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Biomedical subjects

Y Tu

Publications and source records attributed to Y Tu.

At least 19 recordsLinked to original sources
PubMed2003

Modeling of DNA microarray data by using physical properties of hybridization.

A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model.

Algorithms↗
PubMed2003

Clinical features and treatment of hematopoietic stem cell transplantation-associated gastric antral vascular ectasia.

Gastric antral vascular ectasia (GAVE) may occur after hematopoietic stem cell transplantation (HSCT) and cause severe and prolonged gastric bleeding. The underlying pathology of transplant-associated GAVE (HSCT-GAVE) is poorly understood and an effective therapeutic strategy has not been established yet. We retrospectively reviewed the medical records of 230 consecutive allogeneic transplant recipients in our institution between January 1997 and June 2002. We identified five patients who developed HSCT-GAVE (2.2%). Four patients had bleeding from HSCT-GAVE and one patient had HSCT-GAVE discovered incidentally. The clinical features of these patients were similar in that they all received conditioning treatment with busulfan and had history of thrombotic microangiopathy. Furthermore, treatment with a beta-blocker apparently improved the outcome of HSCT-GAVE in three patients.

Adolescent↗
PubMed2002

Quantitative noise analysis for gene expression microarray experiments.

A major challenge in DNA microarray analysis is to effectively dissociate actual gene expression values from experimental noise. We report here a detailed noise analysis for oligonuleotide-based microarray experiments involving reverse transcription, generation of labeled cRNA (target) through in vitro transcription, and hybridization of the target to the probe immobilized on the substrate. By designing sets of replicate experiments that bifurcate at different steps of the assay, we are able to separate the noise caused by sample preparation and the hybridization processes. We quantitatively characterize the strength of these different sources of noise and their respective dependence on the gene expression level. We find that the sample preparation noise is small, implying that the amplification process during the sample preparation is relatively accurate. The hybridization noise is found to have very strong dependence on the expression level, with different characteristics for the low and high expression values. The hybridization noise characteristics at the high expression regime are mostly Poisson-like, whereas its characteristics for the small expression levels are more complex, probably due to cross-hybridization. A method to evaluate the significance of gene expression fold changes based on noise characteristics is proposed.

Gene Expression↗
PubMed2002

Ten-year prospective follow-up study on the relationship between Helicobacter pylori infection and progression of atrophic gastritis, particularly assessed by endoscopic findings.

AIM: To ascertain the progression of atrophic gastritis due to Helicobacter pylori infection, we conducted a 10-year prospective follow-up study with annual endoscopy of the stomach. METHODS: Prospective endoscopic observation was started in 53 subjects in 1989 and 1990 after informed consent was obtained. The progression of atrophic gastritis was evaluated mainly by the endoscopic pattern of atrophy. Histological assessment was performed on biopsy specimens taken from the lesser curvature of the lower corpus. By 2000, 43 patients (20 males, 23 females, mean age 56.7 years at entry) had completed at least 10 years of endoscopic follow-up. RESULTS: Eight H. pylori-negative patients with normal fundic mucosa showed no change endoscopically or histologically. In 35 H. pylori-positive patients, the progression of histological atrophy was observed in 46% and intestinal metaplasia was observed in 49%. Fifteen of 35 H. pylori-positive cases exhibited a cephaloid shift of the endoscopic atrophic border. The cephaloid shift of the atrophic area occured suddenly. The cumulative progression rate of atrophic patterns was 6% after 2 years, 22% after 4 years, 34% after 6 years and 43% after 10 years. These atrophic changes were related to neutrophil infiltration. CONCLUSION: The progression of atrophic gastritis is a result of chronic active gastritis caused by H. pylori infection.

Adult↗
PubMed2001

Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells.

B cell-derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that >50% of CLLs display hypermutated immunoglobulin variable region (IgV) sequences and a more favorable prognosis, suggesting that they may represent a distinct subset of CLLs which have transited through germinal centers (GCs), the physiologic site of IgV hypermutation. To further investigate the phenotype of CLLs, their cellular derivation and their relationship to normal B cells, we have analyzed their gene expression profiles using oligonucleotide-based DNA chip microarrays representative of approximately 12,000 genes. The results show that CLLs display a common and characteristic gene expression profile that is largely independent of their IgV genotype. Nevertheless, a restricted number of genes (<30) have been identified whose differential expression can distinguish IgV mutated versus unmutated cases and identify them in independent panels of cases. Comparison of CLL profiles with those of purified normal B cell subpopulations indicates that the common CLL profile is more related to memory B cells than to those derived from naive B cells, CD5(+) B cells, and GC centroblasts and centrocytes. Finally, this analysis has identified a subset of genes specifically expressed by CLL cells of potential pathogenetic and clinical relevance.

