Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds.

Filamentous fungi may cause food and feed spoilage and produce harmful metabolites to human and animal health such as mycotoxins. Identification of fungi using conventional phenotypic methods is time-consuming and molecular methods are still quite expensive and require specific laboratory skills. In the last two decades, it has been shown that Fourier transform infrared (FTIR) spectroscopy was an efficient tool for microorganism identification. The aims of this study were to use a simple protocol for the identification of filamentous fungi using FTIR spectroscopy coupled with a partial least squares discriminant analysis (PLS-DA), to implement a procedure to validate the obtained results, and to assess the transferability of the method and database. FTIR spectra of 486 strains (43 genera and 140 species) were recorded. An IR spectral database built with 288 strains was used to identify 105 different strains. It was found that 99.17% and 92.3% of spectra derived from these strains were correctly assigned at the genus and species levels, respectively. The establishment of a score and a threshold permitted to validate 80.79% of the results obtained. A standardization function (SF) was also implemented and tested on FTIR data from another instrument on a different site and permitted to increase the percentage of well predicted spectra for this set from 72.15% to 89.13%. This study confirms the good performance of high throughput FTIR spectroscopy for fungal identification using a spectral library of molds of industrial relevance.

Application of capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) analysis for identification of fungal communities in cheese.

As major contributors of the ripening process, yeasts and filamentous fungi play a fundamental role in cheese-making. Still, there is no rapid and affordable identification method available for both yeasts and filamentous fungi encountered in cheeses. In the present study, we developed a method based on CE-SSCP analysis of nuclear ribosomal DNA ITS amplicons, along with a species pattern database comprising 37 fungal species. By combining analyses of the ITS1 and ITS2 conformers, 25 out of 37 species were discriminated using CE-SSCP analysis. This reproducible and sensitive method was applied to determine the fungal community composition of 36 cheeses including blue-veined, pressed-cooked, pressed-uncooked, red-smear and surface-mould ripened cheeses. Overall, each cheese contained between 1 and 6 fungal species and 23 different species of fungi were detected including 8 yeast species, 9 filamentous species and 6 unidentified species. Comparison of the fungal diversity obtained after cloning and sequencing (rDNA ITS) versus CE-SSCP for 8 cheeses showed that CE-SSCP was at least as exhaustive as cloning and sequencing of thirty clones per cheese. In conclusion, this CE-SSCP method was an effective tool to identify the fungi present in various cheese varieties and may be of interest for the cheese industry to rapidly describe the composition of cheese fungal communities.

Influence of Pythium oligandrum on the bacterial communities that colonize the nutrient solutions and the rhizosphere of tomato plants.

The influence exerted by the biocontrol oomycete Pythium oligandrum on the bacterial populations proliferating in the rhizosphere of tomato plants grown in a hydroponic system and in the circulating solutions is studied in the present experiment. Quantitative PCR and single-strand conformation polymorphism were used to investigate the genetic structure and dynamics of the bacterial communities colonizing the root systems and the various circulating solutions. Quantitative PCR assays showed that bacteria heavily colonized the rhizosphere of tomato plants with, however, no significant density changes throughout the cultural season (April-September). Single strand conformation polymorphism fingerprints revealed the occurrence of transient perturbations in the rhizospheric indigenous bacterial communities following P. oligandrum introduction in the root system of plants. This effect was, however, transient and did not persist until the end of the cropping season. Interestingly, the genetic structure of the bacterial microflora colonizing either the roots or the nutrient solutions evolved throughout the cropping season. This temporal evolution occurred whatever the presence and persistence of P. oligandrum in the rhizosphere. Evidence is also provided that bacterial microflora that colonize the root system are different from the ones colonizing the circulating solutions. The relationships between these 2 microflora (at the root and solution levels) are discussed.

Modelling the effect of temperature, water activity and pH on the growth of Serpula lacrymans.

