Structures of soluble amyloid oligomers from computer simulations

Alzheimer's, Parkinson's, and Creutzfeldt-Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid-forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with beta-barrel character, and cross-beta-sheet structures with the meridional but not the equatorial X-ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar-like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs.     

Decades of atmospheric deposition have not resulted in widespread phosphorus limitation or saturation of tree demand for nitrogen in southern New England

It is commonly assumed that nitrogen (N) is the primary mineral resource limiting the productivity of temperate forests. Sustained inputs of N via atmospheric deposition are altering the N status of temperate forests raising the possibility that nutrients such as phosphorus (P) are increasingly limiting productivity. The objective of this study was to determine whether P availability limits tree growth alone or in combination with N. This study was conducted in two forest types common throughout the New England landscape of the northeastern United States; in sugar maple and white ash dominated stands growing on base rich parent material characterized by rapid rates of N cycling and high N availability, and in red oak–beech–hemlock dominated stands growing on base-poor parent material characterized by slow rates of N cycling and low N availability. Starting in 2004, N and P were added to replicate plots in each forest type in factorial combination at a rate of 150 and 50 kg ha⁻¹ year⁻¹, respectively. Diameter growth rates of all trees >10 cm DBH were measured in 2005 and 2006 using dendrometer bands and converted into units of basal area increment (BAI) and wood production. Following 2 years of fertilization, basal area increment in the sugar maple–white ash forests remained strongly N limited. Fertilization with P did not significantly increase BAI alone, although both N and P fertilization tended (P < 0.10) to increase diameter growth in white ash. Wood production in the N-fertilized plots increased by 100 g C m⁻² year⁻¹, roughly doubling production in the non-fertilized plots. In the red oak–beech–hemlock stands, there was no overall effect of N or P fertilization on BAI or wood production because BAI in some species was stimulated by fertilization with N alone (e.g., black cherry, red oak), while in other species BAI was unaffected (e.g., red maple, beech) or negatively affected by fertilization with N or P (e.g., eastern hemlock). Given that BAI in several tree species responded to fertilization with N alone and that only one species responded to P fertilization once N was added, this study suggests that decades of atmospheric N deposition have not (yet) resulted in widespread P limitation or saturation of tree demand for N.     

<Emphasis Type="Italic">Virtual Retina</Emphasis>: A biological retina model and simulator,with contrast gain control

We propose a new retina simulation software, called Virtual Retina, which transforms a video into spike trains. Our goal is twofold: Allow large scale simulations (up to 100,000 neurons) in reasonable processing times and keep a strong biological plausibility, taking into account implementation constraints. The underlying model includes a linear model of filtering in the Outer Plexiform Layer, a shunting feedback at the level of bipolar cells accounting for rapid contrast gain control, and a spike generation process modeling ganglion cells. We prove the pertinence of our software by reproducing several experimental measurements from single ganglion cells such as cat X and Y cells. This software will be an evolutionary tool for neuroscientists that need realistic large-scale input spike trains in subsequent treatments, and for educational purposes.

Mapping of sex hormone receptors and their modulators along the nephron of male and female mice

Renal functions are regulated by steroid sex hormones, but the exhaustive identification of their receptors along the nephron is still lacking. Here, we have localized all known nuclear or membrane-bound sex hormone receptors and some of their activators along the nephron of male and female mice. Almost all receptors are present in male and female kidney, some of them having very restricted localization. Only one gene tested among 11 (ARA54) exhibits a gender difference in the level of its expression. This first “renal map” of sex steroid receptor expression may serve as a pre-requisite for investigating the role of these hormones on kidney functions.     

Optimized genotyping with microsatellite markers in the fungal banana pathogen Mycosphaerella fijiensis (Mycosphaerellaceae)

? Premise of the study: Large-scale population genetics studies are required to investigate the dispersal processes underlying the emergence of Mycosphaerella fijiensis, a fungal pathogen of banana. To this end, we have developed an optimized genotyping procedure combining novel microsatellite markers and a modified DNA extraction protocol. ? Methods and Results: Primers for tetranucleotide loci were designed directly from the recently published genome sequence of M. fijiensis. A total of 19 new polymorphic and easy-to-score markers were developed. Their use was combined with an adapted protocol for total DNA extraction starting from young lesions collected from banana leaves, thus avoiding a pathogen isolation step. ? Conclusions: The combination of the two technical developments presented here will permit the expansion of genotyping capacity in M. fijiensis, allowing large-scale analysis of samples from various geographic locations.     

Bacterial motility complexes require the actin‐like protein,MreB and the Ras homologue,MglA

Gliding motility in the bacterium Myxococcus xanthus uses two motility engines: S‐motility powered by type‐IV pili and A‐motility powered by uncharacterized motor proteins and focal adhesion complexes. In this paper, we identified MreB, an actin‐like protein, and MglA, a small GTPase of the Ras superfamily, as essential for both motility systems. A22, an inhibitor of MreB cytoskeleton assembly, reversibly inhibited S‐ and A‐motility, causing rapid dispersal of S‐ and A‐motility protein clusters, FrzS and AglZ. This suggests that the MreB cytoskeleton is involved in directing the positioning of these proteins. We also found that a ΔmglA motility mutant showed defective localization of AglZ and FrzS clusters. Interestingly, MglA–YFP localization mimicked both FrzS and AglZ patterns and was perturbed by A22 treatment, consistent with results indicating that both MglA and MreB bind to motility complexes. We propose that MglA and the MreB cytoskeleton act together in a pathway to localize motility proteins such as AglZ and FrzS to assemble the A‐motility machineries. Interestingly, M. xanthus motility systems, like eukaryotic systems, use an actin‐like protein and a small GTPase spatial regulator.     

