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Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample. The correlative Raman and Brillouin investigation evidences the role of both extracellular polymeric substances and of hydration water in inducing a marked local softening of the biofilm.

A 62-year-old man developed a blood stream infection and meningitis due to Listeria monocytogenes, 20 days after an episode of pseudo-membranous colitis. The patient, hospitalized for the first time for transurethral prostatectomy, was readmitted 20 days later with watery diarrhea. Pseudo-membranous colitis was diagnosed and treated successfully, without testing for Clostridium difficile infection (CDI). After 15 more days, the patient developed again diarrhea, fever and confusion. Hospitalized again, blood and cerebrospinal fluid cultures resulted positive for L. monocytogenes. The patient was treated successfully and a diagnosis of recurrent CDI was confirmed following culture and nucleic acid amplification assays both positive for C. difficile. This is the first report of an invasive listeriosis after CDI underlines the importance of taking greater awareness in complicated blood stream infections that may arise after CDI.

We report the preparation and the study of the properties of novel deep eutectic solvents (DESs) formed by zwitterionic trimethylglicine and high melting point carboxylic acids. These zwitterionic DESs are liquid at room temperature or at temperatures lower than 70 °C and do not have chloride or any metal ions in their composition. These media were characterized in terms of their viscosity, conductivity, density, ionicity (via Walden plots), surface tension and thermal stability. The values observed are similar to other typical DESs, and the mixtures resulted in “poor ionic liquids” in the Walden plot. The values obtained could be correlated to the carboxylic acids' structures. The toxicity of the pure mixtures was evaluated via an FTIR-bioassay on Saccharomyces cerevisiae cells. This method allowed us to define the action of these media as dehydrating agents on eukaryotic model cells, with a mechanism highly correlated with CaCl2, a well-known dehydrating agent. The Glycolic acid/Trimethylglicine eutectic system can be considered a NADES (Natural Deep Eutectic Solvent) and resulted as the best in our set for many reasons. It is formed by natural, renewable, eco-compatible and cheap compounds (both the molecules can be derived from sugar beet) and it can be used in many applications because it has a low melting point (−36 °C) and it is colorless, and therefore suitable for spectroscopic measurements. For these reasons, the solubility of some α-L-amino acids was investigated in this DES, showing a good solubility for aromatic amino acids, which are normally scarcely soluble in water.

Thirty-six quaternary ammonium salts, of which 28 structurally different non-commercially available surfactants, were tested to screen their biocidal and inhibitory antimicrobial activity. Their activity was compared to commercially available amphiphiles as well as to non-amphiphilic quaternary ammonium salts. As target of these compounds four microbial species were employed of which two (Saccharomyces cerevisiae and Candida albicans) were important yeast in the food and clinical environment and the other two (Escherichia coli and Listeria innocua) represented the Gram negative and positive bacteria, respectively. The surfactants showed the ability to kill the microbial cells in water solution and to variably hamper their growth onto agar medium. The non-amphiphilic compounds (which represent analogues of some surfactants used in this study, since they have the same head group but no hydrophobic portion) had little effect in solution and no effect against the microbial growth on plate. Amphoteric and non-amphoteric zwitterionic surfactants showed reduced biocidal activity. The most active antimicrobial agent was N-tetradecyltropinium bromide (23S) surfactant. The presence of cells did not significantly affect the ability to form micelles, as demonstrated by comparative conductometric measurements.

