Proteomics 2014, 14, 1581–1586
DOI 10.1002/pmic.2014700103
1581
First Systematic Plant Proteomics Workshop in Botany Department, University of Delhi: Transferring Proteomics Knowledge to Next-generation Researchers and Students Renu Deswal1 , Jasmeet Kaur Abat1,2 , Ankita Sehrawat1 , Ravi Gupta1 , Prakriti Kashyap1 , Shruti Sharma1 , Bhavana Sharma1 , Satya Prakash Chaurasia1 , Sougrakpam Yaiphabi Chanu1 , Antonio Masi3 , Ganesh Kumar Agrawal4,5 , Abhijit Sarkar4,5,6,7 , Raj Agrawal7 , Michael J. Dunn8 , Jenny Renaut9 and Randeep Rakwal4,5,10,11 1
Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India 2 Department of Botany, Gargi College, University of Delhi, New Delhi, India 3 DAFNAE, University of Padova, Legnaro, Italy 4 Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal 5 GRADE Academy Private Limited, Adarsh Nagar, Birgunj, Nepal 6 DBT-RAI, Microbiology Laboratory, Department of Botany, University of Kalyani, Kalyani, West Bengal, India 7 International Plant Proteomics Organization (INPPO, www.inppo.com) 8 UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland 9 Centre de Recherche Public-Gabriel Lippman, Department of Environment and Agrobiotechnologies (EVA), Belvaux, GD, Luxembourg 10 Organization for Educational Initiatives, University of Tsukuba, Tsukuba, Japan 11 Department of Anatomy I, Showa University School of Medicine, Shinagawa, Tokyo, Japan
International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to “organize workshops at national and international levels to train manpower and exchange information”. This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26–30, 2013 titled – “1st Plant Proteomics Workshop / Training Program” under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gelbased proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it. Keywords: Collaboration / Funding agency / INPPO / Plant proteomics / Workshop
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1582
1
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
Introduction
Plant proteomics started in the early 1990s at a preliminary stage of identifying and cataloging proteins but has advanced at a rapid pace since then [1, 2]. Two-dimensional gel electrophoresis (2DE) has been a cornerstone of proteomics for the comparative proteome analysis in conjunction with mass spectrometry (MS)-based protein identification utilizing databases. 2DE-based analysis has few drawbacks like identification of merely abundant proteins, gel-to-gel variations, and no automation, leading to development of difference in gel electrophoresis (DIGE) and gel-free methods. In developing countries, universities and institutes have started incorporating equipment’s in their laboratories/central facilities, but there remains an immediate problem of handling and properly operating highend equipment’s, and subsequently training. Training work-force in proteomics requires hands-on training events, such as conducting workshops that provide a platform for exchange of ideas, learning new techniques and creation of networks (Fig. 1). This was the main reason behind initiation of an idea to have a systematic plant proteomics workshop – a first such workshop in the University of Delhi, and in fact a first plant proteomics workshop in India or Nepal. Workshops provide a period of learning and discussion where participants can interact with resource persons and widen their horizons applying the gained knowledge in their research.
2
Workshop goals, planning and organization
Workshop was organized under leadership of Dr. Renu Deswal along with her research students of the Department of Botany (University of Delhi, India) under India-Nepal Plant Proteomics Chapter (http://www.inppo.com/IndoNepallogo.jsp) of INPPO [3]. Selected participants included 10 research scholars and 10 teachers. Five students were from different research groups in Botany Department and five from other Departments/Universities. Of the 10 teachers, five were from different colleges of DU and five from outside Universities/Institutes. Organization of this workshop was itself a learning experience for members of the organizing committee.
Figure 1. Schematic illustration of the drive idea for the workshop and its importance in promoting plant proteomics.
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 1581–1586
1583
Figure 2. Flowchart of all the experiments conducted during the five-day workshop.
