International Biological Engineering Meeting
CONTENT
1. Messages
1
2. Program Schedule
8
3. Speakers abstracts
13
4. Poster Abstracts
37
5. Key Indian labs in synthetic biology
60
6. Sponsorships
63
7. Notes
64
International Biological Engineering Meeting
CORE TEAM
SHAILJA SINGH, Associate Professor, Signaling Biology Group
Special Centre for Molecular Medicine, JNU, New Delhi -110067
e: [email protected] w: http://www.signalingbiology.org
PAWAN K. DHAR, Professor & Head, Synthetic Biology group
School of Biotechnology, JNU, New Delhi - 110067
e: [email protected] w: http://dharlab.net
V. RAVICHANDIRAN
Director, National Institute of Pharmaceutical Education & Research,
Kolkata – 700032
e: [email protected] w: http://www.niperkolkata.edu.in/
SCIENTIFIC ADVISORY BOARD
Prof. Achuthsankar S. Nair, Head, Dept. of Computational Biology and
Bioinformatics, Univ. of Kerala
Prof. BC Tripathy, Dean, School of Life Sciences, JNU
Prof. Ramesh Bamezai, School of Life Sciences, JNU
Prof. Rajiv Bhat, School of Biotechnology, JNU
Prof. Guhan Jayaraman, Dept. of Biotechnology, IIT Madras
Prof. I.S.Bright Singh, CUSAT, Cochin
Prof. Indira Ghosh, School of Computational and Integrative Sciences, JNU
Dr. Joseph Selvin, Pondicherry University
Prof. K.J. Mukherjee, School of Biotechnology, JNU
Prof. Uttam Pati, Dean, School of Biotechnology, JNU
Prof. Vibha Tandon, Chairperson, Special Centre for Molecular Medicine, JNU
International Biological Engineering Meeting
TEAM LEADERS
Dr Siddharth Manvati,
School of Biotechnology, JNU, New Delhi -110067
e: [email protected]
Dr P Kalaiarasan,
School of Biotechnology, JNU, New Delhi -110067
e: [email protected]
TRAVEL & ACCOMMODATION
Mr Raj Kumar Sah
Mr Vijay Kumar
Mr Aditya Nigam
Mr Rahul Yadav
REGISTRATION & OTHERS
Ms Juveria Khan
Ms Monika Kaushik
Ms Ankita Arora
Ms Preeti Yadav
Dr Sonal Gupta
Ms Seema Shah
Dr Mamta Jena
Ms Archita Biswas
Mr Durdam
Mr Mahendra Varma
Ms Rubi
Mr Rupesh Kumar
Ms Shreya Mani Tripathi
Ms Swati Swood
Messages
International Biological Engineering Meeting
Prof. M. Jagadesh Kumar
Vice Chancellor, JNU
I heartily congratulate the organizers of iBEM for launching a new series of synthetic biology
conference in India.
The rational design of biological systems is a bold novel approach that derives motivation from
the engineering community in the form of IEEE standards and rules of composition.
I am delighted to see Jawaharlal Nehru University taking a lead in bringing together brilliant
scientists and students from Universities, IITs, Research Institutes and Private Organizations
on a common innovation platform of engineering biology.
I would like to warmly thank our guests from India and overseas for sharing their immensely
valuable expertise and hope that International Biological Engineering Meeting generates new
knowledge and opportunities for aspiring minds.
My heartiest thanks to NIPER Kolkata for co-organizing this event. Congratulations to
everyone involved and best wishes for the success of this new iBEM series.
1
International Biological Engineering Meeting
SHAILJA SINGH
PAWAN K. DHAR
Greetings and Welcome to JNU ! We are delighted to present the First International Biological
Engineering Meeting
The aim of this conference is bring together outstanding scientists and students from
academia and industry to design and construct biological parts, devices, circuits and cells
towards socially useful applications.
Ever since the term synthetic biology was made popular at MIT, SB 1.0, June 2004, the
community has felt that 'biological engineering' represented the new engineering approach in
biology more accurately. The novel engineering approach calls for rational design of biological
systems from genome sequence to the network and cells.
In the iBEM 1.0, there will be introductory talks on building standards and inventory of
biological components, genome engineering tools, technologies and applications. For the
advanced level users, the talks will focus on genome editing applications, logic gates, cell
factory, synthetic life and so on.
We are delighted to launch a new Indian Biological Engineering Competition (iBEC) for the
Indian community. We thank NIPER for providing important support and highlight the health
and industry applications of this new kind of science.
Welcome to the iBEM 1.0 !
2
International Biological Engineering Meeting
Dr. V. Ravichandiran
Director, NIPER Kolkata
JNU, New Delhi - School of Biotechnology and Special
Centre for Molecular Medicine in collaboration with NIPER
Kolkata are organising iBEM event from 26th to 28th March,
2017 at JNU, New Delhi. Deliberations will focus on
metabolic engineering for production of small molecule
drugs, building standards and inventory of biological
components, developing genome engineering tools,
technologies
and
applications,
genome
editing
applications, logic gates, cell factory, synthetic life and so
on for the best benefit of the emerging synthetic biology in India.
Speakers of the event are from:
Institutes: Indian Institute of Technology, Delhi, Indian Institute of Technology, Madras, Indian
Institute of Technology-BHU, Indian Institute of Technology- Bombay, Saha Institute of
Nuclear Physics, Kolkata, BIRAC, Department of Biotechnology, Government of India, New
Delhi, KIIT School of Biotechnology, Jawaharlal Nehru University, NIPER-Kolkata, Centre for
Computational Biology & Bioinformatics, School of Life Sciences, Central University of
Himachal Pradesh, Dharmashala, CSIR-IGIB Mathura road, New Delhi, CSIR-IICB, CSIR-CFTRI,
IISER Pune.
Institutes from abroad: Johns Hopkins University Baltimore, Maryland, USA, Department of
Biomedical Engineering, University of California Davis, Institute of Molecular and Cellular
Biology Biopolis, Singapore.
Participation from pharma industries in large number from OPPI, IDMA, Sanofi, Natreon US,
Auro Biotech, Chennai, ASG Biochem, etc will contribute immensely to the cause of pharma
education and research in India.
3
International Biological Engineering Meeting
4
International Biological Engineering Meeting
5
International Biological Engineering Meeting
6
International Biological Engineering Meeting
7
International Biological Engineering Meeting
Programe Schedule
DAY 1
SUNDAY MARCH 26, 2017
SESSION ONE
INAUGURAL SESSION
08:00 – 09:00
Registration + Tea
09:00 – 09:10
Lighting the lamp
09:10 – 09:20
Welcome Address, Prof.Satish Chandra Garkoti, Rector II, JNU
09:20 – 09:30
Welcome Address: Prof. Rupesh Chaturvedi, Director, Research, JNU
09:30 – 09:40
Welcome address: Prof. Shailja Singh, SCMM, JNU
09:40 – 09:50
Welcome address: V.Ravichandiran, Director, NIPER Kolkata
09:50 – 10:00
Guest of Honor: Dr Kiran Kaliya, Director NIPER Ahmedabad
10:00 – 10:10
Guest of Honor: Dr. V Nagarajan Member Steering committee, NIPERs
10:10 – 10:20
Guest of Honor: Dr. Rajneesh Tingal, Joint Secretary, Department of
Pharmaceuticals, Government of India
10:20 – 10:30
Guest of Honor: Prof. Ramesh K. Goyal, Vice Chancellor, DPSRU
10:30 – 10:40
Introducing iBEM: Prof. Pawan K. Dhar, SBT, JNU
10:40 – 10:50
CHIEF GUEST: S.S. Chandrasegaran, Johns Hopkins University
10:50 – 11:30
Group photograph, BREAKFAST
CHAIR
Prof V. Nagarajan
11:30 – 12:15
12:15 – 14:00
Keynote: S.S.CHANDRASEGARAN, Johns Hopkins University
Rewriting the blueprint of life by synthetic genomics
L U N C H
8
International Biological Engineering Meeting
SESSION TWO
CELL FACTORY
CHAIRS
ATUL JOHRI, SLS and AMULYA PANDA, NII
14:00 – 14:30
UTTAM SURANA, IMCB, Singapore
Metabolic pathway modulation and yeast surrogacy
14:30 – 15:00
GUHAN JAYARAMAN, IIT Madras
Synthetic biological approaches for regulating metabolic
pathway fluxes in microbial factories
15:00 – 15:30
SHAMS YAZDANI, ICGEB, New Delhi
Microbial Platform for Production of Enzymes, Fuels and Chemicals
15:30 – 16:15
T E A
SESSION THREE
INDUSTRY PERSPECTIVE
PANEL DISCUSSION: Entrepreneurship and Policy
CHAIR: SATYAPRAKASH DASH, BIRAC, New Delhi
16:15 – 17:30
MRUTUYNJAY SUAR, KIIT Bhubneshwar
SHRIRAM RAGAVAN, Evolva Biotech, Chennai
RAVI BHOLA, K & S Partners, Bangalore
K RAJU, Sanofi - Shantha Biotech
A MURUGANANDAM, Director, Natreon Inc.
17:30 – 19:00
Poster presentation
19:00 – 20:30
D I N N E R
DAY 2
MONDAY MARCH27, 2017
08:30 – 9:30
BREAKFAST
9
International Biological Engineering Meeting
CHAIRS
SAIRAM KRISHNAMURTHY, IIT, BHU.
PARASURAMAN JAISANKAR, CSIR IICB Kolkata
09:30 – 10:15
Keynote: BALAJI PRAKASH, CFTRI, Mysore
Designer proteins for the synthetic cell
10:15 – 11:00
T E A
SESSION FOUR
GENOME DESIGN AND EDITING
CHAIRS
UTTAM SURANA, IMCB Singapore, GOBARDHAN DAS, SCMM, JNU
11:00 – 11:30
D.SUNDAR, IIT Delhi
CRISPcut: a novel tool for designing optimal sgRNAs for CRISPR/Cas9 based
experiment in human cells
11:30 – 12:00
SIVAPRAKASH RAMALINGAM, IGIB, New Delhi
Targeted Genome Engineering using Programmable Site-specific Nucleases
12:00 – 12:30
SHAILJA SINGH, JNU, New Delhi
Genome editing approaches and applications in malaria
12:30 – 14:00
L U N C H
SESSION FIVE
SYNTHETIC LIFE - 1
CHAIRS
RAJIV BHAT, SBT, JNU and ANAND RANGANATHAN, SCMM, JNU
14:00 – 14:30
TAN CHEE MENG, University of California, Davis
Engineering programmable, dynamic materials using bio-inspired
communication
14:30 – 15:00
SUDHA RAJAMANI, IISER Pune
What we have learnt from making protocells in the lab
15:00 – 15:30
SANGRAM BAGH, Saha Institute of Nuclear Physics, Kolkata
Towards a synthetic biology platform for cellular robotics and space
bioengineering
15:00 – 16:15
T E A
SESSION SIX
INDUSTRY: TECH TALKS
10
International Biological Engineering Meeting
CHAIRS
RUPESH CHATURVEDI, SBT, JNU , DIPANKAR GHOSH, SCMM, JNU
16:15 – 16:30
RAMA S. VERMA, IIT Madras
16:30 – 16:45
A. MURUGANANDAM
16:45 – 17:00
P.ANNAMALAI, Aura Biotechnologies
Practical approaches in drug development using synthetic biology tools
17:00 – 17:15
MRK Raju Mantena, Shantha Biotech-Sanofi
17:15 – 17:30
AJAY KUMAR, Thermofisher
CRISPR/Cas9 based genome editing tool box from ThermoFisher.
