Stretch triggers microtubule stabilization and MARCKS-dependent membrane incorporation in the shaft of embryonic axons.

Neurons have a unique polarized nature that must adapt to environmental changes throughout their lifespan. During embryonic development, axon elongation is led by the growth cone,1 culminating in the formation of a presynaptic terminal. After synapses are formed, axons elongate in a growth cone-independent manner to accompany body growth while maintaining their ultrastructure and function.2,3,4,5,6 To further understand mechanical strains on the axon shaft, we developed a computer-controlled stretchable microfluidic platform compatible with multi-omics and live imaging. Our data show that sensory embryonic dorsal root ganglia (DRGs) neurons have high plasticity, with axon shaft microtubules decreasing polymerization rates, aligning with the direction of tension, and undergoing stabilization. Moreover, in embryonic DRGs, stretch triggers yes-associated protein (YAP) nuclear translocation, supporting its participation in the regulatory network that enables tension-driven axon growth. Other than cytoskeleton remodeling, stretch prompted MARCKS-dependent formation of plasmalemmal precursor vesicles (PPVs), resulting in new membrane incorporation throughout the axon shaft. In contrast, adolescent DRGs showed a less robust adaptation, with axonal microtubules being less responsive to stretch. Also, while adolescent DRGs were still amenable to strain-induced PPV formation at higher stretch rates, new membrane incorporation in the axon shaft failed to occur. In summary, we developed a new resource to study the biology of axon stretch growth. By unraveling cytoskeleton adaptation and membrane remodeling in the axon shaft of stretched neurons, we are moving forward in understanding axon growth.

Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.

When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and interpret. Therefore, it is useful to have an automated way of collapsing large phylogenetic trees according to a taxonomic term decided by the user (family, class, or order, for instance), in order to highlight the minimal set of sequences that should be used to recapitulate the full history of the gene/gene family being studied at that taxonomic level, that can be refined using additional software. Here we present the Phylogenetic Tree Collapser (PTC) program (https://github.com/pegi3s/phylogenetic-tree-collapser), a flexible tool for automated tree collapsing using taxonomic information, that can be easily used by researchers without a background in informatics, since it only requires the installation of Docker, Podman or Singularity. The utility of PTC is demonstrated by addressing the evolution of the ascorbic acid synthesis pathway in insects. A Docker image is available at Docker Hub (https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser) with PTC installed and ready-to-run.

SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines.

BACKGROUND: The initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initial version of SEDA lacks a command-line interface for more advanced users and does not allow the creation of automated analysis pipelines. RESULTS: The present paper discusses the updates of the new SEDA release, including the addition of a complete command-line interface, new functionalities like gene annotation, a framework for automated pipelines, and improved integration in Linux environments. CONCLUSION: SEDA is an open-source Java application and can be installed using the different distributions available ( https://www.sing-group.org/seda/download.html ) as well as through a Docker image ( https://hub.docker.com/r/pegi3s/seda ). It is released under a GPL-3.0 license, and its source code is publicly accessible on GitHub ( https://github.com/sing-group/seda ). The software version at the time of submission is archived at Zenodo (version v1.6.0, http://doi.org/10.5281/zenodo.10201605 ).

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites.

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.

Post-traumatic stress disorder as a risk factor for major adverse cardiovascular events: a cohort study of a South African medical insurance scheme.

AIMS: Prior research, largely focused on US male veterans, indicates an increased risk of cardiovascular disease among individuals with post-traumatic stress disorder (PTSD). Data from other settings and populations are scarce. The objective of this study is to examine PTSD as a risk factor for incident major adverse cardiovascular events (MACEs) in South Africa. METHODS: We analysed reimbursement claims (2011-2020) of a cohort of South African medical insurance scheme beneficiaries aged 18 years or older. We calculated adjusted hazard ratios (aHRs) for associations between PTSD and MACEs using Cox proportional hazard models and calculated the effect of PTSD on MACEs using longitudinal targeted maximum likelihood estimation. RESULTS: We followed 1,009,113 beneficiaries over a median of 3.0 years (IQR 1.1-6.0). During follow-up, 12,662 (1.3%) persons were diagnosed with PTSD and 39,255 (3.9%) had a MACE. After adjustment for sex, HIV status, age, population group, substance use disorders, psychotic disorders, major depressive disorder, sleep disorders and the use of antipsychotic medication, PTSD was associated with a 16% increase in the risk of MACEs (aHR 1.16, 95% confidence interval (CI) 1.05-1.28). The risk ratio for the effect of PTSD on MACEs decreased from 1.59 (95% CI 1.49-1.68) after 1 year of follow-up to 1.14 (95% CI 1.11-1.16) after 8 years of follow-up. CONCLUSION: Our study provides empirical support for an increased risk of MACEs in males and females with PTSD from a general population sample in South Africa. These findings highlight the importance of monitoring cardiovascular risk among individuals diagnosed with PTSD.

