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EGS Collab Testbed 1: Second Set Tracer Test Results
The EGS Collab project is developing ~10-20 m-scale field sites where fracture stimulation and flow models can be validated against controlled, small-scale, in-situ experiments. The first multi-well experimental site was established at the 4850 level in the Homestake Mine in Lead, South Dakota, where hydraulic fractures were created at an injection well drilled sub-horizontal from the drift. This file contains the second set of tracer data (also include the data uploaded previously, https://gdr.openei.org/submissions/1128) for the EGS Collab testbed. The tracer tests were conducted during October 2018 - November 2019. Injected tracers include DNA, C-dots (fluorescein nano particles), fluorescein, rhodamine-b, sodium chloride, lithium bromide and cesium iodine. The tracers have been detected in three flowing wells located about 7.5 to 9 meters away from the injection interval. The tracer breakthrough curves from these locations have been adjusted to account for the residence time in the injection and production tubing. The details about the tracer test can be found in Background and Methods of Tracer Tests (Mattson et al. (2019,a,b)) (also included in this package). References Mattson, E.D., Neupane, G., Plummer, M.A., Hawkins, A., Zhang, Y. and the EGS Collab Team 2019a. Preliminary Collab fracture characterization results from flow and tracer testing efforts. In Proceedings 44th Workshop on Geothermal Reservoir Engineering, edited, Stanford University, Stanford, California. Mattson, E.D., Neupane, G., Hawkins, A., Burghardt, J., Ingraham, M., Plummer, M., and the EGS Collab Team, 2019b. Fracture tracer injection response to pressure perturbations at an injection well. GRC Transactions, Vol. 43, 2019. Neupane, Ghanashyam, Earl Mattson, Adam Hawkins, Mitchell Plummer, and Yuran Zhang. EGS Collab Testbed 1: Tracer data sets. No. 1128. DOE Geothermal Data Repository; Idaho National Laboratory, 2019.
One-electron redox kinetics of aqueous transition metal couples Zn 2+/+ , Co 2+/+ , and Ni 2+/+ using pulse radiolysis
The one-electron redox potentials for aqueous metal couples Co 2+/+ and Ni 2+/+ have been investigated by using pulse radiolysis using their reactions with a series of reference compounds to establish the most positive upper limits of E 0 . Experiments with Zn + were also carried out to confirm the characteristic shape of the expected reduction kinetics. Both formate ions and t-BuOH were employed to scavenge ˙OH radicals and ˙H atoms. Kinetics and fitted first and second order reaction rates have been reported for reactions with methyl viologen, fluorescein, Ru(NH 3 ) 6 3+ , Co(en) 3 2+ , Co(sepulcrate) 3+ , Ru(bpy) 3 2+ , Cr(bpy)33+, and Ni(Me 6 [14]4,11-dieneN4) 2+ . Previous work demonstrated that both Co 2+ and Ni 2+ can be reduced by CO 2 ˙- radicals, giving a negative E 0 limit of -1.9 V vs. SHE. A definite reaction of Ni + with fluorescein di-anions provides a new upper limit of the Ni 2+/+ couple as -0.906 V vs. SHE. The reaction of Co + with Ru(bpy) 3 2+ has been confirmed, giving E 0 = -1.3 V vs. SHE as a rigorous upper limit of the Co 2+/+ couple. In the case of Co 2+/+ , kinetics were complicated by a self-catalyzed metal clustering phenomenon. Initiation rate constants of this process have also been reported.
