Evolution Of Hotspots Research Articles

Global copy number analyses by next generation sequencing provide insight into pig genome variation.

BackgroundCopy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs.ResultsUsing whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection.ConclusionsOur studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-593) contains supplementary material, which is available to authorized users.

The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas.

Biodiversity is unevenly distributed on Earth and hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history (i.e. tens of millions of years). Understanding the underlying processes that have driven the accumulation of species in some areas and not in others may help guide prioritization in conservation and may facilitate forecasts on ecosystem services under future climate conditions. Consequently, the study of the origin and evolution of biodiversity in mountain systems has motivated growing scientific interest. Despite an increasing number of studies, the origin and evolution of diversity hotspots associated with the Qinghai-Tibetan Plateau (QTP) remains poorly understood. We review literature related to the diversification of organisms linked to the uplift of the QTP. To promote hypothesis-based research, we provide a geological and palaeoclimatic scenario for the region of the QTP and argue that further studies would benefit from providing a complete set of complementary analyses (molecular dating, biogeographic, and diversification rates analyses) to test for a link between organismic diversification and past geological and climatic changes in this region. In general, we found that the contribution of biological interchange between the QTP and other hotspots of biodiversity has not been sufficiently studied to date. Finally, we suggest that the biological consequences of the uplift of the QTP would be best understood using a meta-analysis approach, encompassing studies on a variety of organisms (plants and animals) from diverse habitats (forests, meadows, rivers), and thermal belts (montane, subalpine, alpine, nival). Since the species diversity in the QTP region is better documented for some organismic groups than for others, we suggest that baseline taxonomic work should be promoted.

Spatio-temporal analysis of urbanization and land and water resources efficiency of oasis cities in Tarim River Basin

This paper examines the spatial pattern of land and water resources as well as urbanization and their interactions in the Tarim River Basin, Xinjiang, China. In order to do so, we extract the data associated with efficiency of land and water resources and urbanization for the years of 1995, 2000, 2005 and 2008. Specifically the paper investigates the extent to which agglomeration of population and economic activities varies geographically and interplays with spatial pattern of resources efficiency through computation of Global Moran's I index, Getis-Ord Gi* index and a coordinated development model. The method used provides clear evidence that urbanization, land and water resources efficiency have shown uneven spatial pattern due to oasis distribution, climate, and initial phase of urban development. Some conclusions can be drawn as follows. (1) Agglomeration and dispersion of urbanization are not consistent with those of land and water resources efficiency. (2) Evolution of the hot and cold spots of urbanization, and land and water resources efficiency, in different trajectories, indicate that there are no significant interactions between them. (3) The evidence that numbers of hot and cold spots of the three factors present varying structures reveals the dominance of unequal urban development in the study area. (4) Significant differences are also found between sub-river basins in terms of the three factors, which is a reflection of the complex physical geography of the area. (5) The degree of coordinated development of cities in the Tarim River Basin is generally low in part as a reflection of difference in spatial patterns of the three factors. It is also shown that the pattern of the degree of coordinated development is relatively stable compared with evolution of hot and cold spots of the three factors.

On some necessary conditions for p-11B ignition in the hot spots of a plasma focus

Recently, it has been predicted that hydrogen-boron (p- 11 B) nuclear fusion may attain ignition in the hot spots observed in a plasma focus (PF) pinch, due to their huge values of particle density, magnetic field and (reportedly) ion temperature. Accordingly, large magnetic fields should raise electronic Landau levels, thus reducing collisional exchange of energy from ion to electrons and Bremsstrahlung losses. Moreover, large particle densities, together with ion viscous heating, should allow fulfilment of Lawson criterion and provide effective screening of cyclotron radiation. We invoke both well-known, empirical scaling laws of PF physics, Connor-Taylor scaling laws, Poynting balance of electromagnetic energy and the balance of generalised helicity. We show that the evolution of PF hot spots is a succession of relaxed states, described by the double Beltrami solutions of Hall-MHD equations of motion. We obtain some necessary conditions for ignition, which are violated in most realistic conditions. Large electromagnetic fields in the hot spot accelerate electrons at supersonic velocities and trigger turbulence, which raises electric resistivity and Joule heating, thus spoiling further compression. Ignition is only possible if a significant fraction of the Bremsstrahlung-radiated power is reflected back into the plasma. Injection of angular momentum decreases the required reflection coefficient.

