Biomedical subjects

Young Sook Son

Publications and source records attributed to Young Sook Son.

6 recordsLinked to original sources

PubMed2006

Segmentation and intensity estimation of microarray images using a gamma-t mixture model.

MOTIVATION: We present a new approach to the analysis of images for complementary DNA microarray experiments. The image segmentation and intensity estimation are performed simultaneously by adopting a two-component mixture model. One component of this mixture corresponds to the distribution of the background intensity, while the other corresponds to the distribution of the foreground intensity. The intensity measurement is a bivariate vector consisting of red and green intensities. The background intensity component is modeled by the bivariate gamma distribution, whose marginal densities for the red and green intensities are independent three-parameter gamma distributions with different parameters. The foreground intensity component is taken to be the bivariate t distribution, with the constraint that the mean of the foreground is greater than that of the background for each of the two colors. The degrees of freedom of this t distribution are inferred from the data but they could be specified in advance to reduce the computation time. Also, the covariance matrix is not restricted to being diagonal and so it allows for nonzero correlation between R and G foreground intensities. This gamma-t mixture model is fitted by maximum likelihood via the EM algorithm. A final step is executed whereby nonparametric (kernel) smoothing is undertaken of the posterior probabilities of component membership. The main advantages of this approach are: (1) it enjoys the well-known strengths of a mixture model, namely flexibility and adaptability to the data; (2) it considers the segmentation and intensity simultaneously and not separately as in commonly used existing software, and it also works with the red and green intensities in a bivariate framework as opposed to their separate estimation via univariate methods; (3) the use of the three-parameter gamma distribution for the background red and green intensities provides a much better fit than the normal (log normal) or t distributions; (4) the use of the bivariate t distribution for the foreground intensity provides a model that is less sensitive to extreme observations; (5) as a consequence of the aforementioned properties, it allows segmentation to be undertaken for a wide range of spot shapes, including doughnut, sickle shape and artifacts. RESULTS: We apply our method for gridding, segmentation and estimation to cDNA microarray real images and artificial data. Our method provides better segmentation results in spot shapes as well as intensity estimation than Spot and spotSegmentation R language softwares. It detected blank spots as well as bright artifact for the real data, and estimated spot intensities with high-accuracy for the synthetic data. AVAILABILITY: The algorithms were implemented in Matlab. The Matlab codes implementing both the gridding and segmentation/estimation are available upon request. SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Algorithms↗

PubMed2006

Low-intensity ultrasound stimulation enhances chondrogenic differentiation in alginate culture of mesenchymal stem cells.

Mesenchymal stem cells (MSCs) are regarded as a potential autologous source for cartilage repair, because they can differentiate into chondrocytes by transforming growth factor-beta (TGF-beta) treatment under the 3-dimensional (3-D) culture condition. However, more efficient and versatile methods for chondrogenic differentiation of MSCs are still in demand for its clinical application. Recently, low-intensity ultrasound (LIUS) was shown to enhance fracture healing in vitro and induce chondrogenesis of MSCs in vitro. In this study, we investigated the effects of LIUS on the chondrogenesis of rabbit MSCs (rMSCs) in a 3-D alginate culture and on the maintenance of chondrogenic phenotypes after replating them on a monolayer culture. The LIUS treatment of rMSCs increased: (i) the matrix formation; (ii) the expression of chondrogenic markers such as collagen type II, aggrecan, and Sox-9; (iii) the expression of tissue inhibitor of metalloprotease-2 implicated in the integrity of cartilage matrix; and (iv) the capacity to maintain the chondrogenic phenotypes in a monolayer culture. Notably, LIUS effects were clearly shown even without TGF-beta treatment. These results suggest that LIUS treatment could be an efficient and cost-effective method to induce chondrogenic differentiation of MSCs in vitro for cartilage tissue engineering.

Aggrecans↗

PubMed2006

Isolation of putative corneal epithelial stem cells from cultured limbal tissue.

PURPOSE: To investigate methods of isolating putative corneal epithelial stem cells from cultured limbal tissue. METHODS: Three extraction techniques were compared to identify an efficient method of obtaining a large number of viable corneal epithelial stem cells from the limbus. Limbal tissues were extracted by incubation at 37 degrees C or 4 degrees C for 1 or 16 hours, respectively, with 1.2 U/ml dispase/trypsin or by treatment with 0.05% trypsin and 0.01% ethyldiaminetetraacetic acid (EDTA) at 37 degrees C in single procedure. Collected cells were cultured on NIH/3T3-seeded plates, and colony forming efficiency (CFE) was evaluated. Fluorescence activated cell sorting (FACS) was performed with a Coulter EPICS 753 after incubation with Hoechst 33342 and propidium iodide (PI). Hoechst negative cells were obtained using gates exhibiting low Hoechst blue with a 424/44 nm BP filter. Gated cells of each fraction were re-cultured to assess the capability of colony formation. RESULTS: The mean numbers of viable cells obtained from treatment with dispase and trypsin was 3 x 10(4) cell/ml and 8.06 x 10(5) cell/ml at 37 degrees C and 4 degrees C incubations; the number increased to 1.21 x 10(6) cell/ml with a trypsin/EDTA treatment (p < 0.05). CFE was 9.67 +/- 2.13% and 6.63 +/- 2.35% in rabbit and human cells, respectively. Likewise, the Hoechst negative fraction was 3.61 +/- 0.42% and 5.21 +/- 4.91% in rabbit and human cells, respectively. The sorted Hoechst negative cells were cultured through four passages, forming small round colonies. In rabbit cells, the CFEs of Hoechst negative and positive fractions after FACS, were 12.67 +/- 2.24% and 1.17 +/- 6.13%, respectively (p < 0.05). CONCLUSIONS: Putative corneal epithelial stem cells were efficiently isolated from limbal tissue using a trypsin/EDTA extraction and FACS. This technique may be very useful in tissue engineered stem cell therapy.