An integrative in silico methodology for the identification of modulators of macrophage migration inhibitory factor (MIF) tautomerase activity

Macrophage migration inhibitory factor (MIF) is a major proinflammatory cytokine that has been increasingly implicated in the pathogenesis of several inflammatory, autoimmune, infectious and oncogenic diseases. Accumulating evidence suggests that the tautomerase activity of MIF plays a role in modulating some of its intra- and extra-cellular activities. Therefore, the identification and development of small-molecule inhibitors targeting the catalytic activity of MIF has emerged as an attractive and viable therapeutic strategy to attenuate its function in health and disease. Herein we report a novel virtual screening protocol for the discovery of new inhibitors of MIF’s tautomerase activity. Our protocol takes into account the flexibility and dynamics of the catalytic site by coupling molecular dynamics (MD) simulations aimed at modeling the protein’s flexibility in solution to (i) docking with FlexX, or (ii) docking with FlexX and pharmacophoric filtering with Unity. In addition, we applied in parallel a standalone docking using the new version of Surflex software. The three approaches were used to screen the ChemBridge chemical library and the inhibitory activity of the top-ranked 333 compound obtained from each approach (1000 compound in total) was assessed in vitro using the tautomerase assay. This biochemical validation process resulted in the identification of 12 novel MIF inhibitors corresponding to a 1.2% hit rate. Six of these hits came from Surflex docking; two from FlexX docking with MD simulations and four hits were identified with MDS and pharmacophore filtering with minimal overlap between the hits from each approach. Six hits were identified with IC₅₀ values lower than 10 μM (three hits with IC₅₀ lower than 1 μM); four were shown to be suicide inhibitors and act via covalent modification of the N-terminal catalytic residues Pro1. One additional inhibitor, N-phenyl-N-1,3,4-thiadiazol-2-yl-thiourea, (IC₅₀ = 300 nM) was obtained from FlexX docking combined to pharmacophoric filtering on one of the eight MD structures. These results demonstrate the power of integrative in silico approaches in the discovery of new modulator of MIF’s tautomerase activity. The chemical diversity and mode of action of these compounds suggest that they could be used as molecular probes to elucidate the functions and biology of MIF and as lead candidates in drug developments of anti-MIF drugs.     

Screening for Staphylococcal Superantigen Genes Shows No Correlation with the Presence or the Severity of Chronic Rhinosinusitis and Nasal Polyposis

Background

Staphylococcus aureus secretes numerous exotoxins which may exhibit superantigenic properties. Whereas the virulence of several of them is well documented, their exact biological effects are not fully understood. Exotoxins may influence the immune and inflammatory state of various organs, including the sinonasal mucosa: their possible involvement in chronic rhinosinusitis has been suggested and is one of the main trends in current research. The aim of this study was to investigate whether the presence of any of the 22 currently known staphylococcal exotoxin genes could be correlated with chronic rhinosinusitis.

Methodology/Principal Findings

We conducted a prospective, multi-centred European study, analysing 93 Staphylococcus aureus positive swabs taken from the middle meatus of patients suffering from chronic rhinosinusitis, with or without nasal polyposis, and controls. Strains were systematically tested for the presence of the 22 currently known exotoxin genes and genotyped according to their agr groups. No direct correlation was observed between chronic rhinosinusitis, with or without nasal polyposis, and either agr groups or the presence of the most studied exotoxins genes (egc, sea, seb, pvl, exfoliatins or tsst-1). However, genes for enterotoxins P and Q were frequently observed in nasal polyposis for the first time, but absent in the control group. The number of exotoxin genes detected was not statistically different among the 3 patient groups.

Conclusions/Significance

Unlike many previous studies have been suggesting, we did not find any evident correlation between staphylococcal exotoxin genes and the presence or severity of chronic rhinosinusitis with or without nasal polyposis.     

Modeled production,oxidation, and transport processes of wetland methane emissions in temperate,boreal, and Arctic regions

Wetlands are the largest natural source of methane (CH₄) to the atmosphere. The eddy covariance method provides robust measurements of net ecosystem exchange of CH₄, but interpreting its spatiotemporal variations is challenging due to the co-occurrence of CH₄ production, oxidation, and transport dynamics. Here, we estimate these three processes using a data-model fusion approach across 25 wetlands in temperate, boreal, and Arctic regions. Our data-constrained model—iPEACE—reasonably reproduced CH₄ emissions at 19 of the 25 sites with normalized root mean square error of 0.59, correlation coefficient of 0.82, and normalized standard deviation of 0.87. Among the three processes, CH₄ production appeared to be the most important process, followed by oxidation in explaining inter-site variations in CH₄ emissions. Based on a sensitivity analysis, CH₄ emissions were generally more sensitive to decreased water table than to increased gross primary productivity or soil temperature. For periods with leaf area index (LAI) of ≥20% of its annual peak, plant-mediated transport appeared to be the major pathway for CH₄ transport. Contributions from ebullition and diffusion were relatively high during low LAI (<20%) periods. The lag time between CH₄ production and CH₄ emissions tended to be short in fen sites (3 ± 2 days) and long in bog sites (13 ± 10 days). Based on a principal component analysis, we found that parameters for CH₄ production, plant-mediated transport, and diffusion through water explained 77% of the variance in the parameters across the 19 sites, highlighting the importance of these parameters for predicting wetland CH₄ emissions across biomes. These processes and associated parameters for CH₄ emissions among and within the wetlands provide useful insights for interpreting observed net CH₄ fluxes, estimating sensitivities to biophysical variables, and modeling global CH₄ fluxes.