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cox7a1 functions as SC assembly factor in striated muscle-Part 4
<p><strong><span>Raw data related to manuscript</span></strong></p> <p><strong><span>Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response </span></strong></p> <p><span><span> </span></span></p> <p><span>Carolina García-Poyatos<sup>1,2</sup>,</span><span> </span><span>Prateek Arora<sup>3,4</sup>, Enrique Calvo<sup>1</sup>, Ines J. Marques<sup>3,4</sup>, Nick Kirschke<sup>3,4</sup>, Maria Galardi-Castilla</span><sup><span>1</span></sup><span>, Carla Lembke<sup>3,4</sup>, Marco Meer<sup>3,4</sup>, Paula Rodriguez-Montes<sup>1</sup>, Alexander Ernst<sup>3</sup>, David Haberthür<sup>5</sup>, Ruslan Hlushchuk<sup>5</sup>, Jesús Vázquez<sup>1,6</sup>, Peter Vermathen<sup>7</sup>, José Antonio Enríquez<sup>1,2</sup>* and Nadia Mercader<sup>1,3,4</sup>*</span></p>
cox7a1 functions as SC assembly factor in striated muscle-Part 3
<p>Raw data related to the manuscript "<strong> </strong><span>Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response"</span></p> <p><span>Carolina García-Poyatos<sup>1,2</sup>,</span><span> </span><span>Prateek Arora<sup>3,4</sup>, Enrique Calvo<sup>1</sup>, Ines J. Marques<sup>3,4</sup>, Nick Kirschke<sup>3,4</sup>, Maria Galardi-Castilla</span><sup><span>1</span></sup><span>, Carla Lembke<sup>3,4</sup>, Marco Meer<sup>3,4</sup>, Paula Rodriguez-Montes<sup>1</sup>, David Haberthür<sup>5</sup>, Ruslan Hlushchuk<sup>5</sup>, Jesús Vázquez<sup>1,6</sup>, Peter Vermathen<sup>7</sup>, José Antonio Enríquez<sup>1,2</sup>* and Nadia Mercader<sup>1,3,4</sup>*</span></p> <p><span> </span></p> <p><span> </span></p> <p><sup><span>1</span></sup><span>Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain</span></p> <p><sup><span>2</span></sup><span>Centro de Investigación Biomédica en red en Fragilidad y Envejecimiento saludable (CIBERFES), Madrid, Spain</span></p> <p><sup><span>3</span></sup><span>Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland</span></p> <p><sup><span>4 </span></sup><span>Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland</span></p> <p><sup><span>5</span></sup><span>MikroCT, Institute of Anatomy, University of Bern, Bern, Switzerland</span></p> <p><sup><span>6</span></sup><span>Centro de Investigación Biomédica en red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain</span></p> <p><sup><span>7</span></sup><span>University Institute of Diagnostic and Interventional Neuroradiology, Magnetic Resonance Methodology, University of Bern, Bern, Switzerland</span></p> <p><span> </span></p> <p><span> </span></p>
cox7a1 function as SC assembly factor in striated muscle-Part 1
<p>This Dataset contains raw data related to the manuscirpt entitled "<span>Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response"</span></p> <p> </p> <p><span><span>Carolina García-Poyatos<sup>1,2</sup>,</span><span> </span><span>Prateek Arora<sup>3,4</sup>, Enrique Calvo<sup>1</sup>, Ines J. Marques<sup>3,4</sup>, Nick Kirschke<sup>3,4</sup>, Maria Galardi-Castilla</span><sup><span>1</span></sup><span>, Carla Lembke<sup>3,4</sup>, Marco Meer<sup>3,4</sup>, Paula Rodriguez-Montes<sup>1</sup>, David Haberthür<sup>5</sup>, Ruslan Hlushchuk<sup>5</sup>, Jesús Vázquez<sup>1,6</sup>, Peter Vermathen<sup>7</sup>, José Antonio Enríquez<sup>1,2</sup>* and Nadia Mercader<sup>1</sup></span></span></p> <p><sup><span>1</span></sup><span>Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain</span></p> <p><sup><span>2</span></sup><span>Centro de Investigación Biomédica en red en Fragilidad y Envejecimiento saludable (CIBERFES), Madrid, Spain</span></p> <p><sup><span>3</span></sup><span>Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland</span></p> <p><sup><span>4 </span></sup><span>Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland</span></p> <p><sup><span>5</span></sup><span>MikroCT, Institute of Anatomy, University of Bern, Bern, Switzerland</span></p> <p><sup><span>6</span></sup><span>Centro de Investigación Biomédica en red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain</span></p> <p><sup><span>7</span></sup><span>University Institute of Diagnostic and Interventional Neuroradiology, Magnetic Resonance Methodology, University of Bern, Bern, Switzerland</span></p> <p><span> </span></p>
The ELISA results of serum, skin, and muscle TNF-α, IL-6, IL-1β, iNOS, and β-EP levels and HE staining results of skin and muscle in control group, model group, GSMO group, IMO group, and GSTO group.
