Laboratoire de Génie des Procédés – Environnement – Agro-alimentaire

In this paper, the use of the reassignment method, first applied by Kodera, Gendrin, and de Villedary (1976) to the spectrogram, is generalized to any bilinear time-frequency or time-scale distribution. This method creates a modified version of a representation by moving its values away from where they are computed, so as to produce a better localization of the signal components. We first propose a new formulation of this method, followed by a thorough theoretical study of its characteristics. Its practical use for a large variety of known time-frequency and time-scale distributions is then addressed. Finally, some experimental results are reported to demonstrate the performance of this method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Grafted fat has many attributes of an ideal filler, but the results, like those of any procedure, are technique dependent. Fat grafting remains shrouded in the stigma of variable results experienced by most plastic surgeons when they first graft fat. However, many who originally reported failure eventually report success after altering their methods of harvesting, refinement, and placement. Many surgeons have refined their techniques to obtain long-term survival and volume replacement with grafted fat. They have observed that transplanted fat not only adjusts facial and body proportion but also improves surrounding tissues into which the fat is placed. They have noted not only the improvement in the quality of aging skin and scars but also a remarkable improvement in conditions such as radiation damage, chronic ulceration, breast capsular contracture, and damaged vocal cords. The mechanism of fat graft survival is not clear, and the role of adipose-derived stem cells and preadipocytes in fat survival remains to be determined. Early research has indicated the possible involvement of more undifferentiated cells in some of the observed effects of fat grafting on surrounding tissues. Of particular interest is the research that has pointed to the use of stem cells to repair and even to become bone, cartilage, muscle, blood vessels, nerves, and skin. Further studies are essential to understand grafted fat tissue.

Sugar beet pulp generated by sugar-refining factories has been shown to be an effective adsorbent for the removal of heavy metals from aqueous solutions. The structural components related to the metallic adsorption being determined, batch adsorption studies were performed for several metal ions, namely, Pb2+, Cu2+, Zn2+, Cd2+, and Ni2+ cations. Two simple kinetic models, that is, pseudo-first- and pseudo-second-order, were tested to investigate the adsorption mechanisms. The kinetic parameters of the models were calculated and discussed. For an 8 x 10(-4) M initial metal concentration, the initial sorption rates (v0) ranged from 0.063 mmol x g(-1) x min(-1) for Pb2+ to 0.275 mmol x g(-1) x min(-1) for Ni2+ ions, in the order Ni2+ > Cd2+ > Zn2+ > Cu2+ > Pb2+. The equilibrium data fitted well with the Langmuir and Freundlich models and showed the following affinity order of the material: Pb2+ > Cu2+ > Zn2+ > Cd2+ > Ni2+. The metal removal was strongly dependent on pH and, to a lesser extent, ionic strength. Ion exchange with Ca2+ ions neutralizing the carboxyl groups of the polysaccharide was found to be the predominant mechanism, added with complexation for Pb2+, Cu2+, and Zn2+ metals.

SUMMARY: The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus. AVAILABILITY: PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.

The unicellular green alga Chlamydomonas reinhardtii is a prime model for deciphering processes occurring in the intracellular compartments of the photosynthetic cell. Organelle-specific proteomic studies have started to delineate its various subproteomes, but sequence-based prediction software is necessary to assign proteins subcellular localizations at whole genome scale. Unfortunately, existing tools are oriented toward land plants and tend to mispredict the localization of nuclear-encoded algal proteins, predicting many chloroplast proteins as mitochondrion targeted. We thus developed a new tool called PredAlgo that predicts intracellular localization of those proteins to one of three intracellular compartments in green algae: the mitochondrion, the chloroplast, and the secretory pathway. At its core, a neural network, trained using carefully curated sets of C. reinhardtii proteins, divides the N-terminal sequence into overlapping 19-residue windows and scores the probability that they belong to a cleavable targeting sequence for one of the aforementioned organelles. A targeting prediction is then deduced for the protein, and a likely cleavage site is predicted based on the shape of the scoring function along the N-terminal sequence. When assessed on an independent benchmarking set of C. reinhardtii sequences, PredAlgo showed a highly improved discrimination capacity between chloroplast- and mitochondrion-localized proteins. Its predictions matched well the results of chloroplast proteomics studies. When tested on other green algae, it gave good results with Chlorophyceae and Trebouxiophyceae but tended to underpredict mitochondrial proteins in Prasinophyceae. Approximately 18% of the nuclear-encoded C. reinhardtii proteome was predicted to be targeted to the chloroplast and 15% to the mitochondrion.

