Nonproductive exposure of PBMCs to SARS‐CoV‐2 induces cell‐intrinsic innate immune responses

Cell‐intrinsic responses mounted in PBMCs during mild and severe COVID‐19 differ quantitatively and qualitatively. Whether they are triggered by signals emitted by productively infected cells of the respiratory tract or result from physical interaction with virus particles remains unclear. Here, we analyzed susceptibility and expression profiles of PBMCs from healthy donors upon ex vivo exposure to SARS‐CoV and SARS‐CoV‐2. In line with the absence of detectable ACE2 receptor expression, human PBMCs were refractory to productive infection. RT–PCR experiments and single‐cell RNA sequencing revealed JAK/STAT‐dependent induction of interferon‐stimulated genes (ISGs) but not proinflammatory cytokines. This SARS‐CoV‐2‐specific response was most pronounced in monocytes. SARS‐CoV‐2‐RNA‐positive monocytes displayed a lower ISG signature as compared to bystander cells of the identical culture. This suggests a preferential invasion of cells with a low ISG baseline profile or delivery of a SARS‐CoV‐2‐specific sensing antagonist upon efficient particle internalization. Together, nonproductive physical interaction of PBMCs with SARS‐CoV‐2‐ and, to a much lesser extent, SARS‐CoV particles stimulate JAK/STAT‐dependent, monocyte‐accentuated innate immune responses that resemble those detected in vivo in patients with mild COVID‐19.     

Cyanophages from a less virulent clade dominate over their sister clade in global oceans

Environmental virus communities are highly diverse. However, the infection physiology underlying the evolution of diverse phage lineages and their ecological consequences are largely unknown. T7-like cyanophages are abundant in nature and infect the marine unicellular cyanobacteria, Synechococcus and Prochlorococcus, important primary producers in the oceans. Viruses belonging to this genus are divided into two distinct phylogenetic clades: clade A and clade B. These viruses have narrow host-ranges with clade A phages primarily infecting Synechococcus genotypes, while clade B phages are more diverse and can infect either Synechococcus or Prochlorococcus genotypes. Here we investigated infection properties (life history traits) and environmental abundances of these two clades of T7-like cyanophages. We show that clade A cyanophages have more rapid infection dynamics, larger burst sizes and greater virulence than clade B cyanophages. However, clade B cyanophages were at least 10-fold more abundant in all seasons, and infected more cyanobacteria, than clade A cyanophages in the Red Sea. Models predicted that steady-state cyanophage abundances, infection frequency, and virus-induced mortality, peak at intermediate virulence values. Our findings indicate that differences in infection properties are reflected in virus phylogeny at the clade level. They further indicate that infection properties, together with differences in subclade diversity and host repertoire, have important ecological consequences with the less aggressive, more diverse virus clade having greater ecological impacts.Subject terms: Microbial ecology, Molecular ecology, Bacteriophages, Population dynamics, Microbial biooceanography     

Is There Any Evidence for Rapid,Genetically-Based,Climatic Niche Expansion in the Invasive Common Ragweed?

Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.     

Phylogeography of the Vipera ursinii complex (Viperidae): mitochondrial markers reveal an east–west disjunction in the Palaearctic region

Aim The aim of this study was to elucidate the phylogeographical pattern of taxa composing the Vipera ursinii complex, for which the taxonomic status and the dating of splitting events have been the subject of much debate. The objectives were to delimit potential refugia and to date splitting events in order to suggest a scenario that explains the diversification of this species complex. Location Western Europe to Central Asia. Methods Sequences of the mitochondrial cytochrome b and NADH dehydrogenase subunit 4 (ND4) genes were analysed for 125 individuals from 46 locations throughout the distribution range of the complex. The phylogeographical structure was investigated using Bayesian and maximum likelihood methods. Molecular dating was performed using three calibration points to estimate the timing of diversification. Results Eighty‐nine haplotypes were observed from the concatenation of the two genes. Phylogenetic inferences supported two main groups, referred to in this study as the ‘ursinii clade’ and the ‘renardi clade’, within which several subclades were identified. Samples from Greece (Vipera ursinii graeca) represented the first split within the V. ursinii complex. In addition, three main periods of diversification were revealed, mainly during the Pleistocene (2.4–2.0 Ma, 1.4 Ma and 1.0–0.6 Ma). Main conclusions The present distribution of the V. ursinii complex seems to have been shaped by Quaternary climatic fluctuations, and the Balkan, Caucasus and Carpathian regions are identified in this study as probable refugia. Our results support a south–north pattern of colonization, in contrast to the north–south colonization previously proposed for this complex. The biogeographical history of the V. ursinii complex corroborates other biogeographical studies that have revealed an east–west disjunction (situated near the Black Sea) within a species complex distributed throughout the Palaearctic region.     

Does your lip stick? Evolutionary aspects of the mouth morphology of the Indo‐Pacific clinging goby of the Sicyopterus genus (Teleostei: Gobioidei: Sicydiinae) based on mitogenome phylogeny

Sicydiinae gobies have an amphidromous life cycle. Adults grow, feed, and reproduce in rivers, while larvae have a marine dispersal phase. Larvae recruit back to rivers and settle in upstream habitats. Within the Sicydiinae subfamily, the Sicyopterus genus, one of the most diverse (24 species), is distributed in the tropical islands of the Indo‐Pacific. One of the characters used to determine Sicyopterus species is the upper lip morphology, which can be either smooth, crenulated, or with papillae, and with (2 or 3) or without clefts. The mouth is used as a secondary locomotor organ along with the pelvic sucker. It is thus strongly related to the climbing ability of species and is of major importance for the upstream migration and the colonization of insular freshwater systems. The mouth also has an important role in the feeding mechanism of these herbivorous species. In this paper, we have established a molecular phylogeny of the genus based on the 13 mitochondrial protein‐coding genes to discuss the relationship between 18 Sicyopterus species. There is a well‐supported dichotomy in the molecular phylogeny of the Sicyopterus genus and this separation into two clades is also morphologically visible, with the distinction of species with three clefts and species with 0 or 2 clefts on the upper lip. The mouth morphology can thus be separated with regard to the molecular phylogeny obtained. The evolution of the mouth morphology is discussed in terms of the adaptation of the Sicyopterus genus to settlement and life in tropical insular river systems.     