Open the record for dataset details and reuse information.
Code and exemplificative data for publication titled: Synaptic inputs to motor neurons underlying muscle co-activation for functionally different tasks have different spectral characteristics.
<p>Code implemented in the publication</p> <p>Titled: Synaptic inputs to motor neurons underlying muscle co-activation for functionally different tasks have different spectral characteristics</p> <p>Authors: Borzelli,D; Vieira,TMM; Botter,A; Gazzoni,M; Lacquaniti,F; d’Avella,A</p> <p>Published in: Journal of Neurophysiology</p> <p>Year: 2024</p> <p>When running the function 'coherenceAnalysis_Borzelli_et_al_JNeurophysiol_2024.m', the code load the firings of the motor units identified during two exemplificative trials performed by a participant, saved in 'data_Borzelli_et_al_JNeurophysiol_2024'. One trial was directed toward an horizontal target of the perturbed block and the other was directed toward a supination target of the baseline block.</p> <p>Then the code calculates the coherence between the MUs identified on the BB and on the TB (cross-muscle coherence) and the cross-muscle coherence after excluding the components synchronized with the norm of the endpoint force.</p> <p>Finally, the code plots the results.</p> <p>This code could easily be modified to compute all the relevant analyses presented in the paper, such as the total within muscle coherence and the within muscle coherences after excluding the components synchronized with the norm of the force or the sum of the firings of the antagonist muscle.</p>
The immune landscape of murine skeletal muscle regeneration and aging
<p>This repository contains data associated with the publication Sousa, N.S. <em>et al.</em> (2024) ‘The immune landscape of murine skeletal muscle regeneration and aging’, <em>Cell Reports</em>, 43(11), p. 114975. doi:10.1016/j.celrep.2024.114975.</p> <p>The files are the following: </p> <ul> <li><a href="https://zenodo.org/api/records/14197888/draft/files/srt-all-samples.rds/content" target="_blank" rel="noopener noreferrer">srt-all-samples.rds</a> contains an RDS Seurat object with the dataset comprising all samples and all cells. Metadata, dimensionality reduction coordinates and clustering analysis results reported in the publication are also included.</li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/srt-macs.rds/content" target="_blank" rel="noopener noreferrer">srt-macs.rds</a> contains an RDS Seurat object with the dataset comprising the subset of monocytes and macrophages across all samples. Metadata, dimensionality reduction coordinates and clustering analysis results reported in the publication are also included</li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/metadata_all_samples.txt/content" target="_blank" rel="noopener noreferrer">metadata_all_samples.txt</a> is a table with metadata associated with the dataset comprising all samples. </li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/metadata_macs.txt/content" target="_blank" rel="noopener noreferrer">metadata_macs.txt</a> is a table with metadata associated with the dataset comprising the subset of monocytes and macrophages across all samples. </li> </ul> <p> </p> <div> </div> <p> </p>
Supplemental Material - An IL-6 promoter variant (-174 G/C) augments IL-6 production and alters skeletal muscle transcription in response to exercise in mice.
