Showing papers by "Agrocampus Ouest published in 2015"

A standardised static in vitro digestion method suitable for food – an international consensus

Abstract: Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

Multiple pathways regulate shoot branching

Abstract: Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.

Emergence Shapes the Structure of the Seed Microbiota

Abstract: Seeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment of gyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

Determinants of urban sprawl in European cities

Abstract: This paper provides empirical evidence that helps to answer several key questions relating to the extent of urban sprawl in Europe. Building on the monocentric city model, this study uses existing data sources to derive a set of panel data for 282 European cities at three time points (1990, 2000 and 2006). Two indices of urban sprawl are calculated that, respectively, reflect changes in artificial area and the levels of urban fragmentation for each city. These are supplemented by a set of data on various economic and geographical variables that might explain the variation of the two indices. Using a Hausman-Taylor estimator and random regressors to control for the possible correlation between explanatory variables and unobservable city-level effects, we find that the fundamental conclusions of the standard monocentric model are valid in the European context for both indices. Although the variables generated by the monocentric model explain a large part of the variation of artificial area, their explanatory power for modelling the fragmentation index is relatively low.

Modifications of structures and functions of caseins: a scientific and technological challenge

Abstract: Casein molecules are used in food industry as ingredients. They can be used as isolated forms and under micellar form consisting in an association of different casein molecules and calcium phosphate. In this review, after a brief reminder of the main characteristics of casein molecules and casein micelles, the modifications of caseins induced by physical, chemical, and enzymatic actions are reported. The resulting new physicochemical properties (mineral and casein compositions, charge, hydrophobicity, aggregation state, and morphology) and techno-functionalities (heat stability, viscosity, gelation, emulsifying, and foaming properties) are described and discussed with a special attention paid to the results obtained in our laboratory since several decades.

Effects of global change during the 21st century on the nitrogen cycle

Abstract: . The global nitrogen (N) cycle at the beginning of the 21st century has been shown to be strongly influenced by the inputs of reactive nitrogen (Nr) from human activities, including combustion-related NOx, industrial and agricultural N fixation, estimated to be 220 Tg N yr−1 in 2010, which is approximately equal to the sum of biological N fixation in unmanaged terrestrial and marine ecosystems. According to current projections, changes in climate and land use during the 21st century will increase both biological and anthropogenic fixation, bringing the total to approximately 600 Tg N yr−1 by around 2100. The fraction contributed directly by human activities is unlikely to increase substantially if increases in nitrogen use efficiency in agriculture are achieved and control measures on combustion-related emissions implemented. Some N-cycling processes emerge as particularly sensitive to climate change. One of the largest responses to climate in the processing of Nr is the emission to the atmosphere of NH3, which is estimated to increase from 65 Tg N yr−1 in 2008 to 93 Tg N yr−1 in 2100 assuming a change in global surface temperature of 5 °C in the absence of increased anthropogenic activity. With changes in emissions in response to increased demand for animal products the combined effect would be to increase NH3 emissions to 135 Tg N yr−1. Another major change is the effect of climate changes on aerosol composition and specifically the increased sublimation of NH4NO3 close to the ground to form HNO3 and NH3 in a warmer climate, which deposit more rapidly to terrestrial surfaces than aerosols. Inorganic aerosols over the polluted regions especially in Europe and North America were dominated by (NH4)2SO4 in the 1970s to 1980s, and large reductions in emissions of SO2 have removed most of the SO42− from the atmosphere in these regions. Inorganic aerosols from anthropogenic emissions are now dominated by NH4NO3, a volatile aerosol which contributes substantially to PM10 and human health effects globally as well as eutrophication and climate effects. The volatility of NH4NO3 and rapid dry deposition of the vapour phase dissociation products, HNO3 and NH3, is estimated to be reducing the transport distances, deposition footprints and inter-country exchange of Nr in these regions. There have been important policy initiatives on components of the global N cycle. These have been regional or country-based and have delivered substantial reductions of inputs of Nr to sensitive soils, waters and the atmosphere. To date there have been no attempts to develop a global strategy to regulate human inputs to the nitrogen cycle. However, considering the magnitude of global Nr use, potential future increases, and the very large leakage of Nr in many forms to soils, waters and the atmosphere, international action is required. Current legislation will not deliver the scale of reductions globally for recovery from the effects of Nr deposition on sensitive ecosystems, or a decline in N2O emissions to the global atmosphere. Such changes would require substantial improvements in nitrogen use efficiency across the global economy combined with optimization of transport and food consumption patterns. This would allow reductions in Nr use, inputs to the atmosphere and deposition to sensitive ecosystems. Such changes would offer substantial economic and environmental co-benefits which could help motivate the necessary actions.

