Essential residues in the H-NS binding site of Hha, a co-regulator of horizontally acquired genes in Enterobacteria

Proteins of the Hha/YmoA family co-regulate with H-NS the expression of horizontally acquired genes in Enterobacteria. Systematic mutations of conserved acidic residues in Hha have allowed the identification of D48 as an essential residue for H-NS binding and the involvement of E25. Mutations of these residues resulted in deregulation of sensitive genes in vivo. D48 is only partially solvent accessible, yet it defines the functional binding interface between Hha and H-NS confirming that Hha has to undergo a conformational change to bind H-NS. Exposed acidic residues, such as E25, may electrostatically facilitate and direct the approach of Hha to the positively charged region of H-NS enabling the formation of the final complex when D48 becomes accessible by a conformational change of Hha.

Simulation of growth and development of irrigated cowpea in Piauí State by CROPGRO model

The objective of this work was to adapt the CROPGRO model, which is part of the DSSAT system, for simulating the cowpea (Vigna unguiculata) growth and development under soil and climate conditions of the Baixo Parnaíba region, Piauí State, Brazil. In the CROPGRO, only input parameters that define crop species, cultivars, and ecotype were changed in order to characterize the cowpea crop. Soil and climate files were created for the considered site. Field experiments without water deficit were used to calibrate the model. In these experiments, dry matter (DM), leaf area index (LAI), yield components and grain yield of cowpea (cv. BR 14 Mulato) were evaluated. The results showed good fit for DM and LAI estimates. The medium values of R² and medium absolute error (MAE) were, respectively, 0.95 and 264.9 kg ha-1 for DM, and 0.97 and 0.22 for LAI. The difference between observed and simulated values of plant phenology varied from 0 to 3 days. The model also presented good performance for yield components simulation, excluding 100-grain weight, for which the error ranged from 20.9% to 34.3%. Considering the medium values of crop yield in two years, the model presented an error from 5.6%.

Inversion of multiple intersecting high-resolution crosshole GPR profiles for hydrological characterization at the Boise Hydrogeophysical Research Site

The integration of geophysical data into the subsurface characterization problem has been shown in many cases to significantly improve hydrological knowledge by providing information at spatial scales and locations that is unattainable using conventional hydrological measurement techniques. In particular, crosshole ground-penetrating radar (GPR) tomography has shown much promise in hydrology because of its ability to provide highly detailed images of subsurface radar wave velocity, which is strongly linked to soil water content. Here, we develop and demonstrate a procedure for inverting together multiple crosshole GPR data sets in order to characterize the spatial distribution of radar wave velocity below the water table at the Boise Hydrogeophysical Research Site (BHRS) near Boise, Idaho, USA. Specifically, we jointly invert 31 intersecting crosshole GPR profiles to obtain a highly resolved and consistent radar velocity model along the various profile directions. The model is found to be strongly correlated with complementary neutron porosity-log data and is further corroborated by larger-scale structural information at the BHRS. This work is an important prerequisite to using crosshole GPR data together with existing hydrological measurements for improved groundwater flow and contaminant transport modeling.

Harvest site influences the growth properties of adipose derived stem cells.

The therapeutic potential of adult stem cells may become a relevant option in clinical care in the future. In hand and plastic surgery, cell therapy might be used to enhance nerve regeneration and help surgeons and clinicians to repair debilitating nerve injuries. Adipose-derived stem cells (ASCs) are found in abundant quantities and can be harvested with a low morbidity. In order to define the optimal fat harvest location and detect any potential differences in ASC proliferation properties, we compared biopsies from different anatomical sites (inguinal, flank, pericardiac, omentum, neck) in Sprague-Dawley rats. ASCs were expanded from each biopsy and a proliferation assay using different mitogenic factors, basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) was performed. Our results show that when compared with the pericardiac region, cells isolated from the inguinal, flank, omental and neck regions grow significantly better in growth medium alone. bFGF significantly enhanced the growth rate of ASCs isolated from all regions except the omentum. PDGF had minimal effect on ASC proliferation rate but increases the growth of ASCs from the neck region. Analysis of all the data suggests that ASCs from the neck region may be the ideal stem cell sources for tissue engineering approaches for the regeneration of nervous tissue.

