Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.

Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.

Curvature sensing as an emergent property of multiscale assembly of septins.

The ability of cells to sense and communicate their shape is central to many of their functions. Much is known about how cells generate complex shapes, yet how they sense and respond to geometric cues remains poorly understood. Septins are GTP-binding proteins that localize to sites of micrometer-scale membrane curvature. Assembly of septins is a multistep and multiscale process, but it is unknown how these discrete steps lead to curvature sensing. Here, we experimentally examine the time-dependent binding of septins at different curvatures and septin bulk concentrations. These experiments unexpectedly indicated that septins' curvature preference is not absolute but rather is sensitive to the combinations of membrane curvatures present in a reaction, suggesting that there is competition between different curvatures for septin binding. To understand the physical underpinning of this result, we developed a kinetic model that connects septins' self-assembly and curvature-sensing properties. Our experimental and modeling results are consistent with curvature-sensitive assembly being driven by cooperative associations of septin oligomers in solution with the bound septins. When combined, the work indicates that septin curvature sensing is an emergent property of the multistep, multiscale assembly of membrane-bound septins. As a result, curvature preference is not absolute and can be modulated by changing the physicochemical and geometric parameters involved in septin assembly, including bulk concentration, and the available membrane curvatures. While much geometry-sensitive assembly in biology is thought to be guided by intrinsic material properties of molecules, this is an important example of how curvature sensing can arise from multiscale assembly of polymers.

Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA.

Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in the cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryotic Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so are unclear. We used multiwavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the Escherichia coli transcription cycle. In our experiments, RapA at <5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post termination complex (PTC)-consisting of core RNA polymerase (RNAP)-bound sequence nonspecifically to double-stranded DNA-and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription reinitiation in proteobacterial genomes.

Kinetic modeling identifies targets for engineering improved photosynthetic efficiency in potato (Solanum tuberosum cv. Solara).

Potato (Solanum tuberosum) is a significant non-grain food crop in terms of global production. However, its yield potential might be raised by identifying means to release bottlenecks within photosynthetic metabolism, from the capture of solar energy to the synthesis of carbohydrates. Recently, engineered increases in photosynthetic rates in other crops have been directly related to increased yield - how might such increases be achieved in potato? To answer this question, we derived the photosynthetic parameters Vcmax and Jmax to calibrate a kinetic model of leaf metabolism (e-Photosynthesis) for potato. This model was then used to simulate the impact of manipulating the expression of genes and their protein products on carbon assimilation rates in silico through optimizing resource investment among 23 photosynthetic enzymes, predicting increases in photosynthetic CO2 uptake of up to 67%. However, this number of manipulations would not be practical with current technologies. Given a limited practical number of manipulations, the optimization indicated that an increase in amounts of three enzymes - Rubisco, FBP aldolase, and SBPase - would increase net assimilation. Increasing these alone to the levels predicted necessary for optimization increased photosynthetic rate by 28% in potato.

Optimization-derived blood input function using a kernel method and its evaluation with total-body PET for brain parametric imaging.

Dynamic PET allows quantification of physiological parameters through tracer kinetic modeling. For dynamic imaging of brain or head and neck cancer on conventional PET scanners with a short axial field of view, the image-derived input function (ID-IF) from intracranial blood vessels such as the carotid artery (CA) suffers from severe partial volume effects. Alternatively, optimization-derived input function (OD-IF) by the simultaneous estimation (SIME) method does not rely on an ID-IF but derives the input function directly from the data. However, the optimization problem is often highly ill-posed. We proposed a new method that combines the ideas of OD-IF and ID-IF together through a kernel framework. While evaluation of such a method is challenging in human subjects, we used the uEXPLORER total-body PET system that covers major blood pools to provide a reference for validation. METHODS: The conventional SIME approach estimates an input function using a joint estimation together with kinetic parameters by fitting time activity curves from multiple regions of interests (ROIs). The input function is commonly parameterized with a highly nonlinear model which is difficult to estimate. The proposed kernel SIME method exploits the CA ID-IF as a priori information via a kernel representation to stabilize the SIME approach. The unknown parameters are linear and thus easier to estimate. The proposed method was evaluated using 18F-fluorodeoxyglucose studies with both computer simulations and 20 human-subject scans acquired on the uEXPLORER scanner. The effect of the number of ROIs on kernel SIME was also explored. RESULTS: The estimated OD-IF by kernel SIME showed a good match with the reference input function and provided more accurate estimation of kinetic parameters for both simulation and human-subject data. The kernel SIME led to the highest correlation coefficient (R = 0.97) and the lowest mean absolute error (MAE = 10.5 %) compared to using the CA ID-IF (R = 0.86, MAE = 108.2 %) and conventional SIME (R = 0.57, MAE = 78.7 %) in the human-subject evaluation. Adding more ROIs improved the overall performance of the kernel SIME method. CONCLUSION: The proposed kernel SIME method shows promise to provide an accurate estimation of the blood input function and kinetic parameters for brain PET parametric imaging.

