Molecular identification and characterization of the Arabidopsis delta(3,5),delta(2,4)-dienoyl-coenzyme A isomerase, a peroxisomal enzyme participating in the beta-oxidation cycle of unsaturated fatty acids.

Degradation of unsaturated fatty acids through the peroxisomal beta-oxidation pathway requires the participation of auxiliary enzymes in addition to the enzymes of the core beta-oxidation cycle. The auxiliary enzyme delta(3,5),delta(2,4)-dienoyl-coenzyme A (CoA) isomerase has been well studied in yeast (Saccharomyces cerevisiae) and mammals, but no plant homolog had been identified and characterized at the biochemical or molecular level. A candidate gene (At5g43280) was identified in Arabidopsis (Arabidopsis thaliana) encoding a protein showing homology to the rat (Rattus norvegicus) delta(3,5),delta(2,4)-dienoyl-CoA isomerase, and possessing an enoyl-CoA hydratase/isomerase fingerprint as well as aspartic and glutamic residues shown to be important for catalytic activity of the mammalian enzyme. The protein, named AtDCI1, contains a peroxisome targeting sequence at the C terminus, and fusion of a fluorescent protein to AtDCI1 directed the chimeric protein to the peroxisome in onion (Allium cepa) cells. AtDCI1 expressed in Escherichia coli was shown to have delta(3,5),delta(2,4)-dienoyl-CoA isomerase activity in vitro. Furthermore, using the synthesis of polyhydroxyalkanoate in yeast peroxisomes as an analytical tool to study the beta-oxidation cycle, expression of AtDCI1 was shown to complement the yeast mutant deficient in the delta(3,5),delta(2,4)-dienoyl-CoA isomerase, thus showing that AtDCI1 is also appropriately targeted to the peroxisome in yeast and has delta(3,5),delta(2,4)-dienoyl-CoA isomerase activity in vivo. The AtDCI1 gene is expressed constitutively in several tissues, but expression is particularly induced during seed germination. Proteins showing high homology with AtDCI1 are found in gymnosperms as well as angiosperms belonging to the Monocotyledon or Dicotyledon classes.

Small RNA-dependent expression of secondary metabolism is controlled by Krebs cycle function in Pseudomonas fluorescens.

Pseudomonas fluorescens CHA0, an antagonist of phytopathogenic fungi in the rhizosphere of crop plants, elaborates and excretes several secondary metabolites with antibiotic properties. Their synthesis depends on three small RNAs (RsmX, RsmY, and RsmZ), whose expression is positively controlled by the GacS-GacA two-component system at high cell population densities. To find regulatory links between primary and secondary metabolism in P. fluorescens and in the related species Pseudomonas aeruginosa, we searched for null mutations that affected central carbon metabolism as well as the expression of rsmY-gfp and rsmZ-gfp reporter constructs but without slowing down the growth rate in rich media. Mutation in the pycAB genes (for pyruvate carboxylase) led to down-regulation of rsmXYZ and secondary metabolism, whereas mutation in fumA (for a fumarase isoenzyme) resulted in up-regulation of the three small RNAs and secondary metabolism in the absence of detectable nutrient limitation. These effects required the GacS sensor kinase but not the accessory sensors RetS and LadS. An analysis of intracellular metabolites in P. fluorescens revealed a strong positive correlation between small RNA expression and the pools of 2-oxoglutarate, succinate, and fumarate. We conclude that Krebs cycle intermediates (already known to control GacA-dependent virulence factors in P. aeruginosa) exert a critical trigger function in secondary metabolism via the expression of GacA-dependent small RNAs.

