Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE) time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble the dynamics of known immediate-early genes (IEGs) and this enables a comprehensive comparative study of these genes and their chromatin state. Surprisingly, these data suggest that the earliest transcriptional responses often involve promoters generating non-coding RNAs, many of which are produced in advance of canonical protein-coding IEGs. IEGs are known to be capable of induction without de novo protein synthesis. Consistent with this, we find that the response of both protein-coding and non-coding RNA IEGs can be explained by their transcriptionally poised, permissive chromatin state prior to stimulation. We also explore the function of non-coding RNAs in the attenuation of the immediate early response in a small RNA sequencing dataset matched to the CAGE data: We identify a novel set of microRNAs responsible for the attenuation of the IEG response in an estrogen receptor positive cancer cell line. Our computational statistical method is well suited to meta-analyses as there is no requirement for transcripts to pass thresholds for significant differential expression between time points, and it is agnostic to the number of time points per dataset.

Thermostable small-molecule inhibitor of angiogenesis and vascular permeability that suppresses a pERK-FosB/ΔFosB-VCAM-1 axis.

Vascular permeability and angiogenesis underpin neovascular age-related macular degeneration and diabetic retinopathy. While anti-VEGF therapies are widely used clinically, many patients do not respond optimally, or at all, and small-molecule therapies are lacking. Here, we identified a dibenzoxazepinone BT2 that inhibits endothelial cell proliferation, migration, wound repair in vitro, network formation, and angiogenesis in mice bearing Matrigel plugs. BT2 interacts with MEK1 and inhibits ERK phosphorylation and the expression of FosB/ΔFosB, VCAM-1, and many genes involved in proliferation, migration, angiogenesis, and inflammation. BT2 reduced retinal vascular leakage following rat choroidal laser trauma and rabbit intravitreal VEGF-A165 administration. BT2 suppressed retinal CD31, pERK, VCAM-1, and VEGF-A165 expression. BT2 reduced retinal leakage in rats at least as effectively as aflibercept, a first-line therapy for nAMD/DR. BT2 withstands boiling or autoclaving and several months' storage at 22°C. BT2 is a new small-molecule inhibitor of vascular permeability and angiogenesis.

Influence of Mg/CTAB ratio on the structural, physicochemical properties and catalytic activity of amorphous mesoporous magnesium silicate catalysts.

This study investigated the physicochemical and catalytic properties of mesoporous magnesium silicate catalysts prepared at various Mg/CTAB ratios (0.25, 0.50, 0.75 and 1.00). The XPS analysis detected a mixture of enstatite and magnesium carbonate species when the Mg/CTAB ratio was 0.25, and 0.50. A mixture of forsterite and magnesium carbonate species were detected when the Mg/CTAB ratio was 0.75 whereas for the Mg/CTAB ratio of 1.00, enstatite and magnesium metasilicate species were detected. A catalyst with the Mg/CTAB ratio of 1.00 demonstrated the highest catalytic activity in the oxidation of styrene. The styrene conversion rate was 59.0%, with 69.2% styrene oxide (StO) selectivity. The H2O2 molecules were activated regio-specifically by the magnesium species to prevent rapid self-decomposition while promoting selective interaction with styrene. All the parameters that influence the styrene conversion and product selectivity were evaluated using analysis of variance (ANOVA) with Tukey's test. The ANOVA analysis showed that the reaction time (h), Mg/CTAB ratio, styrene/H2O2 ratio, catalyst loading (mg) and temperature (°C) affect styrene conversion and product selectivity (StO) significantly (p < 0.05). The oxidation of styrene was well fitted to the pseudo-first-order model. The activation energy, E a of the catalysed styrene epoxidation reaction was calculated to be 27.7 kJmol-1. The catalyst can be reused several times without any significant loss in its activity and selectivity. The results from this study will be useful in designing and developing low cost, high activity catalysts from alkaline earth metals.

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1ß.

Smooth muscle cells (SMC) in blood vessels are normally growth quiescent and transcriptionally inactive. Our objective was to understand promoter usage and dynamics in SMC acutely exposed to a prototypic growth factor or pro-inflammatory cytokine. Using cap analysis gene expression (FANTOM5 project) we report differences in promoter dynamics for immediate-early genes (IEG) and other genes when SMC are exposed to fibroblast growth factor-2 or interleukin-1ß. Of the 1871 promoters responding to FGF2 or IL-1ß considerably more responded to FGF2 (68.4%) than IL-1ß (18.5%) and 13.2% responded to both. Expression clustering reveals sets of genes induced, repressed or unchanged. Among IEG responding rapidly to FGF2 or IL-1ß were FOS, FOSB and EGR-1, which mediates human SMC migration. Motif activity response analysis (MARA) indicates most transcription factor binding motifs in response to FGF2 were associated with a sharp induction at 1 h, whereas in response to IL-1ß, most motifs were associated with a biphasic change peaking generally later. MARA revealed motifs for FOS_FOS{B,L1}_JUN{B,D} and EGR-1..3 in the cluster peaking 1 h after FGF2 exposure whereas these motifs were in clusters peaking 1 h or later in response to IL-1ß. Our findings interrogating CAGE data demonstrate important differences in promoter usage and dynamics in SMC exposed to FGF2 or IL-1ß.

