The 1st European Summer School on 'proteomic basics'--the students view. 12-18 August, 2007 Kloster Neustift, Brixen/Bressanone, South Tyrol, Italy

Fifty postgraduate and postdoctoral delegates from all over Europe attended the week-long '1st European Summer School on Proteomic Basics' in Kloster Neustift in the Italian South Tyrol in August 2007. Invited proteomics experts gave tutorial lectures on Proteomics techniques with an emphasis on sample preparation, protein separation and purification in the first of an annual series of Proteomics Summer Schools funded by the EU and the Volkswagen Stiftung.     

Proteomic basics — quantification and post-translational modifications of proteins: The 3rd European Summer School in Kloster Neustift

The field of proteomics is rapidly evolving and has emerged as a routine application in many laboratories. It covers not only the identification of proteins but also the quantification and analysis of post-translational protein modifications. During the last few years a series of summer schools teaching comprehensive knowledge in proteomic research and applied techniques have been held. Various research areas were dealt with by international experts in lectures and workshops. The summer schools were addressed to master's and graduate students as well as young post-docs currently moving into the field of proteomics. Here, we give a report on the third European Summer School “Quantification and Post-translational Modifications of Proteins” held at the monastery in Neustift, Brixen/Bressanone, South Tyrol, Italy from August 2 to 9, 2009.     

Travellers' malaria - 'one shoe does not fit all'

Travellers' malaria is an exciting topic. It is a field in flux with evolving options for chemoprophylaxis, self-diagnosis, self-treatment, risk/strategy analyses and surveillance. Ideologies vary and experts differ but debate is needed and can bring change. The launch of a new thematic series in the Malaria Journal -- " Travellers' malaria " -- creates an ideal forum to bring together research papers, reviews, opinion papers and commentaries, and will hopefully stimulate debate.     

Analysis of longitudinal metabolomics data

MOTIVATION: Metabolomics datasets are generally large and complex. Using principal component analysis (PCA), a simplified view of the variation in the data is obtained. The PCA model can be interpreted and the processes underlying the variation in the data can be analysed. In metabolomics, often a priori information is present about the data. Various forms of this information can be used in an unsupervised data analysis with weighted PCA (WPCA). A WPCA model will give a view on the data that is different from the view obtained using PCA, and it will add to the interpretation of the information in a metabolomics dataset. RESULTS: A method is presented to translate spectra of repeated measurements into weights describing the experimental error. These weights are used in the data analysis with WPCA. The WPCA model will give a view on the data where the non-uniform experimental error is accounted for. Therefore, the WPCA model will focus more on the natural variation in the data. AVAILABILITY: M-files for MATLAB for the algorithm used in this research are available at http://www-its.chem.uva.nl/research/pac/Software/pcaw.zip.     

BIOME 6000: reconstructing global mid-Holocene vegetation patterns from palaeoecological records

Global change research needs data sets describing past states of the Earth system. Vegetation distributions for specified 'time slices' (with known forcings, such as changes in insolation patterns due to the Earth's orbital variations, changes in the extent of ice-sheets, and changes in atmospheric trace-gas composition) should provide a benchmark for coupled climate-biosphere models. Pollen and macrofossil records from dated sediments give spatially extensive coverage of data on vegetation distribution changes. Applications of such data have been delayed by the lack of a global synthesis. The BIOME 6000 project of IGBP aims at a synthesis for 6000 years bp. Success depends on community-wide participation for data compilation and quality assurance, and on a robust methodology for assigning palaeorecords to biomes. In the method summarized here, taxa are assigned to one or more plant functional types (PFTs) and biomes reconstructed using PFT-based definitions. By involving regional experts in PFT assignments, one can combine data from different floras without compromising global consistency in biome assignments. This article introduces a series of articles that substantially extend the BIOME 6000 data set. The list of PFTs and the reconstruction procedure itself are evolving. Some compromises (for example, restricted taxon lists in some regions) limit the precision of biome assignments and will become obsolete as primary data are put into community data bases. This trend will facilitate biome mapping for other time slices. Co-evolution of climate-biosphere modelling and palaeodata synthesis and analysis will continue.     