Long- and short-term evolution of several Mediterranean denudation hot spots: The role of rainfall variations and human impact

Severe slope denudation is one of the most important environmental problems in the Mediterranean region. In particular, badlands are widespread in central Italy as a result of extensive clayey outcrops, current climatic conditions and rapid Quaternary uplift. Human activity may significantly affect the development and evolution of these denudation hot spots, especially through changes in land use. This work is focused on a badland site that has developed over the last 30years on a gently sloping area of cropland in central Italy. The site, named Bargiano, underwent cropland abandonment in 1980 and was selected to evaluate the effects of external forcing (such as human impact and rainfall variations) on the development of water erosion processes. The remnants of the 1980 cropland surface and the present (eroded) surface were sampled using differential global positioning system techniques to perform a volumetric estimation of the eroded material and to calculate the average erosion rate for fairly large time spans. The DGPS survey was coupled with a 2-year monitoring with erosion pins in the region, which permitted comparisons between long- and short-term average erosion rates.In addition, the analysis of the rainfall series recorded at the Orvieto pluviometric station allowed us to assess and evaluate the role of critical rainfall events on denudation intensity.Finally, a further comparison of the measured and estimated erosion rates from the Bargiano site with the data recorded at other long-lasting monitoring stations that are set up in certain key areas of central Italy (the Tevere River and Ombrone River basins) revealed that the Bargiano experimental hillslope experienced considerably higher erosion rates than were noted at the other sites. Our investigations demonstrated that cropland abandonment caused an increase in the erosion rate relative to what happened in natural areas characterized by similar physiographic conditions. This finding is consistent with previously reported results for other badlands found in the Mediterranean area. Moreover, the results obtained suggest that, after the abandonment of its cropland, the Bargiano site evolved in a cyclical manner that was driven by intrinsic thresholds to a greater extent than it was affected by external (climatic) changes.

A Distributed Transfer Function for Non-Premixed Combustion Oscillations

The present study discusses a general distributed transfer function for non-premixed flames based on conservation equations. Also, a distributed transfer function for idealized, two-dimensional, flat, non-premixed flames is calculated using Green's function method. The unsteady heat release can be represented in terms of thermodynamic relationships based on energy conservation equations. By this method, the distributed flame response in physical domain for both combustion zone and its further downstream is intensively investigated. The lumped unsteady heat release can be obtained by the integration along the axial coordination. For distributed heat release transfer function in frequency domain, a dual-peak response of magnitudes is observed in the fuel-rich zone and the fuel-lean zone, respectively. The processes of the generation and the evolution of hot spots in non-premixed flames are also investigated. Analysis of multiple related parameters is conducted to evaluate the effects of the Strouhal number, the Peclet number, and convective velocity on hot spot propagation. The results show that a smaller Strouhal number, a larger Peclet number, or a faster convective velocity causes the hot spots to move farther downstream. These results are valuable for a better understanding of the mechanisms of non-premixed combustion instabilities, which is beneficial to the development of more accurate control techniques.

Energy localization in HMX-Estane polymer-bonded explosives during impact loading

We report the results of a mechanistic study of energy localization in aHMX (High Melting point eXplosive octahydro-1,3,5,7-tetranitro-1,2,3,5-tetrazocine)/Estane PBX system during dynamic loading. The focus is on the thermal-mechanical response over the strain rate range of 104 – 105 s−1 under different confinement conditions. A recently developed cohesive finite element method is used to track and analyze the contributions to heating from different constituents, interfaces, deformation and fracture mechanisms, and internal friction. In particular, energy dissipations due to viscoelastic deformation, grain fracture, interfacial debonding, and friction along crack faces are quantified as functions of time and overall deformation. The materials analyzed have HMX volume fractions between 0.69 and 0.82. Calculations show that variation in strain rate can significantly affect the spatial distribution but not the overall number of hot spots. Higher confining stresses lead to more intense heating in the binder and more uniform distribution of hot spots. The evolution of hot spots is quantified as a function of loading condition, deformation and microstructural attributes. The microstructure-response relations obtained can be used to assess the initiation sensitivity of energetic composites.