19:00 – 20:30
D I N N E R
DAY 3
TUESDAY, MARCH28, 2017
SESSION SEVEN
08:00 –09:00
09:00 – 9:45
BREAKFAST
TUTORIAL: VIKRAM SINGH, CUHP, Dharamshala
Designing gates and networks
SESSION EIGHT
SYNTHETIC LIFE - 2
CHAIRS
SANGRAM BAGH, SINP, Kolkata and DEEPAK GAUR, SBT, JNU
10:00 – 10:30
ARUN SHUKLA, IIT Kanpur
Synthetic antibodies for investigating structure and function of G ProteinCoupled Receptors
10:30 – 11:00
RANJITA GHOSH MOULICK, SPS, JNU
Biomimetic membrane – a synthetic platform
11
International Biological Engineering Meeting
11:00 – 11:30
VIJAI SINGH, Indian Institute of Advanced Research, Gandhinagar
Exploring the potential of RNA-guided CRISPR interference for targeted
11:30 – 11:40
SHORT BREAK
iBEC: Indian Biological Engineering Competition
11:40 – 12:40
Moderator: Pawan K. Dhar, SBT, JNU
Panel: SHAMLAN RESHAMWALA, ICT Mumbai
SHAIKH Z. AHAMMAD, IIT Delhi
SIVAPRAKASH RAMALINGAM, IGIB New Delhi
12:45 – 13:40
L U N C H
SESSION NINE
iGEM [International Genetically Engineered Machines]
CHAIRS
ANDREW M. LYNN, SCIS and VIBHA TANDON, SCMM
13:40 – 14:00
SANGITA KASTURE, DBT, Ministry of S&T, New Delhi
DBT Initiatives in Synthetic Biology
14:00 – 14:30
SHAIKH Z AHAMMAD, IIT Delhi
iGEM 2016: overview
14:30 – 15:00
SHAMLAN RESHAMWALA, ICT Mumbai
iGEM 2017: putreSCENT – designing an environmental application
15:00 – 15:30
T E A
Valedictory : Padma Shri Prof. Ramesh Bamezai, SLS, JNU, Ex Vice
15:30 – 16:00
Chancellor, Shri Mata Vaishno Devi University, Jammu, Fellow National
Academy of Medical Sciences
16:00 – 16:15
Poster awards: Ramesh N.K. Bamezai, SLS, JNU, Rama S. Verma, IIT
Madras
16:15 – 16:30
Vote of Thanks : V. RAVICHANDIRAN, SHAILJA SINGH, PAWAN K. DHAR
12
ABSTRACTS OF THE INVITED TALKS
13
International Biological Engineering Meeting
Prof. SS Chandrasegaran
Johns Hopkins School of Public Health, Maryland
Rewriting the blueprint of life by synthetic genomics
S. S. Chandrasegaran 1, Vijayan Sambasivam 1 , Sivaprakash Ramalingam 2 , Annaluru Narayana 3
1. Department of Environmental Health Sciences, Johns Hopkins School of Public Health, 615 N.
Wolfe Street, Baltimore, Maryland 21205, USA 2. Currently at the CSIR-Institute of Genomics
and Integrative Biology, Mathura Road, New Delhi – 110025, India 3. Currently at Dupont
Pioneer, Iowa, USA
Abstract
We previously reported the total synthesis of a designer version of yeast Saccharomyces
cerevisiae chromosome III, called synIII, with numerous changes from the wild-type sequence. The
changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions,
introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to
enable genome scrambling. SynIII is functional in S. cerevisiae. The synIII alterations does not have
an impact on cell fitness and phenotype, suggesting to the plasticity of the yeast genome. The
project to generate the first synthetic yeast genome - the Sc2.0 Project – is now underway. Sc2.0
is led by a consortium of international scientists. Our lab is currently focused on the completion of
the designer yeast chromosome IX, aka synIX.
14
International Biological Engineering Meeting
Prof. Uttam Surana
Institute of Molecular and Cell Biology, A*STAR,
61 Biopolis Drive, Singapore 138673
Metabolic pathway modulation and yeast surrogacy
Abstract
Yeast Saccharomyces cerevisiae is an established model system well-known for its amenability
to genetic manipulation. It has been extensively used to investigate the fundamental cellular
networks because of their high similarity with those of higher eukaryotes including humans.
Despite a few inherent physiological limitations, it is also frequently employed as a production
host for industrially important metabolites. We are using cellular pathway manipulations in
S.cerevisiae for two disparate aims: (i) to establish “humanized yeast” as a surrogate system for
rapid identification of novel therapeutic agents (ii) to produce lipid derived flavor compounds.
We will discuss our approach to these dissimilar goals and some recent outcomes.
15
International Biological Engineering Meeting
Prof Guhan Jayaraman
Dept of Biotechnology, IIT Madras
Synthetic biological approaches for regulating metabolic pathway fluxes in
microbial factories
Abstract
Regulating metabolic flux imbalances is a key challenge in maximizing the yield of products from
microbial cell factories. Metabolic engineering strategies are mostly based on overexpression of
key pathway enzymes and gene knock-outs to reduce the flux towards competing pathways.
However, such knock-outs are permanent and have undesirable effects in terms of reducing
energy availability and biosynthetic precursors and often affect the overall metabolic
performance and cellular physiology. In cases where competing objectives of cell growth and
product formation are required, a more desirable strategy would be to appropriately regulate the
metabolic fluxes in these pathways at different phases of growth or product formation. This may
involve switching alternately between growth-promoting fluxes and product-formation fluxes.
Riboregulators hold great promise to achieve these objectives by enabling temporary pathway
switching between desired and competing metabolic pathways. This facilitates tuning gene
expression with physiological relevance and environmental signals. This talk will evaluate the
application of this platform for a model problem, viz. Hyaluronic Acid (HA) biosynthesis in
Lactococcus lactis. HA biosynthetic pathway fluxes compete with the major catabolic pathways
used for production of energy and biomass precurors. Insights from this work will enable the
establishment of similar platforms in cell factories used for biotechnological products.
16
International Biological Engineering Meeting
Dr. Syed Shams Yazdani,
Group Leader, Microbial Engineering
Coordinator, DBT-ICGEB Centre for Advanced
Bioenergy Research, ICGEB New Delhi
Microbial Platform for Production of Enzymes, Fuels and Chemicals
AbstractMicrobial platform is an economical and efficient way to produce low value-high volume molecules.
Some of these molecules are biofuels and biochemicals. Excessive use of fossil fuel has already done
significant damages to our environment, and much of these damages are irreversible in nature. Cleaner
fuels in the form of biofuels provide great hope to this problem. However, use of food related feedstock
to produce first generation biofuel seems completely unviable in the long run. Thus, scientists are
looking towards non-food part of plant, such as abundantly available lignocellulosic biomass, to produce
second generation biofuels. However, there are several challenges in extracting fermentable sugars
from lignocellulosic biomass and converting them into appropriate biofuel molecules. Synthetic biology
holds great promise to address these challenges.
One of the key issues in producing second generation biofuel is the low efficiency of enzymes to
hydrolyze cellulosic biomass into fermentable sugars. We had been working on both bacterial and fungal
enzymes to engineer them to improve the efficiency of hydrolysis. We also have been engineering the
genome of fungal host to produce and secrete copious amount of enzymes in the extracellular medium.
Our effort has led to constitution of highly efficient concoction of enzymes for biomass hydrolysis in
comparison to available commercial enzymes. Lignocellulosic biomass may consist of 30% of pentose
sugars, and therefore its effective fermentation will certainly have a positive impact on the economy of
biofuel production. The inability of traditional yeast, Saccharomyces cerevisiae, to ferment pentose
sugars present in biomass in significant quantity into ethanol is the major roadblocks in the
commercialization of lignocellulosic ethanol. E. coli is a robust host for various genetic manipulations
and has been used commonly for bioconversion of hexose and pentose sugars into valuable products.
One of the products that E. coli makes under fermentative condition is ethanol. However, availability of
limited reducing equivalence and generation of competing co-products undermine ethanol yield and
productivity. In our lab, we have constructed an E. coli strain to produce high yield of ethanol from
hexose and pentose sugars by modulating endogenous pathway. The engineering effort was further
extended to produce series of short chain and long chain alcohols to be used as advanced biofuels and
biochemicals.
17
International Biological Engineering Meeting
Dr. Shriram Ragavan
Evolva Biotech Chennai
Synthetic biology in the Consumed Ingredients space
Abstract
Solving the supply chain issues of 21st Century involves optimizing baker’s yeast to produce
ingredients that are commercially scalable & sustainable with reduced carbon footprint. The
technology makes flavours, fragrances, wellness ingredients, molecules for crop & animal
protection, healthy aquaculture, personal care, etc. This is achieved using modern tools (both
structure led and function led) that can allow selection of those yeast cells producing desirable
ingredients from a large background of number of cells which is then coupled with traditional
brewing & pathway optimization techniques. All these enable not only reproduction of ingredients
available in nature but also improvise their attributes tremendously – such as Stevia, saffron,
agarwood, etc. The talk would discuss more about how this is accomplished.
18
International Biological Engineering Meeting
Dr. Ravi Bhola
K & S Partners, Bangalore
Intellectual Property Rights (IPRs) related Issues in Biotechnology –
Opportunities and Challenges!
Abstract
Intellectual Property (IP) Laws provide for protection and enforcement of Inventions, including
Inventions in the area of biotechnology. Patent Laws in particular are relevant here. These laws
have evolved over a period of time to fall in sync with the developments in the field of
biotechnology. And, at the same time, these laws also provide for equity to ensure that monopoly
provided under patent laws is not abused. Also, interestingly, certain technical domains are kept
away from the realm of patents.
International treaties and collaboration on Patent laws among several countries have streamlined
patenting process in the area of biotechnology. This has made the entire procedure simpler and
cost effective.
At the same time, recent court judgements and guidelines for biotech-based inventions have
created new challenges for this Industry. Suddenly, many biotech inventions which were
patentable for past several decades have become non-patentable. This is true for several
countries including US and India.
While the biotech Industry was still trying to dabble these challenges, and the biodiversity law has
created newer challenges for biotech industry using biological resources from India.
Nonetheless, these challenges have also created new opportunities for biotech Industry. And,
these are the opportunities to move up the value chain and develop technological breakthroughs.
19
International Biological Engineering Meeting
Prof. D.Sundar
DuPont Young Professor
Associate Professor, Department of Biochemical
Engineering and Biotechnology, IIT Delhi, New Delhi
RISPcut: a novel tool for designing optimal sgRNAs for CRISPR/Cas9 based
experiment in human cells.
