A quantitative assay for crossover and noncrossover molecular events at individual recombination hotspots in both male and female gametes

AbstractMeiotic recombination is a fundamental process in all eukaryotes. Among organisms in which recombination initiates prior to synapsis, recombination preferentially occurs in short 1-to 2-kb regions, known as recombination hotspots. Among mammals, genotyping sperm DNA has provided a means of monitoring recombination events at specific hotspots in male meiosis. To complement these current techniques, we developed an assay for amplifying all copies of a hotspot from the DNA of male and female germ cells, cloning the products into Escherichia coli, and SNP genotyping the resulting colonies using fluorescence technology. This approach examines the molecular details of crossover and noncrossover events of individual meioses directly at active hotspots while retaining the simplicity of using pooled DNA. Using this technique, we analyzed recombination events at the Hlx1 hotspot located on mouse chromosome 1, finding that the results agree well with a prior genetic characterization of 3026 male and 3002 female meioses

Numerical modelling of climate change impacts on freshwater lenses on the North Sea Island of Borkum using hydrological and geophysical methods

A numerical, density dependent groundwater model is set up for the North Sea Island of Borkum to estimate climate change impacts on coastal aquifers and especially the situation of barrier islands in the Wadden Sea. The database includes information from boreholes, a seismic survey, a helicopter-borne electromagnetic (HEM) survey, monitoring of the freshwater-saltwater boundary by vertical electrode chains in two boreholes, measurements of groundwater table, pumping and slug tests, as well as water samples. Based on a statistical analysis of borehole columns, seismic sections and HEM, a hydrogeological model is set up. The groundwater model is developed using the finite-element programme FEFLOW. The density dependent groundwater model is calibrated on the basis of hydraulic, hydrological and geophysical data, in particular spatial HEM and local monitoring data. Verification runs with the calibrated model show good agreement between measured and computed hydraulic heads. A good agreement is also obtained between measured and computed density or total dissolved solids data for both the entire freshwater lens on a large scale and in the area of the well fields on a small scale. For simulating future changes in this coastal groundwater system until the end of the current century, we use the climate scenario A2, specified by the Intergovernmental Panel on Climate Change and, in particular, the data for the German North Sea coast. Simulation runs show proceeding salinisation with time beneath the well fields of the two waterworks Waterdelle and Ostland. The modelling study shows that the spreading of well fields is an appropriate protection measure against excessive salinisation of the water supply until the end of the current century

Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain of Mus musculus

BACKGROUND: Among the three functions of DNA, mammalian replication and transcription can be subject to epigenetic imprinting specified by the parental origin of chromosomes, and although there is suggestive indication that this is also true for meiotic recombination, no definitive evidence has yet been reported. RESULTS: We have now obtained such evidence on mouse chromosome 7 by assaying meiotic recombination as it occurs in reciprocal F1 mice. A 166 kb region near the Kcnq1 transcriptionally imprinted domain showed significantly higher recombination activity in the CAST x B6 parental direction (p \u3c 0.03). Characterizing hotspots within this domain revealed a cluster of three hotspots lying within a 100 kb span, among these hotspots, Slc22a18 showed a definitive parent of origin effect on recombination frequency (p \u3c 0.02). Comparing recombination activity in the mouse Kcnq1 and neighboring H19-Igf2 imprinted domains with their human counterparts, we found that elevated recombination activity in these domains is a consequence of their chromosomal position relative to the telomere and not an intrinsic characteristic of transcriptionally imprinted domains as has been previously suggested. CONCLUSION: Similar to replication and transcription, we demonstrate that meiotic recombination can be subjected to epigenetic imprinting and hotspot activity can be influenced by the parental origin of chromosomes. Furthermore, transcriptionally imprinted regions exhibiting elevated recombination activity are likely a consequence of their chromosomal location rather than their transcriptional characteristic

Autonomous Configuration of Network Parameters in Operating Systems using Evolutionary Algorithms

By default, the Linux network stack is not configured for highspeed large file transfer. The reason behind this is to save memory resources. It is possible to tune the Linux network stack by increasing the network buffers size for high-speed networks that connect server systems in order to handle more network packets. However, there are also several other TCP/IP parameters that can be tuned in an Operating System (OS). In this paper, we leverage Genetic Algorithms (GAs) to devise a system which learns from the history of the network traffic and uses this knowledge to optimize the current performance by adjusting the parameters. This can be done for a standard Linux kernel using sysctl or /proc. For a Virtual Machine (VM), virtually any type of OS can be installed and an image can swiftly be compiled and deployed. By being a sandboxed environment, risky configurations can be tested without the danger of harming the system. Different scenarios for network parameter configurations are thoroughly tested, and an increase of up to 65% throughput speed is achieved compared to the default Linux configuration.Comment: ACM RACS 201

The Recombinational Anatomy of a Mouse Chromosome

Among mammals, genetic recombination occurs at highly delimited sites known as recombination hotspots. They are typically 1–2 kb long and vary as much as a 1,000-fold or more in recombination activity. Although much is known about the molecular details of the recombination process itself, the factors determining the location and relative activity of hotspots are poorly understood. To further our understanding, we have collected and mapped the locations of 5,472 crossover events along mouse Chromosome 1 arising in 6,028 meioses of male and female reciprocal F1 hybrids of C57BL/6J and CAST/EiJ mice. Crossovers were mapped to a minimum resolution of 225 kb, and those in the telomere-proximal 24.7 Mb were further mapped to resolve individual hotspots. Recombination rates were evolutionarily conserved on a regional scale, but not at the local level. There was a clear negative-exponential relationship between the relative activity and abundance of hotspot activity classes, such that a small number of the most active hotspots account for the majority of recombination. Females had 1.2× higher overall recombination than males did, although the sex ratio showed considerable regional variation. Locally, entirely sex-specific hotspots were rare. The initiation of recombination at the most active hotspot was regulated independently on the two parental chromatids, and analysis of reciprocal crosses indicated that parental imprinting has subtle effects on recombination rates. It appears that the regulation of mammalian recombination is a complex, dynamic process involving multiple factors reflecting species, sex, individual variation within species, and the properties of individual hotspots

