Divalent Concentration Research Articles

Probing the role of ligation and exonuclease digestion towards non-specific amplification in bioanalytical RCA assays.

Non-specific amplification (NSA, amplification in the absence of a target analyte) in bioanalytical rolling circle amplification (RCA) assays, especially those involving pre-synthesized circular DNA (cDNA), affects its analytical sensitivity. Despite extensive development of RCA-based bioanalytical methods, the NSA in RCA remains uncharacterized in terms of its magnitude or origin. NSA may originate from inefficient ligation or succeeding cDNA purification steps. This study comprehensively quantifies NSA across several ligation and digestion techniques for the first time since the innovation of RCA. To quantify the NSA in RCA, cDNAs were prepared using self-annealing, splint-padlock, or cohesive end ligations. The cDNAs were then subjected to nine different exonuclease digestion steps and quantified for NSA under linear as well as hyperbranched RCA conditions. We investigated buffer compositions, divalent ion concentrations, single or dual enzyme digestion, cohesive end lengths, and splint lengths. The optimized conditions successfully mitigated absolute NSA by 30-100-fold and relative NSA (normalized against primer-assisted RCA) to ∼5%. Besides understanding the mechanistic origin of NSA, novel aspects of enzyme-substrate selectivity, buffer composition, and the role of divalent ions were discovered. With increasing bioanalytical RCA applications, this study will help standardize NSA-free assays.

Theoretical and experimental investigation of the impact of oil functional groups on the performance of smart water in clay-rich sandstones

This research investigated the effect of ion concentration on the performance of low salinity water under different conditions. First, the effect of injection water composition on interparticle forces in quartz-kaolinite, kaolinite-kaolinite, and quartz-oil complexes was tested and modeled. The study used two oil samples, one with a high total acid number (TAN) and the other with a low TAN. The results illustrated that reducing the concentration of divalent ions to 10 mM resulted in the electric double layer (EDL) around the clay and quartz particles and the high TAN oil droplets, expanding and intensifying the repulsive forces. Next, the study investigated the effect of injection water composition and formation oil type on wettability and oil/water interfacial tension (IFT). The results were consistent with the modeling of interparticle forces. Reducing the divalent cation concentration to 10 mM led to IFT reduction and wettability alteration in high TAN oil, but low TAN oil reacted less to this change, with the contact angle and IFT remaining almost constant. Sandpack flooding experiments demonstrated that reducing the concentration of divalent cations incremented the recovery factor (RF) in the presence of high TAN oil. However, the RF increment was minimal for the low TAN oil sample. Finally, different low salinity water scenarios were injected into sandpacks containing migrating fines. By comparing the results of high TAN oil and low TAN oil samples, the study observed that fine migration was more effective than wettability alteration and IFT reduction mechanisms for increasing the RF of sandstone reservoirs.

The influence of divalent ions on the osmotic energy conversion performance of 2D cation exchange membrane in reverse electrodialysis process

As reverse electrodialysis (RED) technology evolves, achieving high-performance osmotic energy conversion (OEC) necessitates porous membranes with exceptional ion selectivity and permeability. Two-dimensional membranes crafted from graphene oxide (GO) or MXene stand out for their immensely high surface charges, which facilitate superb ion selectivity during transport. Their unique layered stacking structure further yields ultra-small nanochannel radii, bolstering ion selectivity while maintaining high permeability. This makes them prime candidates for osmotic energy conversion. However, the presence of divalent ions in natural seawater readily alters the surface charge density and interlayer spacing of these 2D membranes, significantly impacting their OEC performance, resulting in a power density reduction of about 6 % -10 %. Prior research focused on the ionic properties of divalent ions but overlooked their impact on the nanochannel structure, including changes in interlayer spacing and surface charge density. This study thus delves into the OEC performance variations of GO and MXene 2D layered membranes under varying divalent ion concentrations and salt ratios. Starting from the ion properties of divalent ions and their impact on the nanochannel structure, combined with simulation research, explain their mechanism of action. This research offers theoretical foundations for the future design and application of 2D layered membranes, providing novel solutions and insights to tackle critical challenges like enhancing power density and adapting to real seawater conditions.