Abstract
The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have
broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other
genomic locations that differ from the intended target site by a few nucleotides, demonstrating
significant off-target activity. Previous studies have sought to predict CRISPR target sites and their
corresponding possible off-targets within a genome that are mainly based on sequence similarity
between CRISPR RNA and the genomic DNA. Moreover, the intricacies of RNA-DNA interaction
recently reported in literature, namely the mismatch, sgRNA and DNA bulges tolerance pattern
are unexplored for screening the off-targets. In this talk, I will discuss the CRISPcut tool that we
have developed to screen the off-targets using the above parameters and predicts the ideal
genomic target for CRISPRs in human cell lines. Predictions can be made for four different
protospacer adjacent motifs (PAM) reported in literature. Direct experimental measurement of
genome-wide DNA accessibility is incorporated that effectively restricts the prediction of CRISPR
targets to open chromatin. An option to predict target sites for paired CRISPR nickases is also
provided. The tool has been validated using a dataset of experimentally used sgRNA and their
identified off-targets.
20
International Biological Engineering Meeting
Sivaprakash Ramalingam
CSIR-Institute for Genomics
and Integrative Biology
Mathura Road, New Delhi 110025
Targeted Genome Engineering using Programmable Site-specific Nucleases
Abstract
Cells use the universal process of homologous recombination (HR) to maintain their genomic
integrity, particularly in the repair of a double-strand break (DSB), which otherwise would be
lethal. Repair of a DSB in a damaged chromosome by HR is a highly accurate form of repair, which
works via a copy and paste process, using the homologous DNA from the undamaged
chromosomal partner as a template. Gene targeting – the process of modifying a gene by HR –
uses an extra-chromosomal fragment of donor template DNA and invokes the cell’s HR for
sequence exchange. Gene targeting is not a very efficient process in mammalian cells; only ~1 in
10 6 cells provided with excess template sequence undergo the desired gene modification.
However, when a defined genomic DSB is introduced, HR is induced efficiently at that site, in a
large fraction of cells in a population. Thus, generation of specific, desired genomic DSB has been
the limiting step in HR technology for gene- modification. ZFNs and the more recent TALENs that
combine the non-specific cleavage domain (N) of FokI endonuclease with either zinc finger
proteins (ZFPs) or transcription activator-like effector (TALE) domains, respectively, and clustered
regularly interspaced palindromic repeats (CRISPR)/ (CRISPR associated protein 9) Cas9 system
offer a general means to cause a site-specific DSB to stimulate local HR. Further, I will discuss the
progress towards the applications of programmable site- specific nucleases (SSNs) in treating
human diseases and other biological applications in economically important plants.
21
International Biological Engineering Meeting
Dr. Shailja Singh
Associate Professor and Head
Signaling Biology, Special Centre for
Molecular Medicine, JNU, New Delhi
Genome editing approaches and applications in malaria
Abstract
In recent years, various technologies have been developed which allow dissecting the function
of the P. falciparum genome. Experimental genetic approaches provide powerful new tools to
study the function of Plasmodium proteins and their roles in biology and disease. Clinical
malaria is associated with the blood stage proliferation of parasite, in which merozoites invade
into and exit from host erythrocytes to continue the life cycle. Invasion by Plasmodium
merozoites is a complex process that requires multiple molecular interactions between the
invading parasite and target erythrocyte. Parasite proteins that mediate such interactions are
localized in membrane bound internal organelles at the apical end of merozoites called
micronemes and rhoptries. The timely secretion of microneme and rhoptry proteins to the
merozoite surface to allow receptor binding is a crucial step in the invasion process. In our
study, we demonstrate that exposure of Plasmodium falciparum merozoites to low potassium
ion concentrations as found in blood plasma provides the natural signal that triggers a rise in
intracellular calcium, which in turn triggers secretion of microneme proteins to the merozoite
surface. Subsequently, we also demonstrated the role of molecular players of calcium mediated
microneme discharge by using genome editing approaches. Moreover, in our recent studies we
demonstrated the role of molecular players such as CDPK and Perforin like proteins in the
process of merozoites egress from host erythrocytes.
22
International Biological Engineering Meeting
Dr. Sudha Rajamani
Assistant Professor and Head
Chemical Origins of Life group
IISER Pune, Maharashtra
What we have learnt from making protocells in the lab.
Abstract
Evolution of life on the early Earth is thought to have been contingent upon encapsulation of the
replicating genetic material in primitive cell membranes. Towards this extent, cutting edge work
is being carried out in a few labs in the world that has shed light on very interesting aspects that
might have facilitated the formation and sustenance of these protocells. I will give an overview
of these results and hope this information will enable the iBEM participants to think about ways
of making synthetic life using a bottom up approach.
23
International Biological Engineering Meeting
Prof. Cheemeng Tan
Department of Biomedical Engineering
University of California Davis,
One Shields Ave, Davis, CA 95616
Engineering programmable, dynamic materials using bio-inspired
communication
Abstract
Dynamic, bio-mimetic materials operate autonomously by sensing and adapting to their
surrounding environment. Engineered to respond to a multitude of extracellular signals (e.g.,
proteases, pH, light), these materials generally react by releasing small molecules into their
surroundings. While these state-of-the-art engineered materials can sense their environment,
two-way communications, like those prevalent in natural systems, remain difficult due to the
myriad of interactions inherent in cell-like environments. Here, we exploit synthetic biology
approaches to develop the first modular dynamic material that can perform two-way
communications with natural cells. The dynamic material, also called artificial cell, mimics
several key properties of natural cells, including synthetic membranes, molecular transport,
gene expression, and cell-cell communication. They are assembled from the bottom up using
lipids, DNA, protein synthesis machineries, NTP, amino acids, and various accessory proteins and
chemicals. We demonstrate cell-cell communication under three scenarios: artificial cells
signaling bacteria, bacteria signaling artificial cells, and artificial cells signaling each other. To
guide the control of the systems, mathematical models are developed to describe the genetic
circuitry of each system as well as the spatial distribution of the transmitters, receivers, and the
diffusing signal molecules. Based on the basic modules, we further implement artificial cells that
synthesize an antimicrobial peptide upon detecting the presence of bacteria. The antimicrobial
peptide inhibits bacterial growth, providing an alternative strategy for the treatment of
antibiotic-resistant bacteria. The development of communication between artificial cells and
living cells provides further insight into cell-cell communication in general, opens the door for
new therapeutic uses of artificial cells, and expands the capacity of artificial systems to mimic
living ones.
24
International Biological Engineering Meeting
Dr. Sangram Bagh
Associate Professor
Biophysics and Structural Genomics Division
Saha Institute of Nuclear Physics, Kolkata
Towards a synthetic biology platform for cellular robotics and space
bioengineering
Abstract
The molecular connectivity between genes and proteins inside a cell shows a good degree of
resemblance with complex electrical circuits. This inspires the possibility of engineering a cell
similar to an engineering device. Synthetic biology is an emerging field of bioengineering, where
scientist use electrical and computer engineering principle to re-program cellular function for
creating new cellular function with a potential to solve next generation challenges in medicine,
energy, and space travel. In this talk, we discuss our synthetic biology efforts to build a
technology platform for cellular computation and robotics and systems biology effort to
understand the effect of zero gravity on human and bacterial cells during space travel.
25
International Biological Engineering Meeting
P. Annamalai
Aura Biotechnologies
Chennai
Practical approaches in drug development using synthetic biology tools
Abstract
Synthetic biology is the effort to apply the concepts of engineering to biological systems with
the aim to create powerful work horses (organisms) with new promising properties. These
engineered organisms might bring the desirable biosynthetic capabilities, act as producer or
help us to understand the complex pathways and its networks of living systems. Synthetic
biology approaches has the potential to support the discovery and production of
pharmaceutically important compounds. This can also improve the existing process by which the
cost of manufacturing can be reduced. New sources of bioactive molecules can be generated in
the form of genetically encoded small molecule libraries. New biosynthetic pathways may be
designed by combining together enzymes with desired activities, and genetic code expansion
can be used to introduce new functionalities into peptides and proteins to increase their
chemical scope and biological stability. In this presentation, we have outlined our approaches
toward utilizing the synthetic biology tools to enhance the production of active pharmaceuticals
that are complex in nature with high therapeutic values. We bring together the metabolic
engineering and chemoenzymatic synthesis of natural products that might serve as parts in a
synthetic biology approach to pharmaceutical biotechnology.
26
International Biological Engineering Meeting
Ajay Kumar, Ph D
Product Specialist III
Thermo Fisher
CRISPR/Cas9 based genome editing tool box from ThermoFisher
Abstract
Today is the era of Genome Editing and CRISPR is more of a misnomer for Genome Editing. The
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas)
system is the latest addition to the genome editing toolbox, offering a simple, rapid, and
efficient solution. The CRISPR/Cas system is a prokaryotic adaptive immune system that uses an
RNA-guided DNA nuclease to silence viral nucleic acids. The type II CRISPR/Cas system from the
bacterium Streptococcus pyogenes has been modified to enable editing of mammalian
genomes. As a simple two-component system composed of Cas9 protein and a noncoding guide
RNA (gRNA), the engineered type II CRISPR/Cas system can be utilized to cleave genomic DNA at
a predefined target sequence of interest. The gRNA has two molecular components, a target
complementary CRISPR RNA (crRNA), and an auxiliary trans-activating crRNA (tracrRNA). The
gRNA unit guides the Cas9 nuclease to a specific genomic locus and the Cas9 protein induces a
double- strand break (DSB) at the specific genomic target sequence. Following CRISPR/ Cas9induced DNA cleavage, the DSB can be repaired by the cellular repair machinery using either
non-homologous end joining (NHEJ) or a homology-directed repair mechanism. Discover the
only complete genome editing solution designed to expedite your research and developed in
house at our Carslbad Labs which is easy-to- use, optimized, and validated spanning the entire
cell engineering workflow, making genome editing accessible to anyone at any level. We’re
continually expanding our suite of genome editing products to span the entire cell engineering
workflow, from reagents for cell culture, transfection, and sample preparation to kits for
genome modification and detection and analysis of known genetic variants. We offer our stateof- the-art online Invitrogen™ CRISPR Search and Design Tool along with Invitrogen™ CRISPRCas9 editing products in four formats: an all-in- one expression vector, Cas9 mRNA, Cas9
protein, and CRISPR library services. These gene editing solutions are paired with optimal cell
culture reagents, delivery methods, and analysis tools, based on your application and cell type.
