Novel acid phosphatase in Candida glabrata suggests selective pressure and niche specialization in the phosphate signal transduction pathway.

Evolution through natural selection suggests unnecessary genes are lost. We observed that the yeast Candida glabrata lost the gene encoding a phosphate-repressible acid phosphatase (PHO5) present in many yeasts including Saccharomyces cerevisiae. However, C. glabrata still had phosphate starvation-inducible phosphatase activity. Screening a C. glabrata genomic library, we identified CgPMU2, a member of a three-gene family that contains a phosphomutase-like domain. This small-scale gene duplication event could allow for sub- or neofunctionalization. On the basis of phylogenetic and biochemical characterizations, CgPMU2 has neofunctionalized to become a broad range, phosphate starvation-regulated acid phosphatase, which functionally replaces PHO5 in this pathogenic yeast. We determined that CgPmu2, unlike ScPho5, is not able to hydrolyze phytic acid (inositol hexakisphosphate). Phytic acid is present in fruits and seeds where S. cerevisiae grows, but is not abundant in mammalian tissues where C. glabrata grows. We demonstrated that C. glabrata is limited from an environment where phytic acid is the only source of phosphate. Our work suggests that during evolutionary time, the selection for the ancestral PHO5 was lost and that C. glabrata neofunctionalized a weak phosphatase to replace PHO5. Convergent evolution of a phosphate starvation-inducible acid phosphatase in C. glabrata relative to most yeast species provides an example of how small changes in signal transduction pathways can mediate genetic isolation and uncovers a potential speciation gene.

Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation-induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants.

Rockfall monitoring by Terrestrial Laser Scanning ¿ case study of the basaltic rock face at Castellfollit de la Roca (Catalonia, Spain)

This case study deals with a rock face monitoring in urban areas using a Terrestrial Laser Scanner. The pilot study area is an almost vertical, fifty meter high cliff, on top of which the village of Castellfollit de la Roca is located. Rockfall activity is currently causing a retreat of the rock face, which may endanger the houses located at its edge. TLS datasets consist of high density 3-D point clouds acquired from five stations, nine times in a time span of 22 months (from March 2006 to January 2008). The change detection, i.e. rockfalls, was performed through a sequential comparison of datasets. Two types of mass movement were detected in the monitoring period: (a) detachment of single basaltic columns, with magnitudes below 1.5 m3 and (b) detachment of groups of columns, with magnitudes of 1.5 to 150 m3. Furthermore, the historical record revealed (c) the occurrence of slab failures with magnitudes higher than 150 m3. Displacements of a likely slab failure were measured, suggesting an apparent stationary stage. Even failures are clearly episodic, our results, together with the study of the historical record, enabled us to estimate a mean detachment of material from 46 to 91.5 m3 year¿1. The application of TLS considerably improved our understanding of rockfall phenomena in the study area.

Ammonium Phosphate/Fly Ash Road Base Construction, HR-294, 1993

The objective of this research project was to evaluate the construction and service performance of ammonium phosphate/fly ash (APFA) treated base courses of crushed fines and/or unprocessed sand. Specific test results related to construction of the test sections were included in the 1987 construction report by Iowa State University. The performance of the experimental sections is dealt with in this final report. This 1986 project demonstrated that in all cases the control sections utilizing a Type B base experienced dramatically less cracking in the surface than the APFA treated base sections. The cost per mix and subsequent surface maintenance costs for the APFA base sections, especially those having a substantial amount of limestone, were higher than the Type B base control sections. This type of construction may prove to be economical only when petroleum product costs escalate.

Members of the PHO1 gene family show limited functional redundancy in phosphate transfer to the shoot, and are regulated by phosphate deficiency via distinct pathways.

