Overview of the Oldest Existing Set of Substrate-optimized Anaerobic Processes: Digestive Tracts

Over millions of years, living organisms have explored and optimized the digestion of a wide variety of substrates. Engineers who develop anaerobic digestion processes for waste treatment and energy production can learn much from this accumulated ‘experience’. The aim of this work is a survey based on the comparison of 190 digestive tracts (vertebrate and insect) considered as ‘reactors’ and their anaerobic processes. Within a digestive tract, each organ is modeled as a type of reactor (continuous stirred-tank, such reactors in series, plug-flow or batch) associated with chemical aspects such as pH or enzymes. Based on this analysis, each complete digestion process has been rebuilt and classified in accordance with basic structures which take into account the relative size of the different reactors. The results show that all animal digestive structures can be grouped within four basic types. Size and/or position in the structure of the different reactors (pre/post treatment and anaerobic microbial digestion) are closely correlated to the degradability of the feed (substrate). Major common features are: (i) grinding, (ii) an extreme pH compartment, and (iii) correlation between the size of the microbial compartment and the degradability of the feed. Thus, shared answers found by animals during their evolution can be a source of inspiration for engineers in designing optimal anaerobic processes.     

Lipid Sorting and Multivesicular Endosome Biogenesis

Intracellular organelles, including endosomes, show differences not only in protein but also in lipid composition. It is becoming clear from the work of many laboratories that the mechanisms necessary to achieve such lipid segregation can operate at very different levels, including the membrane biophysical properties, the interactions with other lipids and proteins, and the turnover rates or distribution of metabolic enzymes. In turn, lipids can directly influence the organelle membrane properties by changing biophysical parameters and by recruiting partner effector proteins involved in protein sorting and membrane dynamics. In this review, we will discuss how lipids are sorted in endosomal membranes and how they impact on endosome functions.It is now well established that membranes along the endocytic and secretory pathway show differences not only in protein but also in lipid composition. For example, lipid gradients exist along the biosynthetic pathway with increasing density of cholesterol and sphingolipids from the endoplasmic reticulum (ER) to the plasma membrane (Maxfield and van Meer 2010). Also, phosphoinositides show distributions restricted to relatively well-characterized membrane territories (Di Paolo and De Camilli 2006). Given the facts that lipids are small and contain little structural information when compared with proteins, that they can diffuse rapidly within membranes, and that membranes are connected by membrane flow during transport, it is not always obvious how different lipids are segregated from each other.In this article, we will evoke different mechanisms that may contribute to the heterogeneous lipid composition of endocytic membranes, including physicochemical properties of the membrane, interactions with other proteins or lipids, and synthesis or degradation. In addition, it has also become apparent that peripheral membrane proteins often interact with membranes via diverse lipid-binding motifs, and thus that lipids directly contribute to the distribution of many peripheral membrane proteins. For example, phosphatidylinositol 3-phosphate (PI(3)P) is detected predominantly on early endosomes, where most characterized PI(3)P-binding proteins encoded by the human genome are found as well (Raiborg et al. 2013). We will also discuss how some lipids may regulate protein sorting and membrane transport within the endosomal system.     

The study of genetic diversity patterns of Coffea commersoniana, an endangered coffee species from Madagascar: a model for conservation of other littoral forest species

Madagascar has 59 described species of Coffea, of which 42 are listed as critically endangered, endangered, or vulnerable by the criteria of the Red List Category system of the World Conservation Union (IUCN). The littoral forest of Madagascar is a distinctive type of humid evergreen forest restricted to unconsolidated sand located within a few kilometers of the Indian Ocean, now persisting only as small fragments with ca. 10 % of its original range remaining. In an attempt to understand the genetic diversity of Madagascan coffee species, we studied ex situ and in situ populations of Coffea commersoniana, an endemic species of the littoral forests of southeastern Madagascar and soon to be impacted by mining activities in that region. The in situ populations studied showed higher genetic diversity than the ex situ population. The genetic partitioning among the two in situ populations of C. commersoniana was high enough to necessitate keeping the two populations separate for restoration purposes. Based on these findings, recommendations for conservation management (in situ and ex situ) are made.     

