Quality evaluation of tandem mass spectral libraries

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

Molecular cytogenetics and gene mapping in sheep (Ovis aries, 2n = 54)

The development of a completely annotated sheep genome sequence is a key need for understanding the phylogenetic relationships and genetic diversity among the many different sheep breeds worldwide and for identifying genes controlling economically and physiologically important traits. The ovine genome sequence assembly will be crucial for developing optimized breeding programs based on highly productive, healthy sheep phenotypes that are adapted to modern breeding and production conditions. Scientists and breeders around the globe have been contributing to this goal by generating genomic and cDNA libraries, performing genome-wide and trait-associated analyses of polymorphism, expression analysis, genome sequencing, and by developing virtual and physical comparative maps. The International Sheep Genomics Consortium (ISGC), an informal network of sheep genomics researchers, is playing a major role in coordinating many of these activities. In addition to serving as an essential tool for monitoring chromosome abnormalities in specific sheep populations, ovine molecular cytogenetics provides physical anchors which link and order genome regions, such as sequence contigs, genes and polymorphic DNA markers to ovine chromosomes. Likewise, molecular cytogenetics can contribute to the process of defining evolutionary breakpoints between related species. The selective expansion of the sheep cytogenetic map, using loci to connect maps and identify chromosome bands, can substantially contribute to improving the quality of the annotated sheep genome sequence and will also accelerate its assembly. Furthermore, identifying major morphological chromosome anomalies and micro-rearrangements, such as gene duplications or deletions, that might occur between different sheep breeds and other Ovis species will also be important to understand the diversity of sheep chromosome structure and its implications for cross-breeding. To date, 566 loci have been assigned to specific chromosome regions in sheep and the new cytogenetic map is presented as part of this review. This review will also summarize the current cytogenomic status of the sheep genome, describe current activities in the sheep cytogenomics research sector, and will discuss the cytogenomics data in context with other major sheep genomics projects.

Building a soil spectral library for Tajikistan comparing local and global modeling approaches

Over the last ~20 years, soil spectral libraries storing near-infrared reflectance (NIR) spectra from diverse soil samples have been built for many places, since almost 10 years also for Tajikistan. Many calibration approaches have been reported and used for prediction from large and heterogeneous libraries, but most are hampered by the high diversity of the soils, where the mineral background is heavily influencing spectral features. In such cases, local learning strategies have the advantage of building locally adapted calibrations, which can deal better with nonlinearities. Therefore, it was our major aim to identify the most efficient approach to develop an accurate and stable locally weigthed calibration model using a spectral library compiled over the past years. Keywords: Tajikistan, Near-Infrared spectroscopy (NIRS), soil organic carbon, locally weighted regression, regional and local spectral library.

Pile-dwellings of the Neolithic and the Bronze Age in Switzerland. Long-term research and future tasks

Swiss lake-side settlements dating between 4300 and 800 BC were first recognized in the early 19th century and between 1854 and 1880 early research boomed due to the first scientific studies and the artificial lowering of lakes in Western Switzerland. In the 20th century underwater and wetland archaeology experienced an enormous surge not only because of large rescue excavations, due to extensive motorway construction projects but also due to the evolution of modern IT technology in the 1970s. For the first time huge quantities of ancient wooden structures could be dated by dendrochronology. This produced a quantum leap in the 150 years of pile-dwelling research. In 2011, the UNESCO World Heritage Committee recognized the outstanding universal value of these sites. This article presents an overview about Swiss pile-dwellings of the Neolithic and the Bronze Age and the results of two recent diploma works (case study Sutz-Lattrigen Haupstation innen and case study Seedorf Lobsigensee) as examples of research and cooperation between universities and government agencies for cultural heritage management.

Education for specialization in prosthodontics in Switzerland and the role of EPA.

Advertisement for any dental treatment was rare in Switzerland. Then the use of digital media became popular, particularly in the field of implant- and esthetic-dentistry. In parallel to the dental schools of public universities, private universities and companies built up centers for continuing education that issue specialists diplomas and M.Sc. degrees. Prosthodontics itself is characterized by many sub-disciplines that incorporated their own associations. These also offer graduate training curricula which diminish the significance of specialization in prosthodontics. Specialized prosthodontists do not have a financial benefit in Switzerland where dentistry is not supported by any insurance. In other European countries funding of prosthodontic treatment depends on their healthcare systems. There are four specialties in Dentistry recognized by the European Union (EU). Specialization in prosthodontics was introduced in Sweden already in 1982 and today it is declared in about 20 European countries, while for others no recognized program exists. Thus there are great variations with more recognized specialists in former east European countries. In Switzerland the prosthodontic specialization curriculum was developed and guided by the Swiss Society for Reconstructive Dentistry, and only in 2001 it became fully acknowledged by the Federal Department of Health. The four Swiss Universities offer the 3-year program under the supervision of the society, while the government remains the executive body. In 2003 EPA tried to set up guidelines and quality standards for an EPA recognized specialization. In spite of these attempts and the Bologna Reform in Europe, it appears that the quality standards and the level of education still may differ significantly among European countries.

NEENAWA: Network in Eastern European Neolithic and Wetland Archaeology: first steps.

Neolithic and Bronze Age wetland sites around the Alps (so called pile-dwellings, Pfahlbauten or palafittes in German/French) are of outstanding universal value (UNESCO-world heritage since 2011). Typical sites are in lakes, rivers and bogs, dating between 5300 and 800 BC. Of common character is the perfect conservation of wood, textiles from plant fabrics and many other organic materials. Larger quantities of sub-fossilized wood, as in the peri-alpine sites, offer the possibility of high-precision dating by dendrochronology. Research in these wetland sites started in the mid-19th century. Through large scale rescue excavations since the 1970s and the evolution of underwater archaeology in the same period the Swiss accumulated a thorough experience with these specific sites. Research in wetland sites is shared between cantonal institutions and universities and led to a worldwide unique accumulation of knowledge. Comparable sites exist outside of the Alpine area, but in much smaller quantities. Regions like Russia (small lakes in NW-Russia) and Macedonia (medium size lakes in the border zone of Macedonia, Albania and Greece) have a high scientific potential; rivers in Ukraine are supposed to have the same type of sites.