Genetic interactions contribute less than additive effects to quantitative trait variation in yeast.

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL-QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL-QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies

Rare variants contribute disproportionately to quantitative trait variation in yeast.

How variants with different frequencies contribute to trait variation is a central question in genetics. We use a unique model system to disentangle the contributions of common and rare variants to quantitative traits. We generated ~14,000 progeny from crosses among 16 diverse yeast strains and identified thousands of quantitative trait loci (QTLs) for 38 traits. We combined our results with sequencing data for 1011 yeast isolates to show that rare variants make a disproportionate contribution to trait variation. Evolutionary analyses revealed that this contribution is driven by rare variants that arose recently, and that negative selection has shaped the relationship between variant frequency and effect size. We leveraged the structure of the crosses to resolve hundreds of QTLs to single genes. These results refine our understanding of trait variation at the population level and suggest that studies of rare variants are a fertile ground for discovery of genetic effects

Genetics of single-cell protein abundance variation in large yeast populations

Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a powerful method for identifying genetic loci that influence protein expression in very large populations of the yeast Saccharomyes cerevisiae. The method measures single-cell protein abundance through the use of green-fluorescent-protein tags. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci cluster at hotspot locations that influence multiple proteins - in some cases, more than half of those examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains

In-situ observation of the formation of laser-induced periodic surface structures with extreme spatial and temporal resolution

Irradiation of solid surfaces with intense ultrashort laser pulses represents a unique way of depositing energy into materials. It allows to realize states of extreme electronic excitation and/or very high temperature and pressure, and to drive materials close to and beyond fundamental stability limits. As a consequence, structural changes and phase transitions often occur along unusual pathways and under strongly non-equilibrium conditions. Due to the inherent multiscale nature - both temporally and spatially - of these irreversible processes their direct experimental observation requires techniques that combine high temporal resolution with the appropriate spatial resolution and the capability to obtain good quality data on a single pulse/event basis. In this respect fourth generation light sources, namely short wavelength, short pulse free electron lasers (FELs) are offering new and fascinating possibilities. As an example, this chapter will discuss the results of scattering experiments carried at the FLASH free electron laser at DESY (Hamburg, Germany), which allowed us to resolve laser-induced structure formation at surfaces on the nanometer to sub-micron length scale and in temporal regimes ranging from picoseconds to several nanoseconds with sub-picosecond resolution

Time-Resolved Measurement of Interatomic Coulombic Decay in Ne_2

The lifetime of interatomic Coulombic decay (ICD) [L. S. Cederbaum et al., Phys. Rev. Lett. 79, 4778 (1997)] in Ne_2 is determined via an extreme ultraviolet pump-probe experiment at the Free-Electron Laser in Hamburg. The pump pulse creates a 2s inner-shell vacancy in one of the two Ne atoms, whereupon the ionized dimer undergoes ICD resulting in a repulsive Ne^{+}(2p^{-1}) - Ne^{+}(2p^{-1}) state, which is probed with a second pulse, removing a further electron. The yield of coincident Ne^{+} - Ne^{2+} pairs is recorded as a function of the pump-probe delay, allowing us to deduce the ICD lifetime of the Ne_{2}^{+}(2s^{-1}) state to be (150 +/- 50) fs in agreement with quantum calculations.Comment: 5 pages, 3 figures, accepted by PRL on July 11th, 201

Multiple ionization and fragmentation dynamics of molecular iodine studied in IR-XUV pump-probe experiments

The ionization and fragmentation dynamics of iodine molecules (I-2) are traced using very intense (similar to 10(14) W cm(-2)) ultra-short (similar to 60 fs) light pulses with 87 eV photons of the Free-electron LASer at Hamburg (FLASH) in combination with a synchronized femtosecond optical laser. Within a pump-probe scheme the IR pulse initiates a molecular fragmentation and then, after an adjustable time delay, the system is exposed to an intense FEL pulse. This way we follow the creation of highly-charged molecular fragments as a function of time, and probe the dynamics of multi-photon absorption during the transition from a molecule to individual atoms

Sequential and Direct Two-Photon Double Ionization of D₂ at Flash

Sequential and direct two-photon double ionization (DI) of D2 molecule is studied experimentally and theoretically at a photon energy of 38.8 eV. Experimental and theoretical kinetic energy releases of D++D+fragments, consisting of the contributions of sequential DI via the D2+(1sσg) state and direct DI via a virtual state, agree well with each other

Nonlinear Coherence Effects in Transient-Absorption Ion Spectroscopy with Stochastic Extreme-Ultraviolet Free-Electron Laser Pulses

We demonstrate time-resolved nonlinear extreme-ultraviolet absorption spectroscopy on multiply charged ions, here applied to the doubly charged neon ion, driven by a phase-locked sequence of two intense free-electron laser pulses. Absorption signatures of resonance lines due to 2$p$--3$d$ bound--bound transitions between the spin-orbit multiplets $^3$P$_{0,1,2}$ and $^3$D$_{1,2,3}$ of the transiently produced doubly charged Ne$^{2+}$ ion are revealed, with time-dependent spectral changes over a time-delay range of $(2.4\pm0.3)\,\text{fs}$. Furthermore, we observe 10-meV-scale spectral shifts of these resonances owing to the AC Stark effect. We use a time-dependent quantum model to explain the observations by an enhanced coupling of the ionic quantum states with the partially coherent free-electron-laser radiation when the phase-locked pump and probe pulses precisely overlap in time

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases