A Simple Empirical Calibration of Energy Dispersive X-Ray Analysis (EDXA) on the Cornea

Monitoring of the corneal electrolyte content is important for the study of chemical eye burns. This paper describes quantitative measurements on gelatin standards, corneas and a cornea homogenate with an energy dispersive X-ray analyzer (EDX) in the scanning electron microscope (SEM). Ten micrometers thick cryosections were freeze-dried and mounted on solid carbon supports. The applied quantification procedure was a local peak background analysis with a specifically designed computer program. Similar chemical and physical properties of gelatin, cornea homogenate, and cornea were proven by EDX-analysis and wet chemical analysis. Gelatin standards with known concentrations of different added salts showed linear correlations with a correlation coefficient higher than 0.95 for all considered elements. The local background generation on carbon supports was the same for gelatin standards and corneal tissue. The results demonstrate that quantitative EDX analysis of semi-thin samples, mounted on neutral carbon supports, can be reliably used for the assessment of the corneal mineral composition

Epigenetic modification of histone 3 at lysine 9 in sheep zygotes and its relationship with DNA methylation

<p>Abstract</p> <p>Background</p> <p>Previous studies indicated that, unlike mouse zygotes, sheep zygotes lacked the paternal DNA demethylation event. Another epigenetic mark, histone modification, especially at lysine 9 of histone 3 (H3K9), has been suggested to be mechanically linked to DNA methylation. In mouse zygotes, the absence of methylated H3K9 from the paternal pronucleus has been thought to attribute to the paternal DNA demethylation.</p> <p>Results</p> <p>By using the immunofluorescence staining approach, we show that, despite the difference in DNA methylation, modification of H3K9 is similar between the sheep and mouse zygotes. In both species, H3K9 is hyperacetylated or hypomethylated in paternal pronucleus relative to maternal pronucleus. In fact, sheep zygotes can also undergo paternal DNA demethylation, although to a less extent than the mouse. Further examinations of individual zygotes by double immunostaining revealed that, the paternal levels of DNA methylation were not closely associated with that of H3K9 acetylation or tri-methylation. Treatment of either 5-azacytidine or Trichostatin A did not induce a significant decrease of paternal DNA methylation levels.</p> <p>Conclusion</p> <p>Our results suggest that in sheep lower DNA demethylation of paternal genomes is not due to the H3K9 modification and the methylated DNA sustaining in paternal pronucleus does not come from DNA <it>de novo </it>methylation.</p

Bayesian Fit of Exclusive b→sℓˉℓb \to s \bar\ell\ell Decays: The Standard Model Operator Basis

We perform a model-independent fit of the short-distance couplings $C_{7,9,10}$ within the Standard Model set of $b\to s\gamma$ and $b\to s\bar\ell\ell$ operators. Our analysis of $B \to K^* \gamma$, $B \to K^{(*)} \bar\ell\ell$ and $B_s \to \bar\mu\mu$ decays is the first to harness the full power of the Bayesian approach: all major sources of theory uncertainty explicitly enter as nuisance parameters. Exploiting the latest measurements, the fit reveals a flipped-sign solution in addition to a Standard-Model-like solution for the couplings $C_i$. Each solution contains about half of the posterior probability, and both have nearly equal goodness of fit. The Standard Model prediction is close to the best-fit point. No New Physics contributions are necessary to describe the current data. Benefitting from the improved posterior knowledge of the nuisance parameters, we predict ranges for currently unmeasured, optimized observables in the angular distributions of $B\to K^*(\to K\pi)\,\bar\ell\ell$.Comment: 42 pages, 8 figures; v2: Using new lattice input for f_Bs, considering Bs-mixing effects in BR[B_s->ll]. Main results and conclusion unchanged, matches journal versio

Implications from clean observables for the binned analysis of B -> K*ll at large recoil