LAV@HAZARD: a web-GIS interface for volcanic hazard assessment

Satellite data, radiative power of hot spots as measured with remote sensing, historical records, on site geological surveys, digital elevation model data, and simulation results together provide a massive data source to investigate the behavior of active volcanoes like Mount Etna (Sicily, Italy) over recent times. The integration of these heterogeneous data into a coherent visualization framework is important for their practical exploitation. It is crucial to fill in the gap between experimental and numerical data, and the direct human perception of their meaning. Indeed, the people in charge of safety planning of an area need to be able to quickly assess hazards and other relevant issues even during critical situations. With this in mind, we developed LAV@HAZARD, a web-based geographic information system that provides an interface for the collection of all of the products coming from the LAVA project research activities. LAV@HAZARD is based on Google Maps application programming interface, a choice motivated by its ease of use and the user-friendly interactive environment it provides. In particular, the web structure consists of four modules for satellite applications (time-space evolution of hot spots, radiant flux and effusion rate), hazard map visualization, a database of ca. 30,000 lava-flow simulations, and real-time scenario forecasting by MAGFLOW on Compute Unified Device Architecture.

Analysis of Forming Mechanism of Thermal Damages on Friction Surfaces of Brake Disc

There exist hotspots, fatigue cracks, and stress fracture on friction surfaces of steel or iron brake disc during service, and these thermal damages greatly contribute to the fatigue crack failure of the friction surfaces. So, it is very significant for researching on the forming mechanism of thermal damages above to prevent the fatigue failure of the friction surfaces from occurring. The method used in the paper is to combine FEM analysis with theoretical analysis. Forming mechanism, influencing factors and preventive measures of the thermal damages above was studied by use of the method. The temperature condition and microstructure evolution of hotspots, the behavior of thermal crack initiation and propagation and the distribution of thermal stress contributed to five constraints all were focused on.

The thermal signature of volcanic eruptions on Io and Earth

We investigate a spectrum-based technique to identify the style of active volcanic eruptions on Jupiter's moon Io. Thermal remote sensing of Io has had to rely primarily on low-spatial-resolution data, similar to low-spatial-resolution satellite data applied to detecting and charting the temporal evolution of terrestrial hot spots. These terrestrial analyses use data from sensors designed to monitor the weather and sea surface temperature. On Io, such low-spatial-resolution data are used to classify eruption styles (modes of emplacement) by means of several criteria related to the temporal evolution of the infrared spectrum associated with the eruptive activity at each hot spot, which we term “thermal signature.” We find that the ratio of the emission at 2 and 5 µm, and how this ratio changes with time, is often diagnostic of eruption style, even in low-spatial-resolution data. Tests using thermal data for terrestrial “ground truth” cases show that our classification system is valid on Earth. The results of our analysis can be used to aid in the design of future space-based instruments that can be used for volcano monitoring on Io, as well as Earth.

Condensins Regulate Meiotic DNA Break Distribution, thus Crossover Frequency, by Controlling Chromosome Structure

Meiotic crossover (CO) recombination facilitates evolution and accurate chromosome segregation. CO distribution is tightly regulated: homolog pairs receive at least one CO, CO spacing is nonrandom, and COs occur preferentially in short genomic intervals called hotspots. We show that CO number and distribution are controlled on a chromosome-wide basis at the level of DNA double-strand break (DSB) formation by a condensin complex composed of subunits from two known condensins: the C. elegans dosage compensation complex and mitotic condensin II. Disruption of any subunit of the CO-controlling condensin dominantly changes DSB distribution, and thereby COs, and extends meiotic chromosome axes. These phenotypes are cosuppressed by disruption of a chromosome axis element. Our data implicate higher-order chromosome structure in the regulation of CO recombination, provide a model for the rapid evolution of CO hotspots, and show that reshuffling of interchangeable molecular parts can create independent machines with similar architectures but distinct biological functions.

Transient cooling response of smart vascular materials for self-cooling

Here we report the transient cooling performance of a body vascularized with tree-shaped channels supplied with coolant, which flows from one side of the body to the other. The vasculature consists of trees that alternate with upside down trees. Heat is generated volumetrically through the body at t=0. A time delay td separates the start of the flow of coolant from the start of heating. Three-dimensional simulations of conduction and convection in the solid-fluid composite show the formation and evolution of hot spots in the material. If the delay is not short enough, the maximum temperature of the body overshoots the maximum allowable level. The paper shows how to design the cooling delay time such that the hot-spot temperature does not exceed the safe level represented by the maximum temperature in the limit of steady state operation. The critical delay time is determined as a function of the applied pressure difference and the complexity of the dendritic flow architecture.

