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Organized byOrganized by
IITG Biotech HubIITG Biotech Hub((Sponsored by DBT, Govt. of IndiaSponsored by DBT, Govt. of India))
Centre for the EnvironmentCentre for the Environment
Indian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiGuwahatiGuwahati--781039, Assam, India781039, Assam, India
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
sohojatrisohojatrisohojatrisohojatri a souvenir on the occasion ofa souvenir on the occasion ofa souvenir on the occasion ofa souvenir on the occasion of
International Symposium onInternational Symposium onInternational Symposium onInternational Symposium on
“BIOENGINEERING 2012”“BIOENGINEERING 2012”“BIOENGINEERING 2012”“BIOENGINEERING 2012”
(ISBE 2012)(ISBE 2012)(ISBE 2012)(ISBE 2012)
December 10, 2012December 10, 2012December 10, 2012December 10, 2012
Organized by
IITG Biotech HubIITG Biotech HubIITG Biotech HubIITG Biotech Hub
(Sponsored by DBT, Govt. of India)
Centre for the EnvironmentCentre for the EnvironmentCentre for the EnvironmentCentre for the Environment
Indian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology GuwahatiIndian Institute of Technology Guwahati Guwahati-781039, Assam, INDIA
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
SOHOJATRI is a souvenir published on the occasion of International Symposium on “BIOENGINEERING
2012” (ISBE 2012), designed and edited by BIOTECH-HUB IIT Guwahati-39, Assam for IBSD.
DISCLAIMER The contents inside SOHOJATRI are personnel opinions and intellectual property of individuals and do not
reflect any institutional or government view, opinion or policy for any matter whatsoever and may thus not be
used for any purpose other than academic and research and validity of facts is a matter of discretion of the user.
The editorial committee and the organizers do not support and endorse any facts, views, conclusions included in
SOHOJATRI and are not responsible for any controversies arising hitherto.
---------------------------------------------------------------------------------------------------------------------------------------
EDITORIAL BOARDEDITORIAL BOARDEDITORIAL BOARDEDITORIAL BOARD
Manav Sharma, Dept. of Biotechnology, IITG
Suradip Das, Dept. of Biotechnology, IITG
Utpal Bora, Dept. of Biotechnology, IITG
VOLUNTEERSVOLUNTEERSVOLUNTEERSVOLUNTEERS
Punuri Jaysekhar Babu, Anil Kumar,
Arghya Sett, Suradip Das, Anuj Kumar Singh,
Nayanmoni Gogoi, Swagata Sharma, Deepika, Sambhavi,
Ajoy Kumar Das, Disco Singh, Rabindra Raut, Manoj Gadewar and Manav Sharma.
CCCCOVER OVER OVER OVER PPPPAGE AGE AGE AGE DDDDETAILSETAILSETAILSETAILS
In the ocean of science bioengineering
is a boat exploring pearl of success, which has different branches
(from left Bioinformatics, Bioelectronics, Biomaterial, Biomolecular engineering,
Environmental Bioengineering), each doing excellent in their individual field; however it is
the precise time to travel together as SOHOJATRI in the boat to achieve the common goal.
Cover page concept & design:Cover page concept & design:Cover page concept & design:Cover page concept & design: Manav Sharma (Dept. of Biotechnology, IITG).
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
International Symposium onInternational Symposium onInternational Symposium onInternational Symposium on
“BIOENGINEERING 2012”“BIOENGINEERING 2012”“BIOENGINEERING 2012”“BIOENGINEERING 2012”
(ISBE 2012)(ISBE 2012)(ISBE 2012)(ISBE 2012)
December 10, 2012December 10, 2012December 10, 2012December 10, 2012
Organizing Committee Coordinators
Dr. Utpal Bora Dr. Chandan Mahanta
Organizing Secretary
Mr. Arghya Sett
Members
Dr. Gopal Das
Dr. Bosanta R Boruah
Dr. Arun Goyal
Dr. Suresh Kartha.
Dr. Ranjan Tamuli
Dr. A. B. Kunnumakkara
Dr. Venkata D Veeranki Dasu
Centre for the Environment
Indian Institute of Technology Guwahati
Guwahati-781039, Assam, India
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
IITG BIOTECH HUBIITG BIOTECH HUBIITG BIOTECH HUBIITG BIOTECH HUB
Background
The Department of Biotechnology, Ministry of Science & Technology initiated the
establishment of Biotech Hubs under the special programme for the northeastern states in
2009. The broad purpose of the programme is to promote education and research in
Biology/Life Science/Biotechnology/Environment and to attract brilliant young students to
build their career in these fields. The fund sanctioned under this programme is to be utilized
for providing the following facilities to each Biotech Hub.
• A biotechnology lab with basic set of equipments
• Support for site preparation/renovation
• A bioinformatics centre with min. of 5 computers with Internet connectivity
• Biotechnology electronic journal access facility
• Recurring budget for procurement of chemicals, glassware and for maintenance of Internet
connectivity
• Support for Organizing Trainings/Workshops for teachers
• Travel Support for Conference allowance, short term training in any Institute in India.
• Student Fellowships etc.
IITG Biotech Hub
Sanction for IITG Biotech Hub was granted on 21/09/2010 and funds arrived in
February 2011. The Biotech Hub is getting established in the new Centre for the Environment
building with three rooms and proposal for constructing two additional rooms has already
been forwarded. Instrumentation purchase is underway and a full facility is expected to be
developed in the next 2-3 months. A BSL 3 facility (first of its kind in the institute), an
environmental biology laboratory with basic facilities like BOD incubators, Bacteriological
incubators, laminar flow, water baths, pH meter, autoclaves, hot air ovens, muffle furnace,
serological water bath, melting point apparatus, Thermal cycler would be in place soon by the
year end. Currently the purchase of computers is complete and the informatics facility is
being developed within the existing Centre for the Environment Computational Laboratory.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
People
The IITG Biotech Hub has one Junior Research Fellow. The Hub is being run by the
involvement of faculty members drawn from multiple disciplines as listed below.
Dr. A. K. Sarma, Physics
Dr. B.R. Boruah, Physics
Dr. M. Sarma, Chemistry
Dr. V.V. Dasu, Biotechnology
Prof. C. Mahanta,
Department of Civil Engineering
(Chairman, IITG Biotech Hub Steering
Committee)
Dr. R. Tamuli, Biotechnology (Co coordinator)
Dr. U. Bora, Biotechnology (Coordinator)
The core group is exploring the possibility of expanding the involvement of additional faculty
members in the near future as soon as the laboratory facilities are in place.
Activities
IITG Biotech Hub has embarked upon the following programmes:
Programme 1. IITG-DBT Biotech Hub Invited Lecture Series:
Under this lecture series speakers having expertise in a particular field are invited to
deliver Lectures to students of the institute. The following lectures have been organized up to
now.
Lecture No. Speaker Name & Affiliation Lecture Topic
1 Dr. Sudip Mitra,
School of Environmental
Sciences
Jawaharlal Nehru University,
New Delhi
Water Management for
Mitigating Green House Gases
from Rice-Paddy Agriculture
Systems
Date: 17-March-2011
2 Dr. Utpal Das,
Department of Neurosciences,
University of California San
Diego
Mechanism of Axonal
Transport of Proteins and
Implications in
Neurodegenerative Disorders
Date: 1-April-2011
3 Dr. Utpal Bora,
Department of Biotechnology
IIT Guwahati
The Herceptin Story
Date: 1-July-2011
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
4 Prof. Toru Shimada, University
of Tokyo, Japan
Genetic and genomic studies on the food habit of
silk worm.
Date: 28th
Feb, 2012
5 Dr. Yumiko Nakajima,
University of Tokyo, Japan
Some Transposable elements in Bombyx
mandarina compared with those of B. mori
Date: 28th
Feb, 2012
6 Dr. Takashi Kiuchi
University of Tokyo, Japan
Positional cloning of the gene responsible for the
black pupa (bp) mutant of the silkworm B.mori
Date: 28th
Feb, 2012
7 Dr. P. Jayprakash,
Central Silk Board, Guwahati
Challenges to Muga silkworm cultures
Date: 28th
Feb, 2012
8 Dr. Utpal Bora, IIT Guwahati
Dr. N.C. Talukdar, IBSD, Imphal
Scope of insect biotechnology in India
Date: 28th
Feb, 2012
9 Prof. J. Nagaraju
CDFD, Hyderabad
Secreats of Silk
Date: 25th
April, 2012
10 Prof. Kim and Prof. Park, Korea Advances in Genome sequencing and Breeding
Date: 2nd
May, 2012
Programme 2. IITG-DBT Biotech Hub Summer Training
Under this programme Biotech Hub offers Summer Training in multidisciplinary
areas of life Sciences to both undergraduate & graduate students of science & engineering
disciplines. In 2011-2012 the following students did summer training.
S.N. Name Affiliation Course
1. Nabasmita Bora Baba Farid Institute of
Technology, Dehradun
B.Sc,
Biotechnology
2 Nilakshi Gohain Guwahati University,
Guwahati
M.Sc,
Biotechnology
3 Abid Rashid Dr. D.Y.Patil
Biotechnology &
Bioinformatics
Institute, Pune
B.Tech,
Bioinformatics
4 Khushboo Jain Sir Padampat Singhania
University,
Udaipur
B.Tech,
Biotechnology
5 Sahil Mishra Sir Padampat Singhania
University,
Udaipur
B.Tech,
Biotechnology
6 Poly Saikia SRM University,
Kancheepuram
B.Tech,
Biotechnology
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
7 Purba Jyoti Hazarika Gautam Buddha
University, Greater
Noida
M.Tech,
Biotechnology
8 Chetna Sangwan Sir Padampat Singhania
University,
Udaipur
B.Tech,
Biotechnology
9 Pulakesh Deka Amity Institute of
Technology, Noida
B.Tech.
10 Faikhie Daimari Sir Padampat Singhania
University,
Udaipur
B.Tech,
Biotechnology
11 Darshana Baruah IST, GU, Guwahati B.Tech
12 Navaneeta Majumdar IST, GU, Guwahati B.Tech
13 Rupjyoti Basumatary IIT, Delhi M.Tech
14 Ruchi Ojha Sir Padampat Singhania
University,
Udaipur
B.Tech
15 Ayushi Jain Sir Padampat Singhania
University,
Udaipur
B.Tech
16 Ishani Goswami Hansraj College, Delhi B.Sc.
17 Parmita Bhuyan University of Madras,
Chennai
M.Sc.
Programme 3. Workshops/ Short Term Courses:
The objectives of the STCs are to upgrade the knowledge and skills of the teachers,
scientists, researchers, students working in the different institutions of the region, in the
emerging areas of Life Sciences/ Environmental Sciences/ etc.
The following STCs have been organized / planned to be organized in the year 2011-2012
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
S.N. Name of the Workshop/
Short
Term Courses
Date Coordinator(s)
1 Introductory Workshop
On Optical
Microscopy
16-17th June 2011 Dr Bosanta R
Boruah,
Department of
Physics
2 Cancer Biology 2011:
Basic Theoretical
Aspects
26-27th August
2011
Dr. Utpal Bora,
Dr. Ranjan Tamuli,
Department of
Biotechnology
3 Photography for
Biodiversity
Documentation
To be announced Dr. Chandan
Mahanta,
Department of Civil
Engineering
4 Mammalian Cell Culture
Techniques
15-25 September
2011
Dr. Utpal Bora,
Department of
Biotechnology
Programme 4. Manpower Development
IITG Biotech Hub will also act a catalyst for manpower development and support
institutional B.Tech, M.Tech and Ph.D. research.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Addresses of SpeakersAddresses of SpeakersAddresses of SpeakersAddresses of Speakers
Name
Address & Email
Bezbaruah,
Achintya Nayan
North Dakota State University , USA
Email: [email protected]
Borah, Probodh Assam Agricultural University, Guwahati
Email: [email protected]
Das, Diganta Kr. Gauhati University
Das, Pranab Jyoti National Research Centre on Yak ,Arunachal Pradesh
Email: [email protected]
Deka, Manab Gauhati University
Email: [email protected]
Fraser, Malcolm
J., Jr.
University of Notre Dame, USA
Email: malcom [email protected]
Kumar, Dinesh Indian Agricultural Statistical Research Institute, Delhi
Email: [email protected]
Kunnumakkara,
A.B.