Direct lithium extraction from Canadian oil and gas produced water using functional ionic liquids – A preliminary study

In this study, a functional ionic liquid system was successfully applied to extract lithium from the Canadian oil and gas produced water samples without further dilution at ambient conditions. The effects of interference cations, dissolved organics and other factors on the extraction were studied in detail. Chemical precipitation method was applied to reduce the concentrations of divalent ions before the ionic liquid extraction. The extraction efficiency is about 70% on average and can be as high as 90%. It appears that this extraction method can be directly applied to the oilfield brine samples with both high Na/Li and Mg/Li ratios. In addition, it seems that the dissolved organics in the produced water did not impact the extraction efficiency. Efforts shall be made in the future to reduce the cost by replacing the diluent with another type of solvent and further improving the recycle and reuse of the IL systems. In summary, the technology can achieve satisfactory lithium extraction from the Canadian oil and gas produced water.

Cation valency in water-in-salt electrolytes alters the short- and long-range structure of the electrical double layer

Highly concentrated aqueous electrolytes (termed water-in-salt electrolytes, WiSEs) at solid-liquid interfaces are ubiquitous in myriad applications including biological signaling, electrosynthesis, and energy storage. This interface, known as the electrical double layer (EDL), has a different structure in WiSEs than in dilute electrolytes. Here, we investigate how divalent salts [zinc bis(trifluoromethylsulfonyl)imide, Zn(TFSI)2], as well as mixtures of mono- and divalent salts [lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) mixed with Zn(TFSI)2], affect the short- and long-range structure of the EDL under confinement using a multimodal combination of scattering, spectroscopy, and surface forces measurements. Raman spectroscopy of bulk electrolytes suggests that the cation is closely associated with the anion regardless of valency. Wide-angle X-ray scattering reveals that all bulk electrolytes form ion clusters; however, the clusters are suppressed with increasing concentration of the divalent ion. To probe the EDL under confinement, we use a Surface Forces Apparatus and demonstrate that the thickness of the adsorbed layer of ions at the interface grows with increasing divalent ion concentration. Multiple interfacial layers form following this adlayer; their thicknesses appear dependent on anion size, rather than cation. Importantly, all electrolytes exhibit very long electrostatic decay lengths that are insensitive to valency. It is likely that in the WiSE regime, electrostatic screening is mediated by the formation of ion clusters rather than individual well-solvated ions. This work contributes to understanding the structure and charge-neutralization mechanism in this class of electrolytes and the interfacial behavior of mixed-electrolyte systems encountered in electrochemistry and biology.

Characterization of aqueous foams of alkyl polyglycoside, GreenZyme, alpha-olefin sulfonate, and cetyltrimethylammonium bromide in the presence of divalent ions

In this study, the impacts of divalent ions (calcium and magnesium) on aqueous foam stability and its rheological properties are investigated. A biodegradable surfactant of alkyl polyglycoside, (APG) and a commercial enzyme (GreenZyme, GZ) are used and their performance were compared with synthetic surfactants of alpha-olefin sulfonate (AOS) and cetyltrimethylammonium bromide (CTAB). The findings of the study revealed that the stability of all foams decreased with increasing concentrations of divalent ions, GZ recorded the lowest foam stability in the presence of the two ions and precipitation occurred in the AOS solution. On the other hand, foams generated by APG achieved the highest stability and the foams generated by CTAB showed the second highest stability among the foaming agents. Through rheological analyses, APG and CTAB exhibited shear thinning behaviour and their behaviour were modelled using a power law model in which the model can incorporate the effects of temperature and salinity.

