BRCC36A is epistatic to BRCA1 in DNA crosslink repair and homologous recombination in Arabidopsis thaliana

BRCA1 is a well-known tumor suppressor protein in mammals, involved in multiple cellular processes such as DNA repair, chromosome segregation and chromatin remodeling. Interestingly, homologs of BRCA1 and several of its complex partners are also found in plants. As the respective mutants are viable, in contrast to mammalian mutants, detailed analyses of their biological role is possible. Here we demonstrate that the model plant Arabidopsis thaliana harbors two homologs of the mammalian BRCA1 interaction partner BRCC36, AtBRCC36A and AtBRCC36B. Mutants of both genes as well as the double mutants are fully fertile and show no defects in development. We were able to show that mutation of one of the homologs, AtBRCC36A, leads to a severe defect in intra- and interchromosomal homologous recombination (HR). A HR defect is also apparent in Atbrca1 mutants. As the Atbrcc36a/Atbrca1 double mutant behaves like the single mutants of AtBRCA1 and AtBRCC36A both proteins seem to be involved in a common pathway in the regulation of HR. AtBRCC36 is also epistatic to AtBRCA1 in DNA crosslink repair. Upon genotoxic stress, AtBRCC36A is transferred into the nucleus

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome- wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material. Methods: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species. Results: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice. Conclusions: Plant-RRBS offers high-throughput and broad, genome- dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations

ROSAT Blank Field Sources I: Sample Selection and Archival Data

We have identified a population of blank field sources (or `blanks') among the ROSAT bright unidentified X-ray sources with faint optical counterparts. The extreme X-ray over optical flux ratio of blanks is not compatible with the main classes of X-ray emitters except for extreme BL Lacertae objects. From the analysis of ROSAT archival data we found no indication of variability and evidence for only three sources, out of 16, needing absorption in excess of the Galactic value. We also found evidence for an extended nature for only one of the 5 blanks with a serendipitous HRI detection; this source (1WGAJ1226.9+3332) was confirmed as a z=0.89 cluster of galaxies. Palomar images reveal the presence of a red (O-E~2) counterpart in the X-ray error circle for 6 blanks. The identification process brought to the discovery of another high z cluster of galaxies, one (possibly extreme) BL Lac, two ultraluminous X-ray sources in nearby galaxies and two apparently normal type1 AGNs. These AGNs, together with 4 more AGN-like objects seem to form a well defined group: they present unabsorbed X-ray spectra but red Palomar counterparts. We discuss the possible explanations for the discrepancy between the X-ray and optical data, among which: a suppressed big blue bump emission, an extreme dust to gas (~40-60 the Galactic ratio), a high redshift (z>3.5) QSO nature, an atypical dust grain size distribution and a dusty warm absorber. These AGN-like blanks seem to be the bright (and easier to study) analogs of the sources which are found in deep Chandra observations. Three more blanks have a still unknown nature.Comment: 23 pages, 8 figures, accepted by ApJ main journa

Hyaluronan and Hyaluronidase, which is better for embryo development?

Our aim was to examine size-specific effects of Hyaluronan (HA) on preimplantation embryo development. We investigated the effects of Hyalovet (HA, 500–750 kDa; the size produced by HA synthase-3, which is abundant in the oviduct), or HA treated with Hyaluronidase-2 (Hyal2; also expressed in the oviduct that breaks down HA into 20 kDa fragments). In experiment 1 (in vivo), oviducts of synchronized and superovulated ewes (n = 20) were surgically exposed on Day 2 post-mating, ligated, and infused with either Hyalovet, Hyalovet + Hyal2, Hyal2, or PBS (control). Ewes were killed 5 days later for recovery of embryos and oviductal epithelial cells (OEC). Blastocyst rates were significantly higher in Hyal2 and Hyalovet + Hyal2 oviducts. Hyaluronidase-2 infusion resulted in higher blastocyst cell numbers and hatching rates. This was associated with increased HSP70 expression in OEC. In contrast, Hyalovet resulted in the lowest development to blastocyst stage and lowest hatching rates, and decreased IGF2 and IGFBP2 expression in OEC. IGF1 and IL1α expression were not affected. In experiment 2, to rule out indirect effects of oviductal factors, ovine embryos were produced and cultured with the same treatments in vitro from Day 2 to 8. Hyaluronidase-2, but not Hyalovet, enhanced blastocyst formation and reduced inner cell mass apoptosis. Hyalovet inhibited hatching. In conclusion, the presence of large-size HA (500–750 kDa) in the vicinity of developing embryos appears to disturb the oviductal environment and embryo development in vivo and in vitro. In contrast, we show evidence that breakdown of HA into smaller fragments is required to maximize embryo development and blastocyst quality