B-Lymphocytes↗
PubMed2001

Atomic charges in molecular mechanical force fields: a theoretical insight.

Based on quantum theory of the Coulombic interactions between a molecule and its surrounding molecules, a theoretical derivation is presented to obtain an atomic charge model. The charge model shows that the appropriate atomic charge, used for example in molecular mechanical force fields, is simply the average value of the electrostatic potential (ESP) derived charge for an isolated molecule and that obtained for the molecule in the interaction system. Computational scheme to calculate the ESP derived atomic charges of a molecule in the interaction system is presented. The method is applied to two common liquids with associated hydrogen bonds: water and methanol. The obtained theoretical atomic charges are similar to those found in the common interaction potential models, such as: SPC, TIP3P, OPLS, etc. However, for methanol they differ considerably from those obtained using the restrained ESP method.

Journal Article↗
PubMed2001

Weighted evolving networks.

Many biological, ecological, and economic systems are best described by weighted networks, as the nodes interact with each other with varying strength. However, most evolving network models studied so far are binary, the link strength being either 0 or 1. In this paper we introduce and investigate the scaling properties of a class of models which assign weights to the links as the network evolves. The combined numerical and analytical approach indicates that asymptotically the total weight distribution converges to the scaling behavior of the connectivity distribution, but this convergence is hampered by strong logarithmic corrections.

Mathematical Computing↗
PubMed2001

CD4+ T cell recognition of a single discordant HLA-A2-transgenic molecule through the indirect antigen presentation pathway induces acute rejection of murine cardiac allografts.

To further define the role of indirect allorecognition, cardiac allografts from HLA-A2-transgenic (HLA-A2+) C57BL/6 mice were heterotopically transplanted into normal C57BL/6, CD4 T cell-knockout (KO) C57BL/6 mice, CD8 T cell-KO C57BL/6 mice, fully MHC-discordant BALB/c mice (allogeneic control), and HLA-A2+ C57BL/6 mice (syngeneic control). HLA-A2+ grafts were acutely rejected when transplanted into BALB/c mice (mean survival time: 10+/-0.8 days), normal C57BL/6 mice (mean survival time: 16.5+/-2.1 days) as well as CD8-KO mice (mean survival time: 12.8+/-1.3 days). Histopathological analysis revealed classical acute cellular rejection with moderate to severe diffuse interstitial CD4+ and CD8+ cellular infiltrates and significant intra-graft deposition of IgG and complement. In contrast, HLA-A2+ grafts were not rejected when transplanted into CD4-KO mice or HLA-A2+ mice. CD8-KO recipients treated with an anti-CD4 monoclonal antibody, but not with an anti-NK monoclonal antibody, failed to reject their allografts with prolonged administration of antibody (30 days). Spleen cells from mice rejecting HLA-A2+ allografts failed to lyse HLA-A2+ target cells indicating a lack of involvement of CD8+ T cells in the rejection process. In contrast, spleen cells from rejecting animals proliferated significantly to both HLA-A2+ cells and to a peptide derived from the HLA-A2 molecule. Development of anti-HLA-A2 antibodies was observed in all animals rejecting HLA-A2+ allografts. These results suggest that indirect allorecognition of donor MHC class I molecules leads to rejection of cardiac allografts and development of alloantibodies in this unique transplant model in which there is a single MHC discordance between donor and recipient.

Acute Disease↗
PubMed2001

Active and passive particles: modeling beads in a bacterial bath.

A simple model for the motion of passive particles in a bath of active, self-propelled ones is introduced. It is argued that this approach provides the correct framework within which to cast the recent experimental results obtained by Wu and Libchaber [Phys Rev. Lett. 84, 3017 (2000)] for the diffusive properties of polystyrene beads displaced by bacteria suspended in a two-dimensional fluid film. Our results suggest that superdiffusive behavior should indeed be generically observed in the transition region marking the onset of collective motion.

Bacterial Physiological Phenomena↗
PubMed2001

A new focal adhesion protein that interacts with integrin-linked kinase and regulates cell adhesion and spreading.

