Robust genetic analysis of the X-linked anophthalmic (Ie) mouse

Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here, we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray-induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ~6 Mb region on the X chromosome. Short- and long-read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000–58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism

Effect of replacing soybean meal (Glycine max) with sesame meal (Sesamum indicum) on productive traits, carcass characteristics, and gross profit margin in fattening lamb's diets.

The objective of this study was to determine the effect of replacing soybean meal (Glycine max) with sesame meal (Sesamum indicum) on productive traits, carcass characteristics, and gross profit margin (GMP) in fattening lamb's diets. For this, 42 Katahdin lambs were divided into three treatments in duplicate: basal diet + soybean meal (100S), basal diet + sesame meal/soybean meal (50/50SA), and basal diet + sesame meal (100A). Dry matter intake, daily weight gain (DWG), total kg gained (KgT), feed conversion (FC), and feed efficiency (FE) were evaluated; upon reaching the weight for sale, the animals were slaughtered, and hot carcass weight (HCW) was evaluated. The results were analyzed with a completely randomized design with repeated measures. Regarding time, no differences were found between treatments, for DWG (0.171 ± 0.006 kg/d), FC (6.7 ± 0.55), FE (0.175 ± 0.02), KgT (2.86 ± 0.13 kg), HCW (50.97 ± 0.79 kg), as well as for chest depth (26.96 ± 0.33 cm), leg width (20.63 ± 0.028 cm), leg diameter (60.7 ± 0.44 cm), and ribs width (24.05 ± 0.14 cm). GPM was 16.50%, 18.63%, and 19.97% for 100S, 50/50SA, and 100A, respectively. Overall, in fatting lamb diets, replacing soybean meal with sesame meal by either 50% or 100% substitution could be a feasible feeding strategy as in both cases, gross profit was increased, and no negative effects were found for productive traits and carcass quality

Association between the plasma/whole blood lead ratio and history of spontaneous abortion: a nested cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Blood lead has been associated with an elevated risk of miscarriage. The plasmatic fraction of lead represents the toxicologically active fraction of lead. Women with a tendency to have a higher plasma/whole blood Pb ratio could tend towards an elevated risk of miscarriage due to a higher plasma Pb for a given whole blood Pb and would consequently have a history of spontaneous abortion.</p> <p>Methods</p> <p>We studied 207 pregnant Mexico City residents during the 1^sttrimester of pregnancy, originally recruited for two cohorts between 1997 and 2004. Criteria for inclusion in this study were having had at least one previous pregnancy, and having valid plasma and blood Pb measurements. Pb was measured in whole blood and plasma by inductively coupled plasma mass spectrometry using ultra-clean techniques. History of miscarriage in previous pregnancies was obtained by interview. The incidence rate of spontaneous abortion was defined as the proportion of previous pregnancies that resulted in miscarriage. Data were analyzed by means of Poisson regression models featuring the incidence rate of spontaneous abortion as the outcome and continuous or categorized plasma/blood Pb ratios as predictor variables. All models were adjusted for age and schooling. Additionally, logistic regression models featuring inclusion in the study sample as the outcome were fitted to assess potential selection bias.</p> <p>Results</p> <p>The mean number of miscarriages was 0.42 (range 0 to 4); mean Pb concentrations were 62.4 and 0.14 μg/L in whole blood and plasma respectively. Mean plasma/blood Pb ratio was 0.22%. We estimated that a 0.1% increment in the plasma/blood Pb ratio lead was associated to a 12% greater incidence of spontaneous abortion (p = 0.02). Women in the upper tertile of the plasma/blood Pb ratio had twice the incidence rate of those in the lower tertile (p = 0.02). Conditional on recruitment cohort, inclusion in the study sample was unrelated to observable characteristics such as number of abortions, number of pregnancies, blood Pb levels, age schooling, weight and height.</p> <p>Conclusion</p> <p>Women with a large plasma/whole blood Pb ratio may be at higher risk of miscarriage, which could be due to a greater availability of placental barrier-crossing Pb.</p

Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon

Rare AGA or AGG codons close to the initiation codon inhibit protein synthesis by a tRNA-sequestering mechanism as toxic minigenes do. To further understand this mechanism, a parallel analysis of protein synthesis and peptidyl-tRNA accumulation was performed using both a set of lacZ constructs where AGAAGA codons were moved codon by codon from +2, +3 up to +7, +8 positions and a series of 3–8 codon minigenes containing AGAAGA codons before the stop codon. β-Galactosidase synthesis from the AGAAGA lacZ constructs (in a Pth defective in vitro system without exogenous tRNA) diminished as the AGAAGA codons were closer to AUG codon. Likewise, β-galactosidase expression from the reporter +7 AGA lacZ gene (plus tRNA, 0.25 μg/μl) waned as the AGAAGAUAA minigene shortened. Pth counteracted both the length-dependent minigene effect on the expression of β-galactosidase from the +7 AGA lacZ reporter gene and the positional effect from the AGAAGA lacZ constructs. The +2, +3 AGAAGA lacZ construct and the shortest +2, +3 AGAAGAUAA minigene accumulated the highest percentage of peptidyl-tRNAArg4. These observations lead us to propose that hungry codons at early positions, albeit with less strength, inhibit protein synthesis by a minigene-like mechanism involving accumulation of peptidyl-tRNA

