Patient Endurance in Sir Gawain and the Green Knight

Medieval patience discussions provide an illuminating context for understanding the type of heroism Sir Gawain manifests in Sir Gawain and the Green Knight. Because of the influence of classical authors on the tradition of virtues and vices, a genre that evolved to guide medieval confession, such discussions circulated widely during the Middle Ages, and the virtue was commonly associated with fortitude, which was divided into aggressive and enduring types and negotiated emotions such as anger and fear. While critics often regard Sir Gawain's heroism as passive, the nature of his quest, his final self-assessment, and, especially, the emotions that the poet foregrounds all suggest the tradition of patience. The necessity that Gawain face death without the possibility of retaliation, and of thereby fortifying himself with anger, naturally threatens his heroic, and particularly martial, identity

Reversible Glucan Phosphorylation in the Red Alga, \u3ci\u3eCyanidioschyzon merolae\u3c/i\u3e

Starch and glycogen are an essential component for the majority of species and have been developed to maintain homeostasis in response to environmental changes. Water-soluble glycogen is an excellent source of quick, short-term energy in response to energy demands. In contrast, plants and algae have developed the macromolecule starch that is elegantly suitable for their dependence on external circumstances. Semi-crystalline starch is water-insoluble and inaccessible to most amylolytic enzymes, thus plants and algae have developed a coordinated system so that these enzymes can gain access to the denser starch energy cache. Starch-like semi-crystalline polysaccharides are also found in red algae, termed floridean starch, and are located outside the plastid in the cytosol. Floridean starch resembles a unique class of polyglucans, intermediate of higher plant starch and mammalian glycogen. Reversible glucan phosphorylation is essential in facilitating normal degradation of starch in many higher plants. However, there is a knowledge gap in regards to this process in other starch-containing organisms such as algae. The relationship between phosphorylation and dephosphorylation activity on the structural consequences of starch are still in their infancy as well. One such organism that produces floridean starch is the thermophilic red microalga, Cyanidioschyzon merolae, which has been rapidly advancing as a model organism. Several studies have shown that C. merolae contains a minimal set of genes required to metabolize a semi-crystalline carbohydrate called semi-amylopectin. Amongst this conservative set of genes, we identified a single glucan phosphatase (laforin) and a putative glucan dikinase (GWD), suggesting that reversible glucan phosphorylation may also be present in C. merolae as a means to metabolize their ‘floridean starch’. Therefore, we proposed that the genetically manipulatable C. merolae provides an excellent model organism to study the basic functions of enzymes involved in reversible glucan phosphorylation and how they affect the main constituent of starch. Our work is the first to show specific effects of reversible glucan phosphorylation in a red algal system. In addition, a sole glucan dikinase (GWD) and phosphatase (laforin) are responsible for phosphorylation and dephosphorylation of semi-amylopectin type floridean starch in C. merolae. They both are highly specific to the C6-hydroxyl of glucose moieties of semi-amylopectin and the loss of either enzymatic activity significantly affects the fine structure of amylopectin and thus granule morphology. Loss of C6-phosphate content of semi-amylopectin in Dgwd lines results in suboptimal organization of semi-amylopectin indicating that C6-phosphate is required for proper synthesis and degradation in C. merolae. In the case of Dlaforin lines, without proper maintenance of C6- phosphate, too much C6-phosphate content can equally be as detrimental to amylopectin organization and thus plant vitality. Proper packing of amylopectin likely has direct biological effects in C. merolae as seen through prolonged energy deprivation. Loss of GWD or laforin in C. merolae resulted in excessive nutrient-scavenging which led to the depletion of critical photosynthetic pigments required to recover cell proliferation upon reintroduction of light. These studies highlight the critical function and conservation of reversible glucan phosphorylation and its effect on starch structure in C. merolae

Insights into membrane protein–lipid interactions from free energy calculations

Integral membrane proteins are regulated by specific interactions with lipids from the surrounding bilayer. The structures of protein–lipid complexes can be determined through a combination of experimental and computational approaches, but the energetic basis of these interactions is difficult to resolve. Molecular dynamics simulations provide the primary computational technique to estimate the free energies of these interactions. We demonstrate that the energetics of protein–lipid interactions may be reliably and reproducibly calculated using three simulation-based approaches: potential of mean force calculations, alchemical free energy perturbation, and well-tempered metadynamics. We employ these techniques within the framework of a coarse-grained force field and apply them to both bacterial and mammalian membrane protein–lipid systems. We demonstrate good agreement between the different techniques, providing a robust framework for their automated implementation within a pipeline for annotation of newly determined membrane protein structures

