The transition of the European Proteomics Association into the future

The following report provides an overview of the discussions and outcome of the EuPA General Council meeting that took place in Estoril 20-21 October 2010. During the annual meeting future policy and action plans in a variety of areas are decided. Several important points were decided upon during this meeting including the expansion of the EuPA Executive Committee by introducing a new EuPA committee - EuPA Developments - that will initially spearhead activities in standardisation, imaging ms and biobanking. The EuPA General Council also invited Russia as its 17th member. More details about these and additional activities are presented in the article.     

EuPA achieves visibility - an activity report on the first three years

Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteomics organizations in their efforts; ii) to co-ordinate and provide educational programs, and iii) to advance the networking of scientists through meetings, workshops and student exchange. Linked to the mission were objectives to emphasise the benefits and contributions of Proteomics to biological and industrial researchers, the general public and science policy makers in Europe. In addition, the EuPA set out to promote scientific exchange for all applications and technology development related to Proteomics, and coordinate joint activities of national Proteomics societies at the European level. To achieve these tasks an organisational structure was conceived whereby four Activity Committees (Conferences/Communications, Education, EuPA-HUPO-Interactions and Funding) were implemented and a General Council consisting of all member countries. The remarkable rise and progress the EuPA has achieved in this small time frame is reported here.     

Promoting proteomics knowledge in Europe: report on the activities of the EuPA Education Committee 2006-2007

The early transition of knowledge from highly specialised and sophisticated proteomics research to a diverse community in need of know-how is a challenge that requires backing from advanced research centres and groups, and a coordinating body for the dissemination of this knowledge. The European Proteomics Association (EuPA) Education Committee signified this as a priority area when the EuPA was formed, and began its program to coordinate proteomics training and knowledge dissemination in 2006. This report serves as an update of our past activities and an announcement of upcoming events. Over the last year the EuPA Education Committee has coordinated or supported different educational activities including basic and advanced courses, a summer school, workshops and tutorials. A new programme of basic courses dubbed "Teaching the Teachers" has been initiated. These courses reach a larger, Europe wide, audience in a short timeframe, thus improving the opportunities for trainees of elementary proteomics techniques. Another important event has been the merger of the EuPA and HUPO (Human Proteome Organisation) Education Committees into a single one in order to combine ideas and ef for ts that will favour global education in proteomics.     

Report on the first congress of the Spanish Proteomics Society

This report describes the first congress of the Spanish Proteomics Society (SEProt) and the Foundation Meeting of the European Proteomics Association (EuPA), which were held in Cordoba, Spain, February 13-17, 2005. The EuPA meeting joined together thirty European representatives from 17 national European proteomics organisations to discuss the opportunity of creating a supranational association aimed to promote all aspects of proteomics as a scientific discipline throughout Europe. The main subjects of the SEProt congress, which was attended by over 350 researchers mainly from Spain and other European countries, were the current status and applications of proteomics in medical and biological sciences.     

C.-E.A. Winslow Day: Proceedings of the June 3, 1977 Centenary Celebration

Sponsored by Yale University, the City of New Haven, and the John B. Pierce Foundation, the C.-E.A. Winslow Day program consisted of speeches by Mr. Leonard Woodcock, President Emeritus, U.A.W., the Honorable Kenneth Gibson, Mayor of Newark, and Dr. Hector Acuña, Director, Pan American Health Organization; reminiscences of Ira Hiscock, Anna M.R. Lauder Professor Emeritus of Public Health, Mary Elizabeth Tennant, Associate Professor Emeritus of Nursing (Public Health), A. Pharo Gagge, Emeritus Fellow, John B. Pierce Foundation, and Mrs. Harriet Welch, Former President of the VNA of New Haven. The proceedings also included the presentation of gifts and the official C.-E.A. Winslow Day Proclamation.     

The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.     

In Remembrance: Professor Qian Ying-Qian(1932-2010)

Professor Qian Ying-Qian,a renowned Chinese plant biologist and a member of the editorial board of Acta Botanica Sinica(predecessor of JIPB)1989-1993,passed away in Beijing on April 20,2010 at the age of 78.Professor Qian was a former Secretary-General(1978-1988),and Vice President of the Chinese Botanical Society(1988-1999).     