BACKGROUND: Protein hydrolysates or hydrolysed proteins (HPs) are high-N organic fertilizers allowing the recovery of by-products (leather meal and fluid hydrolysed proteins) otherwise disposed of as polluting wastes, thus enhancing matter and energy conservation in agricultural systems while decreasing potential pollution. Chemical and biological characteristics of HPs of animal origin were analysed in this work to assess their safety, environmental sustainability and agricultural efficacy as fertilizers. Different HPs obtained by thermal, chemical and enzymatic hydrolytic processes were characterized by Fourier transform infrared spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis, and their safety and efficacy were assessed through bioassays, ecotoxicological tests and soil biochemistry analyses. RESULTS: HPs can be discriminated according to their origin and hydrolysis system by proteomic and metabolomic methods. Three experimental systems, soil microbiota, yeast and plants, were employed to detect possible negative effects exerted by HPs. The results showed that these compounds do not significantly interfere with metabolomic activity or the reproductive system. CONCLUSION: The absence of toxic and genotoxic effects of the hydrolysates prepared by the three hydrolytic processes suggests that they do not negatively affect eukaryotic cells and soil ecosystems and that they can be used in conventional and organic farming as an important nitrogen source derived from otherwise highly polluting by-products. c � 2013 Society of Chemical Industry

The etiology and pathogenesis of Parkinson’s disease (PD) are still unclear. However, multiple lines of evidence suggest a critical role of the toll like receptor 4 (TLR4) in inflammatory response and neuronal death. Neuroinflammation may be associated with the misfolding and aggregation of proteins accompanied by a change in their secondary structure. Recent findings also suggest that biochemical perturbations in cerebral lipid content could contribute to the pathogenesis of central nervous system (CNS) disorders, including PD. Thus, it is of great importance to determine the biochemical changes that occur in PD. In this respect, Fourier Transform Infrared (FTIR) spectroscopy represents a useful tool to detect molecular alterations in biological systems in response to stress stimuli. By relying upon FTIR approach, this study was designed to elucidate the potential role of TLR4 in biochemical changes induced by methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) neurotoxin in a mouse model of PD. The analysis of the FTIR spectra was performed in different brain regions of both wild type (WT) and toll like receptor 4-deficient (TLR4−/−) mice. It revealed that each brain region exhibited a characteristic molecular fingerprint at baseline, with no significant differences between genotypes. Conversely, WT and TLR4−/− mice showed differential biochemical response to MPTP toxicity, principally related to lipid and protein composition. These differences appeared to be characteristic for each brain area. Furthermore, the present study showed that WT mice resulted more vulnerable than TLR4−/− animals to striatal dopamine (DA) depletion following MPTP treatment. These results support the hypothesis of a possible involvement of TLR4 in biochemical changes occurring in neurodegeneration.

Two hundred seventy seven strains from eleven opportunistic species of the genus Candida, isolated from two Italian hospitals, were identified and analyzed for their ability to form biofilm in laboratory conditions. The majority of Candida albicans strains formed biofilm while among the NCAC species there were different level of biofilm forming ability, in accordance with the current literature. The relation between the variables considered, i.e. the departments and the hospitals or the species and their ability to form biofilm, was tested with the assessment of the probability associated to each combination. Species and biofilm forming ability appeared to be distributed almost randomly, although some combinations suggest a potential preference of some species or of biofilm forming strains for specific wards. On the contrary, the relation between biofilm formation and species isolation frequency was highly significant (R2 around 0.98). Interestingly, the regression analyses carried out on the data of the two hospitals separately were rather different and the analysis on the data merged together gave a much lower correlation. These findings suggest that, harsh environments shape the composition of microbial species significantly and that each environment should be considered per se to avoid less significant statistical treatments.

