The Ctp1 protein in Schizosaccharomyces pombe is essential for DNA double-strand break (DSB) repair by homologous recombination. Fission yeast Ctp1 and its budding yeast (Sae2) and human (CtIP) ...homologs control Mre11–Rad50–Nbs1 nuclease complex activity and harbor DNA-binding and -bridging activities. However, the molecular basis for Ctp1–DNA transactions remains undefined. Here, we report atomic force microscopy (AFM) imaging of S. pombe Ctp1–DNA complexes revealing that Ctp1 polymerizes on dsDNA molecules and forms synaptic filaments that bridge two dsDNA strands. We observed that Ctp1 DNA filaments are typified by an average filament length of ∼180 bp of dsDNA and a Ctp1 tetramer footprint of ∼15 bp. Biochemical results characterizing Ctp1 variants with impaired DNA-binding or -bridging properties were consistent with Ctp1-mediated DNA bridging requiring the intact and correctly folded Ctp1 tetramer. Furthermore, mutations altering Ctp1 oligomerization and DNA bridging in vitro conferred cell sensitivity to DSB-producing agents. Together, these results support an important role for Ctp1-regulated DNA strand coordination required for DNA DSB repair in S. pombe.
ABSTRACT
This is the second part of a thorough investigation of the redshift-space effects that affect void properties and the impact they have on cosmological tests. Here, we focus on the ...void-galaxy cross-correlation function, specifically, on the projected versions that we developed in a previous work. The pillar of the analysis is the one-to-one relationship between real and redshift-space voids above the shot-noise level identified with a spherical void finder. Under this mapping, void properties are affected by three effects: (i) a systematic expansion as a consequence of the distortions induced by galaxy dynamics, (ii) the Alcock–Paczynski volume effect, which manifests as an overall expansion or contraction depending on the fiducial cosmology, and (iii) a systematic off-centring along the line of sight as a consequence of the distortions induced by void dynamics. We found that correlations are also affected by an additional source of distortions: the ellipticity of voids. This is the first time that distortions due to the off-centring and ellipticity effects are detected and quantified. With a simplified test, we verified that the Gaussian streaming model is still robust provided all these effects are taken into account, laying the foundations for improvements in current models in order to obtain unbiased cosmological constraints from spectroscopic surveys. Besides this practical importance, this analysis also encodes key information about the structure and dynamics of the Universe at the largest scales. Furthermore, some of the effects constitute cosmological probes by themselves, as is the case of the void ellipticity.
Abstract
The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly ...binds DNA, although the underlying molecular basis and functional significance are unknown. Here, data from Atomic Force Microscopy (AFM) and X-ray structures of PolG2–DNA complexes define dimeric and hexameric PolG2 DNA binding modes. Targeted disruption of PolG2 DNA-binding interfaces impairs processive DNA synthesis without diminishing Pol γ subunit affinities. In addition, a structure-specific DNA-binding role for PolG2 oligomers is supported by X-ray structures and AFM showing that oligomeric PolG2 localizes to DNA crossings and targets forked DNA structures resembling the mitochondrial D-loop. Overall, data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG2 disruption in mitochondrial disease.
Graphical Abstract
Graphical Abstract
ABSTRACT
Voids are promising cosmological probes. Nevertheless, every cosmological test based on voids must necessarily employ methods to identify them in redshift space. Therefore, redshift-space ...distortions (RSD) and the Alcock–Paczyński effect (AP) have an impact on the void identification process itself generating distortion patterns in observations. Using a spherical void finder, we developed a statistical and theoretical framework to describe physically the connection between the identification in real and redshift space. We found that redshift-space voids above the shot noise level have a unique real-space counterpart spanning the same region of space, they are systematically bigger and their centres are preferentially shifted along the line of sight. The expansion effect is a by-product of RSD induced by tracer dynamics at scales around the void radius, whereas the off-centring effect constitutes a different class of RSD induced at larger scales by the global dynamics of the whole region containing the void. The volume of voids is also altered by the fiducial cosmology assumed to measure distances, this is the AP change of volume. These three systematics have an impact on cosmological statistics. In this work, we focus on the void size function. We developed a theoretical framework to model these effects and tested it with a numerical simulation, recovering the statistical properties of the abundance of voids in real space. This description depends strongly on cosmology. Hence, we lay the foundations for improvements in current models of the abundance of voids in order to obtain unbiased cosmological constraints from redshift surveys.
Clathrin- and actin-mediated endocytosis is a fundamental process in eukaryotic cells. Previously, we discovered Tda2 as a new yeast dynein light chain (DLC) that works with Aim21 to regulate actin ...assembly during endocytosis. Here we show Tda2 functions as a dimerization engine bringing two Aim21 molecules together using a novel binding surface different than the canonical DLC ligand binding groove. Point mutations on either protein that diminish the Tda2-Aim21 interaction in vitro cause the same in vivo phenotype as
deletion showing reduced actin capping protein (CP) recruitment and increased filamentous actin at endocytic sites. Remarkably, chemically induced dimerization of Aim21 rescues the endocytic phenotype of
deletion. We also uncovered a CP interacting motif in Aim21, expanding its function to a fundamental cellular pathway and showing such motif exists outside mammalian cells. Furthermore, specific disruption of this motif causes the same deficit of actin CP recruitment and increased filamentous actin at endocytic sites as
deletion. Thus, the data indicate the Tda2-Aim21 complex functions in actin assembly primarily through CP regulation. Collectively, our results provide a mechanistic view of the Tda2-Aim21 complex and its function in actin network regulation at endocytic sites.