Scoping Review of Fall Risk Assessment Tools for Women Who Receive Maternity Care.

OBJECTIVE: To identify and describe fall risk assessment tools used for women who receive maternity care. DATA SOURCES: PubMed, CINAHL Complete, MEDLINE Complete, Cochrane Library, Scopus, SciELO, and Repositórios Científicos de Acesso Aberto de Portugal (RCAAP). STUDY SELECTION: We considered reports published until November 28, 2022, that included women during pregnancy, childbirth, or the postpartum period; involved the use of fall risk assessment tools, regardless of context; and were published in English, French, Portuguese, or Spanish. DATA EXTRACTION: We extracted the following data from the included reports: author(s)/year/country, aim/sample, research design/type of report, tool (i.e., the fall risk assessment tool used), findings, reliability, and validity. DATA SYNTHESIS: We found 13 reports in which the authors addressed nine fall risk assessment tools. Seven of these tools were applied during pregnancy (Kyle's tool, Pregnant Women Information Form and Assessment Scale for Risk of Falling in Pregnant Women, Obstetric Fall Risk Assessment System), labor (Obstetric Fall Risk Assessment System), the postpartum period (Cooksey-Post Obstetric Delivery Fall Risk Assessment, Kyle's tool, Risk of Falling in Post-partum Women (SLOPE), Obstetric Fall Risk Assessment System, Post-epidural Fall Risk Assessment Score, and Maternal Fall Risk Assessment Scale). The Dionne's Egress Test and the Motor Strength Scale do not address the characteristics of the women who receive maternity care. Psychometric characteristics were available for the Pregnant Women Information Form and Assessment Scale for Risk of Falling in Pregnant Women, Post-epidural Fall Risk Assessment Score, Maternal Fall Risk Assessment Scale, and Risk of Falling in Post-partum Women. CONCLUSION: Some fall risk assessment tools are used to assess women who receive maternity care without proper validation in this specific population. The use of fall risk assessment tools that are validated for women who receive maternity care may help nurses make clinical judgments when assessing fall risk and implement measures for fall prevention.

A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH).

Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.

Tool to assess risk of bias in studies estimating the prevalence of mental health disorders (RoB-PrevMH).

OBJECTIVE: There is no standard tool for assessing risk of bias (RoB) in prevalence studies. For the purposes of a living systematic review during the COVID-19 pandemic, we developed a tool to evaluate RoB in studies measuring the prevalence of mental health disorders (RoB-PrevMH) and tested inter-rater reliability. METHODS: We decided on items and signalling questions to include in RoB-PrevMH through iterative discussions. We tested the reliability of assessments by different users with two sets of prevalence studies. The first set included a random sample of 50 studies from our living systematic review. The second set included 33 studies from a systematic review of the prevalence of post-traumatic stress disorders, major depression and generalised anxiety disorder. We assessed the inter-rater agreement by calculating the proportion of agreement and Kappa statistic for each item. RESULTS: RoB-PrevMH consists of three items that address selection bias and information bias. Introductory and signalling questions guide the application of the tool to the review question. The inter-rater agreement for the three items was 83%, 90% and 93%. The weighted kappa scores were 0.63 (95% CI 0.54 to 0.73), 0.71 (95% CI 0.67 to 0.85) and 0.32 (95% CI -0.04 to 0.63), respectively. CONCLUSIONS: RoB-PrevMH is a brief, user-friendly and adaptable tool for assessing RoB in studies on prevalence of mental health disorders. Initial results for inter-rater agreement were fair to substantial. The tool's validity, reliability and applicability should be assessed in future projects.

Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura.

Global warming is forcing insect populations to move and adapt, triggering adaptive genetic responses. Thermal stress is known to alter gene expression, repressing the transcription of active genes, and inducing others, such as those encoding heat shock proteins. It has also been related to the activation of some specific transposable element (TE) families. However, the actual magnitude of this stress on the whole genome and the factors involved in these genomic changes are still unclear. We studied mRNAs and small RNAs in gonads of two Drosophila subobscura populations, considered a good model to study adaptation to temperature changes. In control conditions, we found that a few genes and TE families were differentially expressed between populations, pointing out their putative involvement in the adaptation of populations to their different environments. Under heat stress, sex-specific changes in gene expression together with a trend toward overexpression, mainly of heat shock response-related genes, were observed. We did not observe large changes of TE expression nor small RNA production due to stress. Only population and sex-specific expression changes of some TE families (mainly retrotransposons), or the amounts of siRNAs and piRNAs, derived from specific TE families were observed, as well as the piRNA production from some piRNA clusters. Changes in small RNA amounts and TE expression could not be clearly correlated, indicating that other factors as chromatin modulation could also be involved. This work provides the first whole transcriptomic study including genes, TEs, and small RNAs after a heat stress in D. subobscura.