A nano-liposomal carrier containing p-coumaric acid for induction of targeted apoptosis on melanoma cells and kinetic modeling.

There has been a growth in the use of plant compounds as biological products for the prevention and treatment of various diseases, including cancer. As a phenolic compound, p-Coumaric acid (p-CA) demonstrates preferrable biological effects such as anti-cancer activities. A nano-liposomal carrier containing p-CA was designed to increase the anticancer effectiveness of this compound on melanoma cells (A375). To determine the characteristics of synthesized liposomes, encapsulation efficiency was measured. In addition, the particle size was measured utilizing DLS, FTIR, and morphology examination using SEM. In vitro release was also studied through the dialysis method, while toxicity was evaluated using the MTT assay. To determine apoptotic characteristics, biotechnology tools like flow cytometry, real time PCR, and atomic force microscopy (AFM) were employed. The findings indicated that in the cells treated with the liposomal form of p-CA, the amount of elastic modulus was higher compared to its free form. Kinetic modeling indicated that the best fitting model was zero-order.

Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models.

Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. We transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.

Elucidating uptake and metabolic fate of dipeptides in CHO cell cultures using 13C labeling experiments and kinetic modeling.

The rapidly growing market of biologics including monoclonal antibodies has stimulated the need to improve biomanufacturing processes including mammalian host systems such as Chinese Hamster Ovary (CHO) cells. Cell culture media formulations continue to be enhanced to enable intensified cell culture processes and optimize cell culture performance. Amino acids, major components of cell culture media, are consumed in large amounts by CHO cells. Due to their low solubility and poor stability, certain amino acids including tyrosine, leucine, and phenylalanine can pose major challenges leading to suboptimal bioprocess performance. Dipeptides have the potential to replace amino acids in culture media. However, very little is known about the cleavage, uptake, and utilization kinetics of dipeptides in CHO cell cultures. In this study, replacing amino acids, including leucine and tyrosine by their respective dipeptides including but not limited to Ala-Leu and Gly-Tyr, supported similar cell growth, antibody production, and lactate profiles. Using 13C labeling techniques and spent media studies, dipeptides were shown to undergo both intracellular and extracellular cleavage in cultures. Extracellular cleavage increased with the culture duration, indicating cleavage by host cell proteins that are likely secreted and accumulate in cell culture over time. A kinetic model was built and for the first time, integrated with 13C labeling experiments to estimate dipeptide utilization rates, in CHO cell cultures. Dipeptides with alanine at the N-terminus had a higher utilization rate than dipeptides with alanine at the C-terminus and dipeptides with glycine instead of alanine at N-terminus. Simultaneous supplementation of more than one dipeptide in culture led to reduction in individual dipeptide utilization rates indicating that dipeptides compete for the same cleavage enzymes, transporters, or both. Dipeptide utilization rates in culture and cleavage rates in cell-free experiments appeared to follow Michaelis-Menten kinetics, reaching a maximum at higher dipeptide concentrations. Dipeptide utilization behavior was found to be similar in cell-free and cell culture environments, paving the way for future testing approaches for dipeptides in cell-free environments prior to use in large-scale bioreactors. Thus, this study provides a deeper understanding of the fate of dipeptides in CHO cell cultures through an integration of cell culture, 13C labeling, and kinetic modeling approaches providing insights in how to best use dipeptides in media formulations for robust and optimal mammalian cell culture performance.

Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.

