Hauke Thomsen

Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.

A mammary gland EST showing linkage disequilibrium to a milk production QTL on bovine Chromosome 14

As part of a genome scan, ESTs derived from mammary gland tissue of a lactating cow were used as candidate genes for quantitative trait loci (QTL), affecting milk production traits. Resource families were genotyped with 247 microsatellite markers and 4 polymorphic ESTs. It was shown by linkage analysis that one of these ESTs, KIEL_E8, mapped to the centromeric region of bovine Chromosome (Chr) 14. Regression analysis revealed the presence of a QTL, with significant effect on milk production, in this chromosome region, and analysis of variance showed no significant interaction of marker genotype and family. The estimated significant differences between homozygous marker genotypes were 140 kg milk, −5.02 kg fat yield, and 2.58 kg protein yield for the first 100 days of lactation. Thus, there was strong evidence for a complete or nearly complete linkage disequilibrium between KIEL_E8 and the QTL. To identify the biological function of KIEL_E8, we extended the sequence for 869 bp by 5′-RACE. A 560-bp fragment of this shows a 90.9% similarity to a gene encoding a cysteine- and histidine-rich cytoplasmic protein in mouse. Although such a protein may have a regulatory function for lactation and a linkage disequilibrium between the EST marker and the QTL has been observed, it remains to be elucidated whether they are identical or not. Nevertheless, KIEL_E8 will be an efficient marker to perform marker-assisted selection in the Holstein-Friesian population.

Laser heating of finite two-dimensional dust clusters: A. Experiments

Laser manipulation allows to control the kinetic particle temperature in dusty plasmas. Different methods of laser heating for plasma crystals are benchmarked experimentally. The methods are analyzed with respect to homogeneity and isotropy in a spatial, temporal, and statistical sense. It is shown that it is possible to achieve particle dynamics very close to thermal equilibrium and that laser heating methods allow for a detailed study of phase transitions in finite size systems.

Laser heating of finite two-dimensional dust clusters: B. Simulations

Laser heating of monolayer dusty plasmas is investigated theoretically by Langevin dynamics simulations. The laser radiation pressure is used to externally control the dust temperature without changing the plasma properties. We show that the laser scanning pattern has a major influence on both the velocity distribution function and the stationary structure of the cluster. Furthermore, the heating effect is found to be enhanced when the laser spots move with slightly higher frequencies than the trap frequency. The simulations confirm that a proper thermodynamic excitation of the dust particles is possible.

Controlling strongly correlated dust clusters with lasers

Lasers have been used extensively to manipulate matter in a controlled way ? from single atoms and molecules up to macroscopic materials. They are particularly valuable for the analysis and control of mesoscopic systems such as few-particle clusters. Here we report on recent work on finite size complex (dusty) plasma systems. These are unusual types of clusters with a very strong inter-particle interaction so that, at room temperature, they are practically in their ground state. Lasers are employed as a tool to achieve excited states and phase transitions.The most attractive feature of dusty plasmas is that they allow for a precise diagnostic with single-particle resolution. From such measurements, the structural properties of finite two-dimensional (2D) clusters and three-dimensional (3D) spherical crystals in nearly harmonic traps?so-called Yukawa balls?have been explored in great detail. Their structural features?the shell compositions and the order within the shells?have been investigated and good agreement to theoretical predictions was found. Open questions on the agenda are the excitation behaviour, the structural changes and phase transitions that occur at elevated temperature.Here we report on recent experimental results where laser heating methods were further improved and applied to finite 2D and 3D dust clusters. Comparing to simulations, we demonstrate that laser heating indeed allows to increase the temperature in a controlled manner. For the analysis of thermodynamic properties and phase transitions in these finite systems, we present theoretical and experimental results on the basis of the instantaneous normal modes, pair distribution function and the recently introduced centre-two-particle correlation function.

Heat transport in confined strongly coupled two-dimensional dust clusters

Dusty plasmas are a model system for studying strong correlation. The dust grains’ size of a few micro-meters and their characteristic oscillation frequency of a few hertz allow for an investigation of many-particle effects on an “atomic” level. In this article, we model the heat transport through an axially confined 2D dust cluster from the center to the outside. The system behaves particularly interesting since heat is not only conducted within the dust component but also transferred to the neutral gas. Fitting the analytical solution to the radial temperature profiles obtained in molecular dynamics simulations allows to determine the heat conductivity k. The heat conductivity is found to be constant over a wide range of coupling strengths even including the phase transition from solid to liquid here, as it was also found in extended systems by Nosenko et al. [Phys. Rev. Lett. 100, 025003 (2008)].

Tuning correlations in multi-component plasmas

Spontaneous, correlation-driven structure formation is one of the most fundamental collective processes in nature. In particular, particle ensembles in externally controlled confinement geometries allow for a systematic investigation of strong correlation and quantum effects over broad ranges of the relevant trap and plasma parameters. An exceptional feature inherent to finite systems is the governing role of symmetry and surface effects leading to similar collective behaviour in physical systems on vastly different length and energy scales. Considering (i) confined complex (dusty) plasmas and (ii) charge asymmetric bilayers, the effective range of the pair interaction emerges as a key quantity taking effect on the self-organized structure formation. Additional interest arises from the possible mass asymmetry of the plasma constituents in bilayers. Translating the results from (unconfined) 3D plasmas to bilayer systems, it is shown that the critical mass ratio required for crystallization of the heavy plasma component can be drastically reduced such that this effect becomes experimentally accessible.

Charge Correlations in a Harmonic Trap

A system of N classical Coulomb charges trapped in a harmonic potential displays shell structure and orientational ordering. The local density profile is well understood from theory, simulation, and experiment. Here, pair correlations are considered for this highly inhomogeneous system for both the fluid and ordered states. In the former, it is noted that there is a close relationship to pair correlations in the uniform one component plasma. For the ordered state, it is shown that the disordered “tiling” is closely related to the ground state Thomson sites for a single sphere (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Phase Transitions in Dusty Plasmas

This chapter is devoted to phase transitions in dusty (complex) plasmas which contain micrometer-size highly charged particles. These systems allow for studying the thermodynamic many-body features on a single-particle level. We start with a brief introduction to dusty plasmas and the parameters that can be used to distinguish different phases in harmonically confined dust crystals in two and three dimensions. These finite systems behave differently than bulk systems as their structure is dominated by centric rings in 2D or spherical shells in 3D. Both Monte Carlo and (Langevin) molecular dynamics are addressed as two important simulation methods for classical interacting many body systems. In order to study phase transitions in complex plasma experiments, selective control over the dust kinetic temperature is essential. This control can be achieved by the laser manipulation method where dust grains are accelerated by randomly moving laser spots. Furthermore, parameters are discussed that allow one to detect phase transitions in finite systems in simulations and experiments: the relative inter-particle distance fluctuations and the bond angular order parameter.

Introduction to Streaming Complex Plasmas A: Attraction of Like-Charged Particles

Like-charged particles usually interact via a repulsive force. However, in streaming dusty plasmas one can observe that two negatively charged dust particles may attract each other. This is explained by accumulation of positive ions below the dust particles (with respect to the streaming direction). In this chapter, we describe the dependence of this ion focus and the resulting wakes on discharge rf-power, pressure and thermophoretic force, as the three key parameters, that can be varied in dusty plasma experiments. Moreover, we discuss the impact of this attractive force on the collective properties of many dust particles, in particular, on the structure and on the dynamics of spherically confined clusters.