Visualizing the spatiotemporal dynamics of DNA damage in budding yeast.

Fluorescence microscopy has enabled the analysis of both the spatial distribution of DNA damage and its dynamics during the DNA damage response (DDR). Three microscopic techniques can be used to study the spatiotemporal dynamics of DNA damage. In the first part we describe how we determine the position of DNA double-strand breaks (DSBs) relative to the nuclear envelope. The second part describes how to quantify the co-localization of DNA DSBs with nuclear pore clusters, or other nuclear subcompartments. The final protocols describe methods for the quantification of locus mobility over time.

Photocatalytic Activity of Nanostructured Anatase Coatings Obtained by Cold Gas Spray

This article describes a photocatalytic nanostructured anatase coating deposited by cold gas spray (CGS)supported on titanium sub-oxide (TiO22x) coatings obtained by atmospheric plasma spray (APS) onto stainless steel cylinders. The photocatalytic coating was homogeneous and preserved the composition and nanostructure of the starting powder. The inner titanium sub-oxide coating favored the deposition of anatase particles in the solid state. Agglomerated nano-TiO2 particles fragmented when impacting onto the hard surface of the APS TiO22x bond coat. The rough surface provided by APS provided an ideal scenario for entrapping the nanostructured particles, which may be adhered onto the bond coat due to chemical bonding; a possible bonding mechanism is described. Photocatalytic experiments showed that CGS nano-TiO2 coating was active for photodegrading phenol and formic acid under aqueous conditions. The results were similar to the performance obtained by competitor technologies and materials such as dip-coating P25 photocatalysts. Disparity in the final performance of the photoactive materials may have been caused by differences in grain size and the crystalline composition of titanium dioxide.

Environmental control of the Pom1-dependent cell-size regulation pathway in fission yeast

