Genomic analysis of NE Atlantic sardine (Sardina pilchardus) reveals reduced variation in a recently established North Sea population and directs reconsideration of management units.

The European sardine (Sardina pilchardus) is under intense fishing pressure and exhibits distributional/abundance shifts linked to environmental change. The current understanding of population demographics needed for sustainable management is uncertain due to concerns that previous genetic studies lacked resolution and limited sampling of sardine north of the Bay of Biscay. To address these issues, we performed mtDNA sequencing and genome wide SNP analysis of samples collected across the Bay of Biscay, Celtic Sea, English Channel and North Sea. The complete SNP data reported a lack of structure throughout the sampled area compatible with high gene flow. A consensus suite of positive outlier SNPs was identified which reported a significant correlation with geographical distance with the largest differentiation between the southern Bay of Biscay and North Sea samples which also reported a significant mtDNA ΦST. While the roles of dispersal limitation and environmental heterogeneity underpinning this require further study, this adds to growing evidence that selection is influencing sardine population structure against a background of high gene flow. The results indicate that while there may be a level of demographic independence between North Sea and South Biscay sardine, the current delimitation of central (Biscay) and northern (Channel and Celtic Sea) operational stocks may misrepresent connectivity between the Biscay and Channel. The North Sea sample exhibited markedly lower mtDNA and nuclear variation than other samples. As sardine have only recently invaded the North Sea such reduced genetic variation is compatible with predictions for peripheral leading-edge populations but contrasts with patterns for other small pelagic species and emphasises the need to consider species-specific genetic structure in ecosystem-based management. Nascent management of the North Sea sardine fishery must ensure that current low levels of genetic diversity are not eroded further as this may decrease the species adaptive potential and inhibit its expansion.

Portuguese Recommendations for the management of Raynaud's phenomenon and digital ulcers in systemic sclerosis and other connective tissue diseases.

OBJECTIVE: To develop evidence-based recommendations for the non-pharmacological and pharmacological management of Raynaud's phenomenon (RP) and digital ulcers (DUs) in patients with systemic sclerosis and other immune-mediated connective tissue diseases (CTDs). METHODS: A task force comprising 21 rheumatologists, two surgeons (vascular and plastic), two nurses, and one patient representative was established. Following a systematic literature review performed to inform the recommendations, statements were formulated and discussed during two meetings (one online and one in-person). Levels of evidence, grades of recommendation (GoR), and level of agreement (LoA) were determined. RESULTS: Five overarching principles and 13 recommendations were developed. GoR ranged from A to D. The mean ± standard difference (SD) LoA with the overarching principles and recommendations ranged from 7.8±2.1 to 9.8±0.4. Briefly, the management of RP and DUs in patients with CTDs should be coordinated by a multidisciplinary team and based on shared decisions with patients. Nifedipine should be used as first-line therapy for RP and/or DUs. Sildenafil, tadalafil, and/or iloprost IV are second-line options for severe and/or refractory patients with RP and/or DUs. Sildenafil, tadalafil and/or Iloprost IV, should be prescribed for healing and prevention (also including bosentan) of DUs. In patients with RP and/or DUs, non-pharmacological interventions might be considered as add-ons, but there is limited quality and quantity of scientific evidence supporting their use. CONCLUSIONS: These recommendations will inform rheumatologists, specialist nurses, other healthcare professionals, and patients about a comprehensive and personalized management of RP and DUs. A research agenda was developed to address unmet needs, particularly for non-pharmacologic interventions.

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases.

Genome editing technologies based on DNA-dependent polymerases (DDPs) could offer several benefits compared with other types of editors to install diverse edits. Here, we develop click editing, a genome writing platform that couples the advantageous properties of DDPs with RNA-programmable nickases to permit the installation of a range of edits, including substitutions, insertions and deletions. Click editors (CEs) leverage the 'click'-like bioconjugation ability of HUH endonucleases with single-stranded DNA substrates to covalently tether 'click DNA' (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs and their clkDNAs, we demonstrate the ability to install precise genome edits with minimal indels in diverse immortalized human cell types and primary fibroblasts with precise editing efficiencies of up to ~30%. Editing efficiency can be improved by rapidly screening clkDNA oligonucleotides with various modifications, including repair-evading substitutions. Click editing is a precise and versatile genome editing approach for diverse biological applications.

