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PaSiT: A novel approach based on short oligo-nucleotide frequencies for efficient bacterial identification and typing.
No full textMotivation: One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa
is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore
not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but
at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a
novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.
Results: Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically
well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based
method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover,
the lightweight nature of this method makes it applicable for large-scale analyses.
Availability and implementation: The method introduced here was implemented, together with other existing methods,
in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LMUGent/
GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In
addition, a Java-based graphical user interface that acts as a wrapper for the software is also available
Versicolorin A, a precursor in aflatoxins biosynthesis, is a food contaminant toxic for human intestinal cells
No full textAflatoxin B1 (AFB1) is the most potent carcinogen among mycotoxins. Its biosynthesis involves the formation of
versicolorin A (VerA), whose chemical structure shares many features with AFB1. Our data revealed significant
levels of VerA in foodstuff from Central Asia and Africa. Given this emerging food risk, it was of prime interest to
compare the toxic effects of the two mycotoxins against cells originating from the intestinal tract. We used
human colon cell lines (Caco-2, HCT116) to investigate the cytotoxic process induced by the two mycotoxins.
Contrary to AFB1, a low dose of VerA (1 μM) disturbed the expression level of thousands of genes (18 002 genes).
We show that the cytotoxic effects of low doses of VerA (1–20 μM) were stronger than the same low doses of
AFB1 in both Caco-2 and HCT116 cell lines. In Caco-2 cells, VerA induced DNA strand breaks that led to
apoptosis and reduced DNA replication of dividing cells, consequently inhibiting cell proliferation. Although
VerA was able to induce the p53 signaling pathway in p53 wild-type HCT116 cells, its toxicity process did not
mainly rely on p53 expression since similar cytotoxic effects were also observed in HCT116 cells that do not
express p53. In conclusion, this study provides evidence of the risk of food contamination by VerA and shed light
on its toxicological effect on human colon cells
An Overview of the Applications of Nanomaterials and Nanodevices in the Food Industry
No full textThe efficient progress in nanotechnology has transformed many aspects of food science and the food industry with enhanced investment and market share. Recent advances in nanomaterials and nanodevices such as nanosensors, nano-emulsions, nanopesticides or nanocapsules are intended to bring about innovative applications in the food industry. In this review, the current applications of nanotechnology for packaging, processing, and the enhancement of the nutritional value and shelf life of foods are targeted. In addition, the functionality and applicability of food-related nanotechnologies are also highlighted and critically discussed in order to provide an insight into the development and evaluation of the safety of nanotechnology in the food industry
Evaluating the cost-consequence of a standardized strategy for the etiological diagnosis of uveitis (ULISSE study)
No full textMAIN OBJECTIVE: To prospectively assess the cost-consequence of a standardized diagnostic strategy as to compared to an open one for the etiological diagnosis of uveitis. DESIGN: This was a prospective, non-inferiority, multicentre, randomized controlled trial. METHODS: We included all consecutive patients with uveitis who had visited at least one of the Departments of Ophthalmology. In the standardized group, patients had a minimal work-up regardless of the type of uveitis (including evaluation of the CBC, ESR, C-reactive protein, tuberculin skin test, syphilis serology and chest X-ray). Depending on ophthalmological findings, further investigations could be performed. In the open strategy, ophthalmologists were free to order any kind of investigation. The main outcome was the mean cost per patient of each strategy. RESULTS: 903 uveitis patients were included from January, 2010 to May, 2013. The mean cost per patient of the standardized strategy was 182.97 euros [CI 95% (173.14; 192.80)], and the mean cost per patient of the open strategy was 251.75 euros [CI 95% (229.24; 274.25)]. Therefore, the mean cost per patient of the standardized strategy was significantly lower than the mean cost per patient of the open strategy (p<0.001). There were significantly fewer visits (p<0.001), fewer radiological procedures (p<0.004) and fewer laboratory investigations (p<0.001) in the standardized group. CONCLUSION: A standardized strategy is a cost-saving approach for the etiological diagnosis of uveitis
