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.     

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.     

Some highlights of research on aging with invertebrates, 2006-2007

The invertebrate model organisms continue to be engines of discovery in aging research. Recent work with Drosophila stem cells has thrown light on their human equivalents, and on the role of stem cells and their niches in the decline in fecundity with age. Inspired by observations of aging in bacteria and yeast, a new theoretical study has revealed evolutionary forces that could favour asymmetry in the distribution of damaged cell constituents at division, and hence pave the way for the evolution of aging and selective maintenance of integrity of the germ line. Mechanisms of nutrient sensing and cell signalling in the response of lifespan to dietary restriction have been elucidated. Powerful invertebrate models of human aging-related disease have been produced, and used to start to understand how the aging process acts as a risk factor for disease. In the near future, studies of invertebrate aging are likely to move away from an exclusive reliance on genetic manipulation towards a more biochemical and physiological understanding of these systems.     

Defining the mandate of proteomics in the post-genomics era: workshop report

Research in proteomics is the next step after genomics in understanding life processes at the molecular level. In the largest sense proteomics encompasses knowledge of the structure, function and expression of all proteins in the biochemical or biological contexts of all organisms. Since that is an impossible goal to achieve, at least in our lifetimes, it is appropriate to set more realistic, achievable goals for the field. Up to now, primarily for reasons of feasibility, scientists have tended to concentrate on accumulating information about the nature of proteins and their absolute and relative levels of expression in cells (the primary tools for this have been 2D gel electrophoresis and mass spectrometry). Although these data have been useful and will continue to be so, the information inherent in the broader definition of proteomics must also be obtained if the true promise of the growing field is to be realized. Acquiring this knowledge is the challenge for researchers in proteomics and the means to support these endeavors need to be provided. An attempt has been made to present the major issues confronting the field of proteomics and two clear messages come through in this report. The first is that the mandate of proteomics is and should be much broader than is frequently recognized. The second is that proteomics is much more complicated than sequencing genomes. This will require new technologies but it is highly likely that many of these will be developed. Looking back 10 to 20 years from now, the question is: Will we have done the job wisely or wastefully? This report summarizes the presentations made at a symposium at the National Academy of Sciences on February 25, 2002.     

Recent activities of the Microbiology in Schools Advisory Committee

Ecology and evolution

Agricultural education

Evolution and education

Education division elections

ISII in Europe

Tree project

Science teaching scholarship

Biology of terrestrial arthropods

A microscopied museum     

Prevalence and subtypes of Influenza A Viruses in Wild Waterfowl in Norway 2006-2007

The prevalence of influenza A virus infection, and the distribution of different subtypes of the virus, were studied in 1529 ducks and 1213 gulls shot during ordinary hunting from August to December in two consecutive years, 2006 and 2007, in Norway. The study was based on molecular screening of cloacal and tracheal swabs, using a pan-influenza A RT-PCR. Samples found to be positive for influenza A virus were screened for the H5 subtype, using a H5 specific RT-PCR, and, if negative, further subtyped by a RT-PCR for the 3'-part of the hemagglutinin (HA) gene, encompassing almost the entire HA2, and the full-length of the neuraminidase (NA) gene, followed by sequencing and characterization. The highest prevalence (12.8%) of infection was found in dabbling ducks (Eurasian Wigeon, Common Teal and Mallard). Diving ducks (Common Goldeneye, Common Merganser, Red-breasted Merganser, Common Scoter, Common Eider and Tufted Duck) showed a lower prevalence (4.1%). In gulls (Common Gull, Herring Gull, Black-headed Gull, Lesser Black-headed Gull, Great Black-backed Gull and Kittiwake) the prevalence of influenza A virus was 6.1%. The infection prevalence peaked during October for ducks, and October/November for gulls. From the 16 hemagglutinin subtypes known to infect wild birds, 13 were detected in this study. Low pathogenic H5 was found in 17 dabbling ducks and one gull.     

Dynamics of the 2006/2007 dengue outbreak in Brazil

We analyzed dengue incidence in the period between October 2006-July 2007 of 146 cities around the country were Larval Index Rapid Assay (LIRA) surveillance was carried out in October 2006. Of these, we chosen 61 cities that had 500 or more cases reported during this period. We calculated the incidence coefficient, the force of infection (lambda) and the basic reproduction number (R0) of dengue in those 61 cities and correlated those variables with the LIRA. We concluded that lambda and R0 are more associated with the number of cases than LIRA. In addition, the average R0 for the 2006/2007 dengue season was almost as high as that calculated for the 2001/2002 season, the worst in Brazilian history.     