3
Systematic workshop on plant proteomics
The present workshop/training, spread over five days, aimed to introduce participants to the latest advancements in plant proteomic research providing hands-on training in proteomic techniques and analytical strategies. Each day started with a lecture delivered by an expert in the field followed by discussion and hands-on technical session (Fig. 2). Techniques made available to the participants included: (i) Gel-based proteome mapping – included protein extraction followed by their separation on 2D gels. Staining of gels by silver and colloidal CBB was followed by gel scanning, image analysis, spot picking, trypsin digestion, and MALDI-TOF/TOF analysis; (ii) Immunoblotting – included separation of proteins on SDS-PAGE gel, protein transfer to nitrocellulose membrane, Ponceau-S staining, and immunoblotting for detection of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) protein in crude extract of Brassica juncea seedlings; (iii) Difference-in gel electrophoresis (DIGE) – included extraction of proteins from control and stressed Hippophae rhamnoides seedlings, minimal CyDye labeling of proteins and separation on 2D gels. DIGE gel scanning on Typhoon scanner was followed by gel analysis using Decyder Software (GE Healthcare); and (iv) Gel-free proteomics – included enrichment of phosphoproteins from apoplastic fluid of Hippophae rhamnoides seedlings by TALON PMAC phosphoprotein enrichment kit, in-solution trypsin C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1584
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
Table 1. A list of invited lectures delivered during the workshop.
Session No.
Lecture title
Speakers
Affiliation
1.
Role of proteomics in understanding plant responses under abiotic stresses Evolving proteomics technology, translational proteomics, and INPPO: An open discussion
Prof. S.K. Sopory
3.
Setting up proteins and proteomics facility: An outline
4.
Identifying potential markers for coronary artery disease using quantitative proteomics approach
Dr. Shantanu Sengupta
5.
Computational tools in plant sciences and proteomics
Dr. Arun Jagannath
6.
Structural proteomics of therapeutic proteins in plants
Dr. Pravindra Kumar
7.
Current status and advances in quantitative proteomics
Dr. Kalpana Bhargava
8.
Immunodetection of proteins
Dr. Girish Mishra
9.
Protein analytical methods: Concepts, benefits and issues DeCyder – the 2D software for differential in-gel and biological variation analysis Recent advances in the field of proteomics on MS based approaches Analysis of 2D gels using ImageMaster 2DPlatinum PDQuest softwares Mr. Vipan Manhas
Dr. Prabuddha K. Kundu
Vice Chancellor, Jawaharlal Nehru University President INPPO, Vice President INPPO, University of Padua, Italy Department of Biochemistry, University of Delhi, South Campus Institute of Genomics and Integrative Biology, CSIR, Delhi Department of Botany, University of Delhi Department of Biotechnology, Indian Institute of Technology Roorkee Defence Institute for Physiological and Allied Sciences (DIPAS), DRDO, Delhi Department of Botany, University of Delhi Premas Biotech
Dr. Srijit Khan
GE (Healthcare)
Dr. Annu Uppal
AB Sciex, India
Dr. Srijit Khan Bio-Rad
GE (Healthcare)
2.
10. 11. 12.