Embryonic thermal manipulation has short and long-term effects on the development and the physiology of the Japanese quail
No full textIn vertebrates, the embryonic environment is known to affect the development and the health of individuals. In broiler chickens, the thermal-manipulation (TM) of eggs during the incubation period was shown to improve heat tolerance at slaughter age (35 days of age) in association with several modifications at the molecular, metabolic and physiological levels. However, little is known about the Japanese quail (Coturnix japonica), a closely related avian species widely used as a laboratory animal model and farmed for its meat and eggs. Here we developed and characterized a TM procedure (39.5°C and 65% relative humidity, 12 h/d, from days 0 to 13 of incubation) in quails by analyzing its short and long-term effects on zootechnical, physiological and metabolic parameters. Heat-tolerance was tested by a heat challenge (36°C for 7h) at 35 days of age. TM significantly reduced the hatching rate of the animals and increased mortality during the first four weeks of life. At hatching, TM animals were heavier than controls, but lighter at 25 days of age for both sexes. Thirty-five days after hatching, TM decreased the surface temperature of the shank in females, suggesting a modulation of the blood flow to maintain the internal temperature. TM also increased blood partial pressure and oxygen saturation percentage at 35 days of age in females, suggesting a long-term modulation of the respiration physiology. Quails physiologically responded to the heat challenge, with a modification of several hematologic and metabolic parameters, including an increase in plasma corticosterone concentration. Several physiological parameters such as beak surface temperature and blood sodium concentration revealed that TM birds responded differently to the heat challenge compared to controls. Altogether, this first comprehensive characterization of TM in Japanese quail showed durable effects that may affect the response of TM quails to heat
Opuntia cladode powders inhibit adipogenesis in 3 T3-F442A adipocytes and a high-fat-diet rat model by modifying metabolic parameters and favouring faecal fat excretion
No full textBackground: Obesity is a major public health concern worldwide. A sedentary life and a nutritional transition to processed foods and high-calorie diets are contributing factors to obesity. The demand for nutraceutical foods, such as herbal weight-loss products, which offer the potential to counteract obesity, has consequently increased. We hypothesised that Opuntia cladodes consumption could assist weight management in an obesity prevention context.
Methods: This study was designed to explore the anti-adipogenic effects of lyophilised Opuntia cladode powders (OCP) in an in vitro cellular model for adipocyte differentiation and an in vivo high-fat-diet (HFD)-induced obesity rat model. Two OCP were tested, one from wild species O. streptacantha and the second from the most known species O. ficus-indica.
Results: Pre-adipocytes 3 T3-F442A were treated by OCP during the differentiation process by insulin. OCP
treatment impaired the differentiation in adipocytes, as supported by the decreased triglyceride content and a low glucose uptake, which remained comparable to that observed in undifferentiated controls, suggesting that an antiadipogenic effect was exerted by OCP. Sprague–Dawley rats were fed with a normal or HFD, supplemented or not with OCP for 8 weeks. OCP treatment slightly reduced body weight gain, liver and abdominal fat weights, improved some obesity-related metabolic parameters and increased triglyceride excretion in the faeces. Taken together, these results showed that OCP might contribute to reduce adipogenesis and fat storage in a HFD context, notably by promoting the faecal excretion of fats.
Conclusions: Opuntia cladodes may be used as a dietary supplement or potential therapeutic agent in diet-based therapies for weight management to prevent obesity
Impact de la fréquence des repiquages sur la stabilité du levain utilisé pour la fabrication d'un lait fermenté traditionnel, le Gwell
No full textLe Gwell aussi appelé « gros-lait », est un lait fermenté issu de la tradition culinaire bretonne, produit à partir de lait de vaches locales bretonnes : Froment du Léon, Armoricaine, Nantaise et surtout la race Bretonne Pie Noir. Il est produit par repiquage, c’est-à-dire qu’on l’obtient en ensemençant du lait avec du Gwell de la production précédente, qui sert alors de ferment. Le repiquage ne donne parfois pas lieu à une acidification suffisante, le Gwell est alors dit « perdu ». La seule solution pour le producteur est d’obtenir un nouveau Gwell chez un collègue. L’Union Bretonne Pie Noir qui détient la marque Gwell a pris part à un projet européen soutenant la valorisation des produits issus de races locales. Un volet du projet visait à sécuriser la production de Gwell en identifiant les facteurs potentiellement à l'origine de la perte du ferment.
