Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests

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Negative density-dependent emigration of males in an increasing red deer population

In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deer Cervus elaphus marked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (37 km) than at low density in 1977 (26 km), possibly caused by increasing saturation of deer in areas surrounding the marking sites. Our study highlights that pattern of density dependence in dispersal rates may differ markedly between sexes in highly polygynous species. Contrasting patterns reported in small-scale studies are suggestive that spatial scale of density variation may affect the pattern of temporal density dependence in emigration rates and distances.     

A Conservative Point Mutation in a Dynamic Antigen-binding Loop of Human Immunoglobulin λ6 Light Chain Promotes Pathologic Amyloid Formation

Immunoglobulin light chain (LC) amyloidosis (AL) is a life-threatening human disease wherein free mono-clonal LCs deposit in vital organs. To determine what makes some LCs amyloidogenic, we explored patient-based amyloidogenic and non-amyloidogenic recombinant LCs from the λ6 subtype prevalent in AL. Hydrogen-deuterium exchange mass spectrometry, structural stability, proteolysis, and amyloid growth studies revealed that the antigen-binding CDR1 loop is the least protected part in the variable domain of λ6 LC, particularly in the AL variant. N32T substitution in CRD1 is identified as a driver of amyloid formation. Substitution N32T increased the amyloidogenic propensity of CDR1 loop, decreased its protection in the native structure, and accelerated amyloid growth in the context of other AL substitutions. The destabilizing effects of N32T propagated across the molecule increasing its dynamics in regions ∼30 Å away from the substitution site. Such striking long-range effects of a conservative point substitution in a dynamic surface loop may be relevant to Ig function. Comparison of patient-derived and engineered proteins showed that N32T interactions with other substitution sites must contribute to amyloidosis. The results suggest that CDR1 is critical in amyloid formation by other λ6 LCs.     

Taphonomy and ichnology of cephalopod shells in a Maastrichtian chalk from Western Australia

The post-mortem history of a prolific Maastrichtian ammonite and nautiloid fauna preserved as phosphatic steinkerns in chalk of the upper Miria Formation of Western Australia is described. Sediment infilling of phragmocones, required for their fossilisation, was accomplished by means of perforations in the shell wall induced by the activity of abundant endoliths. These include borings ascribed to clionid sponges (Entobia), thallophytes, polychaete worms (including Caulostrepis and probable Maeandropolydora), phoronids (Talpina and Gnathichnus) and others of conjectural origin. Sediment infilling by this mechanism is considered to be more applicable to the taphonomy of phragmocones in general than sediment entry through the siphuncle and to be indicative of low sedimentation rates for the hosting strata. Nonheteromorph ammonites, and the nautiloid Cimomia, are preserved almost exclusively as phragmocones in the upper Miria Formation, and are numerically subordinate to the heteromorph Eubaculites which, together with Glyptoxoceras, is preserved predominantly as body chambers. This phragmocone/body chamber preservational contrast is attributed to the influence of shell shape on pre-burial mechanical abrasion. The apparent dominance of Eubaculites is considered to be largely a preservational artifact and ascribed to the ease with which body chambers were infilled, and thereby favoured for steinkern formation, relative to phragmocones. Phragmocones, or parts thereof. not filled with sediment were eliminated from the fossil record by diagenetic aragonite dissolution. Many ammonites with open umbilici have the early whorls missing. This we attribute to the trapping of sediment in the umbilicus prior to burial, preventing endolith attack whereby the early whorls avoided a sediment infilling. However, the protected inner whorls of involute ammonites and Cimomia, which have closed umbilici, and the inner whorls of evolute ammonites where a cemented umbilical plug supported the mouldic cavity left by shell dissolution, were preserved and were commonly infilled with calcite spar later in diagenesis. The dearth of cephalopod fossils in chalk underlying the upper Miria Formation is ascribed to diagenesis in which aragonite dissolution was not preceded by cementation.     

A Combined Product Estimator in Sample Survey

For the estimation of the population mean in stratified random sampling a ‘Combined Product Estimator’ is proposed which is more efficient than the ‘Combined Ratio’ and ‘Separate Ratio’ estimators. Also, the proposed estimator have exact expressions for bias and mean square error. An empirical illustration is given to compare the efficiencies of different estimators.     

Does Height Off the Ground Affect Bird Visitation and Fruit Set in the Pollen‐Limited Mistletoe Peraxilla tetrapetala (Loranthaceae)?

For pollination studies of forest species it is sometimes only possible to work on those flowers nearest to the ground. We test whether using low flowers introduces bias, by measuring height effects on bird visitation and fruit set in one mistletoe species pollinated by bellbirds in New Zealand. At this site, previous studies have shown fruit set near the ground to be pollen limited. We measured fruit set on 32 mistletoes at different heights in 11 host trees. Mistletoe fruit set varied significantly among host trees but did not vary with height. Although bellbirds generally forage preferentially in the upper part of the forest, mistletoe flowers appear to be attractive enough to ensure adequate visitation and fruit set at all heights.     

The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-I and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region). Finally, the characteristics of lentiviral codon usage are presented as a phylogenetic tree without the need for prior sequence alignment.Correspondence to: B. Berkhout