Applying network and genetic analysis to the potato metabolome

Compositional traits in potato [Solanum tuberosum L.] are economically important but genetically complex, often controlled by many loci of small effect; new methods need to be developed to accelerate analysis and improvement of such traits, like chip quality. In this study, we used network analysis to organize hundreds of metabolic features detected by mass spectrometry into groups, as a precursor to genetic analysis. 981 features were condensed into 44 modules; module eigenvalues were used for genetic mapping and correlation analysis with phenotype data collected by the Solanaceae Coordinated Agricultural Project. Half of the modules were associated with at least one SNP according to GWAS; 11 of those modules were also significantly correlated with chip color. Within those modules features associated with chipping provide potential targets for selection in addition to selection for reduced glucose. Loci associated with module eigenvalues were not evenly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8. Comparison of GWAS on single features and modules of clustered features often identified the same SNPs. However, features with related chemistries (for example, glycoalkaloids with precursor/product relationships) were not found to be near neighbors in the network analysis and did not share common SNPs from GWAS. Instead, the features within modules were often structurally disparate, suggesting that linkage disequilibrium complicates network analyses in potato. This result is consistent with recent genomic studies of potato showing that chromosomal rearrangements that create barriers to recombination are common in cultivated germplasm

The first total synthesis of (+)-mucosin

The first total synthesis of (+)-mucosin has been completed allowing assignment of the absolute stereochemistry of the natural product. A zirconium induced co-cyclisation was utilised to install the correct stereochemistry of the four contiguous stereocentres around the unusual bicyclo[4.3.0]nonene core

Investigating the Atmospheric Mass Loss of the Kepler-105 Planets Straddling the Radius Gap

An intriguing pattern among exoplanets is the lack of detected planets between approximately $1.5$ R$_\oplus$ and $2.0$ R$_\oplus$. One proposed explanation for this "radius gap" is the photoevaporation of planetary atmospheres, a theory that can be tested by studying individual planetary systems. Kepler-105 is an ideal system for such testing due to the ordering and sizes of its planets. Kepler-105 is a sun-like star that hosts two planets straddling the radius gap in a rare architecture with the larger planet closer to the host star ($R_b = 2.53\pm0.07$ R$_\oplus$, $P_b = 5.41$ days, $R_c = 1.44\pm0.04$ R$_\oplus$, $P_c = 7.13$ days). If photoevaporation sculpted the atmospheres of these planets, then Kepler-105b would need to be much more massive than Kepler-105c to retain its atmosphere, given its closer proximity to the host star. To test this hypothesis, we simultaneously analyzed radial velocities (RVs) and transit timing variations (TTVs) of the Kepler-105 system, measuring disparate masses of $M_b = 10.8\pm2.3$ M$_\oplus$ ($\rho_b = 0.97\pm0.22$ g cm$^{-3}$) and $M_c = 5.6\pm1.2$ M$_\oplus$ ($\rho_c = 2.64\pm0.61$ g cm$^{-3}$). Based on these masses, the difference in gas envelope content of the Kepler-105 planets could be entirely due to photoevaporation (in 76\% of scenarios), although other mechanisms like core-powered mass loss could have played a role for some planet albedos.Comment: 14 pages, 3 figures, 2 table

The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4

In order to gain insight into the function of the Saccharomyces cerevisiae SWI/SNF complex, we have identified DNA sequences to which it is bound genomewide. One surprising observation is that the complex is enriched at the centromeres of each chromosome. Deletion of the gene encoding the Snf2 subunit of the complex was found to cause partial redistribution of the centromeric histone variant Cse4 to sites on chromosome arms. Cultures of snf2Δ yeast were found to progress through mitosis slowly. This was dependent on the mitotic checkpoint protein Mad2. In the absence of Mad2, defects in chromosome segregation were observed. In the absence of Snf2, chromatin organisation at centromeres is less distinct. In particular, hypersensitive sites flanking the Cse4 containing nucleosomes are less pronounced. Furthermore, SWI/SNF complex was found to be especially effective in the dissociation of Cse4 containing chromatin in vitro. This suggests a role for Snf2 in the maintenance of point centromeres involving the removal of Cse4 from ectopic sites

Nucleosome-coupled expression differences in closely-related species

<p>Abstract</p> <p>Background</p> <p>Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown.</p> <p>Results</p> <p>We address this challenge by generating nucleosome positioning and cell cycle expression data for <it>Saccharomyces bayanus </it>and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, <it>S. bayanus </it>and <it>S. cerevisiae</it>. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs).</p> <p>Conclusions</p> <p>Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.</p

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

This study uses high-resolution cryo-electron microscopy to provide a complete structural model of the VEEV alphavirus, bridging the gap between incomplete crystal structures and lower resolution electron microscopy analyses