Department of Biotechnology, IIT Guwahati
Email: [email protected]
Lewis, RV Utah State University, USA
Email: [email protected]
Lim, Yong Pyo Chungnam National University, South Korea
Email: [email protected]
Lynn, Andrew
Michael
Jawaharlal Nehru University, Delhi
Email: [email protected]
Malhotra, BD Delhi Technological University, Delhi
Email: [email protected]
Nahar, Pradip Institute of Genomics & Integrative Biology, Delhi
Email: [email protected]
Okuda, Keiko
Kadono
National Institute of Agrobiological Sciences, Japan
Email: [email protected]
Ramchiary,
Nirala
Jawaharlal Nehru University, Delhi
Email: [email protected]
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Addresses of Addresses of Addresses of Addresses of ParticipantsParticipantsParticipantsParticipants
Name Email Address
Anil Kr. Verma [email protected] Research Scholar, IITG
Anil Kumar [email protected] Research Scholar, IITG
Aniruddha Sarma [email protected]
m
Assistant Prof, Pandu
College, Guwahati
Anuj Kumar Singh [email protected] JRF, IITG
Anupa Agarwal anupa.a @iitg.ernet.in JRF, IITG
Anwesha Ananya
Sharma
anweshaananyasharma13@gmai
l.com
JRF, BN College of
Agriculture, Sonitpure
Arabinda Ghosh [email protected] Research Scholar, IITG
Arghya Sett [email protected] Research Scholar, IITG
Arnish Chakraborty [email protected] Research Scholar, IITG
Arun Dhillon [email protected] Research Scholar, IITG
Arunima Sharma [email protected] IITG
Ashish A Patel [email protected] M.Tech, IITG
Bina Agarwal [email protected] JRF, Rangia College
Bitupona Deuri [email protected] Resaerch Scholar,
AAU,Khanapara
Chandan Kr. Singh [email protected] MVSc, AAU,Khanapara
Deepika [email protected] Research Scholar, IITG
Deeplina Das [email protected] Research Scholar, IITG
Deepmoni Deka [email protected] Research Scholar, IITG
Dollyca Ningombam [email protected] Research Trainee,
Manipur University
Hemant Kumar [email protected] M.Tech, IITG
Hemen Kr. Patowary [email protected] Associate Prof., BPC
College
Himanshu Sharma [email protected] Research Scholar, IITG
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Jadi Praveen Kumar ------------ Research Scholar, IITG
Joy Heikrujam [email protected] Research Trainee,
Manipur University
Joyashri Das [email protected] JRF, Biotech Hub,
BPC college, Ghy
Katla Srikanth [email protected] Research Scholar, IITG
Khullakpam Shaheen [email protected] Research Trainee,
Manipur University
Kimjolly Lhouvum [email protected] Research Scholar, IITG
Lukumoni Borah [email protected] Research Scholar,
Gauhati University
Manav Sharma [email protected] JRF, IIT Guwahati
Mani Shekhar Kumar ------------ Research Scholar, IITG
Manoj Gadewar [email protected] Research Scholar, IITG
Minakshi
Bhattacharjee
[email protected] Research Scholar, IITG
Mridusmita Goswami goswami_mridusmita@rediffma
il.com
JRF, Gauhati University
Nayanmoni Gogoi [email protected] Research Scholar, IITG
Neelima Gudala [email protected] MS(Pharma-
biotech,NIPER)
Nongthombam
Martina Chanu
om
Research Trainee,
Manipur University
Oscar Ningombam [email protected] Research Trainee,
Manipur University
P. Jaya Sekhar Babu [email protected] Research Scholar, IITG
P. Saravanan [email protected] Research Scholar, IITG
Parag Deka [email protected] Assistant prof, Pandu
College, Guwahati
Phairembam
Radharani Devi
[email protected] Research Trainee,
Manipur University
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Pranjal Sarmah [email protected] JRF, Pandu College, Ghy
Rajesh Kumar [email protected] IITG
Rajesh Ahirwar [email protected] JRF,IGIB,New delhi
Rajesh Kr. Shah rajeshkumarshah39@yahoo.
com
Asst Prof,
D.H.S.K.College,Dibrug
arh
Ranendra Kr Das [email protected] Associate Prof, B P
Chaliha College,Kamrup
Ravindra Raut [email protected] M.Tech, IITG
Robin Sachdeva [email protected] B.Tech, IITG
Rohitas Deshmukh [email protected] Research Scholar, IITG
Rupshikha Patowary [email protected] IITG
Salma Jasmine [email protected] Research Scholar, IITG
Sambhavi [email protected] Research Scholar, IITG
Sangeeta Baruah [email protected] SRF, BN College of
Agriculture,
Sonitpure(Assam)
Santhosh M. [email protected] Research Scholar, IITG
Saprativ P. Das [email protected] Research Scholar, IITG
Saumya Sasmal [email protected] Research Scholar, IITG
Shally Sultana
Choudhury
[email protected] Assistant Professor,
Pandu College, Guwahati
Shuchi Singh [email protected] Research Scholar, IITG
Soumyadeep
Chakraborty
[email protected] Research Scholar, IITG
Sudakshina Das [email protected] Associate Prof.,
D.H.S.K.College,Dibrug
arh,
Suradip Das [email protected] Research Scholar, IITG
Surya Kalita [email protected] Co-ordinator, IBT Hub,
BPC College, Ghy
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Sushant Singh [email protected] Research Scholar, IITG
Susma Chityala [email protected] Research Scholar, IITG
Swagata Sharma [email protected] Research Scholar, IITG
T. Jaganmohan Rao [email protected] Research Scholar, IITG
TH Geetanjali Devi [email protected] Research Trainee,
Manipur University
Thoudam Themis [email protected] Research Trainee,
Manipur University
Ujjwal Ranjan Dahiya [email protected] M.Tech, IITG
V.Kohila [email protected] Research Scholar, IITG
Vibha Sinha [email protected] Research Scholar, IITG
Vijay Kumar Mishra [email protected] Research Scholar, IITG
Vikram Kumar [email protected] Research Scholar, IITG
W. Jotinkumar Singh [email protected] Research Trainee,
Manipur University
Wahengbam
Jotinkumar
[email protected] Research Trainee,
Manipur University
Y Disco Singh [email protected] Research Scholar, IITG
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
From the From the From the From the Desk Desk Desk Desk of of of of EditorsEditorsEditorsEditors…..…..…..…..
Science! The ocean of knowledge, mountain of challenge, can be traversed across
through constant struggle or conquered by relentless journey fueled by an eternal
inquisitiveness to unlock the secrets of NATURE. Life! The ultimate gift of nature can be best
understood & enjoyed through the languages of science & innovations of technology.
The complex mechanism of life reflects the supreme engineering prowess of nature
that has captivated the imagination of researchers, philosophers, experimentalists and
theoreticians over time. This quest to decipher life has given birth to Bioengineering which
involves the amalgamation of scientific knowledge with engineering craftsmanship curving
out inventions for the benefit of society. Untiring ventures of scientists has netted many pearls
of success from the ocean of knowledge. However, in the field of Bioengineering to speak in
the words of Sir Isaac Newton “What we know is a drop, what we don’t know is an ocean”.
Bioengineering has diverse branches like Bioinformatics, Environmental engineering,
Bioelectronics, Biomaterials, Biomolecular engineering etc that are pursued individually by
various groups leading to advancement of fundamental concepts in biology, medicine,
behavior and health. However, it’s high time that such experts assemble in the same boat and
travel as “Sohojatri” to augment the human race rowing through the waves of time.
Probably the applications of systems biology to bioengineering are going to deliver us
insights and solutions to problems hitherto unknown.
The name of the souvenir has been given as Sohojatri inspired by the legendary singer
Late Dr. Bhupen Hazarika’s song influenced by the theme of Leadbelly’s famous composition
“We are in the same boat, brother.”
“Bioengineering 2012 (ISBE)” has been organized under DBT BIOTECH HUB
(IITG) to promote interaction between young researchers, students and nationally and
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
internationally acclaimed scientists. We are highly pleased after getting a colossal response
from a galaxy of distinguished speakers and participants with diverse research interests.
The editorial desk pays its gratitude to all those who have contributed in the souvenir
with their valuable writings and findings. At the same time we feel sorry for not providing the
souvenir as hard copy.
We look forward to the day when we, the researchers, return in the boat, churning the
truth of life and passing on the pearls of success to the awaiting society on the shore!
…..Suradip & Manav….
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
“BIOENGINEERING 2012”
(ISBE 2012)
Venue: Convention Centre, IIT
GUWAHATI, Assam, India
Date: 10th December, 2012
Organized by
Biotech Hub,
(Sponsored by Department of Biotechnology, New
Delhi, Govt. of India)
Centre for the Environment,
Indian Institute of Technology Guwahati
Guwahati-781039
PROGRAMME
Registration 830 h
Inauguration 840-900 h
Speaker Name Lecture Title Time
Dr. Bansi Dhar
Malhotra Delhi Technological
University, Delhi
Prospects of Nanomaterials Based Biosensors for
Cancer Detection
900-930 h
Prof. Randolph V.
Lewis
Utah State University,
USA
Spider Silk Bioengineering 930-1000 h
Tea 1000-1015h
Dr. Diganta Das Gauhati University,
Guwahati
Copper(II) complex @ ZSM-5 modified GC electrode:
Voltammetric sensor for dopamine and ascorbic acid
1015-1035 h
Prof Manab Deka
Gauhati University
Effect of host genetic factors and environmental agents
in predisposition of people of north eastern India to
liver disease susceptibility
1035-1055 h
Dr. Dinesh Kumar
Indian Agricultural
Statistical Research
Institute, Delhi
Recent Case Studies in Biopiracy and Bioengineering 1055-1115 h
Dr. Achintya Nayan
Bezbaruah
North Dakota State
University , USA
Looking for Synergies between Iron nanoparticles,
Endemic Microorganisms, and Plants: Can We Address
World Water and Food Security Issues?
1115-1140 h
Dr. Andrew Michael
Lynn Jawaharlal Nehru
University, Delhi
Homology and non-homology based methods of
genome annotation.
1140-1200
noon
Lunch Break Cum Poster Session 12 noon-1400 h
Dr. Probodh Borah Assam Agricultural
University, Guwahati
Phylogenomic Approach to Bacterial Phylogeny 1400-1420 h
Prof. Yong Pyo Lim Chungnam National
University, South
Korea
Brassica Genome 1420-1450h
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
Dr. Keiko Kadono-
Okuda National Institute of
Agrobiological
Sciences, Japan
Bombyx densovirus-susceptibilities in Bombycidae 1450-1520h
Tea Break 1520-1530h
Dr. Pradip Nahar Institute of Genomics
& Integrative
Biology, Delhi
A novel spectrophotometer free colorimetric
assay format
1530-1550h
Dr. Ajaikumar B.
Kunnumakkara IITG, Ghy-39
Chemosensitization of Pancreatic Cancer by Naturally
Occurring Vitamin E Analogues-Tocotrienols
1550-1610h
Dr. Nirala
Ramchiary Jawaharlal Nehru
University, Delhi
Dissecting Glucosinolates Biosynthesis Pathway Genes
for Engineering Better Nutritional Quality in Brassicas
1610-1630h
Dr. Pranab Jyoti Das
National Research
Centre on Yak
Arunachal Pradesh
Gene Mapping and Functional Genomics of Yak with
reference to other Farm Animals.
1630-1700 h
Interaction between Distinguished speakers, Scientists and Research
Scholars AND
Valedictory Session
1700-1800 h
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
CONTENTSCONTENTSCONTENTSCONTENTS
SL NO NAME TOPIC PAGE
CONTRIBUTORY ARTICLECONTRIBUTORY ARTICLECONTRIBUTORY ARTICLECONTRIBUTORY ARTICLE
CA 01 Arghya Sett
Aptamers-the Magic Bullets in Biosensor Technology 1
CA 02 Yengkhom
Disco Singh
Biofuel- A fuel for today, tomorrow from biomass
residue. 4
CA 03: Swagata Sharma Recent Advances in SELEX 7
CA 04 Sambhavi A New Comer in Therapeutic Oligonucleotide:
APTAMER 11
INVITED LECTURESINVITED LECTURESINVITED LECTURESINVITED LECTURES
IL 01 Bansi D.
Malhotra
Prospects of Nanomaterials Based Biosensors for
Cancer Detection
15
IL 02 Diganta Kumar
Das
Copper (II) complex @ ZSM-5 modified GC
electrode: Voltammetric sensor for dopamine and
ascorbic acid.