Microcolumn studies of dye adsorption onto manganese oxides modified diatomite.

The method described here cannot fully replace the analysis of large columns by small test columns (microcolumns). The procedure, however, is suitable for speeding up the determination of adsorption parameters of dye onto the adsorbent and for speeding up the initial screening of a large adsorbent collection that can be tedious if a several adsorbents and adsorption conditions must be tested. The performance of methylene blue (MB), a basic dye, Cibacron reactive black (RB) and Cibacron reactive yellow (RY) was predicted in this way and the influence of initial dye concentration and other adsorption conditions on the adsorption behaviour were demonstrated. On the basis of the experimental results, it can be concluded that the adsorption of RY onto manganese oxides modified diatomite (MOMD) exhibited a characteristic "S" shape and can be simulated effectively by the Thomas model. It is shown that the adsorption capacity increased as the initial dye concentration increased. The increase in the dye uptake capacity with the increase of the adsorbent mass in the column was due to the increase in the surface area of adsorbent, which provided more binding sites for the adsorption. It is shown that the use of high flow rates reduced the time that RY in the solution is in contact with the MOMD, thus allowing less time for adsorption to occur, leading to an early breakthrough of RY. A rapid decrease in the column adsorption capacity with an increase in particle size with an average 56% reduction in capacity resulting from an increase in the particle size from 106-250 microm to 250-500 microm. The experimental data correlated well with calculated data using the Thomas equation and the bed depth-service time (BDST) equation. Therefore, it might be concluded that the Thomas equation and the BDST equations can produce accurate predication for variation of dye concentration, mass of the adsorbent, flow rate and particle size. In general, the values of adsorption isotherm capacity obtained in a batch system show the maximum values and are considerably higher than those obtained in a fixed-bed.

Alpha-Glucosidase Enzyme Biosensor for the Electrochemical Measurement of Antidiabetic Potential of Medicinal Plants.

A biosensor for measuring the antidiabetic potential of medicinal plants was developed by covalent immobilization of α-glucosidase (AG) enzyme onto amine-functionalized multi-walled carbon nanotubes (MWCNTs-NH2). The immobilized enzyme was entrapped in freeze-thawed polyvinyl alcohol (PVA) together with p-nitrophenyl-α-D-glucopyranoside (PNPG) on the screen-printed carbon electrode at low pH to prevent the premature reaction between PNPG and AG enzyme. The enzymatic reaction within the biosensor is inhibited by bioactive compounds in the medicinal plant extracts. The capability of medicinal plants to inhibit the AG enzyme on the electrode correlates to the potential of the medicinal plants to inhibit the production of glucose from the carbohydrate in the human body. Thus, the inhibition indicates the antidiabetic potential of the medicinal plants. The performance of the biosensor was evaluated to measure the antidiabetic potential of three medicinal plants such as Tebengau (Ehretis laevis), Cemumar (Micromelum pubescens), and Kedondong (Spondias dulcis) and acarbose (commercial antidiabetic drug) via cyclic voltammetry, amperometry, and spectrophotometry. The cyclic voltammetry (CV) response for the inhibition of the AG enzyme activity by Tebengau plant extracts showed a linear relation in the range from 0.423-8.29 µA, and the inhibition detection limit was 0.253 µA. The biosensor exhibited good sensitivity (0.422 µA/mg Tebengau plant extracts) and rapid response (22 s). The biosensor retains approximately 82.16 % of its initial activity even after 30 days of storage at 4 °C.

Effect of OH and silanol groups in the removal of dyes from aqueous solution using diatomite.

