An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.

We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

MOTIVATION: Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome. RESULTS: We introduce a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into the RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith-Waterman 3D). The user-friendly interface simplifies parameter setup and input selection. Within seconds, our tool enables visualization of results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB RCSB.org Sequence Annotations viewer and Mol* 3D viewer, respectively. Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB. Moreover, this tool can be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators. By bridging the gap between 1D sequence and 3D structures of proteins, our tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses. AVAILABILITY AND IMPLEMENTATION: The alignment tool is part of the RCSB PDB research-focused RCSB.org web portal and available at rcsb.org/alignment. Programmatic access is available via alignment.rcsb.org. Frontend code has been published at github.com/rcsb/rcsb-pecos-app. Visualization is powered by the open-source Mol* viewer (github.com/molstar/molstar and github.com/molstar/rcsb-molstar) plus the Sequence Annotations in 3D Viewer (github.com/rcsb/rcsb-saguaro-3d).

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

Evaluation of heritability partitioning approaches in livestock populations.

BACKGROUND: Heritability partitioning approaches estimate the contribution of different functional classes, such as coding or regulatory variants, to the genetic variance. This information allows a better understanding of the genetic architecture of complex traits, including complex diseases, but can also help improve the accuracy of genomic selection in livestock species. However, methods have mainly been tested on human genomic data, whereas livestock populations have specific characteristics, such as high levels of relatedness, small effective population size or long-range levels of linkage disequilibrium. RESULTS: Here, we used data from 14,762 cows, imputed at the whole-genome sequence level for 11,537,240 variants, to simulate traits in a typical livestock population and evaluate the accuracy of two state-of-the-art heritability partitioning methods, GREML and a Bayesian mixture model. In simulations where a single functional class had increased contribution to heritability, we observed that the estimators were unbiased but had low precision. When causal variants were enriched in variants with low (< 0.05) or high (> 0.20) minor allele frequency or low (below 1st quartile) or high (above 3rd quartile) linkage disequilibrium scores, it was necessary to partition the genetic variance into multiple classes defined on the basis of allele frequencies or LD scores to obtain unbiased results. When multiple functional classes had variable contributions to heritability, estimators showed higher levels of variation and confounding between certain categories was observed. In addition, estimators from small categories were particularly imprecise. However, the estimates and their ranking were still informative about the contribution of the classes. We also demonstrated that using methods that estimate the contribution of a single category at a time, a commonly used approach, results in an overestimation. Finally, we applied the methods to phenotypes for muscular development and height and estimated that, on average, variants in open chromatin regions had a higher contribution to the genetic variance (> 45%), while variants in coding regions had the strongest individual effects (> 25-fold enrichment on average). Conversely, variants in intergenic or intronic regions showed lower levels of enrichment (0.2 and 0.6-fold on average, respectively). CONCLUSIONS: Heritability partitioning approaches should be used cautiously in livestock populations, in particular for small categories. Two-component approaches that fit only one functional category at a time lead to biased estimators and should not be used.

Long-term effects of the chronic administration of doxorubicin on aged skeletal muscle: An exploratory study in mice.

The widely used chemotherapeutic drug doxorubicin (DOX) has been associated with adverse effects on the skeletal muscle, which can persist for years after the end of the treatment. These adverse effects may be exacerbated in older patients, whose skeletal muscle might already be impaired by aging. Nonetheless, the mediators responsible for DOX-induced myotoxicity are still largely unidentified, particularly the ones involved in the long-term effects that negatively affect the quality of life of the patients. Therefore, this study aimed to investigate the long-term effects of the chronic administration of DOX on the soleus muscle of aged mice. For that and to mimic the clinical regimen, a dose of 1.5 mg kg-1 of DOX was administered two times per week for three consecutive weeks in a cumulative dose of 9 mg kg-1 to 19-month-old male mice, which were sacrificed two months after the last administration. Body wasting and the atrophy of the soleus muscle, as measured by a decrease in the cross-sectional area of the soleus muscle fibers, were identified as long-term effects of DOX administration. The atrophy observed was correlated with increased reactive oxygen species production and caspase-3 activity. An impaired skeletal muscle regeneration was also suggested due to the correlation between satellite cells activation and the soleus muscle fibers atrophy. Systemic inflammation, skeletal muscle energy metabolism and neuromuscular junction-related markers do not appear to be involved in the long-term DOX-induced skeletal muscle atrophy. The data provided by this study shed light on the mediators involved in the overlooked long-term DOX-induced myotoxicity, paving the way to the improvement of the quality of life and survival rates of older cancer patients.