Principal component analysis with missing values: a comparative survey of methods

Abstract: Principal component analysis (PCA) is a standard technique to summarize the main structures of a data table containing the measurements of several quantitative variables for a number of individuals. Here, we study the case where some of the data values are missing and propose a review of methods which accommodate PCA to missing data. In plant ecology, this statistical challenge relates to the current effort to compile global plant functional trait databases producing matrices with a large amount of missing values. We present several techniques to consider or estimate (impute) missing values in PCA and compare them using theoretical considerations. We carried out a simulation study to evaluate the relative merits of the different approaches in various situations (correlation structure, number of variables and individuals, and percentage of missing values) and also applied them on a real data set. Lastly, we discuss the advantages and drawbacks of these approaches, the potential pitfalls and future challenges that need to be addressed in the future.

The downside of eDNA as a survey tool in water bodies

Abstract: Summary 1. There is a growing literature on the detection of species-specific DNA fragments in waterto reveal animals’ presence in aquatic environments. 2. Analysis of Rees et al. (Journal of Applied Ecology, 2014, 51, 1450) and additional publi-cations highlight the downside of the method and suggest that some conclusions have to betoned down. 3. Non-detection of species-specific DNA fragments in a water sample does not automati-cally imply the absence of the target species. A positive signal does not necessarily mean thespecies is present because the environmental DNA (eDNA) could have been transported orpreserved after an animal’s death. Detection of aquatic invertebrates is weakly documented.The effect of species abundance on detection efficiency is not always established. 4. Synthesis and applications. Before successfully becoming an efficient tool to assist propermanagement policies for monitoring of aquatic species, eDNA surveys must implement sam-pling strategies that allow estimating detection rates and scaling up information from watersamples to larger spatial areas. The effects of discharge variations and dendritic organizationin running waters require particular consideration.Key-words: aquatic ecosystem management, detection limit, DNA signal persistence, DNAsignal transport, environmental DNA, false detection, species detectability, survey tools, watersampling

Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing

Abstract: The objective of this study was to examine five different sources of RNA, namely mammary gland tissue (MGT), milk somatic cells (SC), laser microdissected mammary epithelial cells (LCMEC), milk fat globules (MFG) and antibody-captured milk mammary epithelial cells (mMEC) to analyze the bovine mammary gland transcriptome using RNA-Sequencing. Our results provide a comparison between different sampling methods (invasive and non-invasive) to define the transcriptome of mammary gland tissue and milk cells. This information will be of value to investigators in choosing the most appropriate sampling method for different research applications to study specific physiological states during lactation. One of the simplest procedures to study the transcriptome associated with milk appears to be the isolation of total RNA directly from SC or MFG released into milk during lactation. Our results indicate that the SC and MFG transcriptome are representative of MGT and LCMEC and can be used as effective and alternative samples to study mammary gland expression without the need to perform a tissue biopsy.

Organization of lipids in milks, infant milk formulas and various dairy products: role of technological processes and potential impacts

Abstract: The microstructure of milk fat in processed dairy products is poorly known despite its importance in their functional, sensorial and nutritional properties. However, for the last 10 years, several research groups including our laboratory have significantly contributed to increasing knowledge on the organization of lipids in situ in dairy products. This paper provides an overview of recent advances on the organization of lipids in the milk fat globule membrane using microscopy techniques (mainly confocal microscopy and atomic force microscopy). Also, this overview brings structural information about the organization of lipids in situ in commercialized milks, infant milk formulas and various dairy products (cream, butter, buttermilk, butter serum and cheeses). The main mechanical treatment used in the dairy industry, homogenization, decreases the size of milk fat globules, changes the architecture (composition and organization) of the fat/water interface and affects the interactions between lipid droplets and the protein network (concept of inert vs active fillers). The potential impacts of the organization of lipids and of the alteration of the milk fat globule membrane are discussed, and technological strategies are proposed, in priority to design biomimetic lipid droplets in infant milk formulas.