Paratuberculosis, a chronic disease affecting ruminant livestock, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has direct and indirect economic costs, impacts animal welfare and arouses public health concerns. In a survey of 48 countries we found paratuberculosis to be very common in livestock. In about half the countries more than 20% of herds and flocks were infected with MAP. Most countries had large ruminant populations (millions), several types of farmed ruminants, multiple husbandry systems and tens of thousands of individual farms, creating challenges for disease control. In addition, numerous species of free-living wildlife were infected. Paratuberculosis was notifiable in most countries, but formal control programs were present in only 22 countries. Generally, these were the more highly developed countries with advanced veterinary services. Of the countries without a formal control program for paratuberculosis, 76% were in South and Central America, Asia and Africa while 20% were in Europe. Control programs were justified most commonly on animal health grounds, but protecting market access and public health were other factors. Prevalence reduction was the major objective in most countries, but Norway and Sweden aimed to eradicate the disease, so surveillance and response were their major objectives. Government funding was involved in about two thirds of countries, but operations tended to be funded by farmers and their organizations and not by government alone. The majority of countries (60%) had voluntary control programs. Generally, programs were supported by incentives for joining, financial compensation and/or penalties for non-participation. Performance indicators, structure, leadership, practices and tools used in control programs are also presented. Securing funding for long-term control activities was a widespread problem. Control programs were reported to be successful in 16 (73%) of the 22 countries. Recommendations are made for future control programs, including a primary goal of establishing an international code for paratuberculosis, leading to universal acknowledgment of the principles and methods of control in relation to endemic and transboundary disease. An holistic approach across all ruminant livestock industries and long-term commitment is required for control of paratuberculosis.

Postmortem tenderization is caused by enzymatic degradation of key structural proteins in myofibrils as well as in extracellular matrix, and of proteins involved in intermyofibrillar linkages and linkages between myofibrils and the sarcolemma. The function of these proteins is to maintain the structural integrity of myofibrils. Current data indicate that calpains and cathepsins may be responsible for degradation of these proteins. Other phenomena occurring in cells postmortem (pH drop, sarcoplasmic Ca2+ increase, osmotic pressure rise, oxidative processes) may act in synergy with proteases. Our understanding of the underlying mechanisms of muscle degradation should be improved for an accurate evaluation of the postmortem muscle changes and consequently of the fish quality.

Helminth infections are ubiquitous in grazing ruminant production systems, and are responsible for significant costs and production losses. Anthelmintic Resistance (AR) in parasites is now widespread throughout Europe, although there are still gaps in our knowledge in some regions and countries. AR is a major threat to the sustainability of modern ruminant livestock production, resulting in reduced productivity, compromised animal health and welfare, and increased greenhouse gas emissions through increased parasitism and farm inputs. A better understanding of the extent of AR in Europe is needed to develop and advocate more sustainable parasite control approaches. A database of European published and unpublished AR research on gastrointestinal nematodes (GIN) and liver fluke (Fasciola hepatica) was collated by members of the European COST Action "COMBAR" (Combatting Anthelmintic Resistance in Ruminants), and combined with data from a previous systematic review of AR in GIN. A total of 197 publications on AR in GIN were available for analysis, representing 535 studies in 22 countries and spanning the period 1980-2020. Reports of AR were present throughout the European continent and some reports indicated high within-country prevalence. Heuristic sample size-weighted estimates of European AR prevalence over the whole study period, stratified by anthelmintic class, varied between 0 and 48%. Estimated regional (country) prevalence was highly heterogeneous, ranging between 0% and 100% depending on livestock sector and anthelmintic class, and generally increased with increasing research effort in a country. In the few countries with adequate longitudinal data, there was a tendency towards increasing AR over time for all anthelmintic classes in GIN: aggregated results in sheep and goats since 2010 reveal an average prevalence of resistance to benzimidazoles (BZ) of 86%, macrocyclic lactones except moxidectin (ML) 52%, levamisole (LEV) 48%, and moxidectin (MOX) 21%. All major GIN genera survived treatment in various studies. In cattle, prevalence of AR varied between anthelmintic classes from 0-100% (BZ and ML), 0-17% (LEV) and 0-73% (MOX), and both Cooperia and Ostertagia survived treatment. Suspected AR in F. hepatica was reported in 21 studies spanning 6 countries. For GIN and particularly F. hepatica, there was a bias towards preferential sampling of individual farms with suspected AR, and research effort was biased towards Western Europe and particularly the United Kingdom. Ongoing capture of future results in the live database, efforts to avoid bias in farm recruitment, more accurate tests for AR, and stronger appreciation of the importance of AR among the agricultural industry and policy makers, will support more sophisticated analyses of factors contributing to AR and effective strategies to slow its spread.