BRAF is prototypical of oncogenes that can be targeted therapeutically and the treatment of BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression. However, drug-induced rewiring generates a drug adapted state thought to be involved in acquired resistance and disease recurrence. In this article, we study mechanisms of adaptive rewiring in BRAFV600E melanoma cells using an energy-based implementation of ordinary differential equation (ODE) modeling in combination with proteomic, transcriptomic and imaging data. We develop a method for causal tracing of ODE models and identify two parallel MAPK reaction channels that are differentially sensitive to RAF and MEK inhibitors due to differences in protein oligomerization and drug binding. We describe how these channels, and timescale separation between immediate-early signaling and transcriptional feedback, create a state in which the RAS-regulated MAPK channel can be activated by growth factors under conditions in which the BRAFV600E -driven channel is fully inhibited. Further development of the approaches in this article is expected to yield a unified model of adaptive drug resistance in melanoma.

Comparison of parametric imaging and SUV imaging with [68 Ga]Ga-PSMA-11 using dynamic total-body PET/CT in prostate cancer.

PURPOSE: Standardized uptake value (SUV) has been prevalently used to measure [68 Ga]Ga-PSMA-11 activity in prostate cancer, but it is susceptible to multiple factors. Parametric imaging allows for absolute quantification of tracer uptake and provides a better diagnostic accuracy that is crucial for lesion detection. However, the clinical significance of total-body parametric imaging of [68 Ga]Ga-PSMA-11 remains to be fully assessed. Therefore, the aim of our study is to delve into the diagnostic implications of total-body parametric imaging of [68 Ga]Ga-PSMA-11 PET/CT for patients with prostate cancer. METHODS: Twenty prostate cancer patients were included and underwent a dynamic total-body [68 Ga]Ga-PSMA-11 PET/CT scan. An irreversible two-tissue compartment model (2T3k) was fitted for each tissue time-to-activity curve, and the net influx rate (Ki) was obtained. The image quality and semi-quantitative analysis of lesion-to-background ratio (LBR), signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were compared between parametric images and SUV images. RESULTS: Kinetic modeling using 2T3k demonstrated favorable model fitting in both normal organs and lesions. All of the lesions detected on SUV images (55-60 min) could be detected on Ki images. The correlation between Ki, SUVmean, and SUVmax in both normal organs and pathological lesions was found to be positive and statistically significant. Conversely, a moderate positive correlations were found between Ki and K1 (R = 0.69, P < 0.001; R = 0.61, P < 0.001) and Ki and k3 (R = 0.69, P < 0.001; R = 0.62, P < 0.001), in normal organs and pathological lesions, respectively. Visual assessment in Ki images showed less image noise and higher lesions conspicuity compared to SUV images. Ki image-derived LBR, SNR, and CBR of pathological lesions including primary tumors (PTs), lymph node metastases (LNMs) and bone metastases (BMs), exhibited remarkably higher folds (1.4-3.6 folds) compared to those derived from SUV of corresponding lesions. CONCLUSIONS: Total-body parametric imaging of [68 Ga]Ga-PSMA-11 enhanced lesion contrast and improved lesion detectability compared to SUV images. This may potentially serve as an imaging biomarker and theranostic tool for precise diagnosis and treatment evaluation in prostate cancer patients.

Assessment of cerebral drug occupancy in humans using a single PET-scan: A [11C]UCB-J PET study.