The use of acoustic cameras in shallow waters: new hydroacoustic tools for monitoring migratory fish population. A review of DIDSON technology

Abstract: European Union legislation, through the Water Framework Directive (2000/60/ EC), as well as national legislation, such as the ‘Grenelle Environnement’ (2007) in France, requires restoration of ecological connectivity in streams to improve free circulation of migratory fish. Different methods (e.g. capture by trap or net, telemetry, hydroacoustics) are used to evaluate the efficiency of fish passes to estimate the migratory species abundance and analyse changes in their within-river distributions. Among these methods, hydroacoustics is non-intrusive, allowing long-term observation and description of fish populations based on physical properties of sound in water. However, the main limit to hydroacoustic tools is their difficulty in identifying species. Initially designed for military purposes, dual-frequency identification sonar (DIDSON) has been used in environmental management for a decade. This acoustic camera uses higher frequencies and more sub-beams than common hydroacoustic tools, which improves image resolution and then enables observation of fish morphology and swimming behaviour. The ability to subtract static echoes from echograms and directly measure fish length improve the species-identification process. However, some limits have been identified, such as automatic dataset recording and the low range of the detection beam, which decreases accuracy, but efficient tools are now being developed to improve the accuracy of data recording (morphology, species identification, direction and speed). The new technological properties of acoustic cameras, such as the video-like visualization of the data, have greatly improved monitoring of diadromous fish populations (abundance, distribution and behaviour), helping river and fisheries managers and researchers in making decisions.

Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

Abstract: Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit) More than 98% of the sequencing reads were assigned to known pea aphid symbionts The presence of Wolbachia was confirmed in A pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa

The food limitation hypothesis for juvenile marine fish

Abstract: Coastal zones are productive areas that serve as nursery grounds for a large number of marine species. However, the processes involved in survival success during the juvenile phase are not well-known. Some authors suggest that the availability of prey is important to support the production of pre-recruit fish whose fitness is enhanced through optimal feeding conditions. Accordingly, recruitment is limited by the carrying capacity of the nursery habitat. In contrast, other authors state that the carrying capacity of the nursery grounds is not fully exploited, suggesting that there is no effect of food limitation. This study combines an overview of the literature, focused on flatfish that are especially dependent on coastal and estuarine nursery grounds, an extension to other marine fishes and a modelling approach on growth and survival of juvenile fish to explore the controversy of food limitation in their nursery grounds. We demonstrate that the relative lack of growth limitation observed for young marine fishes at the individual scale is related to an observational bias: fish have been affected by size-selective mortality linked to food limitation, but only surviving individuals are observed. As the population is skewed towards the faster-growing juveniles, the growth of survivors remains close to optimal, even when food resources are limited. Food limitation is of major influence in determining the carrying capacity of the nursery habitat. To sustain marine fish populations and related fisheries, management action is needed to protect coastal and estuarine areas and maintain or restore nursery productivity.

Both the Jasmonic Acid and the Salicylic Acid Pathways Contribute to Resistance to the Biotrophic Clubroot Agent Plasmodiophora brassicae in Arabidopsis

Abstract: The role of salicylic acid (SA) and jasmonic acid (JA) signaling in resistance to root pathogens has been poorly documented. We assessed the contribution of SA and JA to basal and partial resistance of Arabidopsis to the biotrophic clubroot agent Plasmodiophora brassicae. SA and JA levels as well as the expression of the SA-responsive genes PR2 and PR5 and the JA-responsive genes ARGAH2 and THI2.1 were monitored in infected roots of the accessions Col-0 (susceptible) and Bur-0 (partially resistant). SA signaling was activated in Bur-0 but not in Col-0. The JA pathway was weakly activated in Bur-0 but was strongly induced in Col-0. The contribution of both pathways to clubroot resistance was then assessed using exogenous phytohormone application and mutants affected in SA or JA signaling. Exogenous SA treatment decreased clubroot symptoms in the two Arabidopsis accessions, whereas JA treatment reduced clubroot symptoms only in Col-0. The cpr5-2 mutant, in which SA responses are constitutively induced, was more resistant to clubroot than the corresponding wild type, and the JA signaling-deficient mutant jar1 was more susceptible. Finally, we showed that the JA-mediated induction of NATA1 drove N(δ)-acetylornithine biosynthesis in infected Col-0 roots. The 35S::NATA1 and nata1 lines displayed reduced or enhanced clubroot symptoms, respectively, thus suggesting that in Col-0 this pathway was involved in the JA-mediated basal clubroot resistance. Overall, our data support the idea that, depending on the Arabidopsis accession, both SA and JA signaling can play a role in partial inhibition of clubroot development in compatible interactions with P. brassicae.