27
International Biological Engineering Meeting
Dr. Vikram Singh
Assistant Professor
Centre for Computational Biology and Bioinformatics,
Central University of Himachal Pradesh, Dharamshala
Computational Design of Synthetic Gene Circuits
Abstract
One of the major goals of synthetic biology is to engineer gene circuits that can perform userdefined tasks in a predictable and reliable manner. Computational modeling of genetic circuits
provides first-hand insights into their topology and parameter space where they may carry out
the desired functions. In this talk, we will briefly overview the mathematical and chemical
kinetic concepts used in designing of genetic circuits. We will then examine the distinct
dynamical behaviours of simple gene networks, starting from the case of a single gene’s selfregulation to the circuits of few interacting genes. Design and dynamics of two model synthetic
genetic circuits – (i) a circuit consisting of two mutually repressing genes (genetic toggle switch),
and (ii) a circuit of three mutually repressing genes (repressilator) will be explained and diverse
behaviours emerging due to alteration in various parameters related to binding and unbinding
of repressors, rates of transcription and translation etc. will be discussed. Students will be
encouraged to design and simulate at least one genetic circuit using the softwares XPP-Aut and
TinkerCell. Those having knowledge of C or PERL programming languages are welcome to
discuss about writing the working codes for such simulations. Towards the end of this talk we
will review the recent advancements in automated design of synthetic genetic circuits.
28
International Biological Engineering Meeting
Dr. Balaji Prakash
Senior Principal Scientist,
Department of Molecular Nutrition,
CSIR-Central Food Technological Research
Institute, Mysuru, Karnataka
Designer Proteins for the synthetic cell
Abstract
A major fascination in my laboratory has been ‘enzymes’. We wish to understand how they
function at the atomic level – so that, in the long term, we develop the ability to tinker these
and tailor new functions into them. This then calls for a detailed understanding of how such
molecules work. For the last 15 years my laboratory has focused on understanding catalysis and
structure function relationships of a large set of enzymes with the aim of designing new
functions or develop new molecules for e.g. designing anti-bacterial activity. From the diverse
enzymes we studied, we realize how small variations bring about different specificities in the
same class of enzymes. To emphasize this, I will present case studies of (1) GTPases that are
critical for ‘ribosome biogenesis (Mishra et.al. 2005, Tomar et.al. 2009, Anand et al, 2013), (2)
Rel - that mediates stringent response in bacteria (Mathew et.al. 2009) (3) GlmU – an enzyme
important for bacterial cell wall formation (Jagtap et.al. 2013) and (4) bacterial serine proteases
that are a part of bacterial defense. Armed with this understanding, we wish to ask ‘can we
make designer proteins, suited for a context?’ and would these find applications in the
hypothetical ‘synthetic cell’? I shall discuss some of these thoughts at this meeting.
29
International Biological Engineering Meeting
Arun Shukla
Department of Biological Science and
Bioengineering, IIT Kanpur
Synthetic antibodies for investigating structure and function of G ProteinCoupled Receptors
Abstract
G Protein-Coupled Receptors (GPCRs) represent the largest class of cell surface receptors in the
human genome. GPCRs are involved in almost every cellular and physiological process in our
body, and they constitute a major class of drug targets for a range of human disorders. We have
utilized a phage display based synthetic antibody platform to generate high-affinity antibody
fragments against GPCRs and their signaling effectors. Using these antibody fragments, we have
deduced novel structural information on receptor-effector coupling, and corresponding signaling
outcomes. We are also employing these antibodies in cellular context to image ligand induced
GPCR activation and trafficking, as well as to rewire GPCR signaling with potential therapeutic
implications.
30
International Biological Engineering Meeting
Ranjita Ghosh Moulick,
SPS,JNU.
Biomimetic membrane- a synthetic platform for studying cell signalling
Abstract
Biological membrane acts as a protective layer of cells and is responsible for several properties. It
consists of two opposed leaflet of lipid molecules. These lipid molecules are the basic component
of the biological membrane. Interestingly such lipid molecules can rearrange themselves on a
solid support and form artificial lipid bilayer. Artificially prepared lipid membrane resembles
biological membrane structurally but needs biological component such as protein to become
identical functionally. Because biological membrane contains protein or sugar molecules for its
functional activity. When protein is embedded into the system, the synthetic membrane is known
as biomimetic membrane. It has an excellent potential to create a natural environment and can
easily replace an interacting cell in cell-cell contact.
In our current work a fusion protein (containing an immunoglobulin G (IgG) – domain) is
embedded into the lipid vesicles using surfactant. The newly proposed method to anchor proteins
into a synthetic membrane does not require complex synthesis. Using this method a neuronal
adhesion protein, Ephrin A5-Fc is homogeneously anchored to the membrane. Ephrin A5 is a
ligand that binds to the Eph receptors of cortical neurons and leads to diverse biological
responses. The biomimetic membrane prepared by this approach is characterized by several
techniques including Fluorescence Recovery After Photobleaching (FRAP) and Quartz crystal
Microbalance (Q-CMD). Such a synthetic system not only enables culturing primary neurons and
testing cell surface-receptor ligand interactions in cell-cell contacts but also facilitates neuronal
maturation shown by early electrophysiological activity. Finally this synthetic membrane is
patterned in the micro-nano range and cells are cultured on them. Live cell Imaging is done to find
out how the cells interact with such confined membrane.
31
International Biological Engineering Meeting
Dr. Vijai Singh
Assistant Professor and Head,
Synthetic Biology Laboratory
School of Biological Sciences and Biotechnology
IIAR, Gandhinagar
Exploring the potential of RNA-guided CRISPR interference for targeted gene
repression in Escherichia coli
Vijai Singh1,2 *, Manish Kushwaha3, Alfonso Jaramillo2,3
1
Synthetic Biology Laboratory, Department of Microbiology, School of Biological Sciences and Biotechnology,
Institute of Advanced Research, Koba Institutional Area, Gandhinagar 382007, India, e:
[email protected] / [email protected] 2 Institute of Systems and Synthetic Biology, Genopole, CNRS,
UEVE, Université Paris-Saclay, Évry, France 3 Warwick Integrative Synthetic Biology Centre (WISB) and School
of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated
proteins (Cas) are an RNA-mediated adaptive immune system of bacteria and archaea that protects
from phages and plasmids. The Type II CRISPR-Cas system utilizes RNA-guided Cas9 endonuclease
which is currently used as a key technology for targeted genome editing in a wide range of
organisms and cell types. We have repurposed CRISPR-Cas9 system which is commonly called
CRISPR interference (CRISPRi) and it was established for transcriptional interference through the
gene silencing. In the present study, we have targeted the sequences close to promoter. We have
constructed a pSEVA pSEVA471_T7_GFP_Pconst_dCas9 plasmid where the T7 promoter has
cognate sequences for small guide RNA (sgRNA) binding. We have also constructed a
pSEVA261+M13+sgRNA where sgRNA was expressed under the control of a constitutive promoter.
We have co-transformed both the plasmid in Escherichia coli BL21[DE3] strain and we optimized
the growth condition and toxicity. We have induced cells with 25 µM IPTG in order to repress the
GFP. We have designed and constructed a set of 20 sgRNAs and tested. Out of 20 sgRNAs, we have
identified 12 sgRNAs that showed the strong repression and also orthogonal to each other. The
CRISPRi could be used as a simple and versatile tool for RNA-guided gene repression in E. coli. This
approach can be further expanded into many organisms towards biomedical, therapeutic,
industrial, and biotechnological applications.
32
International Biological Engineering Meeting
Sivaprakash Ramalingam
CSIR-Institute for Genomics and Integrative Biology,
Mathura Road, New Delhi 110025
Targeted Genome Engineering using Programmable Site-specific Nucleases
Abstract
Cells use the universal process of homologous recombination (HR) to maintain their genomic
integrity, particularly in the repair of a double-strand break (DSB), which otherwise would be
lethal. Repair of a DSB in a damaged chromosome by HR is a highly accurate form of repair, which
works via a copy and paste process, using the homologous DNA from the undamaged
chromosomal partner as a template. Gene targeting – the process of modifying a gene by HR –
uses an extra-chromosomal fragment of donor template DNA and invokes the cell’s HR for
sequence exchange. Gene targeting is not a very efficient process in mammalian cells; only ~1 in
106 cells provided with excess template sequence undergo the desired gene modification.
However, when a defined genomic DSB is introduced, HR is induced efficiently at that site, in a
large fraction of cells in a population. Thus, generation of specific, desired genomic DSB has been
the limiting step in HR technology for gene-modification. ZFNs and the more recent TALENs that
combine the non-specific cleavage domain (N) of FokI endonuclease with either zinc finger
proteins (ZFPs) or transcription activator-like effector (TALE) domains, respectively, and clustered
regularly interspaced palindromic repeats (CRISPR)/ (CRISPR associated protein 9) Cas9 system
offer a general means to cause a site-specific DSB to stimulate local HR. Further, I will discuss the
progress towards the applications of programmable site-specific nucleases (SSNs) in treating
human diseases and other biological applications in economically important plants.
33
International Biological Engineering Meeting
Shaikh Z. Ahammad
Assistant Professor
Department of Biochemical Engineering
and Biotechnology, IIT Delhi, New Delhi
iGEM IIT Delhi – Opportunity and Experience
Abstract
The International Genetically Engineered Machines, or iGEM, is a competition held annually at the
Massachusetts Institute of Technology (MIT), Boston, USA. The Team IIT Delhi has been
participating in the competition for the past 4 years, being the only team Indian team in the 2013
and 2014 editions of iGEM, winning bronze medals in the Asian Jamboree 2013 and the giant
jamboree 2014. In 2015, we were one of five teams from the country, and mentored IIT
Kharagpur, who participated for the first time. We won a bronze medal for our work at the giant
jamboree 2015. In 2016, there were seven teams including ourselves. We won a silver medal in
this edition of the competition
For iGEM 2015, the team worked on the Idea of Air pollution and created a new species of
genetically engineered E.coli bacteria, called “Eco.coli”, for reducing polluting gases (oxides of
nitrogen and sulphur) and particulate matter from the air. We developed a prototype technology
for diesel generators or other polluting exhaust, taking in polluted exhaust and processing it to
give out clean air as the output.
For iGEM 2016, we designed reconfigurable circuits in E.coli using a combination of genetic logic
gates, analogous to electrical circuits. We engineered and created a system that could work as a
bacterial oscillator, and a toggle switch, with a temperature dependent switch between the two
states. Further, we also created a system which was an optogenetic (light based) switch that could
modulate the frequency of the oscillations. These reconfigurable circuits offer field
programmability in these synthetically constructed systems, and confer the ability of multiple
behaviours to be exhibited by the same system. Further, light dependent switching is non
invasive, highly selective, and works without delay that is usually involved in chemical inducers.
Team IIT Delhi has had a colourful experience in the iGEM competition, with medals being
awarded at such a large stage, and we are proud to have represented the team and the country,
and led the synthetic biology revolution in the country. We hope to be the frontrunners in the
field for years to come. Our warmest thanks to the Dept of Biotechnology, Government of India
for their support over the past two years. Our work and idea for 2015 was also appreciated by the
Chief Minister of Delhi, Mr. Arvind Kejriwal, who saw the initiative as the first step towards the
cleaning of Delhi and making the air safe and unpolluted, which is a major concern in the capital
these days.