Effects on the Ocular Surface from Reading on Different Smartphone Screens: A Prospective Randomized Controlled Study
The purpose of this study was to investigate the influence of smartphone reading on the ocular surface and to compare the various effects of different screens and light conditions on the ocular surface. One hundred nineteen volunteers were randomly divided into: light + organic light‐emitting diode (OLED), light + electronic ink (eINK), dark + OLED, and dark + eINK. Ocular surface examinations, including noninvasive break‐up time (NIBUT), noninvasive keratograph tear meniscus height (NIKTMH), ocular redness, fluorescein break‐up time (FBUT), corneal fluorescein staining, meibomian gland assessment, Schirmer I Test, and blinking frequency, were performed before and after a reading task. Symptoms were evaluated using the Ocular Surface Disease Index (OSDI) and Computer Vision Syndrome Questionnaire (CVS‐Q). NIBUT and FBUT were decreased statistically significantly after participants read on an OLED screen for 2 hours compared with the baseline in light and dark environments, whereas no statistically significant decrease was observed on an eINK screen. NIKTMH was statistically significantly decreased after reading on an OLED screen in light and dark settings, and the eINK screen had a lesser effect on NIKTMH. An obvious increase in the ocular redness, OSDI and CVS‐Q scores was observed after reading on an OLED screen, whereas the eINK screen had a lesser effect on these indicators. Blink rate increased gradually in OLED subgroups during the reading task, whereas no statistically significant difference was observed in the eINK subgroups. Our research suggested that reading on an OLED screen can cause ocular surface disorder and obvious subjective discomfort, whereas reading on an eINK screen can minimize ocular surface disorder in both dark and light environments.
Fish scale-loss caused by simulated hydraulic shear stress
Riverine fishes found within streams impacted by hydropower also often pass through hydropower turbines during annual downstream migrations. During turbine passage events, fish may experience a suite of stressors including rapid pressure changes, impacts from turbine blades, and exposure to hydraulic shear. Scale-loss is often observed in fish collected below dams and hydraulic shear is the most likely cause of this trauma. While exposure to shear may cause other injuries, scale-loss appears to be the most common non-lethal injury observed to date. We sought to quantify how hydraulic shear may cause scale-loss in rainbow trout, gizzard shad, and hybrid striped bass by precisely controlling the exposure level (velocity) and duration (seconds) of a water jet. We targeted the same area for all three species found between the operculum and dorsal fin on the left, lateral surface. Exposure velocities ranged from 0 (controls) to 11.0 meters/second but fish were only exposed to the water jet for 1.5 seconds. A 0.2 milligram/milliliter solution of fluorescein was used to stain the areas of scale-loss by submerging each fish in this solution for at least 6 minutes. Fluorescein was used because it interacts with epithelial tissue that has been damaged and it fluoresces under ultraviolet lighting. Fish were photographed under short- and longwave ultraviolet lighting in a dark chamber to capture fluorescence. Fish photographs were analyzed using ImageJ and the proportion of descaled area was estimated for each fish within a 35 by 35-millimeter square. In general, these data highlight how exposure to hydraulic shear may lead to significant levels of descaling in riverine fishes.
NF-κB activation in retinal microglia is involved in the inflammatory and neovascularization signaling in laser-induced choroidal neovascularization in mice
Highlights: • IMD0354 treatment reduced the microglia infiltration, fluorescein leakage and size of the laser CNV spots. • IKK2 inhibition suppressed phospho-IκBα, VEGF-A, and COX-2 in the Laser CNV mouse eyes. • IMD-0354 treated eyes demonstrated reduced microglial migration to the laser injury site. • In vitro, IKK2 inhibition reduced NF-κB activation, COX-2, Actin-F presence, and the microglia cells' migration capacity. To evaluate Nuclear Factor NF-κB (NF-κB) signaling on microglia activation, migration, and angiogenesis in laser-induced choroidal neovascularization (CNV).
