A novel magnetic resonance-based method to measure gene expression in living cells.
Ontology highlight
ABSTRACT:
SUBMITTER: Ki S
PROVIDER: S-EPMC1447650 | biostudies-literature | 2006 Apr
REPOSITORIES: biostudies-literature
Publications
A novel magnetic resonance-based method to measure gene expression in living cells.
Ki Sewon S Sugihara Fuminori F Kasahara Koji K Tochio Hidehito H Okada-Marubayashi Azusa A Tomita Setsuko S Morita Masahito M Ikeguchi Mitsunori M Shirakawa Masahiro M Kokubo Tetsuro T
Nucleic acids research 20060405 6
In unicellular and multicellular eukaryotes, elaborate gene regulatory mechanisms facilitate a broad range of biological processes from cell division to morphological differentiation. In order to fully understand the gene regulatory networks involved in these biological processes, the spatial and temporal patterns of expression of many thousands of genes will need to be determined in real time in living organisms. Currently available techniques are not sufficient to achieve this goal; however, n ...[more]
Similar Datasets
Project description:Background: Pathologically, Meniere's disease symptoms are considered to be associated with endolymphatic hydrops. Examinations revealing endolymphatic hydrops can be useful for accurate Meniere's disease diagnosis. We previously reported a quantitative method for evaluating endolymphatic hydrops, i.e., by measuring the volume of the endolymphatic space using three-dimensional magnetic resonance imaging (MRI) of the inner ear. This study aimed to confirm the usefulness of our methods for diagnosing Meniere's disease. Here, we extracted new explanatory factors for diagnosing Meniere's disease by comparing the volume of the endolymphatic space between healthy volunteers and patients with Meniere's disease. Additionally, we validated our method by comparing its diagnostic accuracy with that of the conventional method. Methods and Findings: This is a prospective diagnostic accuracy study performed at vertigo/dizziness centre of our university hospital, a tertiary hospital. Eighty-six patients with definite unilateral Meniere's disease and 47 healthy volunteers (25 and 33 males, and 22 and 53 females in the control and patient groups, respectively) were enrolled. All participants underwent 3-Tesla MRI 4 h after intravenous injection of gadolinium to reveal the endolymphatic space. The volume of the endolymphatic space was measured and a model for Meniere's disease diagnosis was constructed and compared with models using conventional criteria to confirm the effectiveness of the methods used. The area under the receiver operating characteristic curve of the method proposed in this study was excellent (0.924), and significantly higher than that derived using the conventional criteria (0.877). The four indices, sensitivity, specificity, positive predictive value, and negative predictive value, were given at the threshold; all of these indices achieved higher scores for the 3D model compared to the 2D model. Cross-validation of the models revealed that the improvement was due to the incorporation of the semi-circular canals. Conclusions: Our method showed high diagnostic accuracy for Meniere's disease. Additionally, we revealed the importance of observing the semi-circular canals for Meniere's disease diagnosis. The proposed method can contribute toward providing effective symptomatic relief in Meniere's disease.
| S-EPMC8257926 | biostudies-literature
Project description:Natural killer cells (NK cells) are cytotoxic lymphocytes that play an important role in the innate immune system. In particular, it plays a very important defense function against host cells or cancer cells infected with a specific virus. Recent studies have shown that the activity of NK cells is decreased in patients with various carcinomas compared with normal controls, suggesting that the measurement of activity of NK cells in the blood may be helpful in the early diagnosis of cancer. In a recent study analyzing NK cell activity in 762 patients undergoing colonoscopy, NK cell activity showed performance in diagnosing advanced colorectal adenoma and colorectal cancer with sensitivities 42.2% and 85.7%, and specificity 58.3% and 59.5%, respectively. This finding suggests that NK cell activity may be useful as a screening method for colorectal neoplasms. However, as a single test, this diagnostic power is relatively low. On the other hands, another blood-based colorectal cancer screening test that using 29 gene panels algorithm has recently been reported. According to this study, 29 gene panel algorithms (Colox) showed performance in diagnosing advanced colorectal adenoma and colorectal cancer with sensitivity of 55.4% and 79.5% and specificity of both 90.0%, respectively. for diagnosis of advanced adenoma and colorectal cancer, respectively. Although the Colox test seems to be useful for the colorectal cancer screening using blood test, this diagnostic power is relatively low. In order to overcome low diagnostic performance of aforementioned tests (NK activity and Colox) as a single use, combination of individual biomarkers can be a promising alternative. In this regards, the aim of this study was to evaluate the diagnostic value for predicting advanced colorectal neoplasms by combining Colox and NK cell activity indicators.
