Differences in gene expression between the otic capsule and other bones.
Ontology highlight
ABSTRACT:
SUBMITTER: Stankovic KM
PROVIDER: S-EPMC3586807 | biostudies-literature | 2010 Jun
REPOSITORIES: biostudies-literature
Publications
Differences in gene expression between the otic capsule and other bones.
Stankovic Konstantina M KM Adachi Osamu O Tsuji Kunikazu K Kristiansen Arthur G AG Adams Joe C JC Rosen Vicki V McKenna Michael J MJ
Hearing research 20100208 1-2
Our long term goal is to understand the molecular pathology of otosclerosis and to develop better forms of therapy. Toward this goal, the current study focused on characterizing the molecular factors responsible for the unique biological features of the otic capsule: its minimal rate of remodeling, and lack of healing capacity when fractured. We compared expression levels of 62 genes involved in bone metabolism between the adult murine otic capsule and the tibia and parietal bones; the latter ex ...[more]
Similar Datasets
Project description:The global consumption of flavoured cigarettes, particularly capsule and menthol non-capsule cigarettes, has been rising rapidly. Their attractiveness has been fuelled by perceptions of improved palatability, along with industry marketing tactics such as lower price points in some regions. This study aimed to compare prices of unflavoured, capsule, and menthol non-capsule cigarettes across 65 countries by analysing 2018 cigarette price data from Euromonitor Passport. Median prices of capsule and menthol non-capsule cigarettes were each compared to unflavoured cigarettes at the country-level. Countries were included in the analysis if they contained price data for capsule or menthol non-capsule and unflavoured cigarettes (n = 65). The median price of capsule cigarettes was the same as unflavoured cigarettes in 12 out of 50 countries and not statistically different in another 31 countries (p > 0.05). Capsule cigarettes were more expensive than unflavoured cigarettes in five countries and cheaper in two (p < 0.05). The median price of menthol non-capsule cigarettes was the same as unflavoured cigarettes in 6 out of 51 countries and not statistically different in another 39 countries (p > 0.05). Menthol non-capsule cigarettes were more expensive than unflavoured cigarettes in five countries and cheaper in one country (p < 0.05). There was no pattern found in the pricing of capsule or menthol non-capsule cigarettes, suggesting variability in the tobacco industry’s pricing strategies across countries. Tailoring tobacco control policies to match national market conditions, particularly in countries with significant market shares of capsule and menthol non-capsule cigarettes could help address the public health threat posed by the tobacco epidemic.
| S-EPMC10220479 | biostudies-literature
Project description:We recently established that antibody (Ab)-binding can induce gene expression changes in a serotype A strain (H99) of the pathogenic yeast, Cryptococcus neoformans. That study showed that monoclonal antibodies (mAbs) differing in epitope specificity and protective efficacy elicited differences in gene expression. Because many mAbs bind to serotypes A and D strains differently, we now investigate the binding of one mAb to two strains representing these serotypes. Cells of the serotype A strain H99 and the serotype D strain 24067 were incubated with near saturating concentrations of the IgG1 capsule-binding mAb 18B7 or MOPC, an irrelevant mAb matched control. Comparative immunofluorescence analysis of mAb 18B7 binding revealed that it bound closer to the cell wall in H99 than 24067, where it was associated with decreased or increased cell diameter, respectively. A comparison of encapsulated cell compressibility showed that strain 24067 was more compressible than that of strain H99. RNA was extracted and used for gene expression analysis using the C. neoformans JEC21 genomic microarray. After 1h incubation with mAb 18B7, there were just 2 gene expression changes observed with strain 24067 or strain JEC21, unlike the 43 seen with strain H99. After 4h incubation with mAb 18B7, there were 14 and 140 gene expression changes observed with strain 24067 and JEC21, respectively. Thus, C. neoformans strains differ both in the response and the time of response to mAb binding and these differences may reflect differences in the location of Ab binding, Ab-mediated changes in cell diameter and compressibility of the capsular polysaccharide.