ABSTRACT
The environment within dark matter haloes can quench the star formation of galaxies. However, environmental effects beyond the virial radius of haloes (≳1 Mpc) are less evident. An example ...is the debated correlation between colour or star formation in central galaxies and neighbour galaxies in adjacent haloes at large separations of several Mpc, referred to as two-halo galactic conformity. We use two galaxy catalogues generated from different versions of the semi-analytic model sag applied to the mdpl2 cosmological simulation and the IllustrisTNG300 cosmological hydrodynamical simulation to study the two-halo conformity by measuring the quenched fraction of neighbouring galaxies as a function of the real-space distance from central galaxies. We find that low-mass central galaxies in the vicinity of massive systems (M200c ≥ 1013$h^{-1}~\rm M_{\odot }$) out to 5 $h^{-1}~\rm Mpc$ are preferentially quenched compared to other central galaxies at fixed stellar mass M⋆ or fixed host halo mass M200c at z ∼ 0. In all the galaxy catalogues is consistent that the low-mass (M⋆ < 1010$h^{-1}~\rm M_{\odot }$ or M200c < 1011.8$h^{-1}~\rm M_{\odot }$) central galaxies in the vicinity of clusters and, especially, groups of galaxies mostly produce the two-halo galactic conformity. On average, the quenched low-mass central galaxies are much closer to massive haloes than star-forming central galaxies of the same mass (by a factor of ∼ 5). Our results agree with other works regarding the environmental influence of massive haloes that can extend beyond the virial radius and affect nearby low-mass central galaxies.
The angular momentum of galactic discs in semi-analytic models of galaxy formation is usually updated in time as material is accreted to the disc by adopting a constant dimensionless spin parameter ...and little attention is paid to the effects of accretion with misaligned angular momenta. These effects are the subject of this paper, where we adopt a Monte Carlo simulation for the changes in the direction of the angular momentum of a galaxy disc as it accretes matter based on accurate measurements from dark-matter haloes in the Millennium II simulation. In our semi-analytic model implementation, the flips seen in the dark-matter haloes are assumed to be the same for the cold baryons; however, we also assume that in the latter the flip also entails a difficulty for the disc to increase its angular momentum which causes the disc to become smaller relative to a no-flip case. This makes star formation to occur faster, especially in low-mass galaxies at all redshifts allowing galaxies to reach higher stellar masses faster. We adopt a new condition for the triggering of starbursts during mergers. As these produce the largest flips it is natural to adopt the disc instability criterion to evaluate the triggering of bursts in mergers instead of one based on mass ratios as in the original model. The new implementation reduces the average lifetimes of discs by a factor of ∼2, while still allowing old ages for the present-day discs of large spiral galaxies. It also provides a faster decline of star formation in massive galaxies and a better fit to the bright end of the luminosity function at z = 0.
Context.
The extragalactic vision we have through the Milky Way is very unclear. There is significant extinction of the optical emission from objects located in the region called the zone of ...avoidance (ZOA). NIR wavelengths are less affected by extinction, and therefore the infrared surveys in this zone are a potential source of astronomical discoveries. Nevertheless, these observations need to be compared with cosmological simulations in order to carry out high−accuracy studies.
Aims.
Our aim is to identify extragalactic sources in the ZOA, using infrared images of the VVV survey. We consider mock galaxy catalogues in order to interpret observational results.
Methods.
We studied a region of 1.636 square degrees corresponding to the VVV tile
b
204. Using SExtractor, we analysed photometric data generating a catalogue of extended sources in this area. In order to confirm these sources as galaxy candidates we visually inspected RGB images looking for typical galaxy features. Using 2MASX and GCMW catalogued sources we tested completeness and contamination of our catalogue and define suitable colour cuts to select galaxies. We also compared the observational results with those obtained from two semi-analytical models on Dark Matter simulations. One galaxy catalogue was constructed with the SAG semi-analytic model of galaxy formation, and the other one was constructed with the L-Galaxies semi-analytic model.
Results.
By adopting CLASS_STAR < 0.5,
r
1/2
> 0.7 arcsec and specific colour cuts (
J
−
K
s
> 0.97,
J
−
H
> 0 and
H
−
K
s
> 0) we generated an automatic catalogue of extended sources. After visual inspection we identified 624 sources with 10 <
K
s
< 17 as galaxy candidates. The contamination of the automatic catalogue is 28% when considering visually confirmed galaxies as reliable objects. The estimated completeness is 87% up to magnitude
K
s
= 13.5. We analysed the spatial distribution of galaxy candidates, finding a high concentration of galaxies in a small region of 15 arcmin radius. This region has three times higher density than similar areas in the tile. We compared the number of galaxies in this small area with the mean density values obtained from a suitable sample of galaxies from semi-analytic models finding that our results are consistent with an overdensity region.
Conclusions.
Using VVV near-infrared data and mock catalogues we detect new extragalactic sources that have not been identified by other catalogues. We demonstrate the potentiality of the VVV survey in finding and studying a large number of galaxy candidates and extragalactic structures obscured by the Milky Way.
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