Evaluation of the physical process controlling beach changes adjacent to nearshore dredge pits

Numerical modeling of a beach nourishment project is conducted to enable a detailed evaluation of the processes associated with the effects of nearshore dredge pits on nourishment evolution and formation of erosion hot spots. A process-based numerical model, Delft3D, is used for this purpose. The analysis is based on the modification of existing bathymetry to simulate “what if” scenarios with/without the bathymetric features of interest. Borrow pits dredged about 30 years ago to provide sand for the nourishment project have a significant influence on project performance and formation of erosional hot spots. It was found that the main processes controlling beach response to these offshore bathymetric features were feedbacks between wave forces (roller force or alongshore component of the radiation stress), pressure gradients due to differentials in wave set-up/set-down and bed shear stress. Modeling results also indicated that backfilling of selected borrow sites showed a net positive effect within the beach fill limits and caused a reduction in the magnitude of hot spot erosion.

A combination of cis and trans control can solve the hotspot conversion paradox.

There is growing evidence that in a variety of organisms the majority of meiotic recombination events occur at a relatively small fraction of loci, known as recombination hotspots. If hotspot activity results from the DNA sequence at or near the hotspot itself (in cis), these hotspots are expected to be rapidly lost due to biased gene conversion, unless there is strong selection in favor of the hotspot itself. This phenomenon makes it very difficult to maintain existing hotspots and even more difficult for new hotspots to evolve; it has therefore come to be known as the "hotspot conversion paradox." I develop an analytical framework for exploring the evolution of recombination hotspots under the forces of selection, mutation, and conversion. I derive the general conditions under which cis- and trans-controlled hotspots can be maintained, as well as those under which new hotspots controlled by both a cis and a trans locus can invade a population. I show that the conditions for maintenance of and invasion by trans- or cis-plus-trans-controlled hotspots are broader than for those controlled entirely in cis. Finally, I show that a combination of cis and trans control may allow for long-lived polymorphisms in hotspot activity, the patterns of which may explain some recently observed features of recombination hotspots.

On the dynamical evolution of hotspots in powerful radio-loud active galactic nuclei

We describe the dynamical evolution of hotspots velocity, pressure and mass density in radio-loud active galactic nuclei (AGNs), taking proper account of (1) the conservations of the mass, momentum and kinetic energy flux of the unshocked jet, (2) the deceleration process of the jet by shocks and (3) the cocoon expansion without assuming the constant aspect ratio of the cocoon. By the detailed comparison with two-dimensional relativistic hydrodynamic simulations, we show that our model well reproduces the whole evolution of relativistic jets. Our model can explain also the observational trends of the velocity, the pressure, the size and mass density of hotspots in compact symmetric objects (CSOs) and Fanaroff-Riley type II (FR II) radio galaxies.

Relaxation of a thermal perturbation in a collisional plasma

The relationship between the nonlocal and nonstationary effects in electron heat transport processes in a weakly collisional plasma is investigated by considering the problem of the relaxation of a thermal perturbation as an example. It is shown that, for small-scale perturbations, the electron thermal conductivity depends not only on the temperature scale length but also on time. The consequence is that there exist two qualitatively different characteristic relaxation regimes of thermal perturbations on small and large scale lengths. As a result, the evolution of hot spots in laser plasmas should be described with allowance for the nonstationary nature of electron heat transport. In the course of this evolution, relaxation on the collisional kinetic time scale is clearly seen to change into relaxation on the collisional hydrodynamic time scale.

Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation

Meiotic crossovers in the human genome cluster into highly localized hotspots identifiable indirectly from patterns of DNA diversity and directly by high-resolution sperm typing. Little is known about factors that control hotspot activity and the apparently rapid turnover of hotspots during recent evolution. Clues can, however, be gained by characterizing variation in sperm crossover activity between men. Previous studies have identified single nucleotide polymorphisms within hotspots that appear to suppress crossover activity and which may be involved in hotspot attenuation/extinction. We now analyse a closely spaced pair of hotspots (MSTM1a, MSTM1b) on chromosome 1q42.3, the former being a candidate for a young hotspot that has failed to leave a significant mark on haplotype diversity. Extensive surveys of different men revealed substantial polymorphism in sperm crossover frequencies at both hotspots, but with very different patterns of variation. Hotspot MSTM1b was active in all men tested but with widely differing crossover frequencies. In contrast, MSTM1a was active in only a few men and appeared to be recombinationally inert in the remainder, providing the first example of presence/absence polymorphism of a human hotspot. Haplotype analysis around both hotspots identified active and suppressed men sharing identical haplotypes, establishing that these major variations in the presence/absence of a hotspot and in quantitative activity are not caused by local DNA sequence variation. These findings suggest a role for distal regulators or epigenetic factors in hotspot activity and provide the first direct evidence for the rapid evolution of recombination hotspots in humans.