An Overview of the 2014 ALMA Long Baseline Campaign

A major goal of the Atacama Large Millimeter/submillimeter Array (ALMA) is to make accurate images with resolutions of tens of milliarcseconds, which at submillimeter (submm) wavelengths requires baselines up to ~15 km. To develop and test this capability, a Long Baseline Campaign (LBC) was carried out from September to late November 2014, culminating in end-to-end observations, calibrations, and imaging of selected Science Verification (SV) targets. This paper presents an overview of the campaign and its main results, including an investigation of the short-term coherence properties and systematic phase errors over the long baselines at the ALMA site, a summary of the SV targets and observations, and recommendations for science observing strategies at long baselines. Deep ALMA images of the quasar 3C138 at 97 and 241 GHz are also compared to VLA 43 GHz results, demonstrating an agreement at a level of a few percent. As a result of the extensive program of LBC testing, the highly successful SV imaging at long baselines achieved angular resolutions as fine as 19 mas at ~350 GHz. Observing with ALMA on baselines of up to 15 km is now possible, and opens up new parameter space for submm astronomy.Comment: 11 pages, 7 figures, 2 tables; accepted for publication in the Astrophysical Journal Letters; this version with small changes to affiliation

RPC radiation background simulations for the high luminosity phase in the CMS experiment

The high luminosity expected from the HL-LHC will be a challenge for the CMS detector. The increased rate of particles coming from the collisions and the radioactivity induced in the detector material could cause significant damage and result in a progressive degradation of its performance. Simulation studies are very useful in these scenarios as they allow one to study the radiation environment and the impact on detector performance. Results are presented for CMS RPC stations considering the operating conditions expected at the HL-LHC

DNA Methylation-Independent Reversion of Gemcitabine Resistance by Hydralazine in Cervical Cancer Cells

BACKGROUND: Down regulation of genes coding for nucleoside transporters and drug metabolism responsible for uptake and metabolic activation of the nucleoside gemcitabine is related with acquired tumor resistance against this agent. Hydralazine has been shown to reverse doxorubicin resistance in a model of breast cancer. Here we wanted to investigate whether epigenetic mechanisms are responsible for acquiring resistance to gemcitabine and if hydralazine could restore gemcitabine sensitivity in cervical cancer cells. METHODOLOGY/PRINCIPAL FINDINGS: The cervical cancer cell line CaLo cell line was cultured in the presence of increasing concentrations of gemcitabine. Down-regulation of hENT1 & dCK genes was observed in the resistant cells (CaLoGR) which was not associated with promoter methylation. Treatment with hydralazine reversed gemcitabine resistance and led to hENT1 and dCK gene reactivation in a DNA promoter methylation-independent manner. No changes in HDAC total activity nor in H3 and H4 acetylation at these promoters were observed. ChIP analysis showed H3K9m2 at hENT1 and dCK gene promoters which correlated with hyper-expression of G9A histone methyltransferase at RNA and protein level in the resistant cells. Hydralazine inhibited G9A methyltransferase activity in vitro and depletion of the G9A gene by iRNA restored gemcitabine sensitivity. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that acquired gemcitabine resistance is associated with DNA promoter methylation-independent hENT1 and dCK gene down-regulation and hyper-expression of G9A methyltransferase. Hydralazine reverts gemcitabine resistance in cervical cancer cells via inhibition of G9A histone methyltransferase

High voltage calibration method for the CMS RPC detector

The Resistive Plate Chambers (RPC) are used for muon triggers in the CMS experiment. To calibrate the high voltage working-points (WP) and identify degraded detectors due to radiation or chemical damage, a high voltage scan has been performed using 2017 data from pp collisions at a center-of-mass energy of 13 TeV. In this paper, we present the calibration method and the latest results obtained for the 2017 data. A comparison with all scans taken since 2011 is considered to investigate the stability of the detector performance in time

CMSRPC efficiency measurement using the tag-and-probe method

We measure the efficiency of CMS Resistive Plate Chamber (RPC) detectors in proton-proton collisions at the centre-of-mass energy of 13 TeV using the tag-and-probe method. A muon from a Z(0) boson decay is selected as a probe of efficiency measurement, reconstructed using the CMS inner tracker and the rest of CMS muon systems. The overall efficiency of CMS RPC chambers during the 2016-2017 collision runs is measured to be more than 96% for the nominal RPC chambers

RPC upgrade project for CMS Phase II

The Muon Upgrade Phase II of the Compact Muon Solenoid (CMS) aims to guarantee the optimal conditions of the present system and extend the eta coverage to ensure a reliable system for the High Luminosity Large Hadron Collider (HL-LHC) period. The Resistive Plate Chambers (RPCs) system will upgrade the off-detector electronics (called link system) of the chambers currently installed chambers and place improved RPCs (iRPCs) to cover the high pseudo-rapidity region, a challenging region for muon reconstruction in terms of background and momentum resolution. In order to find the best option for the iRPCs, an R&D program for new detectors was performed and real size prototypes have been tested in the Gamma Irradiation Facility (GIF++) at CERN. The results indicated that the technology suitable for the high background conditions is based on High Pressure Laminate (HPL) double-gap RPC. The RPC Upgrade Phase II program is planned to be ready after the Long Shutdown 3 (LS3)