The PHO1 family comprises 11 members in Arabidopsis thaliana. In order to decipher the role of these genes in inorganic phosphate (Pi) transport and homeostasis, complementation of the pho1 mutant, deficient in loading Pi to the root xylem, was determined by the expression of the PHO1 homologous genes under the control of the PHO1 promoter. Only PHO1 and the homologue PHO1;H1 could complement pho1. The PHO1;H1 promoter was active in the vascular cylinder of roots and shoots. Expression of PHO1;H1 was very low in Pi-sufficient plants, but was strongly induced under Pi-deficient conditions. T-DNA knock-out mutants of PHO1;H1 neither showed growth defects nor alteration in Pi transport dynamics, or Pi content, compared with wild type. However, the double mutant pho1/pho1;h1 showed a strong reduction in growth and in the capacity to transfer Pi from the root to the shoot compared with pho1. Grafting experiments revealed that phenotypes associated with the pho1 and pho1/pho1;h1 mutants were linked to the lack of gene expression in the root. The increased expression of PHO1;H1 under Pi deficiency was largely controlled by the transcription factor PHR1 and was suppressed by the phosphate analogue phosphite, whereas the increase of PHO1 expression was independent of PHR1 and was not influenced by phosphite. Together, these data reveal that although transfer of Pi to the root xylem vessel is primarily mediated by PHO1, the homologue PHO1;H1 also contributes to Pi loading to the xylem, and that the two corresponding genes are regulated by Pi deficiency by distinct signal transduction pathways.

Regional deterministic characterization of fracture networks and its application to GIS-based rock fall risk assessment

The study investigates the possibility to incorporate fracture intensity and block geometry as spatially continuous parameters in GIS-based systems. For this purpose, a deterministic method has been implemented to estimate block size (Bloc3D) and joint frequency (COLTOP). In addition to measuring the block size, the Bloc3D Method provides a 3D representation of the shape of individual blocks. These two methods were applied using field measurements (joint set orientation and spacing) performed over a large field area, in the Swiss Alps. This area is characterized by a complex geology, a number of different rock masses and varying degrees of metamorphism. The spatial variability of the parameters was evaluated with regard to lithology and major faults. A model incorporating these measurements and observations into a GIS system to assess the risk associated with rock falls is proposed. The analysis concludes with a discussion on the feasibility of such an application in regularly and irregularly jointed rock masses, with persistent and impersistent discontinuities.

Microtubule-associated protein 1B binds glyceraldehyde-3-phosphate dehydrogenase.

Microtubule-associated protein 1B, MAP1B, is a major cytoskeletal protein during brain development and one of the largest brain MAPs associated with microtubules and microfilaments. Here, we identified several proteins that bind to MAP1B via immunoprecipitation with a MAP1B-specific antibody, by one and two-dimensional gel electrophoresis and subsequent mass spectrometry identification of precipitated proteins. In addition to tubulin and actin, a variety of proteins were identified. Among these proteins were glyceraldehyde-3-phosphate dehydrogenase (GAPDH), heat shock protein 8, dihydropyrimidinase related proteins 2 and 3, protein-L-isoaspartate O-methyltransferase, beta-spectrin, and clathrin protein MKIAA0034, linking either directly or indirectly to MAP1B. In particular, GAPDH, a key glycolytic enzyme, was bound in large quantity to the heavy chain of MAP1B in adult brain tissue. In vitro binding studies confirmed a direct binding of GAPDH to MAP1B. In PC12 cells, GAPDH was found in cytoplasm and nuclei and partially co-localized with MAP1B. It disappeared from the cytoplasm under oxidative stress or after a disruption of cytoskeletal elements after colcemid or cytochalasin exposure. GAPDH may be essential in the local energy provision of cytoskeletal structures and MAP1B may help to keep this key enzyme close to the cytoskeleton.

Calcium phosphate transfection generates mammalian recombinant cell lines with higher specific productivity than polyfection.