17
IL 03 Manab Deka
Effect of host genetic factors and environmental
agents in predisposition of people of north eastern
India to liver disease susceptibility
18
IL 04 Achintya
Bezbaruah
Looking for Synergies between Iron Nanoparticles,
Endemic
Microorganisms, and Plants: Can We Address World
Water and Food Security Issues?
20
IL 05 Probodh Borah Phylogenomic Approach to Bacterial Phylogeny 21
IL 06 Yong Pyo Lim
A genomic approach to understanding the nutriomics
in Brassica species
22
IL 07 Keiko Kadono-
Okuda
The researches on Insect Technology and
Bioengineering in NIAS
23
IL 08 Pradip Nahar
A Novel Spectrophotometer Free Colorimetric Assay
Format
24
IL 09 Nirala
Ramchiary
Dissecting Glucosinolates Biosynthesis Pathway
Genes for Engineering Better Nutritional Quality in
Brassicas
25
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub
IL 10 Dinesh Kumar Bioengineering and Biopiracy: Sheep DNA SNP chip
case study
26
POSTER APOSTER APOSTER APOSTER ABSTRACTSBSTRACTSBSTRACTSBSTRACTS
P 01 Anil Kumar
Interactions of Curcumin Natural Derivatives with DNA
Topoisomerase I and II-DNA Complexes
27
P 02 Anil Kumar
Verma
Structural characterization and docking analysis of
modeled CtXylGH30 protein family 30 glucoronoxylan
xylanohydrolase of Clostridium thermocellum
29
P 03 V. Kohila The emergence of novel E.coli Uracil
PhosphoRibosyl Transferase mutants in the prospect of
cancer therapeutics : a Bioinformatics Approach
30
P 04 Lukumoni
Borah
Biosorption of Cadmium by Porous Carbon prepared from
Christella hispidula(Decne)Holt
31
P 05 Neelima
Gudala
Blood Group Conversion-Blood Made Suitable to All 32
P 06 Rajesh
Kumar
Peptide self-assembly and biophysical studies of amyloid
aggregation of a short peptide derived from α-synuclein
protein
33
P 07 Rajesh
Kumar Shah
Phytochemical screening and Antimicrobial activity of the
leaf extract of Ficus nervosa Heyne ex Roth.
34
P 08 Dollyca
Ningombam
Studies on feasibility of phylogenetic trees for
characterization of bacteria using the 16S rRNA, rpoB and
gyrB genes of the type strains of Actinomycetes
35
P 09 Th Themis Designing of PCR primer by using Bioinformatics tools 36
P 10 C.K Singh Management of Femur Fracture in Dogs with Biomaterials
(DBM)
37
P 11 Arghya Sett Molecular Signatures of Breast Cancer 38
P 12 Nayanmoni
Gogoi
Development of Majuli Island Bioresource Database
(MIBD)
39
P 13 Rajesh
Ahirwar
A Spectrophotometer-Free Image-Based Assay For
Oligonucleotide Detection
40
Note: Complete details of authors are available in the Abstract Page.
SECTION ISECTION ISECTION ISECTION I
CONTRIBUTORY ARTICLECONTRIBUTORY ARTICLECONTRIBUTORY ARTICLECONTRIBUTORY ARTICLE
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CA 01: Aptamers-the Magic Bullets in Biosensor Technology
Arghya Sett
Dept. of Biotechnology
Indian Institute of Technology, Guwahati, Guwahti-39
Email: [email protected]
Aptamers are small (i.e., 40 to 100 bases), synthetic oligonucleotides that can
specifically recognize and bind to virtually any kind of target, including ions, whole cells,
drugs, toxins, low-molecular-weight ligands, peptides, and proteins. An aptamer's affinity
depends on its target type. Aptamers against small molecules have affinities in the
micromolar range (eg. 2.8 mM for dopamine and ATP 6 mM for adenosine 5
triphosphate)[1,2]. Aptamers have shown affinities in the nanomolar and sub-nanomolar
range against some proteins, such as vascular endothelial growth factor with an affinity of
100 pM, and keratinocyte growth factor of 1 pM [2]. The recent trend is the emergence of
aptamers as sensing elements that has the potential to substitute present ligands. This is
possible due to the unique features of aptamers (sensitivity, specificity, reusability, stability,
non-immunogenicity), which can be easily exploited in biosensor technology. Aptasensors
are thus basically biosensors based on aptamers as ligand molecules.
These specific oligomers are selected from a random pool by an iterative process
called Systemic Evolution of Ligands by Exponential Enrichment (SELEX)[3]. The enriched
pool shows high sensitivity, specificity to their target entities. Due to their versatility,
aptamers are also called as “magic bullets” and are excellent example of functional biological
molecules which are selected in vitro. Since its discovery aptamer based technologies have
been drawn enormous attention in industrial research communities.
Oligonucleotides (both DNA, RNA) , peptide and peptide-nucleic acid (PNA) based
aptasensors offer high reproducibility rate against a wide variety of targets (eg. proteins,
peptides, drugs, small molecules, metal ions, & even whole cells) and are quickly emerging
as suitable candidates for high throughput analytical methods that use minute amount of
analytes (nano-microlitre). Availability of in-depth knowledge of nucleic acid aptamers in
terms of their conformational and ligand binding mechanisms has evoked deep interest
among researchers for developing aptamer based bioassays as reflected in the exponential
increase of published articles related to aptasensors [4].
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Aptasensors were first used in 1996 as the selective component in an optical sensor
application where they were part of a model system consisting of human-neutrophil-elastase-
coated beads that interact with fluorescent-tagged aptamers[5]. Eight months later, two new
examples of aptasensors appeared: one in which a radiolabeled aptamer was used to detect
different protein kinase C isozymes and another in which an enzyme-linked sandwich assay
used a SELEX-derived fluorescently labelled oligonucleotide [6,7]. Since then aptasensors
have been applied in environmental, industrial, defense, and medical fields. In the past
decade, hundreds of aptasensor papers have been published, using an assortment of
transductors. Aptasensor based analysis is continuously evolving with various detection
schemes ranging from label-free methods such as surface plasmon resonance (SPR) [8] and
quartz crystal microbalance (QCM) measurements [9] to label dependant methods such as
electrochemistry, fluorescence, chemiluminescence, field effect transistors [10] etc. However
currently electrochemical and optical aptasensors [11] constitute the two predominant types
under development. However, with advancement in both aptamer generation against a
growing number of targets and their corresponding sensing systems, combined with advances
in micro- and nanotechnology, practical efficient aptasensors will be accessible in near future.
References:
1) M Sassanfar and JW Szostak, “An RNA Motif That Binds ATP,” Nature 364 (1993): 550–
553.
2) LR Paborsky et al., “The Single-Stranded DNA Aptamer-Binding Site of Human
Thrombin,” Journal of Biological Chemistry 268 (1993): 808–811.
3) C. Tuerk and L. Gold, “Systematic Evolution of Ligands by Exponential Enrichment:
RNA Ligands to Bacterio-phage T4 DNA Polymerase,” Science, Vol. 249, No. 4968, 1990,
pp. 505-510.
4) E. N. Brody, M. C. Willis, J. D. Smith, S. Jayasena, D. Zichi and L. Gold, “The Use of
Aptamers in Large Arrays for Molecular Diagnostics,” Molecular Diagnostics, Vol. 4, No. 4,
1999, pp. 381-388.
5) KA Davis et al., “Use of a High Affinity DNA Ligand in Flow Cytometry,” Nucleic Acid
Research 24 (1996): 702–706.
6) D Kiga et al., “nRNA Aptamer to the Xanthine/Guanine Base with a Distinctive Mode of
Purine
Recognition,” Nucleic Acids Research 26 (1998): 1755–1760.
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7) DW Drolet, L Moon-McDermott, and TS Romig, “An Enzyme-Linked Oligonucleotide
Assay,”
Nature Biotechnology 14, no. 8 (1996): 1021–1027.
8) Y. Li, H. J. Lee and R. M. Corn, “Fabrication and Char-acterization of RNA Aptamer
Microarrays for the Study of Protein-Aptamer Interactions with SPR Imaging,” Nu-cleic
Acids Research, Vol. 34, No. 22, 2006, pp. 6416- 6424.
9) Z. M. Dong and G. C. Zhao, “Quartz Crystal Microbal-ance Aptasensor for Sensitive
Detection of Mercury(II) Based on Signal Amplification with Gold Nanoparticles,” Sensors,
Vol. 12, No. 6, 2012, pp. 7080-7094.
10) O. S. Kwon, S. J. Park, J. Y. Hong, A. R. Han, J. S. Lee, J. S. Lee, J. H. Oh and J. Jang,
“Flexible FET-Type VEGF Aptasensor Based on Nitrogen-Doped Graphene Con-verted from
Conducting Polymer,” ACS Nano, Vol. 6, No. 2, 2012, pp. 1486-1493.
11) A. Sassolas, L. J. Blum and B. D. Leca-Bouvier, “Optical Detection Systems Using
Immobilized Aptamers,” Bio-sensors and Bioelectronics, Vol. 26, No. 9, 2011, pp. 3725-
3736.
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CA 02: Biofuel- A fuel for today, tomorrow from biomass residue.
Yengkhom Disco Singh
Biofuel laboratory(BL), Centre for Energy,
Indian Institute of Technology, Guwahati.
Email: [email protected]
Introduction:
Biomass energy or “bioenergy” is one of the most confounding renewable energy
sources in modern fuels. Modern bioenergy sources, such as liquid biofuels, biomass-fired
electricity, or methane from animal wastes are usually second-generation biofuel often
viewed as important components of low carbon, energy-secure future. Global studies suggest
that the need and demand of biofuel will rise significantly by 2050. International Energy
Agency (IEA, 2010) has suggested that in order to reduce the CO2 emissions to half of the
current levels by 2050, the use of biofuel and bioenergy should triple the hand (Chum et al.
2011). Biofuel has greatly stimulated the local economies in developing countries. There has
been 12 bioenergy project set up which examines the 76 document Clean Development
Mechanism (CDM) in countries like India, Brazil and Sub-Saharan Africa. I addition to this
used of agricultural waste, rice straw, coconut husks, bagasse power, sugar cane for
production of biofuel has tremendously increases (Alexeew et al. 2010).
Ethanol or ethyl alcohol is a clear liquid fuel, which is biodegradable and causes low
toxicity to environmental pollution. The chemical formula is C2H5OH. It burns to produce
carbondioxide and water. Ethanol with gasoline is use as blending agent and can replace the
lead as an octane enhancer in petrol. More over Ethanol is being evaluating as a replacement
fuel.
The Ethanol Production Process:
Currently ethanol is produced from biological materials (biomass) by converting
sugars to alcohol through the process called fermentation. Conversion of starch to ethanol
involved two steps: a) liquefaction where starch is making soluble in the respective solvent,
b) Hydrolysis, conversion of starch into glucose. The resulting glucose undergoes
fermentation. Figure 1 illustrates how starch is converted to ethanol. This is the most common
ethanol production process in India.
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Fig. 1. Conversion of biomass to ethanol.
1. The biomass is converted to sugars: The enzyme-catalysed conversion of cellulose to
glucose is slow a process unless biomass is subjected to a process called pretreatment.
Pretreatment helps in increasing the pore size and reducing the cellulose crystallinity. There
are two types of pretreatment techniques, Acid-catalyzed pretreatment and alkali-catalyzed
pretreatment. In acid hydrolysis, hemicelluloses layer is hydrolyzed whereas in alkali
treatment, a part of lignin is removed and hemicellulose has to be removed separately by
hemicellulases.
2. Sugar fermentation to ethanol: In contrast to sucrose and starch based ethanol production,
lignocelluloses based ethanol production is a mixed-sugar fermentation process. Fermentation
with or without oxygen is a biological process where microorganism break down sugars into
simpler compounds like ethanol and carbondioxide (CO2). The yeast Saccharomyces
cerevisiae could not fermented pentose sugars such as xylose and arabinose which are most
abundant in hardwood and agricultural waste (5-20%). Consequently, researcher’s efforts
have been devoted in developing efficient xylose-fermenting micro-organism.
2
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Conclusions:
The commercial production of bioethanol for transportation starts around 1975, during energy
crisis at Brazil. After over 25 years of research and development, commercial plants for the
production of bioethanol are becoming a reality. Eventually, production of bioethanol will
remake the market price. Therefore, during next decade, bioethanol technology is likely to
embarked commercially in bio-refineries throughout the world in response to the
domestically need of the people for transportation fuels. The challenges lie for production of
36 billion gallons of ethanol by the year 2022. The major areas have been made improvised
by the researcher more about the genetic basis of resistance to inhibitors in acid hydrolysate
and pentose fermentation.