Archaeological and archaeomagnetic dating at a site from the ager Tarraconensis (Tarragona, Spain): El Vila-sec Roman pottery

A very accurate archaeological dating of a Roman site in NE Spain (El Vila-sec) was made based on the typology of pottery artifacts. Three different phases were identifi ed with activity ranging from the mid- 1st century BC to the early-3rd century AD. Analyses of bricks from kilns at El Vila-sec produced data on their stored archaeomagnetic vector. These data were compared with the secular variation curve for the Iberian Peninsula and the SCHA.DIF.3K regional archaeomagnetic model. Both, the reference curve and the model, produced probability distributions for the final period of use for two kilns from the second archaeological phase that were not used during the third phase. At a 95% con fidence level, both time distributions cover a wide chronological range including the presumed archaeological age. Both the Iberian secular variation curve and the SCHA.DIF.3K regional model proved to be suitable models for dating the site, although on their own they do not produce a single unambiguous solution. This archaeomagnetic approach could also be applied to neighbouring archaeological sites that have an imprecise archaeological age.

Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain.

In the presence of 2-hydroxybiphenyl, the enhancer binding protein, HbpR, activates the sigma54-dependent P(hbpC) promoter and controls the initial steps of 2-hydroxybiphenyl degradation in Pseudomonas azelaica. In the activation process, an oligomeric HbpR complex of unknown subunit composition binds to an operator region containing two imperfect palindromic sequences. Here, the HbpR-DNA binding interactions were investigated by site-directed mutagenesis of the operator region and by DNA-binding assays using purified HbpR. Mutations that disrupted the twofold symmetry in the palindromes did not affect the binding affinity of HbpR, but various mutations along a 60 bp region, and also outside the direct palindromic sequences, decreased the binding affinity. Footprints of HbpR on mutant operator fragments showed that a partial loss of binding contacts occurs, suggesting that the binding of one HbpR 'protomer' in the oligomeric complex is impaired whilst leaving the other contacts intact. An HbpR variant, devoid of its N-terminal sensing A-domain, was unable to activate transcription from the hbpC promoter while maintaining protection of the operator DNA in footprints. Wild-type HbpR was unable to activate transcription from the hbpC promoter when delta A-HbpR was expressed in the same cell, suggesting the formation of (repressing) hetero-oligomers. This model implies that HbpR can self-associate on its operator DNA without effector recognition or ATP binding. Furthermore, our findings suggest that the N-terminal sensing domain of HbpR is needed to activate the central ATPase domain rather than to repress a constitutively active C domain, as is the case for the related regulatory protein XylR.

Optimization of Snow Drifting Mitigation and Control Methods for Iowa Conditions Part II, TR-626, 2015

