The genome sequence of Podospora anserina, a classic model fungus

The genome sequence of the coprophilous fungus Podospora anserina shows both typical ascomycete features and how this species is adapted to its specialized environment

Ornstein-Zernike equation and Percus-Yevick theory for molecular crystals

We derive the Ornstein-Zernike equation for molecular crystals of axially symmetric particles and apply the Percus-Yevick approximation to this system. The one-particle orientational distribution function has a nontrivial dependence on the orientation and is needed as an input. Despite some differences, the Ornstein-Zernike equation for molecular crystals has a similar structure as for liquids. We solve both equations for hard ellipsoids on a sc lattice. Compared to molecular liquids, the tensorial orientational correlators exhibit less structure. However, depending on the lengths a and b of the rotation axis and the perpendicular axes of the ellipsoids, different behavior is found. For oblate and prolate ellipsoids with b >= 0.35 (units of the lattice constant), damped oscillations in distinct directions of direct space occur for some correlators. They manifest themselves in some correlators in reciprocal space as a maximum at the Brillouin zone edge, accompanied by maxima at the zone center for other correlators. The oscillations indicate alternating orientational fluctuations, while the maxima at the zone center originate from nematic-like orientational fluctuations. For a <= 2.5 and b <= 0.35, the oscillations are weaker. For a >= 3.0 and b <= 0.35, no oscillations occur any longer. For many of the correlators in reciprocal space, an increase of a at fixed b leads to a divergence at the zone center q = 0, consistent with nematic-like long range fluctuations, and for some oblate and prolate systems with b ~< 1.0 a simultaneous tendency to divergence of few other correlators at the zone edge is observed. Comparison with correlators from MC simulations shows satisfactory agreement. We also obtain a phase boundary for order-disorder transitions.Comment: 20 pages, 13 figures, submitted to Phys. Rev.

Characterization of the amyloid bacterial inclusion bodies of the HET-s fungal prion

The formation of amyloid aggregates is related to the onset of a number of human diseases. Recent studies provide compelling evidence for the existence of related fibrillar structures in bacterial inclusion bodies (IBs). Bacteria might thus provide a biologically relevant and tuneable system to study amyloid aggregation and how to interfere with it. Particularly suited for such studies are protein models for which structural information is available in both IBs and amyloid states. The only high-resolution structure of an infectious amyloid state reported to date is that of the HET-s prion forming domain (PFD). Importantly, recent solid-state NMR data indicates that the structure of HET-s PFD in IBs closely resembles that of the infectious fibrils. Here we present an exhaustive conformational characterization of HET-s IBs in order to establish the aggregation of this prion in bacteria as a consistent cellular model in which the effect of autologous or heterologous protein quality machineries and/or anti-aggregational and anti-prionic drugs can be further studied

WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family

<p>Abstract</p> <p>Background</p> <p>Genes involved in non-self recognition and host defence are typically capable of rapid diversification and exploit specialized genetic mechanism to that end. Fungi display a non-self recognition phenomenon termed heterokaryon incompatibility that operates when cells of unlike genotype fuse and leads to the cell death of the fusion cell. In the fungus <it>Podospora anserina</it>, three genes controlling this allorecognition process <it>het-d, het-e </it>and <it>het-r </it>are paralogs belonging to the same <it>hnwd </it>gene family. HNWD proteins are STAND proteins (signal transduction NTPase with multiple domains) that display a WD-repeat domain controlling recognition specificity. Based on genomic sequence analysis of different <it>P. anserina </it>isolates, it was established that repeat regions of all members of the gene family are extremely polymorphic and undergoing concerted evolution arguing for frequent recombination within and between family members.</p> <p>Results</p> <p>Herein, we directly analyzed the genetic instability and diversification of this allorecognition gene family. We have constituted a collection of 143 spontaneous mutants of the <it>het-R </it>(<it>HNWD2</it>) and <it>het-E </it>(<it>hnwd5</it>) genes with altered recognition specificities. The vast majority of the mutants present rearrangements in the repeat arrays with deletions, duplications and other modifications as well as creation of novel repeat unit variants.</p> <p>Conclusions</p> <p>We investigate the extreme genetic instability of these genes and provide a direct illustration of the diversification strategy of this eukaryotic allorecognition gene family.</p

Phase behavior of the Confined Lebwohl-Lasher Model

The phase behavior of confined nematogens is studied using the Lebwohl-Lasher model. For three dimensional systems the model is known to exhibit a discontinuous nematic-isotropic phase transition, whereas the corresponding two dimensional systems apparently show a continuous Berezinskii-Kosterlitz-Thouless like transition. In this paper we study the phase transitions of the Lebwohl-Lasher model when confined between planar slits of different widths in order to establish the behavior of intermediate situations between the pure planar model and the three-dimensional system, and compare with previous estimates for the critical thickness, i.e. the slit width at which the transition switches from continuous to discontinuous.Comment: Submitted to Physical Review

Characterization of the amyloid bacterial inclusion bodies of the HET-s fungal prion