Identification and optimization of the key growth parameters involved in carotenoids production of the marine microalga Pavlova gyrans.

In this work, a multivariate analysis was carried out, using a Plackett-Burman (PB) design involving seventeen growth parameters, on carotenoids production of Pavlova gyrans (p < 0.10). Each assay was analysed regarding its content (mg g-1) of fucoxanthin (Fx), diatoxanthin, diadinoxanthin, ß-carotene (ßCar), α-carotene, and the sum of all carotenoids analysed individually (TCar). According to the statistical analysis, modified medium formulations were developed for the particular cases of Fx, ßCar, and TCar. The study showed that Fx content was positively affected by nitrogen supplementation and lower light intensities. Higher concentrations of nitrogen and iron increased the final content of ßCar as well. Similarly, salinity, light intensity, nitrogen, iron, and cobalt were identified as key factors in TCar production. The PB-based formulations showed significant improvements (p < 0.05) for TCar (11.794 mg g-1) and Fx (6.153 mg g-1) when compared to the control conditions (Walne's medium-2.010 mg g-1). Furthermore, effective control of key variables (e.g., light intensity) throughout P. gyrans growth proved successful (p < 0.05), increasing the productivity of Fx (0.759 mg L-1 d-1) and TCar (1.615 mg L-1 d-1).

The meaning in loss protocol: A clinical trial of online grief therapy.

For a minority of the bereaved, the loss of a significant other can trigger an overwhelming emotional reaction and impaired functioning across life domains, known as prolonged grief disorder (PGD). Hence, ongoing efforts have been made to refine existing treatments to increase their efficacy and to accommodate the idiosyncrasies of grief reactions. This study presents the results of an open clinical trial of the feasibility and effectiveness of the Meaning in Loss (MIL) protocol in an online format. The brief intervention of 12 to 16 sessions combines constructivist and narrative strategies to explore and work through impediments to meaning reconstruction in loss. The sample included 25 participants diagnosed with PGD who were treated by six therapists. Baseline and post-therapy comparisons showed a significant improvement in all clinical measures (grief symptomatology, depression and general distress) and an increase of meaning making regarding the loss. Meaning making was found to be a prospective mediator of symptomatic improvement in grief across the course of therapy. These findings suggest the effectiveness of the MIL protocol in decreasing grief specific and associated symptomatology and argue for the relevance of further controlled evaluations of its efficacy. Moreover, results confirm previous findings that meaning making is a relevant factor in the evolution of grief reactions, including in the context of psychotherapy.

The potential of Pavlovophyceae species as a source of valuable carotenoids and polyunsaturated fatty acids for human consumption.

Microalgae are a group of microorganisms, mostly photoautotrophs with high CO2 fixation capacity, that have gained increased attention in the last decades due to their ability to produce a wide range of valuable metabolites, such as carotenoids and polyunsaturated fatty acids, for application in food/feed, pharmaceutical, and cosmeceutical industries. Their increasing relevance has highlighted the importance of identifying and culturing new bioactive-rich microalgae species, as well as of a thorough understanding of the growth conditions to optimize the biomass production and master the biochemical composition according to the desired application. Thus, this review intends to describe the main cell processes behind the production of carotenoids and polyunsaturated fatty acids, in order to understand the possible main triggers responsible for the accumulation of those biocompounds. Their economic value and the biological relevance for human consumption are also summarized. In addition, an extensive review of the impact of culture conditions on microalgae growth performance and their biochemical composition is presented, focusing mainly on the studies involving Pavlovophyceae species. A complementary description of the biochemical composition of these microalgae is also presented, highlighting their potential applications as a promising bioresource of compounds for large-scale production and human and animal consumption.

Batimastat Induces Cytotoxic and Cytostatic Effects in In Vitro Models of Hematological Tumors.

