Over 200 imprinted genes in rice endosperm are known, but the mechanisms modulating their parental allele‐specific expression are poorly understood. Here we use three imprinted genes, OsYUCCA11, ...yellow2‐like and ubiquitin hydrolase, to show that differential DNA methylation and tri‐methylation of histone H3 lysine 27 (H3K27me₃) in the promoter and/or gene body influences allele‐specific expression or the site of transcript initiation. Paternal expression of OsYUCCA11 required DNA methylation in the gene body whereas the gene body of the silenced maternal allele was hypomethylated and marked with H3K27me₃. These differential markings mirror those proposed to modulate paternal expression of two Arabidopsis genes, PHERES1 and a YUCCA homolog, indicating conservation of imprinting mechanisms. At yellow2‐like, DNA hypomethylation in the upstream flanking region resulted in maternal transcripts that were longer than paternal transcripts; the maternal transcript initiation site was marked by DNA methylation in the paternal allele, and transcription initiated ~700 bp downstream. The paternal allele of an ubiquitin hydrolase gene exhibited gene body DNA methylation and produced full‐length transcripts, while the maternal allele was hypomethylated in the 5′ gene body and transcripts initiated from a downstream promoter. Inhibition of DNA methylation by 5‐azacytidine or zebularine activated the long transcripts from yellow2‐like and enhanced expression of the short transcripts from the ubiquitin hydrolase in seedlings, indicating that DNA methylation prevents transcript initiation from cryptic promoters. These observations suggest a paradigm whereby maternal genome hypomethylation is associated with the production of distinct transcripts, potentially diversifying the gene products from the two alleles.
Data equivalence refers to the extent to which the elements of a research design have the same meaning, and can be applied in the same way, in different cultural contexts. Failure to establish data ...equivalence in cross-cultural studies may bias empirical results and theoretical inferences. Although several authors have encouraged researchers to ensure high levels of data equivalence, no study has assessed the status of the field in relation to compliance with data equivalence standards. Accordingly, this study examines three aspects of data equivalence (construct equivalence, measurement equivalence, and data collection equivalence) within 167 studies that involve cross-cultural data published in the Journal of International Business Studies, Management International Review, Journal of World Business, Strategic Management Journal and the Academy of Management Journal from 1995 to 2005. The findings indicate that international business researchers report insufficient information in relation to data equivalence issues, thus limiting confidence in the findings of many cross-cultural studies. To enhance future research, a guideline for procedures for researchers to follow and report in establishing data equivalence is offered.
Structured Summary Background Carbapenemase-producing Enterobacteriaceae (CPE) can cause healthcare–associated infections with high mortality rates. New Delhi metallo-beta-lactamase-1 (NDM-1) is ...amongst the most recently discovered carbapenemases. Aim To report the first outbreak of NDM-1 CPE in Ireland, including microbiological and epidemiological characteristics, and assessing the impact of infection prevention and control measures. Methods Retrospective microbiological and epidemiological review. Cases were defined as patients with a CPE positive culture. Contacts were designated as roommates or ward mates. Findings This outbreak involved ten patients, with a median age of 71 years (range 45-90 years), located in three separate but affiliated healthcare facilities. One patient was infected (the index case); the nine others were colonised. Nine NDM-1-producing Klebsiella pneumoniae, a NDM-1-producing Escherichia coli and a K. pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae were detected between week 24 2014 and week 37 2014. Pulsed field gel electrophoresis demonstrated similarity. NDM-1 positive isolates were meropenem resistant with MICs ranging from 12 to 32 μg/ml. All were tigecycline susceptible (MICs ≤1 μg/ml). One isolate was colistin resistant (MIC 4.0 μg/ml; mcr- 1 gene not detected). In 2015, four further NDM-1 isolates were detected. Conclusions The successful management of this outbreak was achieved via the prompt implementation of enhanced infection prevention and control practices to prevent transmission. These patients did not have a history of travel outside of Ireland, but a number had frequent hospitalisations in Ireland, raising concerns regarding the possibility of increasing but unrecognised prevalence of NDM-1 and potential decline in value of travel history a marker of colonisation risk.
