Guidelines and recommendations on yeast cell death nomenclature

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research

Theoretical Spectra and Atmospheres of Extrasolar Giant Planets

We present a comprehensive theory of the spectra and atmospheres of irradiated extrasolar giant planets. We explore the dependences on stellar type, orbital distance, cloud characteristics, planet mass, and surface gravity. Phase-averaged spectra for specific known extrasolar giant planets that span a wide range of the relevant parameters are calculated, plotted, and discussed. The connection between atmospheric composition and emergent spectrum is explored in detail. Furthermore, we calculate the effect of stellar insolation on brown dwarfs. We review a variety of representative observational techniques and programs for their potential for direct detection, in light of our theoretical expectations, and we calculate planet-to-star flux ratios as a function of wavelength. Our results suggest which spectral features are most diagnostic of giant planet atmospheres and reveal the best bands in which to image planets of whatever physical or orbital characteristics.Comment: 47 pages, plus 36 postscript figures; with minor revisions, accepted to the Astrophysical Journal, May 10, 2003 issu

Albedo and Reflection Spectra of Extrasolar Giant Planets

We generate theoretical albedo and reflection spectra for a full range of extrasolar giant planet (EGP) models, from Jovian to 51-Pegasi class objects. Our albedo modeling utilizes the latest atomic and molecular cross sections, a Mie theory treatment of extinction by condensates, a variety of particle size distributions, and an extension of the Feautrier radiative transfer method which allows for a general treatment of the scattering phase function. We find that due to qualitative similarities in the compositions and spectra of objects within each of five broad effective temperature ranges, it is natural to establish five representative EGP albedo classes: a ``Jovian'' class (T$_{\rm eff} \lesssim 150$ K; Class I) with tropospheric ammonia clouds, a ``water cloud'' class (T$_{\rm eff} \sim 250$ K; Class II) primarily affected by condensed H$_2$O, a ``clear'' class (T$_{\rm eff} \gtrsim 350$ K; Class III) which lacks clouds, and two high-temperature classes: Class IV (900 K $\lesssim$ T$_{\rm{eff}}$ $\lesssim$ 1500 K) for which alkali metal absorption predominates, and Class V (T$_{\rm{eff}}$ $\gtrsim$ 1500 K and/or low surface gravity ($\lesssim$ 10$^3$ cm s$^{-2}$)) for which a high silicate layer shields a significant fraction of the incident radiation from alkali metal and molecular absorption. The resonance lines of sodium and potassium are expected to be salient features in the reflection spectra of Class III, IV, and V objects. We derive Bond albedos and effective temperatures for the full set of known EGPs and explore the possible effects of non-equilibrium condensed products of photolysis above or within principal cloud decks. As in Jupiter, such species can lower the UV/blue albedo substantially, even if present in relatively small mixing ratios.Comment: revised LaTeX manuscript accepted to Ap.J.; also available at http://jupiter.as.arizona.edu/~burrows/paper

DEM of triaxial tests on crushable sand

This paper presents simulations of high-pressure triaxial shear tests on a crushable sand. The discrete element method is used, featuring a large number of particles and avoiding the use of agglomerates. The triaxial model features a flexible membrane, therefore allowing realistic deformation, and a simple breakage mechanism is implemented using the octahedral shear stress induced in the particles. The simulations show that particle crushing is essential to replicate the realistic behaviour of sand (in particular the volumetric contraction) in high-pressure shear tests. The general effects of crushing during shear are explored, including its effects on critical states, and the influence of particle strength and confining pressure on the degree of crushing are discussed

‘Multi-Epitope-Targeted’ Immune-Specific Therapy for a Multiple Sclerosis-Like Disease via Engineered Multi-Epitope Protein Is Superior to Peptides

Antigen-induced peripheral tolerance is potentially one of the most efficient and specific therapeutic approaches for autoimmune diseases. Although highly effective in animal models, antigen-based strategies have not yet been translated into practicable human therapy, and several clinical trials using a single antigen or peptidic-epitope in multiple sclerosis (MS) yielded disappointing results. In these clinical trials, however, the apparent complexity and dynamics of the pathogenic autoimmunity associated with MS, which result from the multiplicity of potential target antigens and “epitope spread”, have not been sufficiently considered. Thus, targeting pathogenic T-cells reactive against a single antigen/epitope is unlikely to be sufficient; to be effective, immunospecific therapy to MS should logically neutralize concomitantly T-cells reactive against as many major target antigens/epitopes as possible. We investigated such “multi-epitope-targeting” approach in murine experimental autoimmune encephalomyelitis (EAE) associated with a single (“classical”) or multiple (“complex”) anti-myelin autoreactivities, using cocktail of different encephalitogenic peptides vis-a-vis artificial multi-epitope-protein (designated Y-MSPc) encompassing rationally selected MS-relevant epitopes of five major myelin antigens, as “multi-epitope-targeting” agents. Y-MSPc was superior to peptide(s) in concomitantly downregulating pathogenic T-cells reactive against multiple myelin antigens/epitopes, via inducing more effective, longer lasting peripheral regulatory mechanisms (cytokine shift, anergy, and Foxp3+ CTLA4+ regulatory T-cells). Y-MSPc was also consistently more effective than the disease-inducing single peptide or peptide cocktail, not only in suppressing the development of “classical” or “complex EAE” or ameliorating ongoing disease, but most importantly, in reversing chronic EAE. Overall, our data emphasize that a “multi-epitope-targeting” strategy is required for effective immune-specific therapy of organ-specific autoimmune diseases associated with complex and dynamic pathogenic autoimmunity, such as MS; our data further demonstrate that the “multi-epitope-targeting” approach to therapy is optimized through specifically designed multi-epitope-proteins, rather than myelin peptide cocktails, as “multi-epitope-targeting” agents. Such artificial multi-epitope proteins can be tailored to other organ-specific autoimmune diseases