References
Alexeew, J., Bergest, L., Meyer, K., Petersen, J., Schneider, L. and Unger, C. (2010) ‘An
analysis of the relationship between the additionality of CDM projects and their
contribution to sustainable development.’ International Environmental Agreements:
Politics, Law and Economics, 10. 233–48. doi: 10.1007/s10784-010-9121-y.
Chum, H., Faaij, A., Moreira, J., Berndes, G., Dhamija, P., Dong, H., Gabrielle, B., Goss
Eng, A.,Lucht, W., Mapako, M., Masera Cerutti, O., McIntryre, T., Minowa, T. and
Pingoud, K. (2011)‘Bioenergy.’ IPCC Special Report on Renewable Energy Sources
and Climate Change Mitigation,
Dien, B.S. et al. (2003) Bacteria engineered for fuel ethanol production: current status. Appl.
Microbiol. Biotechnol. 63, 258–266
Jeffries, T.W. (2006) Engineering yeasts for xylose metabolism. Curr. Opin. Biotechnol. 17,
1–7
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CA 03: Recent Advances in SELEX
Swagata Sharma
Department of Biotechnology
Indian Institute of Technology, Guwahati, Assam, 781039
Email: [email protected]
Aptamers are generated by an iterative in vitro evolution procedure named SELEX
(Systemic Evolution of Ligands by Exponential Enrichment). Recent modifications in
original SELEX technique provide improved aptamer affinity and specificity as well as
shorter generation time. Such aptamers have great application as therapeutic as well as
diagnostic tool and sensor device in a wide range of fields. Here various modifications in
SELEX techniques to generate aptamer for application in different fields have been discussed
in brief.
1.Introduction:
Aptamers are single stranded DNA or RNA ligands which can be selected for
different targets ranging from protein to small organic dye. Aptamers can be generated
against a wide range of target molecules because of the ability of single stranded nucleic acid
molecules to fold into three dimensional “pocket” structure that fold into to bind with target
molecules. The screening and selection process of aptamer is carried out using SELEX
(Systemic Evolution of Ligands by Exponential Enrichment) technique. SELEX technique
involves iterative process of selection and amplification from a large combinatorial nucleic
acid library. This method was first described in 1990 (Ellington et al. 1990; Tuerk C. et al.,
1990). Since then, various improvements in the original SELEX protocol have been reported
to achieve increased specificity, sensitivity and shorter generation time.
2.Recent advances in SELEX:
2.1 Tailored SELEX:
Aptamers selected by SELEX procedure consist of a central randomized region and
additional fixed primer binding site of size ~60-90nt. Therefore the identified oligomers
generally require additional truncation of the 5’ and 3’ ends before they can be used in
biological system. The identified sequences are also not short enough for efficient chemical
synthesis with low post-SELEX stability. If the primer binding region is a part of the target
recognizing domain, then the truncation process may reduce the efficiency of the aptamer.
Tailored-SELEX involves ligation and cleavage of primer sites before and after
amplification, allowing the selection of shorter aptamer sequences that are more readily
synthesized chemically providing direct and rapid isolation of target binding RNA sequences
(Vater et al, 2003).Tailored SELEX process uses four and six fixed nucleotides at the 5’ and
3’ end of the primer-less library respectively (Yang et al, 2007). Tailored-SELEX has been
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successfully applied to select Speigelmer (mirror-image aptamer) against calcitonin gene
related peptide (Vater et al, 2003).
2.2Capillary electrophoresis SELEX:
Capillary SELEX(CE-SELEX) is a modified procedure where the selection of target
binding aptamer is carried out based on their mobility shift in a column. General SELEX
protocol involves target molecule immobilization with the help of a linker. Binding with a
linker can eliminate a potential target motif. CE-SELEX has been developed to reduce this
limitation by allowing the interaction of nucleotide library with free target. The mix is
allowed to pass through a column and bound aptamers can be separated based on their shift in
mobility (Yang et al, 2007). CE-SELEX has improved selection efficiency with fewer non-
specifics binding.
2.3Toggle SELEX
High specificity of protein-aptamer interaction results in production of aptamers that can
differentiate isoforms of a protein. But sometime species cross-reactivity is desired, usually
during pre-clinical evaluation of a molecule in animal model. Toggle-SELEX procedure can
generate aptamers that are cross reactive between the species by “toggling” the protein target
during alternate selection process (White et al, 2001). Alternations of the target between
homologous proteins of different species ensure selection of aptamers with broader range,
most likely to the conserved domains. Toggle-SELEX should facilitate the isolation of
ligands with needed properties for gene-therapy and other therapeutic and diagnostic
applications (Yang et al, 2007).
2.4 Expression cassette SELEX:
The development of RNA aptamer for gene therapy is limited by the difficulties in
delivering RNA to target cells and tissue. A modified approach has been described to
generate functional expression cassette for previously identified RNA aptamer with inherit
property to bind and inhibit the target protein in vitro. It has been reported that the insertion
of E2F aptamer into a tRNA expression cassette resulted in the production of high level of
chimeric tRNA with high binding affinity to E2F. Moreover these functional E2F aptamers
can inhibit E2F mediated transactivation upto 80% in human 293 cells (Martell et al, 2002).
2.5 Genomic SELEX:
Genomic SELEX is an experimental procedure for the expression condition
independent identification of protein binding RNA (Lorenz et al, 2006). It facilitates the
network study of nucleic acid-protein interaction within any organism. Unlike the general
SELEX, the starting library is not consists of randomized sequences but derived from the
genome of interest (Yang et al, 2007). Genomic SELEX is useful in constructing nucleic
acid-protein linkage map of an organism. A primer-free Genomic SELEX has also been
developed (Wen and Gray, 2004) which can provide improved selection of target binding
nucleic acid sequences.
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2.6 Automated SELEX:
Automation of SELEX protocol can be very useful in order to develop aptamer
sensors with high flexibility and versatility in terms of selection procedure and conditions. A
robotic work station configuration was set up based on an augmented BechmannBiomek
2000 pipetting robot for selection of aptamer for hen egg white lysozyme (Cox et al, 1998).
Further improvements results in coupling of automated selection procedure with a protein
translational system to generate aptamers against target proteins by transcription and
translation of individual gene (Cox et al, 2002). Automated selection of RNA aptamer against
mirror image configuration (D-peptide) of target protein P was designed with high flexibility
in terms of selection of buffers and stringency of selection procedure(Eulberg et al, 2005).
Recently microfluidic based assembly for selection and synthesis of an anti-lysozyme
aptamer was developed based on LabVIEW controlled actuatable valves and a PCR machine
(Hybarger et al, 2006). The microfluidic platform for automated SELEX should lead to high-
throughput SELEX methods with ability of parallel production of aptamers against multiple
targets.
3. Conclusion:
During past two decades, aptamer technology has been grown to become an important
biotechnological tool with the application in therapeutics, diagnostics, sensors and research.
The potential of aptamer to replace the use of antibody can be achieved by development of
easy and automated SELEX technologies. The advancement in SELEX protocol to provide
flexibility and versatility in aptamer selection procedure along with short generation time is
quite desirable. Further research in this area will help in advancing aptamer technology with
wider application.
Reference:
1. Cox, J.C., Hayhurst, A., Hesselberth, J.,Bayer, T.S., Georgiou, G., Ellington, A.D.
(2002) Automated selection of aptamers against protein targets translated in bitro from gene
to aptamer. Nucl. Acids Res.30, e108.
2. Cox, J.C., Rudolph, P., Ellington, A.D. (1998) Automated RNA selection. Biotechol.
Prog. 14, 845-850.
3. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that
bind specific ligands. Nature 346, 818-822.
4. Eulberg, D., Buchner, K., Massch, C., Klussmann, S. (2005) Development of an
automated in vitro selection protocol to obtain RNA- based aptamers: identification of a
biostable substance P antagonist. Nucl. Acids Res. 33, e45.
5. Hybarger, G., Bynum, J., Williams, R.F., Valdes, J.J., Chambers, J.P. (2006) A
microfluidic SELEX prototype. Anal. Bioanal. Chem. 384, 191-198.
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6. Lorenz, C., Pelchrzim, F., Schroeder, R. (2006) Genomic systematic evolution of
ligands by exponential enrichment (Genomic SELEX) for the identification of protein-
binding RNAs independent of their expression levels. Nat. Prot.372, 2204-2212.
7. Martell, R.E., Nevins, J.R., Sullenger, B.A. (2002) Optimizing aptamer activity for
gene therapy applications using expression cassette SELEX. Mol. Ther. 6, 30-34.
8. Tuerk, C. and Gold, L. (1990) Systemic evolution of ligands by exponential
enrichment RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
9. Yan Yang, Dongliang Yang, Schluesener, H.J., Zhang, Z. (2007) Advances in SELEX
and application of aptamer in the central nervous system. ScienceDirect 24, 583-592.
10. Vater, A., Jarosch F., Buchner K., Klussmann, S. (2003) Short bioactive Spiegelmers
to migraine-associated calcitonin gene-related peptide rapidly identified by a noval approach:
Tailored SELEX. Nucl. Acids Res.31,e130.
11. Wen, J.D., Gray, D.M.(2004) Selection of genomic sequences that bind tightly to Ef
gene 5 protein: primer-free genomic SELEX. Nucl. Acids Res. 32, e182.
12. White, R., Rusconi, C., Scardino, E., Wolberg, A., Lawson, J., Hoffman, M.,
Sullenger, B. (2001) Generation of species cross-reactive aptamers using “toggle” SELEX.
Mol. Ther. 4, 567-573.
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CA 04: A New Comer in Therapeutic Oligonucleotide: APTAMER
Sambhavi
Department of Biotechnology,
Indian Institute of Technology Guwahati, Guwahati
Email: [email protected]
Introduction
Nucleic acids are known for their role in the storage and the transfer of genetic
information. However in last few decades it was found that nucleic acids are also involved in
many pathways regulating cellular processes. They can form a myriad of three-dimensional
structures among which some can promote catalytic activity or interaction with proteins or
other partners. Advances in DNA synthetic methods have enabled the generation of large
populations of degenerate oligodeoxynucleotides, while PCR allows small numbers of
molecules to be amplified into amounts that can be readily manipulated by researchers. When
these two advances were iteratively coupled with the ability to partition oligonucleotide on
the basis of their binding or catalytic activities, in vitro selection of functional nucleic acids
(termed SELEX) was born. Nucleic acid ligands generated using SELEX have been termed
APTAMERS, an invented Latin term that means ‘to fit’.
Aptamers are short single-stranded oligonucleotides that recognize their target on the
basis of their 3D shape. They are frequently referred to as ‘chemical antibodies’. As a
consequence aptamers can be raised against any type of molecule or molecular complex:
amino acids, peptides, nucleic acids or even live cells. Proteins constitute by far the largest
class of aptamer targets. The high stability of aptamer–protein complexes, frequently
characterized by a Kd in the low nanomolar range, combined with an exquisite specificity of
interaction make aptamers valuable tools for many applications: as therepeutics, for target
validation, for high thoroughput screening or as diagnostic.
Aptamers in Clinic:
Numerous aptamers have been selected against therapeutic targets, such as IgE, IFN-g,
alpha-thrombin, PTPase and they have shown great efficacy in tissue culture experiments and
animal models. There are now several aptamers that have undergone clinical trials.
• Pegaptanib: To date, the most successful therapeutic application of an aptamer has
been OSI Pharmaceuticals adaptation of an anti-Vascular Endothelial Growth Factor
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(anti-VEGF) aptamer for the treatment of Age-related Macular Degeneration(AMD).
It was approved for therapeutic use by the US Food and Drug Administration in
December 2004 and is currently marketed by Pfizer and Eyetech as MACUGEN.
Pegaptanib is a VEGF-specific aptamer that binds to all isoforms of human VEGFA
except for the smallest (VEGF121). VEGF participates in promoting the growth of
abnormal new blood vessels in the eyes, which eventually leak blood and cause vision
loss. Once pegaptanib is administered it binds to VEGF and inhibits the interaction of
VEGF with its receptors VEGFR1(also known as FLT1) and VEGFR2 (also known as
KDR/ FLK1), with an IC50 value of 49 pm. Although pegaptanib sold well after
regulatory approval, it has more recently lost significant market share to the antibody
fragment RANIBIZUMAB (Lucentis; Genentech), which binds to all isoforms of
human VEGF including VEGF121. However, the story of Pegaptanib is far from
over. Despite being less effective than Ranibizumab, Pegaptanib has fewer side-
effects and is more widely tolerated. As a result of this, new clinical trials are now in
progress to study the long-term effects of Pegaptanib. So it seems with interest in
Pegaptanib very much alive, we may see its return to the clinic in the near future.
