The theory of phase transitions represents a central concept for the characterization of equilibrium matter. In this work we study experimentally an extension of this theory to the nonequilibrium ...dynamical regime termed dynamical quantum phase transitions (DQPTs). We investigate and measure DQPTs in a string of ions simulating interacting transverse-field Ising models. During the nonequilibrium dynamics induced by a quantum quench we show for strings of up to 10 ions the direct detection of DQPTs by revealing nonanalytic behavior in time. Moreover, we provide a link between DQPTs and the dynamics of other quantities such as the magnetization, and we establish a connection between DQPTs and entanglement production.
The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. ...Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network.
•We report mRNA synthesis and degradation rates in 46 yeast gene deletion strains•Eukaryotic cells buffer mRNA levels, and this requires the exonuclease Xrn1•The data reveal interaction networks among mRNA degradation factors
Transcription by RNA polymerase II (RNA Pol II) relies on the elongation factors PAF1 complex (PAF), RTF1, and SPT6. Here, we use rapid factor depletion and multi-omics analysis to investigate how ...these elongation factors influence RNA Pol II elongation activity in human cells. Whereas depletion of PAF subunits PAF1 and CTR9 has little effect on cellular RNA synthesis, depletion of RTF1 or SPT6 strongly compromises RNA Pol II activity, albeit in fundamentally different ways. RTF1 depletion decreases RNA Pol II velocity, whereas SPT6 depletion impairs RNA Pol II progression through nucleosomes. These results show that distinct elongation factors stimulate either RNA Pol II velocity or RNA Pol II progression through chromatin in vivo. Further analysis provides evidence for two distinct barriers to early elongation: the promoter-proximal pause site and the +1 nucleosome. It emerges that the first barrier enables loading of elongation factors that are required to overcome the second and subsequent barriers to transcription.
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•The PAF1 complex and SPT6 have positive roles in transcription elongation•RTF1 and SPT6 stimulate RNA polymerase II elongation in distinct ways•Depletion of RTF1 decreases RNA polymerase II velocity•Loss of SPT6 hinders RNA polymerase II progression through nucleosomes
Metazoan gene transcription requires RNA polymerase II and a large number of factors that help the polymerase to pass through genes. Žumer et al. utilize rapid depletion of endogenous proteins from human cells and sequencing approaches to show two distinct mechanisms of two such elongation factors: one controls polymerase speed, and the other controls polymerase passage through chromatin.
The nationwide multicenter trials of the German Research Network on Neuropathic Pain (DFNS) aim to characterize the somatosensory phenotype of patients with neuropathic pain. For this purpose, we ...have implemented a standardized quantitative sensory testing (QST) protocol giving a complete profile for one region within 30 min. To judge plus or minus signs in patients we have now established age- and gender-matched absolute and relative QST reference values from 180 healthy subjects, assessed bilaterally over face, hand and foot. We determined thermal detection and pain thresholds including a test for paradoxical heat sensations, mechanical detection thresholds to von Frey filaments and a 64 Hz tuning fork, mechanical pain thresholds to pinprick stimuli and blunt pressure, stimulus/response-functions for pinprick and dynamic mechanical allodynia, and pain summation (wind-up ratio). QST parameters were region specific and age dependent. Pain thresholds were significantly lower in women than men. Detection thresholds were generally independent of gender. Reference data were normalized to the specific group means and variances (region, age, gender) by calculating z-scores. Due to confidence limits close to the respective limits of the possible data range, heat hypoalgesia, cold hypoalgesia, and mechanical hyperesthesia can hardly be diagnosed. Nevertheless, these parameters can be used for group comparisons. Sensitivity is enhanced by side-to-side comparisons by a factor ranging from 1.1 to 2.5. Relative comparisons across body regions do not offer advantages over absolute reference values. Application of this standardized QST protocol in patients and human surrogate models will allow to infer underlying mechanisms from somatosensory phenotypes.
