Regulation of the p-hydroxybenzoic acid hydroxylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358

The regulation of the p-hydroxybenzoate hydroxylase gene (pobA) of Pseudomonas putida WC5358 involved in the catabolism of p-hydroxybenzoic acid (PHB) to the central intermediate protocatechuate was studied. Protocatechuic acid (PCA) is then degraded via the beta -ketoadipate pathway to form tricarboxylic acid intermediates. In several Gram-negative bacteria pobA has been found genetically linked to a regulator called pobR which activates pobA expression in response to PHB, In this study the identification and characterization of the pobC-pobA locus of P, putida WCS358 is presented. The p-hydroxybenzoate hydroxylase (PobA) is highly identical to other identified PobA proteins, whereas the regulatory protein PobC did not display very high identity to other PobR proteins studied and belonged to the AraC family of regulatory proteins, hence it has been designated PobC, Using the pobA promoter transcriptionally fused to a promoterless lad gene it was observed that induction via PobC occurred very efficiently when PHB was present and to a lesser but still significant level also in the presence of PCA, This PobC-PCA response was genetically demonstrated by making use of pobC::Tn5 and pcaH::Tn5 mutants of strain WC5358 constructed in this study. In pobC mutants both the p-hydroxybenzoic and PCA response were not observed, whereas in the pcaH mutant, which lacks a functional protocatechuate 3,4-dioxygenase, the protocatechuic-acid-dependent pobA activation was still observed. Finally, the activation of pobA by PHB varied according to the concentration and it was observed that in the pcaR::Tn5 regulatory mutant of strain WCS358 the pobA promoter activity was reduced. PcaR is a regulator involved in the regulation of several loci of the beta -ketoadipate pathway, one of which is pcaK, It was postulated that the reduction of pobA activation in pcaR::Tn5 mutants was because there was no expression of the pcaK gene encoding the PHB transport protein resulting in lower levels of PHB present inside the cell

Longitudinal Variability in Hydrochemistry and Zooplankton Community of a Large River: A Lagrangian‐Based Approach

The variability in water quality and zooplankton community structure during downstream transport was investigated in the Po river (Italy) using for the first time a Lagrangian sampling approach. Two surveys were conducted, one in spring under relatively high discharge levels, and one at low flows in summer. Twelve stations along a 332‐km stretch of the river’s lowland reach and four major tributaries were sampled. A hydrodynamic modelling system was used to determine water transport time along the river, with a satisfying fit between simulated and observed discharge values. No clear downstream trend in phosphorus and nitrogen concentrations was found. Conversely, a marked longitudinal decrease in dissolved silica supports the hypothesis of increasing downstream silica limitation during the phytoplankton growing season.In spring, at low residence time, no apparent plankton growth was observed during downstream transport. In summer, higher temperatures and lower turbulence and turbidity associated with longer residence time stimulated algal growth and in‐stream reproduction of fast‐growing rotifer taxa, with the gradual downstream development of a truly potamal assemblage and the increase of the ratio of euplanktonic to littoral/epibenthic rotifer taxa. Crustacean zooplankton density was generally low. The importance of biotic interactions within the zooplankton in driving community abundance and composition appeared to increase in the downstream direction, paralleled by a decrease in the influence of physical forcing. Tributary influence was especially evident where severe anthropogenic alterations of river hydrology and trophic status resulted in enhanced plankton growth, ultimately affecting zooplankton structure in the main river. Copyright © 2016 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134064/1/rra3028.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134064/2/rra3028_am.pd

