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2,788 results for “remodeling”
Abnormal cytoskeletal remodeling but normal neuronal excitability in a mouse model of the recurrent developmental and epileptic encephalopathy-susceptibility KCNB1-p.R312H variant
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Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome
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An inherited mtDNA mutation remodels inflammatory cytokine responses in macrophages and in vivo
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Sirtuins may mediate temperature-induced metabolic remodeling in threespine stickleback
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Data from: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression
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Data from: Functional remodelling of perinuclear mitochondria alters nucleoplasmic Ca2+ signalling in heart failure
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Data from: Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress
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A multiscale optimization framework for bone remodeling: Integrating material and structural adaptations across hierarchical scales
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Data from: Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants
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Mitochondrial remodeling supports migration in White-crowned Sparrows (Zonotrichia leucophrys)
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Confocal microscopy images for: Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms
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Remodeling dental anatomy vs sham therapy for chronic temporomandibular disorders: A placebo-controlled randomized clinical trial
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Link to dataset related to article "Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells"
<p>Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of <em>cis</em>-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated <em>cis</em>-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.</p>
Meniscus Matrix Remodeling in Response to Compressive Forces in Dogs
<p>Joint motion and postnatal stress of weight bearing are the principal factors that determine the phenotypical and architectural changes that characterize the maturation process of the meniscus. In this study, the effect of compressive forces on the meniscus will be evaluated in a litter of 12 Dobermann Pinschers, of approximately 2 months of age, euthanized as affected by the quadriceps contracture muscle syndrome of a single limb focusing on extracellular matrix remodeling and cell-extracellular matrix interaction (i.e., meniscal cells maturation, collagen fibers typology and arrangement). The affected limbs were considered as models of continuous compression while the physiologic loaded limbs were considered as controls. The results of this study suggest that a compressive continuous force, applied to the native meniscal cells, triggers an early maturation of the cellular phenotype, at the expense of the proper organization of collagen fibers. Nevertheless, an application of a compressive force could be useful in the engineering process of meniscal tissue in order to induce a faster achievement of the mature cellular phenotype and, consequently, the earlier production of the fundamental extracellular matrix (ECM), in order to improve cellular viability and adhesion of the cells within a hypothetical synthetic scaffold.</p>
Data from: A mitochondrial progesterone receptor increases cardiac beta-oxidation and remodeling
Progesterone is primarily a pregnancy related hormone, produced in substantial quantities after ovulation and during gestation. Traditionally known to function via nuclear receptors for transcriptional regulation there is also evidence of non-nuclear action. A previously identified mitochondrial progesterone receptor (PR-M) increases cellular respiration in cell models. In these studies, we demonstrated that expression of PR-M in rat H9c2 cardiomyocytes resulted in a ligand-dependent increase in oxidative cellular respiration and beta-oxidation. Cardiac expression in a TET-On transgenic mouse resulted in gene expression of myofibril proteins for remodeling and proteins involved in oxidative phosphorylation and fatty acid metabolism. In a model of increased afterload from constant transverse aortic constriction (cTAC), mice expressing PR-M showed a ligand-dependent preservation of cardiac function. From these observations, we propose that PR-M is responsible for progesterone-induced increases in cellular energy production and cardiac remodeling to meet the physiological demands of pregnancy.
Data from: Erythrocyte stiffness during morphological remodeling induced by carbon ion radiation
The adverse effect induced by carbon ion radiation (CIR) is still an unavoidable hazard to the treatment object. Thus, evaluation of its adverse effects on the body is a critical problem with respect to radiation therapy. We aimed to investigate the change between the configuration and mechanical properties of erythrocytes induced by radiation and found differences in both the configuration and the mechanical properties with involving in morphological remodeling process. Syrian hamsters were subjected to whole-body irradiation with carbon ion beams (1, 2, 4, and 6 Gy) or X-rays (2, 4, 6, and 12 Gy) for 3, 14 and 28 days. Erythrocytes in peripheral blood and bone marrow were collected for cytomorphological analysis. The mechanical properties of the erythrocytes were determined using atomic force microscopy, and the expression of the cytoskeletal protein spectrin-α1 was analyzed via western blotting. The results showed that dynamic changes were evident in erythrocytes exposed to different doses of carbon ion beams compared with X-rays and the control (0 Gy). The magnitude of impairment of the cell number and cellular morphology manifested the subtle variation according to the irradiation dose. In particular, the differences in the size, shape and mechanical properties of the erythrocytes were well exhibited. Furthermore, immunoblot data showed that the expression of the cytoskeletal protein spectrin-α1 was changed after irradiation, and there was a common pattern among its substantive characteristics in the irradiated group. Based on these findings, the present study concluded that CIR could induce a change in mechanical properties during morphological remodeling of erythrocytes. According to the unique characteristics of the biomechanical categories, we deduce that changes in cytomorphology and mechanical properties can be measured to evaluate the adverse effects generated by tumor radiotherapy. Additionally, for the first time, the current study provides a new strategy for enhancing the assessment of the curative effects and safety of clinical radiotherapy, as well as reducing adverse effects.
Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
<p>Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.</p>
Pathogenic Bacteria Remodel Central Metabolic Enzyme to Build a Cyclopropanol Warhead
<p>MS raw data used for generating Figure 2a/Supplementary Figure 1.</p> <p>NMR raw data of natural gonydiol.</p>
Fig. 6 in From Spinning Silk to Spreading Saliva: Mouthpart Remodeling in Manduca sexta (Lepidoptera: Sphingidae)
Fig. 6. Labio-hypopharyngeal lobe (lb) of the first instar of MaNdUCa SexTa (medial views of longitudinal cross sections). The spigot (sp) of the first instar is elongate and cone shaped and is connected to the salivarium (spr) via arthrodial membrane (dm = dorsal premento-salivarial muscle, lb = labio-hypopharyngeal lobe, lbr = labrum, lsg = labial gland, md = mandible, pm = prementum, pma = premental arm, spr = salivarium (=silk press), t-pm = tentorio-premental muscle, te-ci = tentorio-cibarial muscle, vm = ventral premento-salivarial muscle).
Fig. 5 in From Spinning Silk to Spreading Saliva: Mouthpart Remodeling in Manduca sexta (Lepidoptera: Sphingidae)
Fig. 5. Labio-hypopharyngeal lobe of the third instar of MaNdUCa SexTa. The salivarium (=silk press, spr) and its muscles (vm, dm) of second and later instars are similar to those of the first instar, indicating that the structure plays a similar role (closing and opening of the salivary orifice) in the saliva-producing instars and the silk-producing first instar. Starting with the second instar, the distal margin of the spinneret is equipped with hollow cuticular evaginations (arrowheads in C) that form a fringe.This brush-like structure might be involved in saliva spreading (dm = dorsal premento-salivarial muscle, pma = premental arm, spr = salivarium (=silk press), vm = ventral premento-salivarial muscle).
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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.