Transcription factor exchange enables prolonged transcriptional bursts.

Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcription activation. Here, we devised a microscopy method to simultaneously measure transient TF binding at a single locus and the effect of these binding events on transcription. We show that DNA binding of the yeast TF Gal4 activates transcription of a target gene within a few seconds, with at least ∼20% efficiency and with a high initiation rate of ∼1 RNA/s.

Time will tell: comparing timescales to gain insight into transcriptional bursting.

Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear.

Evaluating the impact of drying on leaching from a solidified/stabilized waste using a monolithic diffusion model.

The release rates of constituents of potential concern from solidified/stabilized cementitious waste forms are potentially impacted by drying, which, however, is not well understood. This study aimed to identify the impacts of drying on subsequent leaching from Cast Stone as an example of a solidified cementitious waste form. The release fluxes of constituents from monoliths after aging under 100, 68, 40, and 15 % relative humidity for 16, 32, and 48 weeks, respectively, were derived from mass transfer tank leaching tests following EPA Method 1315.

Transcription factor clusters enable target search but do not contribute to target gene activation.

Many transcription factors (TFs) localize in nuclear clusters of locally increased concentrations, but how TF clustering is regulated and how it influences gene expression is not well understood. Here, we use quantitative microscopy in living cells to study the regulation and function of clustering of the budding yeast TF Gal4 in its endogenous context. Our results show that Gal4 forms clusters that overlap with the GAL loci.

Impact of oxidation and carbonation on the release rates of iodine, selenium, technetium, and nitrogen from a cementitious waste form.

Evaluation of the long-term retention mechanisms and potential release rates for the primary constituents of potential concern (COPCs) (i.e., Tc, I, Se, and nitrate) is necessary to determine if Cast Stone, a radioactive waste form, can meet performance objectives under near-surface disposal scenarios.

Impact of carbonation on leaching of constituents from a cementitious waste form for treatment of low activity waste at the DOE Hanford site.

Carbonation can be a major aging process during disposal of alkaline cementitious waste forms and can impact constituent leaching by changes in material alkalinity, pore structure, and controlling mineral phases. The effect of carbonation on the leaching of major and trace constituents from Cast Stone, a cementitious waste form developed to treat high salt content low activity waste, was studied through a combination of leaching experiments and reactive transport simulations. Diffusive transport of constituents in the waste form was evaluated using reactive transport modeling of diffusion-controlled leaching test results and a geochemical speciation model derived from pH-dependent leaching.

Following the tracks: How transcription factor binding dynamics control transcription.

Transcription, the process of copying genetic information from DNA to messenger RNA, is regulated by sequence-specific DNA-binding proteins known as transcription factors (TFs). Recent advances in single-molecule tracking (SMT) technologies have enabled visualization of individual TF molecules as they diffuse and interact with the DNA in the context of living cells. These SMT studies have uncovered multiple populations of DNA-binding events characterized by their distinctive DNA residence times.

Development of a Geochemical Speciation Model for Use in Evaluating Leaching from a Cementitious Radioactive Waste Form.

Cast Stone has been developed to immobilize a fraction of radioactive waste at the Hanford Site; however, constituents of potential concern (COPCs) can be released when in contact with water during disposal. Herein, a representative mineral and parameter set for geochemical speciation modeling was developed for Cast Stone aged in inert and oxic environments, to simulate leaching concentrations of major and trace constituents. The geochemical speciation model was verified using a monolithic diffusion model in conjunction with independent monolithic diffusion test results.

Single-Molecule Fluorescence Imaging in Living Cells.

This protocol describes how to image fluorescently tagged proteins, RNA, or DNA inside living cells at the single-molecule level. Imaging inside living cells, as opposed to fixed materials, gives access to real-time kinetic information. Although various single-molecule imaging applications are discussed, we focus on imaging of gene transcription at the single-RNA level.

Transport and degradation of propylene glycol in the vadose zone: model development and sensitivity analysis.