An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability

Proteins of the Fanconi Anemia (FA) complementation group are required for crosslink (CL) repair in humans and their loss leads to severe pathological phenotypes. Here we characterize a homolog of the Fe-S cluster helicase FANCJ in the model plant Arabidopsis, AtFANCJB, and show that it is involved in interstrand CL repair. It acts at a presumably early step in concert with the nuclease FAN1 but independently of the nuclease AtMUS81, and is epistatic to both error-prone and error-free post-replicative repair in Arabidopsis. The simultaneous knock out of FANCJB and the Fe-S cluster helicase RTEL1 leads to induced cell death in root meristems, indicating an important role of the enzymes in replicative DNA repair. Surprisingly, we found that AtFANCJB is involved in safeguarding rDNA stability in plants. In the absence of AtRTEL1 and AtFANCJB, we detected a synergetic reduction to about one third of the original number of 45S rDNA copies. It is tempting to speculate that the detected rDNA instability might be due to deficiencies in G-quadruplex structure resolution and might thus contribute to pathological phenotypes of certain human genetic diseases

The decay energy of the pure s-process nuclide ¹²³ Te

A direct and high-precision measurement of the mass difference of ¹²³Te and ¹²³Sb has been performed with the Penning-trap mass spectrometer SHIPTRAP using the recently introduced phase-imaging ioncyclotron-resonance technique. The obtained mass difference is 51.912(67) keV/c². Using the masses of the neutral ground states and the energy difference between the ionic states an effective half-life of ¹²³Te has been estimated for various astrophysical conditions. A dramatic influence of the electron capture process on the decay properties of ¹²³Te in hot stellar conditions has been discussed

The TRAPSENSOR facility: an open-ring 7 tesla Penning trap for laserbased precision experiments

APenning-trap facility for high-precision mass spectrometry based on a novel detection method has been built. This method consists in measuring motional frequencies of singly-charged ions trapped in strong magnetic fields through the fluorescence photons from laser-cooled 40Ca+ ions, to overcome limitations faced in electronic single-ion detection techniques. The key element of this facility is an open-ring Penning trap coupled upstream to a preparation Penning trap similar to those used at Radioactive Ion Beam facilities. Here we present a full characterization of the trap and demonstrate motional frequency measurements of trapped ions stored by applying external radiofrequency fields in resonance with the ions’ eigenmotions, in combination with time-of-flight identification. The infrastructure developed to observe the fluorescence photons from 40Ca+, comprising the 12 laser beams and the optical system to register the image in a high-sensitive CCD sensor, has been proved by taking images of the trapped and cooled 40Ca+ ions. This demonstrates the functionality of the proposed laser-based mass-spectrometry technique, providing a unique platform for precision experiments with implications in different fields of physics.This work was supported by the European Research Council (contract no. 278648-TRAPSENSOR), from the SpanishMINECO/ FEDER (project nos. FPA2012-32076, FPA2015-67694-P, FIS2015-69983-P, UNGR10-1E- 501, UNGR13-1E-1830), Ramón y Cajal Grant RYC-2012-11391, Juan de la Cierva grant IJCI-2015-26091, Centro Nacional de Partículas, Astropartículas y Nuclear CPAN13-TM01, and ‘Sistema Nacional de Garantía Juvenil y del Programa Operativo de Empleo Juvenil’; from the SpanishMECD(PhD grant nos. FPU15-04679 and FPU17/02596); from Junta de Andalucía/FEDER (project no. IE-57131) and ‘Programa de Empleo Juvenil; from Basque Government (PhD grant no. PRE-2015-1-0394) and (project no. IT986-16), and from the University of Granada ‘Plan propio-Programa de Intensificación de la Investigación PP2017-PRI.I-04’. I.A, L.L. and E.S acknowledge also support from projects OpenSuperQ (820363) and QMiCS (820505) of the EUFlagship on Quantum Technologies