Changes induced by high pressure (HP) treatment (200-600 MPa) on soybean protein isolates (SPI) at pH 3 (SPI3) and pH 8 (SPI8) were analyzed. Changes in protein solubility, surface hydrophobicity (Ho), and free sulfhydryl content (SH(F)) were determined. Protein aggregation and denaturation and changes in secondary structure were also studied. An increase in protein Ho and aggregation, a reduction of free SH, and a partial unfolding of 7S and 11S fractions were observed in HP-treated SPI8. Changes in secondary structure were also detected, which led to a more disordered structure. HP-treated SPI3 was partially denatured and presented insoluble aggregates. A major molecular unfolding, a decrease of thermal stability, and an increase of protein solubility and Ho were also detected. At 400 and 600 MPa, a decrease of the SH(F) and a total denaturation were observed.

The light attenuation in a photobioreactor is determined using a fully predictive model. The optical properties were first calculated, using a data bank of the literature, from only the knowledge of pigments content, shape, and size distributions of cultivated cells which are a function of the physiology of the current species. The radiative properties of the biological turbid medium were then deduced using the exact Lorenz-Mie theory. This method is experimentally validated using a large-size integrating sphere photometer. The radiative properties are then used in a rectangular, one-dimensional two-flux model to predict radiant light attenuation in a photobioreactor, considering a quasi-collimated field of irradiance. Combination of this radiative model with the predictive determination of optical properties is finally validated by in situ measurement of attenuation profiles in a torus photobioreactor cultivating the microalgae Chlamydomonas reinhardtii, after a complete and proper characterization of the incident light flux provided by the experimental set-up.

Starch is a versatile and a widely used ingredient, with applications in many industries including adhesive and binding, paper making, corrugating, construction, paints and coatings, chemical, pharmaceutical, textiles, oilfield, food and feed. However, native starches present limited applications, which impairs their industrial use. Consequently, starch is commonly modified to achieve desired properties. Chemical treatments are the most exploited to bring new functionalities to starch. However, those treatments can be harmful to the environment and can also bring risks to the human health, limiting their applications. In this scenario, there is a search for techniques that are both environmentally friendly and efficient, bringing new desired functionalities to starches. Therefore, this review presents an up-to-date overview of the available literature data regarding the use of environmentally friendly treatments for starch modification. Among them, we highlighted an innovative chemical treatment (ozone) and different physical treatments, as the modern pulsed electric field (PEF), the emerging ultrasound (US) technology, and two other treatments based on heating (dry heating treatment - DHT, and heat moisture treatment - HMT). It was observed that these environmentally friendly technologies have potential to be used for starch modification, since they create materials with desirable functionalities with the advantage of being categorized as clean label ingredients.