PURPOSE: Here, we evaluate a PET displacement model with a Single-step and Numerical solution in healthy individuals using the synaptic vesicle glycoprotein (SV2A) PET-tracer [11C]UCB-J and the anti-seizure medication levetiracetam (LEV). We aimed to (1) validate the displacement model by comparing the brain LEV-SV2A occupancy from a single PET scan with the occupancy derived from two PET scans and the Lassen plot and (2) determine the plasma LEV concentration-SV2A occupancy curve in healthy individuals. METHODS: Eleven healthy individuals (five females, mean age 35.5 [range: 25-47] years) underwent two 120-min [11C]UCB-J PET scans where an LEV dose (5-30 mg/kg) was administered intravenously halfway through the first PET scan to partially displace radioligand binding to SV2A. Five individuals were scanned twice on the same day; the remaining six were scanned once on two separate days, receiving two identical LEV doses. Arterial blood samples were acquired to determine the arterial input function and plasma LEV concentrations. Using the displacement model, the SV2A-LEV target engagement was calculated and compared with the Lassen plot method. The resulting data were fitted with a single-site binding model. RESULTS: SV2A occupancies and VND estimates derived from the displacement model were not significantly different from the Lassen plot (p = 0.55 and 0.13, respectively). The coefficient of variation was 14.6% vs. 17.3% for the Numerical and the Single-step solution in Bland-Altman comparisons with the Lassen plot. The average half maximal inhibitory concentration (IC50), as estimated from the area under the curve of the plasma LEV concentration, was 12.5 µg/mL (95% CI: 5-25) for the Single-Step solution, 11.8 µg/mL (95% CI: 4-25) for the Numerical solution, and 6.3 µg/mL (95% CI: 0.08-21) for the Lassen plot. Constraining Emax to 100% did not significantly improve model fits. CONCLUSION: Plasma LEV concentration vs. SV2A occupancy can be determined in humans using a single PET scan displacement model. The average concentration of the three computed IC50 values ranges between 6.3 and 12.5 µg/mL. The next step is to use the displacement model to evaluate LEV occupancy and corresponding plasma concentrations in relation to treatment efficacy. CLINICAL TRIAL REGISTRATION: NCT05450822. Retrospectively registered 5 July 2022 https://clinicaltrials.gov/ct2/results? term=NCT05450822&Search=Search.

Combined whole-body dynamic and static PET/CT with low-dose [18F]PSMA-1007 in prostate cancer patients.

AIM: In addition to significant improvements in sensitivity and image quality, the recent introduction of long axial field-of-view (LAFOV) PET/CT scanners has enabled dynamic whole-body imaging for the first time. We aim herein to determine an appropriate acquisition time range for static low-dose [18F]PSMA-1007 PET imaging and to investigate the whole-body pharmacokinetics of [18F]PSMA-1007 by dynamic PET with the LAFOV Biograph Vision Quadra PET/CT in a group of prostate cancer patients. METHODOLOGY: In total, 38 prostate cancer patients were enrolled in the analysis for staging or re-staging purposes. Thirty-four patients underwent dynamic whole-body PET/CT (60 min) followed by static whole-body PET/CT and four patients underwent static whole-body PET/CT only. The activity applied was 2 MBq/kg [18F]PSMA-1007. The static PET images of 10-min duration (PET-10) were reconstructed and further split into 8-min (PET-8), 6-min (PET-6), 5-min (PET-5), 4-min (PET-4), and 2-min (PET-2) duration groups. Comparisons were made between the different reconstructed scan times in terms of lesion detection rate and image quality based on SUV calculations of tumor lesions and the spleen, which served as background. Analysis of the dynamic PET/CT data was based on a two-tissue compartment model using an image-derived input function obtained from the descending aorta. RESULTS: Analysis of lesion detection rate showed no significant differences when reducing PET acquisitions from 10 up to 5 min. In particular, a total of 169 lesions were counted with PET-10, and the corresponding lesion detection rates (95% CI for the 90% quantile of the differences in tumor lesions) for shorter acquisitions were 100% (169/169) for PET-8 (95% CI: 0-0), 98.8% (167/169) for PET-6 (95% CI: 0-1), 95.9% (162/169) for PET-5 (95% CI: 0-3), 91.7% (155/169) for PET-4 (95% CI: 1-2), and 85.2% (144/169) for PET-2 (95% CI: 1-6). With the exception of PET-2, the differences observed between PET-10 and the other shorter acquisition protocols would have no impact on any patient in terms of clinical management. Objective evaluation of PET/CT image quality showed no significant decrease in tumor-to-background ratio (TBR) with shorter acquisition times, despite a gradual decrease in signal-to-noise ratio (SNR) in the spleen. Whole-body quantitative [18F]PSMA-1007 pharmacokinetic analysis acquired with full dynamic PET scanning was feasible in all patients. Two-tissue compartment modeling revealed significantly higher values for the parameter k3 in tumor lesions and parotid gland compared to liver and spleen, reflecting a higher specific tracer binding to the PSMA molecule and internalization rate in these tissues, a finding also supported by the respective time-activity curves. Furthermore, correlation analysis demonstrated a significantly strong positive correlation (r = 0.72) between SUV and k3 in tumor lesions. CONCLUSIONS: In prostate cancer, low-dose (2 MBq/kg) [18F]PSMA-1007 LAFOV PET/CT can reduce static scan time by 50% without significantly compromising lesion detection rate and objective image quality. In addition, dynamic PET can elucidate molecular pathways related to the physiology of [18F]PSMA-1007 in both tumor lesions and normal organs at the whole-body level. These findings unfold many of the potentials of the new LAFOV PET/CT technology in the field of PSMA-based diagnosis and theranostics of prostate cancer.