Epidemiology of Huntington's Disease in Latin America: A Systematic Review and Meta-Analysis.

BACKGROUND: Latin America has played a crucial role in advancing our understanding of Huntington's disease (HD). However, previous global reviews include limited data from Latin America. It is possible that English-based medical search engines may not capture all the relevant studies. METHODS: We searched databases in Spanish, Portuguese, and English. The names of every country in Latin America in English-based search engines were used to ensure we found any study that had molecular ascertainment and provided general epidemiological information or subpopulation data. Additionally, we contacted experts across the region. RESULTS: The search strategy yielded 791 citations; 24 studies met inclusion criteria, representing 12 of 36 countries. The overall pooled prevalence was 0.64 per 100,000 (prediction interval, 0.06-7.22); for cluster regions, it was 54 per 100,000 (95% CI, 34.79-84.92); for juvenile HD, it was 8.7% (prediction interval, 5.12-14.35), and 5.9% (prediction interval, 2.72-13.42) for late-onset HD. The prevalence was higher for Mexico, Peru, and Brazil. However, there were no significant differences between Central America and the Caribbean versus South America. CONCLUSION: The prevalence of HD appears to be similar across Latin America. However, we infer that our findings are underestimates, in part because of limited research and underdiagnosis of HD because of limited access to molecular testing and the availability of neurologists and movement disorders specialists. Future research should focus on identifying pathways to improve access to molecular testing and education and understanding differences among different ancestral groups in Latin America. © 2024 International Parkinson and Movement Disorder Society.

Exposing illegal hunting and wildlife depletion in the world's largest tropical country through social media data.

Globally, illegal sport hunting can threaten prey populations when unregulated. Due to its covert nature, illegal sport hunting poses challenges for data collection, hindering efforts to understand the full extent of its impacts. We gathered social media data to analyze patterns of illegal sport hunting and wildlife depletion across Brazil. We collected data for 2 years (2018-2020) across 5 Facebook groups containing posts depicting pictures of illegal sport hunting events of native fauna. We described and mapped these hunting events by detailing the number of hunters involved, the number of species, the mean body mass of individuals, and the number and biomass of individuals hunted per unit area, stratified by Brazilian biome. We also examined the effects of defaunation on hunting yield and composition via regression models, rank-abundance curves, and spatial interpolation. We detected 2046 illegal sport hunting posts portraying the hunting of 4658 animals (∼29 t of undressed meat) across all 27 states and 6 natural biomes of Brazil. Of 157 native species targeted by hunters, 19 are currently threatened with extinction. We estimated that 1414 hunters extracted 3251 kg/million km2. Some areas exhibited more pronounced wildlife depletion, in particular the Atlantic Forest and Caatinga biomes. In these areas, there was a shift from large mammals and reptiles to small birds as the main targeted taxa, and biomass extracted per hunting event and mean body mass across all taxonomic groups were lower than in other areas. Our results highlight that illegal sport hunting adds to the pressures of subsistence hunting and the wild meat trade on Brazil's wildlife populations. Enhanced surveillance efforts are needed to reduce illegal sport hunting levels and to develop well-managed sustainable sport hunting programs. These can support wildlife conservation and offer incentives for local communities to oversee designated sport hunting areas.