Drs. Ganesh Kumar Agrawal, Randeep Rakwal, and Antonio Masi Dr. Suman Kundu
digestion and separation of peptides by reverse-phase column. Separated peptides were identified using LC-MS/MS. Each day started with (a) lectures (Table 1) and (b) hands-on-training, as listed below. Day 1 – Inaugural lecture and technical session I (Gel-based proteome mapping and quantitative proteomics). The “1st Plant Proteomics Workshop / Training Programme” was inaugurated by the Honorable Chief Guest, Vice-Chancellor, University of Delhi, Prof. Dinesh Singh and Honorable Guest of Honor, ViceChancellor, Jawaharlal Nehru University, Prof. Sudhir Kumar Sopory. Day 2 – Technical session II (Immunoblotting and gel-free proteomics). Day 3 – Technical session III (Qualitative proteomics, gel imaging and spot quantification). Day 4 – Technical session IV (Protein visualization, digestion and spot analysis). Day 5 – Technical session V (Protein identification by mass spectrometry-database searching). Final lectures and experiments were followed by wrap-up and troubleshooting sessions. At closing ceremony, Prof. M. M. Chaturvedi (Dean Research-Life Science, University of Delhi) shared some of his scientific experiences with participants (Fig. 3). Organizing secretary, Dr. Deswal shared experiences of organizing this workshop with delegates acknowledging support of each member, associated therein. C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 1581–1586
1585
Figure 3. Workshop participants. Name and affiliation of the participants clockwise last row – Shewta Singh*, Dr. Anjali Anand*, Dr. Kiran Bamel**, Md. Affan Baig (Jamia Millia Islamia), Javed Ahmad (Jamia Millia Islamia), Dr. Sajad Mazar Zagar***, Neha Goyal**, Romeo**, Prof. Randeep Rakwal (University of Tsukuba, Japan), Dr. Arun Jagannath**, Dr. Gayathri. T (Kerala University), Satya Prakash Chaurasia**, Dr. Charu Kalra**, Dr. Jasmeet Kaur Abat**, Dr. Arachna Singh**, Dr. Surinder Kaur**, Prerna Singh****, Neha**, Abha Singh****, Amit Kumar Mishra****, Shivangi Upadhyay**, Shatakshi Pandit**, Prachi Jain**, Pragya Barua (NIPGR), Prakriti Kashyap**, Shruti Sharma**, Ankita Sehrawat**, Bhavana Sharma**, Prof. S.C Bhatla**, Dr. Renu Deswal**, Prof. M.M Chaturvedi**, Dr. Indrakant Singh**, Ravi Gupta** and Dr. Kumar Shantanu. *Indian Agricultural Research Institute, **Delhi University, ***Jammu & Kashmir University, ****Banaras Hindu University.
4
Funding agencies, sponsorship, participant’s response and future prospects
To accomplish our goals and to successfully execute our ideas, good financial support was successfully obtained. Since the workshop consisted of participants from different backgrounds like Zoology, Environmental Science, Biochemistry, Biotechnology, and Botany, and as many of them did not have any prior experience in proteomics, a manual containing basic information of proteomics including experimental procedures of each and every technique used in the workshop was prepared; a print out in a booklet form was provided to all participants. Feedback forms submitted by participants had many positive comments and suggestions, based on which we would like to continue the workshop with certain improvements, such as more attention would be given to the gel-free approaches and DIGE. Workshop will also serve as a model for workshops at other universities and institutes. As it is a universal fact that in biological sciences, majority of the students are women, especially true for Department of Botany, therefore, in this workshop also a large percentage of the participants and instructors were women. This workshop would help in shaping their future as better scientists as well as teachers because with a basic knowledge of proteomics they will have an edge over C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1586
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
others in the competitive field of plant biology. In all, the vision for the workshop and goals that we started with were accomplished during this five-day workshop. However, the true outcome of the workshop will be reflected by the utilization of this training by the participants in their science and publications that follow, along with the establishment of even the basic facilities to do proteomics of plants in their laboratories and in turn train their juniors and/or colleagues. The workshop effort is already bearing fruits as two University of Delhi trainee teachers Drs. Inderkant and Shantanu from this workshop recently organized a two-day workshop in Genomics and Proteomics in March 2014, in a Delhi University associated college.