We perform a frequentist analysis of q^2-dependent B-> K*(->Kpi)ll angular observables at large recoil, aiming at bridging the gap between current theoretical analyses and the actual experimental measurements. We focus on the most appropriate set of observables to measure and on the role of the q^2-binning. We highlight the importance of the observables P_i exhibiting a limited sensitivity to soft form factors for the search for New Physics contributions. We compute predictions for these binned observables in the Standard Model, and we compare them with their experimental determination extracted from recent LHCb data. Analyzing b->s and b->sll transitions within four different New Physics scenarios, we identify several New Physics benchmark points which can be discriminated through the measurement of P_i observables with a fine q^2-binning. We emphasise the importance (and risks) of using observables with (un)suppressed dependence on soft form factors for the search of New Physics, which we illustrate by the different size of hadronic uncertainties attached to two related observables (P_1 and S_3). We illustrate how the q^2-dependent angular observables measured in several bins can help to unravel New Physics contributions to B-> K*(->Kpi)ll, and show the extraordinary constraining power that the clean observables will have in the near future. We provide semi-numerical expressions for these observables as functions of the relevant Wilson coefficients at the low scale.Comment: 50 pages, 21 figures. Improved form factor analysis, conclusions unchanged. Plots with full resolution. Version published in JHE

EOS: a software for flavor physics phenomenology

EOS is an open-source software for a variety of computational tasks in flavor physics. Its use cases include theory predictions within and beyond the Standard Model of particle physics, Bayesian inference of theory parameters from experimental and theoretical likelihoods, and simulation of pseudo events for a number of signal processes. EOS ensures high-performance computations through a C++ back-end and ease of usability through a Python front-end. To achieve this flexibility, EOS enables the user to select from a variety of implementations of the relevant decay processes and hadronic matrix elements at run time. In this article, we describe the general structure of the software framework and provide basic examples. Further details and in-depth interactive examples are provided as part of the EOS online documentation

Embryo cell allocation patterns are not altered by biopsy but can be linked with further development

It has been suggested that first embryo cleavage can be related with the embryonic-abembryonic axis at blastocyst stage in mice. Thus, cells of the 2 cell embryo might be already biased to form the inner cell mass or trophectoderm. This study was conducted to observe the possible effects of embryo biopsy on cell allocation patterns during embryo pre-implantation in two different mouse strains and the effects of these patterns on further development. First, one blastomere of the 2-cell embryo was injected with a lipophilic tracer and cell allocation patterns were observed at blastocyst stage. Blastocysts were classified into orthogonal, deviant or random pattern. For the first experiment, embryos were biopsied at 8-cell stage and total cell counts (TCC) were annotated. Furthermore, non biopsied blastocysts were transferred into foster mothers. Then, pups and their organs were weighed two weeks after birth. Random pattern was significantly recurrent (≈60%), against orthogonal (<22%) and deviant (<22%) patterns among groups. These patterns were not affected by biopsy procedure. However, TCC on deviant embryos were reduced after biopsy. Moreover, no differences were found between patterns for implantation rates, litter size, live offspring and organ weights (lungs, liver, pancreas and spleen). However, deviant pups presented heavier hearts and orthogonal pups presented lighter kidneys among the group. In conclusion, these results suggest that single blastomere removal does not disturb cell allocation patterns during pre-implantation. Nonetheless, the results suggest that embryos following different cell allocation patterns present different coping mechanisms against in-vitro manipulations and further development might be altered

Embryo cell allocation patterns are not altered by biopsy but can be linked with further development

It has been suggested that first embryo cleavage can be related with the embryonic-abembryonic axis at blastocyst stage in mice. Thus, cells of the 2 cell embryo might be already biased to form the inner cell mass or trophectoderm. This study was conducted to observe the possible effects of embryo biopsy on cell allocation patterns during embryo pre-implantation in two different mouse strains and the effects of these patterns on further development. First, one blastomere of the 2-cell embryo was injected with a lipophilic tracer and cell allocation patterns were observed at blastocyst stage. Blastocysts were classified into orthogonal, deviant or random pattern. For the first experiment, embryos were biopsied at 8-cell stage and total cell counts (TCC) were annotated. Furthermore, non biopsied blastocysts were transferred into foster mothers. Then, pups and their organs were weighed two weeks after birth. Random pattern was significantly recurrent (≈60%), against orthogonal (<22%) and deviant (<22%) patterns among groups. These patterns were not affected by biopsy procedure. However, TCC on deviant embryos were reduced after biopsy. Moreover, no differences were found between patterns for implantation rates, litter size, live offspring and organ weights (lungs, liver, pancreas and spleen). However, deviant pups presented heavier hearts and orthogonal pups presented lighter kidneys among the group. In conclusion, these results suggest that single blastomere removal does not disturb cell allocation patterns during pre-implantation. Nonetheless, the results suggest that embryos following different cell allocation patterns present different coping mechanisms against in-vitro manipulations and further development might be altered

