Increased epsilon(gamma-glutamyl)lysine crosslinking associated with increased protein synthesis in the inner layers of healing rat skin wounds.

Three days after biopsy wounds were made in the dorsal skin of rats the animals were killed and explants of wounded and unwounded skin were incubated for 7 h with either [3H]glutamine or [3H]lysine. Both incubated and fresh control explants were then dissected into three layers which were homogenized, extracted, digested and then assayed for epsilon (gamma-glutamyl)lysine. The concentration of epsilon(gamma-glutamyl)lysine was greater in all three wounded layers than in the corresponding unwounded layers. The concentration in the wounded middle (dermal) layer and in the unwounded middle layer of younger rats was greater than in the unwounded outer (keratinized) layer, which has previously been shown to contain epsilon(gamma-glutamyl)lysine crosslinks. The incorporation of label from both [3H]glutamine and [3H]lysine into buffer-insoluble protein of the middle and inner (muscle) layers was much greater in the wounded explants than in the unwounded. Except for [3H]lysine in the inner layer there was also an increase in the fraction of incorporated label which was converted to epsilon(gamma-glutamyl)lysine. These results show that increased protein biosynthesis during repair in the wounded explants is associated with increased formation of epsilon(gamma-glutamyl)lysine. In addition, they indicate that the crosslink is involved in some process in the middle and inner layers which is distinct from its known function in keratinization of the epidermis.     

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

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Associative Processing Is Inherent in Scene Perception

How are complex visual entities such as scenes represented in the human brain? More concretely, along what visual and semantic dimensions are scenes encoded in memory? One hypothesis is that global spatial properties provide a basis for categorizing the neural response patterns arising from scenes. In contrast, non-spatial properties, such as single objects, also account for variance in neural responses. The list of critical scene dimensions has continued to grow—sometimes in a contradictory manner—coming to encompass properties such as geometric layout, big/small, crowded/sparse, and three-dimensionality. We demonstrate that these dimensions may be better understood within the more general framework of associative properties. That is, across both the perceptual and semantic domains, features of scene representations are related to one another through learned associations. Critically, the components of such associations are consistent with the dimensions that are typically invoked to account for scene understanding and its neural bases. Using fMRI, we show that non-scene stimuli displaying novel associations across identities or locations recruit putatively scene-selective regions of the human brain (the parahippocampal/lingual region, the retrosplenial complex, and the transverse occipital sulcus/occipital place area). Moreover, we find that the voxel-wise neural patterns arising from these associations are significantly correlated with the neural patterns arising from everyday scenes providing critical evidence whether the same encoding principals underlie both types of processing. These neuroimaging results provide evidence for the hypothesis that the neural representation of scenes is better understood within the broader theoretical framework of associative processing. In addition, the results demonstrate a division of labor that arises across scene-selective regions when processing associations and scenes providing better understanding of the functional roles of each region within the cortical network that mediates scene processing.     

Structures of ascaroside aglycones

Free and derivatized aglycones and parent ascarosides of Ascaris lumbricoides and A. columnaris (Nematoda) were isolated by thin-layer and gas chromatography and analyzed by mass spectrometry and polarimetry. Results for monol aglycones confirmed previous chain-length assignments and the location of the l-hydroxyl group at C-2. The major monols of even carbon number possessed a methyl branch on the penultimate carbon (ω ? 1). Diol alycones were entirely unbranched homologues, mainly 31 and 33 carbons long, and had hydroxyl groups on C-2 and C-(ω ? 1). These aglycones were truly symmetrical, for they were optically inactive with the center bearing the glycone in diol ascaroside (C-2), being mostly or entirely the l configuration. Three major features of ascaroside structure—chain length composition of the aglycones, molecular weight of the unusual glycone (a dideoxyhexose), the kind and position of acyl groups—were clearly discernible in the spectra of intact ascarosides.     

Heterogeneity of amino acid sequence in hippopotamus cytochrome c.