5
Advanced training and exchange programs
An important issue discussed on the sidelines of the workshop was the meeting between Drs. Renu Deswal (India), Ganesh Kumar Agrawal (Nepal), Antonio Masi (Italy), and Randeep Rakwal (Japan / India) on the development of an advanced training and exchange program for the deserving students and young researchers from India and Nepal, in plant proteomics. The aim was two-fold: first, to develop a collaborative project between India / Nepal and Italy, and, second, to help students in India / Nepal to carry out advanced research in gel-based and gel-free proteomics in an advanced laboratory outside their respective countries by either sending their samples for protein separation and identification by MS or having the candidate visit the collaborative laboratory. It is our hope that such a collaborative research project would help promote the INPPO spirit of open collaboration and exchange between plant proteomics researchers. Authors gratefully acknowledge great support of Department of Botany, University of Delhi, for providing space, technical support, and equipment’s for organizing the workshop. Delhi University Botanical Society (DUBS) is acknowledged for help extended in handling finance of the workshop. The workshop would not have been possible without support from members of organizing committee. Academic and Commercial sources of funding is appreciated from – Department of Biotechnology, Department of Science and Technology, Government of India (printing, travel and hospitality); Delhi University as well as Head, Department of Botany (chemicals); Bio-Rad (consumables and technical assistance); GE Healthcare (consumables, stationary for workshop kit, technical assistance); Abhishek Glass Industrial Corporation (advertisement for manual); and Genetix (advertisement for manual). INPPO is highly grateful to PROTEOMICS and in particular, Professor Michael J. Dunn, Editor-in-Chief, PROTEOMICS, and Dr. Hans-Joachim Kraus, Senior Publishing Editor, Wiley, Weinheim (Germany) for generous support in making possible the INPPO highlights. Authors deeply thank Dr. Thomas Kieselbach (Department of Chemistry, Umea University, 90187, Umea, Sweden) for his reading of the manuscript and critical comments to highlight goals and outcomes of the workshop. The full report on the workshop can be accessed at: http://www.inppo.com/pdf/workshop/DeswaletaFullManuscriptHighlights.pdf The authors have declared no conflict of interest.
6
References
[1] Agrawal, G. K., Rakwal, R. (Eds.), Plant Proteomics: Technologies, Strategies, and Applications. Wiley & Sons, Hoboken, NJ, USA, 2008. [2] Agrawal, G. K., Job, D, Zivy, M, Agrawal, V. P. et al., Time to articulate a vision for the future of plant proteomics – A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 2011, 11, 1559– 1568. [3] Deswal, R., Gupta, R., Dogra, V., Singh, R., et al., Plant proteomics in India and Nepal: Current status and challenges ahead. Physiol. Mol. Biol. Plants 2013, 19, 461–477. C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
DOI 10.1002/pmic.2014700103
1581
First Systematic Plant Proteomics Workshop in Botany Department, University of Delhi: Transferring Proteomics Knowledge to Next-generation Researchers and Students Renu Deswal1 , Jasmeet Kaur Abat1,2 , Ankita Sehrawat1 , Ravi Gupta1 , Prakriti Kashyap1 , Shruti Sharma1 , Bhavana Sharma1 , Satya Prakash Chaurasia1 , Sougrakpam Yaiphabi Chanu1 , Antonio Masi3 , Ganesh Kumar Agrawal4,5 , Abhijit Sarkar4,5,6,7 , Raj Agrawal7 , Michael J. Dunn8 , Jenny Renaut9 and Randeep Rakwal4,5,10,11 1
Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India 2 Department of Botany, Gargi College, University of Delhi, New Delhi, India 3 DAFNAE, University of Padova, Legnaro, Italy 4 Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal 5 GRADE Academy Private Limited, Adarsh Nagar, Birgunj, Nepal 6 DBT-RAI, Microbiology Laboratory, Department of Botany, University of Kalyani, Kalyani, West Bengal, India 7 International Plant Proteomics Organization (INPPO, www.inppo.com) 8 UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland 9 Centre de Recherche Public-Gabriel Lippman, Department of Environment and Agrobiotechnologies (EVA), Belvaux, GD, Luxembourg 10 Organization for Educational Initiatives, University of Tsukuba, Tsukuba, Japan 11 Department of Anatomy I, Showa University School of Medicine, Shinagawa, Tokyo, Japan
International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to “organize workshops at national and international levels to train manpower and exchange information”. This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26–30, 2013 titled – “1st Plant Proteomics Workshop / Training Program” under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gelbased proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it. Keywords: Collaboration / Funding agency / INPPO / Plant proteomics / Workshop
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1582
1
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
Introduction
Plant proteomics started in the early 1990s at a preliminary stage of identifying and cataloging proteins but has advanced at a rapid pace since then [1, 2]. Two-dimensional gel electrophoresis (2DE) has been a cornerstone of proteomics for the comparative proteome analysis in conjunction with mass spectrometry (MS)-based protein identification utilizing databases. 2DE-based analysis has few drawbacks like identification of merely abundant proteins, gel-to-gel variations, and no automation, leading to development of difference in gel electrophoresis (DIGE) and gel-free methods. In developing countries, universities and institutes have started incorporating equipment’s in their laboratories/central facilities, but there remains an immediate problem of handling and properly operating highend equipment’s, and subsequently training. Training work-force in proteomics requires hands-on training events, such as conducting workshops that provide a platform for exchange of ideas, learning new techniques and creation of networks (Fig. 1). This was the main reason behind initiation of an idea to have a systematic plant proteomics workshop – a first such workshop in the University of Delhi, and in fact a first plant proteomics workshop in India or Nepal. Workshops provide a period of learning and discussion where participants can interact with resource persons and widen their horizons applying the gained knowledge in their research.
