Miguel del Nogal Sánchez

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.

Cell cycle control of septin ring dynamics in the budding yeast

Septins constitute a cytoskeletal structure that is conserved in eukaryotes. In Saccharomyces cerevisiae, the Cdc3, Cdc10, Cdc11, Cdc12 and Shs1/Sep7 septins assemble as a ring that marks the cytokinetic plane throughout the budding cycle. This structure participates in different aspects of morphogenesis, such as selection of cell polarity, localization of chitin synthesis, the switch from hyperpolar to isotropic bud growth after bud emergence and the spatial regulation of septation. The septin cytoskeleton assembles at the pre-bud site before bud emergence, remains there during bud growth and duplicates at late mitosis eventually disappearing after cell separation. Using a septin-GFP fusion and time-lapse confocal microscopy, we have determined that septin dynamics are maintained in budding zygotes and during unipolar synchronous growth in pseudohyphae. By means of specific cell cycle arrests and deregulation of cell cycle controls we show that septin assembly is dependent on G1 cyclin/Cdc28-mediated cell cycle signals and that the small GTPase Cdc42, but not Rho1, are essential for this event. However, during bud growth, the septin ring shapes a bud-neck-spanning structure that is unaffected by failures in the regulation of mitosis, such as activation of the DNA repair or spindle assembly checkpoints or inactivation of the anaphase-promoting complex (APC). At the end of the cell cycle, the splitting of the ring into two independent structures depends on the function of the mitotic exit network in which the protein phosphatase Cdc14 participates. Our data support a role of cell cycle control mechanisms in the regulation of septin dynamics to accurately coordinate morphogenesis throughout the budding process in yeast.

Characterization of the CaENG1 Gene Encoding an Endo-1,3-β-Glucanase Involved in Cell Separation in Candida albicans

The Candida albicans CaENG1 gene encoding an endo-1,3-β-glucanase was cloned by screening a genomic library with a DNA probe obtained by polymerase chain reaction using synthetic oligonucleotides designed according to conserved regions found between two Saccharomyces cerevisiae endo-1,3-β-glucanases (Eng1p and Eng2p). The gene contains a 3435-bp open reading frame (ORF), capable of encoding a protein of 1145 amino acids (124,157 Da), that contains no introns. Comparison of the ScEng1p sequence with partial C. albicans genomic sequences revealed the presence of a second protein with sequence similarity (the product of the Ca20C1.22c ORF, which was named CaENG2). Disruption of the CaENG1 gene in C. albicans had no dramatic effects on the growth rate of the strains, but it resulted in the formation of chains of cells, suggesting that the protein is involved in cell separation. Expression of CaENG1 in S. cerevisiae cells afforded a 12-fold increase in the 1,3-β-glucanase activity detected in culture supernatants, showing that the protein has similar enzymatic activity to that of the S. cerevisiae Eng1p. In addition, when the C. albicans protein was expressed under its native promoter in S. cerevisiaeeng1 mutant cells, it was able to complement the separation defect of this mutant, indicating that these two proteins are true functional homologues.

Analysis of the Candida albicans proteome: I. Strategies and applications

The alarming incidence of invasive candidiasis, predominantly among the recent expanding immunocompromised population, the appearance of antifungal-drug resistance, and the lack of specific diagnostic tests for it have demanded more impactful research into Candida albicans pathogenicity. Proteomic approaches can provide accurate clues about its biological complexity. Indeed, initial C. albicans proteome analyses have focused on the understanding of dimorphism, host responses, the cell wall, virulence factors and drug resistance, among others. This review aims to briefly outline the technology available for proteomics-based studies, surveying the main proteomic approaches applied to C. albicans research. Prefractionation techniques, two-dimensional gel electrophoresis and mass spectrometry continue to be the backbone of proteomic projects. Emerging strategies for protein separation, quantification and identification may, however, challenge the pivotal position of 2D-PAGE. Regardless of this, since we are now approaching the completion and annotation of C. albicans genome sequencing, systematic characterization of the proteome of this fungal pathogen, although still in its early stages, heralds an exciting expansion of our knowledge in years to come.

Fast analytical methodology based on mass spectrometry for the determination of volatile biomarkers in saliva.

We report a methodology for the rapid determination of biomarkers in saliva. The method is based on direct coupling of a headspace sampler with a mass spectrometer. The saliva samples are subjected to the headspace generation process, and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of the sample analyzed. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation is required. The following model compounds were studied to check the possibilities of the methodology: methyl tert-butyl ether and styrene as biomarkers of exposure and dimethyl disulfide, limonene, and 2-ethyl-1-hexanol as biomarkers of diseases. The method was applied to the determination of biomarkers in 28 saliva samples: 24 of them were from healthy volunteers, and the others were from patients with different types of illness (including different types of cancer). Additionally, a separative analysis by GC/MS was performed for confirmatory purposes, and both methods provided similar results.