Exposición de la caza ilegal y la reducción de fauna en el país tropical más grande del mundo por medio de datos de las redes sociales Resumen En todo el mundo, la caza recreativa ilegal puede amenazar a las poblaciones de presas cuando no está regulada. Debido a su naturaleza encubierta, la caza recreativa ilegal plantea dificultades para la recopilación de datos, lo que dificulta la comprensión de su impacto. Recopilamos datos de redes sociales para analizar los patrones de caza recreativa ilegal y agotamiento de la vida silvestre en todo Brasil. Recopilamos datos durante 2 años (2018­2020) a través de cinco grupos de Facebook que contenían publicaciones que mostraban imágenes de eventos de caza recreativa ilegal de fauna nativa. Describimos y mapeamos estos eventos de caza detallando el número de cazadores involucrados, el número de especies, la masa corporal media de los individuos y el número y la biomasa de los individuos cazados por unidad de área, estratificados por bioma brasileño. También examinamos los efectos de la deforestación en el rendimiento y la composición de la caza mediante modelos de regresión, curvas de abundancia e interpolación espacial. Detectamos 2,046 puestos de caza recreativa ilegal que mostraban la caza de 4,658 animales (∼29 t de carne sin desollar) en los 27 estados y 6 biomas naturales de Brasil. De las 157 especies autóctonas objetivo de los cazadores, 18 están actualmente en peligro de extinción. Se calcula que 1,414 cazadores extrajeron 3,251 kg/millón de km2. Algunas zonas mostraron una defaunación más pronunciada, en particular los biomas de la Mata Atlántica y la Caatinga. En estas áreas, se produjo un cambio de grandes mamíferos y reptiles a pequeñas aves como principales taxones objetivo, y la biomasa extraída por evento de caza y la masa corporal media en todos los grupos taxonómicos fueron menores que en otras áreas. Nuestros resultados ponen de manifiesto que la caza recreativa ilegal se suma a las presiones de la caza de subsistencia y el comercio de carne salvaje sobre las poblaciones de fauna de Brasil. Es necesario intensificar los esfuerzos de vigilancia para reducir los niveles de caza recreativa ilegal y desarrollar programas de caza recreativa sostenibles y bien gestionados. Estos programas pueden contribuir a la conservación de la fauna y ofrecer incentivos a las comunidades locales para que supervisen las zonas designadas para la caza recreativa.

Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.

BACKGROUND: Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. METHODS: We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD). RESULTS: FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments. CONCLUSIONS: Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.

Quality of life of families and siblings of children and adolescents with meningomyelocele.

BACKGROUND: Children with meningomyelocele may require continuous care. Consequently, there is a risk for caregiver burden and impact on family quality of life (QoL), including siblings' QoL. Some studies analysed caregivers' burden and family QoL separately. However, none of these studies evaluated siblings' QoL and the associations between these three dimensions. This study investigated the associations between caregivers' burden, family QoL and siblings' QoL in Brazilian families of children with meningomyelocele and its correlations with sociodemographic, functional and clinical variables. Siblings' QoL was specifically assessed using as a parameter the QoL of typically developed Brazilian children. METHODS: One hundred and fifty families, 150 caregivers and 68 siblings completed the Family Quality of Life Scale, Burden Interview, KIDSCREEN-27 Child and Adolescent Version and Parents Version questionnaires. RESULTS: Most families and caregivers reported a high family QoL and a low caregiver burden. Family QoL was significantly lower as caregivers' burden increased. Caregiver's burden was significantly lower with increasing family QoL levels. Self-reported siblings' QoL was significantly worse than that of typically developed peers. There were no significant differences between self and parent-reported siblings' QoL. Self-reported siblings' QoL was significantly worse as their age increased and better with increasing family QoL levels. Parent-reported siblings' QoL was significantly worse with increasing levels of caregiver's burden and significantly better as family QoL increased. There were no significant associations with functional and clinical variables. CONCLUSIONS: Despite the cross-sectional nature of the available data precludes any statements of causality, our results reinforce the relevance of knowing the factors that influence the QoL of families and siblings of children and adolescents with meningomyelocele and the relevance of actions aimed at reducing caregivers' burden, improving family QoL and meeting siblings' individual needs. Future multicenter studies may validate the generalizability of our findings.