| 2254885 | ecrin-mdr-crc
Project description:Cell motility is governed by a complex molecular machinery that converts physico-chemical cues into whole-cell movement. Understanding the underlying biophysical mechanisms requires the ability to measure physical quantities inside the cell in a simple, reproducible and preferably non-invasive manner. To this end, we developed BioFlow, a computational mechano-imaging method and associated software able to extract intracellular measurements including pressure, forces and velocity everywhere inside freely moving cells in two and three dimensions with high spatial resolution in a non-invasive manner. This is achieved by extracting the motion of intracellular material observed using fluorescence microscopy, while simultaneously inferring the parameters of a given theoretical model of the cell interior. We illustrate the power of BioFlow in the context of amoeboid cell migration, by modelling the intracellular actin bulk flow of the parasite Entamoeba histolytica using fluid dynamics, and report unique experimental measures that complement and extend both theoretical estimations and invasive experimental measures. Thanks to its flexibility, BioFlow is easily adaptable to other theoretical models of the cell, and alleviates the need for complex or invasive experimental conditions, thus constituting a powerful tool-kit for mechano-biology studies. BioFlow is open-source and freely available via the Icy software.
| S-EPMC5569094 | biostudies-literature
Project description:The salamander axolotl is capable of complete regeneration of amputated heart tissue. However, non-invasive imaging tools for assessing its cardiac function were so far not employed. In this study, cardiac magnetic resonance imaging is introduced as a non-invasive technique to image heart function of axolotls. Three axolotls were imaged with magnetic resonance imaging using a retrospectively gated Fast Low Angle Shot cine sequence. Within one scanning session the axolotl heart was imaged three times in all planes, consecutively. Heart rate, ejection fraction, stroke volume and cardiac output were calculated using three techniques: (1) combined long-axis, (2) short-axis series, and (3) ultrasound (control for heart rate only). All values are presented as mean ± standard deviation. Heart rate (beats per minute) among different animals was 32.2±6.0 (long axis), 30.4±5.5 (short axis) and 32.7±4.9 (ultrasound) and statistically similar regardless of the imaging method (p > 0.05). Ejection fraction (%) was 59.6±10.8 (long axis) and 48.1±11.3 (short axis) and it differed significantly (p = 0.019). Stroke volume (μl/beat) was 133.7±33.7 (long axis) and 93.2±31.2 (short axis), also differed significantly (p = 0.015). Calculations were consistent among the animals and over three repeated measurements. The heart rate varied depending on depth of anaesthesia. We described a new method for defining and imaging the anatomical planes of the axolotl heart and propose one of our techniques (long axis analysis) may prove useful in defining cardiac function in regenerating axolotl hearts.
| S-EPMC5570274 | biostudies-literature
Project description:BackgroundAssessments of subclinical connective tissue disorders depend on complex approaches, emphasizing the need for more accessible methods applicable to clinical routine. Therefore, we aimed to establish a reliable approach assessing cervical vessel tortuosity, which is known to be associated with such disorders.MethodsMagnetic resonance angiography (MRA) images of ReSect study participants [single-center prospective cohort of spontaneous cervical artery dissection (sCeAD) patients] were used. Each patient underwent the same magnetic resonance imaging (MRI) protocol. The segmentation procedure was done using MATrix LABoratory 9.4 [up-sampling of raw MRA images, distance metric (DM) calculation], ITK-SNAP [region of interest (ROI) determination, vessel segmentation] and Vascular Modelling ToolKit (centerline determination). To assess inter-user variability and validity, we (I) had two blinded independent users segment all arteries and we (II) compared the results of our method to visual appraisal of vessel tortuosity done by two blinded expert neuro-radiologists.ResultsA total of 526 extracranial cervical arteries were available for analysis. The inter-user variability of our method users was below 0.5% throughout. Overall, our method outperformed the visual tortuosity appraisal, as the visual grading underestimated the DM in 38.8% subjects when tasked to assess overall cervical artery tortuosity (both vertebral and internal carotid arteries) and in 16.6% and 33.3% respectively if tasked to grade anterior or posterior circulation separately.ConclusionsWe present a reliable method to assess cervical artery tortuosity derived from MRA images applicable in clinical routine and future research investigating the potential correlation of sCeAD and connective tissue disorder.