Zwitterionic sulfobetaine surfactants are used in pharmaceutical or biomedical applications for the solubilization and delivery of hydrophobic molecules in aqueous medium or in biological environments. In a screening on the biocidal activity of synthetic surfactants on microbial cells, remarkable results have emerged with sulfobetaine amphiphiles. The interaction between eight zwitterionic sulfobetaine amphiphiles and Saccharomyces cerevisiae model cells was therefore analyzed. S. cerevisiae yeast cells were chosen, as they are a widely used unicellular eukaryotic model organism in cell biology. Conductivity measurements were used to investigate the interaction between surfactant solution and cells. Viable counts measurements were performed, and the mortality data correlated with the conductivity profiles very well, in terms of the inflection points (IPs) observed in the curves and in terms of supramolecular properties of the aggregates. A Fourier transform infrared (FTIR)-based bioassay was then performed to determine the metabolomic stress-response of the cells subjected to the action of zwitterionic surfactants. The surfactants showed nodal concentration (IPs) with all the techniques in their activities, corresponding to the critical micellar concentrations of the amphiphiles. This is due to the pseudocationic behavior of sulfobetaine micelles, because of their charge distribution and charge densities. This behavior permits the interaction of the micellar aggregates with the cells, and the structure of the surfactant monomers has impact on the mortality and the metabolomic response data observed. On the other hand, the concentrations that are necessary to provoke a biocidal activity do not promote these amphiphiles as potential antimicrobial agents. In fact, they are much higher than the ones of cationic surfactants.

Dekkera bruxellensis—a yeast species associated with wine and beer production—has recently received attention because of its ability to compete with Saccharomyces cerevisiae in distilleries producing fuel ethanol, and due to its resistance to high ethanol and acid levels. The tolerance to acetic acid in 29 strains of D. bruxellensis was investigated by screening growth at different concentrations up to 120 mM at pH 4.5. Different metabolic responses were exhibited in three strains (CBS 98, CBS 2499 and CBS 4482) that were analysed by their FTIR-metabolomic fingerprint. Physiological studies showed that the presence of acetic acid significantly affected their growth, causing a different reduction in growth rate, glucose consumption and ethanol production rates, as well as biomass and ethanol yields. The examined strains were unable to metabolise acetic acid in the presence of glucose, probably due to a glucose repression mechanism on the acetyl-CoA syntethase activity. Interestingly, the cells continued to produce acetic acid as byproduct of their fermentative metabolism. We also showed that the HOG MAP kinase pathway was not activated by phosphorylation upon exposure of the cells to acetic acid.

Trichoderma species are saprophytic filamentous fungi producing localized and invasive infections that are cause of morbidity and mortality, especially in immunocompromised patients, causing up to 53 % mortality. Non-immunocompromised patients, undergoing continuous ambulatory peritoneal dialysis, are other targets of this fungus. Current molecular diagnostic tools, based on the barcode marker ITS, fail to discriminate these fungi at the species level, further increasing the difficulty associated with these infections and their generally poor prognosis. We report on the first case of endocarditis infection caused by Trichoderma longibrachiatum in a 30-year-old man. This patient underwent the implantation of an implantable cardioverter defibrillator in 2006, replaced in 2012. Two years later, the patient developed fever, treated successfully with amoxicillin followed by ciprofloxacin, but an echocardiogram showed large vegetation onto the ventricular lead. After CIED extraction, the patient had high-grade fever. The culturing of the catheter tip was positive only in samples deriving from sonication according to the 2014 ESCMID guidelines, whereas the simple washing failed to remove the biofilm cells from the plastic surface. Subsequent molecular (ITS sequencing) and microbiological (macromorphology) analyses showed that the vegetation was due to T. longibrachiatum. This report showed that T. longibrachiatum is an effective threat and that sonication is necessary for the culturing of vegetations from plastic surfaces. Limitations of the current barcode marker ITS, and the long procedures required by a multistep approach, call for the development of rapid monophasic tests.

Inhibitors commonly found in lignocellulosic hydrolysates impair yeast metabolism and growth, reducing the productivity of the overall bioethanol production process. FTIR spectroscopy was used to analyze the metabolomic alterations induced by acetic and formic acid, furfural and 5-hydroxymethyl-2-furaldehyde (HMF) on yeast metabolism, using three Saccharomyces cerevisiae strains with different sensitivities. IR spectrum alterations were summarized with synthetic descriptors to rapidly visualize the kinds of molecules displaying the more intense reactions and to evaluate the type of interaction between inhibitors in a mixture, at concentrations close to those found at the industrial scale. The four inhibitors induced different levels of mortality and metabolomic changes. The metabolomic response was proportional to the different strain resistance level, further supporting their original classification. Inhibitor mixtures severely hindered the cell viability with the exception of the lowest concentration tested, which was partially biocidal. Furthermore, for the first time, this study revealed antagonistic interactions exerted by inhibitor mixtures on microbial metabolism, closely strain- and dose-dependent. This confirms that yeast strain resistance to single inhibitors cannot be used to predict behaviour on exposure to mixtures. This finding is worth further studies to explain the underlying antagonistic mechanism and to support the selection of highly tolerant strains.