Restoring Skeletal Muscle Health through Exercise in Breast Cancer Patients and after Receiving Chemotherapy.

Breast cancer (BC) stands out as the most commonly type of cancer diagnosed in women worldwide, and chemotherapy, a key component of treatment, exacerbates cancer-induced skeletal muscle wasting, contributing to adverse health outcomes. Notably, the impact of chemotherapy on skeletal muscle seems to surpass that of the cancer itself, with inflammation identified as a common trigger for muscle wasting in both contexts. In skeletal muscle, pro-inflammatory cytokines modulate pathways crucial for the delicate balance between protein synthesis and breakdown, as well as satellite cell activation and myonuclear accretion. Physical exercise consistently emerges as a crucial therapeutic strategy to counteract cancer and chemotherapy-induced muscle wasting, ultimately enhancing patients' quality of life. However, a "one size fits all" approach does not apply to the prescription of exercise for BC patients, with factors such as age, menopause and comorbidities influencing the response to exercise. Hence, tailored exercise regimens, considering factors such as duration, frequency, intensity, and type, are essential to maximize efficacy in mitigating muscle wasting and improving disease outcomes. Despite the well-established anti-inflammatory role of aerobic exercise, resistance exercise proves equally or more beneficial in terms of mass and strength gain, as well as enhancing quality of life. This review comprehensively explores the molecular pathways affected by distinct exercise regimens in the skeletal muscle of cancer patients during chemotherapy, providing critical insights for precise exercise implementation to prevent skeletal muscle wasting.

Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information.

One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies.

MOTIVATION: Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. RESULTS: We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies. AVAILABILITY AND IMPLEMENTATION: https://github.com/rcsb/rcsb-saguaro-3d. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

MOTIVATION: Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. RESULTS: We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. AVAILABILITY AND IMPLEMENTATION: Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The effect of high-voltage monophasic pulsed current on diabetic ulcers and their potential pathophysiologic factors: A systematic review and meta-analysis.

The present review was conducted to determine the efficacy of high-voltage monophasic pulsed current (HVMPC) in treating diabetic ulcers, assess its effect on skin lesions with each of the pathophysiologic factors potentially contributing to diabetic ulcers, evaluate its safety, and identify treatment parameters. Electronic search of PubMed, Scopus, PEDro and Google Scholar databases was conducted. The revised tool for assessing risk of bias in randomised trials (RoB 2), the risk of bias in non-randomised studies-of interventions (ROBINS-I) and the Joanna Briggs Institute (JBI) critical appraisal tool were used to assess risk of bias and methodological quality. Overall quality of evidence was determined using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) principles. Thirty-two studies matched the eligibility criteria, and included 1061 patients with 1103 skin lesions of selected aetiologies; 12 randomised controlled trials were included in quantitative synthesis. HVMPC plus standard wound care (SWC) likely increased the probability of complete wound healing of pressure ulcers (PrUs) compared with sham/no stimulation plus SWC; relative risk (RR) 2.08; 95% CI: [1.42, 3.04], p = 0.0002; I2  = 0%, p = 0.61; eight studies, 358 ulcers. Although conclusive evidence regarding the effect of HVMPC on diabetic ulcers was not found, collateral evidence might suggest a potential benefit. Direct evidence, with moderate certainty, may support its efficacy in treating PrUs, albeit few adverse reactions were reported. Other observations, moreover, might indicate that this efficacy may not be limited to PrUs. Nonetheless, several aspects remain to be clarified for safe and effective application of electrical stimulation for wound healing.

Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals.