2
Workshop goals, planning and organization
Workshop was organized under leadership of Dr. Renu Deswal along with her research students of the Department of Botany (University of Delhi, India) under India-Nepal Plant Proteomics Chapter (http://www.inppo.com/IndoNepallogo.jsp) of INPPO [3]. Selected participants included 10 research scholars and 10 teachers. Five students were from different research groups in Botany Department and five from other Departments/Universities. Of the 10 teachers, five were from different colleges of DU and five from outside Universities/Institutes. Organization of this workshop was itself a learning experience for members of the organizing committee.
Figure 1. Schematic illustration of the drive idea for the workshop and its importance in promoting plant proteomics.
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 1581–1586
1583
Figure 2. Flowchart of all the experiments conducted during the five-day workshop.
3
Systematic workshop on plant proteomics
The present workshop/training, spread over five days, aimed to introduce participants to the latest advancements in plant proteomic research providing hands-on training in proteomic techniques and analytical strategies. Each day started with a lecture delivered by an expert in the field followed by discussion and hands-on technical session (Fig. 2). Techniques made available to the participants included: (i) Gel-based proteome mapping – included protein extraction followed by their separation on 2D gels. Staining of gels by silver and colloidal CBB was followed by gel scanning, image analysis, spot picking, trypsin digestion, and MALDI-TOF/TOF analysis; (ii) Immunoblotting – included separation of proteins on SDS-PAGE gel, protein transfer to nitrocellulose membrane, Ponceau-S staining, and immunoblotting for detection of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) protein in crude extract of Brassica juncea seedlings; (iii) Difference-in gel electrophoresis (DIGE) – included extraction of proteins from control and stressed Hippophae rhamnoides seedlings, minimal CyDye labeling of proteins and separation on 2D gels. DIGE gel scanning on Typhoon scanner was followed by gel analysis using Decyder Software (GE Healthcare); and (iv) Gel-free proteomics – included enrichment of phosphoproteins from apoplastic fluid of Hippophae rhamnoides seedlings by TALON PMAC phosphoprotein enrichment kit, in-solution trypsin C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1584
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
Table 1. A list of invited lectures delivered during the workshop.
Session No.
Lecture title
Speakers
Affiliation
1.
Role of proteomics in understanding plant responses under abiotic stresses Evolving proteomics technology, translational proteomics, and INPPO: An open discussion
Prof. S.K. Sopory
3.
Setting up proteins and proteomics facility: An outline
4.
Identifying potential markers for coronary artery disease using quantitative proteomics approach
Dr. Shantanu Sengupta
5.
Computational tools in plant sciences and proteomics
Dr. Arun Jagannath
6.
Structural proteomics of therapeutic proteins in plants
Dr. Pravindra Kumar
7.
Current status and advances in quantitative proteomics
Dr. Kalpana Bhargava
8.
Immunodetection of proteins
Dr. Girish Mishra
9.