Cells couple their growth and division rate in response to nutrient availability to maintain a constant size. This co-ordination happens either at the G1-S or the G2-M transition of the cell cycle. In the rod-shaped fission yeast, size regulation happens at the G2-M transition prior to mitotic commitment. Recent studies have focused on the role of the DYRK-family protein kinase Pom1, which forms gradients emanating from cell poles and inhibits the mitotic activator kinase Cdr2, present at the cell middle. Pom1 was proposed to inhibit Cdr2 until cells reached a critical size before division. However when and where Pom1 inhibits Cdr2 is not clear as medial Pom1 levels do not change during cell elongation. Here I show that Pom1 gradients are susceptible to environmental changes in glucose. Specifically, upon glucose limitation, Pom1 re-localizes from the poles to the cell sides where it delays mitosis through regulating Cdr2. This re-localization occurs due to microtubule de- stabilization and lateral catastrophes leading to transient deposition of the Pom1 gradient nucleator Tea4 along the cell cortex. As Tea4 localization to cell sides is sufficient to recruit Pom1, this explains the mechanism of Pom1 re-localization. Microtubule destabilization and consequently Tea4 and Pom1 spread depends on the activity of the cAMP-dependent Protein Kinase A (PKA/Pka1), as pka1 mutant cells have stable microtubules and retain polar Tea4 and Pom1 under limited glucose. PKA signaling negatively regulates the microtubule rescue factor CLASP/Cls1, thus reducing its ability to stabilize microtubules. Thus PKA signaling tunes CLASP activity to promote microtubule de-stabilization and Pom1 re-localization upon glucose limitation. I show that the side-localized Pom1 delays mitosis and balances the role of the mitosis promoting, mitogen-associated protein kinase (MAPK) protein Sty1. Thus Pom1 re-localization may serve to buffer cell size upon glucose limitation. -- Afin de maintenir une taille constante, les cellules régulent leur croissance ainsi que leur taux de division selon les nutriments disponibles dans le milieu. Dans la levure fissipare, cette régulation de la taille précède l'engagement mitotique et se fait à la transition entre les phases G2 à M du cycle cellulaire. Des études récentes se sont focalisées sur le rôle de la protéine Pom1, membre de la famille des DYRK kinase. Celle-ci forme un gradient provenant des pôles de la cellule et inhibe l'activateur mitotique Cdr2 présent au centre de la cellule. Le model propose que Pom1 inhibe Cdr2 jusqu'à atteindre une taille critique avant la division. Cependant quand et à quel endroit dans la cellulle Pom1 inhibe Cdr2 n'était pas clair car les niveaux médians de Pom1 ne changent pas au cours de la l'élongation des cellules. Dans cette étude, je montre que les gradients de Pom1 sont sensibles aux changements environnementaux du taux de glucose. Plus spécifiquement, en conditions limitantes de glucose, Pom1 se relocalise des pôles de la cellule pour se distribuer sur les côtés de celle-ci. Par conséquent, un délai d'entrée en mitose est observé dû à l'inhibition Cdr2 par Pom1. Cette délocalisation est due à la déstabilisation des microtubules qui va conduire à une déposition transitoire de Tea4, le nucléateur du gradient de Pom1, tout au long du cortex de la cellule. Comme la localisation de Tea4 sur les côtés de la cellule est suffisante pour recruter la protéine Pom1, ceci explique le mécanisme de relocalisation de celle-ci. La déstabilisation des microtubules et par conséquent la diffusion de Tea4 et Pom1 dépendent de l'activité de la protéine kinase A dépendante de l'AMP cyclique (PKA/Pka1). En absence de pka1, la stabilité des microtubules n'est pas affectée ce qui permet la rétention de Tea4 et Pom1 aux pôles de la cellule même en conditions limitantes de glucose. La signalisation via PKA régule négativement le facteur de sauvetage des microtubules CLASP/Cls1 et permet donc de réduire sa fonction de déstabilisation des microtubules. Ainsi la signalisation via PKA affine l'activité des CLASP pour promouvoir la déstabilisation des microtubules et la relocalisation de Pom1 en conditions limitantes de glucose. Je montre que la localisation sur les côtés retarde l'entrée en mitose et compense l'action de la protéine Sty1, connue pour être une MAPK qui induit l'entrée en mitose. Ainsi, la relocalisation de Pom1 pourrait servir à tamponner la taille de la cellule en condition limitantes de glucose. -- Various cell types in the environment such as bacterial, plant or animal cells have a distinct cellular size. Maintaining a constant cell size is important for fitness in unicellular organisms and for diverse functions in multicellular organisms. Cells regulate their size by coordinating their growth rate to their division rate. This coupling is important otherwise cells would get progressively smaller or larger after each successive cell cycle. In their natural environment cells may face fluctuations in the available nutrient supply. Thus cells have to coordinate their division rate to the variable growth rates shown under different nutrient conditions. During my PhD, I worked with a single-celled rod shaped yeast called the fission yeast. These cells are longer when the nutrient supply is abundant and shorter when the nutrient supply is scarce. A protein that senses changes in the external carbon source (glucose) is called Protein Kinase A (PKA). The rod shape of fission yeast cells is maintained thanks to a structural backbone called the cytoskeleton. One of the components of this backbone is called microtubules, which are small tube like structures spanning the length of the cell. They transport a protein called Tea4, which in turn is important for the proper localization of another protein Pom1 to the cell ends. Pom1 helps to maintain proper shape and size of these rod shaped yeast cells. My thesis work showed that upon reduction in the external nutrient (glucose) levels, microtubules become less stable and show an alteration in their organization. A significant percentage of the microtubules contact the side of the cell instead of touching only the cell tip. This leads to the spreading of the protein Pom1 away from the tips all around the cell periphery. This helps fission yeast cells to maintain the proper size required under these conditions of limited glucose supply. I further showed that the protein PKA regulates microtubule stability and organization and thus Pom1 spreading and maintenance of proper cell size. Thus my work led to the discovery of a novel pathway by which fission yeast cells maintain their size under limited supply of glucose. -- Divers types cellulaires dans l'environnement tels que les bactéries, les plantes ou les cellules animales ont une taille précise. Le maintien d'une taille cellulaire constante est importante pour le fitness des organismes unicellulaire ainsi que pour multiples fonctions dans les organismes multicellulaires. Les cellules régulent leur taille en coordonnant le taux de croissance avec le taux de division. Ce couplage est essentiel sinon les cellules deviendraient progressivement plus petites ou plus grandes après chaque cycle cellulaire. Dans leur habitat naturels les cellules peuvent faire face a des fluctuations dans le taux de nutriment disponible. Les cellules doivent donc coordonner leur taux de division aux taux variables de croissances perçus dans les différentes conditions nutritionnels. Pendant ma thèse, j'ai travaillée sur une levure unicellulaire, en forme de bâtonnet, nommé levure fissipare ou levure de fission. La taille de ces cellules est plus grande quand le taux de nutriments est grand et plus courte quand celui-ci est plus faible. Une protéine qui perçoit les changements dans le taux externe de la source de carbone (glucose) est nommée PKA pour protéine kinase A. La forme en bâtonnet de la cellule est due aux caractères structuraux du cytosquelette. Une composante importante de ce cytosquelette sont les microtubules, dont la structures ressemble à des petit tubes qui vont d'un bout à l'autre de la cellule. Ces microtubules transportent une protéine importante nommée Tea4 qui à leur tour importante pour la bonne localisation d'une autre protéine Pom1 aux extrémités de la cellule. La protéine Pom1 aide à maintenir la taille appropriée des levures fissipares. Mon travail de thèse a montré qu'en présence de taux faible de nutriments (glucose) les microtubules deviennent de moins en moins stables et montrent une désorganisation globale. Un pourcentage significatif des microtubules touche les côtés de la cellule aux lieu d'atteindre uniquement les extrémités. Ceci a pour conséquence une diffusion de Pom1 tout au long du cortex de la cellule. Ceci aide les levures fissipares à maintenir la taille appropriée pendant ce stress nutritionnel. De plus, je montre que PKA régule la stabilité et l'organisation des microtubules et par conséquent la diffusion de Pom1 et le maintien d'une taille constante. En conclusion, mon travail a conduit à la découverte d'un nouveau mécanisme par lequel la levure fissipare maintient sa taille dans des conditions limitantes en glucose.

Patient-adapted treatment for prosthetic hip joint infection.

Hip joint replacement is 1 of the most successful surgical procedures of the last century and the number of replacements implanted is steadily growing. An infected hip arthroplasty is a disaster, it leads to patient suffering, surgeon's frustration and significant costs to the health system. The treatment of an infected hip replacement is challenging, healing rates can be low, functional results poor with decreased patient satisfaction. However, if a patient-adapted treatment of infected hip joints is used a success rate of above 90% can be obtained.Patient-adapted treatment is based on 5 important concepts: teamwork; understanding the biofilm; diagnostic accuracy; correct definition and classification of PJI; and patient-tailored treatment.This review presents a patient-adapted treatment strategy to prosthetic hip infection. It incorporates the best aspects of the single and staged surgical strategies and promotes the short interval philosophy for the 2-stage approach.

Tackling Societal Challenges Related to Ageing and Transport Transition: An Introduction to Philosophical Principles of Causation Adapted to the Biopsychosocial Model

In geriatrics, driving cessation is addressed within the biopsychosocial model. This has broadened the scope of practitioners, not only in terms of assessing fitness to drive, but also by helping to maintain social engagements and provide support for transport transition. Causes can be addressed at different levels by adapting medication, improving physical health, modifying behaviour, adapting lifestyle, or bringing changes to the environment. This transdisciplinary approach requires an understanding of how different disciplines are linked to each other. This article reviews the philosophical principles of causality between fields and provides a framework for understanding causality within the biopsychosocial model. Understanding interlevel constraints should help practitioners overcome their differences, and favor transversal approaches to driving cessation.

Negative feedback regulation of calcineurin-dependent Prz1 transcription factor by the CaMKK-CaMK1 axis in fission yeast

Calcium signals trigger the translocation of the Prz1 transcription factor from the cytoplasm to the nucleus. The process is regulated by the calciumactivated phosphatase calcineurin, which activates Prz1 thereby maintaining active transcription during calcium signalling. When calcium signalling ceases, Prz1 is inactivated by phosphorylation and exported to the cytoplasm. In budding yeast and mammalian cells, different kinases have been reported to counter calcineurin activity and regulate nuclear export. Here, we show that the Ca2+/calmodulin-dependent kinase Cmk1 is first phosphorylated and activated by the newly identified kinase CaMKK2 homologue, Ckk2, in response to Ca2+. Then, active Cmk1 binds, phosphorylates and inactivates Prz1 transcription activity whilst at the same time cmk1 expression is enhanced by Prz1 in response to Ca2+. Furthermore, Cdc25 phosphatase is also phosphorylated by Cmk1, inducing cell cycle arrest in response to an increase in Ca2+. Moreover, cmk1 deletion shows a high tolerance to chronic exposure to Ca2+, due to the lack of cell cycle inhibition and elevated Prz1 activity. This work reveals that Cmk1 kinase activated by the newly identified Ckk2 counteracts calcineurin function by negatively regulating Prz1 activity which in turn is involved in activating cmk1 gene transcription. These results are the first insights into Cmk1 and Ckk2 function in Schizosaccharomyces pombe.

Enzymes of yeast polyphosphate metabolism: structure, enzymology and biological roles.

Inorganic polyphosphate (polyP) is found in all living organisms. The known polyP functions in eukaryotes range from osmoregulation and virulence in parasitic protozoa to modulating blood coagulation, inflammation, bone mineralization and cellular signalling in mammals. However mechanisms of regulation and even the identity of involved proteins in many cases remain obscure. Most of the insights obtained so far stem from studies in the yeast Saccharomyces cerevisiae. Here, we provide a short overview of the properties and functions of known yeast polyP metabolism enzymes and discuss future directions for polyP research.

Microscopy of Fission Yeast Sexual Lifecycle.

