Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR

The Escherichia coli MelR protein is a transcription activator that autoregulates its own promoter by repressing transcription initiation. Optimal repression requires MelR binding to a site that overlaps the melR transcription start point and to upstream sites. In this work, we have investigated the different determinants needed for optimal repression and their spatial requirements. We show that repression requires a complex involving four DNA-bound MelR molecules, and that the global CRP regulator plays little or no role

Age Deficits in Facial Affect Recognition : The Influence of Dynamic Cues

Funding This work was supported by the Australian Research Council, Australia (DP150100302) and the Leverhulme Trust, U.K. (F/00152/W).Peer reviewedPostprin

A multi-sensor approach for volcanic ash cloud retrieval and eruption characterization: the 23 November 2013 Etna lava fountain

Volcanic activity is observed worldwide with a variety of ground and space-based remote sensing instruments, each with advantages and drawbacks. No single system can give a comprehensive description of eruptive activity, and so, a multi-sensor approach is required. This work integrates infrared and microwave volcanic ash retrievals obtained from the geostationary Meteosat Second Generation (MSG)-Spinning Enhanced Visible and Infrared Imager (SEVIRI), the polar-orbiting Aqua-MODIS and ground-based weather radar. The expected outcomes are improvements in satellite volcanic ash cloud retrieval (altitude, mass, aerosol optical depth and effective radius), the generation of new satellite products (ash concentration and particle number density in the thermal infrared) and better characterization of volcanic eruptions (plume altitude, total ash mass erupted and particle number density from thermal infrared to microwave). This approach is the core of the multi-platform volcanic ash cloud estimation procedure being developed within the European FP7-APhoRISM project. The Mt. Etna (Sicily, Italy) volcano lava fountaining event of 23 November 2013 was considered as a test case. The results of the integration show the presence of two volcanic cloud layers at different altitudes. The improvement of the volcanic ash cloud altitude leads to a mean difference between the SEVIRI ash mass estimations, before and after the integration, of about the 30%. Moreover, the percentage of the airborne “fine” ash retrieved from the satellite is estimated to be about 1%–2% of the total ash emitted during the eruption. Finally, all of the estimated parameters (volcanic ash cloud altitude, thickness and total mass) were also validated with ground-based visible camera measurements, HYSPLIT forward trajectories, Infrared Atmospheric Sounding Interferometer (IASI) satellite data and tephra deposits

The Characterization of Ribosomal RNA Gene Chromatin from Physarum Polycephalum

We have isolated ribosomal RNA gene (rDNA) chromatin from Physarum polycephalum using a nucleolar isolation procedure that minimizes protein loss from chromatin and, subsequently, either agarose gel electrophoresis or metrizamide gradient centrifugation to purify this chromatin fraction (Amero, S. A., Ogle, R. C., Keating, J. L., Montoya, V. L., Murdoch, W. L., and Grainger, R. M. (1988) J. Biol. Chem. 263, 10725-10733). Metrizamide-purified rDNA chromatin obtained from nucleoli isolated according to the new procedure has a core histone/DNA ratio of 0.77:1. The major core histone classes comigrate electrophoretically with their nuclear counterparts on Triton-acid-urea/sodium dodecyl sulfate two-dimensional gels, although they may not possess the extent of secondary modification evident with the nuclear histones. This purified rDNA chromatin also possesses RNA polymerase I activity, and many other nonhistone proteins, including two very abundant proteins (26 and 38 kDa) that may be either ribonucleoproteins or nucleolar matrix proteins. Micrococcal nuclease digestion of the metrizamide-purified rDNA chromatin produces particles containing 145-base pair DNA fragments identical in length to those in total chromatin and which contain both transcribed and nontranscribed rDNA sequences. Some smaller fragments (30, 70, and 110 base pairs) are also seen, but their sequence content is not known. These particles sediment uniformly at 11 S in sucrose gradients containing 15 mM NaCl, and at 4-11 S in gradients containing 0.35 M NaCl. Particles enriched in gene or nontranscribed spacer sequences are not resolved in these sucrose gradients or in metrizamide gradients. Our findings suggest that the rDNA chromatin fraction we have identified contains transcriptionally active genes and that an organized, particle-containing structure exists in active rDNA chromatin