Water, ammonia, and H 2S mixing ratios in Jupiter's five-micron hot spots: A dynamical model

The Galileo probe entered the jovian atmosphere at the southern edge of a 5-micron hot spot, one of typically 8–10 quasi-evenly-spaced longitudinal areas of anomalously high 5-micron IR emission that reside in a narrow latitude band centered on +7.5 degrees. These hot spots are characterized primarily by a low abundance of the cloud particles that dominate the 5-micron opacity at other locations on the planet, and by significant desiccation of ammonia, water and hydrogen sulfide in the upper layers of the troposphere. Ortiz et al. [1998. Evolution and persistence of 5-micron hot spots at the Galileo probe entry latitude. J. Geophys. Res. 103, 23,051–23,069] found that the latitude and drift rate of the hot spots could be explained if they are formed by an equatorially trapped Rossby wave of meridional degree 1 moving with a phase speed between 99 and 103 m s −1 relative to System III. Here we model additional properties of the hot spots in terms of the amplitude saturation of such a wave propagating in the weakly stratified deep troposphere. We identify the hot spots with locations where the wave plus mean thermal stratification becomes marginally stable. In these locations, potential temperature isotherms stretch downward to very deep levels in the troposphere. Since fluid parcels follow these isotherms under adiabatic flow conditions, the parcels dive downward when they enter the portion of the wave associated with the hot spot and soar upward upon leaving the spot. We show that this model can account for the anomalous vertical profiles of NH 3, H 2O, and H 2S mixing ratio measured by the Galileo probe. Pressures vary by as much as 20 bar over potential temperature isotherms in solutions that produce sufficient desiccation of water and H 2S in hot spots. Approximately 6 × 10 −2 of Jupiter's internal heat flux must be tapped to maintain the wave over the mean hot spot lifetime of 10 7 s. The results suggest that the phenomenon that causes hot spots may occur widely, although in less dramatic form, across Jupiter's surface, and consequently NH 3, H 2S, and H 2O mixing ratio profiles may vary significantly from location to location in Jupiter's troposphere.

Comparative Linkage-Disequilibrium Analysis of the β-Globin Hotspot in Primates

Recombination rates vary both across the genome and between different species, but little information is available about the temporal and physical scales over which such rates change. To shed light on these questions, we performed a high-resolution analysis of a genomic region within the beta-globin gene cluster that is known to experience elevated recombination rates in humans. For this purpose, we developed new linkage disequilibrium-based methods that thoroughly search for subsets of the data with unusually high or unusually low estimated values of the population-recombination parameter (4Nr, where N is the effective population size and r is the crossover rate between adjacent base pairs). By resequencing a 15-kb segment in a human population sample, we were able to narrow the recombinational hotspot to a segment <2 kb in length that coincides with the beta-globin replication origin. In addition, we analyzed the orthologous region in samples of rhesus macaques and common chimpanzees. Whereas the analysis of the chimpanzee data is complicated by the sample structure, the macaque data imply that this region may not be a hotspot in that species. These results suggest a time scale for the evolution of hotspots in primates. Furthermore, they allow us to propose diverged sequence elements that may contribute to the differences in the recombinational landscape in the two species.

Anomalous diffusion near the Fermi surface

We consider the three-dimensional dynamical evolution of localized hot spots in ultralow temperature Fermi liquids. Within a model calculation, it is found that such perturbations do not relax into a hydrodynamic profile at long times, as might be expected of thermal hot spots under less exotic conditions. Instead, the hot spot expands outward into a shell moving away from its center at a velocity comparable to the Fermi velocity ${v}_{F},$ which is consistent with the ``baked Alaska'' hypothesis proposed earlier by Leggett as a possible solution to the riddle of B-phase nucleation in ${}^{3}\mathrm{He}.$