Rapid characterization of spike variants via mammalian cell surface display

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Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.     

Methodologies for the isolation of alternative binders with improved clinical potentiality over conventional antibodies

The availability of binders to different functional domains of the same protein or to physiologically co-operating proteins allows for the simultaneous inhibition of independent downstream signaling pathways. This multi-target approach represents a promising therapeutic strategy, as demonstrated in the case of the synergistic effect of anti-Her2 treatment based on the combined use of the trastuzumab and pertuzumab monoclonal antibodies that induce cellular cytotoxicity and impair the receptor dimerization, respectively. Therefore, a reliable selection method for the recovery of epitope-specific antibodies is highly needed. Animal immunization with short peptides resembling the epitope sequence for raising conventional antibodies represents an alternative. Panning phage displayed libraries of recombinant antibodies such as scFvs and nanobodies or of other peptide collections is another option. Although recombinant antibodies can provide the same specificity as conventional antibodies, they offer at least two further advantages: i) the protocols for the selection of epitope-specific antibodies can be rationally designed, and ii) their expression as multivalent, bispecific and biparatopic molecules is feasible. This review will analyze the recent literature concerning technical aspects related to the isolation, the expression as multivalent molecules, and the therapeutic applications of binders able to interfere with antigen functional domains. The term binder will be preferred when possible to include those molecules, such as peptides or affibodies, with at least some proven practical uses.     

CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays

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Zebra stripes and tiger stripes: the spatial frequency distribution of the pattern compared to that of the background is significant in display and crypsis

Some striped animals are camouflaged in their natural environment, whereas others are conspicuous. Mammals are known to have spatial frequency analysers in their visual mechanism, and it is suggested that the spatial characteristics of a striped pattern are different in camouflaged and conspicuous animals. Fourier analysis of the stripes of the zebra shows spatial frequencies in the pattern that are unlikely to be present so strongly in their natural background scene. A similar analysis of the camouflaging stripes of a tiger show that the distribution of spatial frequencies are similar to that in the background scene.     

Taxonomic studies ofAsarum sensu lato

The floral vascular anatomy of 12 species representing each ofAsarum s. str.,Asiasarum, Geotaenium, Heterotropa andHexastylis are compared to clarify intergeneric relationships. The five genera have basically similar structures in floral morphology and vasculature, and consistently have a six-carpelled compound ovary and the associated similar placental vasculature. They show, however, a significant difference in the position and the constituent of the “ventral” carpellary bundles in the placental axis betweenAsiasarum-Heterotropa-Hexastylis andAsarum-Geotaenium. InAsiasarum, Heterotropa andHexastylis the ventral bundles of each carpel are basically free and antilocular as expected in the least specialized compound ovary of angiosperms; in contrast, inAsarum andGeotaenium the ventral carpellary bundles are antiseptal and heterogenous (i.e., formed by the lateral fusion of ventral bundles of adjacent carpels). Shared probable apomorphic floral vasculature, as well as shared single style-column, suggests the closest mutual relationships betweenAsarum andGeotaenium. In terms of floral morphology and anatomy,Asiasarum, Heterotropa andHexastylis retain plesiomorphies. Possible chromosomal evolution in the related genera is also discussed.     

Adenosine, a cytoprotective autocoid: effects of adenosine on neutrophil plasma membrane viscosity and chemoattractant receptor display

At inflammatory sites neutrophils are stimulated to produce a variety of toxic agents, yet rarely harm the endothelium across which they migrate. We have recently found that endothelium releases adenosine which, acting via receptors on the surface of human neutrophils, inhibits generation of toxic metabolites by stimulated neutrophils but, paradoxically, promotes chemotaxis. Agents which diminish plasma membrane viscosity affect neutrophil function similarly, possibly by modulating chemoattractant receptor number or affinity. We therefore determined whether adenosine receptor agonists modulate neutrophil function by decreasing membrane viscosity and/or chaning the affinity of chemoattractant (N-fMet-Leu-Phe, FMLP) receptors. Surprisingly, 5′-(N-ethylcar☐amido)adenosine (NECA, 10 μM), the most potent agonist at neutrophil adenosine receptors, increased plasma membrane viscosity, as measured by fluorescence anisotropy of the plasma membrane specific probe 1-(4-trimethylaminophenyl)-6-diphenyl-1,3,5-hexatriene (TMA-DPH), in unstimulated neutrophils from a mean microviscosity of 1.67 ± 0.02 (S.E.) to 1.80 ± 0.02 (p < 0.001) while inosine (10 μM), a poor adenosine receptor agonist, had no effect (1.73 ± 0.04, p =n.s. vs. control, p < 0.01 vs. NECA). Adenosine receptor agonists increased plasma membrane viscosity in neutrophils with the same order of potency previously seen for inhibition of superoxide anion generation and enhancement of chemotaxis (NECA > adenosine = N⁶-phenylisopropyladenosine). The adenosine receptor antagonist 8-(p-sulfophenyl)theophylline reversed the effect of NECA on plasma membrane viscosity. Unlike other agents which modulate plasma membrane viscosity, NECA (10 μM) did not significantly change the number or affinity of [³H]FMLP binding sites on neutrophils. In contrast to the hypothesis of Yuli et al. these results indicate that occupancy of adenosine receptors on neutrophils increases plasma membrane viscosity without affecting chemoattractant receptor display.     