The Purification of Ribosomal RNA Gene Chromatin from Physarum Polycephalum

We have undertaken the purification of ribosomal RNA gene (rDNA) chromatin from the slime mold Physarum polycephalum, in order to study its chromatin structure. In this organism rDNA exists in nucleoli as highly repeated minichromosomes, and one can obtain crude chromatin fractions highly enriched in rDNA from isolated nucleoli. We first developed a nucleolar isolation method utilizing polyamines as stabilization agents that results in a chromatin fraction containing far more protein than is obtained by the more commonly used divalent cation isolation methods. The latter method appears to result in extensive histone loss during chromatin isolations. Two methods were then used for purifying rDNA chromatin from nucleoli isolated by the polyamine procedure. We found that rDNA chromatin migrates as a single band in agarose gels, well separated from other components in the chromatin preparation. Although the utility of this technique is somewhat limited by low yields and by progressive stripping of protein from rDNA chromatin, it can provide useful information about rDNA chromatin protein composition. The application of this technique to the fractionation of gene and spacer chromatin fragments produced by restriction enzyme digestion is discussed. We also found that rDNA chromatin, if RNase-treated, bands discretely in metrizamide equilibrium density gradients with a density lighter than that of non-nucleolar chromatin. These characteristics suggest that we have identified a transcriptionally active rDNA chromatin fraction which possesses a lower protein to DNA ratio than does non-nucleolar chromatin. This technique yields sufficient purified rDNA chromatin for further biochemical studies and does not cause extensive protein stripping. The procedures developed here should be applicable to the analysis of a variety of chromatin fractions in other systems

Conservation of Galliformes in the Greater Himalaya: Is there a need for a higher-quality evidence-base?

Global biodiversity is at a heightened risk of extinction and we are losing species faster than at any other time. It is important to understand the threats that drive a species towards extinction in order to address those drivers. In this paper, we assess our knowledge of the threats faced by 24 Himalayan Galliformes species by undertaking a review of the threats reported in the published literature and the supporting evidence that the threat is having an impact on the species’ populations. Only 24 papers were deemed suitable to be included in the study. We found that biological resource use and agriculture and aquaculture are the predominant threats to the Galliformes in the Greater Himalaya but the evidence available in the studies is quite poor as only one paper quantified the impact on species. This study shows that major gaps exist in our understanding of threats to species, and it is imperative to fill those gaps if we want to prevent species from going extinct

The impact of ensemble meteorology on inverse modeling estimates of volcano emissions and ash dispersion forecasts: Grímsvötn 2011

Volcanic ash can interact with the earth system on many temporal and spatial scales and is a significant hazard to aircraft. In the event of a volcanic eruption, fast and robust decisions need to be made by aviation authorities about which routes are safe to operate. Such decisions take into account forecasts of ash location issued by Volcanic Ash Advisory Centers (VAACs) which are informed by simulations from Volcanic Ash Transport and Dispersion (VATD) models. The estimation of the time-evolving vertical distribution of ash emissions for use in VATD simulations in real time is difficult which can lead to large uncertainty in these forecasts. This study presents a method for constraining the ash emission estimates by combining an inversion modeling technique with an ensemble of meteorological forecasts, resulting in an ensemble of ash emission estimates. These estimates of ash emissions can be used to produce a robust ash forecast consistent with observations. This new ensemble approach is applied to the 2011 eruption of the Icelandic volcano Grímsvötn. The resulting emission profiles each have a similar temporal evolution but there are differences in the magnitude of ash emitted at different heights. For this eruption, the impact of precipitation uncertainty (and the associated wet deposition of ash) on the estimate of the total amount of ash emitted is larger than the impact of the uncertainty in the wind fields. Despite the differences that are dominated by wet deposition uncertainty, the ensemble inversion provides confidence that the reduction of the unconstrained emissions (a priori), particularly above 4 km, is robust across all members. In this case, the use of posterior emission profiles greatly reduces the magnitude and extent of the forecast ash cloud. The ensemble of posterior emission profiles gives a range of ash column loadings much closer in agreement with a set of independent satellite retrievals in comparison to the a priori emissions. Furthermore, airspace containing volcanic ash concentrations deemed to be associated with the highest risk (likelihood of exceeding a high concentration threshold) to aviation are reduced by over 85%. Such improvements could have large implications in emergency response situations. Future research will focus on quantifying the impact of uncertainty in precipitation forecasts on wet deposition in other eruptions and developing an inversion system that makes use of the state-of-the-art meteorological ensembles which has the potential to be used in an operational setting

Preoperative predictors of sternotomy need in mediastinal goiter management

BACKGROUND: The objective of this study was to identify the preoperative risk factors for patients in need of a sternotomy in the management of mediastinal goiters in order to provide better preoperative planning and patient consent. METHODS: We analyzed 98 patients who underwent surgery for mediastinal goiters (goiters extending below the thoracic inlet > or =3 cm with the neck in hyperextension) between 1995 and 2008. Twelve (12.2%) of the patients required a sternotomy. The patients' features were analyzed by the surgical approach performed. Logistic regression analysis was used to study which variables were influencing the surgical strategy. The receiver operating characteristic (ROC) curves were designed when appropriate. RESULTS: The analysis disclosed the following risk factors: radiologic extension of mediastinal goiters below the aortic arch (odds ratio [OR] = 32.87; 95% confidence interval [CI] = 4.04-267.12; p 160 months: OR = 22.8; 95% CI = 5.28-98.53; p < .0001). CONCLUSIONS: Sternotomy need for mediastinal goiter removal can be predicted; in such cases surgeons should not hesitate to perform it for minimizing complications