Recent advances in enzyme assays

Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.     

Starch division and partitioning. A mechanism for granule propagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri

Whereas Glc is stored in small-sized hydrosoluble glycogen particles in archaea, eubacteria, fungi, and animal cells, photosynthetic eukaryotes have resorted to building starch, which is composed of several distinct polysaccharide fractions packed into a highly organized semicrystalline granule. In plants, both the initiation of polysaccharide synthesis and the nucleation mechanism leading to formation of new starch granules are currently not understood. Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, defines the tiniest eukaryote with one of the smallest genomes. We show that it accumulates a single starch granule at the chloroplast center by using the same pathway as higher plants. At the time of plastid division, we observe elongation of the starch and division into two daughter structures that are partitioned in each newly formed chloroplast. These observations suggest that in this system the information required to initiate crystalline polysaccharide growth of a new granule is contained within the preexisting polysaccharide structure and the design of the plastid division machinery.     

Novel secretory vesicle proteins essential for membrane fusion display extracellular-matrix domains

Exocytotic mutants can be obtained in Paramecium that affect the organization of the fusion machinery, visible by electron microscopy. The site of action of the genes in the plasma membrane, cytosol or secretory compartment can easily be determined in such mutants. Functional complementation cloning of exocytotic mutants specifically affected in the secretory compartment, nd2-1 and nd169-1, reported here, and the previously studied nd7-1, led to the discovery of a set of novel proteins that display PSI and EGF domains, normally found in extracellular matrix proteins and involved in transmembrane signaling. The structure of one of these proteins, Nd2p, and of the product of a paralog found in the genome Nd22p, corresponds to that of type I membrane receptors, generally involved in protein and vesicle sorting. Our characterization suggests that the proteins we have identified are required to indicate the presence of a mature secretory vesicle to the plasma membrane, to prepare the machinery for fusion. We propose to name this novel subclass of receptors VEMIF, for Vesicular Extracellular-Matrix-like proteins Involved in preparing membrane Fusion.     

Three-reaction model for the anaerobic digestion of microalgae

Coupling an anaerobic digester to a microalgal culture has received increasing attention as an alternative process for combined bioenergy production and depollution. In this article, a dynamic model for anaerobic digestion of microalgae is developed with the aim of improving the management of such a coupled system. This model describes the dynamics of inorganic nitrogen and volatile fatty acids since both can lead to inhibition and therefore process instability. Three reactions are considered: Two hydrolysis–acidogenesis steps in parallel for sugars/lipids and for proteins, followed by a methanogenesis step. The proposed model accurately reproduces experimental data for anaerobic digestion of the freshwater microalgae Chlorella vulgaris with an organic loading rate of 1 gCOD L^?1 d^?1. In particular, the three‐reaction pathway allows to adequately represent the observed decoupling between biogas production and nitrogen release. The reduced complexity of this model makes it suitable for developing advanced, model‐based control and monitoring strategies. Biotechnol. Bioeng. 2012; 109:415–425. © 2011 Wiley Periodicals, Inc.     

Assessment of the relevance of supported planar bilayers for modeling specific interactions between glycodendrimeric porphyrins and retinoblastoma cells

Glycodendrimeric porphyrins seem promising photosensitizers usable in photodynamic therapy. Evidence of their ability to interact with an artificial supported bilayer membrane exhibiting a model sugar receptor has been previously shown. In the present work, the interaction of the glycodendrimeric porphyrins with retinoblastoma cells bearing the actual sugar receptor has been assessed by both classical cell cultures and an original approach using the quartz crystal microbalance (QCM-D). Our results showed that unlike cell cultures, QCM-D allowed analyzing the mechanism of interaction of the glycodendrimeric porphyrins with the sugar receptor. Not only was molecular recognition demonstrated, but our methodology also proved efficient to discriminate between the studied compounds, depending on the presence of carbohydrate, and the spacer length.     

Equivalence in the strength of deer herbivory on above and below ground communities

Herbivores exert a strong influence on the species composition and richness of plant communities, but the magnitude of their effect on belowground communities remains poorly understood. While an increasing number of studies acknowledge the importance of documenting belowground effects of herbivores, very few of these evaluate variation in the strength of the response from aboveground to belowground communities. Our study documents the long-term consequences of sustained deer herbivory for plant and arthropod communities adjacent to 15 exclosures that have been in place since 1996. We hypothesized that herbivory would alter the composition and diversity of communities, but the strength of the effects of herbivory would weaken from plants, to leaf-litter invertebrates, and to belowground microarthropod communities. First, we found that herbivory negatively impacted plant seedling and sapling abundance and performance, reduced the abundance of ants and the taxonomic richness of arthropods in the litter layer and reduced the richness of soil microarthropod communities. Second, in contrast to our hypothesis, the magnitude of effect size did not vary among trophic levels, indicating that effects of deer herbivory cascade from plants to the leaf-litter and soil arthropod communities with equal strength. While much recent research has focused on how specific traits of plants may mediate the effects of herbivory on associated species, our results suggest that indirect effects of herbivory might influence many components of belowground communities.     

Repression of early lateral root initiation events by transient water deficit in barley and maize

The formation of lateral roots (LRs) is a key driver of root system architecture and developmental plasticity. The first stage of LR formation, which leads to the acquisition of founder cell identity in the pericycle, is the primary determinant of root branching patterns. The fact that initiation events occur asynchronously in a very small number of cells inside the parent root has been a major difficulty in the study of the molecular regulation of branching patterns. Inducible systems that trigger synchronous lateral formation at predictable sites have proven extremely valuable in Arabidopsis to decipher the first steps of LR formation. Here, we present a LR repression system for cereals that relies on a transient water-deficit treatment, which blocks LR initiation before the first formative divisions. Using a time-lapse approach, we analysed the dynamics of this repression along growing roots and were able to show that it targets a very narrow developmental window of the initiation process. Interestingly, the repression can be exploited to obtain negative control root samples where LR initiation is absent. This system could be instrumental in the analysis of the molecular basis of drought-responsive as well as intrinsic pathways of LR formation in cereals.