Estimates of hierarchical variation in flower morphology in natural populations ofScleranthus annuus (Caryophyllaceae), an inbreeding annual

The variation in two sets of morphological characters of the flowers of the highly inbreedingScleranthus annuus (Caryophyllaceae) was assessed using 15–20 plants from each of 20 natural populations from the southernmost region of Sweden. The stamen fertility data set consisted of 10 characters describing the degree of fertility of the ten stamens/staminoids, while the sepal/gynoecium data set comprised 10 sepal characters, together with style and stigma length. Substantial variation was found in both the degree of development and the fertility of the stamens, the degree of variability in stamen fertility being related to stamen position within the flower. Considerable variation was found in the characters of the sepal and the gynoecium. Hierarchical analyses of variance indicated that 29% of the variation in total male reproductive effort was distributed among populations, 28% among plants within populations and 43% represented within-plant variation. The corresponding averages for the characters from the sepal/gynoecium data set are 26, 38, and 35%: a greater proportion of the total variance in female reproductive characters is accounted for by among individual variation than is the case with the male reproductive characters. Significance tests of Mahalanobis distances derived by canonical variate analyses indicated that all populations were significantly separated using the sepal/gynoecium data set, while only 50% of the pairwise comparisons on the basis of the stamen fertility data set were significant. Cluster analysis did not reveal any aggregation of the populations. The incongruence of the two data sets and their ability to discriminate between the populations is discussed.     

Reproductive structures and phylogenetic significance of extant primitive Angiosperms

A brief survey is presented on fossil reproductive structures of early Angiosperms from the Lower and mid-Cretaceous and at the same time on the reproductive structures of those extant Angiosperms which resemble most closely these fossils and which seem to be especially primitive also on other grounds: a first group (Degeneriaceae, Himantandraceae, Eupomatiaceae, Austrobaileyaceae) possessing relatively complicated and conspicuous flowers with elaborated inner staminodes, a second group (Chloranthaceae, Trimeniaceae, Amborellaceae) possessing small and relatively simple, inconspicuous flowers with peculiar features in the carpels, and a third group (Winteraceae) possessing flowers with unusual variability in organ number and size. The three groups exhibit a certain diversity in pollination biology, although cantharophily seems to prevail, however different the cantharophily character syndromes may be between the groups. In the extant primitiveMagnoliidae variability occurs on other morphological levels than in the higher advanced Angiosperms. This has to be taken into consideration in evaluations of the systematic relationships of the various groups of theMagnoliidae. Presumably often their relationships are closer than it may appear at first sight. This is also true for the three groups here discussed.     

Socialization processes in a female lowland gorilla

A low-interactive, captive, female lowland gorilla, Molly, was studied following the introduction into her enclosure of three gorillas, two males and a female, raised from birth in captive gorilla groups. Observations were made 6 mo after the new gorillas were introduced. Throughout the period of observation, Molly interacted in an affiliative manner with one of the males, playing or sitting quietly with him in a tree (where Molly spent most of her time) and occasionally on the ground. Agonistic displays between Molly and the new female decreased after they were released in the enclosure without the males for a series of days. Molly, however, continued to react to the other male, the most dominant, in an agonistic manner, and usually retreated from his reach, climbed the tree, and/or grimaced and piloerected whenever he approached. Although Molly's continued avoidance of the dominant male impeded her complete socialization, we propose that the interventions employed in this study—introduction of new younger gorillas into and an enclosure, and a series of dyadic separations between the noninteractive gorilla and each of the new group members—are possible strategies that can be used to facilitate socialization of captive, noninteractive gorillas.