Transfection with polyethylenimine (PEI) was evaluated as a method for the generation of recombinant Chinese hamster ovary (CHO DG44) cell lines by direct comparison with calcium phosphate-DNA coprecipitation (CaPO4) using both green fluorescent protein (GFP) and a monoclonal antibody as reporter proteins. Following transfection with a GFP expression vector, the proportion of GFP-positive cells as determined by flow cytometry was fourfold higher for the PEI transfection as compared to the CaPO4 transfection. However, the mean level of transient GFP expression for the cells with the highest level of fluorescence was twofold greater for the CaPO4 transfection. Fluorescence in situ hybridization on metaphase chromosomes from pools of cells grown under selective pressure demonstrated that plasmid integration always occurred at a single site regardless of the transfection method. Importantly, the copy number of integrated plasmids was measurably higher in cells transfected with CaPO4. The efficiency of recombinant cell line recovery under selective pressure was fivefold higher following PEI transfection, but the average specific productivity of a recombinant antibody was about twofold higher for the CaPO4-derived cell lines. Nevertheless, no difference between the two transfection methods was observed in terms of the stability of protein production. These results demonstrated the feasibility of generating recombinant CHO-derived cell lines by PEI transfection. However, this method appeared inferior to CaPO4 transfection with regard to the specific productivity of the recovered cell lines.