High-Performance Hemofiltration via Molecular Sieving and Ultra-Low Friction in Carbon Nanotube Capillary Membranes
Conventional dialyzer membranes typically comprise of unevenly distributed polydisperse, tortuous, rough pores, embedded in relatively thick ≈20–50 µm polymer layers wherein separation occurs via size exclusion as well as differences in diffusivity of the permeating species. However, transport in such polymeric pores is increasingly hindered as the molecule size approaches the pore dimension, resulting in significant retention of undesirable middle molecules (≥15–60 kDa) and uremic toxins. Enhanced removal of middle molecules is usually accompanied by high albumin loss (≈66 kDa) causing hypoalbuminemia. Here, the scalable bottom-up fabrication of wafer-scale carbon nanotube (CNT) membranes with highly aligned, low-friction, straight-channels/capillaries and narrow pore-diameter distributions (≈0.5–4.5 nm) is demonstrated, to overcome persistent challenges in hemofiltration/hemodialysis. Using fluorescein isothiocyanate (FITC)-Ficoll 70 and albumin in phosphate buffered saline (PBS) as well as in bovine blood plasma, it is shown that CNT membranes can allow for significantly higher hydraulic permeability (more than an order of magnitude when normalized to pore area) than commercial high-flux hemofiltration/hemodialysis membranes (HF 400), as well as greatly enhance removal of middle molecules while maintaining comparable albumin retention. These findings are rationalized via an N-pore transport model that highlights the critical role of molecular flexing and deformation during size-selective transport within nanoscale confinements of the CNTs. In conclusion, the unique transport characteristics of CNTs coupled with size-exclusion and wafer-scale fabrication offer transformative advances for hemofiltration, and the obtained insight into molecular transport can aid advancements in several other bio-systems/applications beyond hemofiltration/hemodialysis.
Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly
This paper presents an enzyme building block for the assembly of megamolecules. The system is based on the inhibition of the human-derived cellular retinoic acid binding protein II (CRABP2) domain. We synthesized a synthetic retinoid bearing an arylfluorosulfate group, which uses sulfur fluoride exchange click chemistry to covalently inhibit CRABP2. We conjugated both the inhibitor and a fluorescein tag to an oligo(ethylene glycol) backbone and measured a second-order rate constant for the protein inhibition reaction of approximately 3,600 M -1 s -1 . We used this new enzyme-inhibitor pair to assemble multi-protein structures in one-pot reactions using three orthogonal assembly chemistries to demonstrate exact control over the placement of protein domains within a single, homogeneous molecule. This work enables a new dimension of control over specificity, orientation, and stoichiometry of protein domains within atomically precise nanostructures.
On the competition between mixing rate and uniformity in a coaxial hydrodynamic focusing mixer
Fast microfluidic mixers for use with line-of-sight integrating detection schemes pose unique challenges. Such detectors typically cannot discriminate signal from slow moving (e.g. near internal walls) and fast-moving portions of the fluid stream. This convolves reaction rate dynamics with fluid flow residence time dynamics. Further, the small cross sections of typical three-dimensional hydrodynamic focusing devices lead to lower detection signals. The current study focuses on achieving both small time scales of mixing and homogenous residence times. This is achieved by injecting sample through a center capillary and hydrodynamically focusing using a sheath flow within a tapered second capillary. The current design also features a third, larger coaxial capillary. The mixed stream flows into the large cross-section of this third capillary to decelerate and expand the stream by up to 14-fold to improve line-of-sight signal strength of reaction products. Hydrodynamic focusing, mixing, and expansion are studied using analytical and numerical models and also studied experimentally using a fluorescein-iodide quenching reaction. The experimentally validated models are used to explore trade-offs between mixing rate and uniformity. For the first time, this work presents detailed analysis of the Lagrangian time history of species transport during mixing inside coaxial capillaries to measure mixing nonuniformity. The mixing region enables order 100 μs mixing times and residence time widths of the same order (140 μs).
Enzymatically hydrolyzed fluorescence-based chemical probe enables in situ mapping of chitinase activity in the rhizosphere
Rhizosphere microbiomes and root exudates play a pivotal biochemical role in helping to catalyze chitin catabolism. Chitin is a recalcitrant and ubiquitous soil biopolymer, estimated to be the second most abundant organic soil biopolymer on Earth. Despite its abundance, role as a source of C and N in soil, and importance to ecosystem function, the biochemical mechanisms controlling chitin fate in the rhizosphere are elusive and poorly understood. To enable spatial mapping of chitinase activity in the rhizosphere, we designed and synthesized an enzymatically activated fluorogenic substrate, chitotriose-TokyoGreen (chitotriose-TG), by incorporating a fluorescein derivative (TG) onto the trimeric unit of chitin. This non-fluorescent substrate is selectively hydrolyzed by chitinase to release TG and yield a high fluorescence signal, which can be used to spatially image and measure chitinase activity in the rhizosphere. To demonstrate the application of this technique, we grew switchgrass (Panicum virgatum) in rhizoboxes amended with a horizontal layer of chitin. We extracted mobile proteins from the rhizobox using a nitrocellulose membrane blotting technique which offer non-destructive enzyme extraction while preserving the 2D spatial position of the enzymes. We then subjected these membranes to the synthesized chitotriose-TG stain to spatially visualize the distribution of chitinase activity within the rhizosphere. Furthermore, we observed increased chitinase activity near plant roots and higher activity within the soil zone enriched in chitin, showing an adaptive response of chitinase activity with spatial focusing in areas of higher chitin abundance. Thus, the enzyme extraction and visualization strategy we describe here can help enlighten efforts to better understand spatial controls on chitin breakdown in rhizosphere, further elucidating the role of chitin as a C and N source in these systems.