BACKGROUND: Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant associations. RESULTS: After a multiple-step genotype imputation to the sequence-level for 14,762 Belgian Blue beef (BBB) cows, we performed a genome-wide association study (GWAS) for 11 traits related to muscular development and body size. The 37 identified genome-wide significant quantitative trait loci (QTL) could be condensed in 11 unique QTL regions based on their position. Evidence for pleiotropic effects was found in most of these regions (e.g., correlated association signals, overlap between credible sets (CS) of candidate variants). Thus, we applied a multiple-trait approach to combine information from different traits to refine the CS. In several QTL regions, we identified strong candidate genes known to be related to growth and height in other species such as LCORL-NCAPG or CCND2. For some of these genes, relevant candidate variants were identified in the CS, including three new missense variants in EZH2, PAPPA2 and ADAM12, possibly two additional coding variants in LCORL, and candidate regulatory variants linked to CCND2 and ARMC12. Strikingly, four other QTL regions associated with dimension or muscular development traits were related to five (recessive) deleterious coding variants previously identified. CONCLUSIONS: Our study further supports that a set of common genes controls body size across mammalian species. In particular, we added new genes to the list of those associated with height in both humans and cattle. We also identified new strong candidate causal variants in some of these genes, strengthening the evidence of their causality. Several breed-specific recessive deleterious variants were identified in our QTL regions, probably as a result of the extreme selection for muscular development in BBB cattle.

The role of inflammation and antioxidant defenses in the cardiotoxicity of doxorubicin in elderly CD-1 male mice.

Doxorubicin (DOX) is a potent chemotherapeutic agent used against several cancer types. However, due to its cardiotoxic adverse effects, the use of this drug may be also life-threatening. Although most cancer patients are elderly, they are poorly represented and evaluated in pre-clinical and clinical studies. Considering this, the present work aims to evaluate inflammation and oxidative stress as the main mechanisms of DOX-induced cardiotoxicity, in an innovative approach using an experimental model constituted of elderly animals treated with a clinically relevant human cumulative dose of DOX. Elderly (18-20 months) CD-1 male mice received biweekly DOX administrations, for 3 weeks, to reach a cumulative dose of 9.0 mg/kg. One week (1W) or two months (2 M) after the last DOX administration, the heart was collected to determine both drug's short and longer cardiac adverse effects. The obtained results showed that DOX causes cardiac histological damage and fibrosis at both time points. In the 1W-DOX group, the number of nuclear factor kappa B (NF-κB) p65 immunopositive cells increased and a trend toward increased NF-κB p65 expression was seen. An increase of inducible nitric oxide synthase (iNOS) and interleukin (IL)-33 and a trend toward increased IL-6 and B-cell lymphoma-2-associated X (Bax) expression were seen after DOX. In the same group, a decrease in IL-1ß, p62, and microtubule-associated protein 1A/1B-light chain 3 (LC3)-I, p38 mitogen-activated protein kinase (MAPK) expression was observed. Contrariwise, the animals sacrificed 2 M after DOX showed a significant increase in glutathione peroxidase 1 and Bax expression with persistent cardiac damage and fibrosis, while carbonylated proteins, erythroid-2-related factor 2 (Nrf2), NF-κB p65, myeloperoxidase, LC3-I, and LC3-II expression decreased. In conclusion, our study demonstrated that in an elderly mouse population, DOX induces cardiac inflammation, autophagy, and apoptosis in the heart in the short term. When kept for a longer period, oxidative-stress-linked pathways remained altered, as well as autophagy markers and tissue damage after DOX treatment, emphasizing the need for continuous post-treatment cardiac monitoring.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

Validation of complementary non-invasive tools for stress assessment in spotted paca (Cuniculus paca).