Fluid-rock interaction during late stages of the Alpine exhumation

Résumé de la thèseLa fracturation des roches au cours de phases compressives ou extensives est un souvent évoquée pour expliquer la circulation de fluide au sein des roches cristallines. Dans le cadre de cette thèse, la circulation des fluides lors de l'exhumation tardive des Alpes a été étudiée en utilisant deux approches différentes: analyses structurales de la déformation fragile d'une part et analyses géochimiques des roches et des minéraux (isotopes stables, datations U/Pb, thermochronologie (U-Th)/He) d'autre part. Cette approche combinée a permis de mieux comprendre l'interaction existante entre les fluides métamorphiques et les fluides météoriques, ainsi que leur interaction avec les roches encaissantes. Le travail a été effectué dans la zone Pennique du Valais suisse.La première partie était focalisée sur la déformation fragile, le but étant de définir les différents types de déformations existantes et de déterminer l'âge relatif des différentes familles de failles. Dans la région d'étude, quatre domaines ont été distingués. Chacun d'eux comportent deux types de structures fragiles, certaines sont minéralisées alors que d'autre non. Au sein de chaque domaine, la direction principale des structures minéralisées correspond à l'orientation des accidents tectoniques majeurs de la région (Aosta- Ranzola Line au Sud, Rhône Line au Nord et Simplon Fault Zone à l'Est), alors que les structures non- minéralisées montrent des orientations plus variables. Ainsi, le premier type de structure est interprété comme résultant d'une dislocation tectonique alors que le deuxième type de structure résulterait d'une dislocation gravitaire locale. Il n'est néanmoins pas possible de classer chronologiquement la formation de ces deux types de structure ni d'attribuer un âge relatif aux changements d'orientation des contraintes majeures.La deuxième étude a été effectuée dans la région de la zone de faille du Simplon. Dans cette zone, la composition isotopique des minéraux ayant cristallisé à l'intérieur des fractures tardives permet de distinguer différents types de circulation de fluide. Les valeurs δ180 du quartz de la roche encaissante ainsi que ceux des veines tardives du bloque inférieur de la faille sont comparables. Ces valeurs indiquent un rééquilibrage et un tamponnage isotopique des fluides tardifs au contact de la roche encaissante lors de la fracturation de cette dernière et de la cristallisation des veines tardives. La même situation est observée dans la partie nord du bloque supérieur ainsi que dans sa partie sud. Ceci n'est néanmoins pas le cas pour la partie centrale du bloque supérieur où les valeurs isotopiques des minéraux dans les veines tardives sont approximativement 3 %o plus basses (avec des valeurs extrêmes négatifs), indiquant une contribution d'eau météorique aux fluides circulant dans les veines. Ces données suggèrent qu'une infiltration d'eau météorique a pu avoir lieu dans le bloque supérieur, où la fracturation des roches est plus intensive car le déplacement relatif le long de la faille y fut plus important, et la température maximale du métamorphisme plus basse. La troisième contribution traite de la géo-thermochronologie de la zone de contact entre la klippe de la Dent Blanche et la nappe de Tsaté. De petits zircons euhédraux ont été trouvés dans un plan de faille minéralisé (parallèle à la Faille du Rhône, voir première partie de l'étude), riche en hématite et quartz, de la zone d'étude. Les analyses U/Pb donnent des âges radiométriques autour de 270 - 280 Ma aux zircons extraits de la minéralisation ainsi que ceux extraits de la roche encaissante, ce qui correspond à l'âge de la nappe de la Dent Blanche et non celui de la nappe du Tsaté qui est elle-même classiquement interprétée comme une ophiolite Jurassique de l'Océan Liguro-Piémontais. Ces données suggèrent que les zircons contenus dans la veine ont été hérités de la roche encaissante. Les résultats (U-Th)/He indiquent un âge de refroidissement différent pour la roche encaissante (25.5 ± 2.0 Ma) que celui de la minéralisation (17.7 ±1.4 Ma). Le thermomètre isotopique quartz-hématite indique une température d'équilibre, et donc de mise en place de la minéralisation, d'environ 170 °C, température très proche de la température de -180 °C de fermeture du zircon pour le système (U-Th)/He. Ceci suggère que l'âge de refroidissement des zircons de la minéralisation correspond aussi à l'âge de formation de la faille.Thesis abstractFluid circulation in fractured rocks is a common process in geology, and it is generally the consequence of faulting and fracturing during both tectonic compression and extension. This thesis is focused on fluid circulation during late stages of the Alpine exhumation. After a structural analysis of the late brittle deformation of the studied samples, several analytical methods (stable isotope investigations, U/Pb radiometric dating, (U-Th)/He thermochronology) have been applied to understand the interaction of metamorphic and meteoric fluids with one another as well as with the host rock. This thesis is articulated around three study directions. All studies were conducted in the Penninic Zone of the Valais, Switzerland. The first study deals with late, brittle deformation and focuses on the different deformation styles and on the relative age of the different families of fractures. In order to do this, late brittle structures observed in four different domains have been subdivided as a function of the existence (or not) and type of mineralization. Comparisons between mineralized and non-mineralized strike directions for all four domains show that mineralized structures follow the strike orientation of major tectonic movements indicated in the Penninic Zone of the Valais (Aosta-Ranzola Line to the S, Rhône Line to the Ν and Simplon Fault Zone to the E), whereas non-mineralized fractures have a more variable strike orientation. This difference could be interpreted as indicative of tectonic-related faulting (mineralized structures) vs. local, collapse-related faulting (non-mineralized fractures), but it is not strong enough to indicate a relative age of the late brittle structures, and/or a change in the orientation of the strain field in post-Miocene times. The second studied area is focused on the Simplon Fault Zone (SFZ). Stable isotope analyses of minerals filling these late fractures indicate that there are two different fluid circulation systems in the footwall and hanging wall of the SFZ. In the footwall, δ180 values of quartz from both the host rock and the late veins range from +10 %o to +12 %o. This is consistent with buffering of circulating fluids by the host rock during fracturing and vein precipitation. In the hanging