Genome-wide analyses identify KLF4 as an important negative regulator in T-cell acute lymphoblastic leukemia through directly inhibiting T-cell associated genes

é 2015 Li et al. Background: Kruppel-like factor 4 (KLF4) induces tumorigenesis or suppresses tumor growth in a tissue-dependent manner. However, the roles of KLF4 in hematological malignancies and the mechanisms of action are not fully understood. Methods: Inducible KLF4-overexpression Jurkat cell line combined with mouse models bearing cell-derived xenografts and primary T-cell acute lymphoblastic leukemia (T-ALL) cells from four patients were used to assess the functional role of KLF4 in T-ALL cells in vitro and in vivo. A genome-wide RNA-seq analysis was conducted to identify genes regulated by KLF4 in T-ALL cells. Chromatin immunoprecipitation (ChIP) PCR was used to determine direct binding sites of KLF4 in T-ALL cells. Results: Here we reveal that KLF4 induced apoptosis through the BCL2/BCLXL pathway in human T-ALL cell lines and primary T-ALL specimens. In consistence, mice engrafted with KLF4-overexpressing T-ALL cells exhibited prolonged survival. Interestingly, the KLF4-induced apoptosis in T-ALL cells was compromised in xenografts but the invasion capacity of KLF4-expressing T-ALL cells to hosts was dramatically dampened. We found that KLF4 overexpression inhibited T cell-associated genes including NOTCH1, BCL11B, GATA3, and TCF7. Further mechanistic studies revealed that KLF4 directly bound to the promoters of NOTCH1, BCL2, and CXCR4 and suppressed their expression. Additionally, KLF4 induced SUMOylation and degradation of BCL11B. Conclusions: These results suggest that KLF4 as a major transcription factor that suppresses the expression of T-cell associated genes, thus inhibiting T-ALL progression.Link_to_subscribed_fulltex

Rh-Based Mixed Alcohol Synthesis Catalysts: Characterization and Computational Report

The U.S. Department of Energy is conducting a program focused on developing a process for the conversion of biomass to bio-based fuels and co-products. Biomass-derived syngas is converted thermochemically within a temperature range of 240 to 330°C and at elevated pressure (e.g., 1200 psig) over a catalyst. Ethanol is the desired reaction product, although other side compounds are produced, including C3 to C5 alcohols; higher (i.e., greater than C1) oxygenates such as methyl acetate, ethyl acetate, acetic acid and acetaldehyde; and higher hydrocarbon gases such as methane, ethane/ethene, propane/propene, etc. Saturated hydrocarbon gases (especially methane) are undesirable because they represent a diminished yield of carbon to the desired ethanol product and represent compounds that must be steam reformed at high energy cost to reproduce CO and H2. Ethanol produced by the thermochemical reaction of syngas could be separated and blended directly with gasoline to produce a liquid transportation fuel. Additionally, higher oxygenates and unsaturated hydrocarbon side products such as olefins also could be further processed to liquid fuels. The goal of the current project is the development of a Rh-based catalyst with high activity and selectivity to C2+ oxygenates. This report chronicles an effort to characterize numerous supports and catalysts to identify particular traits that could be correlated with the most active and/or selective catalysts. Carbon and silica supports and catalysts were analyzed. Generally, analyses provided guidance in the selection of acceptable catalyst supports. For example, supports with high surface areas due to a high number of micropores were generally found to be poor at producing oxygenates, possibly because of mass transfer limitations of the products formed out of the micropores. To probe fundamental aspects of the complicated reaction network of CO with H2, a computational/ theoretical investigation using quantum mechanical and ab initio molecular dynamics calculations was initiated in 2009. Computational investigations were performed first to elucidate understanding of the nature of the catalytically active site. Thermodynamic calculations revealed that Mn likely exists as a metallic alloy with Rh in Rh-rich environments under reducing conditions at the temperatures of interest. After determining that reduced Rh-Mn alloy metal clusters were in a reduced state, the activation energy barriers of numerous transition state species on the catalytically active metal particles were calculated to compute the activation barriers of several reaction pathways that are possible on the catalyst surface. Comparison of calculations with a Rh nanoparticle versus a Rh-Mn nanoparticle revealed that the presence of Mn enabled the reaction pathway of CH with CO to form an adsorbed CHCO species, which was a precursor to C2+ oxygenates. The presence of Mn did not have a significant effect on the rate of CH4 production. Ir was observed during empirical catalyst screening experiments to improve the activity and selectivity of Rh-Mn catalysts. Thus, the addition of Ir to the Rh-Mn nanoparticles also was probed computationally. Simulations of Rh-Mn-Ir nanoparticles revealed that, with sufficient Ir concentrations, the Rh, Mn and Ir presumably would be well mixed within a nanoparticle. Activation barriers were calculated for Rh-Mn-Ir nanoparticles for several C-, H-, and O-containing transitional species on the nanoparticle surface. It was found that the presence of Ir opened yet another reactive pathway whereby HCO is formed and may undergo insertion with CHx surface moieties. The reaction pathway opened by the presence of Ir is in addition to the CO + CH pathway opened by the presence of Mn. Similar to Mn, the presence of Ir was not found to not affect the rate of CH4 production

Quantitative evaluation of the immunodeficiency of a mouse strain by tumor engraftments