Shallow rainwater lenses in deltaic areas with saline seepage

In deltaic areas with saline seepage, freshwater availability is often limited to shallow rainwater lenses lying on top of saline groundwater. Here we describe the characteristics and spatial variability of such lenses in areas with saline seepage and the mechanisms that control their occurrence and size. Our findings are based on different types of field measurements and detailed numerical groundwater models applied in the south-western delta of the Netherlands. By combining the applied techniques we could extrapolate measurements at point scale (groundwater sampling, temperature and electrical soil conductivity (TEC)-probe measurements, electrical cone penetration tests (ECPT)) to field scale (continuous vertical electrical soundings (CVES), electromagnetic survey with EM31), and even to regional scale using helicopter-borne electromagnetic measurements (HEM). The measurements show a gradual mixing zone between infiltrating fresh rainwater and upward flowing saline groundwater. The mixing zone is best characterized by the depth of the centre of the mixing zone <i>D</i><sub>mix</sub>, where the salinity is half that of seepage water, and the bottom of the mixing zone <i>B</i><sub>mix</sub>, with a salinity equal to that of the seepage water (Cl-conc. 10 to 16 g l<sup>−1</sup>). <i>D</i><sub>mix</sub> is found at very shallow depth in the confining top layer, on average at 1.7 m below ground level (b.g.l.), while <i>B</i><sub>mix</sub> lies about 2.5 m b.g.l. The model results show that the constantly alternating upward and downward flow at low velocities in the confining layer is the main mechanism of mixing between rainwater and saline seepage and determines the position and extent of the mixing zone (<i>D</i><sub>mix</sub> and <i>B</i><sub>mix</sub>). Recharge, seepage flux, and drainage depth are the controlling factors

Combining ground-based and airborne EM through Artificial Neural Networks for modelling glacial till under saline groundwater conditions

Airborne electromagnetic (AEM) methods supply data over large areas in a cost-effective way. We used Artificial Neural Networks (ANN) to classify the geophysical signal into a meaningful geological parameter. By using examples of known relations between ground-based geophysical data (in this case electrical conductivity, EC, from electrical cone penetration tests) and geological parameters (presence of glacial till), we extracted learning rules that could be applied to map the presence of a glacial till using the EC profiles from the airborne EM data. The saline groundwater in the area was obscuring the EC signal from the till but by using ANN we were able to extract subtle and often non-linear, relations in EC that were representative of the presence of the till. The ANN results were interpreted as the probability of having till and showed a good agreement with drilling data. The glacial till is acting as a layer that inhibits groundwater flow, due to its high clay-content, and is therefore an important layer in hydrogeological modelling and for predicting the effects of climate change on groundwater quantity and quality

FRC formation and trapping by counter injection for MTF liner implosions

A new simplified design is being developed for injecting and trapping Field-Reversed Configurations (FRCs) into liners, which is compatible with the energetic liner implosions of interest for Magnetized Target Fusion (MTF). Conical theta pinches that inject from each end of the liner region are proposed. The conical angle can be chosen to make axial translation out of the conical theta pinch into the liner region occur on approximately the same time scale as radial compression. Thus no crowbar switch is needed for the high-voltage fast-rising current pulse. The toroidal field from conical theta-pinch injection and/or Z-pinch preionization should rapidly annihilate upon merging of the two oppositely directed FRCs. Two dc coils in a Helmholtz-like configuration are all that are needed to serve the functions of cusp, translation, and mirror fields for trapping in the liner. The mirror strength required for trapping is not as critical as when using onesided injection because the merging FRCs have no net momentum when they collide. Previously observed damping of axial kinetic energy suggests that viscous damping parallel to B 'is strong for FRCs with mfp comparable to FRC length, and conversion of directed energy to thermal energy should occur on a time scale comparable to the injection time. The electrical/mechanical details will be described, accompanied by numerical simulations of FRC formation using the MACH2 numerical code

Numerical modelling of climate change impacts on freshwater lenses on the North Sea Island of Borkum using hydrological and geophysical methods

A numerical, density dependent groundwater model is set up for the North Sea Island of Borkum to estimate climate change impacts on coastal aquifers and especially the situation of barrier islands in the Wadden Sea. The database includes information from boreholes, a seismic survey, a helicopter-borne electromagnetic (HEM) survey, monitoring of the freshwater-saltwater boundary by vertical electrode chains in two boreholes, measurements of groundwater table, pumping and slug tests, as well as water samples. Based on a statistical analysis of borehole columns, seismic sections and HEM, a hydrogeological model is set up. The groundwater model is developed using the finite-element programme FEFLOW. The density dependent groundwater model is calibrated on the basis of hydraulic, hydrological and geophysical data, in particular spatial HEM and local monitoring data. Verification runs with the calibrated model show good agreement between measured and computed hydraulic heads. A good agreement is also obtained between measured and computed density or total dissolved solids data for both the entire freshwater lens on a large scale and in the area of the well fields on a small scale. <br><br> For simulating future changes in this coastal groundwater system until the end of the current century, we use the climate scenario A2, specified by the Intergovernmental Panel on Climate Change and, in particular, the data for the German North Sea coast. Simulation runs show proceeding salinisation with time beneath the well fields of the two waterworks Waterdelle and Ostland. <br><br> The modelling study shows that the spreading of well fields is an appropriate protection measure against excessive salinisation of the water supply until the end of the current century