We carried out a detailed strong lensing analysis of a sub-sample of eight galaxy clusters of the Cluster Lensing And Supernova survey with Hubble (CLASH) in the redshift range of zcluster = 0.23 − ...0.59 using extensive spectroscopic information, primarily from the Multi Unit Spectroscopic Explorer (MUSE) archival data and complemented with CLASH-VLT redshift measurements. The observed positions of the multiple images of strongly lensed background sources were used to constrain parametric models describing the cluster total mass distributions. Different models were tested in each cluster depending on the complexity of its mass distribution and on the number of detected multiple images. Four clusters show more than five spectroscopically confirmed multiple image families. In this sample, we did not make use of families that are only photometrically identified in order to reduce model degeneracies between the values of the total mass of a cluster source redshifts, in addition to systematics due to the potential misidentifications of multiple images. For the remaining four clusters, we used additional families without any spectroscopic confirmation to increase the number of strong lensing constraints up to the number of free parameters in our parametric models. We present spectroscopic confirmation of 27 multiply lensed sources, with no previous spectroscopic measurements, spanning over the redshift range of zsrc = 0.7 − 6.1. Moreover, we confirm an average of 48 galaxy members in the core of each cluster thanks to the high efficiency and large field of view of MUSE. We used this information to derive precise strong lensing models, projected total mass distributions, and magnification maps. We show that, despite having different properties (i.e. number of mass components, total mass, redshift, etc.), the projected total mass and mass density profiles of all clusters have very similar shapes when rescaled by independent measurements of M200c and R200c. Specifically, we measured the mean value of the projected total mass of our cluster sample within 10 (20)% of R200c to be 0.13 (0.32) of M200c, with a remarkably small scatter of 5 (6)%. Furthermore, the large number of high-z sources and the precise magnification maps derived in this work for four clusters add up to the sample of high-quality gravitational telescopes to be used to study the faint and distant Universe.
Aims.
We strive to explore the differences in the properties and quenching processes of satellite galaxies in a sample of massive clusters with passive and star-forming (SF) brightest cluster ...galaxies (BCGs). One aim is to investigate galactic conformity effects, manifested in a correlation between the fraction of satellite galaxies that halted star formation and the state of star formation in the central galaxy.
Methods.
We explored 18 clusters from the Local Cluster Substructure Survey at 0.15 <
z
< 0.26, using spectra from the Arizona Cluster Redshift Survey Hectospec survey of about 1800 cluster members at
R
<
R
200
in a mass-complete sample. Nine clusters have a SF BCG and nine have a passive BCG, which enable the exploration of galactic conformity effects. We measured the fluxes of emission lines of cluster members, allowing us to derive O/H gas metallicities and to identify active galactic nuclei (AGN). We compared our cluster galaxy sample with a control field sample of about 1300 galaxies with similar masses and at similar redshifts observed with Hectospec as part of the same survey. We used the location of SF galaxies, recently quenched galaxies (RQGs) and AGN in the projected velocity versus the position phase-space (phase-space diagram) to identify objects in the inner regions of the clusters and to compare their fractions in clusters with SF and passive BCGs.
Results.
The metallicities of log(
M
/
M
⊙
)≥10 SF cluster galaxies with
R
<
R
200
were found to be enhanced with respect to the mass-metallicity relation obtained for our sample of coeval field SF galaxies. This metallicity enhancement among SF cluster galaxies is limited to lower-mass satellites (10 < log(
M
/
M
⊙
) < 10.7) of the nine clusters with a passive BCG, with no metallicity enhancement seen for SF galaxies in clusters with active BCGs. Many of the SF galaxies with enhanced metallicities are found in the core regions of the phase-space diagram expected for virialized populations. We find a higher fraction of log(
M
/
M
⊙
)≥10.7 SF galaxies at
R
<
R
500
in clusters with active BCGs as compared to clusters with passive BCGs, which stands as a signal of galactic conformity. In contrast, much higher fractions at
R
<
R
500
of AGN and, particularly of RQGs, are found in clusters with passive BCGs in comparison to clusters with active BCGs.