© 2015 Ye et al. Background: The mouse is an organism that is widely used as a mammalian model for studying human physiology or disease, and the development of immunodeficient mice has provided a valuable tool for basic and applied human disease research. Following the development of large-scale mouse knockout programs and genome-editing tools, it has become increasingly efficient to generate genetically modified mouse strains with immunodeficiency. However, due to the lack of a standardized system for evaluating the immuno-capacity that prevents tumor progression in mice, an objective choice of the appropriate immunodeficient mouse strains to be used for tumor engrafting experiments is difficult. Methods: In this study, we developed a tumor engraftment index (TEI) to quantify the immunodeficiency response to hematologic malignant cells and solid tumor cells of six immunodeficient mouse strains and C57BL/6 wild-type mouse (WT). Results: Mice with a more severely impaired immune system attained a higher TEI score. We then validated that the NOD-scid-IL2Rg-/- (NSI) mice, which had the highest TEI score, were more suitable for xenograft and allograft experiments using multiple functional assays. Conclusions: The TEI score was effectively able to reflect the immunodeficiency of a mouse strain.Link_to_subscribed_fulltex

First-Principles-Based Kinetic Monte Carlo Simulation of Nitric Oxide Reduction over Platinum Nanoparticles under Lean-Burn Conditions

This article discusses first-principles-based kinetic Monte Carlo simulation of Nitric Oxide reduction

Reactivity of hydrogen and methanol on (0 0 1) surfaces of WO₃, ReO₃, WO₃/ReO₃ and ReO₃/WO ₃

Bulk tungsten trioxide (WO3) and rhenium trioxide (ReO3) share very similar structures but display different electronic properties. WO3 is a wide bandgap semiconductor while ReO3 is an electronic conductor. With the advanced molecular beam epitaxy techniques, it is possible to make heterostructures comprised of layers of WO3 and ReO3. These heterostructures might display reactivity different than pure WO3 and ReO3. The interactions of two probe molecules (hydrogen and methanol) with the (0 0 1) surfaces of WO3, ReO3, and two heterostructures ReO3/WO3 and WO3/ReO3 were investigated at the density functional theory level. Atomic hydrogen prefers to adsorb at the mono-coordinated O (O-1C) sites forming a surface hydroxyl on four surfaces. Dissociative adsorption of a hydrogen molecule at the O-1C site leads to formation of a water molecule adsorbed at the penta-coordinated metal (M-5C) site. This is thermodynamically the most stable state. A thermodynamically less stable dissociative state involves two surface hydroxyl groups O1CH and O2CH. The interaction of molecular hydrogen and methanol with pure ReO3 is stronger than with pure WO3 and the strength of the interaction substantially changes on the WO3/ReO3 and ReO3/WO3 heterostructures. The reaction barriers for decomposition and recombination reactions are sensitive to the nature of heterostructure. The calculated adsorption energy of methanol on WO3(001) of -65.6 kJ/mol is consistent with the previous experimental estimation of -67 kJ/mol. (c) 2011 Elsevier B.V. All rights reserved

Catalyst size and morphological effects on the interaction of NO2 with BaO/gamma-Al2O3 materials

The capability of NOx storage on the supported BaO catalyst largely depends on the Ba loading. With different Ba loadings, the supported BaO component exposes various phases ranging from well-dispersed nanoclusters to large crystalline particles on the oxide support materials. In order to better understand size and morphological effects on NO storage over gamma-Al2O3-supported BaO materials, the adsorption structures and energetics of single NO2 molecule, as well as NOx + NOy (NO2 + NO2, NO + NO3 and NO2 + NO3) pairs on the BaO/gamma-Al2O3(1 0 0), (BaO)(2)/gamma-Al2O3(1 00), and (BaO)(S)/gamma-Al2O3(1 0 0) surfaces were investigated using first-principles density functional theory calculations. A single NO2 molecule prefers to adsorb at basic O-Ba site forming anionic nitrate species. Upon adsorption, a charge redistribution in the supported (BaO)(n) clusters occurs. Synergistic effects due to the interaction of NO2 with both the (BaO)(n) clusters and the gamma-Al2O3(1 0 0) support enhance the stability of adsorbed NO2. The interaction between NO2 and the (BaO)(n)/gamma-Al2O3(1 0 0) catalysts was found to be markedly affected by the sizes and morphologies of the supported (BaO),, clusters. The adsorption energy of NO2 increases from -0.98 eV on the BaO/gamma-Al2O3(1 0 0) surface to -3.01 eV on (BaO)(5)/-Al2O3(1 00). NO2 adsorption on (BaO)(2) clusters in a parallel configuration on the gamma-Al2O3(1 0 0) surface is more stable than on dimers oriented in a perpendicular fashion. Similar to the bulk BaO(1 0 0) surface, a supported (BaO)(n) cluster-mediated electron transfer induces cooperative effects that dramatically increase the total adsorption energy of NOx + NOy pairs on the (BaO)(n)/gamma-Al2O3(1 0 0) surfaces. Following the widely accepted NO2 storage mechanism of BaO + 3NO(2)(g) -> Ba(NO3)(2) + NO(g), our thermodynamic analysis indicates that the largest energy gain for this overall process of NO uptake is obtained on the amorphous monolayer-like (BaO)(5)/gamma-Al2O3(1 0 0) surface. This suggests that gamma-Al2O3-supported BaO materials with similar to 6-12 wt% loadings may provide optimum structures for NOx storage. (C) 2010 Elsevier B.V. All rights reservedclose7