Management changes such as drainage, fertilisation, afforestation and harvesting (clearfelling) of forested peatlands influence watertable (WT) position and groundwater concentrations of nutrients. ...This study investigated the impact of clearfelling of a peatland forest on WT and nutrient concentrations. Three areas were examined: (1) a regenerated riparian peatland buffer (RB) clearfelled four years prior to the present study (2) a recently clearfelled coniferous forest (CF) and (3) a standing, mature coniferous forest (SF), on which no harvesting took place. The WT remained consistently below 0.3 m during the pre-clearfelling period. Results showed there was an almost immediate rise in the WT after clearfelling and a rise to 0.15 m below ground level (bgl) within 10 months of clearfelling. Clearfelling of the forest increased dissolved reactive phosphorus concentrations (from an average of 28–230 μg L−1) in the shallow groundwater, likely caused by leaching from degrading brash mats.
•An upland peat forest was studied before and after harvesting (clearfelling).•Watertable fluctuations and groundwater nutrient concentrations were studied.•Clearfelling of a forest on blanket peat raised the watertable.
The structure of the nitrogenase MoFe-protein from Azotobacter vinelandii has been refined to 2.0 Å resolution in two oxidation states. EPR studies on the crystals indicate that the structures ...correspond to the spectroscopically assigned oxidized (POX/MOX) and the native or dithionite-reduced (PN/MN) forms of the enzyme. Both MoFe-protein structures are essentially identical, with the exception of the P-cluster. The MoFe-protein P-cluster in each state is found to contain eight Fe and seven S atoms. Interconversion between the two redox states involves movement of two Fe atoms and an exchange of protein coordination for ligands supplied by a central S atom. In the oxidized POX state, the cluster is coordinated by the protein through six cysteine ligands, Ser-β188 Oγ, and the backbone amide of Cys-α88. In the native PN state, Ser-β188 Oγ and the amide N of Cys-α88 no longer coordinate the cluster due to movement of their coordinated Fe atoms toward the central sulfur. Consequently, this central sulfur adopts a distorted octahedral environment with six surrounding Fe atoms. A previously described model of the P-cluster containing 8Fe-8S likely reflects the inappropriate modeling of a single structure to a mixture of these two P-cluster redox states. These observed redox-mediated structural changes of the P-cluster suggest a role for this cluster in coupling electron transfer and proton transfer in nitrogenase.
Vanadium is reported to undergo a pressure-induced bcc-rhombohedral phase transition at 30–70 GPa, with a transition pressure that is sensitive to the hydrostaticity of the sample environment. ...However, the experimental evidence for the structure of the high-pressure phase being rhombohedral is surprisingly weak. We have restudied vanadium under pressure to 154 GPa using both polycrystalline and single-crystal samples, and a variety of different pressure transmitting media (PTM). We find that only when using single-crystal samples does one observe a rhombohedral high-pressure phase; the high-pressure diffraction profiles from the polycrystalline samples do not fit a rhombohedral lattice, irrespective of the PTM used. The single-crystal samples reveal two rhombohedral phases, with a continuous transition between them, and distortions from cubic symmetry are much smaller than previously calculated.
The high pressure phases of Rb have previously been investigated to 101 GPa, above which Rb is predicted to adopt a double-hexagonal close-packed (dhcp, Pearson hP4) structure similar to that already ...observed in cesium at 72 GPa. Previous ab initio structure searches have indicated that the hP4 phase should become stable in rubidium at 143 GPa . We present data from static compression experiments on Rb up to 264 ( 8 ) GPa , showing the onset of the hP4 phase at 207(6)GPa . The V/V0 of ∼0.121 measured at 264 GPa constitutes the highest compression ratio (more than eightfold) at which structural information has been obtained from a metal using x-ray diffraction methods and is second only to x-ray measurements performed on hydrogen at V/V0 ∼0.094 at 190 GPa. At these extreme compression ratios, the compressive behavior of rubidium shifts from that of a free electron metal to that of a regular d -block metal.
•Two forest catchments were studied to assess efficacy of best management practices.•Concentrations of nitrogen and phosphorus were examined before and after harvesting.•Harvesting impacted ...phosphorus and nitrogen concentrations.•Forest operations should use best management practices where possible.•Concentrations of nutrients in stream were below threshold limits within 15 months.
