Dissecting Oct3/4-Regulated Gene Networks in Embryonic Stem Cells by Expression Profiling

POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation (ChIP) assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks

A Genome-Wide Association Study Identified AFF1 as a Susceptibility Locus for Systemic Lupus Eyrthematosus in Japanese

Systemic lupus erythematosus (SLE) is an autoimmune disease that causes multiple organ damage. Although recent genome-wide association studies (GWAS) have contributed to discovery of SLE susceptibility genes, few studies has been performed in Asian populations. Here, we report a GWAS for SLE examining 891 SLE cases and 3,384 controls and multi-stage replication studies examining 1,387 SLE cases and 28,564 controls in Japanese subjects. Considering that expression quantitative trait loci (eQTLs) have been implicated in genetic risks for autoimmune diseases, we integrated an eQTL study into the results of the GWAS. We observed enrichments of cis-eQTL positive loci among the known SLE susceptibility loci (30.8%) compared to the genome-wide SNPs (6.9%). In addition, we identified a novel association of a variant in the AF4/FMR2 family, member 1 (AFF1) gene at 4q21 with SLE susceptibility (rs340630; P = 8.3×10−9, odds ratio = 1.21). The risk A allele of rs340630 demonstrated a cis-eQTL effect on the AFF1 transcript with enhanced expression levels (P<0.05). As AFF1 transcripts were prominently expressed in CD4+ and CD19+ peripheral blood lymphocytes, up-regulation of AFF1 may cause the abnormality in these lymphocytes, leading to disease onset

Genetics of rheumatoid arthritis contributes to biology and drug discovery

A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological datasets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)1. Here, we performed a genome-wide association study (GWAS) meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ~10 million single nucleotide polymorphisms (SNPs). We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 1012–4. We devised an in-silico pipeline using established bioinformatics methods based on functional annotation5, cis-acting expression quantitative trait loci (cis-eQTL)6, and pathway analyses7–9 – as well as novel methods based on genetic overlap with human primary immunodeficiency (PID), hematological cancer somatic mutations and knock-out mouse phenotypes – to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery

Position-Commanding Anti-Sway Controller for 2-D Overhead Cranes Under Velocity and Acceleration Constraints

This paper proposes an anti-sway controller for two-dimensional overhead cranes. The controller is of the position-commanding type, i.e., it sends position commands to the position-controlled trolley, and it uses the sensor information of the payload sway angle. The position commands are determined so that the trolley tracks the desired position signal sent from an upper-level controller and also so that the payload sway is damped. The sway damping is realized by a leaky integral controller, which employs a high-pass filtered time integral of the sway angle. In addition, arbitrary limits can be imposed on the first and second derivatives of the position command, and thus it is applicable to cases where the desired position signal from the upper-level controller is nonsmooth or discontinuous. Due to these features, the controller is expected to be useful in both human-operated and autonomous systems. The controller was validated with a laboratory setup. This paper also presents an algorithm that can be attached to the proposed controller to prevent the overshoot, which can take place when the desired position signal is discontinuous

Adsorption of pentachlorophenol to a humin-like substance-bentonite complex prepared by polycondensation reactions of humic precursors

Humic substances have natural surfactant characteristics and have a relatively high affinity for pentachlorophenol (PCP). However, humic substances cannot be loaded into bentonite (Bent) via intercalation because of their larger size. In the present study, a humin-like substance (HuLS) was prepared by polycondensation reactions of humic precursors, such as glycine and catechol, and the product was loaded into Bent. XRD patterns showed that the basal spacing, calculated from the montmorillonite peak, for the HuLS-Bent complex was larger than that for Bent itself, indicating that the intercalation of HuLS was successful. The adsorption capabilities of PCP were evaluated from adsorption isotherms at pH 4.0, 5.5 and 6.5. At all pH values, the linear adsorption coefficients of PCP, K-d (L kg(-1)), for the HuLS-Bent complex (37 at pH 6.5, 247 at pH 5.5 and 804 at pH 4.0) were significantly larger than those for Bent itself (not determined at pH 6.5,40 at pH 5.5 and 94 at pH 4.0). These results show that the adsorption capabilities of PCP can be enhanced by loading HuLS onto Bent. In addition, the K-d values for Bent and the HuLS-Bent complex were found to be pH-dependent, in that the K-d value decreased with increasing pH. Because of the pK(a) for PCP (4.75), more than 90% of the PCP was present as the anionic form at pH 5.5 and 6.5. In addition, the values for the Zeta potentials for Bent and the HuLS-Bent complex remained negative at pH 2-12 and decreased with increasing pH. It thus appears that electrostatic repulsion between the anionic form of PCP and the adsorbents can affect the adsorption capabilities. (C) 2013 Elsevier B.V. All rights reserved

Effects of reducing agents on the degradation of 2,4,6-tribromophenol in a heterogeneous Fenton-like system with an iron-loaded natural zeolite

The effects of reducing agents on the degradation of 2,4,6-tribromophennol (TrBP) were investigated in a heterogeneous Fenton-like system using an iron-loaded natural zeolite (Fe-Z). The catalytic activity for TrBP oxidation in the presence of the Fe-Z and H2O2 was not appreciable. The addition of a reducing agent, such as ascorbic acid (ASC) or hydroxylamine (NH2OH), resulted in an enhancement in the degradation and debromination of TrBP. TrBP was completely degraded and debrominated at pH 3 and 5 in the presence of NH2OH, while the degradation was significantly suppressed at pH 7 and 9. Although the rates of TrBP degradation were relatively constant at pH 3, 5, 7 and 9 in the presence of ASC, the percent degradation reached a plateau at 70%. These results show that ASC functions as a strong HO. scavenger, as opposed to NH2OH, at pH 3 and 5. Thus, adding NH2OH is preferable for the degradation of TrBP via a Fenton-like system using Fe-Z as the catalyst. It is noteworthy that the complete mineralization of TrBP was achieved at pH 5, when NH2OH and H2O2 were sequentially added to the reaction mixture. Analysis of the surface of Fe-Z by X-ray photoelectron spectrometry indicated that the Fe(III) on the surface of the catalyst was reduced to Fe(II) after treatment with ASC. Thus, the role of RAs can be of assistance in Fe(III)/Fe(II) redox cycles on the Fe-Z surface and enhance the generation of HO. via the decomposition of H2O2. (C) 2013 Elsevier B.V. All rights reserved

Effects of surface Fe(III) oxides in a steel slag on the formation of humic-like dark-colored polymers by the polycondensation of humic precursors

Carbonated furnace steel slag is effective in enhancing polycondensation reactions of humic precursors such as quinones, amino acids and saccharides. To obtain more detailed information concerning the nature of the catalytic sites on the surface of slag, a pristine slag sample was treated with HNO3, HF and NH2OH to alter the surface states. The catalytic activities for the formation of humic-like dark-colored polymers were significantly decreased for the samples treated with HNO3 or HF compared to untreated slag. Because substantial amounts of iron were eluted as the result of the HNO3 and HF treatments, the minerals remaining on the surface of steel slag were characterized by XRD and SEM, and the results were compared with untreated slag. XRD patterns indicated the significant decrease in Fe(III) oxide content, including magnetite and hematite, as the result of the HNO3 and HF treatment. In addition, when untreated slag was reacted with humic precursors, the hematite and magnetite were largely eluted as a result of the reaction. These results support the conclusion that Fe(III)-oxides on the surface of steel slag, such as hematite and magnetite, serve as catalytic sites for enhancing catalytic activity for the formation of humic-like dark colored-polymers from humic precursors