Efficacy of Modified Magnolia champaca Bark Powder in Sequestration of Divalent Ions from Aqueous Matrices

Noxious effluents let out from large cum small- scale industries has led to acute adverse environmental impact over a time period. In spite of various types of pollutants present in the discharges, heavy metals have been proven to be lethal to all living organisms, whilst exceeding the tolerance levels. In this regard, their confiscation has become inevitable by adoption of varied suitable methodologies. The current inquest is engrossed on probing the efficiency of an eco-derived material, Magnolia champaca Barks (MCB) to trap Zn(II) / Cd(II) ions from laboratory aqueous medium. This ecofriendly material is acid treated (TMCB), so as to improve its surface nature, evidently favoured by microscopic image study. Fourier Transformation Infra-Red and Scanning Electron Microscopy / Energy Dispersive X-Ray Analysis spectra are recorded for sorbent characterization. The factors which influence the sorptive effectiveness of TMCB include particle sizes, initial concentrations of the sorbate molecules, agitation time frames, dosages, pH values and temperatures. The concentrations of divalent ions in the pre and post run samples are assessed using Atomic Absorption Spectrophotometer. Maximum chelation of 98% Zn(II) and 96% Cd(II) had occurred under aligned parametric conditions, with variations in dosage, concentration and contact time interval. The aforementioned observations support the promising nature of the identified bark to adsorb toxic metal species.

Barium Concentration-Dependent Anomalous Electrophoresis of Synthetic DNA Motifs.

The structural integrity, assembly yield, and biostability of DNA nanostructures are influenced by the metal ions used to construct them. Although high (>10 mM) concentrations of divalent ions are often preferred for assembling DNA nanostructures, the range of ion concentrations and the composition of the assembly products vary for different assembly conditions. Here, we examined the unique ability of Ba2+ to retard double crossover DNA motifs by forming a low mobility species, whose mobility on the gel is determined by the concentration ratio of DNA and Ba2+. The formation of this electrophoretically retarded species is promoted by divalent ions such as Mg2+, Ca2+, and Sr2+ when combined with Ba2+ but not on their own, while monovalent ions such as Na+, K+, and Li+ do not have any effect on this phenomenon. Our results highlight the complex interplay between the metal ions and DNA self-assembly and could inform the design of DNA nanostructures for applications that expose them to multiple ions at high concentrations.

Exploring the Effect of Relaxation Time, Natural Surfactant, and Potential Determining Ions (Ca2+, Mg2+, and SO42−) on the Dynamic Interfacial Tension Behavior of Model Oil-Brine Systems

This study examined how the concentration of asphaltene and divalent ions in various salinities affects the interfacial tension (IFT) between a model oil/brine using the pendant drop method. The oleic phase consisted of a mixture of toluene and n-heptane (heptol), to which asphaltene was added to investigate how asphaltene molecules affect the surface properties. The base fluid was prepared with a salinity of 40,000 ppm, and two additional solutions with concentrations of 4000 ppm (low salinity) and 80,000 ppm (high salinity) were created. The results revealed that increasing the concentration of asphaltene within certain salinity ranges led to a decrease in IFT. The lowest IFT was observed at the 40,000 ppm salinity level, indicating that at this optimal salinity, the maximum asphaltene concentration migrated to the heptol/brine interface, reducing the IFT from 23 mN/m to 16 mN/m. Additionally, a 0.5 % wt of asphaltene demonstrated a significant concentration of micellization of natural surfactants, suggesting that the interface was nearly saturated with asphaltene. Consequently, concentrations higher than this value did not significantly alter the IFT. In the final part of the study, the impact of divalent ions was investigated, revealing that as the concentration of Ca2+ ions increased up to fourfold, the IFT decreased to 15 mN/m, about 10 % less than the base case. This value represented the lowest IFT compared to Mg2+ and SO42−. Moreover, modeling the results indicated that the relaxation time decreased with increasing salinity, suggesting that higher salinity accelerated the process of asphaltene absorption at the interface.