5-Methylcytosine and 5-Hydroxymethylcytosine Spatiotemporal Profiles in the Mouse Zygote

Background: In the mouse zygote, DNA methylation patterns are heavily modified, and differ between the maternal and paternal pronucleus. Demethylation of the paternal genome has been described as an active and replication-independent process, although the mechanisms responsible for it remain elusive. Recently, 5-hydroxymethylcytosine has been suggested as an intermediate in this demethylation. Methodology/principal findings: In this study, we quantified DNA methylation and hydroxymethylation in both pronuclei of the mouse zygote during the replication period and we examined their patterns on the pericentric heterochromatin using 3D immuno-FISH. Our results demonstrate that 5-methylcytosine and 5-hydroxymethylcytosine localizations on the pericentric sequences are not complementary; indeed we observe no enrichment of either marks on some regions and an enrichment of both on others. In addition, we show that DNA demethylation continues during DNA replication, and is inhibited by aphidicolin. Finally, we observe notable differences in the kinetics of demethylation and hydroxymethylation; in particular, a peak of 5-hydroxymethylcytosine, unrelated to any change in 5-methylcytosine level, is observed after completion of replication. Conclusion/significance: Together our results support the already proposed hypothesis that 5-hydroxymethylcytosine is not a simple intermediate in an active demethylation process and could play a role of its own during early development

Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways

Understanding the mechanism of resistance of genes to reactivation will help improve the success of nuclear reprogramming. Using mouse embryonic fibroblast nuclei with normal or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2AK119ub1 from transplanted nuclei, we reveal the basis for resistance of genes to transcriptional reprogramming by oocyte factors. A majority of genes is affected by more than one type of treatment, suggesting that resistance can require repression through multiple epigenetic mechanisms. We classify resistant genes according to their sensitivity to 11 chromatin modifier combinations, revealing the existence of synergistic as well as adverse effects of chromatin modifiers on removal of resistance. We further demonstrate that the chromatin modifier USP21 reduces resistance through its H2AK119 deubiquitylation activity. Finally, we provide evidence that H2A ubiquitylation also contributes to resistance to transcriptional reprogramming in mouse nuclear transfer embryos.This work is funded by grants from the Wellcome Trust (101050/Z/13/Z) and the MRC (MR/K011022/1) and supported by the Gurdon Institute core grant from Cancer Research UK (C6946/A14492) and the Wellcome Trust (092096/Z/10/Z). This research was supported in part by the Intramural Research Program of NIAMS at the NIH (1Z01AR041126-17). M.V. was supported by a Svenska Sällskapet för Medicinsk Forskning (SSMF) postdoctoral fellowship. S.W. was supported in part by fellowships from the Gates Cambridge Trust and NIH-Cambridge MD/PhD Program (T32GM007367). M.O. was supported by a postdoctoral fellowship from the Japan Society for the Promotion of Science (JSPS). K.M. is supported by Human Frontier Science Program (RGP0021/2016), JSPS KAKENHI grants JP16H01321 and JP16H01222, and by a Grant for Basic Science Research Projects from The Sumitomo Foundation (150810). V.P. was supported by the Wellcome Trust (081277), the Wallonia-Brussels International Excellence Grant, The Research Foundation – Flanders (FWO) (Odysseus Return Grant G0F7716N), the KU Leuven Research Fund (BOFZAP starting grant StG/15/021BF, C1 grant C14/16/077, and project financing)

Determining the charge states of solar energetic ions during large geomagnetic storms

We give a progress report on a new method of measuring the mean ionic charge states of solar energetic particles (SEPs) and apply this method to oxygen ions at energies of ∼10 MeV/nucleon. We compare simultaneous flux measurements inside and outside the magnetosphere to determine the geomagnetic transmission and use this result to find the corresponding mean ionic charge state. The key to this method is to determine the dependence of the geomagnetic transmission function on the mean ionic charge state of the ions. We report here the results of a new technique to calculate the geomagnetic transmission function, which attempts to account for the cutoff suppression caused by the geomagnetic activity which often accompanies SEP events