Israel Rocker
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PROVIDER: S-EPMC1124824 | biostudies-literature | 2002 Dec
REPOSITORIES: biostudies-literature
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Project description:Differentially DNA methylated regions (DMRs) inform on the role of epigenetic changes in cancer. We present Rocker-meth, a new computational method exploiting a heterogeneous hidden Markov model to detect DMRs across multiple experimental platforms. Through an extensive comparative study, we first demonstrate Rocker-meth excellent performance on synthetic data. Its application to more than 6,000 methylation profiles across 14 tumor types provides a comprehensive catalog of tumor type-specific and shared DMRs, and agnostically identifies cancer-related partially methylated domains (PMD). In depth integrative analysis including orthogonal omics shows the enhanced ability of Rocker-meth in recapitulating known associations, further uncovering the pan-cancer relationship between DNA hypermethylation and transcription factor deregulation depending on the baseline chromatin state. Finally, we demonstrate the utility of the catalog for the study of colorectal cancer single-cell DNA-methylation data.
| S-EPMC8563962 | biostudies-literature
Project description:Rocking-platform perfusion systems rely on hydrostatic pressure differences to perfuse cells in organ-on-chip devices. These systems are popular due to their tubing-free design, which facilitates parallelization, an essential feature for drug discovery, precision medicine, and academic research. However, most of these systems generate bidirectional flow, which does not accurately replicate the physiological conditions experienced by endothelial cells (ECs) in the microvasculature. To address this limitation, pump-based systems are often employed to generate unidirectional flow, though they require external tubing, thereby limiting scalability compared to rocking platforms. In this study, we compared the transcriptomic responses of endothelial cells exposed to flow generated either by a rocking platform or a peristaltic pump, under matched average flow rates. Our results revealed distinct transcriptomic profiles induced by the two flow modalities, with hundreds of genes differentially expressed between the two conditions. After 4 hours of flow exposure, we observed an enrichment in signaling pathways including NF-κB, ERK, BMP and MAPK. Furthermore, after 24 hours of flow exposure, we identified significant changes in the genes involved in biological processes such as immune cell migration, angiogenesis and vascular and extracellular matrix remodeling, highlighting how different flow generated by pump or rokcer can shape endothelial cell behavior at the molecular level.
2025-07-28 | GSE272273 | GEO
Project description:Understanding the signalling function of Ras GTPases has been the focus of much research for over 20 years. Both the catalytic domain and the membrane anchoring C terminal hypervariable region (HVR) of Ras are necessary for its cellular function. However, while the highly conserved catalytic domain has been characterized in atomic detail, the structure of the full-length membrane-bound Ras has remained elusive. Lack of structural knowledge on the full-length protein limited our understanding of Ras signalling. For example, structures of the Ras catalytic domain solved in complex with effectors do not provide a basis for the functional specificity of different Ras isoforms. Recent molecular dynamics simulations in combination with biophysical and cell biological experiments have shown that the HVR and parts of the G domain cofunction with the lipid tails to anchor H-ras to the plasma membrane. In the GTP-bound state, H-ras adopts an orientation that allows read out by Ras effectors and translation into corresponding MAPK signalling. Here we discuss details of an analysis that suggests a novel balance model for Ras functioning. The balance model rationalizes Ras membrane orientation and may help explain isoform specific interactions of Ras with its effectors and modulators.
| S-EPMC2782589 | biostudies-literature
Project description:The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
| S-EPMC10221096 | biostudies-literature
Project description:Goal of the study was to compare gene expression patterns between sites and habitats
2017-07-26 | GSE101884 | GEO
Project description:Biodegradable electrospun polycaprolactone scaffolds can be used to support bone-forming cells and could fill a thin bony defect, such as in cleft palate. Oscillatory fluid flow has been shown to stimulate bone production in human progenitor cells in monolayer culture. The aim of this study was to examine whether bone matrix production by primary human mesenchymal stem cells from bone marrow or jaw periosteal tissue could be stimulated using oscillatory fluid flow supplied by a standard see-saw rocker. This was investigated for cells in two-dimensional culture and within electrospun polycaprolactone scaffolds. From day 4 of culture onwards, samples were rocked at 45 cycles/min for 1 h/day, 5 days/week (rocking group). Cell viability, calcium deposition, collagen production, alkaline phosphatase activity and vascular endothelial growth factor secretion were evaluated to assess the ability of the cells to undergo bone differentiation and induce vascularisation. Both cell types produced more mineralized tissue when subjected to rocking and supplemented with dexamethasone. Mesenchymal progenitors and primary human mesenchymal stem cells from bone marrow in three-dimensional scaffolds upregulated mineral deposition after rocking culture as assessed by micro-computed tomography and alizarin red staining. Interestingly, vascular endothelial growth factor secretion, which has previously been shown to be mechanically sensitive, was not altered by rocking in this system and was inhibited by dexamethasone. Rocker culture may be a cost effective, simple pretreatment for bone tissue engineering for small defects such as cleft palate.
| S-EPMC5836908 | biostudies-literature
Project description:During the past 74 years since its establishment, Israel has evolved into a modernized country with well-established and effective public health care system. Thoracic surgeons in Israel play a central role in the diagnosis and treatment of patients with diseases of the chest wall, diaphragm, mediastinum, airways, Lung, and esophagus as well are taking part in designated trauma teams. Between 2,500-3,000 cases are being performed in 16 designated thoracic surgical units and departments across the country annually, the majority of them being performed in a minimally invasive fashion. Lung cancer is the leading cause of cancer related mortality in Israel and the second most common cancer in Israel. All types of thoracic oncologic cases are being presented routinely during designated multi-disciplinary conferences and treatment plans are designed according to the most up to date international guidelines. Each surgeon undergoes at least 6 years of formal training, followed by certifying exams. Advanced training is usually obtained overseas in centers of excellence. Israeli thoracic surgeons are part of an international societies and are actively involved in academic research. Despite the advancement of the Israeli health care system, thoracic surgeons in Israel are still facing few challenges that are limiting the early diagnosis of thoracic surgical malignancies such as lack of established national lung cancer screening program in Israel although a pilot program is being tested during these days. Tasked with taking care of diseases of the chest, and in order to remain at the forefront of diagnosis and treatment similar to our colleagues across the globe, Thoracic surgeons in Israel are continuously seeking to learn and evolve in order to improve and provide better care to our patients.
| S-EPMC9641345 | biostudies-literature
Project description:In 2008, melioidosis was diagnosed in an agricultural worker from Thailand in the southern Jordan Valley in Israel. He had newly diagnosed diabetes mellitus, fever, multiple abscesses, and osteomyelitis. Burkholderia pseudomallei was isolated from urine and blood. Four of 10 laboratory staff members exposed to the organism received chemoprophylaxis, 3 of whom had adverse events.
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