A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae
The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.
Stream lamination and rapid mixing in a microfluidic jet for X-ray spectroscopy studies
Microfluidic mixers offer new possibilities for the study of fast reaction kinetics down to the microsecond time scale, and methods such as soft X-ray absorption spectroscopy are powerful analysis techniques. These systems impose challenging constraints on mixing time scales, sample volume, detection region size and component materials. The current work presents a novel micromixer and jet device which aims to address these limitations. The system uses a so-called ‘theta’ mixer consisting of two sintered and fused glass capillaries. Sample and carrier fluids are injected separately into the inlets of the adjacent capillaries. At the downstream end, the two streams exit two micron-scale adjoining nozzles and form a single free-standing jet. The flow-rate difference between the two streams results in the rapid acceleration and lamination of the sample stream. This creates a small transverse dimension and induces diffusive mixing of the sample and carrier stream solutions within a time scale of 0.9 microseconds. The reaction occurs at or very near a free surface so that reactants and products are more directly accessible to interrogation using soft X-ray. We use a simple diffusion model and quantitative measurements of fluorescence quenching (of fluorescein with potassium iodide) to characterize the mixing dynamics across flow-rate ratios.
Generalized Protein-Repellent Properties of Ultrathin Homopolymer Films
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Protein-Enabled Size-Selective Defect-Sealing of Atomically Thin 2D Membranes for Dialysis and Nanoscale Separations
Atomically thin 2D materials present the potential for advancing membrane separations via a combination of high selectivity (from molecular sieving) and high permeance (due to atomic thinness). However, the creation of a high density of precise nanopores (narrow-size-distribution) over large areas in 2D materials remains challenging, and nonselective leakage from nanopore heterogeneity adversely impacts performance. Here, we demonstrate protein-enabled size-selective defect sealing (PDS) for atomically thin graphene membranes over centimeter scale areas by leveraging the size and reactivity of permeating proteins to preferentially seal larger nanopores (≥4 nm) while preserving a significant amount of smaller nanopores (via steric hindrance). Our defect-sealed nanoporous atomically thin membranes (NATMs) show stability up to ~35 days during size-selective diffusive separations with a model dialysis biomolecule fluorescein isothiocyanate (FITC)-Ficoll 70 in phosphate buffer saline (PBS) solution as well as outperform state-of-the-art commercially available dialysis membranes (molecular-weight-cutoff ~3.5–5 kDa and ~8–10 kDa) with significantly higher permeance for smaller solutes KCl (~0.66 nm) ~5.1–6 × 10 –5 ms –1 and vitamin B12 (B12, ~1.5 nm) ~2.8–4 × 10 –6 ms –1 compared to small protein lysozyme (Lz, ~4 nm) ~4–6.4 × 10 –8 m s –1 , thereby allowing unprecedented selectivity for B12/Lz ~70 and KCl/Lz ~1280. Our work introduces proteins as nanoscale tools for size-selective defect sealing in atomically thin membranes to overcome persistent issues and advance separations for dialysis, protein desalting, small molecule separations/purification, and other bioprocesses.
