A method for comparison of growth media in objective identification of Penicillium based on multi-spectral imaging

Online Feature Selection for Robust Classification of the Microbiological Quality of Traditional Vanilla Cream by Means of Multispectral Imaging

The performance of an Unsupervised Online feature Selection (UOS) algorithm was investigated for the selection of training features of multispectral images acquired from a dairy product (vanilla cream) stored under isothermal conditions. The selected features were further used as input in a support vector machine (SVM) model with linear kernel for the determination of the microbiological quality of vanilla cream. Model training (n = 65) was based on two batches of cream samples provided directly by the manufacturer and stored at different isothermal conditions (4, 8, 12, and 15 °C), whereas model testing (n = 132) and validation (n = 48) were based on real life conditions by analyzing samples from different retail outlets as well as expired samples from the market. Qualitative analysis was performed for the discrimination of cream samples in two microbiological quality classes based on the values of total viable counts [TVC ≤ 2.0 log CFU/g (fresh samples) and TVC ≥ 6.0 log CFU/g (spoiled samples)]. Results exhibited good performance with an overall accuracy of classification for the two classes of 91.7% for model validation. Further on, the model was extended to include the samples in the TVC range 2-6 log CFU/g, using 1 log step to define the microbiological quality of classes in order to assess the potential of the model to estimate increasing microbial populations. Results demonstrated that high rates of correct classification could be obtained in the range of 2-5 log CFU/g, whereas the percentage of erroneous classification increased in the TVC class (5,6) that was close to the spoilage level of the product. Overall, the results of this study demonstrated that the UOS algorithm in tandem with spectral data acquired from multispectral imaging could be a promising method for real-time assessment of the microbiological quality of vanilla cream samples.

Quantitative analysis of morphological changes in yeast colonies growing on solid medium: the eccentricity and Fourier indices

The colony shape of four yeast species growing on agar medium was measured for 116 days by image analysis. Initially, all the colonies are circular, with regular edges. The loss of circularity can be quantitatively estimated by the eccentricity index, Ei , calculated as the ratio between their orthogonal vertical and horizontal diameters. Ei can increase from 1 (complete circularity) to a maximum of 1.17-1.30, depending on the species. One colony inhibits its neighbour only when it has reached a threshold area. Then, Ei of the inhibited colony increases proportionally to the area of the inhibitory colony. The initial distance between colonies affects those threshold values but not the proportionality, Ei /area; this inhibition affects the shape but not the total surface of the colony. The appearance of irregularities in the edges is associated, in all the species, not with age but with nutrient exhaustion. The edge irregularity can be quantified by the Fourier index, Fi , calculated by the minimum number of Fourier coefficients that are needed to describe the colony contour with 99% fitness. An ad hoc function has been developed in Matlab v. 7.0 to automate the computation of the Fourier coefficients. In young colonies, Fi has a value between 2 (circumference) and 3 (ellipse). These values are maintained in mature colonies of Debaryomyces, but can reach values up to 14 in Saccharomyces. All the species studied showed the inhibition of growth in facing colony edges, but only three species showed edge irregularities associated with substrate exhaustion.

Multispectral image analysis for robust prediction of astaxanthin coating

The aim of this study was to investigate the possibility of predicting the type and concentration level of astaxanthin coating of aquaculture feed pellets using multispectral image analysis. We used both natural and synthetic astaxanthin, and we used several different concentration levels of synthetic astaxanthin in combination with four different recipes of feed pellets. We used a VideometerLab with 20 spectral bands in the range of 385-1050 nm. We used linear discriminant analysis and sparse linear discriminant analysis for classification and variable selection. We used partial least squares regression (PLSR) for prediction of the concentration level. The results show that it is possible to predict the level of synthetic astaxanthin coating using PLSR on either the same recipe, or when calibrating on all recipes. The concentration prediction is adequate for screening for all recipes. Moreover, it shows that it is possible to predict the type of astaxanthin used in the coating using only ten spectral bands. Finally, the most selected spectral bands for astaxanthin prediction are in the visible range of the spectrum.