Abstract: For years, high‐pressure processing has been viewed as useful for pasteurizing food while maintaining the quality of fresh food. However, even at moderate pressure, this process is not without effects on food, especially on meat products. These effects are especially important because pressure greater than 400 MPa is generally necessary to achieve efficient microbial inactivation. In this review, recent advances in the understanding of the impacts of high pressure on the overall quality of raw and processed meat are discussed. Many factors, including meat product formulation and processing parameters, can influence the efficiency of high pressure in pasteurizing meat products. It appears that new strategies are applied either (i) to improve the microbial inactivation that results from high pressure while minimizing the adverse effects of high pressure on meat quality or (ii) to take advantage of changes in meat attributes under high pressure. Most of the time, multiple preservation factors or techniques are combined to produce safe, stable, and high‐quality food products. Among the new applications of high‐pressure techniques for meat and meat‐derivative products are their use in combination with temperature manipulation to texturize and pasteurize new meat products simultaneously.

• COVID-19 pandemic is clearly challenging the entire food system. • A collective action is needed in order to build food systems that are resilient. • Food systems are multidisciplinary and highly interconnected. • Food security is important in times of shocks and crises.

ABSTRACT: An ultra high‐pressure homogenizer (20 to 350 MPa) was used to realize fine food emulsions stabilized by soy proteins. The first aim of the work was to understand how dynamic high‐pressure processing affects soybean globulin conformation. Then, the effect of homogenizing pressure on the emulsions structure and rheology was investigated. High‐pressure homogenization caused denaturation of proteins due to strong mechanical forces and high temperatures encountered in the valve. Droplet sizes of emulsions were greatly reduced with high‐pressure homogenization and Newtonian liquid emulsions were converted into shear‐thinning emulsion gels by homogenization at pressures above 250 MPa. Hydrophobic interactions between proteins were supposed to cause the gel‐like network structure of emulsions.

Anthelmintic resistance has been increasingly reported in cattle worldwide over the last decade, although reports from Europe are more limited. The objective of the present study was to evaluate the efficacy of injectable formulations of ivermectin and moxidectin at 0.2 mg per kg bodyweight against naturally acquired gastro-intestinal nematodes in cattle. A total of 753 animals on 40 farms were enrolled in Germany (12 farms), the UK (10 farms), Italy (10 farms), and France (8 farms). Animals were selected based on pre-treatment faecal egg counts and were allocated to one of the two treatment groups. Each treatment group consisted of between 7 and 10 animals. A post-treatment faecal egg count was performed 14 days (±2 days) after treatment. The observed percentage reduction was calculated for each treatment group based on the arithmetic mean faecal egg count before and after treatment. The resistance status was evaluated based on the reduction in arithmetic mean faecal egg count and both the lower and upper 95% confidence limits. A decreased efficacy was observed in half or more of the farms in Germany, France and the UK. For moxidectin, resistance was confirmed on 3 farms in France, and on 1 farm in Germany and the UK. For ivermectin, resistance was confirmed on 3 farms in the UK, and on 1 farm in Germany and France. The remaining farms with decreased efficacy were classified as having an inconclusive resistance status based on the available data. After treatment Cooperia spp. larvae were most frequently identified, though Ostertagia ostertagi was also found, in particular within the UK and Germany. The present study reports lower than expected efficacy for ivermectin and moxidectin (based on the reduction in egg excretion after treatment) on European cattle farms, with confirmed anthelmintic resistance on 12.5% of the farms.

ABSTRACT High pressure is an innovative non‐thermal food‐preservation technology. We studied the effect of high‐pressure treatment up to 500 MPa for 5 min on physical characteristics of sea bass fillets after 0, 7, and 14 d of refrigerated storage. Color results exhibited an increase of lightness and a slight change of hue, which might be imperceptible in cooked fish. High‐pressure treatment induced a decrease of exudation and water‐holding capacity. Pressure treatment above 300 MPa provoked higher fish hardness after storage than in untreated sample, proving the ability of high pressure to improve textural quality of chilled, stored fish fillet. These assessments were corroborated with microstructure observations. We showed that high‐pressure treatment at 500 MPa allowed, after 7 d of storage, a total aerobic count equivalent to that of untreated fresh fish fillet to be obtained. Thus, high pressure might be considered to be a technology able to improve safety and textural quality of fresh fish fillets.

