Antifungal drug resistance mechanisms in fungal pathogens from the perspective of transcriptional gene regulation.

Fungi are primitive eukaryotes and have adapted to a variety of niches during evolution. Some fungal species may interact with other life forms (plants, insects, mammals), but are considered as pathogens when they cause mild to severe diseases. Chemical control strategies have emerged with the development of several drugs with antifungal activity against pathogenic fungi. Antifungal agents have demonstrated their efficacy by improving patient health in medicine. However, fungi have counteracted antifungal agents in several cases by developing resistance mechanisms. These mechanisms rely on drug resistance genes including multidrug transporters and drug targets. Their regulation is crucial for the development of antifungal drug resistance and therefore transcriptional factors critical for their regulation are being characterized. Recent genome-wide studies have revealed complex regulatory circuits involving these genetic and transcriptional regulators. Here, we review the current understanding of the transcriptional regulation of drug resistance genes from several fungal pathogens including Candida and Aspergillus species.

Field Evaluation of Cold In-Place Recycling of Asphalt Concrete, HR-303, 1993

The average thickness of the existing asphalt cement concrete (ACC) along route E66 in Tama County was 156 mm (6.13 in.). The rehabilitation strategy called for widening the base using the top 75 mm (3 in.) of the existing ACC by a recycling process involving cold milling and mixing with additional emulsion/rejuvenator. The material was then placed into a widening trench and compacted to match the level of the milled surface. The project had the following results: (1) Cold recycled ACC pavement provided adequate pavement structure for a low volume road; (2) Premature cracking of the ACC in the widened pavement area was caused by compaction of the mix over a saturated subgrade; and (3) Considerably less transverse and longitudinal cracking was observed with 75 mm (3 in.) of cold recycled ACC and a 50 mm (2 in.) hot mix ACC overlay than with a conventional hot mix overlay with no cold recycling. More research should be done on efficient construction procedures and incorporating longer test sections for proper evaluation.

Review of Cold In-Place Recycled Asphalt Concrete Projects, HR-392, 1998

Highway Research Project HR-392 was undertaken to evaluate cold in-place asphalt recycled (CIR) projects in the State of Iowa. The research involved assessment of performance levels, investigation of factors that most influence pavement performance and economy, and development of guidelines for CIR project selection. The performance was evaluated in two ways: Pavement Condition Indices (PCI, U.S. Corps of Engineers) were calculated and overall ratings were given on ride and appearance. A regression analysis was extrapolated to predict the future service life of CIR roads. The results were that CIR roads within the State of Iowa, with less than 2000 annual average daily traffic (AADT), have an average predicted service life of fifteen to twenty-six years. Subgrade stability problems can prevent a CIR project from being successfully constructed. A series of Dynamic Cone Penetrometer (DCP) tests were conducted on a CIR project that experienced varying levels of subgrade failure during construction. Based on this case study, and supporting data, it was determined that the DCP test can be used to evaluate subgrades that have insufficient stability for recycling. Overall, CIR roads in Iowa are performing well. It appears that the development of transverse cracking has been retarded and little rutting has occurred. Contracting agencies must pay special attention to the subgrade conditions during project selection. Because of its performance, CIR is a recommended method to be considered for rehabilitating aged low volume (<2000 AADT) asphalt concrete roads in Iowa.

Probing the role of point mutations in the cyp51A gene from Aspergillus fumigatus in the model yeast Saccharomyces cerevisiae.

Azole-resistant strains of Aspergillus fumigatus have been detected and the underlying molecular mechanisms of resistance characterized. Point mutations in the cyp51A gene have been proved to be related to azole resistance in A. fumigatus clinical strains and with different resistance profiles depending on the amino acid change (G54E, G54V, G54R, G54W, M220V, M220K, M220T, M220I). The aim of this work was to express A. fumigatus cyp51A genes in the yeast Saccharomyces cerevisiae in order to better assess the contribution of each independent amino acid substitution to resistance. A tetracycline regulatable system allowing repression of the endogenous essential ERG11 gene was used. The expression of Aspergillus cyp51A alleles could efficiently restore the absence of ERG11 in S. cerevisiae. In general, S. cerevisiae clones expressing. A. fumigatus cyp51A alleles from azole-resistant isolates showed higher MICs to all azoles tested than those expressing alleles from susceptible isolates. The azole susceptibility profiles obtained in S. cerevisiae upon expression of specific cyp51A alleles recapitulated susceptibility profiles observed from their A. fumigatus origins. In conclusion this work supports the concept that characteristics of specific A. fumigatus cyp51A alleles could be investigated in the heterologous host S. cerevisiae.