Apples and pears of four different cultivars from nine companies located in northern Italy have been submitted to the isolation of the blastomycetic flora before and after industrial washing, in order to individuate and isolate the resident yeasts, particularly those resistant to the industrial washing. Cultures of the following species were isolated: Aureobasidium pullulans, Candida oleophila, Debaryomyces hansenii, Hanseniaspora uvarum, Metschnikowia fructicola, Metschnikowia pulcherrima, Wickerhamyomyces anomalus, Meyerozyma guilliermondii, Pichia kluyveri and Rhodotorula glutinis. The most diffuse species was M. guilliermondii, found on all cultivars after washing. Species of the Metschnikowia gender and A. pullulans were also very common. Identification through rDNA 26 S and FTIR characterization made it possible to trace some strains and to establish that these were resistant to the washing treatment. The presence and distribution of superficial microbiota on apples was also shown by scanning electronic microscopy. This preliminary study has shown that the yeast cultures on the surfaces can be differentiated for their resistance to industrial treatments and that an increase of the yeast flora can be easily obtained.

Surfactants are extremely important agents to clean and sanitize various environments. Their biocidal activity is a key factor determined by the interactions between amphiphile structure and the target microbial cells. The object of this study was to analyze the interactions between four structural variants of N-alkyltropinium bromide surfactants with the Gram negative Escherichia coli and the Gram positive Listeria innocua bacteria. Microbiological and conductometric methods with a previously described FTIR bioassay were used to assess the metabolomic damage exerted by these compounds. All surfactants tested showed more biocidal activity in L. innocua than in E. coli. N-tetradecyltropinium bromide was the most effective compound against both species, while all the other variants had a reduced efficacy as biocides, mainly against E. coli cells. In general, the most prominent metabolomic response was observed for the constituents of the cell envelope in the fatty acids (W1) and amides (W2) regions and at the wavenumbers referred to peptidoglycan (W2 and W3 regions). This response was particularly strong and negative in L. innocua, when cells were challenged by N-tetradecyltropinium bromide, and by the variant with a smaller head and a 12C tail (N-dodecylquinuclidinium bromide). Tail length was critical for microbial inhibition especially when acting against E. coli, maybe due the complex nature of Gram negative cell envelope. Statistical analysis allowed us to correlate the induced mortality with the metabolomic cell response, highlighting two different modes of action. In general, gaining insights in the interactions between fine structural properties of surfactants and the microbial diversity can allow tailoring these compounds for the various operative conditions.

Twelve novel deep eutectic solvents (DESs) were prepared and characterized in this work. They are mixtures of (1S)-(+)-10-camphorsulfonic acid (CSA) and differently structured sulfobetaines (SBs) with aliphatic, aromatic and amphiphilic moieties. They are liquids at room temperature, their melting points span, in fact, from −5° to 19 °C, so we can name these mixtures RTDESs (room temperature deep eutectic solvents). These zwitterionic DESs were characterized in terms of their viscosity, conductivity (and therefore ionicity via Walden plots), density, surface tension and toxicity on eukaryotic model cells. The collected data suggest that the interaction between CSA and the SBs can be ascribed as a hydrogen bond instead of a proton transfer, therefore they are not ionic liquids. To our knowledge, their position on the Walden plot, in the left portion close to the diagonal, has not yet been observed for other DESs or ionic liquid systems and indicates the low ionicity of these mixtures. A FTIR-based bioassay was performed to determine the toxicity of these mixtures on eukaryotic model cells (Saccharomyces cerevisiae). The DESs showed merely a dehydrating effect on the cells, similar to that produced by CaCl2, a low cell toxicity salt. This supports these DESs as promising green media. Amphiphilic SBs DESs showed a stronger effect on the cells and a structure-activity trend can be described for this class. A preliminary study on the use of these novel DESs as Bronsted catalyst media was accomplished by the use of one of them in chalcone synthesis, which showed promising catalytic and recycling capabilities.

