventional chemical indus-
trial methods for conversion
of carbon did oxide to meth-
ane.
Reference: Shaoan Cheng, Defeng Xing, Douglas F. Call and Bruce E. Logan. Direct Biological Conver-sion of Electrical Current into Methane by Electro-methanogenesis. Environ. Sci. Technol., 2009 ,Pensylvenia State Uni-
versity. MCROBES-
“A boon or a
bane…???”
New aspects of renewable energy:
Don‘t
worry.. I
am here
just feel
free to eat
Microbe can use electricicity to
convert carbon dioxide and water
into methane a renewable energy
source.Microbial electrolysis re-
quires an electrical voltage in
addition to that is produced by
bacteria using organic materials to
produce current that releases
B I O V A R I A N C E
BY: Anindyo Roy (M.Tech (Biotechnology)), Pallabi Pal (Int PhD Mol Bio)
P A G E 3 6
IN-Sillico Drug
Design need a
novel
ComputationL
biology
knowledge..
DOCKING
From the Alumni’s Desk
Introduction:
Evidence of the use of medicines and drugs can
be found as far back in time as the first Egyp-
tian dynasty, 3100 B.C. The drug discovery and
development process is scientifically complex
and full of risk, and is therefore, expensive and
time-consuming. Typically, a new chemical
entity (NCE) is promoted from discovery into
preclinical development and if it succeeds in
passing all hurdles, it is submitted for an inves-
tigational new drug (IND) application and
eventually enters phase I, II and III clinical
development. If the compound passes all clini-
cal trials, it is submitted for a new drug applica-
tion (NDA) and eventually enters the market
place. For the majority of the time drugs have
been used, discovering them has been a trial-
and-error process. It was not until the 1960's
that some understanding began to develop
about the quantitative relationship between
structure and biological activity. This new un-
derstanding that a quantitative relationship ex-
isted ushered in the beginnings of computer-
aided drug design.
significantly advance the discovery process.
Computer-aided molecular modeling helps
determine which molecules should be synthe-
sized and tested. Special computational tech-
niques are also available to discover biological
targets (proteins, nucleic acids) of a drug.
There has been a manifold increase in the
amount of experimental data because of the
burgeoning progress in high-throughput instru-
mentation and techniques. Accompanying this
progress has been a growing reliance of ex-
perimental researchers on computer-aided
drug design (CADD). CADD, or "rational drug
discovery," helps make it possible to select a
more manageable number of candidates that
can then be tested experimentally. Thus, both
intuition and rational analysis of databases can
be used to generate effective therapeutic com-
pounds. Besides the heavy emphasis on com-
puters, CADD relies extensively on various
Computer-aided drug design is no longer merely
a promising technique. It is a practical and real-
istic way of helping the medicinal chemist. On
its own it is unlikely to lead to pharmaceutical
novelties but it has become a significant tool, an
aid to thought and a guide to synthesis. Still
drugs must be synthesized and tested by the
computational techniques can contribute a clear
molecular rationale and above all provide a spur
to the imagination.
Advances in biomedical and pharmacological
research have continued to benefit
humanity by producing drugs that
either alleviate symptoms of disease
or provide a cure. Exploring the re-
lation between chemical structure
and function of compounds and in
finding a cure for diseases. This re-
cent success demonstrates that with
good experimental backing, the syn-
ergy between experimental and
computational approaches to drug design can
B I O V A R I A N C E
Although no single drug has been designed
solely by computer techniques, the contribu-
tion of these methods to drug discovery is no
longer a matter of dispute. All the world‘s
major pharmaceutical and biotechnology
companies use computational design tools.
At their lowest level the contributions repre-
sent the replacement of crude mechanical
models by display of structure which are a
much more accurate reflection of molecular
reality, capable of demonstrating motion and
solvent effects. Beyond this, theoretical cal-
culations permit the computation of binding
free energies and other relevant molecular
properties.