The amino acid sequences of chymotryptic and tryptic peptides of Hippopotamus amphibius cytochrome c were determined by a recent modification of the manual Edman sequential degradation procedure. They were ordered by comparison with the structure of the hog protein. The hippopotamus protein differs in three positions: serine, alanine, and glutamine replace alanine, glutamic acid, and lysine in positions 43, 92, and 100, respectively. Since the artiodactyl suborders diverged in the mid-Eocene some 50 million years ago, the fact that representatives of some of them show no differences in their cytochromes c (cow, sheep, and hog), while another exhibits as many as three such differences, verifies that even in relatively closely related lines of descent the rate at which cytochrome c changes in the course of evolution is not constant. Furthermore, 10.6% of the hippopotamus cytochrome c preparation was shown to contain isoleucine instead of valine at position 3, indicating that one of the four animals from which the protein was obtained was heterozygous in the cytochrome c gene. Such heterogeneity is a necessary condition of evolutionary variation and has not been previously observed in the cytochrome c of a wild mammalian population.     

A metabolomics based approach for understanding the influence of terroir in Vitis Vinifera L.

This study aims to understand the contribution of ‘terroir’ during the cultivation of Vitis vinifera L. The concept of terroir stems from the French ideal that a region’s soil and local vineyard topography together with a region’s macroclimate, including the mesoclimate and vine microclimate, together define the unique characteristics of a wine. In this current study we have utilized high performance liquid chromatography combined with a Q Exactive quadrupole Orbitrap™ mass analyzer for the direct injection analysis of Vitis vinifera juice samples sourced from two different vineyards from the Santa Ynez AVA of Santa Barbara county. Analysis of the mass spectral data was facilitated by a differential analysis software program—SIEVE 2.0™. Distinct metabolomic signatures in freshly crushed juice samples were elucidated. Interestingly, important and distinct information was revealed from the analysis of both the positive and negative ion data. Hierarchical clustering indicated the negative ion data displayed similarity based on varietal character while results obtained in the positive ion mode clustered primarily on terroir. This may indicate that more acidic compounds are influenced by varietal character while more basic compounds are influenced by terroir. Using a feature of SIEVE 2.0 a flavonoid database was utilized to search the raw data for flavonoids present in the juice samples. This targeted analysis indicated the flavonoid profile of juice samples appears to be a good indicator of varietal character independent of terroir. The analysis presented in this study suggests distinct Vitis vinifera grape juice chemical signatures are present prior to fermentation. Further analysis will aim to attribute which of these compounds is influenced by varietal character and/or terroir.

     

Biogeography of the ecosystems of the healthy human body

Background

Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.

Results

We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies.

Conclusions

The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.     

A biogeographic reversal in sexual size dimorphism along a continental temperature gradient

The magnitude and direction of sexual size dimorphism (SSD) varies greatly across the animal kingdom, reflecting differential selection pressures on the reproductive and/or ecological roles of males and females. If the selection pressures and constraints imposed on body size change along environmental gradients, then SSD will vary geographically in a predictable way. Here, we uncover a biogeographical reversal in SSD of lizards from Central and North America: in warm, low latitude environments, males are larger than females, but at colder, high latitudes, females are larger than males. Comparisons to expectations under a Brownian motion model of SSD evolution indicate that this pattern reflects differences in the evolutionary rates and/or trajectories of sex‐specific body sizes. The SSD gradient we found is strongly related to mean annual temperature, but is independent of species richness and body size differences among species within grid cells, suggesting that the biogeography of SSD reflects gradients in sexual and/or fecundity selection, rather than intersexual niche divergence to minimize intraspecific competition. We demonstrate that the SSD gradient is driven by stronger variation in male size than in female size and is independent of clutch mass. This suggests that gradients in sexual selection and male–male competition, rather than fecundity selection to maximize reproductive output by females in seasonal environments, are predominantly responsible for the gradient.