Blowing and drifting of snow is a major concern for transportation efficiency and road safety in regions where their development is common. One common way to mitigate snow drift on roadways is to install plastic snow fences. Correct design of snow fences is critical for road safety and maintaining the roads open during winter in the US Midwest and other states affected by large snow events during the winter season and to maintain costs related to accumulation of snow on the roads and repair of roads to minimum levels. Of critical importance for road safety is the protection against snow drifting in regions with narrow rights of way, where standard fences cannot be deployed at the recommended distance from the road. Designing snow fences requires sound engineering judgment and a thorough evaluation of the potential for snow blowing and drifting at the construction site. The evaluation includes site-specific design parameters typically obtained with semi-empirical relations characterizing the local transport conditions. Among the critical parameters involved in fence design and assessment of their post-construction efficiency is the quantification of the snow accumulation at fence sites. The present study proposes a joint experimental and numerical approach to monitor snow deposits around snow fences, quantitatively estimate snow deposits in the field, asses the efficiency and improve the design of snow fences. Snow deposit profiles were mapped using GPS based real-time kinematic surveys (RTK) conducted at the monitored field site during and after snow storms. The monitored site allowed testing different snow fence designs under close to identical conditions over four winter seasons. The study also discusses the detailed monitoring system and analysis of weather forecast and meteorological conditions at the monitored sites. A main goal of the present study was to assess the performance of lightweight plastic snow fences with a lower porosity than the typical 50% porosity used in standard designs of such fences. The field data collected during the first winter was used to identify the best design for snow fences with a porosity of 50%. Flow fields obtained from numerical simulations showed that the fence design that worked the best during the first winter induced the formation of an elongated area of small velocity magnitude close to the ground. This information was used to identify other candidates for optimum design of fences with a lower porosity. Two of the designs with a fence porosity of 30% that were found to perform well based on results of numerical simulations were tested in the field during the second winter along with the best performing design for fences with a porosity of 50%. Field data showed that the length of the snow deposit away from the fence was reduced by about 30% for the two proposed lower-porosity (30%) fence designs compared to the best design identified for fences with a porosity of 50%. Moreover, one of the lower-porosity designs tested in the field showed no significant snow deposition within the bottom gap region beneath the fence. Thus, a major outcome of this study is to recommend using plastic snow fences with a porosity of 30%. It is expected that this lower-porosity design will continue to work well for even more severe snow events or for successive snow events occurring during the same winter. The approach advocated in the present study allowed making general recommendations for optimizing the design of lower-porosity plastic snow fences. This approach can be extended to improve the design of other types of snow fences. Some preliminary work for living snow fences is also discussed. Another major contribution of this study is to propose, develop protocols and test a novel technique based on close range photogrammetry (CRP) to quantify the snow deposits trapped snow fences. As image data can be acquired continuously, the time evolution of the volume of snow retained by a snow fence during a storm or during a whole winter season can, in principle, be obtained. Moreover, CRP is a non-intrusive method that eliminates the need to perform man-made measurements during the storms, which are difficult and sometimes dangerous to perform. Presently, there is lots of empiricism in the design of snow fences due to lack of data on fence storage capacity on how snow deposits change with the fence design and snow storm characteristics and in the estimation of the main parameters used by the state DOTs to design snow fences at a given site. The availability of such information from CRP measurements should provide critical data for the evaluation of the performance of a certain snow fence design that is tested by the IDOT. As part of the present study, the novel CRP method is tested at several sites. The present study also discusses some attempts and preliminary work to determine the snow relocation coefficient which is one of the main variables that has to be estimated by IDOT engineers when using the standard snow fence design software (Snow Drift Profiler, Tabler, 2006). Our analysis showed that standard empirical formulas did not produce reasonable values when applied at the Iowa test sites monitored as part of the present study and that simple methods to estimate this variable are not reliable. The present study makes recommendations for the development of a new methodology based on Large Scale Particle Image Velocimetry that can directly measure the snow drift fluxes and the amount of snow relocated by the fence.

