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Background Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database. Results Using a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as “WANCY” for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records. Conclusions We judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank.

Water quality management in large basins demands tools that balance scientific rigor with computational efficiency to avoid paralysis by analysis. While traditional models offer detailed insights, their complexity and resource intensity hinder timely decision-making. To address this gap, we present AFAR-WQS, an open-source MATLAB™ toolbox that introduces a novel integration of assimilation factors with graph theory and a Depth-First Search (DFS) algorithm to rapidly simulate 13 water quality determinants across complex topological networks. AFAR-WQS resolves cumulative processes in networks of up to 30,000 segments in just 163 s on standard hardware, enabling real-time scenario evaluations. Its object-oriented architecture ensures scalability, allowing customization for urban drainage systems or macro-basin studies while maintaining computational efficiency. Case studies demonstrate its utility in prioritizing sanitation investments, assessing water quality at the national scale and fostering stakeholder collaboration through participatory workshops. By bridging the gap between simplified and complex models, AFAR-WQS supports adaptive management in contexts of hydrological uncertainty, regulatory compliance, and climate change. The toolbox is freely available at GitHub, offering a transformative approach for integrated water resource management.

Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.

Railway axles are critical to the safety of railway vehicles. However, railway axle maintenance is currently based on scheduled preventive maintenance using Nondestructive Testing. The use of condition monitoring techniques would provide information about the status of the axle between periodical inspections, and it would be very valuable in the prevention of catastrophic failures. Nevertheless, in the literature, there are not many studies focusing on this area and there is a lack of experimental data. In this work, a reliable real-time condition-monitoring technique for railway axles is proposed. The technique was validated using vibration measurements obtained at the axle boxes of a full bogie installed on a rig, where four different cracked railway axles were tested. The technique is based on vibration analysis by means of the Wavelet Packet Transform (WPT) energy, combined with a Support Vector Machine (SVM) diagnosis model. In all cases, it was observed that the WPT energy of the vibration signals at the first natural frequency of the axle when the wheelset is first installed (the healthy condition) increases when a crack is artificially created. An SVM diagnosis model based on the WPT energy at this frequency demonstrates good reliability, with a false alarm rate of lower than 10% and defect detection for damage occurring in more than 6.5% of the section in more than 90% of the cases. The minimum number of wheelsets required to build a general model to avoid mounting effects, among others things, is also discussed.

An efficient maintenance is a key consideration in systems of railway transport, especially in high-speed trains, in order to avoid accidents with catastrophic consequences. In this sense, having a method that allows for the early detection of defects in critical elements, such as the bogie mechanical components, is a crucial for increasing the availability of rolling stock and reducing maintenance costs. The main contribution of this work is the proposal of a methodology that, based on classical signal processing techniques, provides a set of parameters for the fast identification of the operating state of a critical mechanical system. With this methodology, the vibratory behaviour of a very complex mechanical system is characterised, through variable inputs, which will allow for the detection of possible changes in the mechanical elements. This methodology is applied to a real high-speed train in commercial service, with the aim of studying the vibratory behaviour of the train (specifically, the bogie) before and after a maintenance operation. The results obtained with this methodology demonstrated the usefulness of the new procedure and allowed for the disclosure of reductions between 15% and 45% in the spectral power of selected Intrinsic Mode Functions (IMFs) after the maintenance operation.

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians ( e.g ., corals, octocorals, sea anemones, jellyfish), other marine invertebrates ( e.g. , sponges, molluscs, flatworms), and protists ( e.g ., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

Ecological speciation through adaptation to different habitats can readily occur without strong geographic isolation when the same traits underlie both ecological divergence and reproductive isolation. In light-dependent corals with environment-mediated spawning, adaptation to varying light regimes across depths provides opportunities for such speciation. We show that depth-related distributions are common among sister lineages of corals within the photic zone. We then investigated molecular drivers of depth-associated adaptive divergence by analyzing sequence variation in proteins related to environmental sensing in depth-segregated and light-dependent lineages in the Orbicella species complex. Specifically, we analyzed 1) two genetically divergent ecotypes of Orbicella faveolata across a depth gradient, and 2) two depth-segregated sister species, O. annularis and O. franksi , with different spawning times following sunset. Genome-wide analyses indicate divergence across depths occurred through adaptation via positive selection on G-protein-coupled receptors (GPCRs). These molecules mediate chemo/photo/thermo-reception, enhancing physiological adaptation across environments, and are also involved in reproductive isolation via differences in spawning time. Our study proposes a molecular mechanism for the origin of depth-segregated coral species, common across anthozoans, in which ecological divergence operates at spatial scales smaller than their larval dispersal potential, and highlights avenues contributing to generating biodiversity in the sea. Here, the authors explore mechanisms associated with common depth distributions in sister lineages of corals. They document sequence divergence for proteins related to chemo-, photo-, and thermoreceptors in the Orbicella species complex that have led to ecotype differentiation and speciation.

is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the strains, to identify the relationship of these genes with their phylogeographic origin. The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype. Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of is key information in understanding its pathogenic behavior.

The wandering spider, Phoneutria depilata, is one of Colombia’s most active nocturnal arthropod predators of vertebrates and invertebrates. Its venom has been a relevant subject of study in the last two decades. However, the scarcity of transcriptomic data for the species limits our knowledge of the distinct components present in its venom for linking the mainly neurotoxic effects of the spider venom to a particular molecular target. The transcriptome of the P. depilata venom gland was analyzed to understand the effect of different diets or sex and the impact of these variables on the composition of the venom. We sequenced venom glands obtained from ten males and ten females from three diet treatments: (i) invertebrate: Tenebrio molitor, (ii) vertebrate: Hemidactylus frenatus, and (iii) mixed (T. molitor + H. frenatus). Of 17,354 assembled transcripts from all samples, 65 transcripts relating to venom production differed between males and females. Among them, 36 were classified as neurotoxins, 14 as serine endopeptidases, 11 as other proteins related to venom production, three as metalloprotease toxins, and one as a venom potentiator. There were no differences in transcripts across the analyzed diets, but when considering the effect of diets on differences between the sexes, 59 transcripts were differentially expressed. Our findings provide essential information on toxins differentially expressed that can be related to sex and the plasticity of the diet of P. depilata and thus can be used as a reference for venomics of other wandering spider species.

Introduction: The aim of this study was to compare the histopathological findings in the resected tracheal ring of tracheotomized critically ill patients with or without severe SARS-CoV-2 infection. Material and Methods: This is a prospective case–control study. The data collection period was between May 2020 and 2022. Eighty tracheostomies were performed on patients with long intubation, and the resected tracheal ring was examined by standard microscopy. Forty consecutive tracheotomies were carried out in COVID-19-positive and -negative patients. Results: The mean age was 67.1 (6.9 SD) years in the COVID-19 group and 67.8 (9.6 SD) in the control group (p = 0.3). The number of men in each group was 30 (75.0%) versus 27 (67.5%), respectively (p = 0.5). No relevant histological alterations were found in 82.5% of samples. Chronic subepithelial inflammation was found in 13.8% of cases. Two cases presented with vasculitis (2.5%), and one case presented with thrombotic microangiopathy (1.2%), all of them in the COVID-19 group. We found no statistically significant dependence between relevant histologic findings versus no alterations (X2 = 0.779, p= 0.377) and no significant risk indices (RR = 1.8, OR = 2.032, PAR = 44%). Conclusion: There is no evidence of increased risk of histopathological findings in the resected tracheal ring of patients with long intubation and COVID-19 disease.