• REG1: REG1 is an anticoagulation system that includes RB006, a coagulation factor
IXa-specific aptamer, and its oligonucleotide antidote RB007. A major risk associated
with anticoagulant therapy is uncontrollable bleeding if reversal of the anticoagulation
is not achieved. The current anticoagulant of choice, heparin, is long lasting but its
pharmacokinetics is difficult to control. The use of RB006 and RB007 appears to be
promising anticoagulant candidates. RB006 binds to coagulation factor IXa with an
equilibrium dissociation constant (Kd) of 2.8 nm and prolongs clotting time. RB007
which is complementary to the 5′-terminal region of RB006 rapidly disrupts the
structure of RB006 and inhibits its anticoagulation function. REG1 is being developed
by Regado Biosciences. It is currently in Phase II clinical trials and shows rapid onset
of anticoagulation in vivo after intravenous administration, followed by a rapid return
to baseline levels after dosing of the RB007 antidote.
• AS1411: AS1411, formerly AGRO001, is a G-rich 26-mer oligodeoxynucleotide that
contains only guanines and thymines and exists in solution as a guanine-
quartetmediated dimer. AS1411 inhibits the proliferation of cells in a wide range of
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cancer cell lines. The suggested mechanism of action for the antiproliferative activity
of AS1411 includes binding to, and subsequent internalization by, cell-surface
nucleolin followed by binding to cytoplasmic nucleolin. AS1411 is being developed
by Antisoma and is currently in Phase II clinical trials for acute myeloid leukaemia,
but it has recently been decided not to continue clinical evaluation of AS1411 for
renal cancer.
• ARC1779: ARC1779 is being developed by Archemix and is currently in Phase II
clinical trials for thrombotic microangiopathies and in patients with carotid artery
disease undergoing carotid endarterectomy. It binds to the A1 domain of Von
Willebrand factor19 and inhibits the capacity of this domain to bind to platelet
membrane glycoprotein 1b receptors, thereby eliciting an antithrombotic effect
without significant anticoagulation.
• ARC1905 and E10030: ARC1905 binds to complement component 5 (C5), which is
thought to play a role in AMD (age-related macular degeneration) because it is pro-
inflammatory and has been found in retinal deposits of patients with AMD. Another
aptamer, E10030, binds to platelet-derived growth factor (PDGF), which is known to
play a role in the recruitment and maturation of pericytes that can increase resistance
to the anti-VEGF treatment of AMD. Both aptamer ARC1905 and E10030 is being
developed by Ophthotech and is currently in Phase I clinical trials in which they are
co-dosed with the VEGF-specific antibody fragment Ranibizumab by intravitreal
injection.
• NOX‑‑‑‑E36: NOXXON has several Spiegelmers, mirror image rivals of aptamer, in
clinical development. Amongst the furthest along is the aptamer raised against
monocyte chemotactic protein-1 (MCP-1). This aptamer, referred to as NOX-E36 is
being developed for the treatment of diabetic kidney disease and other complications
associated with type 2 diabetes. In a phase I clinical trial, completed in late 2009,
NOX-E36 showed a dose-dependent effect on blood monocytes, consistent with the
proposed mode of action of NOX-E36. After having successfully completed the first
clinical study, multiple dose studies in healthy volunteers and non-insulin-dependent
diabetic patients are scheduled to begin in coming years.
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• NOX-A12: NOXXON has also recently announced the successful completion of the
First-in-Human, Phase I Clinical Trial with NOX-A12, an aptamer raised against
stromal cell-derived factor-1 (SDF-1). This protein has been shown to bind to several
chemokine receptors and has been shown to play important roles in vasculogenesis,
tumour growth and metastasis. Inhibition of the SDF-1 by NOX-A12 is hoped to be
useful in the treatment of many types of cancer.
Conclusion
Although the aptamer technology was first described in 1990 (Ellington and Szostak,
1990; Tuerk and Gold, 1990), aptamers’ widespread acceptance in therapeutics is still being
realized. Inspite of so much development in this technology the list of aptamers in clinical
development is still limited. Because only one aptamer has been approved and is in the
market, the costs for large scale production aptamers are still high and are affected by the
absence of an adequate technological platform for their development as therapeutics and by a
limited number of companies that are engaged in their development. Aptamers have a number
of advantages in their clinical usage and it is plausible that the global interest for developing
nucleic acid aptamer therapeutics will increase in the next few years.
References:
1. Xiaohua Ni, Mark Castanares, Amarnath Mukherjee, & Shawn E. Lupold, Nucleic
acid aptamers: clinical applications and promising new horizons,Curr Med
Chem. 2011, 18(27): 4206–4214.
2. Anthony D. Keefe, Supriya Pai and Andrew Ellington, Aptamers as therapeutics,
Nature Reviews ,Drug Discovery, July 2010 9:537-550.
3. David HJ Bunka, Olga Platonova & Peter G Stockley, Development of aptamer
therapeutics, Current Opinion in Pharmacology 2010, 10:557–562.
4. Eric Dausse, Sonia Da Rocha Gomes & Jean-Jacques Toulme, Aptamers: a new class
of oligonucleotides in the drug discovery pipeline?,Current Opinion in Pharmacology
2009, 9:602–607.
5. Jennifer F Lee, Gwendolyn M Stovall and Andrew D Ellington, Aptamer therapeutics
advance
Current Opinion in Chemical Biology 2006, 10:282–289.
6. Rebekah R. White, Bruce A. Sullenger,& Christopher P. Rusconi, Developing
aptamers into therapeutics, , The Journal of Clinical Investigation ,October
2000,106:929-934.
SECTION IISECTION IISECTION IISECTION II
INVITED LECTURESINVITED LECTURESINVITED LECTURESINVITED LECTURES
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IL 01: Prospects of Nanomaterials Based Biosensors for Cancer Detection
Bansi D. Malhotra1,2
1Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main
Bawana Road, Delhi-42, India 2Department of Science and Technology Centre on Biomolecular Electronics, Biomedical
Instrumentation Section, National Physical Laboratory, Dr. K. S. Krishnan Marg, New
Delhi-110012, India
Email: [email protected]
Biosensors are rapidly covering the market of clinical diagnostics, toxicity analysis,
food industries, environmental monitoring and quality control1-4
. A biosensor is a special type
of chemical sensor comprising of a biologically sensing element (protein/cell/organelle etc)
in intimate contact with a transducer, which may either be electro-chemical, optical or
thermal(Fig.1). The response generated as a result of bio-chemical reaction is detected by the
transducer to give a signal (optical/electrical/thermal) that can be used with or without
amplification for the estimation of the concentration of an analyte in a given sample. These
interesting bioelectronic devices have the potential to replace or complement the classical
analytical methods by simplifying or eliminating sample preparation protocols and making
field testing easier and faster with significant decrease in costs per analysis.
The nanobiotechnology is rapidly evolving to unravel new materials useful in
solving challenging bioanalytical problems, including specificity, stability and sensitivity. In
this context, nanomaterials are being increasingly used for the development of biosensors.
Their use has extended into all areas of biosensor research. The nanomaterials including
nanostrutured metal oxides are being widely investigated for immobilization of biomolecules
like proteins and single stranded DNA oligomers. Among the various nanostructured metal
oxides, zinc oxide, tin oxide, cerium oxide have recently attracted much attention for the
fabrication of miniaturized biosensing electrodes.
Biosensors have the potential to provide accurate and fast and detection, reliable
imaging of cancer cells, and monitoring of angiogenesis and cancer metastasis, and the ability
to determine the effectiveness of anticancer chemotherapy agents. Effective, accurate
methods of cancer detection and clinical diagnosis are urgently needed. The use of biosensors
in cancer detection and monitoring holds vast potential. This talk will focus on the recent
SOHOJATRI
IITG-DBT Biotech Hub
results obtained in our laboratories relating to fabrication and application of nanopatterned
cadmium selenide quantum dots based Langmuir
References :
1. Biosensors:the new wave in cancer diagnostics,B.Bohunicky and Shaker
A.Mousa,Nanotechnology ,Science and Applications, 2011,Volume4 ,pp1
2. Nanopatterned cadmium selenide Langmuir
detection, Aditya Sharma,C.M.Pandey,Zimple Matharu,Udit Soni, Sameer Sapra
and B.D.Malhotra,Analytical Chemistry, Volume 84, Issue 7, 3 April 2012, Pages
3082-3089
3. Fundamentals and Application of Ordered Molecular Assemblies to Affin
Biosensing, Zimple Matharu, Amay Jairaj Bandodkar, Vinay Gupta and Bansi
Dhar Malhotra,Chemical Society Reviews,
– 1402
4. Chitosan Encapsulated Quantum Dots Platform for Leukemia Detection
Sharmaa, Chandra Mouli Pandey, Gajjala Sumanaa, Udit Soni, Sameer Sapra , A.K.
Srivastava, Tathagat Chatterjee and Bansi D. Malhotra, Biosensors &
Bioelectronics,2012, http://d
“Bioengineering 2012”
results obtained in our laboratories relating to fabrication and application of nanopatterned
cadmium selenide quantum dots based Langmuir–Blodgett films for leukemia detection
Fig.1
Biosensors:the new wave in cancer diagnostics,B.Bohunicky and Shaker
A.Mousa,Nanotechnology ,Science and Applications, 2011,Volume4 ,pp1
Nanopatterned cadmium selenide Langmuir-Blodgett Platform for Lekemia
detection, Aditya Sharma,C.M.Pandey,Zimple Matharu,Udit Soni, Sameer Sapra
and B.D.Malhotra,Analytical Chemistry, Volume 84, Issue 7, 3 April 2012, Pages
Fundamentals and Application of Ordered Molecular Assemblies to Affin
Biosensing, Zimple Matharu, Amay Jairaj Bandodkar, Vinay Gupta and Bansi
Dhar Malhotra,Chemical Society Reviews, Chem. Soc. Rev., 2012, 41 (3),
Chitosan Encapsulated Quantum Dots Platform for Leukemia Detection
Sharmaa, Chandra Mouli Pandey, Gajjala Sumanaa, Udit Soni, Sameer Sapra , A.K.
Srivastava, Tathagat Chatterjee and Bansi D. Malhotra, Biosensors &
http://dx.doi.org/10.1016/j.bios.2012.05.010
“Bioengineering 2012”
16 | P a g e
results obtained in our laboratories relating to fabrication and application of nanopatterned
Blodgett films for leukemia detection2-4
.
Biosensors:the new wave in cancer diagnostics,B.Bohunicky and Shaker
A.Mousa,Nanotechnology ,Science and Applications, 2011,Volume4 ,pp1-10
form for Lekemia
detection, Aditya Sharma,C.M.Pandey,Zimple Matharu,Udit Soni, Sameer Sapra
and B.D.Malhotra,Analytical Chemistry, Volume 84, Issue 7, 3 April 2012, Pages
Fundamentals and Application of Ordered Molecular Assemblies to Affinity
Biosensing, Zimple Matharu, Amay Jairaj Bandodkar, Vinay Gupta and Bansi
, 2012, 41 (3), 1363
Chitosan Encapsulated Quantum Dots Platform for Leukemia Detection , Aditya
Sharmaa, Chandra Mouli Pandey, Gajjala Sumanaa, Udit Soni, Sameer Sapra , A.K.
Srivastava, Tathagat Chatterjee and Bansi D. Malhotra, Biosensors &
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IL 02: Copper (II) complex @ ZSM-5 modified GC electrode:
Voltammetric sensor for dopamine and ascorbic acid.
Diganta Kumar Das
Department of Chemistry
Gauhati University, Guwahati 781 014, Assam, India
Email: [email protected]
A new complex of copper (II), [LCu2+
(CH3COO)2Cu2+
L] (CH3COO)2 where L is N,N
bis(pthalimide)ethylenediamine, has been synthesized and characterized. The complex ion
[LCu2+
(CH3COO)2Cu2+
L]2+
was encapsulated into ZSM-5 zeolite and was used to modify
glassy carbon (GC) electrode surface. This modified electrode, in phosphate buffer solution
(PBS, pH 7.0), exhibited oxidation potential for dopamine (DA) and ascorbic acid (AA) at
electrode potentials +0.230 V and -0.090 V versus Ag-AgCl respectively, a separation by
0.340 V. The electrooxidation of either DA or AA on the modified electrode is independent
of each other. No interference is observed from Na+, K
+, Cl
-, SO4
2-, Mg
2+, Ca
2+, Zn
2+, Fe
2+
and Glucose. The detection limits obtained are 2.91x10-7
M for DA and 3.5 x10-7
M for AA.
