Characteristics of gut microbiota in fracture-related infection patients
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45380 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5986490.fastq.gz | Fastqsanger.gz | |||
| ERR5986500.fastq.gz | Fastqsanger.gz | |||
| ERR5986510.fastq.gz | Fastqsanger.gz | |||
| ERR5986520.fastq.gz | Fastqsanger.gz | |||
| ERR5986530.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 50 |
Similar Datasets
Project description:Age-related delays in fracture healing are prevalent and contribute to morbidity and mortality in elderly populations. Clinical and preclinical studies demonstrate that aging is associated with slower and less complete fracture repair characterized by delayed cartilage and bone formation, impaired matrix resorption, and an increased risk of delayed union or nonunion. Matrix Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI MSI) enables spatially resolved, in situ molecular analysis of proteins directly from murine fracture tissue sections. We applied collagenase type III (MMP 13) mediated proteolytic digestion to formalin fixed, paraffin embedded (FFPE) tibia fracture callus sections harvested 10 days post tibial fracture from young (3 month old) and aged (18 month old) mice to perform spatially resolved proteomic profiling. MALDI MSI revealed pronounced age dependent differences in extracellular matrix protein composition and remodeling within the fracture callus. We identified up regulation of canonical bone and matrix proteins, including Col1a1 and Col1a2 specifically in the young fracture callus demonstrating advancement into harden callus formation. Conversely, Col2a1 and other soft callus proteins were only seen in the aged callus tissues. Further, protein indicators of tissue state, such as fibronectin (up regulated) and calreticulin (down regulated) were selectively regulated aged tissues, demonstrating a failure for aged tissues to fully progress into harden calluses. Spatial proteomic patterns demonstrated a marked delay in progression from cartilaginous to osseous callus in aged mice, consistent with impaired matrix remodeling during fracture repair. Together, these findings establish MALDI MSI based spatial proteomics as a powerful approach to elucidate age related alterations in fracture healing and to identify molecular regulators of impaired skeletal regeneration.
2025-12-22 | MSV000100309 | MassIVE
Project description:Time-point expression analysis of fractures calluses at 1, 3, and 5 days post-fracture in young and old BALB/c mice. Femur fractures were generated on female c57BI6 mice in triplicate: 8 month old retired breeders (old mice) and 6 week old mice (young mice) were used. 1, 3, and 5 days post-fracture, fracture calluses were dissected and total RNA isolated. Expression profiling was performed using Affymetrix's Mouse Genome 430 2.0 array.
2009-09-01 | E-GEOD-17825 | biostudies-arrayexpress
Project description:To further understand the molecular complexity of fracture repair, we investigated miRNA profiling during the first 14 days post fracture. miRNA expression was investigated at post-fracture days 1, 3, 5, 7, 11, 14 as well as in intact (unfractured bone).
2016-04-05 | E-GEOD-76197 | biostudies-arrayexpress
Project description:Purpose The aim of this study was to determine the fracture hematoma (fxH) proteome after multiple trauma using label free proteomics, comparing two different established surgical treatment strategies. Basic procedures A large animal (sus scrofa), multiple trauma animal model was used in which two different trauma surgical treatment methods were compared: Early Total Care (ETC) versus Damage Control Orthopedics (DCO). fxH was harvested after 72 hours and analyzed using liquid chromatography-tandem mass spectrometry. Protein interaction analyses were performed to further elucidate key biomolecular pathways in the early fracture healing phase. Main findings The proteome of the early fxH was characterized by immunomodulatory and osteogenic proteins, as well as proteins involved in the coagulation cascade. Distinct, treatment-specific proteome alterations were observed. The fxH proteome of the ETC group showed increased expression of pro-inflammatory proteins related to, among others, activation of the complement system, neutrophil functioning, and macrophage activation, while showing decreased expression of proteins related to osteogenesis and tissue remodeling. On the other hand, the fxH proteome of the DCO group contained various upregulated or exclusively detected proteins related to tissue regeneration and remodeling, as well as proteins related to anti-inflammatory and osteogenic processes. Principal conclusions The early fxH proteome of the ETC group was characterized by the expression of immunomodulatory, mainly pro-inflammatory, proteins, whereas the early fxH proteome of the DCO group was more regenerative and osteogenic in nature. These findings match clinical observations, in which enhanced surgical trauma after severe multiple trauma causes dysbalanced inflammation, potentially leading to reduced tissue regenerative capabilities, and gained insights into regulatory mechanisms of fracture healing after severe trauma.
