Indian Institute of Technology Guwahati - iitg.ac.in · Nayanmoni Gogoi, Swagata Sharma, Deepika,...

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 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).



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



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.



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



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



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



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.



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


Das, Diganta Kr. Gauhati University

[email protected]

Das, Pranab Jyoti National Research Centre on Yak ,Arunachal Pradesh


Deka, Manab Gauhati University


Fraser, Malcolm

J., Jr.

University of Notre Dame, USA

Email: malcom [email protected]

Kumar, Dinesh Indian Agricultural Statistical Research Institute, Delhi


Kunnumakkara,

A.B.

Department of Biotechnology, IIT Guwahati


Lewis, RV Utah State University, USA


Lim, Yong Pyo Chungnam National University, South Korea


Lynn, Andrew

Michael

Jawaharlal Nehru University, Delhi


Malhotra, BD Delhi Technological University, Delhi


Nahar, Pradip Institute of Genomics & Integrative Biology, Delhi


Okuda, Keiko

Kadono

National Institute of Agrobiological Sciences, Japan


Ramchiary,

Nirala

Jawaharlal Nehru University, Delhi




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



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

[email protected]

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



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



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



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



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….



“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,


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



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



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



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


IITG-DBT Biotech Hub 1 | P a g e

CA 01: Aptamers-the Magic Bullets in Biosensor Technology

Arghya Sett

Dept. of Biotechnology

Indian Institute of Technology, Guwahati, Guwahti-39


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].



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.



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.



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.


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.



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



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



CA 03: Recent Advances in SELEX

Swagata Sharma


Indian Institute of Technology, Guwahati, Assam, 781039


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



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.



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.



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.



CA 04: A New Comer in Therapeutic Oligonucleotide: APTAMER

Sambhavi

Department of Biotechnology,

Indian Institute of Technology Guwahati, Guwahati


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



(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



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.



• 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



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


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


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”


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



Fundamentals and Application of Ordered Molecular Assemblies to Affin


Dhar Malhotra,Chemical Society Reviews, Chem. Soc. Rev., 2012, 41 (3),

Chitosan Encapsulated Quantum Dots Platform for Leukemia Detection



http://dx.doi.org/10.1016/j.bios.2012.05.010

“Bioengineering 2012”

16 | P a g e


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



Fundamentals and Application of Ordered Molecular Assemblies to Affinity


, 2012, 41 (3), 1363

Chitosan Encapsulated Quantum Dots Platform for Leukemia Detection , Aditya





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


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.



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


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,



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.



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.



IL 05: Phylogenomic Approach to Bacterial Phylogeny

Probodh Borah

Professor, Dept. of Microbiology

Assam Agricultural University, Khanapara, Guwahati-22


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.



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


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.



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


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.



IL 08: A Novel Spectrophotometer Free Colorimetric Assay Format

Pradip Nahar

Institute of Genomics & Integrative Biology, Delhi


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.



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


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.



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



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



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.



P 02: Structural characterization and docking analysis of modeled

CtXylGH30 protein family 30 glucoronoxylan xylanohydrolase of

Clostridium thermocellum

Anil Kumar Verma and Arun Goyal


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



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.



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.



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."



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


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.



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



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.



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.



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.



P 11: Molecular Signatures of Breast Cancer

Arghya Sett, Sambhavi and Utpal Bora

Department of Biotechnology,


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.



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.



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.

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