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IL 03: Effect of host genetic factors and environmental agents in
predisposition of people of north eastern India to liver disease susceptibility
Manab Deka
Prof. & Head, Department of Biological Science,
Gauhati University, Guwahati, Assam
Email: [email protected]
Since limited information is available on the underlying molecular aetiology of liver
disease development and progression in Assam and other parts of northeast India, which
incidentally has a high load of liver disease patients of different grades of severity; the
present case-control prospective study was carried out to explore the environmental and
genetic risk factors for liver diseases in Assam using molecular diagnostic tools. The
clinically proven liver disease patients were enrolled from the Central hospital, NF Railway,
Guwahati, with informed consent and all the clinical details; and blood samples were
collected following the standard protocols following the ICMR regulations and guidelines.
The followings are the highlights from the present study:
I. The host genetic factors have been shown to play an important associative role in
liver disease susceptibility, and were thus studied in the present study. Since DNA
repair genes and metabolic pathway genes are instrumental in neutralizing the
genotoxic stress caused due to assaults by different endogenous and exogenous
agents. Genotypes or polymorphism in key genes of BER pathway (hOGG1 and
XRCC1) as well as Cyp2E1 gene was evaluated for their association with the
predisposition of liver disease.
II. Gene environment interaction plays an important role in deciding the rate and fate
of disease progression, and hence, certain key and critical environmental factors were
evaluated for their association with liver disease predisposition in northeastern
population. These included the screening for the presence of nitrite in cases and
controls as well as analysis of food samples which are routinely consumed in
northeast India (some of which are indigenously prepared) for presence of nitrites and
volatile nitrosamines. Presence of 8-oxo-dG, a DNA damaging agent and a marker of
oxidative stress was also analyzed in liver disease cases and compared with control
status.
III. Results: The variant hOGG1 genotype was increased the risk of liver disease
[OR=2.322 at 95%CI, p<0.001] and cirrhosis [OR=3.275, p=0.068] compared to
controls. In Hepatitis B and ALD cohorts, presence of variant hOGG1 genotype was
associated with significantly higher risk of chronic hepatitis and cirrhosis cases
compared to controls and acute cases. The distribution of XRCC1codon399 mutation
significantly increased the risk of liver disease {OR=1.545 at 95%CI, p=0.028} and
cirrhosis [OR=1.816 at 95% CI, p=0.310] compared to controls. In ALD cases,
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presence of XRCC1 variant allele increased the risk of chronic hepatitis compared to
controls and acute hepatitis. The XRCC1 protein expression was down-regulated in
cases of alcoholic-cirrhosis compared to controls. The distribution of variant Cyp2E1
genotype c1/c2 was found to be significantly higher in liver disease cases compared to
controls (p=0.002), and increased the risk of liver disease by almost five folds
[OR=4.937]. Presence of the variant Cyp2E1 genotype significantly increased the risk
of liver disease in alcoholic cases [OR=11.30, p<0.001] and cryptogenic cases
[OR=8.071, p=0.020]; and non-significantly increased the liver disease risk in HAV
[OR=3.477)] and HBV cases [OR=3.082]. The nitrite levels in plasma of liver disease
cases were found to be significantly higher compared to controls (p=0.011). Majority
of the fermented food products showed presence of very high value of nitrite which is
detrimental to health. The highest amount of nitrite in raw material was found in
mustard seed, and the highest amount of nitrite in fermented food was found in
fermented mustard i.e. kharoli which is consumed in large amounts in upper Assam
areas. Detectable amounts of N-nitrosamines were found to be present in raw fish. 8-
OH-dG levels was found to be much higher in liver disease cases compared to
controls (p=0.010). Higher 8-oxoG levels correlated significantly with mutant hOGG1
genotype (p<0.001) which is the key enzyme for the repair of 8-oxoG related DNA
damage.
IV. Conclusion : To conclude, CYP2E1 polymorphism is supposedly associated with the
risk of liver disease, especially in non-viral hepatitis patients, and the presence of
higher nitrite concentration in fermented dietary products in Northeast India, and
nitrosamines in Areca catechu (betel nut) and raw fish, have clinical significance,
because these environmental factors can act as additional risk factors in liver disease
susceptibility, by virtue of the gene-environment interaction. The polymorphism in
BER genes and higher 8-OH-dG may also add to risk of susceptibility/severity of
liver diseases amongst people of this region. The studied factors have prognostic
significance with respect to liver disease susceptibility and severity.
Acknowledgement:
1) This is a part of our team work on health care biotechnology . The following team
members have equal contributions to this work- Dr. Sujoy Bose, Dr. Subhash Medhi and
Miss Moumita Bose.
2) We acknowledge The DBT, Govt of India, New Delhi for financial support to us in
carrying on this research programme.
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IL 04: Looking for Synergies between Iron Nanoparticles, Endemic
Microorganisms, and Plants: Can We Address World Water and Food
Security Issues?
Achintya Bezbaruah
Nanoenvirology Research Group
North Dakota State University, USA
Email: [email protected] Ca-alginate has been used to encapsulate nanoscale zero-valent iron (NZVI)
particles and TCE degrading bacteria for aqueous trichloroethylene (TCE) degradation.
Pseudomonas putida and Dehaloccoides sp. are used in this study. Batch studies using a
combined NZVI-microorganism system achieved removal of TCE below detection limits
within 6-12 h. Such combined systems are expected to completely remove TCE in
groundwater to benign end products. In another study, NZVI particles were used for aqueous
phosphate and selenium removal, and the spent particles were tested for bioavailability of
phosphate, iron, and selenium. Spinaciaoleracea and Selenastrumcapricornutum batch
studies indicated possible bioavailability of iron, phosphate and selenium.
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IL 05: Phylogenomic Approach to Bacterial Phylogeny
Probodh Borah
Professor, Dept. of Microbiology
Assam Agricultural University, Khanapara, Guwahati-22
Email: [email protected]
Traditional classification of bacteria is mainly based on sequence comparisons of
certain homologous genes such as 16S rRNA. However, the classical 16S-rRNA-based
phylogenetic reconstruction does not reflect the overall relationship between bacterial species
with widespread horizontal gene transfer. Methods using comparisons of base on codon
composition have revealed that up to 17% of the genes of bacterial genomes may be of alien
origin derived by horizontal transfer. Moreover, molecular phylogenies based on single or a
few genes often lead to apparently conflicting results. To overcome this limitation, it is
tempting to apply a genome-scale approach to phylogenetic inference (phylogenomics) by
combining many genes or the entire genome. In the recent years, a number of methods based
on whole genome comparisons have been proposed. These include: bacterial phylogeny
based on ribosomal proteins and comparative phylogenomics by microarray analysis or by
estimation of oligonucleotide frequency distances. Whole-genome comparisons typically
identify sets of ‘core genes’, which are shared by all strains in a species, and ‘accessory
genes’, which are present in one or more strains in a species and often result from gene
acquisition. It can be particularly useful for retrospective analyses of the recent (past hundred
years) and the longer term (several thousand years) evolution of bacterial pathogens.
With the advancement of sequencing technologies in the recent past, an increasing
number of genomics sequences of prokaryotes have been deposited to the genomic databases.
As of now, the Genome Online Database (GOLD) has more than 3400 complete sequences of
bacterial genome in addition to more than 1400 draft sequences. Already several bacterial
species (e.g. Escherichia coli, Campylobacter jejuni, Helicobacter pylori, Yersinia pestis,
Neisseria meningitides, Staphylococcus aureus, etc.) have had more than a single
representative sequences. It is expected that with the increasing number of genomics
sequences, these phylogenomic approaches would prove not only to be more appropriate
methods for establishing phylogeny of bacteria but also for studying molecular epidemiology
of pathogenic bacteria.
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IL 06: A genomic approach to understanding the nutriomics in Brassica
species
Yong Pyo Lim
Molecular Genetics and Genomics Lab
Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu,
Daejeon 305-764, Republic of Korea
Email: [email protected]
Genomic study and nutrition research have been developed in parallel for a long time.
Plant nutriomics is a new frontier in plant biology, involving genomic, transcriptomic,
proteomic and metabolomics in a network. Brassica species constitutes one of the world’s
most diverse and economically important plant groups with variations of functional
compounds such as glucosinolates, β-carotene, lutein, phenolic acids, flavonoids, etc.
However, it is still less known about the genetic basis and regulation of their biosynthesis in
Brassica species. Thus, we combined a genome wide comparative study, QTL mapping and
large scale microarray analysis to discover their metabolic pathways and regulatory
mechanisms of related genes. QTL analysis for glucosinolate accumulation in B. rapa seeds
was carried out by using a CRF3 population, derived from a cross between “Chiifu” and rapid
cycling type “RCBr” which showed significant difference in glucosinolate content. Twenty
four loci controlling each ten and total glucosinolate compound were identified, with one
major locus in chromosome A08. Through synteny genomic comparison to A. thaliana,
candidate genes and single nucleotide polymorphisms (SNPs) between parental lines were
identified from whole genome re-sequenced data by NGS. In addition, 57 full length CDs
were identified for carotenoids from Brassica. These genes were also identified in in-home
developed 50K microarray dataset for Chiifu and RCBr, and their levels of differential
expressions were checked. Moreover, numerous collected Brassica accessions and
germplasms supported by Korea Brassica Genome Resource Bank were also used for
important functional compound analysis which paves the way for the gene association study
and evolutionary study in future.
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IL 07: The researches on Insect Technology and Bioengineering in NIAS
Keiko Kadono-Okuda
Insect Genome Research Unit,
National Institute of Agrobiological Sciences
1-2, Owashi, Tsukuba, 305-8634 Japan
Email: [email protected]
The National Institute of Agrobiological Sciences (NIAS), which is the largest agricultural
research institute of basic life science in Japan. It is to be the center for basic studies to develop
innovative agricultural biotechnologies and new bioindustries. Main research subjects of NIASinclude
genome research of plants, insects and animals, development of novel functional crops by gene-
recombination technologies, functional analysis of genes for contribution to breeding applications,
and development of new foundational materials for the creation of novel bioindustries. In 2004, the
Institute had achieved the ultimate goal of decoding the entire rice genome sequence as a leading
country of the 10 counties and regions that had organized the International Rice Genome Sequencing
Project, and also has decoded the silkworm genome sequence. The institute developed technologies
for the recombination of genes in crops, insects (silkworm), and animals, and also focuses on
improvement, diversity and utility of Agrobiological resources – we utilize resources that we have
built up in the course of research on the genes of rice, silkworms, and pigs and we have secured other
genetic resources.
The insect researchesin NIAS consist of Insect Genome Research, Transgenic Silkworm
Research, Insect Mimicry Research (Innate Immunity Research, Anhydrobiosis Research, Silk
Material Research), Insect Interaction Research, Insect-Microbe Research and Pest Management
Research.
I will introduce some topics of the insect research in our institute, silkworm Transgenesis and
anhydrobiosis of a midge, including my research of the virus-resistance genes in Bombyxand of
Spodoptera litura transcriptome analysis.
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IL 08: A Novel Spectrophotometer Free Colorimetric Assay Format
Pradip Nahar
Institute of Genomics & Integrative Biology, Delhi
Email: [email protected]
In this communication, we report a novel ELISA carried out on a polypropylene
microtest plate (PPµTP) which is activated by introducing functional group that binds capture
biomolecules through covalent linkage. Activated polypropylene microtest plate (APPµTP)
eliminates to a large extent non-specific binding of biomolecules prevalent in absorption
based technique and makes ELISA more sensitive and specific which are prerequisites for
such assay. We have quantified the image, taken in a scanner or mobile phone by saturation
percentage (a color space parameter). Efficacy of APPµTP is demonstrated by detecting
human immunoglobulin G (IgG), human immunoglobulin E (IgE) and Aspergillus fumigatus
antibody in patient’s sera. Uniqueness of ELISA on APPµTP is that it is done by ultrasound
waves and even in 8 min, it can convincingly differentiate test sample from control sample.
In short, image-based ELISA on APPµTP is rapid and sensitive and could be a good
substitute for conventional immunoassay procedure.