Two distinct categories of research are
clearly distinguishable:
a) A detailed molecular structure of the target
macromolecule, the drug receptor, is known
from x-ray crystallography, NMR or homol-
ogy modeling.
b) The target receptor-binding site has prop-
erties, which can only be inferred from a
knowledge of the variable activity of other-
Md.Ataul Islam, Alumni WBUT SBT
DRUG DESIGN – Made Easier
P A G E 3 7 V O L U M E 1 , I S S U E 1
Computational scientists need to understand physical
and organic chemistry, biochemistry, biophysics, mo-
lecular biology, statistics, data mining, and mathemat-
ics. They need to be able to study data sets for trends,
categorize and judge the validity of data and the meth-
odology of data collection, and have a drive to under-
stand the problems behind the development of models to
test hypotheses. This broad and diverse field offers tre-
mendous opportunities for scientists who have a variety
of skills such as programming and three-dimensional
visualization. The link between CADD and biology and
chemistry harnesses the tremendous progress in genom-
ics and proteomics that has led to the discovery of new
genes and proteins. Out of 5000 to 10,000 targets, only
about 500 targets have been characterized. This demon-
strates the numerous opportunities for data mining, de-
signing drug candidates, developing models to predict
biological activity, and studying interactions between
cellular targets and synthetic molecules.
In-silico screening of compound databases is presently the
most popular and useful cheminformatics applications in phar-
maceutical discovery. At the moment, virtual screening tech-
niques are roughly segregated into target structure and ligand-
based applications leading to heartening outcomes for novel
drug development. Besides protein-ligand docking, structure-
based approaches include the development of pharmacophore
features from active or binding site. Alternatively, methods
starting from hits or leads range from pharmacophores or
ceutical companies are always searching for new leads
to develop into drug compounds. One search method is
virtual high-throughput screening. In vHTS, protein tar-
gets are screened against databases of small-molecule
compounds to see which molecules bind strongly to the
target. If there is a ―hit‖ with a particular compound, it
can be extracted from the database for further testing.
With today‘s computational resources, several million
compounds can be screened in a few days on sufficiently
large clustered computers. Pursuing a handful of promis-
ing leads for further development can save researchers
considerable time and expense. # Sequence Analysis. In CADD research, one often
knows the genetic sequence of multiple organisms or the
amino acid sequence of proteins from several species. It
is very useful to determine how similar or dissimilar the
organisms are based on gene or protein sequences. With
this information one can infer the evolutionary relation-
ships of the organisms, search for similar sequences in
bioinformatics databases and find related species to
those under investigation.
B I O V A R I A N C E
P A G E 3 8
# Homology Modeling. Another common challenge
in CADD research is determining the 3-D structure
of proteins. Most drug targets are proteins, so it‘s
important to know their 3-D structure in detail. It‘s
estimated that the human body has 500,000 to 1
million proteins. However, the 3-D structure is
known for only a small fraction of these. Homology
modeling is one method used to predict 3-D struc-
ture. In homology modeling, the amino acid se-
quence of a specific protein (target) is known, and
the 3-D structures of proteins related to the target
(templates) are known. Bioinformatics software
tools are then used to predict the 3-D structure of
the target based on the known 3-D structures of the
templates. # Similarity Searches. A common activity in bio-
pharmaceutical companies is the search for drug
analogues. Starting with a promising drug molecule,
one can search for chemical compounds
with similar structure or properties to a
known compound. There are a variety of
methods used in these searches, includ-
ing sequence similarity, 2D and 3D
shape similarity, substructure similarity,
electrostatic similarity and others.
# Drug Lead Optimization. When a
promising lead candidate has been found
in a drug discovery program, the next
step (a very long and expensive step!) is
to optimize the structure and properties
of the potential drug. This usually involves
a series of modifications to the primary
structure (scaffold) and secondary struc-
ture (moieties) of the compound.
# Time-to-Market. The pre-
dictive power of CADD can
help drug research pro-
grams choose only the most
promising drug candidates.
By focusing drug research
on specific lead candidates
and avoiding potential “dead
-end” compounds, biophar-
maceutical companies can
get drugs to market more
quickly.
# Physicochemical Modeling. Drug-receptor inter-
actions occur on atomic scales. To form a deep un-
derstanding of how and why drug compounds bind
to protein targets, we must consider the biochemical
and biophysical properties of both the drug itself
and its target at an atomic level. # Drug Bioavailability and Bioactivity. Most drug
candidates fail in Phase III clinical trials after many
years of research and millions of dollars have been
spent on them. And most fail because of toxicity or
problems with metabolism. The key characteristics
for drugs are Absorption, Distribution, Metabolism,
Excretion, Toxicity (ADMET) and efficacy—in
other words bioavailability and bioactivity. Al-
though these properties are usually measured in
the lab, they can also be predicted in advance with
bioinformatics software
B I O V A R I A N C E
Benefits of CADD
CADD methods and bioinformatics tools offer
significant benefits for drug discovery pro-
grams.