Concept and application of ideal protein for pigs.

Abstract: Knowledge about the amino acid requirements and the response of pigs to the amino acid supply is essential in feed formulation. A deficient AA supply results in a reduction in performance while an oversupply is costly and leads to excessive nitrogen excretion with a potentially negative environmental impact. Amino acid requirements are determined to a large extent by the protein deposition in the body and, for lactating sows, by the protein exported in the milk. The concept of ideal protein was developed more than 50 years ago and refers to a protein with an amino acid profile that exactly meets the animal’s requirement so that all amino acids are equally limiting for performance. Because Lys typically is the first-limiting amino acid, the ideal amino acid profile is often expressed relative to Lys. Although the ideal protein profile is often assumed to be constant for a given production stage, (small) changes in the ideal protein profile can occur within a production stage. This can be caused by changes in the relative contribution of the different components of amino acid requirements during the productive life on the animal (e.g. changes in the relative contribution of growth and maintenance). Amino acids requirements can be determined experimentally using dose–response studies. The design of the study, the chosen response criterion, and the statistical model affect the requirement estimate. Although considerable experimental work has been carried out to determine the requirements for Lys, Met, Thr, and Trp in growing pigs (and to a lesser extent in sows), little is known about the requirements for the other essential amino acids. Experimental dose–response studies generally focus on the requirement and less on the overall response (i.e. what are the consequences of an amino acid deficiency?). This latter aspect is, to some extent, accounted for in modelling approaches that quantify the response of the animal to the amino acid supply in a dynamic way. The paper describes the origin of ideal protein and illustrates how fundamental concepts of amino acid nutrition have been integrated in practical modeling approaches for the nutrition of growing pigs and sows.

Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis

Abstract: Bovine mastitis is a costly disease in dairy cattle worldwide. As of yet, the control of bovine mastitis is mostly based on prevention by thorough hygienic procedures during milking. Additional strategies include vaccination and utilization of antibiotics. Despite these measures, mastitis is not fully under control, thus prompting the need for alternative strategies. The goal of this study was to isolate autochthonous lactic acid bacteria (LAB) from bovine mammary microbiota that exhibit beneficial properties that could be used for mastitis prevention and/or treatment. Sampling of the teat canal led to the isolation of 165 isolates, among which a selection of ten non-redundant LAB strains belonging to the genera Lactobacillus and Lactococcus were further characterized with regard to several properties: surface properties (hydrophobicity, autoaggregation); inhibition potential of three main mastitis pathogens, Staphylococcus aureus, Escherichia coli and Streptococcus uberis; colonization capacities of bovine mammary epithelial cells (bMEC); and immunomodulation properties. Three strains, Lactobacillus brevis 1595 and 1597 and Lactobacillus plantarum 1610, showed high colonization capacities and a medium surface hydrophobicity. These strains are good candidates to compete with pathogens for mammary gland colonization. Moreover, nine strains exhibited anti-inflammatory properties, as illustrated by the lower IL-8 secretion by E. coli-stimulated bMEC in the presence of these LAB. Full genome sequencing of five candidate strains allowed to check for undesirable genetic elements such as antibiotic resistance genes and to identify potential bacterial determinants involved in the beneficial properties. This large screening of beneficial properties while checking for undesirable genetic markers allowed the selection of promising candidate LAB strains from bovine mammary microbiota for the prevention and/or treatment of bovine mastitis.