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IL 09: Dissecting Glucosinolates Biosynthesis Pathway Genes for
Engineering Better Nutritional Quality in Brassicas
Nirala Ramchiary
School of life Sciences
Jawaharlal Nehru University
Aruna Asaf Ali Marg, New Delhi 110067
Email: [email protected]
Glucosinolates are sulphur and nitrogen containing secondary metabolites abundantly
found in plants belonging to order Brassicales including the family Brassicaceae. Low
glucosinolates content in Brassica seeds is important as high glucosinolates causes
abnormality in livestock animals (goiter in animals) upon feeding of seed meal which contain
30-40% protein after extraction of the seed oil. On the other hand, high content of
glucoraphanin, a type of glucosinolates, is very important for human health due to its
anticancer activities. Although genes involved in biosynthesis pathway of glucosinolates have
been already identified in Arabidopsis thaliana, detail genes and genetic networks have not
been identified in Brassicas. Further, the presence of triplicate genome segments giving on
average of three paralogs of a single gene in Brassicas compared to A. thaliana complicates
the identification of functional genes. Therefore, the identification of genes involved in
glucosinolates biosynthesis pathway in Brassicas is prime importance so that the desired level
and content can be engineered through conventional breeding and genetic engineering
technology. Our work in different Brassica species tried to dissect the biosynthesis pathway
genes of glucosinolates. We used combination of different methods such as classical genetic
analysis; comparative mapping between different Brassica species and with the A. thaliana,
candidate gene approach and next generation sequencing technology, and identified the key
regulatory and structural genes involved in the glucosinolates biosynthesis pathway in
Brassicas and developed gene specific molecular markers. These genes based high and low
glucosinolates specific molecular markers are being used for marker assisted breeding to
develop low glucosinolates Brassica lines. Furthermore our result shows that glucosinolates
biosynthesis genes are evolutionarily conserved between different Brassicas and with the A.
thaliana.
SOHOJATRI “Bioengineering 2012”
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IL 10: Bioengineering and Biopiracy: Sheep DNA SNP chip case study
Dinesh Kumar
Centre for Agricultural Bioinformatics
Indian Agricultural Statistics Research Institute
Library Avenue, New Delhi-110012, INDIA
Email:[email protected], [email protected]
The advent of DNA chip of bioengineering and the ever increasing attention to the
germplasm up-gradation and improvement for desirable traits and the new avenues for global
marketing has in fact increased the vulnerability of infringement of germplasm sovereignty
across countries, importantly from an IP perspective. Presentation exemplifies North
hegemony over South where information derived from germplasm of developing and
underdeveloped country is being used encroaching on sovereign rights of native germplasm.
The term "sovereignty” used here is its altruistic legalistic sense which means
exclusivity of “rights” with regard to indigenous native germplasm of the country. In the
global context of intellectual property (IP) rights today, this has an added significance in
unauthorized movement or free –flow of indigenous farm animals and/or their genetic
resources or data across nations and its legal infringement on exclusivity of territorial rights
by other parties/nations.
Sheep SNP chip technology can predict the breeding value of sheep giving better
wool, meat quality, yield, disease resistance thus it’s a better animal selection tool. It reduces
the progeny testing cost and time. Further, this revolutionising technology can be used to
predict breeding value of even a new born lamb thus early stage selection with high accuracy
for low heritable traits which makes it commercially advantageous over traditional method of
animal breeding.
This case study elucidates how the ovine SNP 50 bead chip has been made by pooled
59,494 SNP data of 3004 domestic sheep DNA samples from 71 breeds. This sheep SNP chip
available in both global and Indian market, contains research result of Indian sheep breeds
also. The other breeds are from Africa, Asia, South America, Europe, the Middle East,
Australasia, the USA and the Caribbean country. Out of these 71 breeds, three Indian sheep
breeds viz Garole, Deccani and Changthangi were covered in SNP discovery and sheep hap
map panel. These three sheep breeds represent three divergent agroclimtaic/ecological zones
possessing unique genotypes related to divergent adaptations and disease resistance. Such
unique markers are of immense value of today and looking at climate change and consequent
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need of germplasm or its selection technology is going to be of enormous commercial value
across globe.
Since Indian sheep germplasm has contributed in SNP chip development after post
CBD era and its intellectual scientific finding is getting commercialised by US company
Illumina across the globe thus against this backdrop, the intriguing question that comes to our
mind is whether we are entitled to any IP sharing benefit based on Nagoya Protocol of ABS?
To extend this enquiry further, is it unreasonable to expect some kind of a preferential
treatment in the form of some discount in the price in buying the chip, in question, by a
country that has significantly contributed to the chip discovery process in comparison to other
countries who have had little or no contribution to the R&D process. It also raises concerns
about the strict compliance of statutory guidelines operational on our country under regime of
NBA especially for germplasm movement across border to facilitate collaborative research
purpose in interest of our country or in mutual interest. The transfer of result and
commercialisation has to be protected in the larger interest of the country.
SECTION IISECTION IISECTION IISECTION II
Poster AbstractsPoster AbstractsPoster AbstractsPoster Abstracts
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P 01: Interactions of Curcumin Natural Derivatives with DNA
Topoisomerase I and II-DNA Complexes
Anil Kumar1 and Utpal Bora
1,2
1Computational Biology Laboratory, Department of Biotechnology,
2DBT Biotech Hub, Centre for the Environment
Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
Abstract
The present molecular docking study provides insights into the inhibition of
topoiomerase I and II by curcumin natural derivatives. The binding modes suggested that
curcumin natural derivatives docked at the site of DNA cleavage parallel to the axis of DNA
base pairing. Cyclocurcumin and curcumin sulphate were predicted to be the most potent
inhibitors amongst all the curcumin natural derivatives docked.
Fig. Curcumin sulphate (yellow) and cyclocurcumin (purple-blue) docked parallel to the DNA base pairing at
the site of DNA cleavage superimposed with topotecan (cyan)-topo I-DNA complex (PDB ID: 1K4T)
Keywords: Curcumin natural derivatives; DNA topoisomerases; Cancer drug target; Molecular docking; Polar
interactions; AutoDock.
SOHOJATRI “Bioengineering 2012”
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P 02: Structural characterization and docking analysis of modeled
CtXylGH30 protein family 30 glucoronoxylan xylanohydrolase of
Clostridium thermocellum
Anil Kumar Verma and Arun Goyal
Department of Biotechnology
Indian Institute of Technology Guwahati, Guwahati, Assam, India.
Abstract
CtXylGH30 protein (ABN54208.1), a carbohydrate active modular enzyme is a
component of vast cellulosome of Clostridium thermocellum, belonging to glycosyl
hydrolase (GH) family 30 of glucoronoxylan xylanohydrolase. The molecular architecture of
full length protein contain multiple domains viz. signal peptide (1-30), catalytic domain
CtXylGH30 (34-419), linker (419-424), CBM6 (432-559) and dockerin type I (559-630).
CtXylGH30 was modeled by employing computer programmer Modeller9v8. The crystal
structure of GH30 from Erwinia chrysanthemi (1NOF) and xylanases (GH30) from Bacillus
subtilis (3GTN) were considered as a template to generate a reliable molecular model. Model
refinement was carried out by energy minimization by steepest descent algorithm with
GROMOS96 43a1 force field. Quality assessment of modeled CtXylGH30 at PROCHEAK
server by Ramachandran plot showed that 91% residues lies in most favourable region and
9% residues in additional allowed region. Structural study of modeled CtXylGH30 showed
that the protein has a (β/α)8 barrel folding structure along with obligate β sheet rich structure
which differentiate family GH30 from GH5. Analysis of multiple sequence alignment and
docking results of CtXylGH30 showed that conserved active site residues Glu-137 act as a
catalytic proton donor while Glu-226 act as a catalytic nucleophile and are participating in the
reaction mechanism. The binding mode interaction of ligands depicted that the amino acid
residues Pro81, Trp82, Asn83, Asn136, Tyr140, Trp144, Phe173, His199, Tyr201, Tyr228,
Trp265 and Tyr266 made a binding site pocket around the active site. Xylopentose showed
the maximum affinity with free binding energy (∆G) of -9.39 kcal/mol among the xylo-
oligosaccharides.
Key World: CtXylGH30, Clostridium thermocellum, homology modeling, docking study
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P 03: The emergence of novel E. coli Uracil PhosphoRibosyl Transferase
mutants in the prospect of cancer therapeutics : a Bioinformatics Approach
V. Kohila
a and Siddhartha Sankar Ghosh
a, b
aDepartment of Biotechnology bCentre for Nanotechnology
Indian Institute of Technology Guwahati, Guwahati-39, Assam, India
Abstract
E.coli Uracil Phosphoribosyl Transferase (bUPRT) /5-Fluorouracil (5-FU) based
suicide gene therapy is an enchanting system but the insubstantial binding of the prodrug 5-
FU to the enzyme active site demotes its applications. Hence, the present study aims at
designing mutants of bUPRT to augment its binding affinity towards the prodrug, 5-FU. In
silico site directed mutagenesis (SDM) was performed through molecular docking to
engender novel mutants of bUPRT which show efficient binding to the prodrug than its actual
substrate uracil. The docking results were scrutinized depending on the known substrate
binding and stacking interactions between the protein side chain and the ligands; as well the
binding free energy scores provided by AutoDock. Among the 54 mutants docked, six
mutants showed higher binding capabilities with 5-FU than uracil. Most importantly, the in
silico studies afforded three mutants M101V, I194Y and E105D, which can strongly bind
only to the substrate 5-FU; thereby rendering the mutant proteins to act powerful in the
context of suicide gene therapy (SGT) applications.
Key words: bUPRT, 5-Fluorouracil, Site directed mutagenesis, Suicide gene therapy.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 31 | P a g e
P 04: Biosorption of Cadmium by Porous Carbon prepared from Christella
hispidula(Decne)Holt
Lukumoni Boraha,b
, Mridusmita Goswamia and Prodeep Phukan
a*
aDepartment of Chemistry, Gauhati University, Guwahati-781014, Assam, India
bDepartment of Chemical Engineering, IIT Guwahati, Guwahati-781039, Assam, India
Abstract
Cadmium is considered as a priority pollutant by the USEPA and is extremely toxic
which causes kidney damage, renal disorder, bone faction and red blood cell destruction even
in low concentration. In this study, we have prepared porous carbon (PC) from Bihlangoni
[Christella hispidula (Decne) Holt] with a high surface area of 320.68 m2/g by chemical
activation method. The PC was characterized by SEM, FT-IR and BET surface area analysis
and investigated the potentiality of Cd (II) removal from aqueous solutions by batch
adsorption technique. Adsorption experiments for the biosorbent were optimized by varying
several experimental parameters viz., contact time, initial metal concentration, adsorbent
dosage and adsorbate solution pH which are responsible for effective adsorption. The
equilibrium isotherm data was best fitted to the Langmuir adsorption isotherm model, which
confirms the monolayer chemisorptions of cadmium ions. The results obtained from this
study reveals that PC obtained from locally abundant biomaterials may be used as an efficient
and effective biosorbent for the removal of Cd (II) from aqueous solutions.
Keywords: Christella hispidula (Decne) Holt, Chemical activation, Porous carbon, Cd
removal, Isotherm models.
Acknowledgement: Financial support from the Ministry of Environment and Forest, India
(grant no. 19-27/2008-RE) is gratefully acknowledged.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 32 | P a g e
P 05: Blood Group Conversion-Blood Made Suitable to All
Neelima Gudala and Mangala Lahkar
NIPER, Guwahati, Assam
Abstract
The technique potentially enables blood from groups A, B and AB to be converted
into group O negative, which can be safely transplanted into any patient.The method, which
makes use of newly discovered enzymes, may help relieve shortages of blood for
transfusions. Molecule, while those with group O blood have neither.People The blood cells
of people with group A and B blood contain one of two different sugar molecules, which act
as "antigens", triggering an immune system response. People with AB blood have both types
of produce antibodies against the antigens they lack. This means groups A, B and AB can
only be given to patients with compatible blood, while O - as long as it is rhesus negative -
can be given to anyone. The new technique works by using bacterial enzymes to cut sugar
molecules from the surface of red blood cells. Two bacteria - Elizabethkingia
meningosepticumand Bacterioides fragilis - which contained potentially useful enzymes are
useful in this technique.Enzymes from both bacteria were able to remove both A and B
antigens from red blood cells. "This method may enable manufacture of universal red cells,
which would substantially reduce pressure on the blood supply."