Serum antimüllerian hormone levels remain stable through the menstrual cycle and after oral or vaginal administration of synthetic sex steroids

Rapport de synthèse : Objectif de l'étude : étudier si l'administration orale ou vaginale d'hormones contraceptives influence les concentrations sériques d'hormone antimüllérienne (AMH). Design : essai prospectif chez des femmes recrutées par annonce. Les femmes désireuses d'avoir une contraception ont été randomisées entre une contraception orale et une contraception vaginale. Celles qui ne souhaitaient pas de contraception ont été incluses dans le groupe témoin. Cadre de l'étude : unité de médecine de la reproduction d'un hôpital universitaire. Patientes : vingt-quatre jeunes femmes en bonne santé avec des cycles menstruels réguliers qui n'avaient pas utilisé de contraception hormonale pendant les trois mois précédant l'étude. Intervention : contraception orale ou vaginale du 5ème au 25ème jour du cycle menstruel dans les groupes contraception versus pas de contraception dans le groupe témoin. Mesure d'issue : variations inter et intra-cycle des concentrations sériques d'AMH dans les trois groupes: groupe témoin en cycle spontané et groupes sous contraception oestroprogestative orale ou vaginale. Résultats : les fluctuations d'AMH observées pendant le cycle menstruel (variations intra-cycle) restent dans les valeurs des variations entre deux cycles (variations inter-cycles) tant chez les femmes en cycle spontané que chez les femmes sous contraception orale ou vaginale. Conclusions : nos résultats confirment que les concentrations sériques d'AMH restent stables pendant le cycle menstruel et indiquent qu'elles ne sont pas influencées par l'administration exogène de stéroïdes sexuels contraceptifs, que ce soit par voie orale ou vaginale.

Improved multiple-locus variable-number tandem-repeat assay for Staphylococcus aureus genotyping, providing a highly informative technique together with strong phylogenetic value.

We describe an improved multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme for genotyping Staphylococcus aureus. We compare its performance to those of multilocus sequence typing (MLST) and spa typing in a survey of 309 strains. This collection includes 87 epidemic methicillin-resistant S. aureus (MRSA) strains of the Harmony collection, 75 clinical strains representing the major MLST clonal complexes (CCs) (50 methicillin-sensitive S. aureus [MSSA] and 25 MRSA), 135 nasal carriage strains (133 MSSA and 2 MRSA), and 13 published S. aureus genome sequences. The results show excellent concordance between the techniques' results and demonstrate that the discriminatory power of MLVA is higher than those of both MLST and spa typing. Two hundred forty-two genotypes are discriminated with 14 VNTR loci (diversity index, 0.9965; 95% confidence interval, 0.9947 to 0.9984). Using a cutoff value of 45%, 21 clusters are observed, corresponding to the CCs previously defined by MLST. The variability of the different tandem repeats allows epidemiological studies, as well as follow-up of the evolution of CCs and the identification of potential ancestors. The 14 loci can conveniently be analyzed in two steps, based upon a first-line simplified assay comprising a subset of 10 loci (panel 1) and a second subset of 4 loci (panel 2) that provides higher resolution when needed. In conclusion, the MLVA scheme proposed here, in combination with available on-line genotyping databases (including http://mlva.u-psud.fr/), multiplexing, and automatic sizing, can provide a basis for almost-real-time large-scale population monitoring of S. aureus.