Epidemiologic situation and measures for prevention of infectious diseases in Sverdlovsk region in 2006-2007

Materials characterizing the epidemiologic situation on most significant infectious diseases in Sverdlovsk region are presented. Experience on providing the epidemiologic welfare based on systematic surveillance for activity of various factors influencing the epidemic process is described.     

2006年至2007年我院烧伤创面感染细菌及耐药性监测

目的了解近2年本所分离菌株和耐药情况。方法采用纸片扩散法（KB法）和采用CLSI2006年的判断标准对595株临床分离菌做药敏试验。结果595株细菌中G^-菌占61．51％,G^＋菌占36．3％;G^-球菌占0．84％,真菌占1．75％。发现铜绿假单胞菌对头孢曲松、头孢呋新、头孢塞肟和哌拉西林耐药率高达92．5％-99．1％,更甚者为鲍曼不动杆菌,对头孢唑啉、头孢曲松、头孢哌酮和丁胺卡那霉素耐药率均高达100％。变形杆菌和大肠埃希菌耐药性相对较低。结论烧伤感染常见菌为铜绿假单胞菌、鲍曼不动杆菌、变形杆菌和金葡菌,而且耐药性很强。     

Comments on the sixth report of the Animal Welfare Advisory Committee

The Animal Welfare Advisory Committee (AWAC) was established in July 1996, to consider the care, welfare and use of animals involved in procedures for defence research purposes at Defence and Evaluation Research Agency (DERA) establishments in the UK. Two of the objectives of AWAC are to examine the broad trends in animal use at DERA establishments, and to implement and audit the application of the Three Rs principle. AWAC's sixth report addressed the period from 31 October 2000 to 28 February 2002. The statistics of animal use within the report are briefly examined, and some of the actions undertaken by defence research establishments to facilitate the application of the Three Rs are highlighted. It is recommended that, if possible (subject to security constraints), figures detailing the severity of the procedures undertaken should be included in future issues of the report, in order to provide a more-detailed account. It is concluded that Defence Science and Technology Laboratory establishments have made a contribution to the Three Rs, and that other establishments may be able to incorporate some of their actions into their own research programmes. There was an overall 36% increase in the number of procedures carried out by defence research establishments between 1995 and 2000, from 8,900 to 12,065. This probably reflects alterations in the research programme, which is, in turn, decided primarily by the Ministry of Defence's customers and the progress made with previous research programmes. It is therefore recommended that the UK Government allocates significantly more financial resources for the development and validation of alternatives, in order to maximise the potential for achieving the Three Rs in defence research, and to complement the existing initiatives within the defence research industry.     

Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly

A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5-35 kpsi was demonstrated for proteomic analysis. Successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. Method performance in terms of the number of Shewanella oneidensis peptides and proteins identified in a shotgun approach was evaluated relative to a traditional "overnight" sample preparation method. Advantages of the new method include greatly simplified sample processing, easy implementation, no cross contamination among samples, and cost effectiveness.     

Integrative proteomics: structure, function, and interaction report on the 3rd joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, July 2006

This report summarizes the highlights of the recent British Society for Proteome Research (BSPR) meeting jointly organized with the European Bioinformatics Institute (EBI) which was held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK in July 2006. This was the third annual scientific meeting organized by the BSPR and EBI and the theme of this years meeting was Integrative Proteomics: Structure, function and interaction. A wealth of local and overseas speakers were invited to discuss both their own work and specific challenges present in modern day proteomic based experiments.     

Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer

Functional proteomics approaches that comprehensively evaluate the biological activities of human cDNAs may provide novel insights into disease pathogenesis. To systematically investigate the functional activity of cDNAs that have been implicated in breast carcinogenesis, we generated a collection of cDNAs relevant to breast cancer, the Breast Cancer 1000 (BC1000), and conducted screens to identify proteins that induce phenotypic changes that resemble events which occur during tumor initiation and progression. Genes were selected for this set using bioinformatics and data mining tools that identify genes associated with breast cancer. Greater than 1000 cDNAs were assembled and sequence verified with high-throughput recombination-based cloning. To our knowledge, the BC1000 represents the first publicly available sequence-validated human disease gene collection. The functional activity of a subset of the BC1000 collection was evaluated in cell-based assays that monitor changes in cell proliferation, migration, and morphogenesis in MCF-10A mammary epithelial cells expressing a variant of ErbB2 that can be inducibly activated through dimerization. Using this approach, we identified many cDNAs, encoding diverse classes of cellular proteins, that displayed activity in one or more of the assays, thus providing insights into a large set of cellular proteins capable of inducing functional alterations associated with breast cancer development.