Self-sorting in supramolecular assemblies
Supramolecular self-assembly enables living organisms to form highly functional hierarchical structures with individual components self-organized across multiple length scales. This has inspired work on multicomponent supramolecular materials to understand factors behind co-assembly versus self-sorting of molecules. We report here on a supramolecular system comprised of negatively charged peptide amphiphile (PA) molecules, in which only a tiny fraction of the molecules (0.7 mol%) were covalently conjugated to one of two different fluorophores, half to fluorescein isothiocyanate (FTIC) and the other half to tetramethylrhodamine (TAMRA). Confocal microscopy of the system revealed self-sorting of the two different fluorescent PA molecules, where TAMRA PA is concentrated in micron-scale domains while FITC PA remains dispersed throughout the sample. From Förster resonance energy transfer and fluorescence recovery experiments, we conclude that conjugation of the negatively charged FITC to PA significantly disrupts its co-assembly with the 99.3 mol% of unlabeled molecules, which are responsible for formation of micron-scale domains. Conversely, conjugation of the zwitterionic TAMRA causes no such disruption. Interestingly, this dissimilar behavior between FITC and TAMRA PA causes them to self-sort at large length scales in the supramolecular system, mediated not by specific interactions among the individual fluorophores but instead by their different propensities to co-assemble with the majority component. We also found that greater ionic strength in the aqueous environment of the system promotes mixing by lowering the electrostatic barriers involved in self-sorting. Furthermore, our results demonstrate great thermodynamic subtlety in the driving forces that mediate self-sorting versus co-assembly in supramolecular peptide assemblies.
Asymmetric side-chain engineering in semiconducting polymers: a platform for greener processing and post-functionalization of organic electronics
Organic semiconducting polymers are a powerful platform for the design of next-generation technologies due to their excellent optoelectronic properties and solution processability, allowing access to low-cost and scalable manufacturing techniques such as spin-coating, slot-die coating and roll-to-roll printing. However, their extended π-conjugation results in low solubility, requiring the use of toxic halogenated solvents to generate thin films and devices. Furthermore, accessible post-functionalization of semiconductors toward the development of multifunctional devices and sensors remains a challenge due to limited solid-state chemistry for alkyl side chains. In this work, an asymmetric side-chain engineering approach was used to introduce terminal hydroxyl moieties alongside traditional solubilizing branched alkyl chains into an isoindigo-based polymer. The hydroxyl moieties led to significantly improved processability in alcohol-based solvents without sacrificing electronic performance in thin film organic field-effect transistors. Solid state morphologies of the thin films processed from both alcohol-based and traditional halogenated solvents were further characterized using atomic force microscopy and grazing incidence wide angle X-ray scattering. Additionally, Cryo-EM was utilized in order to characterize the role of asymmetric side-chain functionality in solution state aggregation. The versatility of this design was further probed using fluorescein isothiocyanate to directly functionalize the asymmetric polymer in thin film. Furthermore, this facile solid-state post-functionalization further demonstrates asymmetric side-chain engineering to be a viable approach toward the development of sustainably manufactured multifunctional electronics.
Using Vertically Aligned Carbon Nanofiber Arrays on Rigid or Flexible Substrates for Delivery of Biomolecules and Dyes to Plants
The delivery of biomolecules and impermeable dyes to intact plants is a major challenge. Nanomaterials are up-and-coming tools for the delivery of DNA to plants. As exciting as these new tools are, they have yet to be widely applied. Nanomaterials fabricated on rigid substrate (backing) are particularly difficult to successfully apply to curved plant structures. This study describes the process for microfabricating vertically aligned carbon nanofiber arrays and transferring them from a rigid to a flexible substrate. We detail and demonstrate how these fibers (on either rigid or flexible substrates) can be used for transient transformation or dye (e.g., fluorescein) delivery to plants. We show how VACNFs can be transferred from rigid silicon substrate to a flexible SU-8 epoxy substrate to form flexible VACNF arrays. Further, to overcome the hydrophobic nature of SU-8, fibers in the flexible film were coated with a thin silicon oxide layer (2-3 nm). To use these fibers for delivery to curved plant organs, we deposit a 1 µL droplet of dye or DNA solution on the fiber side of VACNF films, wait 10 min, place the films on the plant organ and employ a swab with a rolling motion to drive fibers into plant cells. With this method, we have achieved dye and DNA delivery in plant organs with curved surfaces.