Oil/Brine Screening for Improved Fluid/Fluid Interactions during Low-Salinity Water Flooding

Low-salinity water flooding/smart water flooding (LSWF/SWF) are used for enhanced oil recovery (EOR) because of the improved extraction efficiency. These methods are more environmentally friendly and in many scenarios more economical for oil recovery. They are proven to increase recovery factors (RFs) by between 6 and 20%, making LSWF/SWF technologies that should be further evaluated to replace conventional water flooding or other EOR methods. Fluid/fluid interaction improvements include interfacial tension (IFT) reduction, viscoelastic behavior (elastic properties modification), and microemulsion generation, which could complement the main mechanisms, such as wettability alteration. In this research, we evaluate the importance of fluid/fluid mechanisms during LSWF/SWF operations. Our study showed that a substantial decrease in IFT occurs when the oil asphaltene content is in the range of 0% to 3 wt.%. An IFT reduction was observed at low salinity (0–10,000 ppm) and a specific oil composition condition. Optimal IFT occurs at higher divalent ion concentrations when oil has low asphaltene content. For the oil with high asphaltene content, the sulfates concentration controls the IFT alteration. At high asphaltene concentrations, the formation of micro-dispersion is not effective to recover oil, and only a 5% recovery factor improvement was observed. The presence of asphaltene at the oil/low-salinity brine interface increases the energy required to disrupt it, inducing significant changes in the elastic moduli. In cases of low asphaltene content, the storage modulus demonstrates optimal performance at higher divalent concentrations. Conversely, at high asphaltene concentrations, the dominant factors to control the interface are paraffin content and temperature.

Investigation of the solid oxidizer effect on the metal geotechnology efficiency

Purpose. The research is aimed at increasing the useful component content in a pregnant solution during in-situ leaching (ISL) using a solid oxidizer and increasing the ferric iron concentration in the leaching solution based on laboratory research. Methods. Laboratory research is performed on a specially developed model electrolyzer for obtaining comparative data on divalent iron oxidation to trivalent iron and the change in the useful component content in a pregnant solution. Firstly, tests are conducted with a basic leaching solution, then on the oxidation of the leaching solution with a solid oxidizer in the form of a lead dioxide plate. Tests are conducted by changing sulphuric acid concentration within 5-50 g/l, amount of divalent iron ions in the solution from 0.5 up to 4.0 g, lead dioxide plate surface area from 19 to 76 cm2. The leaching time is up to 10 hours. Findings. The results of laboratory research on determining the oxidation degree of divalent iron ions and change in the oxidation-reduction potential (ORP) depending on the sulphuric acid concentration and on the initial concentration of divalent iron ions in the initial solution are presented. With a change in the sulphuric acid concentration from 5 to 50 g/l, the oxidation value of divalent iron ions increases from 26.5 to 96.5%, and with an increase in the initial solution concentration of divalent iron, the oxidation degree of divalent iron naturally decreases from 95.2 to 58.8%. In the initial leaching solution, the divalent solution concentration is 312 mg/l, and that of the trivalent solution is 288 mg/l. After oxidation with a solid oxidizer, the divalent and trivalent iron concentrations are 56 and 392 mg/l, respectively. In the course of further laboratory research using core materials from a uranium deposit, it has been revealed that when leaching with a basic solution, the uranium content in the pregnant solution is 19.36 mg/l, and when leaching with a solution after oxidation with a solid oxidizer, it is 27.9 mg/l, which is by 8.54 mg/l more. Originality. New dependences have been determined of the oxidation degree of divalent iron ions to trivalent one on the sulphuric acid concentration and on the initial concentration of divalent iron ions, as well as the useful component content in the pregnant solution on the leaching time when using a solid oxidizer. Practical implications. Using of a solid oxidizer, it is possible to increase the trivalent iron concentration in the leaching solution and the useful component content in the pregnant solution compared with the basic technology, thereby reducing the time of mining uranium reserves. Proposed technology is environmentally friendly, with low capital costs.

DNA Probes for Cas12a-Based Assay with Fluorescence Anisotropy Enhanced Due to Anchors and Salts.