Role of β-TrCP1, variant and homologue in HIV-1 life cycle

Summary The CD4 molecule plays a key role in AIDS pathogenesis, it is required for entry of the virus into permissive cells and its subsequent down-modulation of the cell surface is a hallmark of HN-1 infected cells. The virus encodes no less than three proteins that participate in this process: Nef, Vpu and Env. Vpu protein interacts with CD4 within the endoplasmic reticulum of infected cells, where it targets CD4 for degradation through the interaction with a cellular protein named ß-TrCP1. This F-box protein functions as the substrate recognition subunit of the SCF ß-Trcr E3 ubiquitin ligase, which normally induce the ubiquitination and subsequent degradation of various proteins such as ß-catenin and IxBa. Mammals possess a homologue of ß-TrCP1, HOS, also named ß-TrCP2 which has a cytoplasmic subcellular distribution. Structural analysis of the ligand-binding domain of both homologues shows striking surface similarities. Both F-box proteins have a redundant role in a number of cellular processes; however the potential role of ß-TrCP2 in HIV-1 infected cells has not been evaluated. In the present study, we assessed the existence of génetic variants of BRTC, encoding ß-TrCP1, and evaluated whether these variants would affect CD4 down-modulation. Additionally, we determined whether ß-TrCP2 shares with its homologue structural and functional properties that would allow it to bind Vpu, modulate CD4 expression, and thus participate in HN-1 pathogenesis. We identified a single nucleotide polymorphism present in the human population with an allelic frequency of 0.03 that leads to the substitution of alanine 507 by a serine. However, we showed by transient transfection in HeLa CD4+ cells that this variant behaves as ß-TrCP1 with respect to CD4 down-modulation. We established transient expression systems in HeLa CD4+ cells to test whether ß-TrCP2 is implicated in Vpu-mediated CD4 down-modulation. We show by coimmunoprecipitation experiments that ß-TrCP2 binds Vpu and is able to induce CD4 down-modulation as efficiently as ß-TrCP1. In two different cell lines, HeLa CD4+ and Jurkat, Vpu-mediated CD4 down-modulation could not be completely reversed through the silencing of endogenous ß-TrCP 1 or ß-TrCP2 individually, but required both genes to be silenced simultaneously. We evaluated the role of ß-TrCP1 and ß-TrCP2 in HIV-1 life cycle using silencing prior to actual viral infection. Both ß-TrCP1 and ß-TrCP2 contributed to CD4 down-modulation during aone-cycle viral infection iri Ghost cells. In addition, the combined silencing of both homologues in the absence of env and nef reversed CD4 down-modulation, showing that ß-TrCP 1 and ß-TrCP2 represent the main and additive effectors of HIV-1 encoded Vpu. In addition, we showed that silencing of ß-TrCPI but not ß-TrCP2 induced a decrease of HIV-1 LTR-driven expression. In a transient transfection system with Tat and a LTR luciferase reporter, both homologues modulated LTR-driven expression. The present study revealed that ß-TrCP2 represents a novel protein participating in HIV-1 cycle and complete comprehension of the complex interplay occurring between the two F-Box will improve our understanding of HIV-1 infection. Résumé La molécule CD4 joue un rôle clef dans la pathogenèse du SIDA ; elle est requise pour l'entrée du virus dans les cellules permissives et la diminution de sa concentration au niveau de la surface cellulaire est une importante caractéristique des cellules infectées par le VIH-1. Le virus encode pas moins de trois protéines qui participent à ce processus Nef, Vpu et Env. La protéine Vpu lie CD4 au niveau du réticulum endoplasmique et induit sa dégradation en interagissant avec une protéine cellulaire nommée ß-TrCP 1. Cette protéine de type F-Box est une sous unité du complexe ubiquitine-ligase E3 SCFß-TrCP. Elle permet la reconnaissance du substrat par le complexe qui induit l'ubiquitination et la subséquente dégradation de diverses protéines cellulaires comme la ß-catenin ou IκBα. Les mammifères possèdent un homologue à ß-TrCP1appelé ß-TrCP2 (ou HOS). L'analyse comparative du domaine permettant la reconnaissance des substrats des deux homologues montre de frappantes similarités. Le rôle de ß-TrCP2 dans le cycle viral du VIH-1 n'a pas encore été évalué. Lors de cette étude, nous avons recherché l'existence de variants génétique de BTRC (codant pour ß-TrCP1) et nous avons évalué si ces variants pourraient affecter la dégradation des molécules CD4 induite par le virus. Nous avons ainsi identifié un polymorphisme présent dans la population humaine avec une fréquence allélique de 0.03 qui consiste en une substitution de l'alanine 507 par une sérine. Nous avons cependant montré par transfection dans des cellules HeLa CD4+ que ce variant se comporte comme ß-TrCP 1 en ce qui concerne la modulation de CD4. De plus, nous avons déterminé si ß-TrCP2 partageait avec son homologue des propriétés structurelles et fonctionnelles qui lui permettraient de lier Vpu, moduler la concentration de CD4 et ainsi prendre part à la pathogenèse du SIDA. Pour ce faire, nous avons établi un système d'expression temporaire dans des cellules HeLa CD4+. Par co-immunoprécipitation, nous avons montré que ß-TrCP2 lie Vpu et est capable d'induire la dégradation de CD4 aussi efficacement que ß-TrCP1. Dans deux différentes lignées cellulaires, HeLa CD4+ et Jurkat, la dégradation de CD4 n'a pu être complètement inhibée par le silencing individuel de ß-TrCP 1 ou ß-TrCP2, mais nécessitait le silencing simultané des 2 gènes. Nous avons évalué le rôle des deux homologues dans le cycle viral du VIH-1 en infectant des cellules Ghost avec le virus après avoir effectué un silencing des deux protéines. Nous avons ainsi montré que ß-TrCP 1 et ß-TrCP2 contribuent de manière additive à la dégradation de CD4 induite par une infection du VIH-1. Le silencing combiné des deux homologues inhiba complètement cette dégradation en l'absence de env et nef, prouvant qu'aucune autre voie ne participe à ce processus: En outre, nous avons montré que le silencing de ß-TrCP 1 mais pas celui de ß-TrCP2 induisait une diminution de l'expression virale sous contrôle du LTR. Nous n'avons cependant pas été en mesure de reconstituer cet effet en exprimant Tat et un gène reporteur sous contrôle du LTR dans des cellules HeLa CD4+. Le présent travail révèle que ß-TrCP2 représente une nouvelle protéine participant dans le cycle viral du VIH-1. Une complète compréhension de l'effet de chacun des deux homologues sur le cycle viral permettra d'améliorer notre compréhension de l'infection par le VIH-1.