34
International Biological Engineering Meeting
Sangita Kasture
Scientist ‘E’ / Joint Director
Department of Biotechnology
Ministry of Science & Technology
Lodhi Road, New Delhi
DBT Initiatives in Synthetic Biology
Abstract
Synthetic Biology is the science of designing and building biological components towards practical
applications. In the recent years, it has led to tremendous excitement and investment leading to
great ideas and applications. Many leading universities and industries from US and Europe have
come together in a big way to develop the foundation and generate biological devices and circuits
towards applications in health, food, energy, environment and so on.
Department of Biotechnology (DBT), Ministry of Science and Technology, Govt. of India has been
keen to promote and support this emerging field of synthetic Biology in many ways. A
brainstorming meeting among experts was organized at NII in Oct 2013. Many important
recommendations were provided. Also an Indo-US Workshop in System and Synthetic Biology
was organized in collaboration with JNU in Nov 2014. These meetings have helped in
identification of strategic goals in research, training and awareness towards continued Innovation
in this exciting field.
India is rich in biodiversity and hence has rapidly evolved and adopted stringent guidelines to
conserve, sustain and ensure fair and equitable use of her rich biological resources. The
establishment of recent Convention on Biological Diversity (CBD) is a global initiative and one of
the very appropriate approach is about ethical use of biotechnology in all its variants. DBT
through consultative process has provided views on the Report of Ad Hoc Technical Expert Group
(AHTEG) on Synthetic Biology .
Recently, to crystallize the emerging synthetic biology community in India and create a prominent
conclave of interaction,in 2015 DBT announced a formal Indian Biological Engineering
Competition (iBEC) in partnership with JNU with iGEM (International Genetically Engineering
Machines) as its main module. The idea was to create a stable and long term platform for
developing an Indian standard parts inventory, develop biological standards and applications,
encouraging students and scientists to compete globally and introduce a new generation of
students to synthetic biology and act as a feeder for future iGEMs.
Over last two years, India has seen several innovative participants earn their laurels at the iGEM
awards. The selected teams from IIT /IISER and other Universities have pursued their research and
travel with support from Department of Biotechnology (DBT) last two years. Recently 5 best
teams got selected for funding support to participate in iGEM 2017.
DBT is looking forward to greater participation by scientific community and brilliant students, in
synthetic biology /biological engineering R&D generating novel ideas for useful applications in
various fields.
35
International Biological Engineering Meeting
Prof. Pawan K. Dhar
Head, Synthetic Biology Lab
School of Biotechnology, JNU, New Delhi
iBEC: a new Indian Biological Engineering Competition.
Abstract
iBEC [Indian Biological Engineering Competition] is a novel initiative by the Indian community of
students and scientists to create a registry of standard biological components leading to the
assembly of higher order structures towards useful social outcomes. In the iBEM 1.0, the
fundamentals and scope of the iBEC initiative will be presented and discussed. The idea is to
involve the community in building parameters of future engagement, from responsible
innovation, applications and funding perspectives. The iBEC will be an annual scientific event
starting March 2018. The 2017 primer, will be a curtain raiser, involving a panel of experts and
participants. The expected outcome of this session will be a set of guidelines for the future
engagement of the community.
36
POSTER ABSTRACTS
37
International Biological Engineering Meeting
P01
Communicating Science for all: Simplifying Synthetic biology and Genome
Editing
Susrita Samantaray
KIIT School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
Biological engineering is an interdisciplinary approach to integrate the technology of engineering
into the world of biology and design them for relevant applications. The theory and research in
the scientific world give us the data about the process that goes on within the cell. But we are
unable to visualize the complex functioning of the cells. The innovative emerging technologies in
science can be simplified and better expressed through the creation of art and colors. Through the
diagrammatic representation, I want to illustrate the challenging complexity of cell and examine it
from different angles. Science and art are two different potential fields co-existing naturally. My
focus is to bridge the gap and build a definite bond between both the fields. The overlap of
science and art can leave an impactful image on people about how the cells work and how the
process continues. This collaboration can enable us to analyze the minutiae of the biological world
and gather up creative ideas into science. Art makes the scientific discovery more compelling and
makes the complex steps actionable. The sci-art is also essential for people to get a basic idea
about the new rising techniques in the field of genetics and molecular biology. This convergence
between biology, art and engineering can indeed help in better understanding and
communication of science.
38
International Biological Engineering Meeting
P02
Designing Synthetic Photoreceptor: Lessons from Sequence and Structural
Constraints
Anwesha Deb and Devrani Mitra
Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata-700073
Optogenetics confers light sensitivity to genetically encoded molecule, to control its
down(up)stream activity, thus regulating different signalling pathways at spatio-temporal
precision. The temporal control can be achieved by tailoring the excited state (light state)
lifetime of a photosensor. Further, understanding the role of amino acid residues, playing
significant role in light-dark transition, is essential for optogenetic designs. However, the
structural differences between light and dark-state photoreceptors are subtle. Therefore, a
differential network approach was proposed recently, which not only predicted important
residues but also could highlight their functional significance. We are interested in designing
optogenetic scaffold by tweaking the predicted residues and thereby controlling the excited
state of a photosensor, having Light-Oxygen-Voltage (LOV) sensor in focus. LOV, bearing the
signature PAS (Per-ARNT-Sim) superfamily motif, is ubiquitous throughout different kingdoms
and performs wide variety of biological functions upon sensing blue light. Aureochrome1, a LOV
containing transcription factor is of specific interest because of its unique domain arrangement
with an N-terminal effector (bZIP) and C-terminal LOV sensor domain, promoting upstream
signalling. Therefore, precise manipulation of LOV signalling state lifetime combined with
rational connection of sensor-effector, can lead to successful design of synthetic photoreceptors
to ultimately control transcription factor network using blue light. Our approach not only aims
towards selecting a proper optogenetic scaffold but also to design a synthetic photoreceptor,
having accurate control over its down(up)stream signalling pathways.
39
International Biological Engineering Meeting
P03
Role of cAMP effector EPAC in Regulating Plasmodium falciparum
Merozoite Invasion of Human Erythrocytes
Juveria Khan1, Kalaiarasan Ponnusamy1, Pawan K. Dhar1, Shailja Singh2
1School
of Biotechnology, Jawaharlal Nehru University, New Delhi
2Special
Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi
All pathogenesis and death associated with Plasmodium falciparum malaria is due to parasiteinfected erythrocytes. Invasion of erythrocytes by P. falciparum merozoites requires specific
interactions between host receptors and parasite ligands that are localized in apical organelles
called micronemes. Previously, we have identified cAMP as a key regulator that triggers the
timely secretion of microneme proteins enabling receptor-engagement and invasion. We
demonstrated that exposure of merozoites to a low K+ environment typical of blood plasma
activates a bicarbonate-sensitive cytoplasmic adenylyl cyclase to raise cytosolic cAMP levels and
activate protein kinase A, which regulates microneme secretion. One of the effector molecules
of cAMP is EPAC (exchange protein activated by cAMP). EPAC has shown to regulate several
processes in different systems. We also showed that cAMP regulates merozoite cytosolic Ca2+
levels via induction of an EPAC pathway and demonstrate that increases in both cAMP and Ca2+
are essential for triggering microneme secretion. In the present study, we found that antagonist
of EPAC inhibit parasite growth and microneme discharge. Furthermore, we intend to
investigate specific role of EPAC by genetic manipulation and by designing parasite specific small
molecule antagonist. Identification of the different elements in the cAMP-dependent signaling
pathways that regulate microneme secretion during invasion will provide novel targets to inhibit
blood stage parasite growth and prevent malaria.
40
International Biological Engineering Meeting
P04
Novel micropeptides from non-coding genome - Promising synthetic
peptide drug candidates against Alzheimer's Disease
Navya Raj1, Sidhi P. R.1, Achuthsankar S. Nair1 and Pawan K. Dhar2
1Department
of Computational Biology and Bioinformatics, University of Kerala,
Thiruvananthapuram
2School
of Biotechnology, Jawaharlal Nehru University, New Delhi, India
The non-coding genome is increasingly becoming the preferred hub for the search of novel
functional molecules. Apart from uncovering their fundamental biological role, the scientific
community is also working towards identifying possible therapeutic and industrial applications.
We adopted a ‘junkomics’ approach to generate novel micropeptides from the so-called junk
DNA. The 2000+ intergenic sequences of Escherichia coli genome were computationally
screened for the presence of small open reading frames (sORFs) that can code for short, nonclassical peptides defined as micropeptides. The sORFs were translated and each frame was
subjected to short peptide- specific BLAST search against the known protein databases. An insilico library of 1558 novel micropeptides with no-known similarity was generated and the
physico-chemical properties of the molecules were analysed. In a drug designing perspective,
the micropeptides were further studied for their intestinal stability and toxicity, the major
challenges faced by synthetic peptide drugs. Out of 1558 micropeptides, 36 were found to be
stable and non-toxic. A case study was performed using the drug target Beta secretase 1 (BACE
1) involved in Alzheimer's Disease (AD), to identify the most suitable candidate molecules for
synthetic peptide drug development. The possible micropeptide interactions against BACE 1
protein was studied using peptide-protein docking. Five micropeptides with highest inhibitory
potential against BACE 1 were selected and the stability of the best docked complex was
confirmed by molecular dynamic simulation study. Experimental validation of the lead
micropeptides has just been initiated to confirm their predicted properties in vitro and in vivo.
41
International Biological Engineering Meeting
P05
The Virtual Red Blood Cell Pathway Simulations and Its Application
Archita Biswas, Kalaiarasan Ponnusamy ,Girija Kaushal, Pawan K Dhar
Synthetic Biology Group, School of Biotechnology, Jawaharlal Nehru University, New
Delhi
The ultimate work of blood is to circulate and transport nutrients, hormones and other signaling
molecules, oxygen to various organs. In additions to delivering molecular cargo, the Red Blood
Cells also reclaim wastes for downstream processing at spleen. In the past, scientists have made
attempts to capture network transactions of the RBC. However, a lot more needs to be done
particularly in the space of model quantitative, completion and accuracy. The RBC model
comprises of four pathways i.e. Glycolysis, Pentose Phosphate Pathway, Glutathione pathway
and Purine salvage pathway. A wild type virtual stochastic RBC model was developed and
extended in the direction of pyruvate kinase deficiency and the Aldolase A deficiency. As the
first step, pathways were retrieved from the KEGG pathways database and modeled based on
stochastic values retrieved from the literature. The dynamic stochastic equations were
embedded through C programming and pathway behavior difference between wild type and
enzyme deficiency conditions was studied. By measuring the Changes in the concentration of
the species from neighboring reactions we propose four biomarkers for two mutations. The
gene knock out and gene knock down analyses identified the biomarkers. The PPI model is
constructed to compare the knock out and wild type model model by using String and Network
analyzer. Based on the simulation results, we propose novel biomarkers which are 2phosphoglycerate, phosphoenol pyruvate for mutation one that is pyruvate kinase deficiency
and fructose-1-6-bisphosphate, xylulose-5-phosphate for mutation two which is aldolase A
deficiency for experimental validation.
42
International Biological Engineering Meeting
P06
Investigations into the Spectral Analysis of Retroactivity Phenomenon
Silpa Bhaskaran, Sajil C K, Achuthsankar S Nair
Department of Computational Biology and Bioinformatics, University of Kerala,
Trivandrum, India.