CRISPR/Cas12a is a potent biosensing tool known for its high specificity in DNA analysis. Cas12a recognizes the target DNA and acquires nuclease activity toward single-stranded DNA (ssDNA) probes. We present a straightforward and versatile approach to transforming common Cas12a-cleavable DNA probes into enhancing tools for fluorescence anisotropy (FA) measurements. Our study involved investigating 13 ssDNA probes with linear and hairpin structures, each featuring fluorescein at one end and a rotation-slowing tool (anchor) at the other. All anchors induced FA changes compared to fluorescein, ranging from 24 to 110 mr. Significant FA increases (up to 180 mr) were obtained by adding divalent metal salts (Mg2+, Ca2+, Ba2+), which influenced the rigidity and compactness of the DNA probes. The specific Cas12a-based recognition of double-stranded DNA (dsDNA) fragments of the bacterial phytopathogen Erwinia amylovora allowed us to determine the optimal set (probe structure, anchor, concentration of divalent ion) for FA-based detection. The best sensitivity was obtained using a hairpin structure with dC10 in the loop and streptavidin located near the fluorescein at the stem in the presence of 100 mM Mg2+. The detection limit of the dsDNA target was equal to 0.8 pM, which was eight times more sensitive compared to the common fluorescence-based method. The enhancing set ensured detection of single cells of E. amylovora per reaction in an analysis based on CRISPR/Cas12a with recombinase polymerase amplification. Our approach is universal and easy to implement. Combining FA with Cas12a offers enhanced sensitivity and signal reliability and could be applied to different DNA and RNA analytes.

Reaction of Highly Dispersed Nickel Metal Powders with Pd(II) Aqueous Solutions under Hydrothermal Conditions

The processes of contact reaction of nickel metal powders with aggregated particle sizes of 300–400 nm with aqueous solutions of palladium(II) in autoclaves at elevated temperatures in acidic and alkaline media have been studied. It has been found that when metallic nickel contacts with aqueous solutions of palladium(II) chloride in 0.01 M hydrochloric acid at temperatures of 100 and 130°C for 15 min, the concentration of divalent palladium ions decreases to zero. The process is accompanied by a partial transition of nickel into solution. The precipitates are a mixture of metallic particles of nickel and palladium of variable compositions. In the case of contact of metallic nickel with solutions of tetraammine palladium(II) chloride at temperatures of 160 and 170°C in a medium of 0.1 M potassium hydroxide, metal palladium particles 5–25 nm in size are formed on the surface of larger nickel particles. The structure of bimetallic particles has been determined by X-ray photoelectron microscopy.

Factors influencing the detergent-free membrane protein isolation using synthetic nanodisc-forming polymers

The detergent-free isolation of membrane proteins using synthetic polymers is becoming the desired approach for functional and structural studies of membrane proteins. Since the expression levels for many membrane proteins are low and a high yield of functionalized reconstituted membrane proteins is essential for in vitro studies, it is crucial to optimize the experimental conditions for a given polymer to solubilize target membranes/proteins effectively. The factors that affect membrane solubilization and subsequently the isolation of a target membrane protein include polymer concentration, polymer charge, temperature, pH, and concentration of divalent metal ions. Therefore, it is important to have knowledge about the efficacy of different types of polymers in solubilizing cell membranes. In this study, we evaluate the efficacy of inulin-based non-ionic polymers in solubilizing E. coli membranes enriched with rat flavin mononucleotide binding-domain (FBD) of cytochrome-P450-reductase (CPR) and rabbit cytochrome-b5 (Cyt-b5) under various solubilization conditions. Our results show that a 1:1 (w/w) membrane:polymer ratio, low temperature, high pH and sub-millimolar concentration of metal ions favor the solubilization of E. coli membranes enriched with FBD or Cyt-b5. Conversely, the presence of excess divalent metal ions affected the final protein levels in the polymer-solubilized samples. We believe that the results from this study provide knowledge to assess and plan the use of non-ionic polymers in membrane protein studies.