Mon stage s'inscrivait dans la continuité du projet précédemment cité dans le cadre duquel on a montré que l'écosystème bactérien du Gwell reposait sur un équilibre entre 2 sous espèces de bactéries lactiques majoritaires : Lactococcus lactis sp. cremoris et Lactococcus lactis sp. lactis et que des repiquages trop rapprochés pourraient être responsables de la perte du ferment. Le sujet de mon stage visait donc à étudier l’impact de la fréquence des repiquages sur la stabilité du levain Gwell. Ce sujet a été conduit en étroite collaboration avec Lucas Von Gastrow, un doctorant, au sein de l'équipe CIRM-BIA, un centre de ressources biologiques de l'INRAe dédié aux bactéries d'intérêt alimentaires.
Pour ce faire, en concertation avec 3 producteurs de Gwell, sélectionnés sur la base de résultat antérieurs, deux fréquences de repiquage ont été étudiées : soit un repiquage toutes les semaines, soit un repiquage 3 fois par semaine. Sachant qu'entre 2 repiquages le Gwell est conservé à 4°C et que la fermentation est conduite à 30°C, pour prendre en compte l’environnement varié pendant la fabrication et la conservation, deux contrôles respectivement à 30 et 4°C ont été inclus dans notre suivi. L’analyse de la stabilité du ferment Gwell était évaluée sur sa capacité acidifiante (suivi cinétique du pH pendant la fabrication) et sur l'analyse microbiolgique du Gwell résultats (dénombrement).
Les résultats que nous avons obtenus mettent en évidence que la fréquence de repiquage a un effet direct sur l'équilibre entre les 2 sous espèces de Lactococcus : lactis et cremoris, le repiquage fréquent du Gwell étant responsable d'une augmentation de cremoris au détriment de lactis. La variation environnementale temporelle (passage sucessifs à 30 et 4°C) permet le maintien de l'équilibre entre lactis et cremoris mais la conservation sur une longue durée sans repiquage conduit au déséquilibre du ferment et est responsable d'une diminution de la population de la sous-espèce lactis avec en parallèle une augmentation du nombre de levures
Microstructure and chemical composition of camel and cow milk powders’ surface
No full textThis study aimed at investigating the chemical composition and microstructure of spray dried camel and cow
milk powders' surfaces with two different milk-fat contents (1 and 20g 100 g−1). The SEM (Scanning Electron
Microscopy) micrographs showed that spherical particles with a ‘brain’-type surface for both milk powders were
produced. The surface roughness (Ra) of whole (WDMP) and skimmed (SDMP) camel milk powders
(Ra=7.6 ± 0.4 nm and 5.6 ± 0.7 nm, respectively) were significantly lower as compared with the partially
skimmed (PSCMP) and skimmed (SCMP) cow milk powders. The XPS (X-ray Photoelectron Spectroscopy)
analysis highlighted that the surface of skimmed camel milk powders contained twice the lactose amount
(17.7 ± 0.8%) as compared to cow milk powders (8.7 ± 0.4%). Furthermore, both milk powders showed the
overexposure of proteins and fats at their surfaces regardless of the fat content. The CLSM (Confocal Laser
Scattering Microscopy) micrographs highlighted that most of the camel milk fat globules were encapsulated by
the proteins near the powder surface. Camel milk fat behavior during particle formation was attributed to their
lower size distribution and their higher crystallization temperature
About frame estimation of growth functions and robust prediction in bioprocess modeling
No full textWe address the problem of determining functional framing from experimental data points in view of robust time-varying predictions, which is of crucial importance in bioprocess monitoring. We propose a method that provides guaranteed functional bounds, instead of sets of parameters values for growth functions such as the classical Monod or Haldane functions commonly used in bioprocess modeling. We illustrate the applicability of the method with bioreactor simulations in batch and continuous mode, as well as on real data. We also present two extensions of the method adding flexibility in its application, and discuss its efficiency in providing guaranteed state estimations