Monitoring the concentration of glucocorticoid metabolites (GCMs) in faecal samples is a non-invasive tool for physiological stress evaluation, particularly useful when studying wild species. However, both negative and positive stimuli (distress and eustress, respectively) can lead to a rise in glucocorticoids. Thus, besides validating whether GCM concentration in faeces reflects endogenous adrenal activity, we also need to identify behavioural indicators of distress to avoid misinterpretation. Therefore, we submitted four adult male spotted pacas (Cuniculus paca) to an exogenous adrenocorticotropic hormone (ACTH) challenge-test in a Latin square design (4 × 4) to monitor changes in the GCM concentration in faeces. We also aimed to describe behaviours potentially indicative of distress. We collected excreted faeces and video-recorded the animals' behaviours for five consecutive days, one day before and four days after application of the following four treatments: 1st control (no-handling); 2nd control (intra-muscular [IM] injection of saline solution); low-dose ACTH (IM injection of 0.18 ml ACTH); and high-dose ACTH (IM injection of 0.37 ml ACTH). There was a peak in the concentration of GCM in faeces collected 24 h after the injection of the high-dose ACTH treatment. Additionally, independent of the treatments, spotted pacas spent less time on exploration and feeding states, while spending more time in the inactive but awake (IBA) state following the treatment application (challenge day). The use of GCM concentration in faecal samples together with the behavioural changes (less exploration and feeding, and more IBA) showed to be efficient as a non-invasive tool for welfare assessment of farmed spotted paca.

Protein Turnover in Skeletal Muscle: Looking at Molecular Regulation towards an Active Lifestyle.

Skeletal muscle is a highly plastic tissue, able to change its mass and functional properties in response to several stimuli. Skeletal muscle mass is influenced by the balance between protein synthesis and breakdown, which is regulated by several signaling pathways. The relative contribution of Akt/mTOR signaling, ubiquitin-proteasome pathway, autophagy among other signaling pathways to protein turnover and, therefore, to skeletal muscle mass, differs depending on the wasting or loading condition and muscle type. By modulating mitochondria biogenesis, PGC-1α has a major role in the cell's bioenergetic status and, thus, on protein turnover. In fact, rates of protein turnover regulate differently the levels of distinct protein classes in response to atrophic or hypertrophic stimuli. Mitochondrial protein turnover rates may be enhanced in wasting conditions, whereas the increased turnover of myofibrillar proteins triggers muscle mass gain. The present review aims to update the knowledge on the molecular pathways implicated in the regulation of protein turnover in skeletal muscle, focusing on how distinct muscle proteins may be modulated by lifestyle interventions with emphasis on exercise training. The comprehensive analysis of the anabolic effects of exercise programs will pave the way to the tailored management of muscle wasting conditions.

Regular Voluntary Running is Associated with Increased Tumor Vascularization and Immune Cell Infiltration and Decreased Tumor Growth in Mice.

Tumors present dysfunctional vasculature that limits blood perfusion and hinders immune cells delivery. We aimed to investigate if regular voluntary running promotes tumor vascular remodelling, improves intratumoral immune cells infiltration and inhibits tumor growth. Tumors were induced in C57BL/6 male mice (n=28) by subcutaneous inoculation in the dorsal region with a suspension of RM1 cells (1.5×105 cells/500 µL PBS) and randomly allocated into two groups: sedentary (n=14) and voluntarily exercised on a wheel (n=14). Seven mice from each group were sacrificed 14 and 28 days after cells' inoculation to evaluate tumor weight, microvessel density, vessels' lumen regularity and the intratumoral quantity of NKG2D receptors, CD4+and CD8+T cells, by immunohistochemistry. The statistical inference was done through a two-way ANOVA. Exercised mice developed smaller tumors at 14 (0.17±0.1 g vs. 0.48±0.2 g, p<0.05) and 28 (0.92±0.7 g vs. 2.09±1.3 g, p<0.05) days, with higher microvessel density (21.20±3.2 vs. 15.86±4.0 vessels/field, p<0.05), more regular vessels' lumen (1.06±0.2 vs. 1.43±0.2, p<0.05), and higher CD8+T cells (464.95±48.0 vs. 364.70±49.4 cells/mm2, p<0.01), after 28 days. NKG2D expression was higher in exercised mice at 14 (263.27±25.8 cells/mm2, p<0.05) and 28 (295.06±56.2 cells/mm2, p<0.001) days. Regular voluntary running modulates tumor vasculature, increases immune cells infiltration and attenuates tumor growth, in mice.