Conclusions.
We deduce that strangulation is initiated in clusters with passive BCGs when SF satellite galaxies pass
R
200
, by stopping the pristine gas inflow that would otherwise dilute the interstellar medium and would keep their metallicities at the level of values similar to those of field galaxies at similar redshifts. These satellite galaxies continue to form stars by consuming the available gas in the disk. For galaxies with massses above log(
M
/
M
⊙
)∼10.7 that manage to survive and remain SF when traveling to
R
<
R
500
of clusters with passive BCGs, we assume that they suffer a rapid quenching of star formation, likely due to AGN triggered by the increasing ram pressure stripping toward the cluster center, which can compress the gas and fuel AGN. These AGN can rapidly quench and maintain quenched satellite galaxies. On the other hand, we found that surviving SF massive satellite galaxies around active BCGs are less affected by environment when they enter
R
<
R
500
, since we observe
R
<
R
500
SF galaxies with masses up to
M
∼ 10
11
M
⊙
and with metallicities typical of coeval field galaxies. This observed galactic conformity implies that active BCGs must maintain their activity over timescales of at least ∼1 Gyr.
We present experiments on polarization gradient cooling of Ca+ multi-ion Coulomb crystals in a linear Paul trap. Polarization gradient cooling of the collective modes of motion whose eigenvectors ...have overlap with the symmetry axis of the trap is achieved by two counter-propagating laser beams with mutually orthogonal linear polarizations that are blue-detuned from the S1/2 ↔ P1/2 transition. We demonstrate cooling of linear chains of up to 51 ions and 2D-crystals in zig-zag configuration with 22 ions. The cooling results are compared with numerical simulations and the predictions of a simple model of cooling in a moving polarization gradient.
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3′-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide ...analysis of the 3′-transition in budding yeast. We find that the 3′-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the “torpedo” exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3′-transition can result in increased transcription at downstream genes.
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•Pcf11 and Ysh1 are globally required for the 3′-transition at protein-coding genes•Spt5 binds pre-mRNA near the pA site and contributes to the 3′-transition•Rat1 is globally required for Pol II release from DNA in a narrow termination window
RNA polymerase II undergoes a concerted transition at the 3′ end of protein coding genes. Baejen et al. present a genome-wide analysis of this 3′-transition in budding yeast. They show that this transition requires the Spt5 elongation factor and demonstrate that polymerase II release from DNA requires the Rat1 exonuclease.
ABSTRACT We investigate the physical conditions of ionized gas in high-z star-forming galaxies using diagnostic diagrams based on the rest-frame optical emission lines. The sample consists of 701 ...galaxies with an H detection at , from the Fiber Multi-Object Spectrograph (FMOS)-COSMOS survey, that represent the normal star-forming population over the stellar mass range , with those at being well sampled. We confirm an offset of the average location of star-forming galaxies in the Baldwin-Phillips-Terlevich (BPT) diagram ( versus ), primarily toward higher , compared with local galaxies. Based on the S ii ratio, we measure an electron density ( ), which is higher than that of local galaxies. Based on comparisons to theoretical models, we argue that changes in emission-line ratios, including the offset in the BPT diagram, are caused by a higher ionization parameter both at fixed stellar mass and at fixed metallicity, with additional contributions from a higher gas density and possibly a hardening of the ionizing radiation field. Ionization due to active galactic nuclei is ruled out as assessed with Chandra. As a consequence, we revisit the mass-metallicity relation using and a new calibration including as recently introduced by Dopita et al. Consistent with our previous results, the most massive galaxies ( ) are fully enriched, while those at lower masses have metallicities lower than local galaxies. Finally, we demonstrate that the stellar masses, metallicities, and star formation rates of the FMOS sample are well fit with a physically motivated model for the chemical evolution of star-forming galaxies.
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