The dmf1/mid1 gene is essential for correct positioning of the division septum in fission yeast.

Little is known about the mechanisms that establish the position of the division plane in eukaryotic cells. Wild-type fission yeast cells divide by forming a septum in the middle of the cell at the end of mitosis. Dmf1 mutants complete mitosis and initiate septum formation, but the septa that form are positioned at random locations and angles in the cell, rather than in the middle. We have cloned the dmf1 gene as a suppressor of the cdc7-24 mutant. The dmf1 mutant is allelic with mid1. The gene encodes a novel protein containing a putative nuclear localization signal, and a carboxy-terminal PH domain. In wild-type cells, Dmf1p is nuclear during interphase, and relocates to form a medial ring at the cell cortex coincident with the onset of mitosis. This relocalization occurs before formation of the actin ring and is associated with increased phosphorylation of Dmf1p. The Dmf1p ring can be formed in the absence of an actin ring, but depends on some of the genes required for actin ring formation. When the septum is completed and the cells separate, Dmf1p staining is once again nuclear. These data implicate Dmf1p as an important element in assuring correct placement of the division septum in Schizosaccharomyces pombe cells.

Temporal quantification of MAPK induced expression in single yeast cells.

The quantification of gene expression at the single cell level uncovers novel regulatory mechanisms obscured in measurements performed at the population level. Two methods based on microscopy and flow cytometry are presented to demonstrate how such data can be acquired. The expression of a fluorescent reporter induced upon activation of the high osmolarity glycerol MAPK pathway in yeast is used as an example. The specific advantages of each method are highlighted. Flow cytometry measures a large number of cells (10,000) and provides a direct measure of the dynamics of protein expression independent of the slow maturation kinetics of the fluorescent protein. Imaging of living cells by microscopy is by contrast limited to the measurement of the matured form of the reporter in fewer cells. However, the data sets generated by this technique can be extremely rich thanks to the combinations of multiple reporters and to the spatial and temporal information obtained from individual cells. The combination of these two measurement methods can deliver new insights on the regulation of protein expression by signaling pathways.

Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

Until recently, microbial identification in clinical diagnostic laboratories has mainly relied on conventional phenotypic and gene sequencing identification techniques. The development of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) devices has revolutionized the routine identification of microorganisms in clinical microbiology laboratories by introducing an easy, rapid, high throughput, low-cost, and efficient identification technique. This technology has been adapted to the constraint of clinical diagnostic laboratories and has the potential to replace and/or complement conventional identification techniques for both bacterial and fungal strains. Using standardized procedures, the resolution of MALDI-TOF MS allows accurate identification at the species level of most Gram-positive and Gram-negative bacterial strains with the exception of a few difficult strains that require more attention and further development of the method. Similarly, the routine identification by MALDI-TOF MS of yeast isolates is reliable and much quicker than conventional techniques. Recent studies have shown that MALDI-TOF MS has also the potential to accurately identify filamentous fungi and dermatophytes, providing that specific standardized procedures are established for these microorganisms. Moreover, MALDI-TOF MS has been used successfully for microbial typing and identification at the subspecies level, demonstrating that this technology is a potential efficient tool for epidemiological studies and for taxonomical classification.

Gradation Analysis of Cold Feed and Extracted Bituminuous Mix Samples, MLR-88-2, 1988

Since 1987, the Iowa Department of Transportation has based control of hot asphalt concrete mixes on cold feed gradations. This report presents results of comparisons between cold feed gradations and gradations of aggregate from the same material after it has been processed through the plant and laydown machine. Results are categorized based on mix type, plant type, and method of dust control, in an effort to quantify and identify the factors contributing to those changes. Results of the report are: 1. From the 390 sample comparisons made, aggregate degradation due to asphalt plant processing was demonstrated by an average increase of +0.7% passing the #200 sieve and an average increase in surface area of +1.8 sq. ft. per pound of aggregate. 2. Categories with Type A Mix or Recycling as a sorting criteria generally produced greater degradation than categories containing Type B Mixes and/or plants with scrubbers. 3. None of the averages calculated for the categories should be considered unacceptably high, however, it is information that should be considered when making mix changes in the field, selecting asphalt contents for borderline mix designs, or when evaluating potential mix gradation specification or design criteria changes.