| S-EPMC3482122 | biostudies-literature
Project description:Colorectal cancer studies typically include both colon and rectum tumors as a common entity, though this assumption is controversial and only minor differences have been reported at the molecular and epidemiologic level. We conducted a molecular study based on gene expression data of tumors from colon and rectum to assess the degree of similarity between these cancer sites at transcriptomic level.A pooled analysis of 460 colon tumors and 100 rectum tumors from four data sets belonging to three independent studies was conducted. Microsatellite instable tumors were excluded as these are known to have a different expression profile and have a preferential proximal colon location. Expression differences were assessed with linear models, and significant genes were identified using adjustment for multiple comparisons.Minor differences at a gene expression level were found between tumors arising in the proximal colon, distal colon, or rectum. Only several HOX genes were found to be associated with tumor location. More differences were found between proximal and distal colon than between distal colon and rectum.Microsatellite stable colorectal cancers do not show major transcriptomic differences for tumors arising in the colon or rectum. The small but consistent differences observed are largely driven by the HOX genes. These results may have important implications in the design and interpretation of studies in colorectal cancer.
| S-EPMC3229689 | biostudies-literature
Project description:ObjectivePatients with peripheral vestibular dysfunction because of gravitational receptor asymmetries display signs of cognitive dysfunction and are assumed to have neurobehavioral sequelae. This was tested with pre- and postoperatively quantitative measurements in three cohort groups with superior semicircular canal dehiscence syndrome (SSCDS) symptoms with: 1) superior canal dehiscence (SCD) repaired via a middle cranial fossa craniotomy and canal plugging only; 2) otic capsule defects not visualized with imaging (no-iOCD) repaired with round window reinforcement (RWR) only; or 3) both SCD plugging and subsequent development of no-iOCD followed by RWR.Study designProspective patient series.SettingTertiary referral center.PatientsThere were 13 adult and 4 pediatric patients with SSCDS who had completion of neuropsychology test batteries pre- and every 3 months postoperatively. Eight patients had no-iOCD and RWR exclusively, 5 had SCD and plugging exclusively, and 4 had both SCD plugging and then development of no-iOCD with RWR. These cohorts included SSCDS with 2 different dehiscence locations.InterventionsCompletion of a neuropsychology test battery preoperatively and at 3, 6, 9, and 12 months postoperatively that included: Beck Depression Inventory-II (BDI); Wide Range Intelligence Test (WRIT FSIQ) including average verbal (crystallized intelligence) and visual (fluid intelligence); Wide Range Assessment of Memory and Learning (WRAML), including the four domains of verbal memory, visual memory, attention/concentration, and working memory; and Delis-Kaplan Executive Function System (D-KEFS). The Dizziness Handicap Inventory (DHI) and the Headache Impact Test (HIT-6) were also completed to assess the impact of their disease on activities pre- and postoperatively.Main outcome measuresQuantitative and statistical analysis of their cognitive and neurobehavioral function.ResultsThe pattern of differences between the SCD group and the no-iOCD group from WRAML verbal, visual, and attention test performance indicate different postoperative clinical trajectories. For the WRAML, there was a statistically significant improvement for visual memory and verbal memory for the no-iOCD only and both (SCD and subsequent no-iOCD) groups, but no mean improvement for the SCD only group. By contrast, the no-iOCD group had significantly lower scores on the WRAML attention test preoperatively, but they recovered postoperatively to match the other groups. The preoperative findings and postoperative outcomes did not differ significantly among patient groups on the WRAML working memory test, D-KEFS motor scores, D-KEFS number and letter scores, or Wide Range Intelligence Test scores. There was a significant decrease in the BDI for all groups. The IQ scores were unchanged. There was a statistically significant improvement in the DHI and HIT-6 scores postoperatively in all groups.ConclusionsThere was a marked overall improvement in cognitive and neurobehavioral function postoperatively. Variability may result from duration of underlying disease before intervention. The initial decrement or delay in performance improvement measured in several patients may represent brain reorganization. Greater longitudinal data and greater subject numbers are necessary to better understand and optimize cognitive recovery.