Secular Evolution and the Formation of Pseudobulges in Disk Galaxies

We review internal processes of secular evolution in galaxy disks, concentrating on the buildup of dense central features that look like classical, merger-built bulges but that were made slowly out of disk gas. We call these pseudobulges. As an existence proof, we review how bars rearrange disk gas into outer rings, inner rings, and gas dumped into the center. In simulations, this gas reaches high densities that plausibly feed star formation. In the observations, many SB and oval galaxies show central concentrations of gas and star formation. Star formation rates imply plausible pseudobulge growth times of a few billion years. If secular processes built dense central components that masquerade as bulges, can we distinguish them from merger-built bulges? Observations show that pseudobulges retain a memory of their disky origin. They have one or more characteristics of disks: (1) flatter shapes than those of classical bulges, (2) large ratios of ordered to random velocities indicative of disk dynamics, (3) small velocity dispersions, (4) spiral structure or nuclear bars in the bulge part of the light profile, (5) nearly exponential brightness profiles, and (6) starbursts. These structures occur preferentially in barred and oval galaxies in which secular evolution should be rapid. So the cleanest examples of pseudobulges are recognizable. Thus a large variety of observational and theoretical results contribute to a new picture of galaxy evolution that complements hierarchical clustering and merging.Comment: 92 pages, 21 figures in 30 Postscript files; to appear in Annual Review of Astronomy and Astrophysics, Vol. 42, 2004, in press; for a version with full resolution figures, see http://chandra.as.utexas.edu/~kormendy/ar3ss.htm

Post-stroke inhibition of induced NADPH oxidase type 4 prevents oxidative stress and neurodegeneration

Ischemic stroke is the second leading cause of death worldwide. Only one moderately effective therapy exists, albeit with contraindications that exclude 90% of the patients. This medical need contrasts with a high failure rate of more than 1,000 pre-clinical drug candidates for stroke therapies. Thus, there is a need for translatable mechanisms of neuroprotection and more rigid thresholds of relevance in pre-clinical stroke models. One such candidate mechanism is oxidative stress. However, antioxidant approaches have failed in clinical trials, and the significant sources of oxidative stress in stroke are unknown. We here identify NADPH oxidase type 4 (NOX4) as a major source of oxidative stress and an effective therapeutic target in acute stroke. Upon ischemia, NOX4 was induced in human and mouse brain. Mice deficient in NOX4 (Nox4(-/-)) of either sex, but not those deficient for NOX1 or NOX2, were largely protected from oxidative stress, blood-brain-barrier leakage, and neuronal apoptosis, after both transient and permanent cerebral ischemia. This effect was independent of age, as elderly mice were equally protected. Restoration of oxidative stress reversed the stroke-protective phenotype in Nox4(-/-) mice. Application of the only validated low-molecular-weight pharmacological NADPH oxidase inhibitor, VAS2870, several hours after ischemia was as protective as deleting NOX4. The extent of neuroprotection was exceptional, resulting in significantly improved long-term neurological functions and reduced mortality. NOX4 therefore represents a major source of oxidative stress and novel class of drug target for stroke therapy