AIMS: To predict the risk factors for building infestation by Serpula lacrymans, which is one of the most destructive fungi causing timber decay in buildings. METHODS AND RESULTS: The growth rate was assessed on malt extract agar media at temperatures between 1.5 and 45°C, at water activity (a(w)) over the range of 0.800-0.993 and at pH ranges from 1.5 to 11.0. The radial growth rate (µ) and the lag phase (λ) were estimated from the radial growth kinetics via the plots radius vs time. These parameters were then modelled as a function of the environmental factors tested. Models derived from the cardinal model (CM) were used to fit the experimental data and allowed an estimation of the optimal and limit values for fungal growth. Optimal growth rate occurred at 20°C, at high a(w) level (0.993) and at a pH range between 4.0 and 6.0. The strain effect on the temperature parameters was further evaluated using 14 strains of S. lacrymans. The robustness of the temperature model was validated on data sets measured in two different wood-based media (Quercus robur L. and Picea abies). CONCLUSIONS: The two-step procedure of exponential model with latency followed by the CM with inflection gives reliable predictions for the growth conditions of a filamentous fungus in our study. The procedure was validated for the study of abiotic factors on the growth rate of S. lacrymans. SIGNIFICANCE AND IMPACT OF THE STUDY: This work describes the usefulness of evaluating the effect of physico-chemical factors on fungal growth in predictive building mycology. Consequently, the developed mathematical models for predicting fungal growth on a macroscopic scale can be used as a tool for risk assessment of timber decay in buildings.

Application of denaturing high-performance liquid chromatography (DHPLC) for yeasts identification in red smear cheese surfaces.

AIMS: To evaluate and optimize the use of denaturing high-performance liquid chromatography (DHPLC) for yeasts identification in red smear cheese surfaces. METHODS AND RESULTS: The resolution of DHPLC was first evaluated and optimized using a mixture of PCR amplicons of the internal transcribed spacer 2 (ITS2) region of 19 yeast reference strains representing 18 species that are common in the cheese microbiota. Sixteen of the 18 yeast species could be resolved by combining runs at temperatures of 57.5 and 59 degrees C. Then, DHPLC was used to investigate the yeast microbiota of pasteurized Maroilles, Munster and Livarot cheese surfaces by comparing their peak profiles with our reference yeast database and by collecting/sequencing of peak fractions. Debaryomyces hansenii and Geotrichum candidum for Munster and Maroilles cheeses, and Candida catenulata, Candida intermedia and G. candidum for Livarot cheese were identified using the reference database and collecting/sequencing of peak fractions. CONCLUSIONS: DHPLC technique was found to have good resolution properties and to be useful for investigating the yeast microbiota of red smear cheese surfaces. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first time that DHPLC is applied to study the yeast microbiota of red smear cheese surfaces.

Epiphysiolysis Type Salter I of the Medial Clavicle with Posterior Displacement: A Case Series and Review of the Literature.

Physeal fractures of the medial clavicle with posterior displacement of the metaphysis are very rare injuries, but additional injuries can be life-threatening. Due to the specific clavicular ossification process, skeletally immature patients present usually not true sternoclavicular joint (SCJ) dislocations accordingly to adults but rather displaced physeal fractures. There is no consensus in the current literature on the best treatment of this lesion. Conservative treatment is not resulting in good outcome; closed reduction is often not successful, and open reduction with internal fixation is finally required. Several methods are described for stabilizing these physeal fractures. We treated three osseous immature patients with this lesion. Due to the small dimension of the medial clavicular epiphysis, we performed in one case a transosseous figure-of-eight suture of the clavicular metaphysis towards the sternum, and in the two other cases, a transosseous suture from the clavicular metaphysis on the anterior clavicular periosteum. The latter technique avoids harm to the small epiphysis or the SCJ and minimizes the risk of retrosternal complications.

The adenylosuccinate synthetase from the hyperthermophilic archaeon Pyrococcus species displays unusual structural features.

The first example of a hyperthermophilic adenylosuccinate synthetase is reported, which is an enzyme that must maintain its folded structure at temperatures as high as 102 degrees C. The amino acid sequence of this key enzyme has been determined after cloning and sequencing the purA-like gene from the archaeal Pyrococcus sp. strain ST700. The corresponding protein displays two unexpected features: (1) it is 21% shorter than the homologous mesophilic enzymes and this shortening corresponds to the loss of two alpha-helices and three beta-strands present in the Escherichia coli enzyme; (2) surprisingly, the archaeal adenylosuccinate synthetase has a significant number of substitutions in residues that are conserved in all other homologous enzymes from bacteria to man. In E. coli, the conserved residues have been described as essential for catalytic activity and/or for maintaining the folded structure of the homodimer. Despite these drastic differences, the purA-like archaeal gene seems to be normally expressed and its product functions in vivo in bacteria, since it complemented an E. coli purA auxotroph. The archaeal adenylosuccinate synthetase appears to be a good example of a bona fide orthologous protein. Reconstruction of phylogenetic trees showed that the archaeal gene is equally distantly related to both eukaryotes and bacteria, independently of the numerous substitutions observed at critical positions.

A putative SOS repair gene (dinF-like) in a hyperthermophilic archaeon.

