Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays ad gene expression arrays

Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prognosis has not significantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technologies-single nucleotide polymor-phism (SNP) array and gene expression array-with gene motifs considered transcription factor-binding sites (TFBS). We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS. The potential regulation of SNP-containing motifs affects only when certain mutations occur. These motifs can be identified from a group of co-expressed genes with copy number variation. Then, we used a sliding window to identify motif candidates near SNPs on gene sequences. The candidates were filtered by coarse thresholding and fine statistical testing. Using the regression. based LARS-EN algorithm and a level. wise sequence combination procedure, we identified 28 SNP-containing motifs as candidate TFBS. We confirmed 21 of the 28 motifs with ChIP-chip fragments in the TRANSFAC database. Another six motifs were validated by TRANSFAC via searching binding fragments on co-regulated genes. The identified motifs and their location genes can be considered potential biomarkers for myelodysplastic syndromes. Thus, our proposed method, a novel strategy for associating two data categories, is capable of integrating information from different sources to identify reliable candidate regulatory SNP-containing motifs introduced by genetic variation and mutation

Chemical ordering in PtNi nanocrystals

We investigated the chemical ordering in PtNi nanocrystals fabricated on sapphire substrate using in-situ synchrotron X-ray scattering. Nanocrystals with composition close to 1:1 were ordered in the tetragonal L1(0) structure at low temperatures. The transition to disordered FCC structure occurred at around 640 degrees C and substantial hysteresis of about 50 K was observed. Nanocrystals of smaller sizes fabricated under the same conditions were Ni rich and ordered into Cu3Au type L1(2) structure. Significantly higher degree of chemical ordering was observed in L1(2) structure than in L1(0) structure. (C) 2016 Elsevier B.V. All rights reserved.1144Ysciescopu

Initial validation of Chinese Pain Assessment in Advanced Dementia Scale (C-PAINAD)

2007-2008 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

C5 Extract Induces Apoptosis in B16F10 Murine Melanoma Cells through Extrinsic and Intrinsic Apoptotic Pathways and Sub-G1 Phase Arrest

Purpose: To investigate the anti-cancer activities of C5 extract (C5E), a new herbal preparation from Korea, on B16F10 cells.Methods: The anti-proliferative effects of C5E were assessed by culturing B16F10 cells in the presence or absence of C5E. Cell cycle progression was analyzed by PI staining using flow cytometry. The quantities of apoptosis-inducing proteins were measured by Western blot.Results: C5E inhibited the proliferation of B16F10 cells but not human keratinocytes. C5E induced S phase arrest by interfering with cell regulatory factors such as cyclins B1, D1, D3, and E, and cyclindependent kinase 2, in B16F10 cells. Furthermore, immunoblot analysis confirmed that treatment with C5E induced apoptosis and cleaved caspase-3, poly (ADP-ribose) polymerase, via extrinsic pathway, whereas Bcl-2 expression was down-regulated. In addition, the suppression of cell proliferation by C5E is through down-regulation of p-Akt, up-regulation of phosphatase and tensin homolog protein expression via phosphoinositol 3 kinase survival signaling pathways in B16F10 cells. The combined cytotoxic effects of C5E and vinblastine generated 10 % increase in activity in contrast to the sum of the inhibitory effects of the individual agents.Conclusion: C5E shows promising anti-cancer activity and can be a useful adjuvant with vinblastine in combination therapeutic treatment of skin cancer.Keywords: Melanoma, Apoptosis, Anti-cancer, p53, Vinblastine, Cell cycle arrest, Caspas

Respiratory viral infections in exacerbation of chronic airway inflammatory diseases: novel mechanisms and insights from the upper airway epithelium.

Respiratory virus infection is one of the major sources of exacerbation of chronic airway inflammatory diseases. These exacerbations are associated with high morbidity and even mortality worldwide. The current understanding on viral-induced exacerbations is that viral infection increases airway inflammation which aggravates disease symptoms. Recent advances in in vitro air-liquid interface 3D cultures, organoid cultures and the use of novel human and animal challenge models have evoked new understandings as to the mechanisms of viral exacerbations. In this review, we will focus on recent novel findings that elucidate how respiratory viral infections alter the epithelial barrier in the airways, the upper airway microbial environment, epigenetic modifications including miRNA modulation, and other changes in immune responses throughout the upper and lower airways. First, we reviewed the prevalence of different respiratory viral infections in causing exacerbations in chronic airway inflammatory diseases. Subsequently we also summarized how recent models have expanded our appreciation of the mechanisms of viral-induced exacerbations. Further we highlighted the importance of the virome within the airway microbiome environment and its impact on subsequent bacterial infection. This review consolidates the understanding of viral induced exacerbation in chronic airway inflammatory diseases and indicates pathways that may be targeted for more effective management of chronic inflammatory diseases

Quasi-Two-Dimensional Heterostructures (KM1 – xTe)(LaTe3) (M = Mn and Zn) with Charge Density Waves