Bacterial Colonies in Solid Media and Foods: A Review on Their Growth and Interactions with the Micro-Environment

Abstract: Bacteria, either indigenous or added, are immobilized in solid foods where they grow as colonies. Since the 80's, relatively few research groups have explored the implications of bacteria growing as colonies and mostly focused on pathogens in large colonies on agar/gelatine media. It is only recently that high resolution imaging techniques and biophysical characterization techniques increased the understanding of the growth of bacterial colonies, for different sizes of colonies, at the microscopic level and even down to the molecular level. This review covers the studies on bacterial colony growth in agar or gelatine media mimicking the food environment and in model cheese. The following conclusions have been brought to light. Firstly, under unfavorable conditions, mimicking food conditions, the immobilization of bacteria always constrains their growth in comparison with planktonic growth and increases the sensibility of bacteria to environmental stresses. Secondly, the spatial distribution describes both the distance between colonies and the size of the colonies as a function of the initial level of population. By studying the literature, we concluded that there systematically exists a threshold that distinguishes micro-colonies (radius 200 μm). Micro-colonies growth resembles planktonic growth and no pH microgradients could be observed. Macro-colonies growth is slower than planktonic growth and pH microgradients could be observed in and around them due to diffusion limitations which occur around, but also inside the macro-colonies. Diffusion limitations of milk proteins have been demonstrated in a model cheese around and in the bacterial colonies. In conclusion, the impact of immobilization is predominant for macro-colonies in comparison with micro-colonies. However, the interaction between the colonies and the food matrix itself remains to be further investigated at the microscopic scale.

Towards validation of ammonia (NH 3 ) measurements from the IASI satellite

Abstract: . Limited availability of ammonia (NH3) observations is currently a barrier for effective monitoring of the nitrogen cycle. It prevents a full understanding of the atmospheric processes in which this trace gas is involved and therefore impedes determining its related budgets. Since the end of 2007, the Infrared Atmospheric Sounding Interferometer (IASI) satellite has been observing NH3 from space at a high spatio-temporal resolution. This valuable data set, already used by models, still needs validation. We present here a first attempt to validate IASI-NH3 measurements using existing independent ground-based and airborne data sets. The yearly distributions reveal similar patterns between ground-based and space-borne observations and highlight the scarcity of local NH3 measurements as well as their spatial heterogeneity and lack of representativity. By comparison with monthly resolved data sets in Europe, China and Africa, we show that IASI-NH3 observations are in fair agreement, but they are characterized by a smaller variation in concentrations. The use of hourly and airborne data sets to compare with IASI individual observations allows investigations of the impact of averaging as well as the representativity of independent observations for the satellite footprint. The importance of considering the latter and the added value of densely located airborne measurements at various altitudes to validate IASI-NH3 columns are discussed. Perspectives and guidelines for future validation work on NH3 satellite observations are presented.

Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov.

Abstract: Since 2008, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis) caused by Pseudomonas syringae pv. actinidiae (Psa) has resulted in severe economic losses worldwide. Four biovars of Psa can be distinguished based on their biochemical, pathogenicity and molecular characteristics. Using a range of biochemical, molecular and pathogenicity assays, strains collected in France since the beginning of the outbreak in 2010 were found to be genotypically and phenotypically diverse, and to belong to biovar 3 or biovar 4. This is the first time that strains of biovar 4 have been isolated outside New Zealand or Australia. A multilocus sequence analysis based on four housekeeping genes (gapA, gltA, gyrB and rpoD) was performed on 72 strains representative of the French outbreak. All the strains fell into two phylogenetic groups: one clonal corresponding to biovar 3, and the other corresponding to biovar 4. This second phylogenetic group was polymorphic and could be divided into four lineages. A clonal genealogy performed with a coalescent approach did not reveal any common ancestor for the 72 Psa strains. Strains of biovar 4 are substantially different from those of the other biovars: they are less aggressive and cause only leaf spots whereas Psa biovars 1, 2 and 3 also cause canker and shoot die-back. Because of these pathogenic differences, which were supported by phenotypic, genetic and phylogenetic differences, it is proposed that Psa biovar 4 be renamed Pseudomonas syringae pv. actinidifoliorum pv. nov. Strain CFBP 8039 is designated as the pathotype strain.

Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle

Abstract: Improving feed efficiency is a relevant strategy to reduce feed cost and environmental waste in livestock production. Selection experiments on residual feed intake (RFI), a measure of feed efficiency, previously indicated that low RFI was associated with lower feed intake, similar growth rate, and greater lean meat content compared with high RFI. To gain insights into the molecular mechanisms underlying these differences, 24 Large White females from 2 lines divergently selected for RFI were examined. Pigs from a low-RFI ("efficient") and high-RFI ("inefficient") line were individually fed ad libitum from 67 d of age (27 kg BW) to slaughter at 115 kg BW (n = 8 per group). Additional pigs of the high-RFI line were feed restricted to the daily feed intake of the ad libitum low-RFI pigs (n = 8) to investigate the impact of selection independently of feed intake. Global gene and protein expression profiles were assessed in the LM collected at slaughter. The analyses involved a porcine commercial microarray and 2-dimensional gel electrophoresis. About 1,000 probes were differentially expressed (P < 0.01) between RFI lines. Only 10% of those probes were also affected by feed restriction. Gene functional classification indicated a greater expression of genes involved in protein synthesis and a lower expression of genes associated with mitochondrial energy metabolism in the low-RFI pigs compared with the high-RFI pigs. At the protein level, 11 unique identified proteins exhibited a differential abundance (P < 0.05) between RFI lines. Differentially expressed proteins were generally not significantly affected by feed restriction. Mitochondrial oxidative proteins such as aconitase hydratase, ATP synthase subunit α, and creatine kinase S-type had a lower abundance in the low-RFI pigs, whereas fructose-biphosphate aldolase A and glyceraldehyde-3-phosphate dehydrogenase, 2 proteins involved in glycolysis, had a greater abundance in those pigs compared with high-RFI pigs. Antioxidant proteins such as superoxide dismutase and glutathione peroxidase 3 at the mRNA level and peroxiredoxin-6 at the protein level were also less expressed in LM of the most efficient pigs, likely related to lower oxidative molecule production. Collectively, both the transcriptomic and proteomic approaches revealed a lower oxidative metabolism in muscle of the low-RFI pigs and all these modifications were largely independent of differences in feed intake.

Transit time distributions, legacy contamination and variability in biogeochemical 1/fα scaling: how are hydrological response dynamics linked to water quality at the catchment scale?

Abstract: In spite of recent progress, hydrological processes underlying observed water quality response patterns, such as the emergence of near-chemostatic conditions and fractal 1/f(alpha) scaling of stream chemistry, are not completely understood. Analysing hydrological and Cl- tracer data for two intensely managed, hydrologically contrasting yet biogeochemically similar catchments we tested if (1) a semi-distributed, conceptual model can simultaneously reproduce catchment scale hydrological and biogeochemical responses, (2) legacy stores, allowing for long-term storage of nutrient inputs can be identified and (3) a model can reproduce 1/f(alpha) scaling. Further we analysed (4) transit (TTD) and residence time distributions (RTD) and the associated response dynamics of legacy stores, to explore (5) what controls fluctuations in the scaling exponent a, thereby establishing a process based link between 1/f(alpha) scaling, legacy stores and age distributions. We found that the model could reproduce the variable hydrological and the stable Cl- responses. This was possible through Cl- accumulation in hydrologically passive legacy stores that are mainly associated with the groundwater store, where Cl- age is well above 2000 days, one magnitude above the Cl- age in other components, such as the root zone (similar to 200 d). The results indicate that legacy stores can cause stable nutrient concentrations in streams for several decades after the end of nutrient input. It was further found that the model could reproduce fractal scaling of stream Cl- in both catchments, with higher values of alpha for the catchment with the smaller legacy store and faster response (alpha = -0.88 vs -1.29). Further analysing the spectral properties of model components, it was found that the parts of the system with less storage are characterized by higher values of alpha. This suggests a plausible processes-based link between the fluctuations of alpha, legacy stores and RTDs: the smaller the legacy store and the higher the flow contribution from faster responding system components, the higher alpha, suggesting that fractal scaling may potentially not be a universally emerging property of the biogeochemical response in streams.

Drying of a single droplet to investigate process–structure–function relationships: a review

Abstract: Drying usually results in various types of particle morphology that influence the properties and the functionality of powders. Understanding how the final shape of the particle is formed is therefore a key issue for industrial applications. However, it is difficult to carry out relevant studies and interpret them on an industrial scale, mainly because of the complexity and scale of the drying operation and the difficulty of monitoring drying parameters in situ. To overcome these difficulties, experiments are currently performed with the simplest system conceivable: drying of a single droplet in a controlled environment. Different approaches are available in the literature in order to study the drying of a single droplet, from a sessile droplet to a free-flying droplet. This review aims to illustrate results obtained with these experiments, and their key contributions to fundamental and applied understanding of drying (or evaporation) phenomena are discussed. It is shown that investigation of a single droplet may be a key approach to spray drying in order to improve understanding of the chemical and physical mechanisms involved in particle processing and governing the properties of the final particle.