The hyperthermophilic archaeon, Pyrococcus (strain IFREMER AL585), contains an ORF that encodes a polypeptide with a high similarity to the Escherichia coli dinF (DNA damage-inducible) gene product. The conservation of this protein between Archaea and Bacteria suggests that a SOS repair system might operate in Archaea.

Purification, molecular properties and specificity of a thermoactive and thermostable proteinase from Pyrococcus abyssi, strain st 549, hyperthermophilic archaea from deep-sea hydrothermal ecosystem.

A protease was isolated and purified from the supernatant of a culture of hyperthermophilic archaebacteria: Pyrococcus abyssi strain st 549. Purification consisted of three chromatographic steps. The enzyme purification yield was 4% and the purification factor 890. This protease is a seryl-protease hydrolyzing proteins and peptides with a preference for cleavage at the aromatic and hydrophobic residues in P1 and P'1 positions. Its activity is optimal at 95 degrees C and at pH 9. The electrophoretic mobility of the protease observed by zymogram suggests that it can adopt several oligomer forms. Three of them predominate displaying apparent molecular masses of 150, 105 and 60 kDa. Interdependence of the observed bands was revealed by changing the denaturation conditions of the samples (temperature, SDS concentration) before electrophoresis.

Microbial diversity in smoked salmon examined by a culture-independent molecular approach--a preliminary study.

Microbial biodiversity in sliced vacuum-packed cold smoked salmon was investigated using culture-independent molecular biology techniques. Sliced smoked salmon was stored for 25 days after being packed at 4 degrees C. DNA was extracted from sliced vacuum-packed cold smoked salmon. PCR DNA amplification were carried out using universal eubacterial primers corresponding to Escherichia coli 16S rRNA gene. 16S rRNA genes were amplified, cloned in E. coli and compared using Amplification Ribosomal DNA Restriction Analysis (ARDRA). 106 clones were studied and classified into 13 Operational Taxonomic Units (OTUs). Sequences obtained to describe those 13 OTUs were compared to GenBank data. They indicated the presence of Vibrio species. Enterobacteraceae and also marine psychrophilic clones related to Alteromonas macleodii, which were not encountered within cultures, but no Gram-positive species have been obtained. Those results indicate that bias in description of microbial diversity may be encountred in both molecular and cultural techniques.

Clinical rationale for the use of an ultra-short acting beta-blocker: esmolol.

Esmolol is a unique cardioselective, intravenous, ultra-short acting, beta-adrenergic blocking agent. A 9-minute half-life with rapid clinical onset and offset of action and the ability to titrate the drug to changing circumstances makes esmolol a useful addition to our treatment armamentarium. The efficacy and safety of esmolol have been shown in specific clinical settings, i.e. in patients with unstable angina, myocardial infarction, atrial fibrillation or flutter and supraventricular tachycardia. In the emergency management of hypertension, tachycardia or arrhythmia in critical care units, emergency room and surgery, esmolol is effective by attenuating hemodynamic responses from sympathetic activation or endogenous catecholamine release. With careful titration and monitoring of the patient, esmolol is relatively safe in the management of hypertension or tachyarrhythmias associated with congestive heart failure or chronic obstructive lung disease where beta-blockers are otherwise contraindicated. Different dosage schedules have been employed as per the clinical setting and the diagnosis. Generally, esmolol is infused intravenously in doses ranging from 25-300 micrograms/kg/min, along with a loading dose or bolus. The most frequently reported adverse effect associated with esmolol infusion was hypotension. Adverse effects due to beta-blockade can be corrected by down-titrating or discontinuing the infusion with complete disappearance of clinical effects in 20-30 minutes. Therefore, as an ultra-short acting beta-blocker, esmolol is an important therapeutic option in the acute clinical setting.

Unpredictable response to vasodilator therapy in primary pulmonary hypertension.

A 49-year-old man with severe primary pulmonary hypertension unresponsive to multiple vasodilators showed beneficial response to intravenous (i.v.) isoproterenol with significant decrease in the pulmonary vascular resistance and increase in the cardiac output. However, the patient became dependent on i.v. isoproterenol and eventually died suddenly following an episode of bradyarrhythmia. Autopsy confirmed severe primary pulmonary hypertension. As the response to vasodilator therapy can be unpredictable in PPH, sequential hemodynamic evaluation of drugs is necessary for finding an optimal therapeutic agent.

[Comparison of tacrine hepatotoxicity in patients with Alzheimer disease or AIDS]. / Comparaison de l'hépatoxicité de la tacrine chez des patients atteints de la maladie d'Alzheimer ou du SIDA.