Potential fungal inhibition by immobilized hydrolytic enzymes from Trichoderma asperellum

The use of cell wall degrading enzymes from Trichoderma asperellum immobilized on biodegradable support is an alternative for food packaging. In this study, hydrolytic enzymes produced by T. asperellum were tested as a fungal growth inhibitor, in free form or immobilized on a biodegradable film composed of cassava starch and poly(butylene adipate-co-terephtalate) (PBAT). The inhibitory activity was tested against Aspergillus niger , Penicillium sp., and Sclerotinia sclerotiorum , microorganisms that frequently degrade food packaging. The use of chitin as carbon source in liquid medium induced T. asperellun to produce N-acetylglucosaminidase, β-1,3-glucanase, chitinase, and protease. The presence of T. asperellun cell wall degradating enzymes (T-CWD) immobilized by adsorption or covalent attachment resulted in effective inhibition of fungal growth. The enzymatic activity of T-CWD was stronger on S. sclerotiorum than on the Aspergillus or Penicillum isolates tested. These results suggest that T-CWD can be used in a free or immobilized form to suppress fungi that degrade food packaging.

Applying Parallel Factor Analysis models to HPLC diode array detector datasets reveals strain dependent regulation of polyketide biosynthesis in Fusarium graminearum, Fusarium culmorum and Fusarium pseudograminearum

Fungal secondary metabolites confer an indiscriminate resource of bioactive compounds with both pharmaceutical and industrial relevance. Synthesis of these compounds is tightly controlled through regulatory networks. These networks act in response to the environmental conditions in which the fungus grows. One class of fungal secondary metabolites that have drawn increased attention, is the polyketides produced by a high number of fungi and bacteria. The increasing number of publicly available genomic sequences of filamentous fungi, combined with new and highly efficient DNA-cloning techniques, has allowed the use of new efficient approaches to study the regulation and synthesis of these compounds. With the availability of new molecular genetic tools, a new bottleneck has occurred in fungal molecular biology; the analytical chemical analysis of the generated transgenic mutants. In this study, a method based on PARAFAC data analysis of HPLC data is presented and shown useful for gaining overview of complex and diverse datasets. Further, the strain specific and nutrient dependent regulation of polyketide synthesis is discussed.

European species of Hypocrea Part I. The green-spored species

At present 75 species of Hypocrea have been identified in temperate Europe. Nineteen green-spored species and their Trichoderma asexual states are here described in detail. Extensive searches for Hypocrea teleomorphs in 14 European countries, with emphasis on Central Europe, yielded more than 620 specimens within five years. The morphology of fresh and dry stromata was studied. In addition, available types of species described from Europe were examined. Cultures were prepared from ascospores and used to study the morphology of cultures and anamorphs, to determine growth rates, and to extract DNA that was used for amplification and sequencing of three genetic markers. ITS was used for identification, while RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) were analyzed for phylogenetic reconstruction of the genus.SEVERAL UNEXPECTED FINDINGS RESULTED FROM THIS PROJECT: 1) The previous view that only a small number of Trichoderma species form a teleomorph is erroneous. 2) All expectations concerning the number of species in Europe are by far exceeded. Seventy-five species of Hypocrea, two species of Protocrea, and Arachnocrea stipata, are herein identified in temperate Europe, based on the ITS identification routine using fresh material, on species described earlier without molecular data and on species recently described but not collected during this project. 3) Current data suggest that the biodiversity of Hypocrea / Trichoderma above soil exceeds the number of species isolated from soil. 4) The number of Trichoderma species forming hyaline conidia has been considered a small fraction. In Europe, 26 species of those forming teleomorphs produce hyaline conidia, while 42 green-conidial species are known. Three of the detected Hypocrea species do not form an anamorph in culture, while the anamorph is unknown in four species, because they have never been cultured.This work is a preliminary account of Hypocrea and their Trichoderma anamorphs in Europe. Of the hyaline-spored species, H. minutispora is by far the most common species in Europe, while of the green-spored species this is H. strictipilosa.General ecology of Hypocrea is discussed. Specific associations, either with host fungi or trees have been found, but the majority of species seems to be necrotrophic on diverse fungi on wood and bark.The taxonomy of the genus will be treated in two parts. In this first part 19 species of Hypocrea with green ascospores, including six new teleomorph and five new anamorph species, are described in detail. All green-spored species belong to previously recognised clades, except H. spinulosa, which forms the new Spinulosa Clade with two additional new species, and H. fomiticola, which belongs to the Semiorbis Clade and forms effuse to large subpulvinate stromata on Fomes fomentarius, a trait new for species with green ascospores. Anamorph names are established prospectively in order to provide a basis for possible policy alterations towards their use for holomorphs.