University of Victoria

About: University of Victoria is a education organization based out in Victoria, British Columbia, Canada. It is known for research contribution in the topics: Population & Galaxy. The organization has 14994 authors who have published 41051 publications receiving 1447972 citations. The organization is also known as: Victoria College.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Simulations of the formation, evolution and clustering of galaxies and quasars

Abstract: The cold dark matter model has become the leading theoretical picture for the formation of structure in the Universe. This model, together with the theory of cosmic inflation, makes a clear prediction for the initial conditions for structure formation and predicts that structures grow hierarchically through gravitational instability. Testing this model requires that the precise measurements delivered by galaxy surveys can be compared to robust and equally precise theoretical calculations. Here we present a simulation of the growth of dark matter structure using 2,1603 particles, following them from redshift z = 127 to the present in a cube-shaped region 2.230 billion lightyears on a side. In postprocessing, we also follow the formation and evolution of the galaxies and quasars. We show that baryon-induced features in the initial conditions of the Universe are reflected in distorted form in the low-redshift galaxy distribution, an effect that can be used to constrain the nature of dark energy with future generations of observational surveys of galaxies.

Modules for Experiments in Stellar Astrophysics (MESA)

Abstract: Stellar physics and evolution calculations enable a broad range of research in astrophysics. Modules for Experiments in Stellar Astrophysics (MESA) is a suite of open source, robust, efficient, thread-safe libraries for a wide range of applications in computational stellar astrophysics. A one-dimensional stellar evolution module, MESAstar, combines many of the numerical and physics modules for simulations of a wide range of stellar evolution scenarios ranging from very low mass to massive stars, including advanced evolutionary phases. MESAstar solves the fully coupled structure and composition equations simultaneously. It uses adaptive mesh refinement and sophisticated timestep controls, and supports shared memory parallelism based on OpenMP. State-of-the-art modules provide equation of state, opacity, nuclear reaction rates, element diffusion data, and atmosphere boundary conditions. Each module is constructed as a separate Fortran 95 library with its own explicitly defined public interface to facilitate independent development. Several detailed examples indicate the extensive verification and testing that is continuously performed and demonstrate the wide range of capabilities that MESA possesses. These examples include evolutionary tracks of very low mass stars, brown dwarfs, and gas giant planets to very old ages; the complete evolutionary track of a 1 M ☉ star from the pre-main sequence (PMS) to a cooling white dwarf; the solar sound speed profile; the evolution of intermediate-mass stars through the He-core burning phase and thermal pulses on the He-shell burning asymptotic giant branch phase; the interior structure of slowly pulsating B Stars and Beta Cepheids; the complete evolutionary tracks of massive stars from the PMS to the onset of core collapse; mass transfer from stars undergoing Roche lobe overflow; and the evolution of helium accretion onto a neutron star. MESA can be downloaded from the project Web site (http://mesa.sourceforge.net/).

The ATLAS Experiment at the CERN Large Hadron Collider

Abstract: The ATLAS detector as installed in its experimental cavern at point 1 at CERN is described in this paper. A brief overview of the expected performance of the detector when the Large Hadron Collider begins operation is also presented.