Layered heterostructure materials with two different functional building blocks can teach us about emergent physical properties and phenomena arising from interactions between the layers. We report intergrowth compounds KLaM1 – xTe4 (M = Mn and Zn; x ≈ 0.35) featuring two chemically distinct alternating layers [LaTe3] and [KM1 – xTe]. Their crystal structures are incommensurate, determined by single X-ray diffraction for the Mn compound and a transmission electron microscope study for the Zn compound. KLaMn1 – xTe4 crystallizes in the orthorhombic superspace group Pmnm(01/2γ)s00 with lattice parameters a = 4.4815(3) Å, b = 21.6649(16) Å, and c = 4.5220(3) Å. It exhibits charge density wave order at room temperature with a modulation wave vector q = 1/2b* + 0.3478c* originating from electronic instability of Te-square nets in [LaTe3] layers. The Mn analog exhibits a cluster spin glass behavior with spin freezing temperature Tf ≈ 5 K attributed to disordered Mn vacancies and competing magnetic interactions in the [Mn1 – xTe] layers. The Zn analog also has charge density wave order at room temperature with a similar q-vector having the c* component ∼0.346 confirmed by selected-area electron diffraction. Electron transfer from [KM1 – xTe] to [LaTe3] layers exists in KLaM1 – xTe4, leading to an enhanced electronic specific heat coefficient. The resistivities of KLaM1 – xTe4 (M = Mn and Zn) exhibit metallic behavior at high temperatures and an upturn at low temperatures, suggesting partial localization of carriers in the [LaTe3] layers with some degree of disorder associated with the M atom vacancies in the [M1 – xTe] layers

The subchalcogenides Ir₂In₈Q (Q = S, Se, Te): Dirac semimetal candidates with re-entrant structural modulation

Subchalcogenides are uncommon compounds where the metal atoms are in unusually low formal oxidation states. They bridge the gap between intermetallics and semiconductors, and can have unexpected structures and properties because of the exotic nature of their chemical bonding, as they contain both metal-metal and metal-main group (e.g. halide, chalcogenide) interactions. Finding new members of this class of materials presents synthetic challenges, as attempts to make them often result in phase separation into binary compounds. We overcome this difficulty by utilizing indium as a metal flux to synthesize large (mm scale) single crystals of novel subchalcogenide materials. Herein, we report two new compounds Ir2In8Q (Q = Se, Te) and compare their structural and electrical properties to the previously reported Ir2In8S analogue. Ir2In8Se and Ir2In8Te crystallize in the P42/mnm space group and are isostructural to Ir2In8S but also have commensurately modulated (with q-vectors q = 1/6a* + 1/6b* and q= 1/10a* + 1/10b* for Ir2In8Se and Ir2In8Te, respectively) low temperature phase transitions, where the chalcogenide anions in the channels experience a distortion in the form of In-Q bond alternation along the ab plane. Both compounds display re-entrant structural behavior, where the supercells appear on cooling but revert to the original subcell below 100 K, suggesting competing structural and electronic interactions dictate the overall structure. Notably, these materials are topological semimetal candidates with symmetry-protected Dirac crossings near the Fermi level, and exhibit high electron mobilities (~1500 cm2 V-1 s-1 at 1.8 K) and moderate carrier concentrations (~1020 cm-3) from charge transport measurements. This work highlights metal flux as a powerful synthetic route to high quality single crystals of novel intermetallic subchalcogenides

A two-dimensional type I superionic conductor

Superionic conductors possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I superionic conductors (for example, AgI, Ag2Se and so on) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I superionic conductor, α-KAg3Se2, by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag+ ions are confined to subnanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that compose the immobile charge-balancing layers. Our work thus extends the known classes of superionic conductors and will facilitate the design of new materials with tailored ionic conductivities and phase transitions

Kinetic roughening of ion-sputtered Pd(001) surface: Beyond the Kuramoto-Sivashinsky model

The kinetic roughening of Ar+ ion-sputtered Pd(001) surface was investigated. The facet formation on the sputtered surface was studied by tracing the extradiffraction peaks or satellites around the diffraction peaks corresponding to the sample surface. The morphological evolution of the sputtered Pd(001) surface was also investigated by an scanning tunneling microscopy (STM). It was shown that the nanoscale adatom islands form and grow with increasing sputter time.open313

Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.

Obesity-associated insulin resistance plays a central role in type 2 diabetes. As such, tyrosine phosphatases that dephosphorylate the insulin receptor (IR) are potential therapeutic targets. The low-molecular-weight protein tyrosine phosphatase (LMPTP) is a proposed IR phosphatase, yet its role in insulin signaling in vivo has not been defined. Here we show that global and liver-specific LMPTP deletion protects mice from high-fat diet-induced diabetes without affecting body weight. To examine the role of the catalytic activity of LMPTP, we developed a small-molecule inhibitor with a novel uncompetitive mechanism, a unique binding site at the opening of the catalytic pocket, and an exquisite selectivity over other phosphatases. This inhibitor is orally bioavailable, and it increases liver IR phosphorylation in vivo and reverses high-fat diet-induced diabetes. Our findings suggest that LMPTP is a key promoter of insulin resistance and that LMPTP inhibitors would be beneficial for treating type 2 diabetes