<p>Supplemental Material for article: "An IL-6 promoter variant (-174 G/C) augments IL-6 production and alters skeletal muscle transcription in response to exercise in mice."</p>
PWB Muscle SR - Supplementary Table S2 (Reasons for Exclusion)
<p>Supplementary material for the manuscript entitled ' Skeletal Muscle Deconditioning During Partial Weight-Bearing in Rodents – A Systematic Review and Meta-Analysis'</p>
PWB Muscle SR - Supplementary Table S1 - PRISMA Checklist
<p>Supplementary material for the manuscript entitled 'Skeletal Muscle Deconditioning During Partial Weight-Bearing in Rodents – A Systematic Review and Meta-Analysis'</p>
Validation data Set: Development and validation of a quantitative method for 15 antiviral drugs in poultry muscle using liquid chromatography coupled to tandem mass spectrometry
<p>Validation dataset for paper published in the Journal of Chromatography A.</p> <p> </p> <p>Clément Douillet, Mary Moloney, Melissa Di Rocco, Christopher Elliott, Martin Danaher,<br> Development and validation of a quantitative method for 15 antiviral drugs in poultry muscle using liquid chromatography coupled to tandem mass spectrometry, Journal of Chromatography A, Volume 1665, 2022, 462793, ISSN 0021-9673,</p> <p><br> Abstract:</p> <p>The objective of this work was to develop a quantitative multi-residue method for analysing antiviral drug residues and their metabolites in poultry meat samples. Antiviral drugs are not licensed for the treatment of influenza in food producing animals. However, there have been some reports indicating their illegal use in poultry. In this study, a method was developed for the analysis of 15 antiviral drug residues in poultry muscle (chicken, duck, quail and turkey) using liquid chromatography coupled to tandem mass spectrometry. This included 13 drugs against influenza and associated metabolites, but also two drugs employed for the treatment of herpes (acyclovir and ganciclovir). The method required the development of a novel chromatographic separation using a hydrophilic interaction chromatographic (HILIC) BEH amide column, which was necessary to retain the highly polar compounds. The analytes were detected using a triple quadrupole mass spectrometer operating in positive electrospray ionization mode. A range of different sample preparation protocols suitable for polar compounds were evaluated. The most effective procedure was based on a simple acetonitrile-based protein precipitation step followed by a further dilution in a methanol/water solution. The confirmatory method was validated according to the EU 2021/808 guidelines on different species including chicken, duck, turkey and quail. The validation was performed using various calibration curves ranging from 0.1 µg kg−1to 200 µg kg−1, according to the analyte. Depending on the analyte sensitivity, decision limits achieved ranged from 0.12 µg kg−1 for arbidol to 34.7 µg kg−1 for ribavirin. Overall, the reproducibility precision values ranged from 2.8% to 22.7% and the recoveries from 84% to 127%. The method was applied to 120 commercial poultry samples from the Irish market, which were all found to be residue-free.<br> Keywords: Antiviral drug residues; Influenza; HILIC; LC-MS/MS; Poultry muscle</p>
Molecular and biochemical markers of oxidative stress in skeletal muscle
<p>Dataset of experimental animal study involved high-intensity interval training and molecular aspects of skeletal muscle.</p>
Interrelationship among thigh intermuscular adipose tissue, cross-sectional area, muscle strength and functional mobility in older subjects
<p><strong>Objectives:</strong> The aim of this cross-sectional study was to investigate the association between lower limb strength, muscle mass and composition and balance ability in elders. <strong>Methods:</strong> Thirthy-four older participants (Age: 65.6±4.73 years; male=10 and female=24) were assessed for muscle strength (maximal isometric strength of knee extensors and one repetition maximum by leg press, 1RM), balance and gait capacity (Mini-BESTest), body composition by DXA (obtaining Appendicular Skeletal Muscle Mass Index, ASMMI) and magnetic resonance imaging of thigh to evaluate Intermuscular Adipose Tissue (IMAT) and muscle Cross Sectional Area (CSA). <strong>Results:</strong> Positive correlations between 1RM leg press and ASMMI (r<sub>s</sub>=0.64, P<.0001) and thigh CSA (r<sub>s</sub>=0.52, P=.0017), but not with thigh IMAT, were found. In addition, significant correlations between knee extensors strength and ASMMI (r<sub>s</sub>=0.48, P=.004) and thigh CSA (r<sub>s</sub>=0.49, P=.0033) and IMAT (r<sub>s</sub>=-0.35, P=.043) were observed whereas no significant correlations between the Mini-BESTest with ASMMI, thigh CSA and IMAT were observed. <strong>Discussion:</strong> Lower limb strength positively correlated with appendicular muscle mass. Further, the maximal isometric strength of knee extensors negatively correlated with thigh IMAT in elderly patients whereas the dynamic balance ability did not correlate with any of the morphological variables of the muscle (i.e. ASMMI, CSA and IMAT). A reduced muscle size and strength could affect movement and reduce physical function in older patients. Improving the composition and size of muscle in elder subjects could reduce frailty and risk of falls.</p>