Evaluation of Long-Term Field Performance of Cold In-Place Recycled Roads: Field Distress Survey, TR-502, 2007

Cold in-place recycling (CIR) has become an attractive method for rehabilitating asphalt roads that have good subgrade support and are suffering distress related to non-structural aging and cracking of the pavement layer. Although CIR is widely used, its use could be expanded if its performance were more predictable. Transportation officials have observed roads that were recycled under similar circumstances perform very differently for no clear reason. Moreover, a rational mix design has not yet been developed, design assumptions regarding the structural support of the CIR layer remain empirical and conservative, and there is no clear understanding of the cause-effect relationships between the choices made during the design/construction process and the resulting performance. The objective of this project is to investigate these relationships, especially concerning the age of the recycled pavement, cumulative traffic volume, support conditions, aged engineering properties of the CIR materials, and road performance. Twenty-four CIR asphalt roads constructed in Iowa from 1986 to 2004 were studied: 18 were selected from a sample of roads studied in a previous research project (HR-392), and 6 were selected from newer CIR projects constructed after 1999. This report summarizes the results of a comprehensive program of field distress surveys, field testing, and laboratory testing for these CIR asphalt roads. The results of this research can help identify changes that should be made with regard to design, material selection, and construction in order to lengthen the time between rehabilitation cycles and improve the performance and cost-effectiveness of future recycled roads.

Functional and topological characterization of transcriptional cooperativity in yeast

This work was supported by grants from Spanish Ministry of Science andInnovation (MICINN) BIO2011-22568 & BIO2008-205.

Ripening and quality of 'Laetitia' plums following harvest and cold storage as affected by inhibition of ethylene action

The inhibition of ethylene action by 1-methylcyclopropene (1-MCP) extends shelf and storage life of many climacteric fruits. However, 1-MCP appears to have limited effects on stone fruit depending on specie and cultivar. The effects of 1-MCP on ripening and quality of 'Laetitia' plums were determined during ripening at 23ºC following harvest and cold storage. Japanese plums (Prunus salicina, cv. Laetitia) were harvested at mature pre-climacteric stage, cooled to 2ºC within 36 hours of harvest and then treated with 0, 0.05, 0.10, 0.50 or 1.00 muL L-1 of 1-MCP at 1°C for 24 hours. Following treatment, fruits were either held at 23ºC for 16 days or stored at 1ºC for 50 days. Fruits were removed from cold storage at 10-day intervals and allowed to ripe at 23°C for five days. A delay of climacteric respiration and ethylene production by 1-MCP treatment during ripening following harvest and cold storage was associated to a slow rate of fruit softening. 1-MCP treatment also delayed the loss of titratable acidity and changes of flesh and skin color, whereas it had little or no effect on soluble solids content. 1-MCP effects were concentration- and storage duration-dependent and, generally, a saturation fruit response to 1-MCP occurred between 0.5 and 1.0 muL L-1. During ripening, 1-MCP treated fruits attained quality similar to that of controls. Results indicated that 1-MCP treatment may extend shelf life (23ºC) and storage life (1ºC) of 'Laetitia' plums by approximately six and 20 days, respectively.