Transport and degradation of de-icing chemical (containing propylene glycol, PG) in the vadose zone were studied with a lysimeter experiment and a model, in which transient water flow, kinetic degradation of PG and soil chemistry were combined. The lysimeter experiment indicated that aerobic as well as anaerobic degradation occurs in the vadose zone. Therefore, the model included both types of degradation, which was made possible by assuming advection-controlled (mobile) and diffusion-controlled (immobile) zones.

Testing copper-speciation predictions in freshwaters over a wide range of metal-organic matter ratios.

The harsh chemical conditions involved in the isolation of fulvic acids (FA) and humic acids (HA) have been identified as a possible contributing factor to the significant mismatch between in situ measurements and model predictions of trace metal speciation in freshwaters, resulting from the use of isolated FA and HA in model calibration. A set of experimental assays were developed to enable Cu binding to DOM to be measured over the full range of [Cu]/[DOC] ratios (∼1-460 μmol g(-1)) observed in surface freshwaters. They were applied to the widely used and traditionally isolated Suwannee River HA and FA and to DOM isolated from headwater streams by a mild procedure using minimal chemical treatment.

Evaluation of a generic multisurface sorption model for inorganic soil contaminants.

The performance of a multisurface sorption model approach, composed of well-accepted surface complexation models in combination with published "generic" parameter sets, is evaluated for its possible use in risk assessment. For that purpose, the leaching of a broad range of potential soil contaminants (Ni, Cu, Zn, Cd, Pb, Ba, Cr, Co, Mo, V, Sn, Sb, S, As, Se) from eight diffusely and industrially contaminated soils is predicted simultaneously without any parameter optimization. The model approach includes aqueous speciation in combination with sorption to organic matter (NICA-Donnan model), Fe/Al(hydr)oxides (Generalized Two-Layer Model), and clay (Donnan model).

BIOCHEM-ORCHESTRA: a tool for evaluating chemical speciation and ecotoxicological impacts of heavy metals on river flood plain systems.

The chemical speciation model BIOCHEM was extended with ecotoxicological transfer functions for uptake of metals (As, Cd, Cu, Ni, Pb, and Zn) by plants and soil invertebrates. It was coupled to the object-oriented framework ORCHESTRA to achieve a flexible and dynamic decision support system (DSS) to analyse natural or anthropogenic changes that occur in river systems. The DSS uses the chemical characteristics of soils and sediments as input, and calculates speciation and subsequent uptake by biota at various scenarios.

Effect of accelerated aging of MSWI bottom ash on the leaching mechanisms of copper and molybdenum.

The effect of accelerated aging of Municipal Solid Waste Incinerator (MSWI) bottom ash on the leaching of Cu and Mo was studied using a "multisurface" modeling approach, based on surface complexation to iron/aluminum (hydr)oxides, mineral dissolution/precipitation, and metal complexation by humic substances. A novel experimental method allowed us to identify that the solid/liquid partitioning of fulvic acids (FA) quantitatively explains the observed beneficial effect of accelerated aging on the leaching of Cu. Our results suggestthat iron/aluminum (hydr)oxides are the major reactive surfaces that retain fulvic acid in the bottom ash matrix, of which the aluminum (hydr)oxides were found to increase after aging.

Test method selection, validation against field data, and predictive modelling for impact evaluation of stabilised waste disposal.

In setting criteria for landfill classes in Annex II of the EU Landfill Directive, it proved to be impossible to derive criteria for stabilised monolithic waste due to the lack of information on release and release controlling factors in stabilised waste monofills. In this study, we present a scientific basis, which enables a realistic description of the environmental impact of stabilised waste landfills. The work in progress involves laboratory testing of different stabilisation recipes, pilot scale studies on site and evaluation of field leachate from a full-scale stabilisation landfill.

Competitive sorption and diffusion of chromate and sulphate in a flow system with goethite in gel beads.