MALDI imaging mass spectrometry for direct tissue analysis: technological advancements and recent applications

Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a method that allows the investigation of the molecular content of tissues within its morphological context. Since it is able to measure the distribution of hundreds of analytes at once, while being label free, this method has great potential which has been increasingly recognized in the field of tissue-based research. In the last few years, MALDI-IMS has been successfully used for the molecular assessment of tissue samples mainly in biomedical research and also in other scientific fields. The present article will give an update on the application of MALDI-IMS in clinical and preclinical research. It will also give an overview of the multitude of technical advancements of this method in recent years. This includes developments in instrumentation, sample preparation, computational data analysis and protein identification. It will also highlight a number of emerging fields for application of MALDI-IMS like drug imaging where MALDI-IMS is used for studying the spatial distribution of drugs in tissues.     

The future of high-throughput screening

High-throughput screening (HTS) is a well-established process in lead discovery for pharma and biotech companies and is now also being set up for basic and applied research in academia and some research hospitals. Since its first advent in the early to mid-1990s, the field of HTS has seen not only a continuous change in technology and processes but also an adaptation to various needs in lead discovery. HTS has now evolved into a quite mature discipline of modern drug discovery. Whereas in previous years, much emphasis has been put toward a steady increase in capacity ("quantitative increase") via various strategies in the fields of automation and miniaturization, the past years have seen a steady shift toward higher content and quality ("quality increase") for these biological test systems. Today, many experts in the field see HTS at the crossroads with the need to decide either toward further increase in throughput or more focus toward relevance of biological data. In this article, the authors describe the development of HTS over the past decade and point out their own ideas for future directions of HTS in biomedical research. They predict that the trend toward further miniaturization will slow down with the implementation of 384-well, 1536-well, and 384 low-volume-well plates. The authors predict that, ultimately, each hit-finding strategy will be much more project related, tailor-made, and better integrated into the broader drug discovery efforts.     

Apoptosis-an introduction

Apoptosis has become a major research area in the biomedical sciences. As there are more than 13,000 papers published annually on the topic, it is impossible to keep track on all developments in the area. The individual aspects of molecular control of apoptosis are well reviewed, but more general, introductory recent reviews into the field are lacking. This review aims to give a brief overview of the field, providing an introduction into the literature for students and newcomers; as it is written for the un-initiated, wherever possible, review articles will be cited rather than original papers.     

Ethical Issues in Adolescents' Sexual and Reproductive Health Research in Nigeria

There is increasing interest in the need to address the ethical dilemmas related to the engagement of adolescents in sexual and reproductive health (SRH) research. Research projects, including those that address issues related to STIs and HIV, adverse pregnancy outcomes, violence, and mental health, must be designed and implemented to address the needs of adolescents. Decisions on when an individual has adequate capacity to give consent for research most commonly use age as a surrogate rather than directly assessing capacity to understand the issues and make an informed decision on whether to participate in research or not. There is a perception that adolescents participating in research are more likely to be coerced and may therefore not fully comprehend the risk they may be taking when engaging in research. This paper examines the various ethical issues that may impact stakeholders' decision making when considering engaging adolescents in SRH research in Nigeria. It makes a case for lowering the age of consent for adolescents. While some experts believe it is possible to extrapolate relevant information from adult research, studies on ethical aspects of adolescents' participation in research are still needed, especially in the field of sexual and reproductive health where there are often differences in knowledge, attitudes and practices compared to adults. The particular challenges of applying the fundamental principles of research ethics to adolescent research, especially research about sex and sexuality, will only become clear if more studies are conducted.     

Neuroethology, its roots and future

Scholars in a particular scientific field should be familiar with its historical roots. Such knowledge will put their own research into a historical perspective, and, in addition, will allow them to assess current strengths and weaknesses in their particular area of research. To keep an exciting field like neuroethology alive and close to fast moving scientific frontiers, it is necessary to constantly adapt and broaden its approaches to newly emerging ideas from other fields, and to quickly incorporate new methodologies. The following article tries to expose some of the roots of neuroethology, and, in addition, will present some evidence as to why the authors think this field needs a broader definition than that formulated in the past. Doing so after the 5th International Congress of Neuroethology in San Diego in August 1998 seems to the authors the most appropriate time. Accepted: 17 June 1999     

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

‘Proteomics for Biological Discovery’ edited byTimothy D. Veenstra and John R. Yates III (342 pages, John-Wiley& Sons, publishers), defines the modern analytical challengesof proteomics in terms of quantification, detection and accuracyfor biomedical research. The logic and possibly the eleganceof this text comes from the way that the reader is able to conversewith more than two dozen experts on a nearly complete collectionof separation, automation and bioinformatics techniques requiredfor quantitative and functional proteomic analysis. The bookis divided into three parts: Part I is on the fundamentals ofprotein separations and mass spectrometry, Part II is on functionalproteomic analysis and Part III discusses new methods that areat the frontier of the proteomics field. All of     

Climate change and marine life

A Marine Climate Impacts Workshop was held from 29 April to 3 May 2012 at the US National Center of Ecological Analysis and Synthesis in Santa Barbara. This workshop was the culmination of a series of six meetings over the past three years, which had brought together 25 experts in climate change ecology, analysis of large datasets, palaeontology, marine ecology and physical oceanography. Aims of these workshops were to produce a global synthesis of climate impacts on marine biota, to identify sensitive habitats and taxa, to inform the current Intergovernmental Panel on Climate Change (IPCC) process, and to strengthen research into ecological impacts of climate change.     

Adaptive landscape genetics: pitfalls and benefits

Landscape genetics offers a promising framework for assessing the interactions between the environment and adaptive genetic variation in natural populations. A recent workshop held at the University of Neuchatel brought together leading experts in this field to address current insights and future research directions in adaptive landscape genetics. Considerable amounts of genetic and/or environmental data can now be collected, but the forthcoming challenge is to do more with such manna. This requires a markedly better understanding of the genetic variation that is adaptive and prompts for advances in information management together with the development of a balance between theory and data. Moreover, showing the links between landscapes and adaptive genetic variation will ultimately move the field beyond association studies.     

Expert status and performance

Expert judgements are essential when time and resources are stretched or we face novel dilemmas requiring fast solutions. Good advice can save lives and large sums of money. Typically, experts are defined by their qualifications, track record and experience. The social expectation hypothesis argues that more highly regarded and more experienced experts will give better advice. We asked experts to predict how they will perform, and how their peers will perform, on sets of questions. The results indicate that the way experts regard each other is consistent, but unfortunately, ranks are a poor guide to actual performance. Expert advice will be more accurate if technical decisions routinely use broadly-defined expert groups, structured question protocols and feedback.     

Ikaros in hematopoiesis and leukemia

Ikaros is a gene whose activity is essential for normal hematopoiesis.Ikaros acts as a master regulator of lymphoid and myeloid development as well as a tumor suppressor.In cells,Ikaros regulates gene expression via chromatin remodeling.During the past 15 years tremendous advances have been made in understanding the role of Ikaros in hematopoiesis and leukemogenesis.In this Topic Highlights series of reviews,several groups of international experts in this field summarize the experimental data that is shaping the emerging picture of Ikaros function at the biochemical and cellular levels.The articles provide detailed analyses of recent scientific advancements and present models that will serve as a basis for future studies aimed at developing a better understanding of normal hematopoiesis and hematological malignancies and at accelerating the application of this knowledge in clinical practice.     