Data from: Computational Modeling of Gluteus Medius Muscle Moment Arm in Caviomorph Rodents Reveals Ecomorphological Specializations
<p>The data stored in this repository allow the reproduction of the study described in the following. Vertebrate musculoskeletal locomotion is realized through lever-arm systems. The instantaneous muscle moment arm (IMMA), which is expected to be under selective pressure and thus of interest for ecomorphological studies, is a key aspect of these systems. The IMMA changes with joint motion and its length change is technically difficult to acquire—usually, proxies such as osteological in-levers are used instead—and has not been compared in a larger phylogenetic ecomorphology framework, yet. We used 18 species of the ecologically diverse clade of caviomorph rodents to test whether its diversity is reflected in the IMMA of the hip extensor M. gluteus medius. A large IMMA is beneficial for torque generation; a small IMMA facilitates fast joint excursion. We expected large IMMAs in scansorial species, small IMMAs in fossorial species, and somewhat intermediate IMMAs in cursorial species, depending on the relative importance of acceleration and joint angular velocity. We modelled the IMMA over the entire range of possible hip extensions and applied macroevolutionary model comparison to selected joint poses. We also obtained the osteological in-lever of the M. gluteus medius to compare it to the IMMA. At small hip extension, the IMMA was largest on average in scansorial species, while the other two lifestyles were similar. We interpret this as an emphasized need for increased hip joint torque when climbing on inclines, especially in a crouched posture. Cursorial species might benefit from a fast joint excursion, but their similarity with the fossorial species is difficult to interpret and could hint at ecological similarities. At larger extension angles, cursorial species displayed the second-largest IMMAs after scansorial species. The larger IMMA optimum results in powerful hip extension which coincides with forward acceleration at late stance beneficial for climbing, jumping, and escaping predators. This might be less relevant for a fossorial lifestyle. The results of the in-lever only matched the IMMA results of larger hip extension angles, suggesting that the modelling of the IMMA provides more nuanced insights into adaptations of musculoskeletal lever arm systems than this osteological proxy.</p>
Drosophila muscle
<p>TEM image of Drosophila muscle tissue</p>
Sleep characteristics, MRI- and DXA-based morphological parameters, muscle strength and risk of falls in sedentary older subjects: a cross sectional study
<p>The aims of this study were: 1) to assess actigraphy-based and subjective sleep parameters in a sample of healthy older subjects and compare them to normative values for this specific population; 2) to assess the differences in muscle morphological parameters (muscle mass and composition) and physical performance (strength and balance) between short- vs normal-sleepers and poor- vs good-sleepers; 3) to assess the possible correlations between sleep variables and muscle morphological and physical function parameters in elderly subjects.</p>
Coding and noncoding genes involved in atrophy and compensatory muscle growth in Nile Tilapia
<p><strong>Electronic Supplementary Material</strong><strong>: </strong>Supplementary Table S1;Supplementary Table S2;Supplementary Table S3</p>
Rapid unloading experiments from Ttn112-158 muscles