Pushing the boundaries of phosphorylase cascade reaction for cellobiose production I: Kinetic model development.

One-pot cascade reactions of coupled disaccharide phosphorylases enable an efficient transglycosylation via intermediary α-d-glucose 1-phosphate (G1P). Such transformations have promising applications in the production of carbohydrate commodities, including the disaccharide cellobiose for food and feed use. Several studies have shown sucrose and cellobiose phosphorylase for cellobiose synthesis from sucrose, but the boundaries on transformation efficiency that result from kinetic and thermodynamic characteristics of the individual enzyme reactions are not known. Here, we assessed in a step-by-step systematic fashion the practical requirements of a kinetic model to describe cellobiose production at industrially relevant substrate concentrations of up to 600 mM sucrose and glucose each. Mechanistic initial-rate models of the two-substrate reactions of sucrose phosphorylase (sucrose + phosphate → G1P + fructose) and cellobiose phosphorylase (G1P + glucose → cellobiose + phosphate) were needed and additionally required expansion by terms of glucose inhibition, in particular a distinctive two-site glucose substrate inhibition of the cellobiose phosphorylase (from Cellulumonas uda). Combined with mass action terms accounting for the approach to equilibrium, the kinetic model gave an excellent fit and a robust prediction of the full reaction time courses for a wide range of enzyme activities as well as substrate concentrations, including the variable substoichiometric concentration of phosphate. The model thus provides the essential engineering tool to disentangle the highly interrelated factors of conversion efficiency in the coupled enzyme reaction; and it establishes the necessary basis of window of operation calculations for targeted optimizations toward different process tasks.

Pushing the boundaries of phosphorylase cascade reaction for cellobiose production II: Model-based multiobjective optimization.

The inherent complexity of coupled biocatalytic reactions presents a major challenge for process development with one-pot multienzyme cascade transformations. Kinetic models are powerful engineering tools to guide the optimization of cascade reactions towards a performance suitable for scale up to an actual production. Here, we report kinetic model-based window of operation analysis for cellobiose production (≥100 g/L) from sucrose and glucose by indirect transglycosylation via glucose 1-phosphate as intermediate. The two-step cascade transformation is catalyzed by sucrose and cellobiose phosphorylase in the presence of substoichiometric amounts of phosphate (≤27 mol% of substrate). Kinetic modeling was instrumental to uncover the hidden effect of bulk microviscosity due to high sugar concentrations on decreasing the rate of cellobiose phosphorylase specifically. The mechanistic-empirical hybrid model thus developed gives a comprehensive description of the cascade reaction at industrially relevant substrate conditions. Model simulations serve to unravel opposed relationships between efficient utilization of the enzymes and maximized concentration (or yield) of the product within a given process time, in dependence of the initial concentrations of substrate and phosphate used. Optimum balance of these competing key metrics of process performance is suggested from the model-calculated window of operation and is verified experimentally. The evidence shown highlights the important use of kinetic modeling for the characterization and optimization of cascade reactions in ways that appear to be inaccessible to purely data-driven approaches.

Unveiling the Mechanism and Kinetics of Pollutant Attenuation by Free Radicals Triggered from Goethite in Water Distribution Systems.