Edible insects are advocated as sustainable and healthy food and feed. However, commercially produced insects are often low in n-3 fatty acids and have suboptimal n-6/n-3 ratios. A certain amount and proportion of these FAs is required to optimize human health. Flaxseed oil consists primarily (57%) out of alpha-linolenic acid. An experiment was conducted to quantify the effect of flaxseed oil provision on fatty acid composition and to determine the quantity needed to attain a beneficial n-6/n-3 ratio. Three species were used in the experiment: house crickets (Acheta domesticus [L.]), lesser mealworms (Alphitobius diaperinus [Pfanzer]) and black soldier flies (Hermetia illucens [L.]). These were provided with either a control diet or a diet enriched with 1%, 2%, or 4% flaxseed oil during their larval/nymphal stage. Fatty acid profiles of diets and insects were determined via GC-MS. The three species had distinct fatty acid profiles on all four diets, but responded similarly to flaxseed oil addition. For each percent added to the diet, the alpha-linolenic acid content of the insects increased by 2.3%-2.7%. Four percent addition increased the n-3 fatty acid content 10-20 fold in the three species and thereby strongly decreased n-6/n-3 ratios from 18-36 to 0.8-2.4. A ratio below 5 is considered optimal for human health and was achieved by 2% flaxseed oil inclusion for house crickets and lesser mealworms, and at 1% inclusion for black soldier flies. Adding a source of n-3 fatty acids to insect diets can thus improve the nutritional quality of insects.

The past decade has seen a surge in the interest in microalgae culture for biodiesel production and other applications as renewable biofuels as an alternative to petroleum transport fuels. The development of new technologies for the culture of these photosynthetic microorganisms and improved knowledge of their biochemical composition has spurred innovation in the field of high-value biomolecules. These developments are only economically viable if all the microalgae fractions are valorized in a biorefinery strategy. Achieving this objective requires an understanding of microalgae content and the cellular localization of the main biomolecular families in order to develop efficient harvest and sequential recovery technologies. This review summarizes the state of the art in microalgae compositions and topologies using some examples of the main industrially farmed microalgae.

In Chlamydomonas reinhardtii cells, H2 photoproduction can be induced in conditions of sulfur deprivation in the presence of acetate. The decrease in photosystem II (PSII) activity induced by sulfur deprivation leads to anoxia, respiration becoming higher than photosynthesis, thereby allowing H2 production. Two different electron transfer pathways, one PSII dependent and the other PSII independent, have been proposed to account for H2 photoproduction. In this study, we investigated the contribution of both pathways as well as the acetate requirement for H2 production in conditions of sulfur deficiency. By using 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), a PSII inhibitor, which was added at different times after the beginning of sulfur deprivation, we show that PSII-independent H2 photoproduction depends on previously accumulated starch resulting from previous photosynthetic activity. Starch accumulation was observed in response to sulfur deprivation in mixotrophic conditions (presence of acetate) but also in photoautotrophic conditions. However, no H2 production was measured in photoautotrophy if PSII was not inhibited by DCMU, due to the fact that anoxia was not reached. When DCMU was added at optimal starch accumulation, significant H2 production was measured. H2 production was enhanced in autotrophic conditions by removing O2 using N2 bubbling, thereby showing that substantial H2 production can be achieved in the absence of acetate by using the PSII-independent pathway. Based on these data, we discuss the possibilities of designing autotrophic protocols for algal H2 photoproduction.

Combined sewer overflows (CSOs) are of major environmental concern for impacted surface waterbodies. In the last decades, major storm events have become increasingly regular in some areas, and meteorological scenarios predict a further rise in their frequency. Consequently, control and treatment of CSOs with respect to best practice examples, innovative treatment solutions, and management of sewer systems are an inevitable necessity. As a result, the number of publications concerning quality, quantity, and type of treatments has recently increased. This review therefore aims to provide a critical overview on the effects, control, and treatment of CSOs in terms of impact on the environment and public health, strict measures addressed by regulations, and the various treatment alternatives including natural and compact treatments. Drawing together the previous studies, an innovative treatment and control guideline are also proposed for the better management practices.