The role of metalloproteinases (MMPs) in hematological malignancies, like acute myeloid leukemia (AML), myelodysplastic neoplasms (MDS), and multiple myeloma (MM), is well-documented, and these pathologies remain with poor outcomes despite treatment advancements. In this study, we investigated the effects of batimastat (BB-94), an MMP inhibitor (MMPi), in single-administration and daily administration schemes in AML, MDS, and MM cell lines. We used four hematologic neoplasia cell lines: the HL-60 and NB-4 cells as AML models, the F36-P cells as an MDS model, and the H929 cells as a model of MM. We also tested batimastat toxicity in a normal human lymphocyte cell line (IMC cells). BB-94 decreases cell viability and density in a dose-, time-, administration-scheme-, and cell-line-dependent manner, with the AML cells displaying higher responses. The efficacy in inducing apoptosis and cell cycle arrests is dependent on the cell line (higher effects in AML cells), especially with lower daily doses, which may mitigate treatment toxicity. Furthermore, BB-94 activated apoptosis via caspases and ERK1/2 pathways. These findings highlight batimastat's therapeutic potential in hematological malignancies, with daily dosing emerging as a strategy to minimize adverse effects.

Malignant tumour in pregnancy: Ewing-like sarcoma of the gluteal region.

We report a case of an Ewing-like sarcoma of the gluteal region with ongoing growth during the second trimester of pregnancy and noted during the third trimester. This lesion was consequently studied to infer its malignant potential. Several examinations were conducted to characterise this lesion, such as ultrasound and MR, which showed signs of tumourous invasion of the deep tissues of the gluteal region.Given that the pregnancy was at the end of the third trimester, the decision was made to schedule the delivery at 37 weeks of gestation and treat the tumour afterwards to balance maternal and fetal health.This case illustrates the need for a detailed investigation and guidance by a multidisciplinary team to provide prenatal counselling regarding a malignant tumour during pregnancy.

Evaluating the User Experience of a Smartphone-Delivered Sexual Health Promotion Program for Older Adults in the Netherlands: Single-Arm Pilot Study.

BACKGROUND: Sexual health is an important component of quality of life in older adults. However, older adults often face barriers to attaining a fulfilling sexual life because of issues such as stigma, lack of information, or difficult access to adequate support. OBJECTIVE: We aimed to evaluate the user experience of a self-guided, smartphone-delivered program to promote sexual health among older adults. METHODS: The mobile app was made available to community-dwelling older adults in the Netherlands, who freely used the app for 8 weeks. User experience and its respective components were assessed using self-developed questionnaires, the System Usability Scale, and semistructured interviews. Quantitative and qualitative data were descriptively and thematically analyzed, respectively. RESULTS: In total, 15 participants (mean age 71.7, SD 9.5 years) completed the trial. Participants showed a neutral to positive stance regarding the mobile app's usefulness and ease of use. Usability was assessed as "Ok/Fair." The participants felt confident about using the mobile app. To increase user experience, participants offered suggestions to improve content and interaction, including access to specialized sexual health services. CONCLUSIONS: The sexual health promotion program delivered through a smartphone in a self-guided mode was usable. Participants' perception is that improvements to user experience, namely in content and interaction, as well as connection to external services, will likely improve usefulness and acceptance.

Olfactory Receptor OR2K2 Expression in Human Choroid Plexus as a Potential Marker in Early Sporadic Alzheimer's Disease.

Epithelial cells comprising the choroid plexus (CP) form a crucial barrier between the blood and the cerebrospinal fluid, thereby assuming a central position in brain homeostasis and signaling. Mounting evidence suggests that the impairment of CP function may be a significant contributor to Alzheimer's disease (AD) pathogenesis. CP function relies on the expression of specific receptors, and the potential involvement of olfactory receptors (ORs) and taste receptors (TASRs) in chemical surveillance within the CP is being investigated. Previous studies have implicated ORs and TASRs in neurodegenerative disorders like AD, although the direct evidence of their expression in the human CP remains to be established. In this study, we conducted a transcriptomic analysis encompassing eleven ORs and TASRs in the CP, comparing samples from healthy age-matched controls to those from patients with AD spanning Braak stages I to VI. Among these receptors, a striking finding emerged-OR2K2 exhibited robust expression, with a statistically significant upregulation noted at Braak stage I. Surprisingly, at the protein level, OR2K2 showed a significant decrease in both Braak stage I and VI. Additionally, we identified CP epithelial cells as the source of OR2K2 expression, where it colocalized with autophagy markers LC3 and p62. We postulate that OR2K2 could be subjected to degradation by autophagy in the early stages of AD, triggering a compensatory mechanism that leads to increased OR2K2 mRNA transcription. This study uncovers a potential role for OR2K2 in AD pathogenesis, offering a novel perspective on the intricate dynamics at play in this neurodegenerative disorder.

Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum.

Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.

Carbapenemase-producing Enterobacterales strains causing infections in companion animals-Portugal.