Ensemble modeling informs hypoxia management in the northern Gulf of Mexico

A large region of low-dissolved-oxygen bottom waters (hypoxia) forms nearly every summer in the northern Gulf of Mexico because of nutrient inputs from theMississippi River Basin andwater column stratification. Policymakers developed goals to reduce the area of hypoxic extent because of its ecological, economic, and commercial fisheries impacts. However, the goals remain elusive after 30 y of research and monitoring and 15 y of goal-setting and assessment because there has been little change in river nitrogen concentrations. An intergovernmental Task Force recently extended to 2035 the deadline for achieving the goal of a 5,000-km(2) 5-y average hypoxic zone and set an interim load target of a 20% reduction of the spring nitrogen loading from the Mississippi River by 2025 as part of their adaptive management process. The Task Force has asked modelers to reassess the loading reduction required to achieve the 2035 goal and to determine the effect of the 20% interim load reduction. Here, we address both questions using a probabilistic ensemble of four substantially different hypoxia models. Our results indicate that, under typical weather conditions, a 59% reduction in Mississippi River nitrogen load is required to reduce hypoxic area to 5,000 km(2). The interim goal of a 20% load reduction is expected to produce an 18% reduction in hypoxic area over the long term. However, due to substantial interannual variability, a 25% load reduction is required before there is 95% certainty of observing any hypoxic area reduction between consecutive 5-y assessment periods

Ensemble Modeling Informs Hypoxia Management In The Northern Gulf Of Mexico

A large region of low-dissolved-oxygen bottom waters (hypoxia) forms nearly every summer in the northern Gulf of Mexico because of nutrient inputs from theMississippi River Basin andwater column stratification. Policymakers developed goals to reduce the area of hypoxic extent because of its ecological, economic, and commercial fisheries impacts. However, the goals remain elusive after 30 y of research and monitoring and 15 y of goal-setting and assessment because there has been little change in river nitrogen concentrations. An intergovernmental Task Force recently extended to 2035 the deadline for achieving the goal of a 5,000-km(2) 5-y average hypoxic zone and set an interim load target of a 20% reduction of the spring nitrogen loading from the Mississippi River by 2025 as part of their adaptive management process. The Task Force has asked modelers to reassess the loading reduction required to achieve the 2035 goal and to determine the effect of the 20% interim load reduction. Here, we address both questions using a probabilistic ensemble of four substantially different hypoxia models. Our results indicate that, under typical weather conditions, a 59% reduction in Mississippi River nitrogen load is required to reduce hypoxic area to 5,000 km(2). The interim goal of a 20% load reduction is expected to produce an 18% reduction in hypoxic area over the long term. However, due to substantial interannual variability, a 25% load reduction is required before there is 95% certainty of observing any hypoxic area reduction between consecutive 5-y assessment periods

CDKL5 expression is modulated during neuronal development and its subcellular distribution is tightly regulated by the C-terminal tail

Mutations in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been identified in patients with Rett syndrome (RTT), West syndrome, and X-linked infantile spasms, sharing the common feature of mental retardation and early seizures. CDKL5 is a rather uncharacterized kinase, but its involvement in RTT seems to be explained by the fact that it works upstream of MeCP2, the main cause of Rett syndrome. To understand the role of this kinase for nervous system functions and to address if molecular mechanisms are involved in regulating its distribution and activity, we studied the ontogeny of CDKL5 expression in developing mouse brains by immunostaining and Western blotting. The expression profile of CDKL5 was compared with that of MeCP2. The two proteins share a general expression profile in the adult mouse brain, but CDKL5 levels appear to be highly modulated at the regional level. Its expression is strongly induced in early postnatal stages, and in the adult brain CDKL5 is present in mature neurons, but not in astroglia. Interestingly, the presence of CDKL5 in the cell nucleus varies at the regional level of the adult brain and is developmentally regulated. CDKL5 shuttles between the cytoplasm and the nucleus and the C-terminal tail is involved in localizing the protein to the cytoplasm in a mechanism depending on active nuclear export. Accordingly, Rett derivatives containing disease-causing truncations of the C terminus are constitutively nuclear, suggesting that they might act as gain of function mutations in this cellular compartment

Advanced 3D modeling versus Building Information Modeling: the case study of Palazzo Ettoreo in Sacile (Italy)