| S-EPMC4674143 | biostudies-literature
Project description:Identifying the molecular programs underlying human organ development and how they differ from model species is key for understanding human health and disease. Developmental gene expression profiles provide a window into the genes underlying organ development and a direct means to compare them across species. We use a transcriptomic resource covering the development of seven organs to characterize the temporal profiles of human genes associated with distinct disease classes and to determine, for each human gene, the similarity of its spatiotemporal expression with its orthologs in rhesus macaque, mouse, rat, and rabbit. We find clear associations between spatiotemporal profiles and the phenotypic manifestations of diseases. We also find that half of human genes differ from their mouse orthologs in their temporal trajectories in at least one of the organs. These include more than 200 genes associated with brain, heart, and liver disease for which mouse models should undergo extra scrutiny.
| S-EPMC7610014 | biostudies-literature
Project description:ObjectivesThis study was aimed to assess the relationship between the type of temporal bone area involved and conductive hearing loss.MethodsWe enrolled 97 patients who visited the otolaryngology clinics of Seoul National University Hospital or Boramae Medical Center, Seoul Metropolitan Government-Seoul National University with temporal bone fracture between January 2004 and January 2014. Audiometric parameters, including initial and improved air-bone (AB) conduction gap values, were reviewed in accordance with the temporal bone computed tomography (external auditory canal [EAC], middle ear [ME], mastoid [M], and ossicle [O]).ResultsPatients with ossicular chain involvement exhibited a larger AB gap compared to those with no ossicular chain involvement at 250, 1,000, 2,000, and 4,000 Hz. Among the groups without ossicular chain involvement, the initial AB gap was largest in patients with EAC+ME+M involvement, followed by the ME+M and M-only involvement groups. The greatest improvement in the AB gap was observed in the EAC+ME+M group followed by the ME+M and M-only groups, irrespective of ossicular chain involvement. Improvements in AB gap values were smallest at 2,000 Hz.ConclusionConductive hearing loss pattern differed according to the temporal bone area involved. Therefore, areas such as the hematoma and hemotympanum, as well as the fracture line of the temporal bone area, must be evaluated to predict audiologic patterns with otic capsule preserving temporal bone fracture.
| S-EPMC4996100 | biostudies-literature
Project description:Atherosclerotic carotid stenosis is an important risk factor for stroke. Carotid plaques (CPs) causing stroke may present a distinct type of molecular pathology compared with transient ischemic attack (TIA)-associated or asymptomatic plaques. We compared the gene expression profiles of CPs from stroke patients (n?=?12) and asymptomatic patients (n?=?9), both with similar risk factors and severity of carotid stenosis (>70%). Sixty probes showed over 1.5-fold expression difference at 5% false discovery rate. Functional clustering showed enrichment of genes in 51 GO categories and seven pathways, the most significant of which relate to extracellular-matrix interaction, PPAR gamma signaling, scavanger receptor activity, and lysosomal activity. Differential expression of ten genes was confirmed in an extended replication group (n?=?43), where the most significant expression differences were found in CD36 (2.1-fold change, p?=?0.005), CD163 (1.7-fold change, p?=?0.007) and FABP4 (2.2-fold change, p?=?0.015). These include four genes not previously linked to plaque destabilization: GLUL (2.2-fold change, p?=?0.016), FUCA1 (2.2-fold change, p?=?0.025), IL1RN (1.6-fold change, p?=?0.034), and S100A8 (2.5-fold change, p?=?0.047). Strong correlations were found to plaque ulceration, plaque hemorrhage, and markers of apoptosis and proliferation (activated caspase 3, TUNEL, and Ki67). Protein expression of these genes was confirmed by immunohistochemistry and was found in the atheromatous areas of CPs critical for plaque destabilization. This study presents a comprehensive transcriptional analysis of stroke-associated CPs and demonstrates a significant transcriptome difference between stroke-associated and asymptomatic CPs. Follow-up studies on the identified genes are needed to define whether they could be used as biomarkers of symptomatic CPs or have a role in plaque destabilization.