| S-EPMC10895094 | biostudies-literature
Project description:A novel high-throughput magnetic tweezers-based 3D microchannel electroporation system capable of transfecting 40 000 cells/cm(2) on a single chip for gene therapy, regenerative medicine, and intracellular detection of target mRNA for screening cellular heterogeneity is reported. A single cell or an ordered array of individual cells are remotely guided by programmable magnetic fields to poration sites with high (>90%) cell alignment efficiency to enable various transfection reagents to be delivered simultaneously into the cells. The present technique, in contrast to the conventional vacuum-based approach, is significantly gentler on the cellular membrane yielding >90% cell viability and, moreover, allows transfected cells to be transported for further analysis. Illustrating the versatility of the system, the GATA2 molecular beacon is delivered into leukemia cells to detect the regulation level of the GATA2 gene that is associated with the initiation of leukemia. The uniform delivery and a sharp contrast of fluorescence intensity between GATA2 positive and negative cells demonstrate key aspects of the platform for gene transfer, screening and detection of targeted intracellular markers in living cells.
| S-EPMC4397144 | biostudies-literature
Project description:The thalamus is an essential relay station in the cortical-subcortical connections. It is characterized by a complex anatomical architecture composed of numerous small nuclei, which mediate the involvement of the thalamus in a wide range of neurological functions. We present a novel framework for segmenting the thalamic nuclei, which explores the orientation distribution functions (ODFs) from diffusion magnetic resonance images at 3 T. The differentiation of the complex intra-thalamic microstructure is improved by using the spherical harmonic (SH) representation of the ODFs, which provides full angular characterization of the diffusion process in each voxel. The clustering was performed using the k-means algorithm initialized in a data-driven manner. The method was tested on 35 healthy volunteers and our results show a robust, reproducible and accurate segmentation of the thalamus in seven nuclei groups. Six of them closely matched the anatomy and were labeled as anterior, ventral anterior, medio-dorsal, ventral latero-ventral, ventral latero-dorsal and pulvinar, while the seventh cluster included the centro-lateral and the latero-posterior nuclei. Results were evaluated both qualitatively, by comparing the segmented nuclei to the histological atlas of Morel, and quantitatively, by measuring the clusters' extent and the clusters' spatial distribution across subjects and hemispheres. We also showed the robustness of our approach across different sequences and scanners, as well as intra-subject reproducibility of the segmented clusters using additional two scan-rescan datasets. We also observed an overlap between the path of the main long-connection tracts passing through the thalamus and the spatial distribution of the nuclei identified with our clustering algorithm. Our approach, based on SH representations of the ODFs, outperforms the one based on angular differences between the principle diffusion directions, which is considered so far as state-of-the-art method. Our findings show an anatomically reliable segmentation of the main groups of thalamic nuclei that could be of potential use in many clinical applications.