Field Monitoring of Curved Girder Bridges with Integral Abutments, TPF-5(169), 2014

Nationally, there are questions regarding the design, fabrication, and erection of horizontally curved steel girder bridges due to unpredicted girder displacements, fit-up, and locked-in stresses. One reason for the concerns is that up to one-quarter of steel girder bridges are being designed with horizontal curvature. There is also an urgent need to reduce bridge maintenance costs by eliminating or reducing deck joints, which can be achieved by expanding the use of integral abutments to include curved girder bridges. However, the behavior of horizontally curved bridges with integral abutments during thermal loading is not well known nor understood. The purpose of this study was to investigate the behavior of horizontal curved bridges with integral abutment (IAB) and semi-integral abutment bridges (SIAB) with a specific interest in the response to changing temperatures. The long-term objective of this effort is to establish guidelines for the use of integral abutments with curved girder bridges. The primary objective of this work was to monitor and evaluate the behavior of six in-service, horizontally curved, steel-girder bridges with integral and semi-integral abutments. In addition, the influence of bridge curvature, skew and pier bearing (expansion and fixed) were also part of the study. Two monitoring systems were designed and applied to a set of four horizontally curved bridges and two straight bridges at the northeast corner of Des Moines, Iowa—one system for measuring strains and movement under long term thermal changes and one system for measuring the behavior under short term, controlled live loading. A finite element model was developed and validated against the measured strains. The model was then used to investigate the sensitivity of design calculations to curvature, skew and pier joint conditions. The general conclusions were as follows: (1) There were no measurable differences in the behavior of the horizontally curved bridges and straight bridges studied in this work under thermal effects. For preliminary member sizing of curved bridges, thermal stresses and movements in a straight bridge of the same length are a reasonable first approximation. (2) Thermal strains in integral abutment and semi-integral abutment bridges were not noticeably different. The choice between IAB and SIAB should be based on life – cycle costs (e.g., construction and maintenance). (3) An expansion bearing pier reduces the thermal stresses in the girders of the straight bridge but does not appear to reduce the stresses in the girders of the curved bridge. (4) An analysis of the bridges predicted a substantial total stress (sum of the vertical bending stress, the lateral bending stress, and the axial stress) up to 3 ksi due to temperature effects. (5) For the one curved integral abutment bridge studied at length, the stresses in the girders significantly vary with changes in skew and curvature. With a 10⁰ skew and 0.06 radians arc span length to radius ratio, the curved and skew integral abutment bridges can be designed as a straight bridge if an error in estimation of the stresses of 10% is acceptable.

