Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications.

During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging to samples taken from COVID-19 patients from October 2020 to April 2021 at the "Reina Sofía" Hospital (Murcia, Spain) focused to variant appeared later. The results at the mentioned stage show the turning point since the 20E (EU1) variant was still prevalent (71.6%), but Alpha was bursting to 14.8%. Concern mutations have been found in 5 genomes classified as 20E (EU1), which were not characteristic of this still little evolved variant. Most of those mutations are found in the spike protein, namely Δ69-70, E484K, Q675H and P681H. However, a relevant deletion in ORF1a at positions 3675-3677 was also identified. These mutations have been reported in many later SARS-CoV-2 lineages, including Omicron. Taken together, our data suggest that preferential emergence mutations could already be present in the early converging evolution. Aside from this, the molecular information has been contrasted with clinical data. Statistical analyses suggest that the correlation between age and severity criteria is significantly higher in the viral samples with more accumulated changes.

Monitoring for Anguillicoloides crassus, Anguillid herpesvirus 1, aquabirnavirus EVE and rhabdovirus EVEX in the European eel population of southern Spain.

European eel is critically endangered in Europe. Among other stressors, pathogens are well-known to harm eels' fitness. One hundred and eighty-two eels were captured in three Eel Management Units in Andalucía (SE Spain) and analysed for Anguillicoloides crassus, Anguillid herpesvirus 1 (AngHV1), the rhabdovirus Eel Virus European X (EVEX) and the aquabirnavirus Eel Virus European (EVE). A. crassus adults and preadults were isolated and morphometrically identified, and the eel swimbladders were artificially digested to count A. crassus larvae. Also, eel tissues were examined by PCRs for the presence of viruses. EVEX and EVE were not detected in any of the eels. The estimated prevalence (95% confidence limits) was 71 (64-78)% for A. crassus and 35 (28-42)% for AngHV-1, varying these prevalences significantly between and within EMUs. Moreover, A. crassus prevalence was highest in smaller eels, in sites closest to the sea and eels sampled in the autumn. By contrast, AngHV-1 prevalence was highest in biggest eels, in sites far from the sea and sampled in the summer or winter. However, in mixed effects logistic models including site as a random variable, the risk of infection was associated with distance to the sea in both A. crassus and AngHV-1 infections and also to winter sampling in the case of AngHV-1 and not to other variables. These results are evidence that both pathogens are highly endemic in eels from Andalusian habitats. Further studies are needed to better understand the risk factors associated with these pathogens on eel populations.

Generation of Nonmosaic, Two-Pore Channel 2 Biallelic Knockout Pigs in One Generation by CRISPR-Cas9 Microinjection Before Oocyte Insemination.

Studies of knockout (KO) mice with defects in the endolysosomal two-pore channels (TPCs) have shown TPCs to be involved in pathophysiological processes, including heart and muscle function, metabolism, immunity, cancer, and viral infection. With the objective of studying TPC2's pathophysiological roles for the first time in a large, more humanlike animal model, TPC2 KO pigs were produced using CRISPR-Cas9. A major problem using CRISPR-Cas9 to edit embryos is mosaicism; thus, we studied for the first time the effect of microinjection timing on mosaicism. Mosaicism was greatly reduced when in vitro produced embryos were microinjected before insemination, and surgical embryo transfer (ET) was performed using such embryos. All TPC2 KO fetuses and piglets born following ET (i.e., F0 generation) were nonmosaic biallelic KOs. The generation of nonmosaic animals greatly facilitates germ line transmission of the mutation, thereby aiding the rapid and efficient generation of KO animal lines for medical research and agriculture.

A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix.

Direct targeting of critical DNA-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. Structural descriptions for this, though often proposed for bacterial and phage repressor-antirepressor systems, are unavailable. Here, we describe the structural and functional basis of how the Myxococcus xanthus CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarA and CarH repress the carB operon in the dark. CarS, produced in the light, physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB. The NMR structure of CarS1, a functional CarS variant, reveals a five-stranded, antiparallel beta-sheet fold resembling SH3 domains, protein-protein interaction modules prevalent in eukaryotes but rare in prokaryotes. NMR studies and analysis of site-directed mutants in vivo and in vitro unveil a solvent-exposed hydrophobic pocket lined by acidic residues in CarS, where the CarA DNA recognition helix docks with high affinity in an atypical ligand-recognition mode for SH3 domains. Our findings uncover an unprecedented use of the SH3 domain-like fold for protein-protein recognition whereby an antirepressor mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription.

Blood-cell-specific acetylcholinesterase splice variations under changing stimuli.

Developmental and trauma-induced mechanism(s) that modify inflammation and immune responses in blood cells were recently found to be regulated by acetylcholine. Here, we report corresponding blood cell-specific changes in acetylcholinesterase splice variants. Plasmon resonance and flow cytometry using acetylcholinesterase variant-specific antibody probes, revealed a progressive increase in myeloid cell fractions expressing the apoptosis-related acetylcholinesterase-S variant from newborns to adult controls and post-delivery mothers. Hematopoietic cell fractions positive for the myeloproliferative acetylcholinesterase-R variant, were similarly high in post-partum blood, both intracellular and on the cell surface. Moreover, intracellular acetylcholinesterase-S protein amounts as reflected by fluorescence intensity measurements remained unchanged in myeloid cells from post-partum mothers as compared with matched controls. Unlike brain neurons, which over-express intracellular acetylcholinesterase-R under stress, lymphocytes from post-partum mothers presented increased surface acetylcholinesterase-S and pronounced decreases in both the expression and contents of surface acetylcholinesterase-R. Peripheral stimuli-induced modulations in acetylcholine regulation may hence reflect blood cell lineage-dependent acetylcholinesterase splice variations.

From brain to blood: alternative splicing evidence for the cholinergic basis of Mammalian stress responses.

Three principal features of mammalian stress responses are that they span peripheral and CNS changes, modify blood cell composition and activities, and cover inter-related alterations in a large number of gene products. The finely tuned spatiotemporal regulation of these multiple events suggests the hierarchic involvement of modulatory neurotransmitters and modified process(es) in the pathway of gene expression that together would enable widely diverse stress responses. We report evidence supporting the notion that acetylcholine (ACh) acts as a stress-response-regulating transmitter and that altered ACh levels are variously associated with changes in the alternative splicing of pre-mRNA transcripts in brain neurons and peripheral blood cells. We used acetylcholinesterase (AChE) gene expression as a case study and developed distinct probes for its alternative splice variants at the mRNA and protein levels. In laboratory animals and human-derived cells, we found stress-induced changes in the alternative splicing patterns of AChE pre-mRNA, which attributes to this gene and its different protein products diverse stress responsive functions that are associated with the enzymatic and noncatalytic properties of AChE. Together, these approaches provide a conceptually unified view of the studied pathways for controlling stress responses in brain and blood.