The removal of methylene blue, reactive black (C-NN), and reactive yellow (MI-2RN) from aqueous solution by calcined and raw diatomite at 980 degrees C was studied. These studies demonstrated the importance of the various functional groups on the mechanism of adsorption. The role of pore size distribution in the dye adsorption studies was also investigated. The adsorption isotherms were pH dependent. Henry and Freundlich adsorption isotherms were used to model the adsorption behavior and experimental results for all dyes used exhibited heterogeneous surface binding. The removal of the ionisable functional groups increased the pH(ZPC) value from 5.4 to 7.7, while FTIR, SEM and XRD analysis showed a remarkable decrease of the characteristic Si-OH peaks after calcinations at 980 degrees C. The removal of hydroxyl groups from the surface of diatomite lead to a decrease in the adsorption. It was evident from pH and infrared spectra results that mechanisms of methylene blue and reactive yellow adsorption differed from that of reactive black. Accordingly, adsorption on the external surface by n-pi interaction between the pi system of the RB and the electron lone pairs of the oxygen atoms of siloxane group and columbic attraction between the dye and the surface of calcined diatomite was proposed as a possible adsorption mechanism.

Thermodynamic behaviour and the effect of temperature on the removal of dyes from aqueous solution using modified diatomite: a kinetic study.

The effect of solution temperature and the determination of the thermodynamic parameters of adsorption of methylene blue (MB), Cibacron Reactive black C-NN (RB) and Cibacron Reactive golden yellow MI-2RN (RY) onto manganese-oxides-modified diatomite (MOMD), such as activation energy, E, enthalpy of activation, DeltaH*, entropy of activation, DeltaS*, and free energy of activation, DeltaG*, on the adsorption rates is important in understanding the adsorption mechanism. The rate and the transport/kinetic processes of dye adsorption onto the adsorbents were described by applying various kinetic adsorption models. This would lead to a better understanding of the mechanisms controlling the adsorption rate. The pseudo-second-order model was the best choice among all the kinetic models to describe the adsorption behaviour of RB onto MOMD, suggesting that the adsorption mechanism might be a chemisorption process. The activation energies, E, for RB, RY and MB were -6.74, 56.65 and 99.80 kJ/mol, respectively. The negative value of the activation energy suggested that the rise in the solution temperature did not favour RB adsorption onto MOMD. Moreover, the activation energy of the diffusion process, E', for RB, RY and MB increased as MB > RY >> RB. It means that the RB molecules are much faster moving and a lower energy is needed to diffuse into MOMD than RY and MB molecules. E', the activation energy for adsorption into pores, of RY is higher than E, indicating that the rate-limiting step of RY adsorption onto MOMD might be diffusion controlled, while the activation energy of the diffusion process, E', of MB is slightly lower than E, suggesting that the rate-limiting step is a combination of chemical and diffusion adsorption.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

Chloroquine polymeric membrane electrodes: Development and applications.

Three main types of PVC solvent polymeric membrane ion-selective electrodes for chloroquine are described. They are based on three ion-pairing agents namely dipicrylamine (DPA), tetraphenylborate (TPB) or tetrakis(4-chlorophenyl)borate (TCPB) with either dioctylphenyl phosphonate (DOPP) or trioctyl phosphate (TOP) solvent mediator. All electrodes exhibit Nernstian responses, fast dynamic response times and a wide useful pH range. The best all-round electrode is based on TPB and TOP plasticizing solvent mediators with a limit of detection of 7.1 x 10(-6)M and was utilized for the assay of chloroquine in tablets. Direct potentiometric determinations with either the analyte addition method or the normal calibration method gave results comparable to the official method.

The effect of pH, temperature, and molecular size on the removal of dyes from textile effluent using manganese oxides-modified diatomite.

This work is an investigation on the use of manganese oxides-modified diatomite (MOMD) for the removal of color from textile wastewaters. The modification of the diatomite was carried out by treatment with manganese oxides; delta-bimessite type resulted. The surface area, pH(ZPC), Fourier transform infrared (FTIR), and scanning electron microscopy of MOMD were studied. The influence of concentration, pH, particle size, and temperature on the adsorption capacities of methylene blue (MB) and hydrolyzed reactive black (RB) and reactive yellow (RY) was investigated. Key thermodynamic parameters such as deltaH degrees, deltaS degrees, and deltaG degrees were also determined. The deltaH degrees of MB and hydrolyzed RB and RY was +94.64, -143.1, and -38.78 kJ/mol, respectively, whereas the deltaG degrees values of -17.68, -27.93, and -23.26 kJ/mol were obtained, indicating a spontaneous process with low activation-energy requirements. The findings further indicated that coulomb interaction, molecular size, and orientation of the dye and its surface charge played an important role in the adsorption and attachment of the dyes to the bimessite layers of MOMD.

The adsorption of heavy metal by Bornean oil palm shell and its potential application as constructed wetland media.