| S-EPMC5504280 | biostudies-literature
Project description:PurposeCoil-by-coil reconstruction methods are followed by coil combination to obtain a single image representing a spin density map. Typical coil combination methods, such as square-root sum-of-squares and adaptive coil combining, yield images that exhibit spatially varying modulation of image intensity. Existing practice is to first combine coils according to a signal-to-noise criterion, then postprocess to correct intensity inhomogeneity. If inhomogeneity is severe, however, intensity correction methods can yield poor results. The purpose of this article is to present an alternative optimality criterion for coil combination; the resulting procedure yields reduced intensity inhomogeneity while preserving contrast.Theory and methodsA minimum mean squared error criterion is adopted for combining coils via a subspace decomposition. Techniques are compared using both simulated and in vivo data.ResultsExperimental results for simulated and in vivo data demonstrate lower bias, higher signal-to-noise ratio (about 7×) and contrast-to-noise ratio (about 2×), compared to existing coil combination techniques.ConclusionThe proposed coil combination method is noniterative and does not require estimation of coil sensitivity maps or image mask; the method is particularly suited to cases where intensity inhomogeneity is too severe for existing approaches.
| S-EPMC4568182 | biostudies-literature
Project description:Bile acid transporters, including the ileal apical sodium-dependent bile acid transporter (ASBT) and the hepatic sodium-taurocholate cotransporting polypeptide (NTCP), are crucial for the enterohepatic circulation of bile acids. Our objective was to develop a method for measuring bile acid transporter activity in real time to precisely evaluate rapid changes in their function. We designed a reporter system relying on a novel probe: cholic acid attached to luciferin via a disulfide-containing, self-immolating linker (CA-SS-Luc). Incubation of human embryonic kidney-293 cells coexpressing luciferase and ASBT with different concentrations of CA-SS-Luc (0.01-1 μM) resulted in bioluminescence with an intensity that was concentration- and time-dependent. The bioluminescence measured during incubation with 1 μM CA-SS-Luc was dependent on the levels of ASBT or NTCP expressed in the cells. Coincubation of CA-SS-Luc with natural bile acids enhanced the bioluminescence in a concentration-dependent manner with kinetic parameters for ASBT similar to those previously reported using conventional methods. These findings suggest that this method faithfully assesses ASBT function. Further, incubation with tyrosine phosphatase inhibitor III (PTPIII) led to significantly increased bioluminescence in cells expressing ASBT, consistent with previous studies showing an increase in ASBT function by PTPIII. We then investigated CA-SS-Luc in isolated mouse intestinal epithelial cells. Ileal enterocytes displayed significantly higher luminescence compared with jejunal enterocytes, indicating a transport process mediated by ileal ASBT. In conclusion, we have developed a novel method to monitor the activity of bile acid transporters in real time that has potential applications both for in vitro and in vivo studies. NEW & NOTEWORTHY This article reports the development of a real-time method for measuring the uptake of bile acids using a bioluminescent bile acid-based probe. This method has been validated for measuring uptake via the apical sodium-dependent bile acid transporter and the sodium-taurocholate cotransporting polypeptide in cell culture and ex vivo intestinal models.
| S-EPMC6230696 | biostudies-literature
Project description:Many studies reported that spontaneous fluctuation of the blood oxygen level-dependent signal exists in multiple frequency components and changes over time. By assuming a reliable energy contrast between low- and high-frequency bands for each voxel, we developed a novel spectrum contrast mapping (SCM) method to decode brain activity at the voxel-wise level and further validated it in designed experiments. SCM consists of the following steps: first, the time course of each given voxel is subjected to fast Fourier transformation; the corresponding spectrum is divided into low- and high-frequency bands by given reference frequency points; then, the spectral energy ratio of the low- to high-frequency bands is calculated for each given voxel. Finally, the activity decoding map is formed by the aforementioned energy contrast values of each voxel. Our experimental results demonstrate that the SCM (1) was able to characterize the energy contrast of task-related brain regions; (2) could decode brain activity at rest, as validated by the eyes-closed and eyes-open resting-state experiments; (3) was verified with test-retest validation, indicating excellent reliability with most coefficients > 0.9 across the test sessions; and (4) could locate the aberrant energy contrast regions which might reveal the brain pathology of brain diseases, such as Parkinson's disease. In summary, we demonstrated that the reliable energy contrast feature was a useful biomarker in characterizing brain states, and the corresponding SCM showed excellent brain activity-decoding performance at the individual and group levels, implying its potentially broad application in neuroscience, neuroimaging, and brain diseases.
| S-EPMC8455948 | biostudies-literature