Retinal degeneration depends on Bmi1 function and reactivation of cell cycle proteins.

The epigenetic regulator Bmi1 controls proliferation in many organs. Reexpression of cell cycle proteins such as cyclin-dependent kinases (CDKs) is a hallmark of neuronal apoptosis in neurodegenerative diseases. Here we address the potential role of Bmi1 as a key regulator of cell cycle proteins during neuronal apoptosis. We show that several cell cycle proteins are expressed in different models of retinal degeneration and required in the Rd1 photoreceptor death process. Deleting E2f1, a downstream target of CDKs, provided temporary protection in Rd1 mice. Most importantly, genetic ablation of Bmi1 provided extensive photoreceptor survival and improvement of retinal function in Rd1 mice, mediated by a decrease in cell cycle markers and regulators independent of p16(Ink4a) and p19(Arf). These data reveal that Bmi1 controls the cell cycle-related death process, highlighting this pathway as a promising therapeutic target for neuroprotection in retinal dystrophies.

Epigenetic regulation of the bacterial cell cycle.

N(6)-methyl-adenines can serve as epigenetic signals for interactions between regulatory DNA sequences and regulatory proteins that control cellular functions, such as the initiation of chromosome replication or the expression of specific genes. Several of these genes encode master regulators of the bacterial cell cycle. DNA adenine methylation is mediated by Dam in gamma-proteobacteria and by CcrM in alpha-proteobacteria. A major difference between them is that CcrM is cell cycle regulated, while Dam is active throughout the cell cycle. In alpha-proteobacteria, GANTC sites can remain hemi-methylated for a significant period of the cell cycle, depending on their location on the chromosome. In gamma-proteobacteria, most GATC sites are only transiently hemi-methylated, except regulatory GATC sites that are protected from Dam methylation by specific DNA-binding proteins.

Inclusion of soil erosion impacts in life cycle assessment on a global scale: application to energy crops in Spain

Purpose: Despite the fundamental role of ecosystem goods and services in sustaining human activities, there is no harmonized and internationally agreed method for including them in life cycle assessment (LCA). The main goal of this study was to develop a globally applicable and spatially resolved method for assessing land-use impacts on the erosion regulation ecosystem service.Methods: Soil erosion depends much on location. Thus, unlike conventional LCA, the endpoint method was regionalized at the grid-cell level (5 arc-minutes, approximately 10×10 km2) to reflect the spatial conditions of the site. Spatially explicit characterization factors were not further aggregated at broader spatial scales. Results and discussion: Life cycle inventory data of topsoil and topsoil organic carbon (SOC) losses were interpreted at the endpoint level in terms of the ultimate damage to soil resources and ecosystem quality. Human health damages were excluded from the assessment. The method was tested on a case study of five three-year agricultural rotations, two of them with energy crops, grown in several locations in Spain. A large variation in soil and SOC losses was recorded in the inventory step, depending on climatic and edaphic conditions. The importance of using a spatially explicit model and characterization factors is shown in the case study.Conclusions and outlook: The regionalized assessment takes into account the differences in soil erosion-related environmental impacts caused by the great variability of soils. Taking this regionalized framework as the starting point, further research should focus on testing the applicability of the method trough the complete life cycle of a product and on determining an appropriate spatial scale at which to aggregate characterization factors, in order to deal with data gaps on location of processes, especially in the background system. Additional research should also focus on improving reliability of the method by quantifying and, insofar as it is possible, reducing uncertainty.