Investigating the fate of persistent organic pollutants in water distribution systems (WDSs) is of great significance for preventing human health risks. The role of iron corrosion scales in the migration and transformation of organics in such systems remains unclear. Herein, we determined that hydroxyl (•OH), chlorine, and chlorine oxide radicals are generated by Fenton-like reactions due to the coexistence of oxygen vacancy-related Fe(II) on goethite (a major constituent of iron corrosion scales) and hypochlorous acid (HClO, the main reactive chlorine species of residual chlorine at pH ∼ 7.0). •OH contributed mostly to the decomposition of atrazine (ATZ, model compound) more than other radicals, producing a series of relatively low-toxicity small molecular intermediates. A simplified kinetic model consisting of mass transfer of ATZ and HClO, •OH generation, and ATZ oxidation by •OH on the goethite surface was developed to simulate iron corrosion scale-triggered residual chlorine oxidation of organic compounds in a WDS. The model was validated by comparing the fitting results to the experimental data. Moreover, the model was comprehensively applicable to cases in which various inorganic ions (Ca2+, Na+, HCO3-, and SO42-) and natural organic matter were present. With further optimization, the model may be employed to predict the migration and accumulation of persistent organic pollutants under real environmental conditions in the WDSs.

Critical Role of Mineral Fe(IV) Formation in Low Hydroxyl Radical Yields during Fe(II)-Bearing Clay Mineral Oxygenation.

In subsurface environments, Fe(II)-bearing clay minerals can serve as crucial electron sources for O2 activation, leading to the sequential production of O2•-, H2O2, and •OH. However, the observed •OH yields are notably low, and the underlying mechanism remains unclear. In this study, we investigated the production of oxidants from oxygenation of reduced Fe-rich nontronite NAu-2 and Fe-poor montmorillonite SWy-3. Our results indicated that the •OH yields are dependent on mineral Fe(II) species, with edge-surface Fe(II) exhibiting significantly lower •OH yields compared to those of interior Fe(II). Evidence from in situ Raman and Mössbauer spectra and chemical probe experiments substantiated the formation of structural Fe(IV). Modeling results elucidate that the pathways of Fe(IV) and •OH formation respectively consume 85.9-97.0 and 14.1-3.0% of electrons for H2O2 decomposition during oxygenation, with the Fe(II)edge/Fe(II)total ratio varying from 10 to 90%. Consequently, these findings provide novel insights into the low •OH yields of different Fe(II)-bearing clay minerals. Since Fe(IV) can selectively degrade contaminants (e.g., phenol), the generation of mineral Fe(IV) and •OH should be taken into consideration carefully when assessing the natural attenuation of contaminants in redox-fluctuating environments.

Evaluating Possible Formation Mechanisms of Criegee Intermediates during the Heterogeneous Autoxidation of Squalene.

Organic molecules in the environment oxidatively degrade by a variety of free radical, microbial, and biogeochemical pathways. A significant pathway is heterogeneous autoxidation, in which degradation occurs via a network of carbon and oxygen centered free radicals. Recently, we found evidence for a new heterogeneous autoxidation mechanism of squalene that is initiated by hydroxyl (OH) radical addition to a carbon-carbon double bond and apparently propagated through pathways involving Criegee Intermediates (CI) produced from ß-hydroxy peroxy radicals (ß-OH-RO2•). It remains unclear, however, exactly how CI are formed from ß-OH-RO2•, which could occur by a unimolecular or bimolecular pathway. Combining kinetic models and multiphase OH oxidation measurements of squalene, we evaluate the kinetic viability of three mechanistic scenarios. Scenario 1 assumes that CI are formed by the unimolecular bond scission of ß-OH-RO2•, whereas Scenarios 2 and 3 test bimolecular pathways of ß-OH-RO2• to yield CI. Scenario 1 best replicates the entire experimental data set, which includes effective uptake coefficients vs [OH] as well as the formation kinetics of the major products (i.e., aldehydes and secondary ozonides). Although the unimolecular pathway appears to be kinetically viable, future high-level theory is needed to fully explain the mechanistic relationship between CI and ß-OH-RO2• in the condensed phase.

Utilizing an Integrated Flow Cathode-Membrane Filtration System for Effective and Continuous Electrochemical Hydrodechlorination.

