'Proteomic basics--sample preparation and separation': the 1st European Summer School in Kloster Neustift, 12-18 August, 2007 Brixen/Bressanone, South Tyrol, Italy

Proteomics is rapidly developing into a routine approach for protein analysis in many laboratories. The series of European-wide Summer Schools 'Proteomics Basics' (http://www.proteomic-basics.eu/) aims at teaching of comprehensive knowledge in proteomics research and applied technologies for master and graduate students and postdocs currently moving into the field of proteomic research. In the next 3 years the series will cover the theoretical basis of the fundamental topics in the various areas of proteomic analysis, i.e. sample preparation and handling, mass spectrometry, post-translational modifications and quantitation given by leading experts in the field. This summer school series embodies a unique advantage in comparison with conventional scientific meetings and university curricula: internationally renowned experts will give a detailed perspective view of the fundamentals of their particular proteome research area, something which is usually not encountered at conferences and congresses. Here, we give a report on the first European Summer School 'Sample Preparation and Handling' within the series 'Proteomic Basics' that was held at the monastery in Neustift close to Bressanone/Brixen, Italy from August 12 to 18, 2007.     

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea

Proteomics Data Collection (ProDaC) is an EU-funded "Coordination Action" within the 6th framework programme. It aims to simplify the publication, dissemination and utilization of proteomics data by establishing standards that will support broad data collection from the research community. As a part of ProDaC, regular workshops are organized on a half-yearly basis to enable communication and discussion of the involved partners and to report on project progress. After the kick-off meeting (October 2006) in Long Beach, CA, USA and the 1st workshop in Lyon, France (April 2007), the 2nd ProDaC workshop took place at the COEX InterContinental Hotel in Seoul, Korea, on 5th October 2007, shortly before the HUPO World Congress. The progress achieved within the first year was presented by the leaders of the work packages. Additionally, a Journal's representative talked about his experiences and future plans concerning Proteomics standards; and two further external speakers presented their research related to data handling and Proteomics repositories.     

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation provided an opportunity to update delegates on the progress of the work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) to develop and implement standards in the field of proteomics. Significant advances have been made since the previous congress, with several of the interchange standards and minimal requirements documents being submitted for publication in the literature and being more widely adopted by both manufacturers and data repositories. An exciting development over the interim twelve months is the ongoing merger of the two existing mass spectrometry standards, the PSI mzData and Institute for Systems Biology mzXML, into a single product. This should be achieved by early in 2007.     

Quality meets quantity - quality control, data standards and repositories

In recent years, standardization and quality control have become important key points in industry, e.g. in drug discovery and for developing medical products. Is quality control in academic Proteomics a minor problem nowadays, where standard data formats and public repositories for data sharing exist? In this article, it is discussed how standard formats and repositories already support the documentation of quality control criteria in protein identification and quantification, and what has to be improved in the future: It is stated that the Proteomics community (represented by a group like the Proteomics Standards Initiative) will have to define a minimum document regarding quality control and to extend existing standards with additional quality control criteria enabling a substantial and standardized quality control process.     

承德市避暑山庄植被生态规划有关问题的探讨

本文首先对避暑山庄现状植被及存在的问题进行研究,绘制了现状植被图;然后分析了旅游及城市化对避暑山庄土壤及植物的影响程度以及不同生境土壤中N,P、K、有机质、水分含量及pH大小,针对避暑山庄不同游览区存在的植物配置不协调、生境不适、环境污染等问题,从植被生态角度出发对避暑山庄进行了规划和设计,最后完成了1:10000规划植被图。     

Protein in gels, computers, crystals and camels

The IBC's Proteomics 2001 meeting was held in Philadelphia, PA, USA, 14-17 May 2000.     

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.     

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.     

Rejuvenating rice proteomics: facts, challenges, and visions

Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.     

On an introduced weevil <Emphasis Type="Italic">Polydrusus formosus</Emphasis> (Mayer) (Coleoptera,Curculionidae: Entiminae) in the Summer Garden,St. Petersburg

In the summer of 2015, Polydrusus formosus was found in the Summer Garden, St. Petersburg on Tilia cordata in the trellises and berceau restored in 2011. This weevil was known in the European part of the former USSR only in Moldova and Crimea. The finding of 6 individuals of Polydrusus formosus only on the linden trellises may be due to an unintended introduction of the weevils (probably only a single fertilized female) with the plants from Germany and maintenance of the population in the Summer Garden for already five years.     

Genomics,proteomics and bioinformatics: all in the same boat

A report on the Genomics, Proteomics and Bioinformatics for Medicine (GPBM) 2002 meeting, St. Petersburg to Moscow, Russia, 22-30 June 2002.     

The AOHUPO Membrane Proteomics Initiative, Fourth Workshop 22 June 2008, Cairns, Australia

The Fourth Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative (AOHUPO MPI) Workshop took place on 22 June 2008 in Cairns, Australia, with approximately 90 attendees from academia and industry. Participants from ten of the seventeen collaborating centres presented workshop papers. This was part of the pre-conference programme of the Joint Fourth Asian Oceania Human Proteome Organisation Conference and the Second Pacific Rim International Conference on Protein Structure.     

Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow

The European Proteomics Association (EuPA) 2012 Scientific Congress ‘New Horizons and Applications for Proteomics’, hosted by the British Society for Proteome Research (BSPR)

Glasgow, Scotland, UK, 12 July 2012

Cross-linking/mass spectrometry ended decades of method developments and entered the era of applications at this year’s European Proteomics Association meeting. The train has started moving, with successful applications of this tool by multiple pioneering laboratories addressing biological and structural problems. Proteomics, on the other side, sees ever increasing data volumes, leading to questions as to how to store the data mountain publically, use it and convert it into testable hypotheses. The European Proteomics Association meeting has been complementary to the American Society for Mass Spectrometry meeting in many ways, also thanks to its more manageable size and the vision of the organizers in inviting some of Europe’s best emerging minds.     

Anti-phase oscillation of Asian monsoons during the Younger Dryas period: Evidence from peat cellulose δC of Hani, Northeast China

Significant changes in the global atmospheric and oceanic circulation system occurred during the Younger Dryas cold period. Several researchers have demonstrated a weakening of intensity of the Indian Ocean Summer Monsoon during that period. However, the exact characteristics of the East Asian Summer Monsoon still remain vague. Here we present a late-glacial precipitation proxy record of the East Asian Summer Monsoon, based on the peat cellulose δ¹³C found in Hani, Northeast China. Both the peat cellulose record and a pollen record from Lake Sihailongwan sediment indicate an abrupt increase in precipitation in the region during the Younger Dryas period. These results support the occurrence of wet conditions in the north and of dry conditions in the south of the Chinese Mainland during that period. By examining the activity of the East Asian Summer Monsoon on an interannual timescale, we propose a theory for the anomalous precipitation distribution that we attribute to the occurrence of an El Niño-like phenomenon in the Equatorial Pacific Ocean during the Younger Dryas. In this case, the intensity of the Western Pacific subtropical high may strengthen, and its position over the western Pacific Ocean may move northward. This could cause an enhancement of the East Asian Summer Monsoon and migration of a monsoonal rainbelt towards the northern region of the Chinese mainland, resulting in a precipitation distribution of wet conditions in the north and dry conditions in the south. Therefore, this anomalous rainfall distribution should be considered to indicate the strengthening of the East Asian Summer Monsoon, in anti-phase with the Indian Ocean Summer monsoon that weakened during the same period. This agrees with the previously revealed anti-phase variations of the two monsoons during the ice-rafted debris cold events of the North Atlantic Ocean. It appears that, in relation to the abrupt temperature drop in the Northern Hemisphere on centennial to millennial time scales, anti-phase variations of the two Asian summer monsoons occurred.     

蛋白质组学在结核分枝杆菌研究中的应用

蛋白质组学是在基因组学基础上发展起来的新兴学科, 其基本技术包括样品制备、蛋白质分离和蛋白质鉴定分析, 其中的核心技术是双向凝胶电泳技术(2-Dimensional Electrophoresis, 2-DE)和质谱技术(Mass Spectrometry, MS)。近年来, 蛋白质组学技术已应用于结核分枝杆菌的研究领域。应用蛋白质组学技术分离、鉴定、检测结核分枝杆菌致病株的全菌蛋白及分泌蛋白, 分析其蛋白组成, 可深入解析结核分枝杆菌的致病机理和耐药机制。通过对结核分枝杆菌致病株抗原的分析, 为研制预防结核病的新型疫苗拓展了空间。通过对结核分枝杆菌临床分离株的蛋白组成分析还发现了一些有意义的结核病早期诊断标志物。蛋白质组学技术还应用于寻找新的药物靶标, 在研制和筛选新的抗结核药物等方面展示了一些有价值的研究成果, 为更好地开展结核病的预防、早期诊断及治疗打下了基础。     

Virtual Labs in proteomics: new E-learning tools

Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/.     

Proteomics for Biological Discovery * Edited by T.D. Veenstra and John R. Yates

An understanding of the roles and interactions of proteins withincells is vital to our understanding of biology. Proteomics hascome a long way, and covers many areas now, since the inventionof 2 dimensional gel electrophoresis in the 1970s, or the coiningof the term proteomics in the 1990s. As more people move intothis important area, there is a need for guides to aid thesemoves. Proteomics for Biological Discovery aims to serve assuch a guide. The format of this multi-author book is well laidout, with fifteen chapters in three main parts: I. Foundationsof Proteomics; II. Functional Proteomics; and III. Novel Approachesin Proteomics. The editors have selected a strong team of respectedexperts in the various proteomics niches to write the fifteenconstituent chapters. The chapters are, for the most part, self-contained,and there is no     

The current state of microbial proteomics: where we are and where we want to go

Proteomics allows the assessment of cellular processes in an unprecedented scale by providing a comprehensive quantitative and qualitative overview of the protein content of a cell. Consequently, proteomics has been employed to investigate a multitude of bacterial processes ranging from the analysis of environmental communities, identification of virulence factors to the proteome-guided optimization of production strains. Proteomics has, in short, become an indispensable tool for the global analysis of bacterial physiology. Nonetheless, challenges exist, especially in the accurate prediction of phenotypic consequences based on any given proteome composition. In this review, we will give an overview of current highlights in the area of microbial proteomics, discuss some current challenges and present new developments that may help in overcoming them.     

Building integrated approaches for the proteomics of complex, dynamic systems: NIH programs in technology and infrastructure development

Proteomics technology and methods remain inadequate. Technological constraints contribute to an artificially static view of complex biological systems and a barrier between quantitative and interaction studies. Several NIH programs combine proteomics technology development with research on challenging biological problems to drive progress. A new initiative of the NIH Roadmap focuses on characterization of dynamic systems. The success of these programs will be judged by their impact on relevant biological problems.