| S-EPMC3170468 | biostudies-literature
Project description:Coral reefs provide habitats for a disproportionate number of marine species relative to the small area of the oceans that they occupy. The mutualism between the cnidarian animal hosts and their intracellular dinoflagellate symbionts provides the nutritional foundation for coral growth and formation of reef structures, because algal photosynthesis can provide >90% of the total energy of the host. Disruption of this symbiosis ("coral bleaching") is occurring on a large scale due primarily to anthropogenic factors and poses a major threat to the future of coral reefs. Despite the importance of this symbiosis, the cellular mechanisms involved in its establishment, maintenance, and breakdown remain largely unknown. We report our continued development of genomic tools to study these mechanisms in Aiptasia, a small sea anemone with great promise as a model system for studies of cnidarian-dinoflagellate symbiosis. Specifically, we have generated de novo assemblies of the transcriptomes of both a clonal line of symbiotic anemones and their endogenous dinoflagellate symbionts. We then compared transcript abundances in animals with and without dinoflagellates. This analysis identified >900 differentially expressed genes and allowed us to generate testable hypotheses about the cellular functions affected by symbiosis establishment. The differentially regulated transcripts include >60 encoding proteins that may play roles in transporting various nutrients between the symbiotic partners; many more encoding proteins functioning in several metabolic pathways, providing clues regarding how the transported nutrients may be used by the partners; and several encoding proteins that may be involved in host recognition and tolerance of the dinoflagellate.
| S-EPMC3931562 | biostudies-literature
Project description:This study compares the visualization of otic capsule anatomy by thin-section three-dimensional Fourier transformation (3DFT) MR imaging with that by high-resolution CT. The osseous margins of the otic capsule are delineated by high-resolution CT, while MR displays the soft-tissue structures. Routine two-dimensional Fourier transformation (2DFT) spin-echo MR techniques have been limited by slice thickness and signal to noise. Previous longer TE 3DFT gradient-echo MR images of the otic structures have been degraded by magnetic susceptibility effects, which limit spatial resolution and decrease signal to noise. These effects are especially prevalent in the otic capsule, where small soft-tissue structures interface with surrounding air and bone. We developed a high-resolution 3DFT MR technique to image five normal subjects. MR images were compared with high-resolution CT images of the same subjects. Axial, sagittal, and coronal 3DFT gradient-echo MR images with a short TR/TE and 15 degrees flip angle were acquired on a General Electric 1.5-T Signa unit using a 3-in. circular, receive-only surface coil. Axial, sagittal, and coronal 1.5-mm-thick contiguous high-resolution CT bone-algorithm images were obtained also. There was a high correlation between the MR and CT findings. The 3DFT MR images demonstrated significantly higher spatial resolution and soft-tissue detail than the high-resolution CT images did. For example, the endolymphatic duct was seen on twice the number of consecutive sagittal and axial MR slices. Other soft-tissue otic capsule structures routinely seen on the 3DFT MR images included the entire facial nerve, membranous labyrinth including cochlea, and tensor tympani muscle. This study demonstrates a new high-resolution 3DFT MR technique for visualizing the soft-tissue microstructures of the otic capsule and achieves a level of spatial resolution beyond that possible with high-resolution CT.
| S-EPMC8367544 | biostudies-literature
Project description:Strabismic extraocular muscles (EOMs) differ from normal EOMs in structural and functional properties, but the gene expression profile of these two types of EOM has not been examined. Differences in gene expression may inform about causes and effects of the strabismic condition in humans.EOM samples were obtained during corrective surgery from patients with horizontal strabismus and from deceased organ donors with normal EOMs. Microarrays and quantitative PCR identified significantly up- and down-regulated genes in EOM samples. Analysis was performed on probe sets with more than 3-fold differential expression between normal and strabismic samples, with an adjusted P value of ? 0.05.Microarray analysis showed that 604 genes in these samples had significantly different expression. Expression predominantly was upregulated in genes involved in extracellular matrix structure, and down-regulated in genes related to contractility. Expression of genes associated with signaling, calcium handling, mitochondria function and biogenesis, and energy homeostasis also was significantly different between normal and strabismic EOM. Skeletal muscle PCR array identified 22 (25%) of 87 muscle-specific genes that were significantly down-regulated in strabismic EOMs; none was significantly upregulated.Differences in gene expression between strabismic and normal human EOMs point to a relevant contribution of the peripheral oculomotor system to the strabismic condition. Decreases in expression of contractility genes and increases of extracellular matrix-associated genes indicate imbalances in EOM structure. We conclude that gene regulation of proteins fundamental to contractile mechanics and extracellular matrix structure is involved in pathogenesis and/or consequences of strabismus, suggesting potential novel therapeutic targets.
| S-EPMC3416046 | biostudies-literature