The formation of amyloid aggregates is related to the onset of a number of human diseases. Recent studies provide compelling evidence for the existence of related fibrillar structures in bacterial inclusion bodies (IBs). Bacteria might thus provide a biologically relevant and tuneable system to study amyloid aggregation and how to interfere with it. Particularly suited for such studies are protein models for which structural information is available in both IBs and amyloid states. The only high-resolution structure of an infectious amyloid state reported to date is that of the HET-s prion forming domain (PFD). Importantly, recent solid-state NMR data indicates that the structure of HET-s PFD in IBs closely resembles that of the infectious fibrils. Here we present an exhaustive conformational characterization of HET-s IBs in order to establish the aggregation of this prion in bacteria as a consistent cellular model in which the effect of autologous or heterologous protein quality machineries and/or anti-aggregational and anti-prionic drugs can be further studied

Climate change is an important predictor of extinction risk on macroevolutionary timescales

Anthropogenic climate change is increasing rapidly and already impacting biodiversity. Despite its importance in future projections, understanding of the underlying mechanisms by which climate mediates extinction remains limited. We present an integrated approach examining the role of intrinsic traits versus extrinsic climate change in mediating extinction risk for marine invertebrates over the past 485 million years. We found that a combination of physiological traits and the magnitude of climate change is necessary to explain marine invertebrate extinction patterns. Our results suggest that taxa previously identified as extinction resistant may still succumb to extinction if the magnitude of climate change is great enough.</p

Small-Angle Excess Scattering: Glassy Freezing or Local Orientational Ordering?

We present Monte Carlo simulations of a dense polymer melt which shows glass-transition-like slowing-down upon cooling, as well as a build up of nematic order. At small wave vectors q this model system shows excess scattering similar to that recently reported for light-scattering experiments on some polymeric and molecular glass-forming liquids. For our model system we can provide clear evidence that this excess scattering is due to the onset of short-range nematic order and not directly related to the glass transition.Comment: 3 Pages of Latex + 4 Figure

Theme and variations: evolutionary diversification of the HET-s functional amyloid motif

International audienceIn mammals and fungi, Nod-like receptors (NLR) activate downstream cell death execution proteins by a prion-like mechanism. In Podospora anserina, the NWD2 NLR activates the HET-S Helo-domain pore-forming protein by converting its prion-forming domain into a characteristic β-solenoid amyloid fold. The amyloid forming region of HET-S/s comprises two repetitions of a 21 amino acid motif. Herein, we systematically analyze the sequences of C-terminal regions of fungal HeLo and HeLo-like domain proteins to identify HET-s-related amyloid motifs (HRAM). We now identify four novel HRAM subfamilies in addition to the canonical HET-S/s subfamily. These novel motifs share the pseudo-repeat structure of HET-S/s and a specific pattern of distribution of hydrophobic and polar residues. Sequence co-variance analyses predict parallel in-register β-stacking of the two repeats and residue-residue interactions compatible with the β-solenoid fold. As described for HET-S, most genes encoding the HeLo proteins are adjacent to genes encoding NLRs also displaying HRAMs. The motifs of the NLRs are similar to those of their cognate HeLo-domain protein, indicating concerted evolution between repeats. This study shows that HET-s-related amyloid motifs are more common than anticipated and that they have diversified into discrete subfamilies that apparently share a common overall fold. Amyloids are self-templating protein polymers assembled by stacking of β-strands 1. Amyloid formation is often associated with disease, in particular neurodegenerative age-related pathologies such as Alzheimer's or Parkinson's diseases or other conditions like type 2 diabetes 2,3. Amyloid formation has also been linked to cancer with a proposed role of p53 amyloids in tumorogenesis 4. Yet, amyloids also fulfill a range of different functions inside and outside cells 5–7. Such so-called functional amyloids are involved in hormone and toxin storage and release, formation of cell surface structures in microorganisms and scaffolding of pigment synthesis. A role in the regulation of cell states is also described in yeast, where prion amyloids behave as epigenetic regulatory switches 8. Recently, it has also been reported that functional amyloids play a role in cell fate controlling sig-naling cascades both in mammals and fungi. In mammals, the RIP1 and RIP3 kinases which control the necroptosis cell death pathway form an amyloid-like complex assembled via short conserved motifs termed RHIM (for RIP homotypic interaction motifs)

Poisson-Bracket Approach to the Dynamics of Nematic Liquid Crystals. The Role of Spin Angular Momentum

Nematic liquid crystals are well modeled as a fluid of rigid rods. Starting from this model, we use a Poisson-bracket formalism to derive the equations governing the dynamics of nematic liquid crystals. We treat the spin angular momentum density arising from the rotation of constituent molecules about their centers of mass as an independent field and derive equations for it, the mass density, the momentum density, and the nematic director. Our equations reduce to the original Leslie-Ericksen equations, including the inertial director term that is neglected in the hydrodynamic limit, only when the moment of inertia for angular momentum parallel to the director vanishes and when a dissipative coefficient favoring locking of the angular frequencies of director rotation and spin angular momentum diverges. Our equations reduce to the equations of nematohydrodynamics in the hydrodynamic limit but with dissipative coefficients that depend on the coefficient that must diverge to produce the Leslie-Ericksen equations.Comment: 10 pages, to be published in Phys. Rev. E 72(5