Meyerozyma guilliermondii is a yeast species widely isolated from several natural environments and from fruit; in medical microbiology it is known as the teleomorph of the opportunistic pathogen Candida guilliermondii, which causes about 2% of the human blood infections. This yeast is also promising in a variety of biotechnological applications as vitamins production and post-harvest control. The question if isolates from different sources are physiologically and genetically similar, or if the various environments induced significant differences, is crucial for the understanding of this species structure and to select strains appropriate for each application. This question was addressed using LSU and ITS sequencing for taxonomic assignment, i-SSR (GACA4) for the molecular characterization and FTIR for the metabolomic fingerprint. All data showed that fruit and environmental isolates cluster separately with a general good agreement between metabolomics and molecular analysis. An additional RAPD analysis was able to discriminate strains according to the isolation position within the pineapple fruit. Although all strains are members of the M. guilliermondii species according to the current standards, the distribution of large variability detected suggests that some specialization occurred in the niches inhabited by this yeast and that food related strains can be differentiated from the medical isolates.

Forty-two yeast strains from 27 species belonging to seven genera, selected for their ability to grow in 10% NaCl, have been analysed for their resistance to salt concentrations up to 5 M, by calculating the Minimum Inhibitory Concentrations (MIC). Using eight different NaCl concentrations from 0 to 5M, results show that halotolerance (MIC) ranges from 1.7 to 3.8 M NaCl, with an avera ge around 2.5 M and confirm that the most halotolerant strains belong to the speciesDebaryomyces hansenii. Since a real halophily could not be found in these isolates, and is generally questioned to be present among the yeast, the effects of NaCl has been measured as salt enhancement effect on growth (MSE), which is defined as the rate between the growth at a given NaCl concentration and theowth in the medium without addition of salt. The implications of these findings in food microbial ecology and technology are discussed.

The improvement of yeast starters for wine making, with classical genetic techniques, relays on the effective independence of the main oenological traits in order to combine them optimally. The analysis of three characters (ethanol production, volatile acidity and fermenting rate) in 787Saccharomyces cerevisiae strains, isolated from several parts of the world and substrates, shows moderate correlation between the volatile acidity and the other two traits, whereas ethanol production and fermenting rate appear more correlated. The minimum number of strains necessary to start selection or genetic improvement programs is discussed. The correlation between the oenological traits and the source of isolation showed that the best strains can be obtained from wineries and wine, whereas the isolates from grapes and must are less performing on the average.

The activity of surfactants against fungal cells has been studied less than against bacteria, although the medical and industrial importance of the former is of paramount importance. In this paper the surfactant biocidal effect was measured in the yeasts Saccharomyces cerevisiae and Candida albicans with a previously described FTIR bioassay which estimates the stress level as function of the FTIR spectra variation of the cells upon exposition to the chemicals. N-tetradecyltropinium bromide was chosen as stressing agent on the basis of previous preliminary study demonstrating its ability to kill prokaryotic and especially eukaryotic cells at concentration around or over the critical micellar concentration (c.m.c.). Here we show that this surfactant is able to inactivate S. cerevisiae cells at 0.4mM and C. albicans cells at 0.6mM after 1h exposition. FTIR analysis revealed that the surfactant induced metabolomics reactions of S. cerevisiae cells in the regions of amides (W2) and fatty acids (W1). In the same way C. albicans cells showed the maximum stress response in amides (W2) and mixed (W3) regions. Variations of the hydrophobic tail of this surfactant produced a reduced level of cell stress with both the 12C and 16C variants; although these two compounds were more effective in inducing cell mortality in S. cerevisiae but not in C. albicans. In conclusion, this paper has shown that, for this surfactant, the n-alkyl chain must vary between 12C and 16C and that the hydrophilic head size is not as critical as the tail length.