Regulation of Tyrosine Phosphatase STEP61 by Protein Kinase A during Motor Skill Learning in Mice

Recently, striatal-enriched protein tyrosine phosphatase (STEP) and its upstream regulator protein kinase A (PKA) have been suspected to play a role in the intracellular mechanisms of fear conditioning and spatial memory. However, whether they contribute to the learning and memory of motor skills is totally unknown. In this study, we have investigated the role of STEP and PKA activities during motor skill learning associated with the accelerating rotarod task. We observed that learning the rotarod task differentially modulated the levels of phosphorylated STEP61 at serine 221, a site directly regulated by PKA, in the hippocampus, motor cortex and striatum. In a second set of experiments, we have pharmacologically inhibited PKA by the injection of Rp-cAMPS directly into the dorsal striatum of mice before rotarod trainings. PKA phosphorylation of STEP prevents the dephosphorylation of STEP substrates, whereas inhibition of PKA promotes STEP activity. Striatal PKA inhibitions dose-dependently impaired mice performances on the accelerating rotarod task. General motor abilities testing revealed an intact motor control in mice treated with 5 and 20 µg of Rp-cAMPS, but not at the highest dose of 40 µg. This suggested that motor learning was selectively affected by PKA inhibition at lower doses. Most notably, striatal inhibition of PKA reduced the levels of phosphorylated STEP61 at serine 221. Our data support that inactivation of STEP61 by the PKA activity is part of the molecular process associated with motor skill learning.     

Spiralin Diversity Within Iranian Strains of Spiroplasma citri

The first-cultured and most-studied spiroplasma is Spiroplasma citri, the causal agent of citrus stubborn disease, one of the three plant-pathogenic, sieve-tube-restricted, and leafhopper vector-transmitted mollicutes. In Iranian Fars province, S. citri cultures were obtained from stubborn affected citrus trees, sesame and safflower plants, and from the leafhopper vector Circulifer haematoceps. Spiralin gene sequences from different S. citri isolates were amplified by PCR, cloned, and sequenced. Phylogenetic trees based on spiralin gene sequence showed diversity and indicated the presence of three clusters among the S. citri strains. Comparison of the amino acid sequences of eleven spiralins from Iranian strains and those from the reference S. citri strain GII-3 (241 aa), Palmyre strain (242 aa), Spiroplasma kunkelii (240 aa), and Spiroplasma phoeniceum (237 aa) confirmed the conservation of general features of the protein. However, the spiralin of an S. citri isolate named Shiraz I comprised 346 amino acids and showed a large duplication of the region comprised between two short repeats previously identified in S. citri spiralins. We report in this paper the spiralin diversity in Spiroplasma strains from southern Iran and for the first time a partial internal duplication of the spiralin gene.     

Fluorescent Biosensor of CDK5 Kinase Activity in Glioblastoma Cell Extracts and Living Cells

CDK5 plays a major role in neuronal functions, and is hyperactivated in neurodegenerative pathologies as well as in glioblastoma and neuroblastoma. Although this kinase constitutes an established biomarker and pharmacological target, there are few means of probing its activity in cell extracts or in living cells. To this aim a fluorescent peptide reporter of CDK5 kinase activity, derived from a library of CDK5‐specific substrates, is engineered and its ability to respond to recombinant CDK5/p25 is established and CDK5 activity in glioblastoma cell extracts is reported on through sensitive changes in fluorescence intensity. A cell‐penetrating variant of this biosensor which can be implemented to image CDK5 activation dynamics in space and in time is further implemented. This original biosensor constitutes a potent tool for quantifying differences in CDK5 activity following treatment with selective inhibitors and for monitoring CDK5 activation, following inhibition or stimulation, in a physiologically relevant environment. As such it offers attractive opportunities to develop a diagnostic assay for neuronal pathologies associated with hyperactivated CDK5, as well as a companion assay to evaluate response to new therapies targeting this kinase.     

Phylogeny and evolution of shallow‐water squat lobsters (Decapoda,Galatheoidea) from the Indo‐Pacific

Squat lobsters have a worldwide distribution and are highly visible crustaceans living in a broad range of habitats. In this study, partial sequences of two mitochondrial DNA genes (16S rRNA and COI) and a nuclear gene (H3) were obtained for all but one of the known species of the shallow‐water genera Sadayoshia (Munididae) and Lauriea, Macrothea and Triodonthea (Galatheidae). Lauriea siagiani appeared to be phylogenetically closer to Triodonthea and Macrothea than to other Lauriea species, suggesting the need for taxonomic re‐evaluation of these taxa. All species of Sadayoshia formed a monophyletic group that would have diverged during the Paleogene (around 50 Mya). Our results support the hypothesis that the late Paleogene–Neogene transition was a period of rapid diversification for shallow‐water species of both Galatheidae and Munididae in the Indo‐Pacific region. This is probably related to high tectonic activity among the Eurasian, Philippine Sea, Indo‐Australian and Pacific plates and corresponding changes in distribution of habitats and ocean currents during the late Paleogene. Finally, the tropical south‐west Pacific province is identified as a major diversification centre for shallow‐water squat lobsters, from where species dispersed to other Pacific and Indian Ocean regions.