<p>Evidence suggests that the giant muscle protein, titin, functions as a tunable spring in active muscle. However, the mechanisms for increasing titin stiffness with activation are not well understood. Previous studies have suggested that during muscle activation, titin binds to actin which engages the PEVK region of titin thereby increasing titin stiffness. In this study, we investigated the role of PEVK titin in active muscle stiffness during rapid unloading. We measured elastic recoil of active and passive soleus muscles from Ttn<sup>112-158</sup> mice characterized by a 75% deletion of PEVK titin and increased passive stiffness. We hypothesized that activated Ttn<sup>112-158</sup> muscles are stiffer than wild-type muscles as a result of the increased stiffness of PEVK titin. Using a servomotor force lever, we compared the stress-strain relationships of elastic elements in active and passive muscles during rapid unloading and quantified the change in stiffness upon activation. The results show that the elastic modulus of Ttn<sup>112-158</sup> muscles increased with activation. However, elastic elements developed force at 7% longer lengths and exhibited 50% lower active stiffness in Ttn<sup>112-158</sup> soleus muscles than wild-type muscles. Thus, despite having a shorter, stiffer PEVK segment, during rapid unloading, Ttn<sup>112-158</sup> soleus muscles exhibited reduced active stiffness compared to wild-type soleus muscles. These results are consistent with the idea that PEVK titin contributes to active muscle stiffness, however, the reduction in active stiffness of Ttn<sup>112-158</sup> muscles suggests that other mechanisms compensate for the increased PEVK stiffness.</p>
The effect of dietary supplementation with blueberry, cyanidin-3-O-β-glucoside, yoghurt and its peptides on gene expression associated with glucose metabolism in skeletal muscle obtained from a high-fat-high-carbohydrate diet induced obesity model
<p><span>Obesity is a leading global health problem contributing to various chronic diseases, including type II diabetes mellitus</span> <span>(T2DM). The aim of this study was to investigate whether blueberries, yoghurt, and their respective bioactive components, Cyanidin-3-O-β-glucoside (C3G) and peptides alone or in combinations, alter the expression of genes related to glucose metabolism in skeletal muscles from diet-induced obese mice. In extensor digitorum longus (EDL), yoghurt up-regulated the expression of activation of 5'adenosine monophosphate-activated protein kinase (AMPK), insulin receptor substrate-1 (IRS-1), phosphatidylinositol-3 kinase (PI3K) and glucose transporter 4 (GLUT4), and down-regulated the expression of angiotensin II receptor type 1 (AGTR-1). The combination of blueberries and yoghurt down-regulated the mRNA expression of AGTR-1 and Forkhead box protein O1 (FoxO1) in the EDL. Whereas the combination of C3G and peptides down-regulated AGTR-1 and up-regulated GLUT4 mRNA expression in the EDL. In the soleus, blueberries and yoghurt alone, and their combination down-regulated AGTR-1 and up-regulated GLUT4 mRNA expression. In summary blueberries and yoghurt, regulated multiple genes associated with glucose metabolism in skeletal muscles, and therefore may play a role in the management and prevention of T2DM.</span></p>
Locomotor resilience through load-dependent modulation of muscle co-contraction
<p>Terrestrial locomotor behavior in variable environments requires resilience to sudden changes in substrate properties. For example, walking animals can adjust to substantial changes in slope and corresponding changes in load distribution among legs. In insects, slope-dependent adjustments have mainly been examined under steady-state conditions, whereas the transition dynamics have been largely neglected. In a previous study, we showed that steady-state adjustments of stick insects to ±45° slopes involve substantial changes in joint torques and muscle activity with only minor changes in leg kinematics. Here, we take a close look at the time course of these adjustments as stick insects compensate for various kinds of disturbances to load distribution. In particular, we test whether the transition from one steady state to another involves distinct transition steps or follows a graded process. To resolve this, we combined simultaneous recordings of whole-body kinematics and hind leg muscle activity to elucidate how freely walking <em>Carausius morosus</em> negotiated a step-change in substrate slope. Step-by-step adjustments reveal that muscle activity changed in a graded manner as a function of body pitch relative to gravity. We further show analogous transient adjustment of muscle activity in response to destabilizing lift-off events of neighboring legs and the disappearance of antagonist co-activation during crawling episodes. Given these three examples of load-dependent regulation of antagonist muscle co-contraction, we conclude that stick insects respond to both transient and sustained changes in load distribution by regulating joint stiffness rather than through distinct transition steps.</p>
Humans trade-off whole-body energy cost to avoid overburdening muscles while walking
<p>See ReadMe_MATLAB.txt and ReadMe_Excel.txt for more information.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.