# Cost Savings. The Tufts Report suggests that
the cost of drug discovery and development
has reached $800 million for each drug suc-
cessfully brought to market. Many biopharma-
ceutical companies now use computational
methods and bioinformatics tools to reduce
this cost burden. Virtual screening, lead opti-
mization and predictions of bioavailability and
bioactivity can help guide experimental re-
search. Only the most promising experimental
lines of inquiry can be followed and experi-
mental dead-ends can be avoided early based
on the results of CADD simulations.
# Insight.
One of the non-quantifiable benefits of CADD and
the use of bioinformatics tools is the deep insight that
researchers acquire about drug-receptor interactions.
Molecular models of drug compounds can reveal
intricate, atomic scale binding properties that are
difficult to envision in any other way. When we show
researchers new molecular models of their putative
drug compounds, their protein targets and how the
two bind together, they often come up with new ideas
on how to modify the drug compounds for improved
fit. This is an intangible benefit that can help design
research programs.
P A G E 3 9 V O L U M E 1 , I S S U E 1
In the early 1990‘s there was a great deal of opti-
mism that computer aided drug design would revo-
lutionize the way in which drugs could be devel-
oped. The enduring exponential increase in com-
puting power had progressed to the point that rudi-
mentary estimations of ligand receptor comple-
mentarity could be performed. Furthermore, com-
puter graphics technology had achieved the ability
to generate vector models of chemical structures
and manipulate them in real-time. This offered,
for the first time, the ability to interactively study
computer models of ligand structures and their
binding interactions with a receptor. The use of
mass screening and combinatorial chemistry al-
lowed researchers to discover lead compounds in a
rapid and efficient manner. As such, denovo de-
sign tools and their associated problems were no
longer needed to generate lead structures. One
would surmise that computer-aided drug design
technology would have soon ceased to exist.
On the contrary, it soon became apparent that
computational tools were needed that could opti-
mize these lead compounds into potent drugs. The
concept of drug optimization versus denovo de-
sign is an important one. The difficulty with de-
novo ligand generation is that an entire structure
is being created from scratch. The confidence
one has of accurately predicting how this struc-
ture will interact and bind within a target receptor
is shaky at best. In drug optimization, we begin
with a lead compound whose bound structure
within the receptor has been characterized, most
likely through x-ray crystallography. Subtle
modifications are then performed to generate de-
rivative compounds using structure based drug
design to improve binding affinity. Because we
are making much smaller changes, our faith in the
validity of the resulting structures is far
greater.These derivatives then undergo testing to
determine which modifications improve binding.
allowing the chemist to focus, synthesize, and
test only the most promising ligands. Thus, util-
izing computer aided drug design software to aid
in the refinement of weak binding lead com-
pounds is the most effective manner in which
these tools can be employed. The use of com-
puter modeling to refine structures has become
standard practice in modern drug design. There-
fore, CADD and bioinformatics together are a
powerful combination in drug research and devel-
opment. An important challenge for us going for-
ward is finding skilled, experienced people to man-
age all the bioinformatics tools available to us.
The structures of the best ligands can then be eluci-
dated to verify the accuracy of the modifica-
tions. This refinement process continues iteratively
until optimal binding ligands are produced.
In addition, the act of generating chemical
derivatives is highly amenable to computerized auto-
mation. Consider the application of targeted structure
based combinatorial chemistry as discussed
above. Libraries of derivative components are assem-
bled based upon the analysis of the active site. Be-
cause of the combinatorial nature of this method, an
extremely large number of candidate structures may
be possible. A computer can rapidly generate and
predict the binding of all potential derivatives, creat-
ing a list of the best potential candidates. In essence,
the computer filters all weak-binding compounds,
BIOTECH-
“A technology
for the
future.”
B I O V A R I A N C E
P A G E 4 0
“Democratic
sophistication is
the ultimate
sophistication…”
Caption describing
picture or graphic.