Report. Proteomics education, an important challenge for the scientific community: report on the activities of the EuPA Education Committee

The main missions of the EuPA Education Committee (EuPA-EC) are to promote and enhance the quality of proteomics knowledge by creating educational programs and to initiate European-wide scientific exchange programs for young proteomics researchers. In this first report we present the initial actions we have undertaken in relation to the missions of the EuPA-EC, and the educational activities that have been planned for 2007-2008. These activities include courses (basic and advanced courses and a summer school), workshops, laboratory networking and tutorials.     

The Chromosome‐centric Human Proteome Project at FEBS Congress

In the summer of 2013, distinguished global representatives of proteome science gathered to discuss the futuristic visions of the chromosome‐centric human proteome project (C‐HPP) (Cochairs: Y. K. Paik, G. Omenn; hosted by A. Archakov, Institute of Biomedical Chemistry, Russia) that was broadcast to the annual Federation of European Biochemical Societies Congress (St. Petersburg, Russia, July 10–11, 2013). Technology breakthroughs presented included a new ultra‐sensitive Tribrid mass‐spectrometer from Thermo and SOMAmers—Slow Off‐rate Modified Aptamers (SOMAlogic, USA), a new type of protein capture reagents. Professor Archakov's group introduced the “rectangle” concept of proteome size as a product of proteome width and depth. The discussion on proteome width culminated with the introduction of digital biomarkers—low‐copied aberrant proteins that differ from their typical forms by PTMs, alternative splicing, or single amino acid polymorphisms. The aberrant proteoforms, a complement to whole‐genome proteomic surveys, were presented as an ultimate goal for the proteomic community.     

The current status of cardiovascular surgery in the People's Republic of China

Dr. David Bregman was invited to participate in a thirteen-physician American Teaching Delegation led by Dr. Tsung O. Cheng, Professor of Medicine at George Washington University Medical Center in Washington, D.C. The trip was sponsored by the American College of Physicians. Deputy Director of the delegation was Dr. Samuel Asper, Deputy Executive Vice President of the American College of Physicians and Professor of Medicine at Johns Hopkins University. The American Teaching Delegation was the first of its kind to be invited to lecture and impart new medical-surgical techniques throughout the People's Republic of China. The trip lasted approximately one month, from September to October, 1979, and included the September 30 to October 1 celebrations in Peking commemorating the 30th Anniversary of the founding of the People's Republic of China. Principal cities visited were Peking and Shanghai, as well as Chengtu, Chungking, and Wuhan. Dr. Bregman demonstrated, for the first time in the People's Republic of China, intraaortic balloon pumping, a new percutaneous intraaortic balloon, and other cardiac assist techniques.     

Reflections on a Life in Biomedicine: Leading Change

Dr. Elizabeth Nabel delivered the following presentation as the Lee E. Farr Lecturer on May 7, 2013, which served as the culmination of the annual Student Research Day at Yale School of Medicine. Dr. Nabel is President of the Brigham and Women’s Hospital in Boston, Massachusetts, and Professor of Medicine at Harvard Medical School. Her lecture to Yale medical students portrayed her own personal and professional journey through medicine as a series of opportunities. Dr. Nabel focused on the roles and responsibilities of physicians to recognize need and to make change through focused advocacy.     

The manzanar project: Towards a solution to poverty, hunger, environmental pollution, and global warming through sea water aquaculture and silviculture in deserts

Summary Dr. Gordon Sato is a former Editor-in-Chief of In Vitro Cellular and Developmental Biology, President of the Tissue Culture Association (now Society for In Vitro Biology), and Director of the W. Alton Jones Cell Science Center (now Adirondack Biomedical Center). He began pilot experiments on the Manzanar Project at test sites in the Salton Sea while a Professor of Biology at the University of California, San Diego and continued the project in the laboratory at the Cell Center in Lake Placid, NY and at Eritrean test sites during their war of independence. Since 1994, he spends up to 10 mo. per yr in Eritrea where he directs the Manzanar Project and trains young Eritrean scientists in the field in the area of what he refers to as “low-tech biotech.” The name of the Manzanar Project was inspired by the camp in California where Dr. Sato and his family were interned during World War II.—The Editor     

The management of European estuaries: A comparison of the features,controls and management framework of the Tagus (Portugal) and Humber (England)