Oil palm shell, a waste from palm oil industry, was cleaned and utilized as adsorbent. Its particle size distribution gave the uniformity coefficient of approximately two indicating that it can be used as filter bed media for continuous operation without resting. Its measured pH(pzc) of 4.1 is below the common pH of constructed wetland water body suggesting positive adsorption for heavy metal. The effect of various parameters on its adsorption was studied via batch experiments. The adsorption of Cu(II) and Pb(II) ions by oil palm shell showed a slightly better fit with the Freundlich compared to Langmuir. Its monolayer adsorption capacities were found to be 1.756 and 3.390mg/g for Cu(II) and Pb(II), respectively. High correlation coefficient of over 0.99 given by the pseudo-second-order model suggests that the rate limiting factor may be chemisorption. These findings suggest its potential application as constructed wetland media for the removal of heavy metal.

Adsorption characteristics of reactive dyes in columns of activated carbon.

Adsorption behaviour of reactive dyes in fixed-bed adsorber was evaluated in this work. The characteristics of mass transfer zone (MTZ), where adsorption in column occurs, were affected by carbon bed depth and influent dye concentration. The working lifetime (t(x)) of MTZ, the height of mass transfer zone (HMTZ), the rate of mass transfer zone (RMTZ), and the column capacity at exhaustion (q(column)) were estimated for the removal of remazol reactive yellow and remazol reactive black by carbon adsorber. The results showed that column capacity calculated at 90% of column exhaustion was lower than carbon capacity obtained from equilibrium studies. This indicated that the capacity of activated carbon was not fully utilized in the fixed-bed adsorber. The bed-depth service time model (BDST) was applied for analysis of reactive yellow adsorption in the column. The adsorption capacity of reactive yellow calculated at 50% breakthrough point (N(0)) was found to be 0.1 kg kg(-1) and this value is equivalent to about 14% of the available carbon capacity. The results of this study indicated the applicability of fixed-bed adsorber for removing remazol reactive yellow from solution.

Magnetization transfer imaging diagnosis of intracranial tuberculomas.

Tuberculomas (TB) can mimic brain tumors and abscesses. We performed prospective magnetization transfer ratio (MTR) analysis on 60 patients with 52 intracranial TB, 13 pyogenic abscesses and 65 tumors to determine the efficacy of magnetization transfer (MT) imaging in the differential diagnosis of brain tumors and infection. The nonenhancing cores of TB had significantly higher (P=.026) MTR (0.14+/-0.29) than necrotic components of high-grade gliomas (-0.19+/-0.22). The MTR of cores of TB were also higher than those of the cystic areas of low-grade gliomas (-0.53+/-0.32), benign (-0.09+/-0.21) and malignant (-0.07+/-0.25) tumors, and abscesses (-0.03+/-0.13), but the differences were not significant because of the small number of tumors and abscesses. There was also no significant difference between the MTR of abscesses, malignant and benign tumors. Using the criteria of MTR of necrotic center > 0.14 (mean MTR of TB) for diagnosing TB, MTR <-0.03 (mean MTR of abscesses) for diagnosing tumors and MTR between these values for diagnosing abscesses, MTI had diagnostic sensitivity of 68.42%, specificity of 80.49%, and accuracy of 76.67%. The improved diagnostic accuracy of MRI with the addition of MTR analysis from 86.67% to 91.67% and from 85.71% to 87.50% for both radiologists respectively was not significant. MTR analysis helped us to differentiate solitary TB or abscess from low-grade glioma in five patients and to diagnose multiple TB, abscesses, and metastases in four.

The removal of dyes from textile wastewater: a study of the physical characteristics and adsorption mechanisms of diatomaceous earth.

The feasibility of using diatomite for the removal of the problematic reactive dyes as well as basic dyes from textile wastewater was investigated. Methylene blue, Cibacron reactive black and reactive yellow dyes were considered. Physical characteristics of diatomite such as pHsolution, pHZPC, surface area, Fourier transform infrared, and scanning electron microscopy were investigated. The surface area of diatomite was found to be 27.80 m2g(-1) and the pHZPC occurred around pH of 5.4. The results indicated that the surface charge of diatomite decreased as the pH of the solution increased with the maximum methylene blue removal from aqueous solution occurring at basic pH of around (10-11). Adsorption isotherms of diatomite with methylene blue, hydrolysed reactive black and yellow dyes were constructed at different pH values, initial dye concentrations and particle sizes. The experimental results were fitted to the Langmuir, Freundlich, and Henry models. The study indicated that electrostatic interactions play an important role in the adsorption of dyes onto diatomite. A model of the adsorption mechanism of methylene blue onto diatomite is proposed.