This paper presents an experience of 3D modeling starting from laser scanning data and following two alternative approaches: the first one, called \u201cAdvanced 3D modeling\u201d, based on an original meshing algorithm, while the second make use of Revit BIM software. The case study in Palace Ettoreo in Sacile (Pordenone, Italy), constructed in Renaissance Venetian style in the 16th century: it has a trapezoid plan and is developed on three floors, with the ground one endowing a portico on two fa\ue7ades. The palace has been surveyed by two terrestrial laser scanners: a Riegl Z420i for 5 external scans and a FARO Photon 120 for 53 internal scans; also a topographic surveying of 270 targets have been carried out. The final TLS cloud has 1,4 billions of points. The Advanced 3D modeling has produced a \u201csmart\u201d mesh, allowing also to model the elements with deformations (out of plumb, bulges and troughs). Moreover, this model drastically reduce the stored data: the whole palace is modeled by 111.496 polygons only. The modeling with Revit follows the classical flowchart where the principal architectonical elements are gradually composed: this HBIM process has required a strong manual work in exploiting the available parametric objects and/or in the definition of new objects. Comparing the two models with respect the points cloud, both have evidenced advantages and limitations: therefore, the best solution is a process involving their combination. At the beginning, the Advanced 3D modeling is performed onto the points cloud, so well exploiting the segmentation tools and the smart meshing of the surfaces preserving any geometrical irregularity. Such obtained model allows metrical and morphological evaluation on the various structural and architectonical elements. Afterwards, this very light model becomes the entry data for the modeling in BIM environment, where also the shape of irregular elements are so imported

Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.

Published onlinePseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.G.U. and M.K. were funded by the Ministry of Education, Science and Technological Development, Republic of Serbia (grant no. 173019). G.U. is also the beneficiary of FEMS Research Fellowship 2014-1. The laboratory of V.V. was financed by ICGEB core funding

AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens

This is the final version. Available on open access from the Microbiology Society via the DOI in this recordAzelaic acid is a dicarboxylic acid that has recently been shown to play a role in plant-bacteria signalling and also occurs naturally in several cereals. Several bacteria have been reported to be able to utilize azelaic acid as a unique source of carbon and energy, including Pseudomonas nitroreducens. In this study, we utilize P. nitroreducens as a model organism to study bacterial degradation of and response to azelaic acid. We report genetic evidence of azelaic acid degradation and the identification of a transcriptional regulator that responds to azelaic acid in P. nitroreducens DSM 9128. Three mutants possessing transposons in genes of an acyl-CoA ligase, an acyl-CoA dehydrogenase and an isocitrate lyase display a deficient ability in growing in azelaic acid. Studies on transcriptional regulation of these genes resulted in the identification of an IclR family repressor that we designated as AzeR, which specifically responds to azelaic acid. A bioinformatics survey reveals that AzeR is confined to a few proteobacterial genera that are likely to be able to degrade and utilize azelaic acid as the sole source of carbon and energy

Functional consequences of mutations in CDKL5, an X-linked gene involved in infantile spasms and mental retardation

Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been identified in patients with Rett syndrome, West syndrome, and X-linked infantile spasms sharing the common features of generally intractable early seizures and mental retardation. Disease-causing mutations are distributed in both the catalytic domain and in the large COOH terminus. In this report, we examine the functional consequences of some Rett mutations of CDKL5 together with some synthetically designed derivatives useful to underline the functional domains of the protein. The mutated CDKL5 derivatives have been subjected to in vitro kinase assays and analyzed for phosphorylation of the TEY (Thr-Glu-Tyr) motif within the activation loop, their subcellular localization, and the capacity of CDKL5 to interact with itself. Whereas wild-type CDKL5 autophosphorylates and mediates the phosphorylation of the methyl-CpG-binding protein 2 (MeCP2) in vitro, Rett-mutated proteins show both impaired and increased catalytic activity suggesting that a tight regulation of CDKL5 is required for correct brain functions. Furthermore, we show that CDKL5 can self-associate and mediate the phosphorylation of its own TEY (Thr-Glu-Tyr) motif. Eventually, we show that the COOH terminus regulates CDKL5 properties; in particular, it negatively influences the catalytic activity and is required for its proper sub-nuclear localization. We propose a model in which CDKL5 phosphorylation is required for its entrance into the nucleus whereas a portion of the COOH-terminal domain is responsible for a stable residency in this cellular compartment probably through protein-protein interactions