Science Academies’ Lecture Workshop on
‘OMICS: Basics and Applications’
held at IWSA Campus, Vashi, Navi Mumbai.
A two day lecture workshop sponsored and supported by the three National Science Academies – Indian Academy of Sciences (Bengaluru), Indian National Science Academy (New Delhi) and The National Academy of Sciences, India (Allahabad) on ‘OMICS: Basics and Applications’ was held on 8 – 9 July 2017 at Indian Women Scientists’ Association, Sector 10-A, Dr. Mar Theophilus Road, Vashi, Navi Mumbai 400703. Dr. Rita Mulherkar, Fellow NASI was Course Convenor and Dr. Susan Eapen, Member, Board of Trustees, IWSA was Course Co-ordinator.
The circular was sent to about 40 colleges and 15 research institutes in Mumbai and Navi Mumbai. The applications could be downloaded from www.iwsa.net and was to be forwarded to Co-ordinator, OMICS Lecture Workshop at firstname.lastname@example.org The last date of receiving applications was ‘first-cum-first served’ basis. Hundred and twenty five candidates from different colleges of Mumbai like St. Xavier’s College, K. B. Patil College, SIES College, ICLE’s Motilal Junjunwala College, D. Y. Patil University, R. D. National College, Amity University, Vaze College, Junjunwala College, Ruia College and institutes like P. D. Hinduja Hospital, BARC, NIRRH, Haffkine Institute, MGM Medical College etc participated in the workshop. There were 3 students from IISER, Bhopal.
There were 16 lectures on selected topics on Genomics, Metagenomics, RNA omics, Biobanking, and Ethical issues, Proteomics, Metabolomics, and Instrumentation. Two speakers delivered two lectures each.At the end of each lecture, there was an active discussion.
Workshop on ‘OMICS: Basics and Applications’
The workshop began with Dr. Susan Eapen, Co-ordinator of the workshop, welcoming all the delegates. She mentioned that the workshop had received an overwhelming response with more than 200 applications. On a first-come-first-serve basis 125 candidates were selected. This was followed by a short presentation about the organization and activities of the host institute – IWSA, by Dr. Surekha Zingde, President, IWSA.
The scientific session commenced with a brief introductory talk on Genomics by Dr. Rita Mulherkar, Convenor of the workshop. She traced the remarkable path leading to Genomics, starting with Gregor Mendel’s discovery of Laws of Genetics, in 1865, to completion of Human Genome Project (HGP) in 2003. HGP not only provided the essential reference map for the human genome but also stimulated the development of technology and analytic tools to process massive quantities of genomic data.
Dr. M. Seshadri spoke on instrumentation for studying genetic variations and diseases. He too dwelled upon how HGP had led to our understanding of the variations among various human populations. He spoke about the complexities of the genome such as multiple genes but same phenotype, or single gene mutation causing a disease but with number of mutations spanning the same gene. Dr. Seshadri gave an excellent account of how the sequencing technology had evolved bringing down the cost as well as time taken to sequence the whole human genome. The latest sequencing technology – nanostring technology can sequence a single DNA molecule as it passes through a nano pore.
Dr. Sarin gave a medical practitioner’s perspective with real life examples, on medical ethics. Besides mentioning about the challenges related to counseling patients with hereditary cancers and their relatives, he also spoke about issues arising due to genome analysis. Variants of Unknown clinical Significance (VUS) identified in genome sequencing pose a special challenge in counseling patients.
Dr. Sanjeev Galande gave two talks which held the audience captive for more than one hour. First he spoke on bioinformatics and sequencing data analysis. He described the different softwares like BOWTIE, CUFFLINKS, TOPHAT, CUMMERBUND – all part of the TUXEDO. He described how Phred score was important in determining the quality of base calling. The second talk was on Epigenomics. We carry the imprinting on our genome from our forefathers. He mentioned how the germ cells carry the epigenetic changes to the progeny. Fat fathers give birth to girls who develop diabetes when they grow up. He described some elegant experiments carried out on fat fed and control mice for over 50 generations to demonstrate germ cell Epigenomics and their effect on the progeny.
Dr. Yogesh Shouche had to travel out of the country and so his colleague Dr. Dhiraj Dhotre replaced him. His talk was on human microbiome. It was quite surprising to hear that there are 10 microbial cells per human cell in our body. The microbes in different parts of our body – skin, gut, oral and vagina, are different and they play a role in shaping the overall health and disease condition of an individual. He mentioned that the human microbiome in the Indian population is different from the west due to difference in the diet, environment, etc and needs to be studied.