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 33 | P a g e
P 06: Peptide self-assembly and biophysical studies of amyloid aggregation
of a short peptide derived from α-synuclein protein
Rajesh Kumar and Nitin Chaudhary
Department of Biotechnology
Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
Abstract
Parkinson's disease (PD), the second most common neurodegenerative disorder is caused due
to accumulation of Lewy bodies in the substantia nigra of the midbrain in the age of 65 years. These
Lewy bodies are pathological hallmark of PD and formed due to aggregation of α-synuclein and other
associated proteins. The cytosolic α-synuclein protein self-assembles into ordered crossed β-sheet
amyloid like fibrils similar to amyloid beta (Aβ) peptide in Alzheimer’s disease. Upon axon damage
in the substantia nigra, the aggregated α-synuclein species are released into the extracellular space
which can cause oxidative stress in nearby neuron cells. The amyloidogenic Alzheimer Aβ (16–22)
peptide sequence (Ac-KLVFFAE-am) was shown to form short fibrous aggregates similar to full
length Aβ peptide (42 residues) in organic solvents such as hexafluoroisopropanol. According to
AMYLPRED tool, the short peptide sequence from 69-78 (AVVTGVTAVA) derived from full length
α-synuclein (140 residues) has the tendency to form amyloid fibrils. The sequence may provide a new
insight in understanding the mechanism of amyloid formation of α-synuclein protein and developing
potential therapeutics against PD. The peptide sequence has Boman index -1.73 kcal/mol and
hydrophobic ratios of 70% predicted by APD tool which suggests that the 69-78 peptide stretch might
have antimicrobial activity similarly recently shown by Aβ peptide that normally functions as an
antimicrobial peptide (AMP) of the host innate immune system.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 34 | P a g e
P 07: Phytochemical screening and Antimicrobial activity of the leaf
extract of Ficus nervosa Heyne ex Roth.
Rajesh Kumar Shah1 and R.N.S.Yadav
2
1Assistant Professor, Deptt. Of Zoology,D.H.S.K.College
Dibrugarh-01
2Professor, Deptt. of Life Sciences, Dibrugarh University,Assam.
Abstract
NE Region of India is rich source of biodiversity which includes high potential of
naturally occurring medicinal plants. Nature has been a source of medicinal agents for
thousands of years and an impressive number of modern drugs have been isolated from
natural sources. Many of these isolations were based on the uses of the agents in traditional
medicine. The present study was undertaken to evaluate the phytochemical constituents and
antimicrobial activity in the leaf extract of Ficus nervosa,a traditionally used medicinal
plant. The crude extracts from leaf of Ficus nervosa. in different solvent, were subjected to
phytochemical analysis., indicated that the leaf contain a broad spectrum of secondary
metabolites which were also quantified and presence of these medicinally important bioactive
compounds justifies their use in the traditional medicines for the treatment of different
diseases. The antibacterial activity of methanolic and ethanolic extracts was carried out using
agar well diffusion method against Escherichia coli and Streptococcus epidermidis
.Methanolic extract was found to be effective against Escherichia coli and both methanolic
and ethanolic extract were found to be effective against Streptococcus epidermidis. The
standard antibiotic Cefotaxime was found to have no inhibition against Streptococcus
epidermidis. Streptococcus epidermidis in human produces slime layers, which forms a
hydrophobic biofilm. This film is adhesive to hydrophobic biopolymers The biofilm of S.
epidermidis consists of clusters of cells that are embedded in extracellular slime. Biofilms as
such act as a diffusion barrier to antibiotics and others. Since the plant shows a high degree of
antimicrobial activity , there is a possibility that the plant may be a source of antimicrobial
agent, and further investigation are necessary to find the bioactive principle.
Key Words: Phytochemical, Leaf extract, Ficus nervosa, E.coli, S. epidermidis antimicrobial
activity
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 35 | P a g e
P 08: Studies on feasibility of phylogenetic trees for characterization of
bacteria using the 16S rRNA, rpoB and gyrB genes of the type strains of
Actinomycetes
Dollyca Ningombam,
Joy Heikrujam,Oscar Ningombam,Phairembam Radharani Devi, Salam Nimaichand,
Suchitra Sanasam, Debananda S. Ningthoujam
DBT State Biotech Hub, Manipur University
Abstract
16S rRNA gene is the most commonly used gene for the characterization of bacteria.
However, due to its large copy number, the characterization based on 16s rRNA sequence
analysis is sometimes ambiguous as more than one type of 16S rRNA genes may be present
owing to horizontal gene transfer in bacteria. Hence, multilocus sequence analysis is being
currently investigated for proper denotation of bacteria in the phylogenetic clade. In the
resent study, comparative studies have been undertaken on feasibility of phylogenetic trees of
type strains of actinomycetes using three different genes, viz. 16S RNA, rpoB and gyrB
enes. The detailed findings of this investigation shall be discussed in this paper.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 36 | P a g e
P 09: Designing of PCR primer by using Bioinformatics tools
Th Themis, N Martina,
Th Geetanjali, Kh Shaheen,
Suchitra Sanasam, Debananda S.
Ningthoujam
*Microbial Biotechnology Research Laboratory (MBRL), Department of Biochemistry,
Manipur University, Canchipur, Imphal, India
Abetract
Bioinformatics has become an essential tool for basic research and applied research in
biotechnology and biomedical sciences. Polymerase chain reaction (PCR) is a commonly
used method to amplify DNA of interest in many fields such as biomedical research,
diagnostics testing and forensic sciences. Selection of appropriate oligonucleotide primer is
crucial in Polymerase chain reaction (PCR), oligonucleotide hybridization and DNA
sequencing protocols. Choosing appropriate primers is probably the single most important
factor affecting the polymerase chain reaction (PCR). Primer sequences are needed to be
chosen uniquely for a selected region of DNA to avoid the possibility of mishybridization to
a similar sequence nearby leading to undesired amplification. Optimal primer sequence and
appropriate primer concentration are essential for maximal specificity and efficiency of PCR.
A poorly designed primer can result in little or no product due to non-specific amplification
and/or primer-dimer formation, which can become competitive enough to suppress product
formation. The use of software in biological applications has given a new dimension to the
field of bioinformatics. A number of primer design tools or software packages such as Oligo,
Primer-BLAST, Primer Premier etc are available that can assist in PCR primer design and
alleviate the difficulty in designing target-specific primers. These tools reduce the cost and
time involved in experimentation by lowering the chances of failed experimentation. This
paper will highlight the use of these bioinformatics tools and techniques.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 37 | P a g e
P 10: Management of Femur Fracture in Dogs with Biomaterials (DBM)
C.K Singh, B Deuri, K.K.Sarma, B. Sarma, P.J. Nath,
L. Sailo, M.G. Kaur, R. Lashkar, S. Ali and J. Kachari
Department of Veterinary Surgery & Radiology
College of Veterinary Science, Khanapara, Guwahati-781022, Assam.
Abstract
A study was conducted in the Department of Veterinary Surgery and Radiology, C.V.Sc,
AAU Khanapara, Guwahati-22 from 1st Aug 2011 to 31st July 2012 for incidence and management of
femur fractures in dogs. Fifteen dogs of either sex having femur fracture were under taken for the
study where diagnosis for fracture was based on history, clinical assessment and radiography. The
animals were randomly divided into three equal groups’ viz. GROUP -A –where fracture management
was done with closed reduction and external fixation; GROUP –B- open reduction with intra-
medullary pinning was done and in GROUP-C- the management was done with internal fixation
along with DBM (Demineralized Bone Matrix). The healing was recorded with both radiographic and
clinical assessment on the 21st, 45th and 60th days postoperatively. The complications like delayed
union, non-union etc. were observed in Group A; in GROUP B, the dislodgment of the intra-
medullary pin were observed and healing took longer time in both the groups compared to GROUP
C, where the healing was early and other complications were least observed. Application of DBM in
fracture management has shown a promising result as it reduces the postoperative complications
associated with fracture healing.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 38 | P a g e
P 11: Molecular Signatures of Breast Cancer
Arghya Sett, Sambhavi and Utpal Bora
Department of Biotechnology,
Indian Institute of Technology Guwahati
Guwahati 781039, Assam, India
Abstract
Breast cancer is a collection of clinically, histopathologically and molecularly
heterogeneous disease which is the most prevalent invasive cancer. Biomarkers are useful for
diagnosis, monitoring disease progression, predicting disease recurrence, & therapeutic
treatment efficacy. Predicting cancer outcome & influencing the cancer treatment will have a
major role in determining the cost effectiveness in clinical cancer management. Recently, an
increasing number of markers have been identified that aim to predict cancer outcome rather
than to detect it early. This progress stems from the advent of novel techniques in genomics
and proteomics to discover the mechanisms in genes and proteins associated with various
carcinoma. Even though mammography is widely used to detect incipient breast carcinoma,
the technique is unable to provide any caution of ultimate disease outcome. Consequently
several recent studies have sought to identify different marker protein like Her2, ER, PR,
marker genes like ki67, BRCA I, BRCAII, that contribute to the ‘metastatic signature of
breast cancer’. Thus Recent development of novel biomarkers results in early prognosis of
disease and increasing survival of cancer patients worldwide.
Keywords: breast cancer, biomarkers, metastatic signatures.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 39 | P a g e
P 12: Development of Majuli Island Bioresource Database (MIBD)
Nayanmoni Gogoi1, Anil Kumar
2, Utpal Bora
1, 2 and Chandan Mahanta
1, 3
1Centre for the Environment,
2Department of Biotechnology,
3 Department of Civil Engineering
Indian Institute of Technology, Guwahati, Assam
Abstract
Wetlands play a significant role in maintaining some of the key activities of large
rivers like the Brahmaputra and the Ganga. Wetlands can be regarded as the heart of a
riverine ecosystem, they play an important role in nutrient cycling, water purification, climate
regulation, flood regulation, coastal protection, recreational activities and increasingly,
tourism (Millennium Ecosystem Assessment, 2005). Rising environmental impacts and over
exploitation of high concentration of natural and socio-economic resources highlight the need
for regional to global assessments of wetlands. It is necessary to review the status and
management of wetlands in Majuli River Island and identify the ecosystem services of the
potential bioresources Database provides details of wetlands and help in establishing a
baseline, conservation, management and sustainable use of resources. Components included
in database development are water and soil quality, agriculture, rainfall, temperature, flood
and erosion, microbial component of soil and water, nutrient budget of soil, bioresource
application and land use management. An attempt has been made to compile the basic
information available through various resources and data obtained through experimental
analysis, the database developed consists of information on geographic location, area,
locality, water quality, soil quality, nutrient budget and vegetation in Majuli Island.
Keywords: Wetland, ecosystem, exploitation, resources, database.
SOHOJATRI “Bioengineering 2012”
IITG-DBT Biotech Hub 40 | P a g e
P 13: A Spectrophotometer-Free Image-Based Assay For Oligonucleotide
Detection
Rajesh Ahirwar, Shahila Parween, Ishita Rehman and Pradip Nahar*
CSIR- Institute of Genomics and Integrative Biology
Mall Road, Delhi – 110 007, India
Abstract
Image-based diagnostic assay is a new area and is mostly carried out on paper.
However, paper gives high non-specific binding leading to false positive result. In this report,
we have responded to this problem by performing image - based assay on activated
polypropylene microtest plate (APPµTP). Hydrophobic and inert test zone of PPµTP is
photochemically activated to enable covalent immobilize of capture biomolecule. In the
present work, 20bp oligonucleotides were attachment on APPµTP and detected hybridization
non-spectrophotometrically. APPµTP is a white hydrophobic polypropylene surface having
photochemically activated test zones. It binds oligonucleotide probes covalently instead of
absorption. The probe binding and hybridization parameters were optimized for different
temperature and time periods on APPµTP. A temperature of 60⁰C for 60min and 50⁰C for 60
min was found to be optimal for probe immobilization and hybridization detection,
respectively. The FNAB (1-fluoro-2-nitro-4-azido-benzene) activated zones bind labelled
probes only. It eliminates non-specific binding prevalent in absorption based techniques.
Biotin labelled target oligonucleotides were hybridized with probes and detected by
photocolorimetric method. The captured image color was quantified by colour saturation
based assay using desktop scanner instead of Lambert-Beer absorbance based method. A
linear correlation is observed between colour saturation percentage and absorbance based
quantification. The method is sensitive, require femto molar concentration of target
oligonucleotides and can detect even single mismatch target. This image-based
spectrophotometer-free assay could be a potentially useful alternative to absorbance- based
conventional assay system.