The paper describes the local, national, European and wider-area framework, statutes, and formal and voluntary mechanisms for managing European estuaries. These aspects are discussed in relation to two large and representative estuarine systems, the Tagus, Portugal, and the Humber, on the English North Sea coast As estuaries are sites of many activities and uses, most of which are encouraged or at least condoned, management has the role of preventing and resolving conflicts between those uses and users. Accepted uses of estuaries include the discharge and dumping of waste materials, fin and shell-fisheries, conservation, land reclamation, natural usage, abstraction by industry, and recreation. Estuarine management is now being carried out within the constraints of local and regional government planning, planning and activities of water pollution control bodies, fisheries control bodies, and navigation and port authorities The Tagus and Humber estuaries support all of the above activities and uses, and have controls within a European legislative framework but have differing histories of management and planning in order to resolve conflicts. In addition the Humber is subject to controls placed on North Sea areas. The paper discusses the relevant national and European legislation (Directives) and accepted practices for management. Furthermore, the paper discusses the formulation and practice of estuarine management plans as used by various bodies (nature conservation, water quality and regional authority). It is of particular note that the lessons from these two estuaries are relevant to many other European estuaries.     

Dietary protein source affects lipid metabolism in the European seabass (Dicentrarchus labrax)

The study was undertaken to evaluate the effects of dietary protein sources on lipogenesis and fat deposition in a marine teleost, the European seabass (Dicentrarchus labrax). Four isonitrogenous (crude protein (CP, Nx6.25), 44% DM) and isoenergetic (22-23 kJ/g DM) diets were formulated to contain one of the following as the major protein source: fish meal (FM), one of two soy protein concentrates (SPC) and corn gluten meal (CGM). Apparent digestibility coefficients of the diets and raw ingredients, as well as soluble nitrogen (ammonia and urea) and phosphorus excretion were measured. Growth rates of seabass fed plant protein-based diets were significantly lower than those fed fish meal based diet. The protein utilisation was strongly correlated to the dietary essential amino acids index. Measurements of N excretion (ammonia and urea nitrogen) confirmed these data. Daily fat gain at the whole body level ranged between 1.1 to 1.7 g/kg BW, with the highest values being recorded in fish fed the fish meal based diet. Levels of plasma triglycerides and cholesterol were lower in fish fed soy protein diets than in those fed the diet solely based on fish meal. Soy protein rich diets decreased the activities of selected hepatic lipogenic enzymes (glucose 6-phosphate dehydrogenase, malic enzyme, ATP-citrate lysase, acetylcoenzyme A carboxylase and fatty acid synthetase). Highest lipogenic enzyme activities where found in fish fed the fish meal diet, except for fatty acid synthetase which was increased in seabass fed the corn-gluten meal based diets. Overall data suggest that dietary protein sources affects fat deposition and the lipogenic potential in European seabass.     

Surgical transfer of in vivo produced farmed European polecat (Mustela putorius) embryos

Surgical embryo transfer of farmed European polecat (Mustela putorius) was investigated as part of an ex situ preservation project. The long-term objective of the project is to develop effective technology for ex situ conservation of the European mink (Mustela lutreola), which is a highly endangered aboriginal European species. Twenty European polecat females, which served as a model species for the European mink, were humanely killed 4-9 days after first mating and embryos were recovered from oviducts and uteri. Donor-recipient pairs (n = 16) were generated by mating the donors (n = 20) once a day for 2 consecutive days with fertile males and by mating the corresponding recipients (n = 16) on the same days with vasectomized males. An embryo recovery rate of 70% (200 recovered embryos/284 corpora lutea) was achieved from 20 donors. Morulae and blastocysts were recovered between Days 5 and 9 after first mating and were regarded as the best developmental stages for uterine embryo transfer. A total of 172 embryos were transferred surgically under general anaesthesia into the ovarian third of the left uterine horn of 16 recipients with a thin glass capillary. Eleven recipients (69%) produced 72 pups equivalent to an average success rate of 42% (72 pups/172 transferred embryos). The average litter size was 4.5 (range 0-9). These results with this model species, farmed European polecat, demonstrate the potential of embryo transfer as an effective method for the preservation of the endangered European mink (M. lutreola). These species are closely related and have a similar reproductive physiology. However, success of applying embryo transfer in conserving European mink is still dependent on further studies both into its reproductive physiology and developing of improved flushing techniques for anaesthetized donors and the successful transfer of frozen-thawed embryos.     