Dr. Mulherkar gave a talk on genomics in health and agriculture. With all the genomic data available after HGP and advances in sequencing technology and bioinformatics, it has dramatically changed biomedical research and disease management. It provided the first systematic approach to identify genes and cellular pathways in health and disease. A number of diseases are being mapped to the genome, mutations are being unraveled and drugs matching the mutations are being discovered. But unfortunately biology and our understanding of the human body is still lagging behind. On the agriculture front, Dr. Mulherkar mentioned that genomics was helping in improving the yield and quality of agricultural products and improving sustainability. She mentioned about Indian contribution in decoding rice, tomato, chickpea, potato, pigeon pea and wheat genomes.
Dr. Mukesh Jaiswal from Agilent Technologies delivered a talk on pre-implantation genetic screening using Agilent microarrays. Agilent has been leaders in microarray and CGH technologies. They have now developed a single cell high resolution CGH array technology which can accurately and rapidly screen single cells from 3-5 day embryos before implantation. This has improved IVF rate to 72%.
The last talk on the first day was delivered by Dr. Rita Mukhopadhyaya. She gave a thought provoking talk on RNomics. RNomics deals with small and long non-protein coding RNAs. These are regulatory proteins and play an important role in cellular processes and human diseases. However, the biological role of most of them remains elusive.
All the talks were very informative and were well received by the audience. There was very good participation from the audience, specially the students who asked very pertinent questions.
On the second day of the OMICS lecture workshop the focus was on Proteomics and Metabolomics.
The first lecture was delivered by Dr. Surekha Zingde, President, IWSA, formerly from ACTREC, who gave an overview of proteomics describing how the transition from proteins to proteomics has taken place after the first draft human genome sequence was announced. She informed about the Human Proteome Organization which through its various projects is targeted towards getting detailed information of all the proteins coded for by the human genome, their post translational modifications, expression, location in the cells/tissues and variations in clinical conditions. The lecture also covered the three major proteomic tools, mass spectrometry, antibodies and bioinformatics which are being used for the proteomic studies. Information on the different approaches to obtain the identity and quantity of each protein and the challenges to be addressed was also given.
The second lecture was given by Dr. Ajit Datar, Shimadzu Instruments Pvt Ltd. He spoke on Mass spectrometry and explained the basic principles of the technique and the main components ie ion source, mass analyser and detector. Dr Datar informed about the configurations of some of the mass spectrometers which are being used for proteomics and the different parameters such as resolution and sensitivity which are essential for identification and quantitation of proteins.
The third lecture was on Metabolomics with specific reference to plant secondary metabolites and the pathways regulating their generation. Dr. Ashok Giri, from NCL Pune informed that the metabolites belong to the terpenoid, flavonoid and alkaloid family. He explained how these molecules regulate the physiology and flavour of strawberries and mangos. He showed how his research has identified the key molecules which regulate the expression of the metabolites and in turn the flavour of the fruits. He emphasized that basic research was necessary for translation into the field.
In the afternoon session, three speakers, Dr. Bhakti Basu, BARC, Dr Geetanjali Sachdeva, NIRRH, spoke on the applications of Proteomics and Genomics. Dr. Basu described the identification of several molecules which are responsible for the radio resistance of the microbe Dienococus. She further showed how this information was used to understand the signalling pathways for DNA repair.
Dr.Sachdeva spoke on how her group has used the OMICS technology to understand endometrium receptivity. She explained the identification of key molecules and their functional role and their potential as biomarkers.
These presentations were followed by lectures from company application specialists who informed the participants about Western blotting and chromatography.
Dr.Abhijit Dixit from BioRad spoke on the different equipment and reagents for Western blotting. He also explained the basic principles and the key points that need to be followed to ensure optimal transfer and immunodetection.
With increasing complexity of the number of proteins in tissues it has become necessary to separate proteins by chromatography prior to mass spectrometry. Dr. Shailesh Damale gave a brief history of chromatography and the principles of separation. He described the different chromatography column materials which are based on polarity, size and ionic charge and their use. He informed how instrumentation is evolving to meet the requirements of the times ie equipment which can be used to analyse nano litres of material and resolve them in the shortest time. Dr Damale explained how the separated material is then analysed by mass spectrometry.
The participants enjoyed all the presentations. Many of the students asked some very intelligent and relevant questions. All of them informed that the presentations gave them an idea of the latest in Proteomics Research.
Breakfast, lunch and high tea were served to the participants, speakers and ohers who participated in the workshop. Three students from KBP College, Xavier’s College and D Y Patil University spoke at the feed back session. A few feedback points are enclosed. Dr Rita Mulherkar and Dr Surekha Zingde summarised the workshop lectures and Dr Susan Eapen proposed the vote of thanks.
Indian Women Scientists’ Association is happy to place on record their special thanks to the three Science Academies for supporting the lecture workshop on “OMICS:Basics and Applications”.
Dr. Susan Eapen
Co-ordinator, OMICS Workshop