Integrin-linked kinase (ILK) is a multidomain focal adhesion (FA) protein that functions as an important regulator of integrin-mediated processes. We report here the identification and characterization of a new calponin homology (CH) domain-containing ILK-binding protein (CH-ILKBP). CH-ILKBP is widely expressed and highly conserved among different organisms from nematodes to human. CH-ILKBP interacts with ILK in vitro and in vivo, and the ILK COOH-terminal domain and the CH-ILKBP CH2 domain mediate the interaction. CH-ILKBP, ILK, and PINCH, a FA protein that binds the NH(2)-terminal domain of ILK, form a complex in cells. Using multiple approaches (epitope-tagged CH-ILKBP, monoclonal anti-CH-ILKBP antibodies, and green fluorescent protein-CH-ILKBP), we demonstrate that CH-ILKBP localizes to FAs and associates with the cytoskeleton. Deletion of the ILK-binding CH2 domain abolished the ability of CH-ILKBP to localize to FAs. Furthermore, the CH2 domain alone is sufficient for FA targeting, and a point mutation that inhibits the ILK-binding impaired the FA localization of CH-ILKBP. Thus, the CH2 domain, through its interaction with ILK, mediates the FA localization of CH-ILKBP. Finally, we show that overexpression of the ILK-binding CH2 fragment or the ILK-binding defective point mutant inhibited cell adhesion and spreading. These findings reveal a novel CH-ILKBP-ILK-PINCH complex and provide important evidence for a crucial role of this complex in the regulation of cell adhesion and cytoskeleton organization.

Actinin↗
PubMed2001

Binding of regulator of G protein signaling (RGS) proteins to phospholipid bilayers. Contribution of location and/or orientation to Gtpase-activating protein activity.

Regulator of G protein signaling (RGS) proteins must bind membranes in an orientation that permits the protein-protein interactions necessary for regulatory activity. RGS4 binds to phospholipid surfaces in a slow, multistep process that leads to maximal GTPase-activating protein (GAP) activity. When RGS4 is added to phospholipid vesicles that contain m2 or m1 muscarinic receptor and G(i), G(z), or G(q), GAP activity increases approximately 3-fold over 4 h at 30 degrees C and more slowly at 20 degrees C. This increase in GAP activity is preceded by several other events that suggest that, after binding, optimal interaction with G protein and receptor requires reorientation of RGS4 on the membrane surface, a conformational change, or both. Binding of RGS4 is initially reversible but becomes irreversible within 5 min. Onset of irreversibility parallels initial quenching of tryptophan fluorescence (t(12) approximately 30 s). Further quenching occurs after binding has become irreversible (t(12) approximately 6 min) but is complete well before maximal GAP activity is attained. These processes all appear to be energetically driven by the amphipathic N-terminal domain of RGS4 and are accelerated by palmitoylation of cysteine residues in this region. The RGS4 N-terminal domain confers similar membrane binding behavior on the RGS domains of either RGS10 or RGSZ1.

Animals↗
PubMed2001

Enantioselective synthesis and stereoselective rearrangements of enol ester epoxides.

Enol esters can be epoxidized with high enantioselectivities using the fructose-derived chiral ketone 1 as catalyst and Oxone as oxidant. A detailed study of enantiomerically enriched enol ester epoxides has revealed that the acid-catalyzed rearrangement can proceed through two distinct pathways, one with retention of configuration and the other with inversion. The competition between the two pathways is highly dependent upon the nature of the acid catalyst. A strong acid favors retention of configuration and a weak acid favors inversion of configuration. Under thermal conditions, these epoxides rearrange highly stereoselectively with inversion of configuration. Either enantiomer of an alpha-acyloxy ketone can be formed from one enantiomer of an enol ester epoxide by judicious choice of reaction conditions.

Catalysis↗
PubMed2001

Identification and kinetic analysis of the interaction between Nck-2 and DOCK180.

Nck-2 is a newly identified adapter protein comprising three N-terminal SH3 domains and one C-terminal SH2 domain. We have identified in a yeast two-hybrid screen DOCK180, a signaling protein implicated in the regulation of membrane ruffling and migration, as a binding protein for Nck-2. Surface plasmon resonance analyses reveal that the second and the third SH3 domains interact with the C-terminal region of DOCK180. The interactions mediated by the individual SH3 domains, however, are much weaker than that of the full length Nck-2. Furthermore, a point mutation that inactivates the second or the third SH3 domain dramatically reduced the interaction of Nck-2 with DOCK180, suggesting that both SH3 domains contribute to the DOCK180 binding. A major Nck-2 binding site, which is recognized primarily by the third SH3 domain, has been mapped to residues 1819-1836 of DOCK180. Two additional, albeit much weaker, Nck-2 SH3 binding sites are located to DOCK180 residues 1793-1810 and 1835-1852 respectively. Consistent with the mutational studies, kinetic analyses by surface plasmon resonance suggest that two binding events with equilibrium dissociation constants of 4.15+/-1.9x10(-7) M and 3.24+/-1.9x10(-9) M mediate the binding of GST-Nck-2 to GST fusion protein containing the C-terminal region of DOCK180. These studies identify a novel interaction between Nck-2 and DOCK180. Furthermore, they provide a detailed analysis of a protein complex formation mediated by multiple SH3 domains revealing that tandem SH3 domains significantly enhance the weak interactions mediated by each individual SH3 domain.