Elevated levels of nutrients and suspended sediment (SS), and changes to other environmental parameters, are frequently associated with forestry harvesting (clearfelling) operations, and are indicative of the potentially complex changing environment associated with clearfelling. Current and future recommended best management practices (BMPs) for forestry clearfelling on upland peat catchments must provide for a healthy soil and good water quality. The aim of this study was to quantify the effects of implementation, or violation, of BMPs in the clearfelling of an upland peat conifer forest. Over periods of 12 months prior to clearfelling and 15 months after clearfelling, two peatland forests, comprising a study control (no clearfelling) and a study site (clearfelling), were monitored for the release of phosphorus (P) and nitrogen (N) species (dissolved reactive phosphorus (DRP), total phosphorus (TP), total oxidised nitrogen (TON) and ammonium nitrogen (NH4+-N)), SS, dissolved oxygen (DO), electrical conductivity (EC), pH and stream water temperature. Clearfelling was conducted during poor weather conditions and a watercourse, which drained the study site, was not protected. The maximum recorded concentration exported from the study site after clearfelling was 471μgL−1 for DRP, 611μgL−1 for TP, 1336μgL−1 for NH4+-N, and 194μgL−1 for TON. Concentrations of SS exiting the study site increased in one of the two samples taken during clearfelling (maximum release of 481mgL−1, with 68% of this organic) and returned to pre-clearfelling levels, or below, within 6 months of the commencement of clearfelling. Exports of TP and DRP from the study site were 0.9 and 0.4kgha−1yr−1, which were greater than the study control (0.6 and 0.2kgha−1yr−1, respectively). This indicated that the mitigation practices employed on site were not effective in phosphorus retention.
► A riparian buffer zone was studied for nutrients and vegetation. ► Degrading brash (tree branches/needles) fertilized the peat. ► Higher dissolved reactive phosphorus concentrations were found ...under brash mats. ► The adjacent water course was protected from elevated nutrients. ► The buffer zone was capable of providing nutrients for survival of planted saplings.
Forestry on peatland throughout the world is now focused on minimising destructive effects to the surrounding environment, especially during harvesting. These effects may be mitigated through the use of well-developed riparian buffers zones (RBZs). However, much of the commercial forestry planted in Ireland and the UK in the mid-20th century was planted without adequate RBZs. The creation of new RBZs prior to clearfelling may be a possible mitigation measure in these circumstances. The aim of this paper was to assess the nutrient content and phosphorus (P) adsorption capacity of the soil, and survival of planted saplings in a RBZ, positioned downslope from a standing forest and partly covered with brash mats, five years after its establishment. Dissolved reactive phosphorus (DRP) concentrations were significantly higher under the brash mats in the RBZ when compared to all other areas. The standing forest had the highest concentrations of ammonium nitrogen (NH4-N), while total oxidised nitrogen (TON) was similar for all areas. Water extractable phosphorus and desorption–adsorption testing also confirmed the high concentrations of P under the brash mats, but P did not leach through the peat to the stream. The overall survival rate of the saplings was relatively high, with over half of Quercus robur (oak) (57%), Sorbus aucuparia (rowan) (57%) and Betula pendula (birch) (51%) surviving. Salix cinerea (willow) (22%), Alnus glutinosa (alder) (25%) and Ilex aquifolium (holly) (44%) did not survive as successfully. The RBZ was capable of providing nutrients for the survival of planted saplings, fertilizing the peat with degrading brash material and preventing elevated levels of nutrients entering the adjacent aquatic ecosystem.
Rapid detection of patients with carbapenemase-producing Enterobacteriaceae (CPE) is essential for the prevention of nosocomial cross-transmission, allocation of isolation facilities and to protect ...patient safety. Here, we aimed to design a new laboratory work-flow, utilizing existing laboratory resources, in order to reduce time-to-diagnosis of CPE. A review of the current CPE testing processes and of the literature was performed to identify a real-time commercial polymerase chain reaction (PCR) assay that could facilitate batch testing of CPE clinical specimens, with adequate CPE gene coverage. Stool specimens (210) were collected; CPE-positive inpatients (n = 10) and anonymized community stool specimens (n = 200). Rectal swabs (eSwab™) were inoculated from collected stool specimens and a manual DNA extraction method (QIAamp® DNA Stool Mini Kit) was employed. Extracted DNA was then processed on the Check-Direct CPE® assay. The three step process of making the eSwab™, extracting DNA manually and running the Check-Direct CPE® assay, took <5 min, 1 h 30 min and 1 h 50 min, respectively. It was time efficient with a result available in under 4 h, comparing favourably with the existing method of CPE screening; average time-to-diagnosis of 48/72 h. Utilizing this CPE work-flow would allow a 'same-day' result. Antimicrobial susceptibility testing results, as is current practice, would remain a 'next-day' result. In conclusion, the Check-Direct CPE® assay was easily integrated into a local laboratory work-flow and could facilitate a large volume of CPE screening specimens in a single batch, making it cost-effective and convenient for daily CPE testing.
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