A comprehensive review of viscoelastic polymer flooding in sandstone and carbonate rocks

Polymer flooding is a proven chemical Enhanced Oil Recovery (cEOR) method that boosts oil production beyond waterflooding. Thorough theoretical and practical knowledge has been obtained for this technique through numerous experimental, simulation, and field works. According to the conventional belief, this technique improves macroscopic sweep efficiency due to high polymer viscosity by producing moveable oil that remains unswept after secondary recovery. However, recent studies show that in addition to viscosity, polymer viscoelasticity can be effectively utilized to increase oil recovery by mobilizing residual oil and improving microscopic displacement efficiency in addition to macroscopic sweep efficiency. The polymer flooding is frequently implemented in sandstones with limited application in carbonates. This limitation is associated with extreme reservoir conditions, such as high concentrations of monovalent and divalent ions in the formation brine and ultimate reservoir temperatures. Other complications include the high heterogeneity of tight carbonates and their mixed-to-oil wettability. To overcome the challenges related to severe reservoir conditions, novel polymers have been introduced. These new polymers have unique monomers protecting them from chemical and thermal degradations. Monomers, such as NVP (N-vinylpyrrolidone) and ATBS (2-acrylamido-2-methylpropane sulfonic acid), enhance the chemical resistance of polymers against hydrolysis, mitigating the risk of viscosity reduction or precipitation in challenging reservoir conditions. However, the viscoelasticity of these novel polymers and their corresponding impact on microscopic displacement efficiency are not well established and require further investigation in this area. In this study, we comprehensively review recent works on viscoelastic polymer flow under various reservoir conditions, including carbonates and sandstones. In addition, the paper defines various mechanisms underlying incremental oil recovery by viscoelastic polymers and extensively describes the means of controlling and improving their viscoelasticity. Furthermore, the polymer screening studies for harsh reservoir conditions are also included. Finally, the impact of viscoelastic synthetic polymers on oil mobilization, the difficulties faced during this cEOR process, and the list of field applications in carbonates and sandstones can also be found in our work. This paper may serve as a guide for commencing or performing laboratory- and field-scale projects related to viscoelastic polymer flooding.

Evaluating the effect of food components on the digestion of dietary nucleic acids in human gastric juice in vitro.

Nucleic acids (NAs) were recently shown to be digested by pepsin in vitro; however, NAs digestion in human gastric juice in vivo is more complicated because of the complex gastric environment and ingestion of other food components. The purpose of this study was to investigate the digestibility of NAs in real human gastric juices after ingestion of other food components. As a result, DNA digestion was not affected when carbohydrates, proteins, and metal elements were ingested within the recommended dietary intake levels. Separately, protein exerted an inhibitory effect on DNA digestion when the mass ratio of protein:DNA was greater than 40:1. DNA exists in the nucleoprotein, which is closer to the state of DNA in real food, and was digested efficiently in human gastric juice. Meanwhile, DNA digestion was rarely affected even when the concentrations of monovalent ion (Na+) and divalent ions (Mg2+) were as high as 500 and 100 mM, respectively, and high concentration of Mg2+ ranged from 20 to 100 mM accelerated the digestion. In particular, short-stranded DNA (<100 nt) and miRNAs (19 ~ 25 nt) were not obviously degraded in human gastric juice. In conclusion, dietary NAs were digested efficiently and were not affected by other food components in human gastric juice, which may facilitate further digestion and utilization of DNA in the intestinal tract.

Dual brine concentration for the beneficial use of two concentrate streams from desalination plant - Concept proposal and pilot plant demonstration

A dual brine concentration concept is proposed and proved in a pilot plant demonstration with commercial membranes. To utilize the dissolved ions in seawater (45,000 mg/L) effectively for various applications, a nanofiltration (NF) system is introduced in the upstream of the reverse osmosis (RO) system, and a membrane brine concentration (MBC) system is introduced after RO to concentrate the RO brine to the desired point, i.e., 15 wt% (166,000 mg/L) and higher. In the proposed NF-RO-MBC system two valuable brines are produced: 1) Concentrate 1, which is highly concentrated and purified monovalent ion stream at a TDS of about 170,000 mg/L after HPRO and 2 stage OARO, and 2) Concentrate 2, which has a high concentration of divalent ions, such as 3.41 times the Ca and 5.17 times the Mg concentration compared to those in seawater. Based on the successful pilot demonstration data and performance evaluation of a novel NF membrane and a single OARO module, a commercial-scale NF-RO-MBC system was designed for the capacity of 1 mil. dry ton/year production of NaCl salt in the form of 169,000 mg/L concentrated brine. With the proposed configuration, 65.2 % of the seawater will be recovered as fresh water, 19.3 % will be Concentrate 1, and the remainder 15.5 % will be Concentrate 2. The specific electricity consumption of the NF-RO-MBC system is estimated as 6.90 kWh/t of the fresh water produced, and the techno-economic analysis estimated the production cost of fresh water as 0.57 USD/m3 and that of NaCl brine as 28.87 USD/dry t NaCl.