The fission yeast Schizosaccharomyces pombe has been an invaluable model system in studying the regulation of the mitotic cell cycle progression, the mechanics of cell division and cell polarity. Furthermore, classical experiments on its sexual reproduction have yielded results pivotal to current understanding of DNA recombination and meiosis. More recent analysis of fission yeast mating has raised interesting questions on extrinsic stimuli response mechanisms, polarized cell growth and cell-cell fusion. To study these topics in detail we have developed a simple protocol for microscopy of the entire sexual lifecycle. The method described here is easily adjusted to study specific mating stages. Briefly, after being grown to exponential phase in a nitrogen-rich medium, cell cultures are shifted to a nitrogen-deprived medium for periods of time suited to the stage of the sexual lifecycle that will be explored. Cells are then mounted on custom, easily built agarose pad chambers for imaging. This approach allows cells to be monitored from the onset of mating to the final formation of spores.

Setting priorities in clinical and health services research: Properties of an adapted and updated method

Objectives: The objectives of this study is to review the set of criteria of the Institute of Medicine (IOM) for priority-setting in research with addition of new criteria if necessary, and to develop and evaluate the reliability and validity of the final priority score. Methods: Based on the evaluation of 199 research topics, forty-five experts identified additional criteria for priority-setting, rated their relevance, and ranked and weighted them in a three-round modified Delphi technique. A final priority score was developed and evaluated. Internal consistency, test–retest and inter-rater reliability were assessed. Correlation with experts’ overall qualitative topic ratings were assessed as an approximation to validity. Results: All seven original IOM criteria were considered relevant and two new criteria were added (“potential for translation into practice”, and “need for knowledge”). Final ranks and relative weights differed from those of the original IOM criteria: “research impact on health outcomes” was considered the most important criterion (4.23), as opposed to “burden of disease” (3.92). Cronbach’s alpha (0.75) and test–retest stability (interclass correlation coefficient = 0.66) for the final set of criteria were acceptable. The area under the receiver operating characteristic curve for overall assessment of priority was 0.66. Conclusions: A reliable instrument for prioritizing topics in clinical and health services research has been developed. Further evaluation of its validity and impact on selecting research topics is required

Calculation of the critical crack size for cold form rectangular hollow section tube (CRHS) under bending load at -40º C temperature

To predict the capacity of the structure or the point which is followed by instability, calculation of the critical crack size is important. Structures usually contain several cracks but not necessarily all of these cracks lead to failure or reach the critical size. So, defining the harmful cracks or the crack size which is the most leading one to failure provides criteria for structure’s capacity at elevated temperature. The scope of this thesis was to calculate fracture parameters like stress intensity factor, the J integral and plastic and ultimate capacity of the structure to estimate critical crack size for this specific structure. Several three dimensional (3D) simulations using finite element method by Ansys program and boundary element method by Frank 3D program were carried out to calculate fracture parameters and results with the aid of laboratory tests (loaddisplacement curve, the J resistance curve and yield or ultimate stress) leaded to extract critical size of the crack. Two types of the fracture which is usually affected by temperature, Elastic and Elasti-Plastic fractures were simulated by performing several linear elastic and nonlinear elastic analyses. Geometry details of the weldment; flank angle and toe radius were also studied independently to estimate the location of crack initiation and simulate stress field in early stages of crack extension in structure. In this work also overview of the structure’s capacity in room temperature (20 ºC) was studied. Comparison of the results in different temperature (20 ºC and -40 ºC) provides a threshold of the structure’s behavior within the defined range.

Xylitol from rice husks by acid hydrolysis and Candida yeast fermentation

An investigation was conducted into the production of xylose by acid hydrolysis of rice husks and its subsequent bioconversion to xylitol. The parameters were optimised using the response surface methodology. The fermentation stage took place with the aid of the yeast species Candida guilliermondii and Candida tropicalis. An evaluation of the influence of several biomass pre-treatments was also performed. The effects of the acid concentration and hydrolysate pH on xylitol global yield were also assessed, and the highest yield of xylitol was 64.0% (w/w). The main products, xylose and xylitol, were identified and quantified by means of liquid chromatography.

EVALUATION OF A BUFFERED SOLID PHASE DISPERSION PROCEDURE ADAPTED FOR PESTICIDE ANALYSES IN THE SOIL MATRIX

An evaluation of the pesticides extracted from the soil matrix was conducted using a citrate-buffered solid phase dispersion sample preparation method (QuEChERS). The identification and quantitation of pesticide compounds was performed using gas chromatography-mass spectrometry. Because of the occurrence of the matrix effect in 87% of the analyzed pesticides, the quantification was performed using matrix-matched calibration. The method's quantification limits were between 0.01 and 0.5 mg kg-1. Repeatability and intermediate precision, expressed as a relative standard deviation percentage, were less than 20%. The recoveries in general ranged between 62% and 99%, with a relative standard deviation < 20%. All the responses were linear, with a correlation coefficient (r) ≥0.99.