Amino Acid Sequence↗
PubMed2001

Src homology 3 domain-dependent interaction of Nck-2 with insulin receptor substrate-1.

Insulin receptor substrate-1 (IRS-1) is a multi-domain protein that mediates signal transduction from receptors for insulin and other growth factors to a variety of downstream molecules through both tyrosine-phosphorylation-dependent and -independent interactions. While the tyrosine-phosphorylation-dependent interactions mediated by IRS-1 have been well characterized, the molecular basis underlying the tyrosine-phosphorylation-independent IRS-1 interactions is largely unknown. We previously detected, in an in vitro binding assay, interactions of Nck-2 Src homology (SH) 3 domains with IRS-1. We show here that IRS-1 associates with Nck-2 in vivo. Additionally, we have investigated the molecular basis underlying the IRS-1-Nck-2 complex formation. We have found that (i) mutations at the highly conserved tryptophan within the Nck-2 SH3 domains markedly reduced the association with IRS-1, (ii) interactions mediated by multiple SH3 domains enhance the complex formation of Nck-2 with IRS-1, (iii) deletion of either the phosphotyrosine-binding/Shc and IRS-1 NPXY-binding (PTB/SAIN) domains or the Pre-C-terminal domain of IRS-1, but not the pleckstrin homology (PH) domain, reduced the Nck-2 binding, (iv) PTB/SAIN domains or the Pre-C-terminal domain alone is capable of interacting with Nck-2, and (v) the IRS-1-Nck-2 interaction occurs in the absence of other proteins and therefore is direct. These results establish that IRS-1 is a bona fide target of the Nck-2 SH3 domains and reveal that IRS-1 forms a complex with Nck-2 via direct interactions mediated by multiple domains from both binding partners.

Adaptor Proteins, Signal Transducing↗
PubMed2001

A study on the expression of interleukin (IL)-10 and IL-12 P35, P40 mRNA in the psoriatic lesions.

To investigate the possible role of interleukin (IL)-10 and IL-12 in the pathogenesis of psoriatic lesions and to supply theoretical basis for the gene therapy for psoriasis, the expression of IL-10 and IL-12 P35, P40 mRNA in 12 cases of psoriatic lesions and 6 normal skin tissues was detected by using RT-PCR technique. The results showed that the expression of IL-10 mRNA in the psoriatic lesions was significantly lower than that in the normal skin tissues (P < 0.001). The expression of IL-12 P35 was positive both in the psoriatic lesions and in the normal skin tissues. IL-12 P40 mRNA was expressed positively only in the psoriatic lesions but negatively in the normal skin tissues. It was suggested that IL-12 might take an important role in the occurrence and progression of psoriasis, but IL-10 might have certain role in the regression of psoriasis.

Adult↗
PubMed2001

The expression of Fas/FasL in peripheral blood lymphocytes and the level of IL-2 in serum of patients with condyloma acuminata.

In order to investigate the role of the expression of the Fas/FasL in peripheral blood lymphocytes (PBLC) and the level of IL-2 in serum of patients with condyloma acuminata (CA) in the immune pathogenesis of CA, flow cytometry, indirect immunofluorescence labeling and ELISA were performed to detect the expression of the apoptotic regulatory proteins Fas/FasL in PBLC and the level of IL-2 in serum of 60 patients with different course of CA. The results showed that the expression of Fas/FasL in PBLC of the group of short course in CA was significantly higher than that of the normal controls (P < 0.05); the expression of Fas, FasL in PBLC of the group of long course CA was significantly higher than that of the group of short course and the normal controls (P < 0.05 and P < 0.01, respectively); the level of IL-2 in serum of the group of short and long course CA was significantly lower than that of the group of normal controls (P < 0.01); the negative relation was revealed between the expression of Fas/FasL in PBLC and the level of IL-2 in serum of patients with CA (r = -0.76, P < 0.01). It was suggested that the abnormal apoptosis in PBLC and decreased level of IL-2 in serum of CA might play an important role in the course of CA.

Adolescent↗