Pd-based electrodes are recognized to facilitate effective electrochemical hydrodechlorination (EHDC) as a result of their superior capacity for atomic hydrogen (H*) generation. However, challenges such as electrode stability, feasibility of treating complex matrices, and high cost associated with electrode synthesis hinder the application of Pd-based electrodes for EHDC. In this work, we investigated the feasibility of degrading 2,4-dichlorophenol (2,4-DCP) by EHDC employing Pd-loaded activated carbon particles, prepared via a simple wet-impregnation method, as a flow cathode (FC) suspension. Compared to other Pd-based EHDC studies, a much lower Pd loading (0.02-0.08 mg cm-2) was used. Because of the excellent mass transfer in the FC system, almost 100% 2,4-DCP was hydrodechlorinated to phenol within 1 h. The FC system also showed excellent performance in treating complex water matrices (including hardness ion-containing wastewater and various other chlorinated organics such as 2,4-dichlorobenzoic acid and trichloroacetic acid) with a relatively low energy consumption (0.26-1.56 kW h m-3 mg-1 of 2,4-DCP compared to 0.32-7.61 kW h m-3 mg-1 of 2,4-DCP reported by other studies). The FC synthesized here was stable over 36 h of continuous operation, indicating its potential suitability for real-world applications. Employing experimental investigations and mathematical modeling, we further show that hydrodechlorination of 2,4-DCP occurs via interaction with H*, with no role of direct electron transfer and/or HO•-mediated processes in the removal of 2,4-DCP.

Kinetic Model for Predicting Perfluoroalkyl Acid Degradation During UV-Sulfite Treatment.

Hydrated electron (eaq-) treatment processes show great potential in remediating recalcitrant water contaminants, including perfluoroalkyl and polyfluoroalkyl substances (PFAS). However, treatment efficacy depends upon many factors relating to source water composition, UV light source characteristics, and contaminant reactivity. Here, we provide critical insights into the complex roles of solution parameters on contaminant abatement through application of a UV-sulfite kinetic model that incorporates first-principles information on eaq- photogeneration and reactivity. The model accurately predicts decay profiles of short-chain perfluoroalkyl acids (PFAAs) during UV-sulfite treatment and facilitates quantitative interpretation of the effects of changing solution composition on PFAS degradation rates. Model results also confirm that the enhanced degradation of PFAAs observed under highly alkaline pH conditions results from changes in speciation of nontarget eaq- scavengers. Reverse application of the model to UV-sulfite data collected for longer chain PFAAs enabled estimation of bimolecular rate constants (k2, M-1 s-1), providing an alternative to laser flash photolysis (LFP) measurements that are not feasible due to the water solubility limitations of these compounds. The proposed model links the disparate means of investigating eaq- processes, namely, UV photolysis and LFP, and provides a framework to estimate UV-sulfite treatment efficacy of PFAS in diverse water sources.

Ultrasound-assisted extraction of phenolics from Sargassum carpophyllum - A kinetics study.

The species of the brown macroalgal genus Sargassum are distributed globally and contain many bioactive compounds. In this study, ultrasound-assisted extraction (UAE) was applied to obtain phenolic compounds with strong antioxidant activity from Sargassum carpophyllum collected along the coastline of Weizhou Island in the South China Sea. The influence of different variables such as the solid-liquid ratio (1:5-1:30 g · mL-1), ultrasonic power (160-280 W), duty circle ratio (DCR, 1/3-1/1), and ethanol concentration (30% to ~90%) were studied using a single factor design. The extraction kinetics were investigated using the Peleg model and second-order kinetics model, and the second-order model described the extraction procedure better than the Peleg model. Total phenol content (TPC) values of 3.316, 2.964, 2.741, and 3.665 mg phloroglucinol (PHG) · g-1 algae were achieved at a higher solid-liquid ratio (1:30 g · mL-1), higher ultrasonic power (280 W), a higher DCR (1/1), and a moderate ethanol concentration (50%), respectively. However, a slightly different result was observed in the extract obtained, with total phenol contents (TPCextract) of 52.99, 65.00, 46.22, and 55.10 mg PHG · g-1 extract and DPPH radical scavenging activity (IC50) of 0.096, 0.066, 0.131, and 0.136 mg extract · mL-1 observed at 50% ethanol, 1:5 g m· mL-1, 2/3 DCR, and 200 W respectively. All variables studied influenced the extraction kinetics by altering the extraction rate and the TPC at equilibrium. As for the bioactivities in the extract, a larger solid-liquid ratio and greater ultrasonic power may not contribute because of their ability to extract non-phenolic components simultaneously, leading to reduced overall bioactivities. The results of the present study provide essential information for future UAE process design and optimization for extracting phenolics from S. carpophyllum through mathematical modeling and could be regarded as important reference for obtaining value-added products from other macroalgae species.