The fission yeast FANCM ortholog directs non-crossover recombination during meiosis

Peer reviewedPostprin

Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits

Scaling of 1/f noise in tunable break-junctions

We have studied the $1/f$ voltage noise of gold nano-contacts in electromigrated and mechanically controlled break-junctions having resistance values $R$ that can be tuned from 10 $\Omega$ (many channels) to 10 k$\Omega$ (single atom contact). The noise is caused by resistance fluctuations as evidenced by the $S_V\propto V^2$ dependence of the power spectral density $S_V$ on the applied DC voltage $V$. As a function of $R$ the normalized noise $S_V/V^2$ shows a pronounced cross-over from $\propto R^3$ for low-ohmic junctions to $\propto R^{1.5}$ for high-ohmic ones. The measured powers of 3 and 1.5 are in agreement with $1/f$-noise generated in the bulk and reflect the transition from diffusive to ballistic transport

Electrolyte gate dependent high-frequency measurement of graphene field-effect transistor for sensing applications

We performed radiofrequency (RF) reflectometry measurements at 2.4 GHz on electrolyte-gated graphene field-effect transistors (GFETs) utilizing a tunable stub-matching circuit for impedance matching. We demonstrate that the gate voltage dependent RF resistivity of graphene can be deduced even in the presence of the electrolyte which is in direct contact with the graphene layer. The RF resistivity is found to be consistent with its DC counterpart in the full gate voltage range. Furthermore, in order to access the potential of high-frequency sensing for applications, we demonstrate time-dependent gating in solution with nanosecond time resolution.Comment: 14 pages, 4 figure

Slx8 removes Pli1-dependent protein-SUMO conjugates including SUMOylated Topoisomerase I to promote genome stability

Peer reviewedPublisher PD

The multilevel trigger system of the DIRAC experiment

The multilevel trigger system of the DIRAC experiment at CERN is presented. It includes a fast first level trigger as well as various trigger processors to select events with a pair of pions having a low relative momentum typical of the physical process under study. One of these processors employs the drift chamber data, another one is based on a neural network algorithm and the others use various hit-map detector correlations. Two versions of the trigger system used at different stages of the experiment are described. The complete system reduces the event rate by a factor of 1000, with efficiency $\geq$95% of detecting the events in the relative momentum range of interest.Comment: 21 pages, 11 figure

Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue

\ua9 2024 by the authors.A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at −80 \ub0C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19). The RNA from fresh tissue in RNAlater resulted in higher amounts and a better quality of RNA than that from the paraffin-embedded tissue. The reference gene evaluation exhibited four stably expressed reference genes (B2M, HPRT1, GAPDH and GUSB). The selected reference genes were then used to examine the effect on the expression outcome of target genes (OTOF and TECTA), which are known to be regulated during inner ear development. The selected reference genes displayed no differences in the expression profile of OTOF and TECTA, which was confirmed by immunostaining. The results underline the importance of the choice of the RNA extraction method and reference genes used in gene expression studies

A Measurement of the Electric Form Factor of the Neutron through d⃗(e⃗,e′n)p\vec{d}(\vec{e},e'n)p at Q2=0.5Q^2 = 0.5 (GeV/c)2^2

We report the first measurement of the neutron electric form factor $G_E^n$ via $\vec{d}(\vec{e},e'n)p$ using a solid polarized target. $G_E^n$ was determined from the beam-target asymmetry in the scattering of longitudinally polarized electrons from polarized deuterated ammonia, $^{15}$ND$_3$. The measurement was performed in Hall C at Thomas Jefferson National Accelerator Facility (TJNAF) in quasi free kinematics with the target polarization perpendicular to the momentum transfer. The electrons were detected in a magnetic spectrometer in coincidence with neutrons in a large solid angle segmented detector. We find $G_E^n = 0.04632\pm0.00616 (stat.) \pm0.00341 (syst.)$ at $Q^2 = 0.495$ (GeV/c)$^2$.Comment: Latex2e 5 pages, 3 figure

Imaging signatures of the local density of states in an electronic cavity

We use Scanning Gate Microscopy to study electron transport through an open, gate-defined resonator in a Ga(Al)As heterostructure. Raster-scanning the voltage-biased metallic tip above the resonator, we observe distinct conductance modulations as a function of the tip-position and voltage. Quantum mechanical simulations reproduce these conductance modulations and reveal their relation to the partial local density of states in the resonator. Our measurements illustrate the current frontier between possibilities and limitations in imaging the local density of states in buried electron systems using scanning gate microscopy

RF Discharge Mirror Cleaning for ITER Optical Diagnostics Using 60 MHz Very High Frequency

For the fusion reactor ITER, a mandatory monitor of the fusion device and plasma will be performed with optical diagnostic systems. For the metallic first mirrors, the recovery of the reflectivity losses due to dust deposition is proposed to be carried out for 14 different optical diagnostic systems by the plasma cleaning technique. In this work, we studied the influence of the electrode area on the electrode potential as a function of the applied power with a 60 MHz radio very high frequency source. Unshielded copper disks with different diameters were constructed to study the impact of the electrode area in the range of 90 cm2 to 1200 cm2, which corresponds to an Edge Thomson Scattering area ratio of 0.15 to 2. It was observed that the absolute value of the resulting bias decreased from 280 V to 15 V with the increase of the area for a given RF power. Moreover, the power consumption was reduced by 43 langid = english, keywords = End-of-Cleaning indicator,First mirror,ITER,Plasma cleanin