Towards a cohesive,holistic view of top predation: a definition,synthesis and perspective

Research on the ecology of top predators – upper trophic level consumers that are relatively free from predation once they reach adult size – has provided regular contributions to general ecology and is a rapidly expanding and increasingly experimental, multidisciplinary and technological endeavour. Yet, an exponentially expanding literature coupled with rapid disintegration into specialized, disconnected subfields for study (e.g. vertebrate predators versus invertebrate predators, community ecology versus biological control etc.) increasingly means that we are losing a coherent, integrated understating of the role and importance of these species in ecosystems. This process of canalization is likely to hinder sharing of scientific discovery and continued progress, especially as there is a growing need to understand the generality of the top–down forcing, as demonstrated for some members of this group. Here, we propose ways to facilitate synthesis by promoting changes in mentality and awareness among specialists through increased debate and collaboration, conceptual reviews and a series of exemplary case studies. The strategy will rely on the collective contribution by all scientists in the field and will strive to consolidate and formalise top‐order predation as a holistic, cohesive, cross‐taxonomical field of research studying the ecology, evolution and behaviour of apex predators and their capability to exert top–down forcing on lower trophic levels. Synthesis The ongoing global loss of top predators and their recolonization of various regions are causing a rapid upsurge of studies on these species and a consequent fragmentation of this field into disconnected, specialized subcompartments: this will weaken efforts to produce synthetic generalisations of broader ecological interest. Here, we show that top predation provides regular contributions to general ecology, is well grounded in theoretical ecology and is a rapidly expanding and increasingly experimental, multidisciplinary and technological field of research. The novelty of this forum lies in providing a concise synthesis of this area of ecology, in attempting to formalise “top predation” as a specific, inter‐connected area of investigation, and in proposing a marked change of mentality by stressing the need for cross‐taxonomic approaches enabling broader views of the role of predators in ecosystems.     

Exploration of Ellsworth Subglacial Lake: a concept paper on the development, organisation and execution of an experiment to explore, measure and sample the environment of a West Antarctic subglacial lake

Antarctic subglacial lakes have, over the past few years, been hypothesised to house unique forms of life and hold detailed sedimentary records of past climate change. Testing this hypothesis requires in situ examinations. The direct measurement of subglacial lakes has been considered ever since the largest and best-known lake, named Lake Vostok, was identified as having a deep water-column. The Subglacial Antarctic Lake Environments (SALE) programme, set up by the Scientific Committee on Antarctic Research (SCAR) to oversee subglacial lakes research, state that prior exploration of smaller lakes would be a “prudent way forward”. Over 145 subglacial lakes are known to exist in Antarctica, but one lake in West Antarctica, officially named Ellsworth Subglacial Lake (referred to hereafter as Lake Ellsworth), stands out as a candidate for early exploration. A consortium of over 20 scientists from seven countries and 14 institutions has been assembled to plan the exploration of Lake Ellsworth. An eight-year programme is envisaged: 3 years for a geophysical survey, 2 years for equipment development and testing, 1 year for field planning and operation, and 2 years for sample analysis and data interpretation. The science experiment is simple in concept but complex in execution. Lake Ellsworth will be accessed using hot water drilling. Once lake access is achieved, a probe will be lowered down the borehole and into the lake. The probe will contain a series of instruments to measure biological, chemical and physical characteristics of the lake water and sediments, and will utilise a tether to the ice surface through which power, communication and data will be transmitted. The probe will pass through the water column to the lake floor. The probe will then be pulled up and out of the lake, measuring its environment continually as this is done. Once at the ice surface, any water samples collected will be taken from the probe for laboratory analysis (to take place over subsequent years). The duration of the science mission, from deployment of the probe to its retrieval, is likely to take between 24 and 36 h. Measurements to be taken by the probe will provide data about the following: depth, pressure, conductivity and temperature; pH levels; biomolecules (using life marker chips); anions (using a chemical analyzer); visualisation of the environment (using cameras and light sources); dissolved gases (using chromatography); and morphology of the lake floor and sediment structures (using sonar). After the probe has been retrieved, a sediment corer may be dropped into the lake to recover material from the lake floor. Finally, if time permits, a thermistor string may be left in the lake water to take time-dependent measurements of the lake’s water column over subsequent years. Given that the comprehensive geophysical survey of the lake will take place in two seasons during 2007–2009, a two-year instrument and logistic development phase from 2008 (after the lake’s bathymetry has been assessed) makes it possible that the exploration of Lake Ellsworth could take place at the beginning of the next decade.