When Scenes Look Like Materials: René Magritte’s Reversible Figure–Ground Motif

We draw attention to a frequent motif in the work of the Belgian surrealist René Magritte (1898–1967). In the motif, a scene is depicted that contains a silhouette, which itself contains another depicted scene. The silhouette is bistable, appearing either as a figural region whose positive space is covered, or filled, with the interior scene texture, or as a ground region providing a window onto a more distant scene. We call this the ‘reversible figure–ground motif’. Because the stimulus does not change when our percept changes, the motif’s appearance at any particular moment cannot be explained by its local or global image statistics. Instead principles of perceptual organization, and in particular image segmentation and figure–ground assignment, appear crucial for determining whether the interior of the silhouette is processed as a material vs. a scene — which in turn reflects the fundamental role of visual segmentation in material and scene perception more generally.

Climate Change in Literature, Television and Film from Norway

Environmental and climatic change has become a frequent motif in contemporary Norwegian literature, television and film, and Norway has the worldwide first organization of writers committed to climate action (The Norwegian Writers’ Climate Campaign, founded in 2013). In this article, we argue that Norwegian climate change fiction and related works draw on elements that relate to specific national and/or Nordic cultural, societal and historical aspects, and that these elements give these works their distinct identity. We focus on four such aspects: (1) references to Norwegian petroculture (since the Norwegian economy is largely based on the export of fossil fuels); (2) an (imagined) intimate connection between Norwegianness and nature, and thus of what often is seen as a typical element of Norwegian national identity; (3) notions of “Nordicity”, and (4) an atmosphere of gloom and melancholia in many of the works (which often has been ascribed to Nordic landscapes, and usually is characteristic for the genre of Nordic noir).

The Old Man and the Bee – Zur Entwicklung eines literarischen Motivs

Although bees are a frequent motif in ancient literature, the people who work with bees are often left in the background. An exception is the motif of the older man on his – usually small – farm who lives from and with his bees. The article shows that this motif is a topos that appears in various texts of Greek and Latin literature of the imperial period. Depending on the intention behind these representations, different elements of the motif may be emphasised or omitted. These variations, and how the motif develops, are here shown through the example of different passages.

The architecture of SARS-CoV-2 transcriptome

SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces a large number of transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif being AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the internal modification and the 3′ tail. Functional investigation of the unknown ORFs and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.HighlightsWe provide a high-resolution map of SARS-CoV-2 transcriptome and epitranscriptome using nanopore direct RNA sequencing and DNA nanoball sequencing.The transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical.In addition to the genomic and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces transcripts encoding unknown ORFs.We discover at least 41 potential RNA modification sites with an AAGAA motif.

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level.

Microsatellites in the Genome of the Edible Mushroom,Volvariella volvacea

Using bioinformatics software and database, we have characterized the microsatellite pattern in theV. volvaceagenome and compared it with microsatellite patterns found in the genomes of four other edible fungi:Coprinopsis cinerea,Schizophyllum commune,Agaricus bisporus,andPleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in theV. volvaceagene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.

ASYMMETRIC TRANSITION AND TIME-SCALE SEPARATION IN INTERLINKED POSITIVE FEEDBACK LOOPS

In [Brandman et al., 2005] it was proposed that interlinked fast and slow positive feedback loops are a frequent motif in biological signaling, because such a device can allow for a rapid response to an external stimulus (sensitivity) along with a certain noise-buffering capacity (robustness), as soon as the two loops operate on different time scales. Here we explore the properties of the nonlinear system responsible for this behavior. We argue that (a) the noise buffering is not linked to the stochastic nature of the stimulus, but only to the time scale of the stimulus variation compared to the intrinsic time scales of the system, and (b) this buffering of stimulus variations follows from the stabilization of a region of the state space away from the equilibrium branches of the system. Our analysis is based on a slow-fast decomposition of the dynamics. We analyze the strength of this buffering as a function of the time scales involved and the Boolean logic of the coupling between dynamic variables, as well as of the amplitude of the stimulus variations. We underline that such a nonequilibrium regime is universal as soon as the stimulus time scale is smaller than the larger time scale of the system, preventing the prediction of the behavior from the features of the bifurcation diagram or using a linear analysis.