The undesired signals transmitted by the downstream modules in a synthetic biology network
due to its interconnection with the upstream modules, remains as a challenge yet to be
effectively addressed. The effect generated by these signals, called retroactivity, is crucial as it
challenges the reliability and predictability of synthetic biology devices. Comparing with the
loading effect in electrical, mechanical or hydraulic systems, retroactivity is also being viewed
and explored using the common engineering approaches. We propose spectral analysis as a tool
to explore this unwanted phenomenon in synthetic biology networks and presents results of
preliminary investigations on spectral analysis of signals that generate retroactive effect. We
select the system constituted by an input protein, which phosphorylates another protein to
become the output, which further binds to another module in the downstream. It was observed
that the dynamics of both the input and output has a significant difference when connected to
the downstream and when it is not connected. We spectrally decompose the input-output
signals and select five prominent components that contribute a significant modification to the
original signals. We report the dynamics of the system and analyse how it varies for each
spectral component. This provides insights into the role of each component in generating the
retroactive effect and gives perceptions about the underlying biological mechanisms that can
mitigate retroactivity.
43
International Biological Engineering Meeting
P07
Synthetic microRNA on its biogenesis processing unit regulation in human
Kalaiarasan Ponnusamy, Pawan K Dhar
Synthetic Biology Group, School of Biotechnology, Jawaharlal Nehru University, New
Delhi, India
MicroRNAs (miRNA), ~22 nucleotide molecules that pairs to mRNAs to regulate the expression
of various disease related genes. Recent studies improved the knowledge on RNA interferences,
but understanding the dynamics of multiple microRNAs is still limited. By studying the regulation
of microRNA biogenesis pathway with help of synthetic microRNA will provide significant
develop in dynamics of microRNAs.
We developed a model with microRNA biogenesis proteins with its regulators. The model
captures the quantitative relationship between miRNA and target gene expression levels as a
function of parameters, including seed match, evolutionary conservation, target-sites,
transcriptional regulation and mRNA half-life. We linked the synthetic microRNA with the genes
encoding regulator proteins using computational predictions. The synthetic circuits were further
incorporated with protein-protein interaction switches. The study designed a disease model on
dynamic of the proteins with its concentration and compared with control.
Our results highlight the importance of methods for guiding microRNA dynamics and its
influence in biogenesis proteins with the help of synthetic microRNA.
44
International Biological Engineering Meeting
P08
ORGANIC CONTACT LENS FOR 20/4 VISUAL ACUITY
Rajesh Babu. A, Umesh.P, Achuthsankar S. Nair
Dept. of Computational Biology and Bioinformatics, University of Kerala, India
Eagles are the one of few species of birds that has sharp vision 4 to 8 times than average human.
It is capable of watching its prey from 3.2km in the flight. It can even locate fish below water.
Eagle eye has multi-layered retina structure the reason behind the sharp vision. When light falls
on the retina top layer which contains photoreceptor proteins called opn5 which belong to opsin
family and has pigment called retinal the light gets transduced into second layer fovea which has
rods and cones a high-density photoreceptor region with proteins like rhodopsin and photopsins
respectively which are responsible for light reception and colour vision respectively. cone cells
are tetra chromatic which has capacity to detect different colours. The proteins opsin, rhodopsin
and protopsin acts as photoreceptors and high density of the receptors in con cells play a major
role in eagle’s sharp vision and magnifying capacity than humans.
The idea of synthetic biology can pave way for organic contact lenses that can attain the visual
acuity of 20/4 by engineering these proteins opn5, photopsin and rhodopsin at high volumes
and convert them into contact lens which can be sandwich structure here and it can be treated
as internal and external layer and opn5 and phot opsin proteins can be used in their
manufacture whose function can be like eagle eye’s which is sharper than human. The reindeer
which is the only mammal which has ultra-violet sensitive eye sight. The chimeric gene formed
when combined with the protein sequence of eagle eye both traits can be inherited and a
powerful contact lens that can magnify, look in the water and observe ultraviolent light
wavelength and the objects that reflect the ultraviolet light can be visualized. Normal human
visual acuity is 20/20 but with this chimeric gene translated fusion protein visual acuity of 20/4
can be attained. Also, camera lens can be manufactured which can attain high resolution
imaging capacity even at far distances
45
International Biological Engineering Meeting
P09
Exploiting Fatty Acid Metabolic Pathway for Production of Short Chain
Fatty Acids in E. coli
Kamran Jawed 1, Anu J Mattam1, Zia Fatma1, Saima Wajid3, Malik Z. Abdin3 and Syed S
Yazdani1,2
1
Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology,
Aruna Asaf Ali Marg, New Delhi-110067 (India) (E-mail: [email protected])
2
DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic
Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067 (India);
3
Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi – 110062 (India)
Worldwide demand of sustainable fuels and chemicals has encouraged researchers for
microbial synthesis of short chain fatty acids (SCFAs), such as such as butyric acid (C4), as
they are attractive precursors to replace petroleum-based fuels and chemicals. In this
study, we explore the fatty acid metabolism for production of butyric acid in E. coli with
the help of three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from
Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron. We found that
E. coli strain transformed with gene for TesBT and grown in presence of 8 g/L glucose
produced maximum butyric acid titer at 1.46 g/L, followed by that of TesBF at 0.85 g/L
and TesAT at 0.12 g/L, showing that these thioesterases were efficiently converting
short chain fatty acyl-ACP into corresponding acid. Depending upon the plasmid copy
number and strain genotype, the titer of butyric acid varied significantly. Deletion of
genes involved in initiating the fatty acid degradation such as fatty acyl-CoA synthetase
and acyl-CoA dehydrogenase and overexpression of FadR, which is a dual transcriptional
regulator, exerts negative control over fatty acid degradation pathway, reduced up to
30% of butyric acid titer. This observation suggested that β-oxidation pathway is
working synergistically with fatty acid synthesis pathway in production of butyric acid.
Moreover, accelerating the fatty acid elongation cycle by overexpressing acetyl-CoA
carboxyltransferase (Acc) and 3-hydroxy-acyl-ACP dehydratase (FabZ) or by deleting
FabR, the transcription suppressor of elongation, did not improve the butyric acid titer,
rather favored the long chain fatty acid production. Use of chemical inhibitor cerulenin,
which limits the fatty acid elongation cycle, increased the butyric acid titer by 1.7-fold in
case of TesBF, while it had adverse impact in case of TesBT. In vitro enzyme assay
showed that cerulenin also inhibited the short chain specific thioesterases, though
inhibitory concentration varied according to the type of thioesterase used. Further
process optimization followed by fed-batch cultivation under phosphorous limited
condition led to production of 14.3 g/L butyric acid and 17.5 g/L total free fatty acid at
28% of theoretical yield. The strategy used in this study resulted in highest reported
titers of butyric acid and FFAs in engineered E. coli and could be used to replace the
traditional chemical methods for production of butyric acid.
46
International Biological Engineering Meeting
P10
A peptidomimetic approach to identify the therapeutic potential of noncoding peptides.
Sidhi P. R1 Navya Raj1, Achuthsankar S. Nair1 and Pawan K. Dhar1,2
1Centre
for Systems and Synthetic Biology, Department of Computational Biology &
Bioinformatics, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala, India.
2School
of Biotechnology, Jawaharlal Nehru University, New Delhi, India
Can we make functional peptides from Non-coding regions? The major part of genome in most
organisms doesn’t encode proteins. Recent studies have demonstrated that many non-coding
regions once considered as junk are in fact being transcribed to functional molecules involved in
various biological processes such as differentiation, embryogenesis, cell signaling and regulation
of innate immunity. It is possible that many such sequence regions might have been missed out
during the annotation processes. In the present study, a peptidomimetic approach was used to
identify novel therapeutic peptide of junk origin. Intergenic region of Saccharomyces cerevisiae
was used in the study. Sequence and structural based studies was performed with non-coding
peptides to check similarity with known therapeutic peptides that are used for the treatment of
diseases such as cancer, diabetics and osteoporosis. Peptide derived from the intergenic regions
was found to have sequence and structural similarity with a peptide that are used for the
treatment of cancer. Protein interaction analysis reveals that non-coding peptide has
comparable binding mode and affinity as that of the existing peptide and may act as an analog
to the existing therapeutic peptide. The present work demonstrated that non-coding regions has
untapped potential of making useful proteins and peptides which would have a wide range of
applications including protein engineering and therapeutics.
47
International Biological Engineering Meeting
P11
LAB-ON-A-CHIP TECHNOLOGY: AN INNOVATIVE APPROACH FOR
BIOLOGICAL ENGINEERING
M. Mohana1, V. Murugan2, K. Balamurugan1, 2, V. Ravichandran2
1Department
of Biotechnology, Alagappa University, Karaikudi- 630 003, Tamil Nadu,
India;
2National Institute of Pharmaceutical Education and Research (NIPER), Kolkata-700 032,
West Bengal, India
Microfluidics is a multi-disciplinary field exploring the behaviour and the manipulation of minute
quantity of fluid with the characteristic range from nanolitres to hundreds of microliters.
Microfluidics possess great promise to revolutionize multiple areas of biological engineering,
such as single-cell analysis, environmental screening, tissue engineering, and point-of-care
diagnostics. Tissue engineering could benefit significantly from microfluidic technology, given
that the biomaterials and biocompatible processes should be appropriately interfaced with
conventional microfabrication techniques. To develop a functional tissue or organ, it is
necessary to culture or grow cells in three dimensions. We report a couple of microfluidic
platform designed and developed for synthesizing a porous micro fibrous scaffold and a 3D
cancer tissue model. One of the microfluidic chips generates microfibers of wide diameter range
(2-200µm) providing the broad loading accessibility from proteins to drugs and the scaffold's
high porous nature helps for controlled/sustained release of protein/drug for tissue
regeneration. Furthermore, 3D cancer tissue (Spheroid), an in vitro model, with significantly
linear sizes of 100-600µm grown on an integrated microfluidic platform, which has various onchip utilities including synthesis, drug treatment, staining and imaging for facilitating the highthroughput chemotherapeutic drug screening. Currently, a microfluidic platform is being
developed to utilize a high human genome relevant C. elegans model for screening and
characterizing the mode of action of various natural extracts for implementing as possible
combinatorial therapeutics against neurodegenerative disorders. Advancements of these
microfluidic strategies expected to pave a way for translational lab-on-a-chip systems for a wide
spectrum of biological engineering applications.
48
International Biological Engineering Meeting
P12
METAL-DYE POLYMER NANOSYSTEM ENGINEERED WITH
BIOMACROMOLECULES AS SENSOR PLATFORM FOR DIAGNOSIS OF
DENGUE ANTIGEN
Murugan Veerapandian1, Mohana Marimuthu2, PramodK Avti3, K. Balamurugan1,2, V.