Habitat use under predation risk: hunting, roads and human dwellings influence the spatial behaviour of roe deer

Wildlife populations are subjected to increasing pressure linked to human activities, which introduce multiple stressors. Recently, in addition to direct effects, it has been shown that indirect (non-lethal) effects of predation risk are predominant in many populations. Predation risk is often structured in space and time, generating a heterogeneous “landscape of fear” within which animals can minimize risks by modifying their habitat use. Furthermore, for ungulates, resource quality seems to be positively correlated with human-related sources of risk. We studied the trade-off between access to resources of high-quality and risk-taking by contrasting habitat use of roe deer during daytime with that during nighttime for 94 roe deer in a hunted population. Our first hypothesis was that roe deer should avoid human disturbance by modifying their habitat use during daytime compared to nighttime. Our results supported this, as roe deer mainly used open fields during nighttime, but used more forested habitats during daytime, when human disturbance is higher. Moreover, we found that diel patterns in habitat use were influenced by hunting disturbance. Indeed, the roe deer decreased their use of high-crops during daytime, an important source of cover and food, during the hunting season. The proximity of roads and dwellings also affected habitat use, since roe deer used open fields during daytime to a greater extent when the distance to these sources of disturbance was higher. Hence, our results suggest that roe deer resolve the trade-off between the acquisition of high-quality resources and risk avoidance by modifying their habitat use between day and night.     

Crop seed oil bodies: From challenges in protein identification to an emerging picture of the oil body proteome

Oleaginous seeds store lipids in specialized structures called oil bodies (OBs). These organelles consist of a core of neutral lipids bound by proteins embedded in a phospholipid monolayer. OB proteins are well conserved in plants and have long been grouped into only two categories: structural proteins or enzymes. Recent work, however, which identified other classes of proteins associated with OBs, clearly shows that this classification is obsolete. Proteomics‐mediated OB protein identification is facilitated in plants for which the genome is sequenced and annotated. However, it is not clear whether this knowledge can be dependably transposed to less well‐characterized plants, including the well‐established commercial sources of seed oil as well as the many others being proposed as novel sources for biodiesel, especially in Africa and Asia. Toward an update of the current data available on OB proteins this review discusses (i) the specific difficulties for proteomic studies of organelles; (ii) a 2012 census of the proteins found in seed OBs from various crops; (iii) the oleosin composition of OBs and their role in organelle stability; (iv) PTM of OB proteins as an emerging field of investigation; and finally we describe the emerging model of the OB proteome from oilseed crops.     

Brachypodium distachyon as a model plant toward improved biofuel crops: Search for secreted proteins involved in biogenesis and disassembly of cell wall polymers

Polysaccharides make up about 75% of plant cell walls and can be broken down to produce sugar substrates (saccharification) from which a whole range of products can be obtained, including bioethanol. Cell walls also contain 5–10% of proteins, which could be used to tailor them for agroindustrial uses. Here we present cell wall proteomics data of Brachypodium distachyon, a model plant for temperate grasses. Leaves and culms were analyzed during active growth and at mature stage. Altogether, 559 proteins were identified by LC‐MS/MS and bioinformatics, among which 314 have predicted signal peptides. Sixty‐three proteins were shared by two organs at two developmental stages where they could play housekeeping functions. Differences were observed between organs and stages of development, especially at the level of glycoside hydrolases and oxidoreductases. Differences were also found between the known cell wall proteomes of B. distachyon, Oryza sativa, and the Arabidopsis thaliana dicot. Three glycoside hydrolases could be immunolocalized in cell walls using polyclonal antibodies against proteotypic peptides. Organ‐specific expression consistent with proteomics results could be observed as well as cell‐specific localization. Moreover, the high number of proteins of unknown function in B. distachyon cell wall proteomes opens new fields of research for monocot cell walls.     

Biodiversity gap analysis of the protected area system in poorly-documented Chad

Chad is amongst the richest countries in terms of biodiversity in Sahelo-Sudanian Africa with some of the last remaining populations of large mammals that once roamed West-Central Africa. Its protected area (PA) system, made up of three national parks (NP) and seven faunal reserves (FR) and introduced 40 years ago to focus on the protection of large game, has never been reviewed in terms of biodiversity coverage. This study (i) assesses whether the PA network captures Chad's current biodiversity (focusing on ecoregions and threatened mammal species), (ii) identifies gaps in the PA system and (iii) proposes recommendations to improve the representativeness of the PA system, in a country characterised by the lack of biological data. Of the seven ecoregions in Chad, three are not covered by PAs and two are represented only once and have less than 10% of their area included in the PA network. Of the 31 large mammal species used in the analysis, five occur only once in the network and five species are not represented. Analysis of the persistence of species shows that, of the nine historical PAs, all have lost at least one (and up to six) species of large mammals. The Ouadi Rimé-Ouadi Achim FR was found to have the highest irreplaceability index, with the Bahr Salamat FR and Zakouma NP second and third respectively. Zakouma NP has the highest number of large mammal populations of an internationally important size. Threatened large mammals, many depending on large-scale migration, and (migratory) waterbird populations highlight the lack of wetlands in the formal PA system. We recommend a more effective protection of these wetlands, an extension of the PA system into ecoregions not covered by current PAs and provide details on the realignment of several of the PAs that have been encroached upon and are no longer viable.     