Auto-évaluation de la qualité d'un site Internet de pharmacie hospitalière

Introduction: L'unité d'Assistance Pharmaceutique de la Pharmacie des HUG fonctionne comme centre d'information sur les médicaments et gère des informations mises à disposition sur le web. Celles-ci sont destinées prioritairement au personnel soignant des HUG et accessibles sur le site intranet/Internet (http://www.hcuge.ch/Pharmacie), mis en service en 1998. L'objectif de ce travail était d'évaluer la qualité de l'information du site intranet/Internet et d'y apporter les améliorations nécessaires. Méthode: Le site intranet/Internet de la pharmacie des HUG a été évalué en automne 2004 à l'aide de 2 outils : NetScoring : grille d'évaluation de la qualité de l'information de santé sur Internet (http://www.chu-rouen.fr/netscoring/). Elle comporte 49 critères répartis en 8 catégories. Chaque critère est noté sur une échelle de 5 occurrences puis pondéré selon son importance (multiplication par 3 si le critère est essentiel, par 2 s'il est important ou par 1 s'il est mineur). Analyse AMDEC : méthode permettant de séquencer un processus et d'en Analyser les Modes de Défaillance, leur Effet et leur Criticité (Qual Saf Health Care 2005 :14(2);93-98). Un score est attribué à chaque mode de défaillance identifié en terme de fréquence, de sévérité et de détectabilité. La multiplication des 3 scores fournit un résultat global de criticité (indice de criticité IC, max. 810), permettant de hiérarchiser les risques. Résultats: Etat des lieux NetScoring : La qualité globale du site intranet/Internet était bonne (202 pts/312). Les points forts concernaient la pertinence et l'utilité du site, la qualité du contenu, du moteur de recherche et du design, la rapidité de chargement du site, la sélection des liens externes proposés et le respect du secret médical. Les faiblesses résidaient dans l'absence de politique de mise à jour régulière, d'annotation systématique de l'état d'actualisation des documents, d'un comité éditorial et scientifique, de mots-clés en anglais et d'une liste permettant l'identification des auteurs. Analyse AMDEC : Quatre catégories (création du document, conversion, structure du site et publication du document) et 19 modes de défaillances ont été caractérisés. Trois modes de défaillance étaient associés à un IC important: erreurs lors de la création d'un document (IC 256), information inadéquate car pratique non validée ou recommandation non généralisable (IC 147) et absence de relecture après la conversion du document en format publiable (ex : PDF) (IC 144). Mesures correctives: Une procédure standard (SOP) a été élaborée pour la gestion du site intranet/Internet. Le format standard des informations (initiales de l'auteur, dates de création et de mise à jour, logo de la pharmacie), la validation et la politique de mise à jour des documents ainsi que la procédure d'archivage y sont clairement définis. Une fiche de suivi accompagnant chaque document a été créée pour la traçabilité de toutes les modifications effectuées et la fréquence de révision à respecter. Discussion et conclusion Cette étude a permis de déterminer et de quantifier les points critiques à améliorer sur le site intranet/Internet de la Pharmacie des HUG. Les mesures correctives entreprises doivent permettre d'améliorer les principales faiblesses et défaillances mises en évidence. La mise en place d'un comité éditorial et scientifique devra être évaluée à l'avenir. Le NetScoring et l'analyse AMDEC sont des outils utiles pour l'évaluation et l'amélioration continue de la qualité d'un site Internet, sous réserve d'une interprétation critique des résultats obtenus avant la mise en place de mesures correctives. Malgré une approche totalement différente, ces outils ont permis de mettre en évidence des lacunes similaires.

Evaluation of High-Slump Concrete for Bridge Deck Overlays, TR-427, 2005

The Iowa Method for bridge deck overlays has been very successful in Iowa since its adoption in the 1970s. This method involves removal of deteriorated portions of a bridge deck followed by placement of a layer of dense (Type O) Portland Cement Concrete (PCC). The challenge encountered with this type of bridge deck overlay is that the PCC must be mixed on-site, brought to the placement area and placed with specialized equipment. This adds considerably to the cost and limits contractor selection, because not all contractors have the capability or equipment required. If it is possible for a ready-mix supplier to manufacture and deliver a dense PCC to the grade, then any competent bridge deck contractor would be able to complete the job. However, Type O concrete mixes are very stiff and generally cannot be transported and placed with ready-mix type trucks. This is where a “super-plasticizer” comes in to use. Addition of this admixture provides a substantial increase in the workability of the concrete – to the extent that it can be delivered to the site and placed on the deck directly out of a ready-mix truck. The objective of this research was to determine the feasibility of placing a deck overly of this type on county bridges within the limits of county budgets and workforce/contractor availability.

Nutrient and light availability to white spruce seedlings in partial and clearcut harvested aspen stands

Abstract

Rhizosphere properties of rice genotypes as influenced by anoxia and availability of zinc and iron

The objective of this work was to study possible mechanisms involved in root-induced changes of rhizosphere physicochemical properties of rice genotypes, under anoxia and low supply of Zn and Fe. Two rice genotypes, including an upland and a lowland ones, were grown in hydroponic medium under adequate and low supply of Zn and Fe, with or without aeration. Anoxia increased shoot dry weight, root length and uptake of Zn and Fe in lowland Amol genotype, but reduced these parameters in upland Gasrol-Dashti genotype. The amount of oxygen released by roots was statistically higher in 'Amol'. The highest acidification potential of roots was observed in the lowland genotype under low supply of Zn, and in the upland genotype under Fe starvation. The highest oxalate (only organic acid detected) exudation from roots was observed in Zn and Fe deficient Gasrol-Dashti genotype. Zinc deficiency caused reduction of alcohol dehydrogenase and stimulation of lactate dehydrogenase activity, particularly in shoot. The ability to induce changes in the rhizosphere properties has a great contribution for the adaptation of both lowland and upland rice genotypes to specific soil conditions.