Column experiments and model simulations were employed to evaluate the processes involved in multicomponent solute transport in a system with heterogeneous flow. Column experiments were performed with goethite embedded in polyacrylamide gel beads. The gel forms an immobile water region that can be accessed by diffusion.

The implications of integrated assessment and modelling studies for the future remediation of chromite ore processing residue disposal sites.

Chromite ore processing residue (COPR) waste from a former chromium chemical works (1830-1968) is still contaminating groundwater in Glasgow, Scotland, with carcinogenic hexavalent chromium, Cr(VI). An integrated analytical, experimental and modelling approach has identified and accounted for mineral phases and processes responsible for the retention and release of Cr(VI) under prevailing field conditions. Both the nature of mineral phase retention and the buffered high pH of the sites, however, militate against direct remediative treatment of the source material, for example by the application of generic methods (e.

Sorption kinetics of strontium in porous hydrous ferric oxide aggregates II. Comparison of experimental results and model predictions.

In a previous paper, we introduced the Donnan diffusion model to describe cation diffusion into microporous solids with variably charged surfaces, such as hydrous ferric oxides (HFO). Here, we present experiments investigating slow diffusion and sorption of strontium by HFO aggregates with well-characterized porosity. Adsorption of protons and strontium at the HFO surface was evaluated by acid-base titration and batch adsorption experiments with dispersed HFO.

Sorption kinetics of strontium in porous hydrous ferric oxide aggregates I. The Donnan diffusion model.

Sorption of ions by hydrous ferric oxide (HFO) often shows a fast initial sorption reaction followed by a much slower sorption process. The second step is diffusion-controlled and can continue for days or months before equilibrium is reached. In this paper, we demonstrate that the diffusion rate may be explained by electrostatic interactions.

Leaching of heavy metals from contaminated soils: an experimental and modeling study.

In this paper, we characterize the leaching of heavy metals (Ni, Cu, Zn, Cd, and Pb) from eight contaminated soils over a wide range of pH (pH 0.4-12) using an original approach based on batch pH-static leaching experiments in combination with selective chemical extractions and geochemical modeling. The leached concentrations of the heavy metals are generally much lower than the total concentrations and show a strong pH dependency, resulting in "V-shaped" leaching curves with orders of magnitude changes in solution concentrations.

Chromium remediation or release? Effect of iron(II) sulfate addition on chromium(VI) leaching from columns of chromite ore processing residue.

Chromite ore processing residue (COPR), derived from the so-called high lime processing of chromite ore, contains high levels of Cr(III) and Cr(VI) and has a pH between 11 and 12. Ferrous sulfate, which is used for remediation of Cr(VI) contamination in wastewater and soils via reduction to Cr(III) and subsequent precipitation of iron(III)/chromium(III) hydroxide, has also been proposed for remediation of Cr(VI) in COPR. Instead, however, addition of FeSO4 to the infiltrating solution in column experiments with COPR greatly increased leaching of Cr(VI).

ORCHESTRA: an object-oriented framework for implementing chemical equilibrium models.

This work presents a new object-oriented structure for chemical equilibrium calculations that is used in the modeling framework ORCHESTRA (Objects Representing CHEmical Speciation and TRAnsport). In contrast to standard chemical equilibrium algorithms, such as MINEQL, MINTEQ2A, PHREEQC, and ECOSAT, model equations are not hard-coded in the source code, but instead all equations are defined in text format and read by the ORCHESTRA calculation kernel at run time. This makes model definitions easily accessible and extendible by users.

The effect of EDTA and fulvic acid on Cd, Zn, and Cu toxicity to a bioluminescent construct (pUCD607) of Escherichia coli.

The hypothesis, that metal toxicity is dominated by free ion activity, was tested by comparing calculated metal activities with measured toxic responses to a genetically modified, luminescent bacterium, Escherichia coli. The toxicity of Cd, Cu, and Zn sulphate salts in the presence of EDTA and fulvic acid in well-defined solutions was measured. Good agreement between free metal activity and toxicity was found for Cu but not for Zn and Cd.