Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.

Loop formulation of supersymmetric Yang-Mills quantum mechanics

We derive the fermion loop formulation of N=4 supersymmetric SU(N) Yang-Mills quantum mechanics on the lattice. The loop formulation naturally separates the contributions to the partition function into its bosonic and fermionic parts with fixed fermion number and provides a way to control potential fermion sign problems arising in numerical simulations of the theory. Furthermore, we present a reduced fermion matrix determinant which allows the projection into the canonical sectors of the theory and hence constitutes an alternative approach to simulate the theory on the lattice.

Symbol/Meaning paired-associate recall: an "archetypal memory" advantage?

The theory of the archetypes and the hypothesis of the collective unconscious are two of the central characteristics of analytical psychology. These provoke, however, varying reactions among academic psychologists. Empirical studies which test these hypotheses are rare. Rosen, Smith, Huston and Gonzales proposed a cognitive psychological experimental paradigm to investigate the nature of archetypes and the collective unconscious as archetypal (evolutionary) memory. In this article we report the results of a cross-cultural replication of Rosen et al. conducted in the German-speaking part of Switzerland. In short, this experiment corroborated previous findings by Rosen et al., based on English speakers, and demonstrated a recall advantage for archetypal symbol meaning pairs vs. other symbol/meaning pairings. The fact that the same pattern of results was observed across two different cultures and languages makes it less likely that they are attributable to a specific cultural or linguistic context.

The genomic substrate for adaptive radiation in African cichlid fish

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Compactified N = 1 supersymmetric Yang-Mills theory on the lattice: continuity and the disappearance of the deconfinement transition

Fermion boundary conditions play a relevant role in revealing the confinement mechanism of N=1 supersymmetric Yang-Mills theory with one compactified space-time dimension. A deconfinement phase transition occurs for a sufficiently small compactification radius, equivalent to a high temperature in the thermal theory where antiperiodic fermion boundary conditions are applied. Periodic fermion boundary conditions, on the other hand, are related to the Witten index and confinement is expected to persist independently of the length of the compactified dimension. We study this aspect with lattice Monte Carlo simulations for different values of the fermion mass parameter that breaks supersymmetry softly. We find a deconfined region that shrinks when the fermion mass is lowered. Deconfinement takes place between two confined regions at large and small compactification radii, that would correspond to low and high temperatures in the thermal theory. At the smallest fermion masses we find no indication of a deconfinement transition. These results are a first signal for the predicted continuity in the compactification of supersymmetric Yang-Mills theory.