Selection of antimalarial drug resistance after intermittent preventive treatment of infants and children (IPTi/c) in Senegal

Senegal has since 2003 used sulphadoxine-pyrimethamine (SP) for Intermittent Preventive Treatment (IPT) of malaria in risk groups. However, the large-scale IPT strategy may result in increasing drug resistance. Our study investigated the possible impact of SP-IPT given to infants and children on the prevalence of SP-resistant haplotypes in the Plasmodium falciparum genes Pfdhfr and Pfdhps, comparing sites with and without IPTi/c. P. falciparum positives samples (n = 352) were collected from children under 5 years of age during two cross-sectional surveys in 2010 and 2011 in three health districts (two on IPTi/c and one without IPTi/c intervention) located in the southern part of Senegal. The prevalence of SP-resistance-related haplotypes in Pfdhfr and Pfdhps was determined by nested PCR followed by sequence-specific oligonucleotide probe (SSOP)–ELISA. The prevalence of the Pfdhfr double mutant haplotypes (CNRN and CICN) was stable between years at < 10% in the control group (P = 0.69), while it rose significantly in the IPTi/c group from 2% in 2010 to 20% in 2011 (P = 0.008). The prevalence of the Pfdhfr triple mutant haplotype (CIRN) increased in both groups, but only significantly in the IPTi/c group from 41% to 65% in 2011 (P = 0.005). Conversely, the Pfdhps 437G mutation decreased in both groups from 44.6% to 28.6% (P = 0.07) and from 66.7% to 47.5% (P = 0.02) between 2010 and 2011 in the control and the IPTi/c groups, respectively. Combined with Pfdhfr, there was a weak trend for decreasing prevalence of quadruple mutants (triple Pfdhfr + Pfdhps 437G) in both groups (P = 0.15 and P = 0.34). During the two cross-sectional surveys, some significant changes were observed in the SP-resistance-related genes. However, since these changes were observed in the two groups, the IPTi/c strategy does only seem to have limited impact on resistance development and other factors as well. However, continuous monitoring will be needed, due to the up-scaling of the IPTi/c strategy in Senegal according to WHO recommendations.     

In Situ Monitoring of the 2D Aggregation Process of Thiol-Coated Gold Nanoparticles Using Interparticle Plasmon Coupling

Near-field plasmon coupling between neighboring gold nanoparticles, measured by polarized optical waveguide lightmode spectroscopy, is employed to study the surface self-assembly of alcanethiol-capped gold nanoparticles during solvent evaporation. The waveguide used is a monomode optical fiber half-coupler. The sample is deposited on the surface of the waveguide and absorption spectra are continuously collected during the solvent evaporation process with a temporal resolution of 0.2 s. The absorption spectra show a progressive red shift of the plasmon peak caused by increasing interparticle near-field coupling. This shift can be used to determine the distance between particles by comparison to theoretical values calculated using the discrete dipoles approximation. The technique is demonstrated for the assembly of 10 nm gold particles capped with thiol ligands of two different lengths. Interestingly, in the case of dodecanethiol-capped particles, the extinction spectrum not only shifts to longer wavelengths, but also changes in shape during the drying process. About half a second before the solvent completely evaporates, the spectrum broadens as a second component appears. This feature is tentatively attributed to the formation of a significant population of particle clusters as a result of incomplete screening of van der Waals attractions by the shorter ligand.     

On-Line Optical and Morphological Studies of Silver Nanoparticles Growth Formed by Nanosecond Laser Irradiation of Silver-Exchanged Silicate Glass

Silver-exchanged silicate glass has been irradiated by 532-nm pulsed Nd:YAG laser in order to locally form metallic nanoparticles. The particular interest of this process is to locally control the silver nanoparticles (NPs) growth. Silver ions are exchanged with sodium ions near the glass surface after dumping of a silicate glass few minutes in silver and sodium nitrates molten salt. A low-energy density laser exposure (0.239 J/cm²) chosen at the ablation threshold allows to observe the kinetics of the silver NPs growth according to the increasing shots number. An on-line optical measurement is carried out after each shot to identify the most important steps during the irradiation process. According to this measurement, we have determined four steps highlighted by UV/Visible spectrophotometry and we have identified the influence of located surface plasmon resonance. Three combined material analysis methods were used to understand the glass/laser interaction mechanism: we outlined the material volume variations by profilometric method, the element distribution by scanning electron microscopy and finally the structural distribution of the irradiated region by a local infrared investigation. The trend for NPs formation revealed by the UV/Visible spectrophotometry is thus explained by the formation of a ring expelled from a central hole. We highlight that the on-line extinction measurement can be used to data process the NPs evolution.