The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana

The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β‐(1,4)‐linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one‐half of the xylosyl residues are O‐acetylated at C‐2 or C‐3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecular dynamics simulation, we found that a twofold helical screw conformation of xylan is stable in interactions with both hydrophilic and hydrophobic cellulose faces. Tight docking of xylan on the hydrophilic faces is feasible only for xylan decorated on alternate residues and folded as a twofold helical screw. The findings suggest an explanation for the importance of acetylation for xylan–cellulose interactions, and also have implications for our understanding of cell wall molecular architecture and properties, and biological degradation by pathogens and fungi. They will also impact strategies to improve lignocellulose processing for biorefining and bioenergy.     

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python.     

Stability of Staphylococcus aureus Phage ISP after Freeze-Drying (Lyophilization)

Staphylococcus aureus phage ISP was lyophilized, using an Amsco-Finn Aqua GT4 freeze dryer, in the presence of six different stabilizers at different concentrations. Stability of the lyophilized phage at 4°C was monitored up to 37 months and compared to stability in Luria Bertani broth and physiological saline at 4°C. Sucrose and trehalose were shown to be the best stabilizing additives, causing a decrease of only 1 log immediately after the lyophilization procedure and showing high stability during a 27 month storage period.     

CD25- T cells generate CD25+Foxp3+ regulatory T cells by peripheral expansion

Naturally occurring CD4(+) regulatory T cells are generally identified through their expression of CD25. However, in several experimental systems considerable T(reg) activity has been observed in the CD4(+)CD25(-) fraction. Upon adoptive transfer, the expression of CD25 in donor-derived cells is not stable, with CD4(+)CD25(+) cells appearing in CD4(+)CD25(-) T cell-injected animals and vice versa. We show in this study that CD25(+) cells arising from donor CD25(-) cells upon homeostatic proliferation in recipient mice express markers of freshly isolated T(reg) cells, display an anergic state, and suppress the proliferation of other cells in vitro. The maintenance of CD25 expression by CD4(+)CD25(+) cells depends on IL-2 secreted by cotransferred CD4(+)CD25(-) or by Ag-stimulated T cells in peripheral lymphoid organs.     

Embryonic shell structure of Early–Middle Jurassic belemnites,and its significance for belemnite expansion and diversification in the Jurassic

Early Jurassic belemnites are of particular interest to the study of the evolution of skeletal morphology in Lower Carboniferous to the uppermost Cretaceous belemnoids, because they signal the beginning of a global Jurassic–Cretaceous expansion and diversification of belemnitids. We investigated potentially relevant, to this evolutionary pattern, shell features of Sinemurian–Bajocian Nannobelus, Parapassaloteuthis, Holcobelus and Pachybelemnopsis from the Paris Basin. Our analysis of morphological, ultrastructural and chemical traits of the earliest ontogenetic stages of the shell suggests that modified embryonic shell structure of Early–Middle Jurassic belemnites was a factor in their expansion and colonization of the pelagic zone and resulted in remarkable diversification of belemnites. Innovative traits of the embryonic shell of Sinemurian–Bajocian belemnites include: (1) an inorganic–organic primordial rostrum encapsulating the protoconch and the phragmocone, its non‐biomineralized component, possibly chitin, is herein detected for the first time; (2) an organic rich closing membrane which was under formation. It was yet perforated and possessed a foramen; and (3) an organic rich pro‐ostracum earlier documented in an embryonic shell of Pliensbachian Passaloteuthis. The inorganic–organic primordial rostrum tightly coating the protoconch and phragmocone supposedly enhanced protection, without increase in shell weight, of the Early Jurassic belemnites against explosion in deep‐water environment. This may have increased the depth and temperature ranges of hatching eggs, accelerated the adaptation of hatchlings to a nektonic mode of life and promoted increasing diversity of belemnoids. This study supports the hypothesis that belemnite hatchlings were ‘a miniature of the adults’.     

Establishment of tree seedlings in the understory of restoration plantations: natural regeneration and enrichment plantings

Little is known about the potential of restoration plantations to provide appropriate understory conditions to support the establishment of seeds arriving from neighboring native forests. In this article, we investigated how seedling establishment is affected in the understory of restoration sites of different ages and assessed some of the potential environmental factors controlling this ecological process. We first compared the density and richness of native tree seedlings among 10‐, 22‐, and 55‐year‐old restoration plantations within the Atlantic Forest region of southeastern Brazil. Then, we undertook a seed addition experiment in each study site, during the wet season, and compared seedling emergence, survival, and biomass on local versus old‐growth forest soil (transferred from a reference ecosystem), in order to test whether local substrate could hamper seedling establishment. As expected, the oldest restoration site had higher density and richness of spontaneously regenerating seedlings. However, seedling establishment was less successful both in the oldest restoration planting and using substrate transferred from a reference ecosystem, where emergence and survival were lower, but surviving seedlings grew better. We attribute these results to lower light availability for seedlings in the understory of the oldest site and speculate that higher incidence of pathogens on old‐growth forest soil may have increased seedling mortality. We conclude that the understory of young restoration plantations provides suitable microsite conditions at the early establishment phases for the spontaneous regeneration or enrichment planting of native trees.     

Ultraviolet B and A irradiation induces fibromodulin expression in human fibroblasts in vitro

Ultraviolet (UV) radiation affects the extracellular matrix (ECM) of the human skin. The small leucine-rich repeat protein fibromodulin interacts with type I and II collagen fibrils, thereby affecting ECM assembly. The aim of this study was to evaluate whether short wave UV (UVB) or long wave UV (UVA) irradiation influences fibromodulin expression. Exponentially growing human fibroblasts (IMR-90 cells) were exposed to increasing doses of UVB (2.5–60 mJ/cm²) or UVA (0.5–10 J/cm²). After UV irradiation fibromodulin, p21 and GADD45 levels were evaluated as well as cell viability, reactive oxygen species formation (ROS) and DNA damage. We found that fibromodulin expression: (i) increased after UVB and UVA irradiation; (ii) was 10-fold higher after UVA (10 J/cm²) versus 5-fold with UVB (10 mJ/cm²); (iii) correlated with reactive oxygen species formation, particularly after UVA; and (iv) was linked to the DNA damage binding protein (DDB1) translocation in the nucleus, particularly after UVB. These results further suggest that the UV-induced fibromodulin increase could counteract the UV-induced connective tissue damage, promoting the assembly of new collagen fibrils.     

A new era in forest restoration monitoring

Monitoring ecological restoration has been historically dependent on traditional inventory methods based on detailed information obtained from field plots. New paradigms are now needed to successfully achieve restoration as a large‐scale, long‐lasting transformative process. Fortunately, advances in technology now allow for unprecedented shifts in the way restoration has been planned, implemented, and monitored. Here, we describe our vision on how the use of new technologies by a new generation of restoration ecologists may revolutionize restoration monitoring in the coming years. The success of the many ambitious restoration programs planned for the coming decade will rely on effective monitoring, which is an essential component of adaptive management and accountability. The development of new remote sensing approaches and their application to a restoration context open new avenues for expanding our capacity to assess restoration performance over unprecedented spatial and temporal scales. A new generation of scientists, which have a background in remote sensing but are getting more and more involved with restoration, will certainly play a key role for making large‐scale restoration monitoring a viable human endeavor in the coming decade—the United Nations' decade on ecosystem restoration.