Protein analytical methods: Concepts, benefits and issues DeCyder – the 2D software for differential in-gel and biological variation analysis Recent advances in the field of proteomics on MS based approaches Analysis of 2D gels using ImageMaster 2DPlatinum PDQuest softwares Mr. Vipan Manhas
Dr. Prabuddha K. Kundu
Vice Chancellor, Jawaharlal Nehru University President INPPO, Vice President INPPO, University of Padua, Italy Department of Biochemistry, University of Delhi, South Campus Institute of Genomics and Integrative Biology, CSIR, Delhi Department of Botany, University of Delhi Department of Biotechnology, Indian Institute of Technology Roorkee Defence Institute for Physiological and Allied Sciences (DIPAS), DRDO, Delhi Department of Botany, University of Delhi Premas Biotech
Dr. Srijit Khan
GE (Healthcare)
Dr. Annu Uppal
AB Sciex, India
Dr. Srijit Khan Bio-Rad
GE (Healthcare)
2.
10. 11. 12.
Drs. Ganesh Kumar Agrawal, Randeep Rakwal, and Antonio Masi Dr. Suman Kundu
digestion and separation of peptides by reverse-phase column. Separated peptides were identified using LC-MS/MS. Each day started with (a) lectures (Table 1) and (b) hands-on-training, as listed below. Day 1 – Inaugural lecture and technical session I (Gel-based proteome mapping and quantitative proteomics). The “1st Plant Proteomics Workshop / Training Programme” was inaugurated by the Honorable Chief Guest, Vice-Chancellor, University of Delhi, Prof. Dinesh Singh and Honorable Guest of Honor, ViceChancellor, Jawaharlal Nehru University, Prof. Sudhir Kumar Sopory. Day 2 – Technical session II (Immunoblotting and gel-free proteomics). Day 3 – Technical session III (Qualitative proteomics, gel imaging and spot quantification). Day 4 – Technical session IV (Protein visualization, digestion and spot analysis). Day 5 – Technical session V (Protein identification by mass spectrometry-database searching). Final lectures and experiments were followed by wrap-up and troubleshooting sessions. At closing ceremony, Prof. M. M. Chaturvedi (Dean Research-Life Science, University of Delhi) shared some of his scientific experiences with participants (Fig. 3). Organizing secretary, Dr. Deswal shared experiences of organizing this workshop with delegates acknowledging support of each member, associated therein. C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 1581–1586
1585
Figure 3. Workshop participants. Name and affiliation of the participants clockwise last row – Shewta Singh*, Dr. Anjali Anand*, Dr. Kiran Bamel**, Md. Affan Baig (Jamia Millia Islamia), Javed Ahmad (Jamia Millia Islamia), Dr. Sajad Mazar Zagar***, Neha Goyal**, Romeo**, Prof. Randeep Rakwal (University of Tsukuba, Japan), Dr. Arun Jagannath**, Dr. Gayathri. T (Kerala University), Satya Prakash Chaurasia**, Dr. Charu Kalra**, Dr. Jasmeet Kaur Abat**, Dr. Arachna Singh**, Dr. Surinder Kaur**, Prerna Singh****, Neha**, Abha Singh****, Amit Kumar Mishra****, Shivangi Upadhyay**, Shatakshi Pandit**, Prachi Jain**, Pragya Barua (NIPGR), Prakriti Kashyap**, Shruti Sharma**, Ankita Sehrawat**, Bhavana Sharma**, Prof. S.C Bhatla**, Dr. Renu Deswal**, Prof. M.M Chaturvedi**, Dr. Indrakant Singh**, Ravi Gupta** and Dr. Kumar Shantanu. *Indian Agricultural Research Institute, **Delhi University, ***Jammu & Kashmir University, ****Banaras Hindu University.