Kernel-based Mapping of Meteorological Fields in Complex Orography

Due to the advances in sensor networks and remote sensing technologies, the acquisition and storage rates of meteorological and climatological data increases every day and ask for novel and efficient processing algorithms. A fundamental problem of data analysis and modeling is the spatial prediction of meteorological variables in complex orography, which serves among others to extended climatological analyses, for the assimilation of data into numerical weather prediction models, for preparing inputs to hydrological models and for real time monitoring and short-term forecasting of weather.In this thesis, a new framework for spatial estimation is proposed by taking advantage of a class of algorithms emerging from the statistical learning theory. Nonparametric kernel-based methods for nonlinear data classification, regression and target detection, known as support vector machines (SVM), are adapted for mapping of meteorological variables in complex orography.With the advent of high resolution digital elevation models, the field of spatial prediction met new horizons. In fact, by exploiting image processing tools along with physical heuristics, an incredible number of terrain features which account for the topographic conditions at multiple spatial scales can be extracted. Such features are highly relevant for the mapping of meteorological variables because they control a considerable part of the spatial variability of meteorological fields in the complex Alpine orography. For instance, patterns of orographic rainfall, wind speed and cold air pools are known to be correlated with particular terrain forms, e.g. convex/concave surfaces and upwind sides of mountain slopes.Kernel-based methods are employed to learn the nonlinear statistical dependence which links the multidimensional space of geographical and topographic explanatory variables to the variable of interest, that is the wind speed as measured at the weather stations or the occurrence of orographic rainfall patterns as extracted from sequences of radar images. Compared to low dimensional models integrating only the geographical coordinates, the proposed framework opens a way to regionalize meteorological variables which are multidimensional in nature and rarely show spatial auto-correlation in the original space making the use of classical geostatistics tangled.The challenges which are explored during the thesis are manifolds. First, the complexity of models is optimized to impose appropriate smoothness properties and reduce the impact of noisy measurements. Secondly, a multiple kernel extension of SVM is considered to select the multiscale features which explain most of the spatial variability of wind speed. Then, SVM target detection methods are implemented to describe the orographic conditions which cause persistent and stationary rainfall patterns. Finally, the optimal splitting of the data is studied to estimate realistic performances and confidence intervals characterizing the uncertainty of predictions.The resulting maps of average wind speeds find applications within renewable resources assessment and opens a route to decrease the temporal scale of analysis to meet hydrological requirements. Furthermore, the maps depicting the susceptibility to orographic rainfall enhancement can be used to improve current radar-based quantitative precipitation estimation and forecasting systems and to generate stochastic ensembles of precipitation fields conditioned upon the orography.

Combined effect of natural antimicrobials and high pressure processing to prevent Listeria monocytogenes growth after a cold chain break during storage of cooked ham

The effect of high pressure processing (400 MPa for 10 min) and natural antimicrobials 2 (enterocins and lactate-diacetate) on the behaviour of L. monocytogenes in sliced cooked ham 3 during refrigerated storage (1ºC and 6ºC) was assessed. The efficiency of the treatments after a 4 cold chain break was evaluated. Lactate-diacetate exerted a bacteriostatic effect against L. 5 monocytogenes during the whole storage period (3 months) at 1ºC and 6ºC, even after 6 temperature abuse. The combination of low storage temperature (1ºC), high pressure 7 processing (HPP) and addition of lactate-diacetate reduced the levels of L. monocytogenes 8 during storage by 2.7 log CFU/g. The most effective treatment was the combination of HPP, 9 enterocins and refrigeration at 1ºC, which reduced the population of the pathogen to final counts 10 of 4 MPN/g after 3 months of storage, even after the cold chain break.

Mitochondrial dysfunction increases oxidative stress and decreases chronological life span in fission yeast

Background: Oxidative stress is a probable cause of aging and associated diseases. Reactive oxygen species (ROS) originate mainly from endogenous sources, namely the mitochondria. Methodology/Principal Findings: We analyzed the effect of aerobic metabolism on oxidative damage in Schizosaccharomyces pombe by global mapping of those genes that are required for growth on both respiratory-proficient media and hydrogen-peroxide-containing fermentable media. Out of a collection of approximately 2700 haploid yeast deletion mutants, 51 were sensitive to both conditions and 19 of these were related to mitochondrial function. Twelve deletion mutants lacked components of the electron transport chain. The growth defects of these mutants can be alleviated by the addition of antioxidants, which points to intrinsic oxidative stress as the origin of the phenotypes observed. These respiration-deficient mutants display elevated steady-state levels of ROS, probably due to enhanced electron leakage from their defective transport chains, which compromises the viability of chronologically-aged cells. Conclusion/Significance: Individual mitochondrial dysfunctions have often been described as the cause of diseases or aging, and our global characterization emphasizes the primacy of oxidative stress in the etiology of such processes.