The New (Old) Genetics, Version 1.0

The field of Genetics started flourishing after the rediscovery of the Mendelian laws of inheritance at the beginning of the 20th century. These laws are based on a discrete classification of phenotypes and their causative genes. Such a Mendelian way of thinking forms the foundation of modern molecular biology, with its experimental paradigm that a gene function is inferred from the knock-out of the gene. However, most phenotypes are not discrete. Human height, for example, is a continuous phenotype and height measures approximate a Gaussian distribution. The statistical foundation for the genetics of human height was worked out by GALTON at the end of the 19th century. He established the basis of quantitative genetics, a field that has driven the agricultural and breeding programs in the past century. It is not until very recently that the technical developments behind the human genome project have paved the way to reconcile the two contrasting ways of genetic thinking – Mendelian genetics and statistical genetics – through genome-wide analyses. It has now become clear that most phenotypes are rarely determined by single Mendelian genes, but instead, many genes contribute to their determination and variation. It has even been suggested in the omnigenic model that all genes that are expressed at the appropriate time contribute to any given phenotype. These insights are stimulating a major rethinking of how the linear genetic information laid down in the deoxyribonucleic acid (DNA) is converted into the threedimensional structure of an individual. The new conceptual and experimental paradigms have already revolutionized animal and plant breeding. In the field of human genetics, the realization that common diseases also have a polygenic basis is raising new challenges for treatment. And finally, in basic sciences like molecular and evolutionary biology, researchers are starting to revisit traditional, but oversimplified concepts on how genes act and how evolutionary adaptation works

Use of a natural hybrid zone for genome-wide association mapping of craniofacial traits in the house mouse

The identification of the genes involved in morphological variation in nature is still a major challenge. Here we explore a new approach: we combine 178 samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus), and high coverage of the genome (~145K SNPs) to identify loci underlying craniofacial shape variation. Due to the long history of recombination in the hybrid zone, high mapping resolution is anticipated. The combination of genomes from subspecies allows the mapping of both, variation within subspecies and intersubspecific differences, thereby increasing the overall amount of causal genetic variation than can be detected. Skull and mandible shape were measured using 3D landmarks and geometric morphometrics. Using principle component axes as phenotypes, and a linear mixed model accounting for genetic relatedness in the mapping populations, we identified 9 genomic regions associated with skull and 10 with mandible shape. High mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. Some of the genes act as regulators or modifiers of signaling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. The significant associations combined explain 13% and 7% of the skull and mandible shape variation. In addition, a positive correlation was found between chromosomal length and proportion of variation explained. Our results suggest a complex genetic architecture for shape traits, and support a polygenic model

Surfactant-Mediated Epitaxial Growth of Single-Layer Graphene in an Unconventional Orientation on SiC

We report the use of a surfactant molecule during the epitaxy of graphene on SiC(0001) that leads to the growth in an unconventional orientation, namely $R0^\circ$ rotation with respect to the SiC lattice. It yields a very high-quality single-layer graphene with a uniform orientation with respect to the substrate, on the wafer scale. We find an increased quality and homogeneity compared to the approach based on the use of a pre-oriented template to induce the unconventional orientation. Using spot profile analysis low energy electron diffraction, angle-resolved photoelectron spectroscopy, and the normal incidence x-ray standing wave technique, we assess the crystalline quality and coverage of the graphene layer. Combined with the presence of a covalently-bound graphene layer in the conventional orientation underneath, our surfactant-mediated growth offers an ideal platform to prepare epitaxial twisted bilayer graphene via intercalation.Comment: 7 pages, 3 figure

Growth rates of the Weibel and tearing mode instabilities in a relativistic pair plasma

We present an algorithm for solving the linear dispersion relation in an inhomogeneous, magnetised, relativistic plasma. The method is a generalisation of a previously reported algorithm that was limited to the homogeneous case. The extension involves projecting the spatial dependence of the perturbations onto a set of basis functions that satisfy the boundary conditions (spectral Galerkin method). To test this algorithm in the homogeneous case, we derive an analytical expression for the growth rate of the Weibel instability for a relativistic Maxwellian distribution and compare it with the numerical results. In the inhomogeneous case, we present solutions of the dispersion relation for the relativistic tearing mode, making no assumption about the thickness of the current sheet, and check the numerical method against the analytical expression.Comment: Accepted by PPC

Numerical solution of the linear dispersion relation in a relativistic pair plasma

We describe an algorithm that computes the linear dispersion relation of waves and instabilities in relativistic plasmas within a Vlasov-Maxwell description. The method used is fully relativistic and involves explicit integration of particle orbits along the unperturbed equilibrium trajectories. We check the algorithm against the dispersion curves for a single component magnetised plasma and for an unmagnetised plasma with counter-streaming components in the non-relativistic case. New results on the growth rate of the Weibel or two-stream instability in a hot unmagnetised pair plasma consisting of two counter-streaming relativistic Maxwellians are presented. These are relevant to the physics of the relativistic plasmas found in gamma-ray bursts, relativistic jets and pulsar winds.Comment: Accepted by Plasma Physics and Controlled Fusio

Quantum transport through STM-lifted single PTCDA molecules

Using a scanning tunneling microscope we have measured the quantum conductance through a PTCDA molecule for different configurations of the tip-molecule-surface junction. A peculiar conductance resonance arises at the Fermi level for certain tip to surface distances. We have relaxed the molecular junction coordinates and calculated transport by means of the Landauer/Keldysh approach. The zero bias transmission calculated for fixed tip positions in lateral dimensions but different tip substrate distances show a clear shift and sharpening of the molecular chemisorption level on increasing the STM-surface distance, in agreement with experiment.Comment: accepted for publication in Applied Physics