wall, δΙ80 values for quartz crystals from the host rock and the late veins are similar in both the northern and southern parts of the detachment that are both affected by the same degree of metamorphism (greenschist to the Ν and amphibolite to the S). This is not the case in the central part of the SFZ, where there is a jump from amphibolite facies in the footwall to greenschist facies in the hanging wall. δ,80 values for quartz from the hanging wall late veins are approximately 3.0 %o lower (down to negative values in some cases) than the values observed in the footwall These data suggest that infiltration of meteoric water may have occurred in the most fractured parts of the hanging wall, where relative displacement on the SFZ was the greatest and the peak temperature lower. In the less fractured footwall the δ180 values reflect a host rock-buffered system.The third study is focused on geo-thermochronology at the contact between the Dent Blanche nappe and the Tsaté nappe where small, euhedral zircons were found in a hematite- and quartz-rich mineralization on a late normal fault plane parallel to the Rhône Line (see first part of the study). U/Pb analysis indicates that the zircons - both in the late mineralization and in the host rock - have absolute radiometric ages clustering around 270 - 280 Ma, which is the accepted age for intrusive rocks from the Austroalpine Dent Blanche units but not for the Tsaté nappe. The latter is classically interpreted as an ophiolitic remnant of the Jurassic Liguro-Piemontais Ocean. U/Pb analyses suggest that zircons in late mineralization are all inherited from the host rock; however, results of (U-Th)/He analyses indicate that cooling ages for the host rocks are different to the cooling ages for the zircons in late mineralization. Indeed, the calculated cooling age for the Arolla gneiss is 25.5 ± 2.0 Ma, whilst the cooling age for the associated mineralized fault plane is 17.7 ±1.4 Ma. Oxygen stable isotope fractionation between quartz and hematite in the same late mineralization corresponds to temperatures of about 170 °C. The proximity of the calculated emplacement temperature for the mineralization and the lower accepted closure temperature for zircon in the (U-Th)/He system (-180 °C) imply that the age of 17.7 ± 1.4 Ma can also be interpreted as the formation age of this late brittle fault.Résumé grand publicLa circulation des fluides dans les roches fracturées est typique de nombreux processus géologiques, et très souvent est la conséquence de la fracturation des roches. Cette thèse aborde la question de la circulation des fluides pendant les dernières phases du soulèvement des Alpes. Après une analyse structurale de la fracturation directement sur le terrain, plusieurs méthodes géochimiques ont été appliquées pour comprendre l'interaction entre les différents fluides circulants, et avec leur propre roche mère. L'étude, concentrée sur trois directions principales, a été conduite dans la zone Pennique du Valais suisse. La première partie traite de la déformation cassante dans le secteur cité. L'analyse détaillée des fractures a permis de les subdiviser en structures minéralisées et non-minéralisées, sur quatre domaines différents. La comparaison entre les directions des structures minéralisées et non-minéralisées a permis de montrer que les premières suivent l'orientation des accidents tectoniques majeurs de la région, alors que les structures non- minéralisées ont une orientation plus variable. Cette différence pourrait être interprétée comme indication d'une dislocation tectonique (structures minéralisées) contre une dislocation gravitaire locale (structures non-minéralisées), mais elle n'est pas assez forte pour indiquer un âge relatif des structures tardives et/ou un changement de l'orientation des contraintes après -20 Ma vers le présent.A partir de ces observations, la deuxième étude est concentrée dans la région de la faille du Simplon. Les analyses géochimiques sur les minéraux remplissant les structures tardives indiquent qu'il y a deux différents systèmes de circulation des fluides dans les deux parties (toit et mur) de la faille. Dans le mur, les valeurs isotopiques des minéraux cristallisés à partir d'un fluide tardif sont les mêmes de ceux de la roche mère, donc il y a eu rééquilibration chimique entre fluide et roche pendant la fracturation de cette dernière et la précipitation des minéraux. Dans le toit, les valeurs isotopiques dans la roche mère et dans les minéraux des veines tardives sont comparables dans les parties Ν et S de la faille, où les roches du toit et du mur ont atteint une température maximale - pendant phase prograde de la formation des Alpes - comparable. Au contraire, dans la partie centrale, où le mur a atteint des températures maximales plus élevées par rapport au toit, les valeurs géochimiques des minéralisations tardives du toit sont parfois plus basses que les valeurs observées dans le mur. Ces données suggèrent que l'infiltration de l'eau de surface aurait pu se produire dans la partie plus fracturée du toit, où le déplacement relatif le long de la faille était majeur et les températures maximales mineures. Au contraire, les données géochimiques du mur de la partie centrale indiquent un système isotopique équilibré par la roche mère.La troisième partie de ce travail se base sur l'étude géochimique intégrée des isotopes stables d'Oxygène et radioactifs du Plomb, Uranium, Thorium et Hélium, auprès d'une faille normale minéralisée et des roches de la région à cheval entre deux nappes, la nappe de la Dent Blanche et la nappe de Tsaté. Ici, des petits zircons ont été trouvés dans la minéralisation citée, riche en hématite et quartz. L'analyse radiométrique Uranium/Plomb a montré que les zircons dans la minéralisation et dans les roches autour ont des âges comparables (autour 280 Ma). Cela signifie que les zircons dans la minéralisation tardive ont été hérités de la roche mère pendant la fracturation et la circulation des fluides tardives. De l'autre coté, les résultats des analyses Uranium-Thorium/Hélium indiquent que les âges de refroidissement pour les roches mères sont différents comparés aux âges de refroidissement pour les zircons dans la minéralisation tardive: ces derniers sont plus jeunes d'environ 8 Ma (autour 25 Ma et autour 17 Ma respectivement). Les analyses des isotopes de l'oxygène sur quartz et hématite dans la même minéralisation donnent une température de mise en place de cette dernière d'environ 170° C. La température de fermeture du système chimique des zircons dans le système (Uranium-Thorium)/Hélium est d'environ 180 °C: la proximité de ces deux températures implique que l'âge de refroidissement de la minéralisation tardive peut également être interprété comme âge de formation de la faille.