4
Funding agencies, sponsorship, participant’s response and future prospects
To accomplish our goals and to successfully execute our ideas, good financial support was successfully obtained. Since the workshop consisted of participants from different backgrounds like Zoology, Environmental Science, Biochemistry, Biotechnology, and Botany, and as many of them did not have any prior experience in proteomics, a manual containing basic information of proteomics including experimental procedures of each and every technique used in the workshop was prepared; a print out in a booklet form was provided to all participants. Feedback forms submitted by participants had many positive comments and suggestions, based on which we would like to continue the workshop with certain improvements, such as more attention would be given to the gel-free approaches and DIGE. Workshop will also serve as a model for workshops at other universities and institutes. As it is a universal fact that in biological sciences, majority of the students are women, especially true for Department of Botany, therefore, in this workshop also a large percentage of the participants and instructors were women. This workshop would help in shaping their future as better scientists as well as teachers because with a basic knowledge of proteomics they will have an edge over C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
1586
R. Deswal et al.
Proteomics 2014, 14, 1581–1586
others in the competitive field of plant biology. In all, the vision for the workshop and goals that we started with were accomplished during this five-day workshop. However, the true outcome of the workshop will be reflected by the utilization of this training by the participants in their science and publications that follow, along with the establishment of even the basic facilities to do proteomics of plants in their laboratories and in turn train their juniors and/or colleagues. The workshop effort is already bearing fruits as two University of Delhi trainee teachers Drs. Inderkant and Shantanu from this workshop recently organized a two-day workshop in Genomics and Proteomics in March 2014, in a Delhi University associated college.
5
Advanced training and exchange programs
An important issue discussed on the sidelines of the workshop was the meeting between Drs. Renu Deswal (India), Ganesh Kumar Agrawal (Nepal), Antonio Masi (Italy), and Randeep Rakwal (Japan / India) on the development of an advanced training and exchange program for the deserving students and young researchers from India and Nepal, in plant proteomics. The aim was two-fold: first, to develop a collaborative project between India / Nepal and Italy, and, second, to help students in India / Nepal to carry out advanced research in gel-based and gel-free proteomics in an advanced laboratory outside their respective countries by either sending their samples for protein separation and identification by MS or having the candidate visit the collaborative laboratory. It is our hope that such a collaborative research project would help promote the INPPO spirit of open collaboration and exchange between plant proteomics researchers. Authors gratefully acknowledge great support of Department of Botany, University of Delhi, for providing space, technical support, and equipment’s for organizing the workshop. Delhi University Botanical Society (DUBS) is acknowledged for help extended in handling finance of the workshop. The workshop would not have been possible without support from members of organizing committee. Academic and Commercial sources of funding is appreciated from – Department of Biotechnology, Department of Science and Technology, Government of India (printing, travel and hospitality); Delhi University as well as Head, Department of Botany (chemicals); Bio-Rad (consumables and technical assistance); GE Healthcare (consumables, stationary for workshop kit, technical assistance); Abhishek Glass Industrial Corporation (advertisement for manual); and Genetix (advertisement for manual). INPPO is highly grateful to PROTEOMICS and in particular, Professor Michael J. Dunn, Editor-in-Chief, PROTEOMICS, and Dr. Hans-Joachim Kraus, Senior Publishing Editor, Wiley, Weinheim (Germany) for generous support in making possible the INPPO highlights. Authors deeply thank Dr. Thomas Kieselbach (Department of Chemistry, Umea University, 90187, Umea, Sweden) for his reading of the manuscript and critical comments to highlight goals and outcomes of the workshop. The full report on the workshop can be accessed at: http://www.inppo.com/pdf/workshop/DeswaletaFullManuscriptHighlights.pdf The authors have declared no conflict of interest.
6
References
[1] Agrawal, G. K., Rakwal, R. (Eds.), Plant Proteomics: Technologies, Strategies, and Applications. Wiley & Sons, Hoboken, NJ, USA, 2008. [2] Agrawal, G. K., Job, D, Zivy, M, Agrawal, V. P. et al., Time to articulate a vision for the future of plant proteomics – A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 2011, 11, 1559– 1568. [3] Deswal, R., Gupta, R., Dogra, V., Singh, R., et al., Plant proteomics in India and Nepal: Current status and challenges ahead. Physiol. Mol. Biol. Plants 2013, 19, 461–477. C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
