MolabIS - An integrated information system for storing and managing molecular genetics data

BACKGROUND: Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects. RESULTS: We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration. CONCLUSIONS: MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org

Northern Hemisphere Glaciation during the Globally Warm Early Late Pliocene

The early Late Pliocene (3.6 to ~3.0 million years ago) is the last extended interval in Earth's history when atmospheric CO2 concentrations were comparable to today's and global climate was warmer. Yet a severe global glaciation during marine isotope stage (MIS) M2 interrupted this phase of global warmth ~3.30 million years ago, and is seen as a premature attempt of the climate system to establish an ice-age world. Here we propose a conceptual model for the glaciation and deglaciation of MIS M2 based on geochemical and palynological records from five marine sediment cores along a Caribbean to eastern North Atlantic transect. Our records show that increased Pacific-to-Atlantic flow via the Central American Seaway weakened the North Atlantic Current and attendant northward heat transport prior to MIS M2. The consequent cooling of the northern high latitude oceans permitted expansion of the continental ice sheets during MIS M2, despite near-modern atmospheric CO2 concentrations. Sea level drop during this glaciation halted the inflow of Pacific water to the Atlantic via the Central American Seaway, allowing the build-up of a Caribbean Warm Pool. Once this warm pool was large enough, the Gulf Stream–North Atlantic Current system was reinvigorated, leading to significant northward heat transport that terminated the glaciation. Before and after MIS M2, heat transport via the North Atlantic Current was crucial in maintaining warm climates comparable to those predicted for the end of this century

Towards Uniform Gene Bank Documentation In Europe – The Experience From The EFABISnet Project

In the EFABISnet project, a collaborative effort of EAAP, FAO and partners from 14 European countries, in cooperation with the European Regional Focal Point for Animal Genetic Resources (ERFP), national information systems for monitoring the animal genetic resources on breed level were established in Austria, Cyprus, Estonia, Georgia, Iceland, Ireland, Italy, Netherlands, Slovakia, Slovenia, Switzerland, and United Kingdom. The network was soon extended beyond the project plans, with the establishment of EFABIS databases in Finland, Greece, and Hungary. The network was then complemented by a set of inventories of national gene bank collections to strengthen the documentation of ex situ conservation programmes. These documentation systems were established by the National Focal Points for management of farm animal genetic resources. Here we present the experience gained in establishment of these national inventories of gene banks and their relevance to the Strategic Priority Areas of the Global Plan of Action which could be useful for other areas in the world

Nonequilibrium Electron Interactions in Metal Films

Ultrafast relaxation dynamics of an athermal electron distribution is investigated in silver films using a femtosecond pump-probe technique with 18 fs pulses in off-resonant conditions. The results yield evidence for an increase with time of the electron-gas energy loss rate to the lattice and of the free electron damping during the early stages of the electron-gas thermalization. These effects are attributed to transient alterations of the electron average scattering processes due to the athermal nature of the electron gas, in agreement with numerical simulations

Ultrafast quasiparticle relaxation dynamics in normal metals and heavy fermion materials

We present a detailed theoretical study of the ultrafast quasiparticle relaxation dynamics observed in normal metals and heavy fermion materials with femtosecond time-resolved optical pump-probe spectroscopy. For normal metals, a nonthermal electron distribution gives rise to a temperature (T) independent electron-phonon relaxation time at low temperatures, in contrast to the T^{-3}-divergent behavior predicted by the two-temperature model. For heavy fermion compounds, we find that the blocking of electron-phonon scattering for heavy electrons within the density-of-states peak near the Fermi energy is crucial to explain the rapid increase of the electron-phonon relaxation time below the Kondo temperature. We propose the hypothesis that the slower Fermi velocity compared to the sound velocity provides a natural blocking mechanism due to energy and momentum conservation laws.Comment: 10 pages, 11 figure

Ventilation history of Nordic Seas overflows during the last (de)glacial period revealed by species-specific benthic foraminiferal 14C dates