An increase in Klebsiella pneumoniae carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the blaOXA-48-like and blaKPC-like genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January-December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (n = 5/977). Thus, five strains were characterized: (i) one OXA-181-producing K. pneumoniae ST273, (ii) two KPC-3-producing K. pneumoniae ST147; (iii) one KPC-3-producing K. pneumoniae ST392; and (iv) one OXA-48-producing E. coli ST127. The blaKPC-3 gene was located on transposon Tn4401d on IncFIA type plasmid for the K. pneumoniae ST147 strains and on a IncN-type plasmid for the K. pneumoniae ST392 strain, while blaOXA-181 gene was located on an IncX3 plasmid. All de novo assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing E. coli ST127. The dissemination of carbapenem resistance is occurring horizontally via plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed. IMPORTANCE: This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.

Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies.

The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.

Glial-restricted precursors stimulate endogenous cytogenesis and effectively recover emotional deficits in a model of cytogenesis ablation.

Adult cytogenesis, the continuous generation of newly-born neurons (neurogenesis) and glial cells (gliogenesis) throughout life, is highly impaired in several neuropsychiatric disorders, such as Major Depressive Disorder (MDD), impacting negatively on cognitive and emotional domains. Despite playing a critical role in brain homeostasis, the importance of gliogenesis has been overlooked, both in healthy and diseased states. To examine the role of newly formed glia, we transplanted Glial Restricted Precursors (GRPs) into the adult hippocampal dentate gyrus (DG), or injected their secreted factors (secretome), into a previously validated transgenic GFAP-tk rat line, in which cytogenesis is transiently compromised. We explored the long-term effects of both treatments on physiological and behavioral outcomes. Grafted GRPs reversed anxiety-like deficits and demonstrated an antidepressant-like effect, while the secretome promoted recovery of only anxiety-like behavior. Furthermore, GRPs elicited a recovery of neurogenic and gliogenic levels in the ventral DG, highlighting the unique involvement of these cells in the regulation of brain cytogenesis. Both GRPs and their secretome induced significant alterations in the DG proteome, directly influencing proteins and pathways related to cytogenesis, regulation of neural plasticity and neuronal development. With this work, we demonstrate a valuable and specific contribution of glial progenitors to normalizing gliogenic levels, rescuing neurogenesis and, importantly, promoting recovery of emotional deficits characteristic of disorders such as MDD.

Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures.

The successful translation of therapeutic nucleic acids (NAs) for the treatment of neurological disorders depends on their safe and efficient delivery to neural cells, in particular neurons. DNA nanostructures can be a promising NAs delivery vehicle. Nonetheless, the potential of DNA nanostructures for neuronal cell delivery of therapeutic NAs is unexplored. Here, tetrahedral DNA nanostructures (TDN) as siRNA delivery scaffolds to neuronal cells, exploring the influence of functionalization with two different reported neuronal targeting ligands: C4-3 RNA aptamer and Tet1 peptide are investigated. Nanostructures are characterized in vitro, as well as in silico using molecular dynamic simulations to better understand the overall TDN structural stability. Enhancement of neuronal cell uptake of TDN functionalized with the C4-3 Aptamer (TDN-Apt), not only in neuronal cell lines but also in primary neuronal cell cultures is demonstrated. Additionally, TDN and TDN-Apt nanostructures carrying siRNA are shown to promote silencing in a process aided by chloroquine-induced endosomal disruption. This work presents a thorough workflow for the structural and functional characterization of the proposed TDN as a nano-scaffold for neuronal delivery of therapeutic NAs and for targeting ligands evaluation, contributing to the future development of new neuronal drug delivery systems based on DNA nanostructures.

Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells.

Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.

Generation of IGGi003-A induced pluripotent stem cell line from a patient with Sotos Syndrome carrying c.1633delA NSD1 variant in exon 5.

Sotos syndrome (SoS) is a neurodevelopmental disorder that results from NSD1 mutations that cause haploinsufficiency of NSD1. Here, we generated an induced pluripotent stem cell (iPSC) line from fibroblasts of a SoS patient carrying the pathogenic variant (c.1633delA). The cell line shows typical iPSC morphology, high expression of pluripotent markers, normal karyotype, and it differentiates into three germ layers in vitro. This line is a valuable resource for studying pathological pathways involved in SoS.