Evaluation of Crushed Limestone Rock as a Mulch Material, HR-171, 1975

Earthen fills and back slopes resulting from highway building and other construction projects pose problems with respect to erosion stabilization and establishing vegetation cover. Sediments from such slopes create stream pollution while the erosion itself results in maintenance problems. Furthermore, adverse conditions aggravated by erosion prevent satisfactory establishing of vegetative cover. A dense vegetative cover is very effective in controlling erosion but even with optimum weather and soil conditions there is a delay of about 10 weeks between seeding and the establishment of a vegetative cover. Under actual field conditions, 3 months to a year may elapse between completion of construction and establishment of a vegetative cover. A research project was initiated early in 1974 to determine the effectiveness of a rock mulch of crushed limestone aggregates in controlling soil losses on highway construction back slopes in Iowa and to find the influence of such treatments on stand establishment of grasses and legumes.

Thin Asphalt Concrete Pavement on Crushed Rock Base - Cass County, Construction Report, HR-2075, 1997

The road paving cost continues to increase and the backlog of projects waiting for funding is growing. Finding a more cost-effective way to use the available money to pave roads will result in more miles of road being paved with the same amount of money. This project is in Cass County on G35 between US 71 and Norway-Center. It consists of a thin layer of asphalt over a base designed to achieve stability while having some permeability. This project was paved in 1996. An asphalt cement concrete pavement was chosen for the project based on cost, convenience, and historic portland cement concrete problems in Cass County. The new pavement gives quicker access time to farms and residences.

Rock Island Centennial Bridge, Final Report on Construction of the Mississippi River Bridge Between Rock Island, Illinois and Davenport, Iowa, 1945

The Rock Island Centennial Bridge spanning the Mississippi River between Rock Island, Illinois and Davenport, Iowa was opened to traffic on July 12, 1940. It is a thoroughly modern, four-lane highway bridge, adequate in every respect for present day high speed passenger and transport traffic. The structure is ideally situated to provide rapid transit between the business districts of Rock Island and Davenport and serves not only the local or shuttle traffic in the Tri-City Area, but also heavy through motor travel on U.S. Highways 67 and 150. The Centennial Bridge is notable in several respects. The main spans are box girder rib tied arches, a type rather unusual in America and permitting simplicity in design with pleasing appearance. The Centennial Bridge is the only bridge across the Mississippi providing for four lanes of traffic with separation of traffic in each direction. It is a toll bridge operating alongside a free bridge and has the lowest rates of toll of any toll bridge on the Mississippi River. It was financed entirely by the City of Rock Island with no obligation on the taxpayers; there was no federal or state participation in the financing. But perhaps the most outstanding feature of the new bridge is its great need. A few remarks on the communities served by the new structure, the services rendered, and some statistics on cross-river traffic in the Tri-City Area will emphasize the reasons for constructing the Centennial Bridge.