Formation of deep water in the high-latitude North Atlantic is important for the global meridional ocean circulation, and its variability in the past may have played an important role in regional and global climate change. Here we study ocean circulation associated with the last (de)glacial period, using water-column radiocarbon age reconstructions in the Faroe-Shetland Channel, southeastern Norwegian Sea, and from the Iceland Basin, central North Atlantic. The presence of tephra layer Faroe Marine Ash Zone II, dated to ~26.7 ka, enables us to determine that the middepth (1179 m water depth) and shallow subsurface reservoir ages were ~1500 and 1100 14C years, respectively, older during the late glacial period compared to modern, suggesting substantial suppression of the overturning circulation in the Nordic Seas. During the late Last Glacial Maximum and the onset of deglaciation (~20–18 ka), Nordic Seas overflow was weak but active. During the early deglaciation (~17.5–14.5 ka), our data reveal large differences between 14C ventilation ages that are derived from dating different benthic foraminiferal species: Pyrgo and other miliolid species yield ventilation ages >6000 14C years, while all other species reveal ventilation ages <2000 14C years. These data either suggest subcentennial, regional, circulation changes or that miliolid-based 14C ages are biased due to taphonomic or vital processes. Implications of each interpretation are discussed. Regardless of this “enigma,” the onset of the Bølling-Allerød interstadial (14.5 ka) is clearly marked by an increase in middepth Nordic Seas ventilation and the renewal of a stronger overflow

Catch comparison of pulse trawls vessels and a tickler chain beam trawler

Comparative fishing trials were conducted in May 2011 (week 19) on commercial beam trawlers fishing with conventional tickler chain beam trawls (on MFV GO4), pulse wings made by HFK-Engineering of Baarn, the Netherlands (MFV TX36), and pulse trawls produced by the DELMECO-Group of Goes, the Netherlands (version used on MFV TX68). The three vessels fished side-by-side as much as possible. Landings and discards of these vessels were monitored. Special emphasis was given on cod and whiting, that were dissected to study possible spinal damage. Result for TX36 and TX68 are expressed in terms of percentages of GO4. The pulse characteristics were as follows: TX36: voltage 45 V0 to peak, pulse frequency: 45 Hz, pulse duration 380 μs; electric power on single gear: 7.0 kW; TX68: voltage 50 V0 to peak, pulse frequency: 50 Hz, pulse duration 220 μs; electric power on single gear: 8.5 kW. The fuel consumption recorded over the whole week was considerably lower for the pulse trawls, i.e. on TX36 (40%) and on TX68 (54%), than for the tickler chain beam trawls used on the GO4. The net earnings (taken as gross earnings minus fuel costs) for the TX36 were almost twice as large at 186%, and for the TX68 also considerably higher at 155%. The vessels with pulse trawls caught fewer (65-69%) target species, but also less (30-50%) immature and non-target fish ('discards'), and benthic species (48-73%) than the vessel with tickler chains on these fishing grounds and in this period. The pulse gears caught fewer (19-42%) kg per hour cod than the tickler chain beam trawls, but the catches of cod on all three vessels were very small. For plaice and dab these differences were statistically proven, for brill, turbot and cod this was not the case. There was no marked difference between both pulse trawl vessels in total landings. The TX68 caught less marketable sole, but not significantly less undersized sole than the GO4. The TX36 caught less undersized sole, but here the difference in marketable fish was not significant. Catches of brill and turbot were so small that no statistically substantiated conclusion could be drawn. Only for undersized turbot the TX36 caught less. For whiting we found a demonstrable reduction in both marketable and undersized fish in both pulse fishing vessels. The TX36 caught less whiting in number per hour. The CPUEs found from the auction data and the sampled hauls correlated reasonably well for the most abundant species, such as plaice and sole. However, for less abundant species the results did not match very well, and care should be taken to increase the sampling rate in future comparative fishing studies. Spinal fracture in cod occurred under pulse stimulation but to a limited extent in both marketable and undersized fish. There is an indication that this happens slightly more on TX68 (11%) than on TX36 (7%). Whiting hardly seems to suffer any damage