Ravichandiran1
1 National Institute of Pharmaceutical Education and Research, Kolkata 700032, West
Bengal, India
2 Depatment of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, 630003
3 Department of Biophysics, Postgraduate institute of Medical Education and Research,
Sector-12, Chandigarh160012, India
In the recent past, India has seen outbreaks of infectious diseases. Dengue, mosquito bornevirus infection, is a global epidemic with an estimated 390 million infections worldwide every
year. Laboratorial methods currently available for dengue diagnosis such as viral culture, reverse
transcriptase PCR and ELISAs are having limited scope due to expensive assay cost, time- and
labor-intensive operation. Electrochemical approach is a promising method for rapid detection
of various biomarkers. However, fabrication of label-free electrochemical system with durable
electrochemical property, controllable bio-affinity, timely operation and low-cost is challenging.
NS1 is a non-structural dengue protein that is secreted from infected cells and has been used as
an early surrogate biomarker for viremia and/or infected cell mass in patients. Herein, we
developed an advanced nanomaterial composite (hybrid nanoparticles: PEGylated-molybdenum
oxide-[Ru(bpy)3]2+) modified biochip/electrode as sensor platform, potential for immunosensing
of NS1 protein. Physico-chemical investigations revealed that the prepared hybrid
nanostructures are chemically bonded. Further, the hybrid nanostructures exhibited a metal-toligand charge transfer absorbance and emission bands in the range of 450 nm and 605 nm,
respectively. Electrode modified with molybdenum oxide-[Ru(bpy)3]2+ and molybdenum oxide[Ru(bpy)3]2+/PEG3k exhibit improved voltammetric properties than pristine molybdenum oxide.
Confocal cellular imaging supported that these hybrid particles were easily uptaken by
endothelial cells with minimal cytotoxic effects. The hybrid nanocomplex displayed unique optoelectrochemical and cellular biocompatibility that may be an ideal platform for electrochemical
immunosensor device development. Investigations on bioengineering of antibodies related to
dengue NS1 proteins on sensor platform and its immunosensing efficiency are in progress.
Outcomes of the invention in early diagnosis of dengue infection would provide better healthcare to individual as well as contribute the socio-economy to the country.
49
International Biological Engineering Meeting
P13
Converting “PSEUDO” genes into” NOVEL” proteins using Synthetic
Biology Approaches.
Aditya Nigam, Juveria khan, Monica Kaushik, Siddharth Manvati, Kalaiarasan
Punnaswami, Pawan K Dhar.
Pseudogenes which have long been called as junk DNA are the stretches of the nucleotides that
resembles the functional genes but, are no longer translated or transcribed. Recently growing
evidence suggest that some families of pseudogenes are transcribed into RNA which have a wide
range of functionality ex RN7SL family of processed (retrotransposed) pseudogenes.
In this work, an attempt has been made to synthesize novel proteins from the yeast
(Saccharomyces cerevisiae) pseudogenes. What are the functions of these novel proteins and
how would the organism react to the artificial or the untimely re-activation of the pseudogenes?
16 full-length protein equivalents of pseudogenes were studied out of which only 4 were chosen
to be expressed.
50
International Biological Engineering Meeting
P14
Structural and functional studies of antimicrobial proteins from seeds of
Datura stramonium
Monika Jain and Amit Kumar Singh
Department of Biotechnology, School of Engineering and Technology, Sharda University,
Greater Noida
The worldwide problem of emerging antibiotic resistance has created a need to explore
alternative approaches of treatment. Our ability to effectively treat disease is dependent on the
development of new pharmaceuticals, and one potential source of novel drugs is traditional
medicine. One such approach is based on evaluating herbal compounds for their activity against
pathogens causing infections. Antimicrobial compounds present in different plants are active
against a large spectrum of Infectious bacterial strains.
The present study was conducted to investigate the antimicrobial property of proteins present
in seeds of Datura stramonium. The isolated and extracted proteins was subjected to Dialysis in
which all the salt was removed and then purified using Ion-exchange chromatography to obtain
acidic and basic proteins which were also subjected to sodium dodecyl sulphate polyacrylamide
gel Electrophoresis (SDS-PAGE) to visualise their different molecular weight. Antibacterial
activities of both acidic and basic proteins were determined by the microbiological technique
using paper –discs –diffusion method against clinical bacterial isolates namely E. coli,
Pseudomonas and Klebsiella. More antimicrobial activity was observed in basic protein fraction
compared with acidic fraction. Further we will do structural characterization of the targeted
proteins in their native as well as with their specific ligands. This will provide insight for
redesigning the binding/active site of antimicrobial protein. Also by using computational biology
we will remodel antimicrobial proteins from Datura seeds, so that they become more specific for
their function. This information can be used in site directed mutations in active site of targeted
proteins to enhance their antimicrobial effect.
51
International Biological Engineering Meeting
P15
Synthetic Biology: A Boon to Future Diagnostics
Wamika Sharma
Bachelor of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, 182320
Synthetic biology is that new field of biomedical research which deals with the conception and
construction of new biological parts, devices and circuits with the help of the pathways that are
not existing in nature. It aims to deliver an unconventional solution to big challenges in a variety
of fields, including the discovery of new drugs, production of chemicals, renewable bio fuels,
value-added products and cellular reprogramming. Researchers have also been made to design
and particularize synthetic genetic parts which includes finding promoters, transcription factors,
degradation tags and transcriptional terminators. With the assembly of these genetic parts the
assembly of various synthetic devices and circuits like oscillators, toggle switches, amplifiers and
biologic gates was made possible. Synthetic biology also plays a role in cell reprogramming
which better explains cellular mechanisms and control of biological process and have also
proved to be helpful for the frequent and tunable production of drugs, fine chemicals, vaccines
and much more. Synthetic biology broadly categorized into two forms. One that utilizes
unnatural molecules for the reproduction of emergent behaviours from natural biology, hence
creating artificial life while the other cast about the interchangeable parts from natural biology
to merge into the systems that work efficiently. Either way, a synthetic objective urges scientists
to solve problems that are not easily encountered through analysis. With the advent of synthetic
biology, we have made diagnostic tools. The aim of this review would be to assist and boom up
the future research in synthetic biology.
52
International Biological Engineering Meeting
P16
A pH based translational regulator for gene expression and conversion of
its translation based regulation into transcriptional based regulation.
B. Ramit and Prof. Nalinkanth.V.Ghone
Sri Venkateswara College of Engineering,Chennai,TamilNadu.
Synthetic biologists over the years have designed various regulators for gene expression which
respond to stimuli such as light, temperature, specific proteins etc. However there has been an
acute lack of genetic parts that regulate genes based on pH. It is observed that alx gene which is
a putative transporter protein in Escherichia Coli is expressed in high amounts under alkaline
conditions. Upstream of the alx gene a 5’UTR is present which when transcribed is capable of
forming two stable RNA secondary structures, one structure is termed as structure N denoting
it’s stable at neutral pH and the other is termed as structure H denoting it’s stable at higher pH.
The N structure is such that it has five stem-loop domains which occlude the Shine Dalgarno
sequence thereby preventing the binding of ribosomes and hence inhibiting translation of
downstream genes. In comparison, the stem loops in the H structure do not occlude the Shine
Dalgarno sequence and allow the translation of downstream genes. This 5’UTR called the SraF
gene hence serves as a Riboswitch which translates genes only under alkaline conditions. By
placing any gene downstream of this riboswitch, we can control pH sensitive gene expression.
However, this riboswitch serves as a translational regulator, in order to additionally convert the
riboswitch into a transcriptional regulator, the leader peptide element from the tna operon,
called the tnaC element can be placed upstream of the gene to be expressed and the riboswitch
can be placed upstream of the tnaC element. The leader peptide element takes advantage of
the fact that in prokaryotes translation and transcription is coupled, in the sense that depending
on whether the leader peptide element gets translated, the genes downstream of it get
transcribed. Hence, the tnaC element can be used as an adaptor to convert translational
regulation into transcriptional regulation.
53
International Biological Engineering Meeting
P17
Pollutant detector and consumer for toxic gasses
J. Ashwin Kumar, Prateek Chawla, Nitish Tayal, Manisha Wadhwa, Bhupinder Singh
Indian Institute of Science Education and Research, Mohali, Punjab 140306, INDIA.
Air is essential for survival of living organisms. It’s the quality of air that affects health of living
beings. When the pollutants increase above their allowed limits in the air, the air quality
declines resulting in increase in different health problems like stroke, heart diseases and lung
cancer. The major pollutants are xylene and acetaldehyde whose level drastically increases at
closed vehicles due to enormous aerosol accumulation. These different pollutants are measured
by different techniques- GC-FID, PTRMS which are very costly and cannot be installed at every
place. Due to limitation of these sophisticated techniques, alternative and cost effective
approaches are required for the measurement and reducing the levels of pollutants. Therefore,
to curb this problem, many groups have tried to engineer the microorganisms to respond to
levels of pollutants present in the environment. But they were not so successful in their
approaches as they compromise on one of the two factors sensitivity and efficiency. We also
tried to approach this problem in more systematic manner and designed the synthetic circuit for
the measurement of major pollutants of air – NO, acetaldehyde, xylene and CO. These synthetic
circuits are designed by kinetic equations and simulated for their feasibility. These designer
circuits when engineered in E. coli will change the color of E. coli based on levels of pollutants
present in the environment/air. Our approach not only senses the pollutants but also reduces
their levels in the air.
54
International Biological Engineering Meeting
P18
Structural and Functional Studies of Lactoperoxidase: Crystal Structures of
Lactoperoxidase in Complex with aromatic ligands
Amit k. Singh
Department of Biotechnology, Sharda University, Greater Noida, India
Lactoperoxidase (LPO), (EC. 1.11.1.7) is a member of the family of glycosylated mammalian
heme-containing peroxidase enzymes which also includes myeloperoxiadse (MPO), eosinophil
peroxidase (EPO) and thyroid peroxidase (TPO). The binding and structural studies of bovine
lactoperoxidase with three aromatic ligands, acetyl salicylic acid (ASA), salicylhydoxamic acid
(SHA) and benzylhydroxamic acid (BHA) show that all the three compounds bind to
lactoperoxidase at the substrate binding site on the distal heme side. The binding of ASA occurs
without perturbing the position of conserved heme water molecule W-1 whereas both SHA and
BHA displace it by the hydroxyl group of their hydroxamic acid moieties. The acetyl group
carbonyl oxygen atom of ASA forms a hydrogen bond with W-1 which in turn makes three other
hydrogen bonds one each with heme iron, His-109 N2 and Gln-105 N2. In contrast, in the
complexes of SHA and BHA, the OH group of hydroxamic acid moiety in both complexes
interacts with heme iron directly with Fe - OH distances of 3.0Å and 3.2Å respectively. The OH is
also hydrogen bonded to His-109 N2 and Gln-105N2. The plane of benzene ring of ASA is
inclined at 70.7° from the plane of heme moiety while the aromatic planes of SHA and BHA are
nearly parallel to the heme plane with inclinations of 15.7° and 6.2° respectively.
The mode of ASA binding provides the information about the mechanism of action of aromatic
substrates while the binding characteristics of SHA and BHA indicate the mode of inhibitor
binding. Using all these structural insights, we can remodel and modify the stereochemistry of
the active site of lactoperoxidase to achieve the desired function.