EBI2 is highly expressed in multiple sclerosis lesions and promotes early CNS migration of encephalitogenic CD4 T cells

Arrival of encephalitogenic T cells at inflammatory foci represents a critical step in development of experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis. EBI2 and its ligand, 7{alpha},25-OHC, direct immune cell localization in secondary lymphoid organs. CH25H and CYP7B1 hydroxylate cholesterol to 7{alpha},25-OHC. During EAE, we found increased expression of CH25H by microglia and CYP7B1 by CNS-infiltrating immune cells elevating the ligand concentration in the CNS. Two critical pro-inflammatory cytokines, interleukin-23 (IL-23) and interleukin-1 beta (IL-1{beta}), maintained expression of EBI2 in differentiating Th17 cells. In line with this, EBI2 enhanced early migration of encephalitogenic T cells into the CNS in a transfer EAE model. Nonetheless, EBI2 was dispensable in active EAE. Human Th17 cells do also express EBI2, and EBI2 expressing cells are abundant within multiple sclerosis (MS) white matter lesions. These findings implicate EBI2 as a mediator of CNS autoimmunity and describe mechanistically its contribution to the migration of autoreactive T cells into inflamed organs

Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations

Progress in our understanding of ultrafast light-induced processes in molecules is best achieved through a close combination of experimental and theoretical approaches. Direct comparison is obtained if theory is able to directly reproduce experimental observables. Here, we present a joint approach comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay of the photoelectron signal and an induction time prior to excited state depopulation in dynamics simulations. As a benchmark molecule, we have chosen hexamethylcyclopentadiene, which shows an unprecedentedly large spectral delay of (310 \ub1 20) fs in TRPES experiments. For the dynamics simulations, methyl groups were replaced by "hydrogen atoms" having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 \ub1 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close connection between the two phenomena could be elucidated, allowing for a comparison with other polyenes and supporting the general validity of this finding for their excited state dynamics. Thus, the combination of TRPES and AIMS proves to be a powerful tool for a thorough understanding of ultrafast excited state dynamics in polyenes.Peer reviewed: YesNRC publication: Ye

The Kuiper Belt and Other Debris Disks

We discuss the current knowledge of the Solar system, focusing on bodies in the outer regions, on the information they provide concerning Solar system formation, and on the possible relationships that may exist between our system and the debris disks of other stars. Beyond the domains of the Terrestrial and giant planets, the comets in the Kuiper belt and the Oort cloud preserve some of our most pristine materials. The Kuiper belt, in particular, is a collisional dust source and a scientific bridge to the dusty "debris disks" observed around many nearby main-sequence stars. Study of the Solar system provides a level of detail that we cannot discern in the distant disks while observations of the disks may help to set the Solar system in proper context.Comment: 50 pages, 25 Figures. To appear in conference proceedings book "Astrophysics in the Next Decade

The qualification of collective absolutes and the individuality of persons and events in mid-nineteenth-century Spain

This article argues, on the basis of intellectual, literary, and art history, against the view that mid-nineteenth-century notions of individuality in Spain were products of a social structure based around a bourgeoisie, or, in other accounts, based around a failed effort to establish a bourgeoisie. Instead, it argues that an emphasis on individuality could take radically different forms, that there was no core shared idea of 'individuality'. The article argues that the key motivating factor in these varying notions of individuality was a conflict between and concerning different factions within an oligarchic elite over the future of that elite

Folding-competent and folding-defective forms of Ricin A chain have different fates following retrotranslocation from the endoplasmic reticulum

We report that a toxic polypeptide retaining the potential to refold upon dislocation from the endoplasmic reticulum (ER) to the cytosol (ricin A chain; RTA) and a misfolded version that cannot (termed RTAΔ), follow ER-associated degradation (ERAD) pathways in Saccharomyces cerevisiae that substantially diverge in the cytosol. Both polypeptides are dislocated in a step mediated by the transmembrane Hrd1p ubiquitin ligase complex and subsequently degraded. Canonical polyubiquitylation is not a prerequisite for this interaction because a catalytically inactive Hrd1p E3 ubiquitin ligase retains the ability to retrotranslocate RTA, and variants lacking one or both endogenous lysyl residues also require the Hrd1p complex. In the case of native RTA, we established that dislocation also depends on other components of the classical ERAD-L pathway as well as an ongoing ER–Golgi transport. However, the dislocation pathways deviate strikingly upon entry into the cytosol. Here, the CDC48 complex is required only for RTAΔ, although the involvement of individual ATPases (Rpt proteins) in the 19S regulatory particle (RP) of the proteasome, and the 20S catalytic chamber itself, is very different for the two RTA variants. We conclude that cytosolic ERAD components, particularly the proteasome RP, can discriminate between structural features of the same substrate