The Human Liver Proteome Project (HLPP) workshop during the 4th HUPO World Congress

The Human Liver Proteome Project (HLPP) is the first initiative of the Human Proteome Organisation (HUPO) to target a human organ/tissue and aims at the establishment of a biological atlas of the liver to advance our understanding of liver functions and to provide the tools to develop new diagnostics and therapeutics for liver diseases. The major achievements of HLPP during its pilot phase (2003-2005) were presented during a one-day workshop held on August 27, 2005, immediately prior to the 4th HUPO World Congress in Munich, Germany. These include (i) the participation of a large number of laboratories worldwide and the initiation of international research collaborations; (ii) the establishment of a management infrastructure and (iii) the development of standard operating procedures and the generation and collection of a first set of expression profile data. A summary of the workshop was subsequently presented by Professor Fuchu He, the Chair of this initiative, during the HUPO 4th Annual World Congress.     

The International Proteomics Tutorial Programme--reaching out to the next generation proteome scientists

One of the most critical functions of the various Proteomics organizations is the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with the other local proteomics associations are therefore launching a joint Tutorial Program to meet these needs. The level is aimed at Masters/PhD level students with good basic training in biology, biochemistry, mathematics and statistics. The Tutorials will consist of a review/teaching article with an accompanying talk slide presentation for classroom teaching. The Tutorial Program will cover core techniques and basics as an introduction to scientists new to the field. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organizations homepages.     

Retinohypothalamic pathway in the duck (Anas platyrhynchos)

Summary Retinohypothalamic connections were studied in the duck after unilateral optic nerve transection using both light and electron microscopic techniques. Degenerated endings of optic fibers were found only in a circumscribed part of the anterior hypothalamic area, i.e. the ventral region of the contralateral suprachiasmatic nucleus. Images of degenerating boutons were observed in frozen sections (method according to Johnstone-Bowsher), and their presence confirmed by electron microscopic examination. These degenerating boutons make synaptic contacts with dendrites or dendritic spines of neurons of the suprachiasmatic nucleus.In the same material, the decussation of the optic chiasma was studied with the light microscope. Uncrossed retinal fibers were found in the marginal optic tract, the basal optic root and occasionally also in the isthmo-optic tract.Dedicated to Professor Dr. W. Bargmann on the occasion of his 70th birthdaySupported by the DGRST and European Training Program Brain and Behaviour ResearchI wish to express my gratitude to Professor Andreas Oksche, who repeatedly offered me the scientific facilities at the Department of Anatomy of the University of Giessen, and who provided me with valuable neuroanatomical suggestions throughout the progress of these studies.     

Four Children and Yale: The Making of a Human Geneticist: The Grover Powers Lecture 2014

Dr. Leon E. Rosenberg delivered the following presentation as the Grover Powers Lecturer on May 14, 2014, which served as the focal point of his return to his “adult home” as a Visiting Professor in the Department of Pediatrics. Grover F. Powers, MD, was one of the most influential figures in American Pediatrics and certainly the leader who created the modern Department of Pediatrics at Yale when he was recruited in 1921 from Johns Hopkins and then served as its second chairman from 1927 to 1951. Dr. Powers was an astute clinician and compassionate physician and fostered and shaped the careers of countless professors, chairs, and outstanding pediatricians throughout the country. This lectureship has continued yearly since it first honored Dr. Powers in 1956. The selection of Dr. Rosenberg for this honor recognizes his seminal role at Yale and throughout the world in the fostering and cultivating of the field of human genetics. Dr. Rosenberg served as the inaugural Chief of a joint Division of Medical Genetics in the Departments of Pediatrics and Internal Medicine; he became Chair when this attained Departmental status. Then he served as Dean of the Medical School from 1984 to 1991, before he became President of the Pharmaceutical Research Institute at Bristol-Myers Squibb and later Senior Molecular Biologist and Professor at Princeton University, until his recent retirement. Dr. Rosenberg has received numerous honors that include the Borden Award from the American Academy of Pediatrics, the McKusick Leadership Award from the American Society for Human Genetics, and election to the Institute of Medicine and the National Academy of Sciences.