Structure and ion-dependent folding of k-junctions.

k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.

Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions.

Misfolding of the cellular prion protein (PrPC) is associated with the development of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs). Metal ions appear to play a crucial role in PrPC misfolding. PrPC is a combined Cu(II) and Zn(II) metal-binding protein, where the main metal-binding site is located in the octarepeat (OR) region. Thus, the biological function of PrPC may involve the transport of divalent metal ions across membranes or buffering concentrations of divalent metal ions in the synaptic cleft. Recent studies have shown that an excess of Cu(II) ions can result in PrPC instability, oligomerization, and/or neuroinflammation. Here, we have used biophysical methods to characterize Cu(II) and Zn(II) binding to the isolated OR region of PrPC. Circular dichroism (CD) spectroscopy data suggest that the OR domain binds up to four Cu(II) ions or two Zn(II) ions. Binding of the first metal ion results in a structural transition from the polyproline II helix to the β-turn structure, while the binding of additional metal ions induces the formation of β-sheet structures. Fluorescence spectroscopy data indicate that the OR region can bind both Cu(II) and Zn(II) ions at neutral pH, but under acidic conditions, it binds only Cu(II) ions. Molecular dynamics simulations suggest that binding of either metal ion to the OR region results in the formation of β-hairpin structures. As the formation of β-sheet structures can be a first step toward amyloid formation, we propose that high concentrations of either Cu(II) or Zn(II) ions may have a pro-amyloid effect in TSE diseases.

New Insights into Hybrid Low-Salinity Polymer Flooding through a Coupled Geochemical-Based Modeling Approach

Summary Low-salinity polymer (LSP) flooding is a synergic emergent enhanced oil recovery (EOR) technique. Previous laboratory experiments showed noticeable improvements in displacement efficiency, polymer rheology, injectivity, and viscoelasticity. Nevertheless, when it comes to modeling LSP flooding, it is still challenging to develop a mechanistic predictive model that captures polymer-brine-rock (PBR) interactions. Therefore, this study uses a coupled MATLAB reservoir simulation toolbox (MRST)-IPhreeqc simulator to investigate the effect of water chemistry on PBR interactions during LSP flooding through varying overall salinity and the concentrations of divalent and monovalent ions. For describing the related geochemistry, the presence of polymer in the aqueous phase was considered by introducing novel solution species (Poly) to the Phreeqc database. The developed model’s parameters were validated and history matched with experimental data reported in the literature. Moreover, different injection schemes were analyzed, including low-salinity (LS) water, LSP injection (1 × LSP), and 5-times spiked LSP injection (5 × LSP) with their related effects on polymer viscosity. Results showed that polymer viscosity during LSP flooding is affected directly by Ca2+ and Mg2+ and indirectly by SO42− owing to PBR interactions on a dolomite rock-forming mineral. Monovalent ions (viz. Na+ and K+) have minor effects on polymer viscosity. Ca2+ and Mg2+ ions discharged from dolomite dissolution create polymer complexes (acrylic acid, C3H4O2) to reduce polymer viscosity significantly. The increased SO42− concentration in the injected LSP solution affects the interactions between the polymer and positively charged aqueous species, leading to minimized polymer viscosity loss. For LSP flood derisking measures, the cation’s effect was related to the charge ratio (CR). Thus, it is key to obtain an optimal CR where viscosity loss is minimal. This paper is among the few to detail the mechanistic geochemical modeling of the LSP flooding technique. The validated MRST-IPhreeqc simulator evaluates the previously overlooked effects of water chemistry on polymer viscosity during the LSP process. Using this coupled simulator, several other geochemical reactions and parameters can be assessed, including rock and injected-water compositions, injection schemes, and other polymer characteristics.