Conductometry is widely used to determine critical micellar concentration and micellar aggregates surface properties of amphiphiles. Current conductivity experiments of surfactant solutions are typically carried out by manual pipetting, yielding some tens reading points within a couple of hours. In order to study the properties of surfactant-cells interactions, each amphiphile must be tested in different conditions against several types of cells. This calls for complex experimental designs making the application of current methods seriously time consuming, especially because long experiments risk to determine alterations of cells, independently of the surfactant action. In this paper we present a novel, accurate and rapid automated procedure to obtain conductometric curves with several hundreds reading points within tens of minutes. The method was validated with surfactant solutions alone and in combination with Saccharomyces cerevisiae cells. An easy-to use R script, calculates conductometric parameters and their statistical significance with a graphic interface to visualize data and results. The validations showed that indeed the procedure works in the same manner with surfactant alone or in combination with cells, yielding around 1000 reading points within 20 min and with high accuracy, as determined by the regression analysis.

Candida milleri , together with Candida humilis , is the most representative yeast species found in type I sourdough ecosystems. In this work, comparison of the ITS region and the D1/D2 domain of 26S rDNA gene partial sequences, karyotyping, mtDNA-RFLP analysis, Intron Splice Site dispersion (ISS-PCR) and (GTG) 5 microsatellite analyses, assimilation test of different carbohydrates, and metabolome assessment by FT-IR analysis, were investigated in seventeen strains isolated from four different companies as well as in type strains CBS6897 T and CBS5658 T . Most isolates were ascribed to C. milleri , even if a strong relatedness was confirmed with C. humilis as well, particularly for three strains. Genetic characterization showed a high degree of intraspecific polymorphism since 12 different genotypes were discriminated. The number of chromosomes varied from 9 to 13 and their size ranged from less than 0.3 to over 2 Mbp. Phenotypic traits let to recognize 9 different profiles of carbon sources assimilation. FT-IR spectra from yeast cells cultivated in different media and collected at different growth phases revealed a diversity of behaviour among strains in accordance with the results of PCR-based fingerprinting. A clear evidence of the polymorphic status of C. milleri species is provided thus representing an important feature for the development of technological applications in bakery industries.

During an investigation of olive oil microbiota, three yeast strains were found to be divergent from currently classified yeast species according to the sequences of the D1/D2 domain of the gene encoding the rRNA large subunit (LSU) and the internal transcribed spacer region including the gene for 5.8S rRNA. Phylogenetic analysis revealed that these strains, designated CBS 12509, CBS 12510T and CBS 12511, represent a novel anascosporogenous species described herein as Yamadazyma terventina sp. nov; the type strain is DAPES 1924T ( = CBS 12510T = NCAIM Y.02028T). This novel species was placed in the Yamadazyma clade, with Yamadazyma scolyti, Candida conglobata and Candida aaseri as closest relatives. Y. terventina differs from the above-mentioned species in the ability to strongly assimilate dl-lactate and weakly assimilate ethanol.

A novel species of ascomycetous yeast, Candida coquimbonensis sp. nov., from the necrotic tissue of cacti in Chile and Australia is described. C. coquimbonensis sp. nov. is closely related and phenotypically similar to Phaffomyces opuntiae. There is no overlap in the geographical distribution between C. coquimbonensis and any species in the Phaffomyces clade. However, this is the first member of the clade to be collected in both native (Chile) and non-native (Australia) cactus habitats. The type strain of C. coquimbonensis sp. nov. is TSU 00-206.4BT ( = CBS 12348T = USCFST 12-103T).