Comparison of PLS and kinetic models for a second-order reaction as monitored using ultraviolet visible and mid-infrared spectroscopy

A second-order reaction between benzophenone and phenylhydrazine to give benzophenone phenylhydrazone was followed using UV/vis and mid-infrared spectroscopic probes. Established kinetic (hard) and partial least squares (soft) modelling chemometrics methods were applied to both datasets in order to compare the information acquired with each probe. To this purpose, an experimental design with 25 samples and a test set with 5 samples were used to build a partial least squares calibration model to predict the concentration profiles of the compounds present in the reaction vessel. In addition, multivariate kinetic modelling was also performed on the spectroscopic data. Using a guess of the rate constant, concentration profiles were estimated. The profiles are then used to calculate the estimated spectroscopic profile, which is compared to the data acquired experimentally. The residual is minimised and the rate constant estimated; this procedure is iterated until convergence. A total of four profiles were obtained for each compound, corresponding to two sets of probes and two sets of models. The results were compared and discussed. It is shown that several different spectroscopic techniques can be used in reaction monitoring, with increasing benefits in terms of information and interpretation of the results. The profiles obtained agreed well which was also demonstrated when comparing the different rate constants obtained.

A method based on microextraction by packed sorbent-programmed temperature vaporizer–fast gas chromatography–mass spectrometry for the determination of aromatic amines in environmental water samples

We report a sensitive method for the determination of 15 aromatic amines in environmental water samples. They have been included in the list of priority pollutants in surface water by the European Union. The method is based on analyte enrichment using microextraction by packed sorbent (MEPS) and later analysis using programmed temperature vaporizer–gas chromatography–mass spectrometry (PTV-GC-MS). All MEPS steps were carried out manually. The detection limits were of the order of nanograms per liter for most of the compounds. The results were compared with those obtained without MEPS using the method exclusively based on direct injection of the sample into the PTV-GC-MS. External calibration in ultrapure water was used in the determination of the compounds studied in five types of water samples (sea, river, tap, influent, and effluent waste water) since no significant matrix effect was found. The results obtained can be considered highly satisfactory and they revealed the presence of aniline in the sea and the influent and effluent waste water samples.

Determination of aromatic and polycyclic aromatic hydrocarbons in gasoline using programmed temperature vaporization-gas chromatography–mass spectrometry

A sensitive method is presented for the fast analysis of three aromatic and six polycyclic aromatic hydrocarbons (biphenyl, 3-methylbiphenyl, 4-methylbiphenyl, fluorene, phenanthrene, fluoranthene, pyrene, 1,2-benz(a)anthracene and chrysene) in gasoline samples. The applicability of a GC device equipped with a programmable temperature vaporizer (PTV) and an MS detector is explored. Additionally, a modular accelerated column heater (MACH) was used to control the temperature of the capillary gas chromatography column. This module can be heated and cooled very rapidly, making total analysis cycle times very short. The proposed method does not require any previous analyte extraction and preconcentration step, as in most methods described to date. Sample preparation is reduced to simply diluting the gasoline samples in methanol. This reduces the experimental errors associated with this step of the analytical process. By using sampling injection in the solvent vent mode, and through choice of a suitable temperature, the lightest major components of the gasoline were removed. Moreover, use of a liner packed with Tenax-TA allowed the compounds of interest to be retained during the process. This working strategy could be extended to other groups of compounds through the choice of different venting temperatures. In this way, a large part of the gasoline components are eliminated, the life of the liner is prolonged, and it is possible to inject sample volumes that will not saturate the chromatographic column. The limits of detection ranged from 0.61 microg/L (pyrene) to 6.1 microg/L (biphenyl), and precision (measured as the relative standard deviation) was equal to or lower than 7.3%. The method was applied to the determination of analytes in gasoline samples and the results obtained can be considered highly satisfactory.

Factors affecting signal intensity in headspace mass spectrometry for the determination of hydrocarbon pollution in beach sands

One of the main limitations to the use of direct coupling of headspace mass spectrometry (HS-MS) for the quantitative determination of analytes in a sample is related to factors affecting the signal intensity. The importance of strategies aimed at compensating this problem is considerable in the case of classification, and is indeed critical as regards the problems involved in quantification. This paper reports the effects of the different factors affecting HS-MS signal intensity in the quantification of the pollution of beach sands by hydrocarbons—the matrix effect, signal instability over time and nature of the different pollutants present in the polluted sands—and proposes possible solutions. Signal instability was solved by using a multiplicative calibration transfer algorithm. A three-factor Box–Behnken experimental design was used to study the matrix effect, mainly as regards the moisture of the samples, and the results are discussed.

Sensitivity Enhancement in the Determination of Volatile Biomarkers in Saliva Using a Mass Spectrometry-Based Electronic Nose with a Programmed Temperature Vaporizer

With a view to improving the sensitivity of direct coupling of a headspace sampler (HS) with a mass spectrometer (MS), here we propose the use of a programmed temperature vaporizer (PTV) in solvent-vent injection mode before the sample is introduced into the MS. This preconcentration scheme has been used for some time in many methods based on gas chromatography (GC), but to the best of our knowledge it has not yet been used in an electronic nose based on MS. The increase in the S/N ratio with the proposed instrumental configuration (HS-PTV/MS) lies between 6.9- and 22-fold. The main advantage of using this injector lies in the fact that it does not involve time-consuming steps. To check the possibilities of this methodology, saliva samples from healthy volunteers and patients with different types of illnesses (including some types of cancer) were analyzed. None of the compounds studied was detected in the samples corresponding to the healthy volunteers. One or more biomarkers, at levels ranging from 13 to 500 μg/L, were found in five of the samples from the patients. Additionally, separative analysis by HS-PTV-GC/MS was performed for confirmatory purposes and both methods provided similar results. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required.