ISSUES ON CAMPUS
B I O V A R I A N C E
WBUT-SCHOOL OF BIOTECH POLLS
As it is said, the first step in solving a problem is to first realize that there is a
problem and polls are generally conducted to create awareness about the pros
and cons of the situation prevailing in any system. The response obtained by the
organizers from all the members of the School Of Biotechnology was amazing and
we would like to thank them for their kind consideration and support for making
this attempt a grand success. In future also, we hope each and every individual
will help us in creating awareness about the common issues and get them sorted
out positively for making WBUT - SBT a better place to live and work in.
What WBUT-SBT thinks about these issues:
General scientific scenario in India
A. What improvements can be done in our methodology so that the
society can be benefited with science? 1. Ability to think out of the box 2.Improvement in policy making 3.Lack of high impact factor research 4.Lack of applied research and innovate 5.Others
B. What basic measures and policies should be there to promote
basic science at the school level? 1.Stress on practical oriented teaching 2.Quality of teachers should be improved 3.Stress on understanding concepts 4. No changes to be made 5.Others
C. What do you think is better in this scenario to achieve your goals in
science? 1.Smart work
2.Hard work
3.Basic understanding
4.Common sense
5.Others
D. What could be done to improve the research quality
among the Students?
1.Improvement of financial incentives
2.Providing the freedom of thought 3. Improve on basic knowledge 4.Encouraging logical approach
5.Others
P A G E 4 1 V O L U M E 1 , I S S U E 1
E. The faculties in the department:
1.Sufficient and has good technical knowledge
2.Efficient in making students understand concepts
3.Faculties for interdisciplinary fields is needed
4.none of the above 5.Others
F. What could be done to maintain the equipments and chemicals in the lab
in a good and working state
1.Annual maintenance contracts
2.Lab technicians should be appointed 3. Students should be made responsible 4.Instruments should work at least once in a month
5.Others
G. Is our University clean enough to be called as the 'Center Of Excellence’?
To what extent is the college and classroom infrastructure suitable enough to
create a good atmosphere for creative sustainable learning?
1.It‘s in our reach
2.Still a long way to go
3.If drastic changes in the system are made 4. Do not wish to comment
5.Others
H. Regarding the campus placements:
1.The efforts taken are sufficient 2.Higher studies should be encouraged instead 3.Training and awareness should be given to enhance industry compatibility 4.There is ample scope for improvement for us to be competent and suitable
enough for companies to recognize. 5.Others
I. E journals:
1.Subscription should be at par with other IITs 2.Only free abstracts would suffice my research 3.I do not have any idea about it.
4.Consumes a lot of time in obtaining paid papers
B I O V A R I A N C E
P A G E 4 2 V O L U M E 1 , I S S U E 1
What you need for Biotech career?
Big question isn‘t it. Well, most of the forums on internet, biotech aspirants always
ask or looking for good answer. Mostly it is frustrating you don‘t get right answer.
Somethings that are useful are:
#1 PLANNING :
If you are looking for a career in BIOTECHNOLOGY, you definitely need to plan
ahead. Most of the biotech aspirants are not truly opted for BIOTECHNOLOGY.
Reason is simple, before coming to BIOTECHNOLOGY, they might have tried their
luck in Medicine entrance exams.
It is not because we don‘t have jobs, it‘s just planning and finding information
start ahead and plan at least one year before what you want to do.
#2 Mentor:
Everybody needs a mentor in life. It is true for BIOTECHNOLOGY as well. Find a
lecturer in your college or research institute, whom you believe successful/active
interested in what you want to do and take help from him/her. He/She will guide you
not only in project/future work; moreover you get a good reference letter.
#3 Field :
Best thing is find a subject you really like during your course.
Choose your field according to the opportunities
#4 Internet:
Now a days with internet, we are flooded with information. Please
spend some time on web find out which sites are offering admis-
“BIOVARIANCE”-The Team
CHIEF EDITOR -
NOTIFICATIONS
Dr. Joydeep Mitra, Reader ,WBUT
CONVEENER - Abhinav.K.V, M.Tech (Biotech)
MAGAZINE WING GENERAL SECRETARY– Amit Rai,M.Tech (Biotech)