Animals↗

PubMed2002

TGFbeta1 -mediated epithelial to mesenchymal transition is accompanied by invasion in the SiHa cell line.

It has recently been suggested by several investigators that the epithelial-mesenchymal transition-inducing capacity of TGFbetas contributes to invasive transition of tumors at later stages of carcinogenesis. In the present study, we examined the possibility of TGFbeta1-stimulated epithelial-mesenchymal transition in SiHa cell line, detailed molecular events in the process, and its possible contribution to the invasive transition of tumors. TGFbeta1-induced epithelial-mesenchymal transition of SiHa cells was based on morphological and biochemical criteria; actin stress fiber formation, focal translocalization of integrin alphav, talin, and vinculin, fibronectin-based matrix assembly at the cell periphery, and translocalization and down-regulation of E-cadherin. TGFbeta1 also stimulated surface expression of integrin alphavbeta3 and FAK activation. Focal translocalization of integrin alphav preceded actin reorganization and fibronectin matrix assembly, and functional blocking of the integrin suppressed actin stress fiber formation. Furthermore, induction of actin reorganization and fibronectin matrix assembly by TGFbeta1 were shown to be mutually independent events. These changes were irreversible because 5 minutes pulse exposure to TGFbeta1 was sufficient to stimulate progress of actin reorganization and fibronectin matrix assembly. In further studies with raft culture, TGFbeta1 was found to stimulate invasion of SiHa cells into a type I collagen gel matrix. In conclusion, TGFbeta1 stimulated epithelial-mesenchymal transition of SiHa cells, indicating a positive role in the invasive transition of tumors.

Actins↗

PubMedDate not supplied

Heterogeneity of capillary endothelial cells for basic fibroblast growth factor-induced paracrine signaling.

In this study, the authors isolated morphologically different capillary endothelial cells, designated as BCE-1 and BCE-2 cells, from bovine adrenal cortex. By a series of experiments involving proliferation, migration, and tubular-like structure formation assays, the authors found that the two BCE clones showed a clearly different response to basic fibroblast growth factor (bFGF). Similar to these results, the ERK-1/2 in the BCE-1 cells was phosphorylated by bFGF or vascular endothelial growth factor (VEGF), whereas that of the BCE-2 cells was phosphorylated only by VEGF. However, when the BCE-2 cells were transfected with FGF receptor 1 cDNA, the ERK-1/2 of these cells was phosphorylated by exogenous bFGF. Receptor binding experiments revealed that BCE-2 cells expressed high-affinity tyrosine-kinase FGF receptors approximately twofold less than BCE-1 cells. Transfection and receptor binding studies suggest a possibility that the poor response of the BCE-2 cells to exogenous bFGF is derived from the limitation of functional availability of high affinity FGF receptors. On the other hand, when both BCE clones were treated with anti-bFGF antibodies, basal formation of tubular-like structure in both clones were strongly inhibited, indicating that endogenous bFGF plays a role in in vitro angiogenesis of both BCE clones. Taken together, these data show that the isolated capillary endothelial cells are heterogeneous for paracrine but not autocrine bFGF signaling, and suggest that the diversity of capillary endothelial cells can occur by angiogenic factors, such as bFGF.

Adrenal Cortex↗

PubMedDate not supplied

Application of physical force is essential to enrich for epidermal stem cells in primary human keratinocyte isolation.

We present an improved method to isolate epidermal cells and to enrich stem cell populations. The new method utilizes magnetic stirring during digestion of skin with trypsin-EDTA (magnetic stirring method). The magnetic stirring method significantly improves both cell yield and colony-forming efficiency (CFE) relative to conventional epidermal cell isolation methods, such as those involving trypsin-EDTA only, thermolysin, or dispase. The cell yield and the total number of colony-forming cells per square centimeter of adult foreskin were 7,064,000 +/- 95,000 cells and 96,030 +/- 31,990 cells by the magnetic stirring method, 1,128,000 +/- 111,000 cells and 10,192 +/- 2941 cells by trypsin-EDTA only, 3,279,000 +/- 842,000 cells and 5851 +/- 2989 cells by thermolysin, and 1,443,000 +/- 507,000 cells and 8843 +/- 3388 cells by dispase, respectively. The CFE was 1.15 +/- 0.32% by magnetic stirring, 0.95 +/- 0.35% by trypsin-EDTA only, 0.28 +/- 0.12% by thermolysin, and 0.83 +/- 0.30% by dispase. The levels of surface beta(1)-integrin expression skewed to the right with the magnetic stirring method, implying increased proportion of beta(1)-integrin-bright cells (putative stem cells). Isolated keratinocytes developed fully differentiated epidermis when they were grafted onto nude mice. In conclusion, cell isolation by the magnetic stirring method is advantageous over conventional epidermal cell isolation methods, by which full range of basal epidermal cells including stem cells, transiently amplifying cells, and differentiating cells can be isolated and allow shorter expansion time for maximal coverage of wound sites after biopsies are taken from patients.

Animals↗