55
International Biological Engineering Meeting
P19
Microbe as a tool for fabrication of three dimensional structures and their
potential engineering applications
Sunita Mehta, Saravanan Murugeson2, Balaji Prakash2†, Deepak1
1Department
of Materials Science & Engineering and Samtel Center for Display
Technologies, Indian Institute of Technology Kanpur, Kanpur-208016
2Department of Biological Sciences & Bioengineering, Indian Institute of Technology
Kanpur, Kanpur- 208016
†Department of molecular nutrition, CSIR-Central Food Technological Research Institute,
Mysore-570020, India
Inspired by the wound healing property of certain trees, we report a novel microbe based
additive process for producing three dimensional patterns. Imposing a two-dimensional pattern
of microbes on a gel media and allowing them to grow in the third dimension is known from its
use in biological studies. Instead, we have introduced an intermediate porous substrate
between the gel media and the microbial growth, which enables three dimensional patterns in
specific forms that can be lifted off and used in engineering applications. The described process
involves two approaches – microbial approach, where microbes can grow on selected regions;
and antimicrobial approach, where microbial growth is restricted on specified regions. To
demonstrate the applicability of this idea in a diverse set of areas, different applications are
selected. One of them includes the fabrication of microlenses for enhancement of light
extraction in organic light emitting diodes. Among the two approaches, microbial approach
results into a densely-packed array of microlenses leading to luminance enhancement by a
factor of 1.24X. In another application, these three dimensional microbial patterns are utilized as
tactile dots of braille text. Braille dot patterns thus prepared meet the standard specifications
(size and spacing) for braille books. In the last application, these microbial patterns serve as
masters for preparing stamps for micro-contact printing. The stamps thus prepared have been
successfully used for fabricating source-drain electrodes of gold ink on Si/SiO2 substrate for thin
film transistors.
56
International Biological Engineering Meeting
P20
Computational and experimental evidences for presence of purinergic
receptor in P. falciparum: Implications for therapeutic target.
Sonal Gupta, Shailja Singh
Special Centre for Molecular Medicine, Jawaharlal Nehru University, India
Purinergic signaling is one of the classical signaling pathways that regulate numerous cellular
and physiological functions including calcium signaling in living organisms. The role of purinergic
signaling is implicated in neurodegenerative diseases, cardiac dysfunction, inflammation,
arthritis and other important pathological conditions. Several pharmacological compounds and
FDA approved drugs specifically target purinergic receptors in case of different diseases.
Purinergic receptors are a class of GPCRs that binds to purines such as ADP, ATP and UTP.
Malaria, caused by a protozoan parasite Plasmodium sp., is one of the major devastating
infectious diseases worldwide. The previous studies suggested the role of secondary messengers
like calcium and cAMP in pathogenesis of Plasmodium. However, the receptors associated with
calcium signaling and their relation with parasite growth remains undefined. Here, we found by
bioinformatics studies that P. falciparum has serpentine receptor PfSR12 which possess 7
transmembrane domains and a nucleotide binding consensus P-loop sequence. Using docking
studies, we confirmed binding of P-loop residues of PfSR12 with ATP. The presence of conserved
GPCR like topology and a consensus nucleotide binding sequence (P-loop) suggest that PfSR12
could be a putative purinergic receptor. Next, we confirmed the expression of PfSR12 in parasite
using antibodies against P-loop sequence containing domain of PfSR12 by immunofluorescence
assay. Further using different antagonists and FDA approved drugs affecting purinergic signaling,
we found good inhibition effect on growth cycle of malaria parasites. Growth Inhibition by
purinergic receptors antagonist shows the importance of purinergic signaling in malaria parasite
pathogenesis. Further studies in this direction would lead to identification of novel drug targets
against malaria parasite.
57
International Biological Engineering Meeting
P21
Insights from Codon Usage Pattern and Structural Stability Of mRNA
Manish Prakash Victor, Tina Begum, Debarun Acharya, Tapash Chandra Ghosh.
Bose Institute, West Bengal, Kolkata India-700009.
Reasons for the selection of codon composition of genes in organism have been well accounted
in literatures stating ambient temperatures, tRNA pool, translational efficiency and fidelity as
instigating factors. But the holistic picture remains unclear. It’s because the studies circle around
the translational domain only; and it constitutes the terminal domain of central dogma, which is
an outcome of events after transcription. Properties of mRNAs i.e. mRNA abundance and its
secondary structure stability show a great deal of influence on the processes following it. They
include- its reduced degradation hence greater translation time, appropriate ribosomal
abundance, co-translational folding, and close correlations between positions of folding in mRNAs
and their polypeptide products. These secondary structures reveal the inherent property of
mRNA arising out of its codon composition. We carried out an intense mutational analysis
encompassing synonymous codon shuffling as well as usage of all possible synonymous codons
within genes of Saccharomyces cerevisiae. The results astonishingly indicate a harmonious
articulation of trio i.e. codon composition, mRNA secondary structure stability and mRNA
abundance. The results show that, even under high stability and narrow selection of codon pool
does not suffice for the appropriate selection for gene expression level, which is accounted from
earlier studies. Our study here confirms that the existent codon composition has not a mere
influence of translational domain only, as transcription and translation are both articulated
process. Rather, it indicates that both mRNA stability and meticulous codon usage fine tunes the
apt gene expression level.
58
International Biological Engineering Meeting
P22
Model system to functionally validate novel Regulatory-RNA-Molecules for
various therapeutic potentials.
Ankita Arora, Siddharth Manvati, Pawan K Dhar
Synthetic Biology Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi
MicroRNAs (miRNA) are small non coding RNA molecules (20-25 nucleotides long) that regulate
around 60% of human genes, and the key cellular processes associated with them, at post
transcriptional level by interacting with 3' or 5' UTR regions of target mRNA. Dysregulation of such
known regulatory RNA molecules has been associated with various multi gene diseases such as
cancer, neurodegenerative disorder etc. Such an association highlights the biomarker functions
that these may posses for various diseases. We have generated a model system to functionally
validate the novel micro-RNA for various therapeutic potentials in less time interval possible. It
involves identification and analysis of miRNA involved in various diseases using various
bioinformatic tools like DAVID, TargetScan, PicTar. The in-silico preliminary data obtained are then
analysed in-vitro using various traditional techniques. The model system discussed is currently
being tested for validating the function of hsa-miR-760. Such an approach has helped understand
the novel role of hsa-miR-760 in Epithelial-Mesynchemyl Transition (EMT) and cAMP production.
Previous studies had suggested that EMT regulation can be used to control metastatic behaviour
of cancer cells. From the aproach applied it could be hypothesized that hsa-miR-760 may
regualate metastasis by altering EMT and cAMP production. This model system can be used to
bioinformatically identify and validate the function of novel regulatory RNA molecules from noncoding DNA regions for various therapeutic potentials and implementations.
59
International Biological Engineering Meeting
KEY INDIAN LABS SYNTHETIC BIOLOGY
ARCHANA CHUGH
Assistant Professor
Kusuma School of Biological Sciences,
IIT Delhi, New Delhi - 110016
RAMAN PARKESH
Associate Professor, IMTECH
Sector 39, Chandigarh - 160036
ARUN K. SHUKLA
Assistant Professor
Wellcome Trust-DBT Intermediate Fellow
Department of Biological Sciences and Bioengineering
Indian Institute of Technology Kanpur 208 016
RAMANUJAM SRINIVASAN
Reader-F, School of Biological Sciences,
National Institute of Science Education and Research,
Bhubaneswar, Odisha - 752050
CHAITANYA ATHALE
Associate Professor, Div. of Biology, IISER Pune
Dr. Homi Bhabha Road, Pashan, Pune - 411008
S. RAMASWAMY
CEO and Co-Founder, Center for Cellular and Molecular Platforms,
Professor, Institute for Stem Cell Biology and Regenerative Medicine
(inStem), Bangalore, Karnataka - 560065
D.SUNDAR
DuPont Young Professor, Associate Professor
Department of Biochemical Engineering and Biotechnology
IIT Delhi, New Delhi - 110016
SANGRAM BAGH
Associate Professor
Saha Institute of Nuclear Physics,
Bidhan Nagar, Kolkata- 700064
GUHAN JAYARAMAN
Professor, Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences
IIT Madras, Chennai - 600036
SEEMA MISHRA
Assistant Professor, Department of Biochemistry
School of Life Science University of Hyderabad,
Hyderabad - 500046
60
International Biological Engineering Meeting
H. V. THULASIRAM
Scientist, Division of Organic Chemistry,
National Chemical Laboratory, Pune - 411008
SOMENATH ROY CHOWDHURY
Senior Research Fellow
India-Brazil Bilateral Scientific Cooperation
CSIR-Indian Institute of Chemical Biology, Kolkata -700 032
INDIRA GHOSH
Professor, School of Integrative and Computational Sciences
JNU, New Delhi - 110067
SOUVIK MAITI
Scientist, CSIR-IGIB,
Mathura Road, New Delhi - 110 025
I S BRIGHT SINGH
Professor, UGC-BSR Faculty
National Centre for Aquatic Animal Health
Cochin University of Science and Technology
Kochi, Kerala - 682 016
SUVENDRA N. BHATTACHARYYA
Principal Scientist & Head
Molecular & Human Genetics Division
CSIR-Indian Institute of Chemical Biology , Kolkata 700 032
JOSEPH SELVIN
Associate Professor, Co-ordinator
Department of Microbiology, School of Life Sciences
Pondicherry University, Puducherry – 605014
SYED SHAMS YAZDANI
Coordinator, DBT-ICGEB Centre for Advanced Bioenery Research
Group Leader, Synthetic Biology and Biofuel Group,
ICGEB, New Delhi - 110067
KAILASH C. PANDEY
Scientist E, Departmnt of Biochemistry
National Institute for Research in Environmental Health
Indian Council of Medical Research, Bhopal-462001
UMESH P
Centre for Systems and Synthetic Biology,
Department of Computational Biology and Bioinformatics
University of Kerala, Trivandrum, Kerala - 695581
K J MUKHERJEE
Professor, Metabolic Engineering
School of Biotechnology, JNU, New Delhi - 110067
UTPAL MOHAN
Assistant Professor
Department of Biotechnology,
NIPER, Guwahati - 781 032
61
International Biological Engineering Meeting
MRINAL K. MAITI
Associate Professor, Department of Biotechnology
Indian Institute of Technology, Kharagpur - 721302
VIKAS JAIN
Associate Professor, Department of Biological Sciences
IISER Bhopal, Bhopal, Madhya Pradesh - 462 066
PAWAN K. DHAR
Professor & Head, Synthetic Biology Group
School of Biotechnology, JNU, New Delhi - 110067
VIKRAM SINGH
Assistant Professor, School of Life Sciences
Central University of Himachal Pradesh
Dharamshala, – Kangra, H.P - 176215
62
International Biological Engineering Meeting
OUR SPONSORS
63
International Biological Engineering Meeting
NOTES
64
International Biological Engineering Meeting
NOTES
65
66