08019-011 Staff Beaver Creek Final Report

Staff and Beaver Creeks are two tributaries of the Upper Iowa River (UIR). Additional acres that drain directly into the UIR bring the size of the project area to 41,328 acres. The goal of the project is to reduce sediment loading and excess nutrients from reaching the streams which ultimately reach the UIR. Staff/Beaver Water Quality Project initially received funding as part of the FY 2005 WSPF/319 grant application cycle. Tremendous progress has been accomplished towards the original goals of the project. Due to the large number of Best Management Practices (BMPs) installed and the continued high interest for those practices, more work remains to be done. The heavy rains received in 2008 caused severe erosion and has dramatically increased interest in conservation practices. A thorough watershed assessment was completed in the fall of 2008. Data from this assessment indicates additional work is needed. The initial grant funding will be exhausted within fiscal year 2009. Therefore, the Howard Soil and Water Conservation District is seeking 3 years of funding. The District believes interest in the water quality project is at an all time high and that with an additional three years of funding, even more progress can be achieved in reducing sediment delivery and excess nutrients to these priority streams.

Fluorodeoxyuridine mediated cell cycle synchronization in S-phase increases the Auger radiation cell killing with 125I-iododeoxyuridine.

Aim: 125I-iododeoxyuridine is a potential Auger radiation therapy agent. Its incorporation in DNA of proliferating cells is enhanced by fluorodeoxyuridine. Here, we evaluated therapeutic activities of 125I-iododeoxyuridine in an optimized fluorodeoxyuridine pre-treatment inducing S-phase synchronization. Methods: After S-phase synchronization by fluorodeoxyuridine, cells were treated with 125I-iododeoxyuridine. Apoptosis analysis and S-phase synchronization were studied by flow cytometry. Cell survival was determined by colony-forming assay. Based on measured growth parameters, the number of decays per cell that induced killing was extrapolated. Results: Treatment experiments showed that 72 to 91% of synchronized cells were killed after 0.8 and 8 kBq/ml 125I-iododeoxyuridine incubation, respectively. In controls, only 8 to 38% of cells were killed by corresponding 125I-iododeoxyuridine activities alone and even increasing the activity to 80 kBq/ml gave only 42 % killing. Duplicated treatment cycles or repeated fluorodeoxyuridine pre-treatment allowed enhancing cell killing to >95 % at 8 kBq/ml 125I-iododeoxyuridine. About 50 and 160 decays per S-phase cells in controls and S-phase synchronization, respectively, were responsible for the observed cell killing at 0.8 kBq/ml radio-iododeoxyuridine. Conclusion: These data show the successful application of fluorodeoxyuridine that provided increased 125I-iododeoxyuridine Auger radiation cell killing efficacy through S-phase synchronization and high DNA incorporation of radio-iododeoxyuridine.

Passive immunization with neutralizing antibodies interrupts the mouse mammary tumor virus life cycle.

Mouse mammary tumor virus (MMTV) infects the host via mucosal surfaces and exploits the host immune system for systemic spread and chronic infection. We have tested a neutralizing rat monoclonal antibody specific for the retroviral envelope glycoprotein gp52 for its efficiency in preventing acute and chronic mucosal and systemic infection. The antibody completely inhibits the superantigen response and chronic viral infection following systemic or nasal infection. Surprisingly however, the antibody only partially inhibits the early infection of antigen-presenting cells in the draining lymph node. Despite this initially inefficient protection from infection, superantigen-specific B- and T-cell responses and systemic viral spread are abolished, leading to complete clearance of the retroviral infection and hence interruption of the viral life cycle. In conclusion, systemic neutralizing monoclonal antibodies can provide an efficient protection against chronic retroviral amplification and persistence.