2024-05-24 | PXD049002 | Pride
Project description:It is commonly observed that patients with bone fracture concomitated with traumatic brain injury (TBI) had significantly increased fracture healing while the underlying mechanisms were not fully revealed. Long non-coding RNAs (lncRNAs) were known for paly complicated roles in bone homeostasis while its role in TBI accelerated fracture were rarely reported. The present study was designed to determine the role of lncRNAs in TBI accelerated fracture via transcriptome sequencing and further bioinformatical analysis. Blood samples from 3 fracture only patients, 3 fracture concomitated with TIB patients and 3 healthy controls were harvested and were subsequently subjected to transcriptome lncRNAs sequencing. Differentially expression genes were identified, and pathway enrichment were performed by Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyze. High high-dimensional data portraying by self-organizing map (SOM) machine learning was applied to further interpret the data. A xCell method were then used to predict cellular behavior in all samples based on gene expression profiles and a lncRNA-cell interaction network were generated. A total of 874 differentially expressed genes were identified, of which about 26% were lncRNAs. Those identified lncRNAs were mainly enriched on traumatic brain injury related- and damage repair related-pathways. SOM analyzes revealed that those differentially expressed lncRNAs could be divided into three major module implications and were mainly enriched on transcriptional regulation and immune related signal pathways, which promote us to further explore cellular behaviors based on differentially expressed lncRNAs. We have predicted that basophils, CD8+ T effector memory cells, B cells, and naïve B cells were significantly down-regulated while microvascular endothelia cells were predicated significantly up-regulated with TBI/Fr group was the lowest or highest, respectively. ENSG00000278905, ENSG00000240980, ENSG00000255670, and ENSG00000196634 were the most differentially expression lcnRNA that related to all changes of cellular behavior. The present study has revealed for the first time that several critical lncRNAs may participate in TBI accelerated fracture potentially via regulating cellular behaviors of basophils, cytotoxic T cells, B cells and endothelia cells.
2021-05-24 | GSE171718 | GEO
Project description:Periosteum deficiency affects bone regeneration, especially in the case of the bone disorder congenital pseudarthrosis of the tibia (CPT). We investigated a new mouse model of CPT caused by Nf1 inactivation in boundary cap-derivatives, the Prss56Cre; R26tdTom; Nf1fl/fl model. To investigate altered healing in this CPT model, we generated a dataset of the injured periosteum and fracture callus at day-7 post fracture from Prss56Cre; R26tdTom; Nf1fl/fl mice.
2024-07-24 | GSE232517 | GEO
Project description:10% of the fifteen million bone fractures each year that occur in the US fail to heal, which leads to significant loss of function, morbidity, and mortality. However, very little is known about the cellular and molecular mechanisms underpinning inferior healing. Two perturbed fracture models, surgically induced ischemia and the genetic deletion of the self-antigen CD47, were studied to identify unifying cellular and molecular mechanisms. C57Bl/6 wild-type (WT) mice with intact vasculature (WT Intact), WT mice with induced ischemia (WT Ischemic), and CD47-null mice with intact vasculature (CD47-KO) underwent transverse tibial fractures. Single-cell RNA-sequencing (scRNAseq) was performed during the inflammatory stage (4 days post-fracture) and the stromal stage (7 days post fracture) to assess transcriptomic alterations in perturbed fracture calluses.
2026-01-10 | GSE292578 | GEO
Project description:Genome-wide comparative gene expression analysis of callus tissue of osteoporotic mice (Col1a1-Krm2 and Lrp5-/-) and wild-type were performed to identify candidate genes that might be responsible for the impaired fracture healing observed in Col1a1-Krm2 and Lrp5-/- mice. To investigate bone healing in osteoporosis, we performed fracture healing studies in wild-type mice (C57BL/6 genetic background) and the low bone mass strains Col1a1-Krm2 and Lrp5-/- (Schulze et al., 2010; Kato et al., 2002). Osteotomy was set in femora of female mice and stabilized by a semi-rigid fixator to allow fast bone healing (RM-CM-6ntgen et al., 2010). 21 days post surgery we analyzed the fracture calli by biochemical/histological methods, as well as micro-computed tomography, and observed impaired fracture healing in Col1a1-Krm2 and Lrp5-/- mice in comparison to wild-type. To identify genes that may be responsible for the impaired healing in osteoporotic mice, we performed microarray analysis of three independent callus samples of each genotype. The callus tissue was taken 10 days after surgery, because extensive bone formation took place at this point.
2013-10-25 | E-GEOD-51686 | biostudies-arrayexpress
Project description:Inflammation, as a crucial initial phase of bone healing, typically commences in the early stages of fracture repair. The cGAS-STING pathway serves as a key mediator of inflammation. The aim of this study is to explore the biological role and molecular mechanisms of the cGAS-STING pathway in the fracture healing process, with a particular focus on its function during the early inflammatory phase.
2025-09-19 | GSE308052 | GEO
Project description:Clinical study of critically ill patients with sepsis and sepsis-related ARDS with whole blood RNA collected within the first 24 hours of admission Goal of the study was to determine whether biologically relevant genes were identified to be differentially expressed genes in patients with sepsis alone and sepsis with ARDS Prospective observational study, case cohort design
2015-04-01 | E-GEOD-66890 | biostudies-arrayexpress