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.     

Geographical focus. Proteomics initiatives in Spain: ProteoRed

The Spanish National Network of Proteomic Facilities--ProteoRed has been created as an initiative for the coordination, integration and development of the proteomics facilities and laboratories distributed throughout Spain. ProteoRed's main objective is to give support to the scientific community allowing them wide access to emerging proteomics technologies and thus encouraging the science of proteomics. In addition, standardization of protocols and robustness of workflows are addressed by multi-centric laboratory activities. Educational, training and dissemination issues are part of the core activities of ProteoRed. To reach these objectives, specific activities have been developed through six working groups (WG1-WG6) covering functional, technical, educational and scientific aspects of proteomics.     

Boosting the globalization of plant proteomics through INPPO: current developments and future prospects

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific).     

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/.     

Opportunity gaps in out-of-school learning: How structural and process features of programs relate to race and socioeconomic status

Abstract

Out-of-school learning programs can be a context for positive development and learning for children and youth. However, research points to potential racial and socioeconomic disparities, or opportunity gaps, in this context. In this study, we use survey and video data from 106 staff across 30 out-of-school programs to examine how three features, staff, activities, and adult–child interactions, differ based on the racial and socioeconomic makeup of programs. We find that staff at programs serving children from low-income families on average have less experience and education. Also, programs serving children from African American and low-income families tend to offer more academic-focused activities. Finally, we found no differences in adult–child interaction quality across programs in the sample. Our findings suggest that a racial and socioeconomic opportunity gap may exist in the out-of-school context. This has implications for educational equity and the positive development of children that participate in this context.     

Investigating the feeding behaviour of brine shrimps

Genomics and proteomics projects have produced a huge amount of raw biological data including DNA and protein sequences. Although these data have been stored in data banks, their evaluation is strictly dependent on bioinformatics tools. These tools have been developed by multidisciplinary experts for fast and robust analysis of biological data. However, there is a gap in the development of educational materials in the bioinformatics area for undergraduate students in bioscience departments. A sample in silico laboratory manual on the prediction of N-glycosylation sites in phosphoethanolamine transferases is presented in this study. The method proposed in this study is simple to apply in laboratory courses and is dependent on the use of internet-based bioinformatics tools such as ProtParam, ClustalW2 and NetNGlyc. In conclusion, this application can stimulate the interest of undergraduate students in bioscience departments and may also contribute to the development of bioinformatics.     

Relevance of proteomics standards for the ProteoRed Spanish organization

ProteoRed, a Spanish Initiative in the field of proteomics, is reaching international standards. Here we present ProteoRed as an example of collaborative initiative in the field of proteomics. Being established as a high level proteomics service provider, it also has consolidated as one of the first institutions really involved in implementing proteomics standards developed by the HUPO consortium. As a collaborative network it has proved a valuable platform to coordinate multi-centric experiments aiming at evaluating the robustness of laboratory workflows as well as the implementation of standards. In addition, this initiative has been very active in promoting the interaction between clinicians and basic researchers by means of courses, workshops or symposia like the one highlighted in this report, which was devoted to clinical proteomics and took place in La Coruña, Spain, last September.     

Integrating recent advances in neuroscience into undergraduate neuroscience and physiology courses

Neuroscience has enjoyed tremendous growth over the past 20 years, including a substantial increase in the number of neuroscience departments, programs, and courses at the undergraduate level. To meet the need of new neuroscience courses, there has also been growth in the number of introductory neuroscience textbooks designed for undergraduates. However, textbooks typically trail current knowledge by five to ten years, especially in neuroscience where our understanding is increasing rapidly. Consequently, it is often important to supplement neuroscience and physiology textbooks with information about recent findings in neuroscience. To design supplementary educational material, it is essential first to identify the educational objectives of the program and the characteristics of the learners, which can differ dramatically between undergraduate and graduate or professional students. Four principles that may serve the selection and design of supplementary material for undergraduate neuroscience and physiology courses are that (1) material must be interesting to the undergraduates, (2) material should reinforce previously learned concepts, (3) students must be adequately prepared, and (4) the teacher and student must have sufficient appropriate resources.     

The Changing Face of Natural Resources Students,Education, and the Profession

ABSTRACT There are many challenges facing natural resources programs in North American higher education today. Pressures exerted by a new generation of students, changing workplace requirements (including undergraduate core-knowledge requirements), and an increasingly specialized professoriate are great but not insurmountable. We discuss each of these issues and pose potential solutions to address each including adopting new pedagogical techniques for content delivery (e.g., adapting courses to be inclusive of new technologies), revising curriculum to meet the needs of a new suite of learners (e.g., developing curricula that allow structured flexibility of choices, designing a core curriculum that is a mix of single-discipline courses and courses that integrate across disciplines), and new strategies for faculty engagement in discipline-specific survey courses. By remaining deliberate and effective in our pursuit of quality higher education we have the opportunity to ensure we are delivering the best possible education to the future professionals of our disciplines.     