Previously used in Alzheimer disease Tacrine (THA): tetrahydroaminoacridine has shown a rise of hepatic transaminase enzyme activity (TEA) in 18% of patients for Summers and 19% for Ames. Although studies using THA from USA or Canada have noticed a rise of TEA in 30% of the patients, after a treatment course with French THA we also have noted a rise of TEA in 12% of the Alzheimer patients. However, these secondary effects yielded to the end of treatment. These studies have been done with THA from different origins and different associations. Summers, the Canadian group and the French one have used THA in association with lecithin, when american group study has been made with no additional product. Therefore we have initiated a trial with oral THA in AIDS patients. 52 patients with HIV infection (26 in the IVC1 group and 26 in IVC2 group) have been treated with the same THA as the one used for Alzheimer french group. The common dosage was 150 to 200 mg (3 to 4 of 50 mg dosing capsules per day). The THA has been synthetized such as having an over 99% pureness product. After a period of 260 months/patient no elevation of TEA has been noted in any patients of our group. These results observed in HIV advanced patients with this THA are discordant with the one observed in Alzheimer's study. The dosage used in AIDS is twice higher than the one used for Alzheimer which gives us credit to the lack of hepatic toxicity in HIV advanced patient after 7 months of treatment.

Differentiation and identification of filamentous fungi by high-throughput FTIR spectroscopic analysis of mycelia.

Routine identification of fungi based on phenotypic and genotypic methods can be fastidious and time-consuming. In this context, there is a constant need for new approaches allowing the rapid identification of molds. Fourier-transform infrared (FTIR) spectroscopy appears as such an indicated method. The objective of this work was to evaluate the potential of FTIR spectroscopy for an early differentiation and identification of filamentous fungi. One hundred and thirty-one strains identified using DNA sequencing, were analyzed using FTIR spectroscopy of the mycelia obtained after a reduced culture time of 48 h compared to current conventional methods. Partial least square discriminant analysis was used as a chemometric method to analyze the spectral data and for identification of the fungal strains from the phylum to the species level. Calibration models were constructed using 106 strains pertaining to 14 different genera and 32 species and were used to identify 25 fungal strains in a blind manner. Identification levels of 98.97% and 98.77% achieved were correctly assigned to the genus and species levels respectively. FTIR spectroscopy with its high discriminating power and rapidity therefore shows strong promise for routine fungal identification. Upgrading of our database is ongoing to test the technique's robustness.

Biodiversity of antifungal lactic acid bacteria isolated from raw milk samples from cow, ewe and goat over one-year period.

Antifungal lactic acid bacteria (ALAB) biodiversity was evaluated in raw milk from ewe, cow and goat over one year period. Lactic acid bacteria were enumerated using 8 semi-selective media, and systematically screened for their antifungal activity against 4 spoilage fungi commonly encountered in dairy products. Depending on the selective medium, between 0.05% (Elliker agar) and 5.5% (LAMVAB agar) screened colonies showed an antifungal activity. The great majority of these active colonies originated from cow (49%) and goat (43%) milks, whereas only 8% were isolated from ewe milk. Penicillium expansum was the most frequently inhibited fungus with 48.5% of colonies active against P. expansum among the 1235 isolated, followed by Mucor plumbeus with 30.6% of active colonies, Kluyveromyces lactis with only 12.1% of active colonies and Pichia anomala with 8.7% of active colonies. In the tested conditions, 94% of the sequenced active colonies belonged to Lactobacillus. Among them, targeted fungal species differed according to the Lactobacillus group, whose presence largely depended on year period and milk origin. The Lb. casei and Lb. reuteri groups, predominantly recovered in summer/fall, were overrepresented in the population targeting M. plumbeus, whereas isolates from the Lb. plantarum group, predominantly recovered in spring, were overrepresented in the population targeting K. lactis, the ones belonging to the Lb. buchneri group, predominantly recovered in spring, were overrepresented in the population targeting P. anomala. Raw milk, especially cow and goat milks from the summer/fall period appeared to be a productive reservoir for antifungal lactobacilli.

Quantification of Penicillium camemberti and P. roqueforti mycelium by real-time PCR to assess their growth dynamics during ripening cheese.