Potassium metabisulphite (PMB) is a common antimicrobial additive in the food industry. In aqueous solutions, PMB leads to complex equilibria according to its concentration, pH and temperature, and different chemical species can be present. In winemaking, PMB is used at low pH, suggesting that the biocidic activity is exerted by sulphur dioxide while, in other applications, it is employed at higher pH values with little if any dissociation. This observation leads to the question of which chemical form is biologically active. For this reason, Saccharomyces cerevisiae cells were subjected to PMB solutions at different pH values and analysed with a Fourier transform infrared spectroscopy (FTIR)-based bioassay, to assess the entity and the type of stress. Cell viability was determined and compared to the metabolomics (FTIR) stress indices, which revealed that the metabolomics fingerprint was an effective description of the cell health state. GC-MS metabolite profiles were obtained to describe (in detail) the changes caused by PMB in the fatty acids region. Human dermal fibroblasts (HDF) were also subjected to PMB stress at pH 7.0 and analysed with the FTIR protocol, in order to compare the response spectra of yeast and human cell cultures.

During an investigation of yeast biota in the rhizosphere of lentisk in Sardinian semi-arid areas, a strain was isolated that could not be assigned to any known species. The sequence of the D1/D2 domain of the large subunit rDNA gene revealed that the strain belonged to the genus Kazachstania and was phylogenetically related to a clade including Kazachstania aerobia, Kazachstania servazzii, Kazachstania solicola and Kazachstania unispora. The novel isolate differed from members of this clade in its ability to assimilate d-glucono-1,5-lactone and its very weak fermentation of glucose and sucrose; its assimilation profile was unique within the genus Kazachstania. Monosporal colonies were able to sporulate, indicating that the species is homothallic. It is proposed that the isolate represents a novel species, Kazachstania ichnusensis sp. nov., with LCF 1675T ( = CBS 11859T) as type strain.

Fourier Transform InfraRed spectroscopy (FTIR) is an emerging technique in biology. One of the analytical problems inherent with this approach is the extreme variability typical of biological systems. Extrinsic fonts of variations are the growth media and the growth phase of the microbial culture. In order to gain knowledge on the relations between these two factors and the spectral variability, metabolomic changes in Saccharomyces cerevisiae cells during growth were analyzed with FTIR spectroscopy. Spectral variations reflected the changes occurring in all cellular compartments and components during the different growth stages and describe the metabolomic evolution of cell cultures during growth. Three different media were tested. Different mathematical and statistical treatments were used to describe and evaluate the changes occurring during growth. Variations were mainly concentrated in the exponential phase, whereas fewer changes occurred in stationary phase cells. The three different media caused different metabolomic behaviours during growth. The mathematical distance between the peak areas of amide I, amide II and of two distinct peaks in the carbohydrates region could give a synthetic description of growth and produced similar trends in all the conditions tested. The distance between the two carbohydrate peaks could be used to determine the mid exponential phase and the entrance in the stationary phase. Growth phase was shown to influence the sensitivity of a FTIR-based cell stress bioassay. The knowledge of the metabolomic variations during growth could be used in the future to optimize FTIR applications in microbiology.

The problem of species and in particular microbial species is central in biology. An active collaboration of various specialists such as taxonomists, epistemologists, mathematicians and bioinformatics experts is desirable for its solution. This article intended to show the possibilities and perspectives of bioinformatics research in understanding the ontological problem of species, i.e. the problem of the existence of the microbial species. The approach undertaken of this paper is based on the concept that if microbial species exist, then there should be detectable discontinuities or disconnections between microorganisms assigned to different species. A yeast model has been used to show how the distances from a reference organism raise with the increase of the number of different strains included in the study.