No "Rip Van Winkles" Here: Amish Education Since Wisconsin v. Yoder

This study examines the educational implications of the shift in economic livelihood in a Ohio Amish community since a landmark 1972 Supreme Court decision paved the way for control of their schools. The clash between tradition and economic pragmatism, and their multiple interpretations, has led to diverse educational pathways, including public schools, charter schools, homeschooling, GED programs, and vocational courses. The diverse ways in which the Amish continue to renegotiate social boundaries with their English neighbors suggests the need for more attention to internal diversity in the anthropological study of schooling in so called "folk societies."     

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics

Background  

In proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for these programs have become prohibitive, particularly in searches for modified proteins. Recently, methods to limit the number of spectra to be searched based on spectral quality have been proposed by different research groups, but rankings of spectral quality have thus far been based on arbitrary cut-off values. In this work, we develop a more readily interpretable spectral quality statistic by providing probability values for the likelihood that spectra will be identifiable.     

On the teaching of ecological restoration in Brazil: an analysis of postgraduate courses

Several ambitious restoration targets have been set for recovering degraded ecosystems in Brazil (21 million hectares with a legal deficit of native vegetation). The development of scientific knowledge and skilled professionals is necessary to meet this demand and is fundamental for achieving success in medium‐ and long‐term restoration. In this study, we describe the availability and profile of postgraduate courses on ecological restoration in Brazil. We surveyed 272 postgraduate programs, comprising six specific areas of concentration (forestry, soil sciences, botany, environmental engineering, ecology, and environmental science). We analyzed all selected courses in terms of location, approach (economic, social, and legal), and restoration techniques. Only 27% of the postgraduate programs analyzed offer ecological restoration courses, and 49% of these are offered in the southeast region of the country. Regions covered by nonforest ecosystems, such as Pampas, Caatinga, and Pantanal, were poorly represented. Legal aspects were considered in 51% of the courses, whereas social and economic approaches were only considered in 2.7 and 11% of the courses, respectively. Seedling planting (85%) and nucleation (68%) were the most frequently cited techniques of active restoration, and passive restoration was mentioned in 63% of the courses. Our findings highlight the need for increasing postgraduate courses in areas with nonforest ecosystems, especially due to a lack of knowledge about restoration of these areas. The incorporation of economic and social approaches is highly recommended, considering the importance of these attributes in achieving success in large‐scale restoration initiatives.     

Small-molecule probes elucidate global enzyme activity in a proteomic context

The recent dramatic improvements in high-resolution mass spectrometry (MS) have revolutionized the speed and scope of proteomic studies. Conventional MS-based proteomics methodologies allow global protein profiling based on expression levels. Although these techniques are promising, there are numerous biological activities yet to be unveiled, such as the dynamic regulation of enzyme activity. Chemical proteomics is an emerging field that extends these types proteomic profiling. In particular, activity-based protein profiling (ABPP) utilizes small-molecule probes to monitor enzyme activity directly in living intact subjects. In this mini-review, we summarize the unique roles of smallmolecule probes in proteomics studies and highlight some recent examples in which this principle has been applied. [BMB Reports 2014; 47(3): 149-157]     

New Insight into Neurodegeneration: the Role of Proteomics

Recent advances within the field of proteomics, including both upstream and downstream protocols, have fuelled a transition from simple protein identification to functional analysis. A battery of proteomics approaches is now being employed for the analysis of protein expression levels, the monitoring of cellular activities and for gaining an increased understanding into biochemical pathways. Combined, these approaches are changing the way we study disease by allowing accurate and targeted, large scale protein analysis, which will provide invaluable insight into disease pathogenesis. Neurodegenerative disorders, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), prion disease, and other diseases that affect the neuromuscular system, are a leading cause of disability in the aging population. There are no effective intervention strategies for these disorders and diagnosis is challenging as it relies primarily on clinical symptomatic features, which often overlap at early stages of disease. There is, therefore, an urgent need to develop reliable biomarkers to improve early and specific diagnosis, to track disease progression, to measure molecular responses towards treatment regimes and ultimately devise new therapeutic strategies. To accomplish this, a better understanding of disease mechanisms is needed. In this review we summarize recent advances in the field of proteomics applicable to neurodegenerative disorders, and how these advances are fueling our understanding, diagnosis, and treatment of these complex disorders.