Real-time PCR has been applied to quantify mycelium of Penicillium camemberti and Penicillium roqueforti during ripening of model cheese curd and surface mould-ripened cheeses. Total fungal DNA was first validated as an indicator of mycelial biomass in pure liquid culture and then in model curds at different stages of ripening. To imitate cheese matrix effects, DNA was extracted from curd mixed with known amounts of fresh mycelium of P. camemberti or P. roqueforti and was used as biomass standards for further quantitative real-time PCR. Mycelial mass per cheese (mg/g) was then directly obtained from fluorescence data. In model cheese curd, mycelial mass of P. camemberti increased from 2.8 at d4 to 596 mg/g at d11 whereas P. roqueforti increased from 0.3 to 6.3 mg/g during the same period. P. camemberti showed a fast development in Coulommiers from d2 to d9 (66 to 119 mg/g) and a 100-fold increase in Carré (0.85 to 85 mg/g). While mycelial biomass reached a maximum at d9 in Coulommiers, it still developed in Carré until d45. For the first time, cheese manufacturers have a powerful technique to monitor mycelial growth dynamics of their fungal cultures, which represents an important step for controlling cheese making.

Physiological traits of Penicillium glabrum strain LCP 08.5568, a filamentous fungus isolated from bottled aromatized mineral water.

Penicillium glabrum is a ubiquitous fungus distributed world wide. This fungus is a frequent contaminant in the food manufacturing industry. Environmental factors such as temperature, water activity and pH have a great influence on fungal development. In this study, a strain of P. glabrum referenced to as LCP 08.5568, has been isolated from a bottle of aromatized mineral water. The effects of temperature, a(w) and pH on radial growth rate were assessed on Czapeck Yeast Agar (CYA) medium. Models derived from the cardinal model with inflection [Rosso et al., 1993 An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model. J. Theor. Bio. 162, 447-463.] were used to fit the experimental data and determine for each factor, the cardinal parameters (minimum, optimum and maximum). Precise characterisation of the growth conditions for such a fungal contaminant, has an evident interest to understand and to prevent spoilage of food products.

Isolation and analysis of differentially expressed genes in Penicillium glabrum subjected to thermal stress.

Penicillium glabrum is a filamentous fungus frequently involved in food contamination. Numerous environmental factors (temperature, humidity, atmospheric composition, etc.) or food characteristics (water activity, pH, preservatives, etc.) could represent potential sources of stress for micro-organisms. These factors can directly affect the physiology of these spoilage micro-organisms: growth, conidiation, synthesis of secondary metabolites, etc. This study investigated the transcriptional response to temperature in P. glabrum, since this factor is one of the most important for fungal growth. Gene expression was first analysed by using suppression subtractive hybridization to generate two libraries containing 445 different up- and downregulated expressed sequence tags (ESTs). Expression of these ESTs was then assessed for different thermal stress conditions, with cDNA microarrays, resulting in the identification of 35 and 49 significantly up- and downregulated ESTs, respectively. These ESTs encode heat-shock proteins, ribosomal proteins, superoxide dismutase, trehalose-6-phosphate synthase and a large variety of identified or unknown proteins. Some of these may be molecular markers for thermal stress response in P. glabrum. To our knowledge, this work represents the first study of the transcriptional response of a food spoilage filamentous fungus under thermal stress conditions.

Characterization of Bacillus and Pseudomonas strains with suppressive traits isolated from tomato hydroponic-slow filtration unit.

Bacillus and Pseudomonas spp. are known to be involved in plant pathogenic fungi elimination during the slow filtration process used in tomato soilless cultures. We isolated 6-8 strains of both Bacillus and Pseudomonas from the top, middle, and bottom sections of filters and identified them after 16S rDNA sequencing. Four Pseudomonas strains were identified as Pseudomonas fulva, 5 as Pseudomonas plecoglossicida, and 12 as Pseudomonas putida. The use of specific oligonucleotide polymerase chain reaction primer sets designed from gyrB gene sequences additionally permitted the identification of 17 Bacillus cereus and 3 Bacillus thuringiensis strains. Ribotyping with EcoRI pointed out an important polymorphism within Bacillus and Pseudomonas strains. Molecular characterization did not reveal a correlation between the location of isolates within the filter (top, middle, or bottom) and bacterial identification or riboclusters. Functional aspects assessed by community-level physiological profiling showed marked phenotypic differences between Pseudomonas communities isolated from the top and bottom filter layers; differences were lower between Bacillus communities of different layers and far less noticeable between mixed communities of Bacillus and Pseudomonas. These strains were tested for several suppressive activities. Conversely to most Bacillus, the majority of Pseudomonas strains were auxin producers and promoted the growth of tomato plantlet roots. On the other hand, only Bacillus strains displayed antagonistic activities by inhibiting the growth of pathogenic fungi frequently detected in soilless cultures. Siderophores were produced by nearly all bacteria, but at higher amounts by Pseudomonas than Bacillus strains. The biocontrol agent potentiality of certain strains to optimize the slow filtration process and to promote the suppressive potential of nutrient solution is discussed.