Typology is based on the concept that one individual (the type) can represent the whole group. In yeast taxonomy the type strain is the representative of the whole species and is considered an important tool for classification. Although the evolutionary, phylogenetic and biological species concepts are in contrast with this approach, the International Codes of nomenclature still use typology, which remains one of the most operative systems. These incongruities demand a multidisciplinary investigation on the nature of the type, its characteristics and the possibility of the type to be defined on the basis of a shareable criterion. In this paper we present an approach to the problem of type centrality based on mathematical demonstrations and numerical examples. This paper intended to show the possibilities offered to bioinformatics research by the implementation of multidisciplinary approaches in biology and in proposing a general approach to the definition of the type representing any sort of set, described with multiple descriptors.

Fourier transform infrared spectroscopy (FTIR) was used to analyze the metabolomic alterations caused to yeast cells by four chemical compounds: ethanol, sodium hypochlorite, sodium chloride and sulfur dioxide, each tested at five different concentrations. The complex of four stressing agents at different concentrations, inducing cell mortalities ranging from 1% to 100%, has given the opportunity to prove that FTIR can individuate the presence of a stress before the cells start dying. A series of "Stress Indexes" was calculated with an expressly designed "R" script, to estimate the level of stress induced by the chemical agents at different concentrations. These estimation procedures allowed the direct comparison of the stress induced by the four agents at different concentrations. The response spectra, calculated as difference between the spectrum of the cells under stress and that of the cells maintained in water, showed different shapes in the diverse experimental conditions, suggesting a specificity of the response and the possibility to classify it. The contribution of five different spectral regions (fatty acids, amides, mixed zone, carbohydrates and typing region) could be calculated separately, gaining additional information on the stressing effects. Spectral alterations were detected at concentrations as low as 10% ethanol, 20 ppm bleach, 1 M NaCl and 100 mg L(-1) SO(2). These preliminary findings suggest that FTIR technology and a series of simple algorithms can be employed to study response of cells to various stressing situations, not limited to chemical agents. The ease and rapidity of the FTIR analysis suggest that this approach could be used as a bioassay in several applications and particularly in ecotoxicology and in environmental microbiology.

Iprodione is a contact fungicide used to control several pathogens such as Botrytis cinerea, Monilia, and Sclerotinia. This paper reports the ability of an iprodione-resistant strain of Zygosaccharomyces rouxii to degrade iprodione at a concentration of 1 mg L(-1). The yeast Z. rouxii was chosen also for its ability to grow at high osmolarity. Also of note is that in bioremediation situations and in the food industry such resistance could be important. The kinetic and metabolic behaviors of the fungicide in the media are described. The results show a new transformation pathway of iprodione by the yeast leading to the formation of N-(3,5-dichlorophenyl)-2,4-dioxoimidazoline, 3-isopropylhydantoin, and 3,5-dichloroaniline. These compounds were identified by 1H NMR, 13C NMR, and GC-MS analyses. This study provides a basis to employ yeast strains in biodegradation studies in relation to their ability in the disappearance and degradation of xenobiotics into simpler molecules.

Different phenotypical or molecular techniques can be used to describe and classify microorganisms for taxonomic, phylogenetic or genetic purposes. In yeast taxonomy the official hierarchic classification, based on morphological and physiological characters, is used together with more convenient molecular techniques such as the DNA sequencing. The question on whether these procedures produce coherent classifications is critical both to interpret taxonomic data consistently and to outline species correctly. In this paper, a set of type strains from the major genera of the budding hemiascomycetes yeast is examined with a series of physiological and molecular techniques, widely employed in taxonomy, in order to compare the among-strains correlations obtained with different methods. Results showed that the level of correlation among different techniques is relatively low, showing that different classifications and species organization could be obtained with diverse approaches. This is particularly interesting, considering that the official description of the yeast species is based on characters different from those becoming increasingly popular in the routine identification.

Aims: Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains. Methods and Results: A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques Conclusions: The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method. Significance and Impact of the Study: The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology.