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1. Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

   https://doi.org/10.3390/cryst12010049  

   Ward, Abigail R. ; Dmytriw, Sara ; Vajapayajula, Ananya ; Snow, Christopher D. ( January 2022 , Crystals)

   Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide crosslinking agent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) under various optimization conditions: 5′ vs. 3′ terminal phosphate, EDC concentration, EDC incubation time, and repeated EDC dose. This crosslinking and DNA ligation route did not destroy crystal diffraction. In fact, the ligation of DNA across the DNA–DNA junctions was clearly revealed via X-ray diffraction structure determination. Furthermore, crystal macrostructure was fortified. Neither the loss of counterions in pure water, nor incubation in blood serum, nor incubation at low pH (2.0 or 4.5) led to apparent crystal degradation. These findings motivate the use of crosslinked biomolecular co-crystals for purposes beyond structural biology, including biomedical applications.
2. Freshwater salinization syndrome: from emerging global problem to managing risks

   https://doi.org/10.1007/s10533-021-00784-w  

   Kaushal, Sujay S. ; Likens, Gene E. ; Pace, Michael L. ; Reimer, Jenna E. ; Maas, Carly M. ; Galella, Joseph G. ; Utz, Ryan M. ; Duan, Shuiwang ; Kryger, Julia R. ; Yaculak, Alexis M. ; et al ( June 2021 , Biogeochemistry)

   null (Ed.)

   Abstract Freshwater salinization is an emerging global problem impacting safe drinking water, ecosystem health and biodiversity, infrastructure corrosion, and food production. Freshwater salinization originates from diverse anthropogenic and geologic sources including road salts, human-accelerated weathering, sewage, urban construction, fertilizer, mine drainage, resource extraction, water softeners, saltwater intrusion, and evaporative concentration of ions due to hydrologic alterations and climate change. The complex interrelationships between salt ions and chemical, biological, and geologic parameters and consequences on the natural, social, and built environment are called Freshwater Salinization Syndrome (FSS). Here, we provide a comprehensive overview of salinization issues (past, present, and future), and we investigate drivers and solutions. We analyze the expanding global magnitude and scope of FSS including its discovery in humid regions, connections to human-accelerated weathering and mobilization of ‘chemical cocktails.’ We also present data illustrating: (1) increasing trends in salt ion concentrations in some of the world’s major freshwaters, including critical drinking water supplies; (2) decreasing trends in nutrient concentrations in rivers due to regulations but increasing trends in salinization, which have been due to lack of adequate management and regulations; (3) regional trends in atmospheric deposition of salt ions and storage of salt ions in soils and groundwater, andmore »(4) applications of specific conductance as a proxy for tracking sources and concentrations of groups of elements in freshwaters. We prioritize FSS research needs related to better understanding: (1) effects of saltwater intrusion on ecosystem processes, (2) potential health risks from groundwater contamination of home wells, (3) potential risks to clean and safe drinking water sources, (4) economic and safety impacts of infrastructure corrosion, (5) alteration of biodiversity and ecosystem functions, and (6) application of high-frequency sensors in state-of-the art monitoring and management. We evaluate management solutions using a watershed approach spanning air, land, and water to explore variations in sources, fate and transport of different salt ions ( e.g. monitoring of atmospheric deposition of ions, stormwater management, groundwater remediation, and managing road runoff). We also identify tradeoffs in management approaches such as unanticipated retention and release of chemical cocktails from urban stormwater management best management practices (BMPs) and unintended consequences of alternative deicers on water quality. Overall, we show that FSS has direct and indirect effects on mobilization of diverse chemical cocktails of ions, metals, nutrients, organics, and radionuclides in freshwaters with mounting impacts. Our comprehensive review suggests what could happen if FSS were not managed into the future and evaluates strategies for reducing increasing risks to clean and safe drinking water, human health, costly infrastructure, biodiversity, and critical ecosystem services.« less
3. Radium in hydraulic fracturing wastewater: distribution in suspended solids and implications to its treatment by sulfate co-precipitation

   https://doi.org/10.1039/C8EM00311D  

   Ouyang, Bingjie ; Renock, Devon J. ; Ajemigbitse, Moses A. ; Van Sice, Katherine ; Warner, Nathaniel R. ; Landis, Joshua D. ; Feng, Xiahong ( February 2019 , Environmental Science: Processes & Impacts)

   High concentrations of barium (Ba), strontium (Sr) and radium (Ra) are present in both the liquid and suspended solid portions of wastewater produced from hydraulic fracturing. These high concentrations often require special treatment in which the solid and liquid portions are separated and then independently treated prior to disposal. The solids are typically disposed in landfills while the liquids are further treated, recycled for future hydraulic fracturing, or disposed via injection wells. Finding optimal treatment methods of both the solid and the liquid fractions requires a thorough understanding of potential Ra mobility from both the raw suspended solids and mineral precipitates formed during treatment. Using a sequential extraction procedure, we found that, without treatment, more than 50% of Ra-226 in the suspended solids was associated with soluble salts and readily exchangeable fractions. When the liquid portion of the wastewater was treated by mixing with acid mine drainage (AMD), which contained high sulfate concentrations, approximately 80–97% of the total Ra-226 in the mixture solution is found in the insoluble sulfate fraction of the precipitate. The activity of Ra-226 sequestered in the precipitated solid sulfate fractions is positively correlated with the Sr/Ba ratio of the wastewater-AMD solution. We discuss implications of thesemore »findings for effective long-term management of elevated radium in both solid and liquid wastes.« less
4. Formaldehyde Analysis in Non-Aqueous Methanol Solutions by Infrared Spectroscopy and Electrospray Ionization

   https://doi.org/10.3389/fchem.2021.678112  

   Barakoti, Krishna K. ; Subedi, Pradeep ; Chalyavi, Farzaneh ; Gutierrez-Portocarrero, Salvador ; Tucker, Matthew J. ; Alpuche-Aviles, Mario A. ( July 2021 , Frontiers in Chemistry)

   We present the analysis of formaldehyde (HCHO) in anhydrous methanol (CH 3 OH) as a case study to quantify HCHO in non-aqueous samples. At higher concentrations (C > 0.07 M), we detect a product of HCHO, methoxy methanol (MM, CH 3 OCH 2 OH), by Fourier transform infrared spectroscopy, FTIR. Formaldehyde reacts with CH 3 OH, CD 3 OH, and CD 3 OD as shown by FTIR with a characteristic spectral feature around 1,195 cm −1 for CH 3 OH used for the qualitative detection of MM, a formaldehyde derivative in neat methanol. Ab initio calculations support this assignment. The extinction coefficient for 1,195 cm −1 is in the order of 1.4 × 10 2  M −1 cm −1 , which makes the detection limit by FTIR in the order of 0.07 M. For lower concentrations, we performed the quantitative analysis of non-aqueous samples by derivatization with dinitrophenylhydrazine (DNPH). The derivatization uses an aqueous H 2 SO 4 solution to yield the formaldehyde derivatized hydrazone. Ba(OH) 2 removes sulfate ions from the derivatized samples and a final extraction with isobutyl acetate to yield a 1:1 methanol: isobutyl acetate solvent for injection for electrospray ionization (ESI). The ESI analysis gave a linear calibration curve formore »concentrations from 10 to 200 µM with a time-of-flight analyzer (TOF). The detection and quantification limits are 7.8 and 26 μM, respectively, for a linear correlation with R 2 > 0.99. We propose that the formaldehyde in CH 3 OH is in equilibrium with the MM species, without evidence of HCHO in solution. In the presence of water, the peaks for MM become less resolved, as expected from the well-known equilibria of HCHO that favors the formation of methylene glycol and polymeric species. Our results show that HCHO, in methanol does not exist in the aldehyde form as the main chemical species. Still, HCHO is in equilibrium between the production of MM and the formation of hydrated species in the presence of water. We demonstrate the ESI-MS analysis of HCHO from a non-aqueous TiO 2 suspension in methanol. Detection of HCHO after illumination of the colloid indicates that methanol photooxidation yields formaldehyde in equilibrium with the solvent.« less
5. Heterosynaptic plasticity in biomembrane memristors controlled by pH

   https://doi.org/10.1557/s43577-022-00344-z  

   McClintic, William T. ; Scott, Haden L. ; Moore, Nick ; Farahat, Mustafa ; Maxwell, Mikayla ; Schuman, Catherine D. ; Bolmatov, Dima ; Barrera, Francisco N. ; Katsaras, John ; Collier, C. Patrick ( January 2023 , MRS Bulletin)

   Abstract In biology, heterosynaptic plasticity maintains homeostasis in synaptic inputs during associative learning and memory, and initiates long-term changes in synaptic strengths that nonspecifically modulate different synapse types. In bioinspired neuromorphic circuits, heterosynaptic plasticity may be used to extend the functionality of two-terminal, biomimetic memristors. In this article, we explore how changes in the pH of droplet interface bilayer aqueous solutions modulate the memristive responses of a lipid bilayer membrane in the pH range 4.97–7.40. Surprisingly, we did not find conclusive evidence for pH-dependent shifts in the voltage thresholds ( V* ) needed for alamethicin ion channel formation in the membrane. However, we did observe a clear modulation in the dynamics of pore formation with pH in time-dependent, pulsed voltage experiments. Moreover, at the same voltage, lowering the pH resulted in higher steady-state currents because of increased numbers of conductive peptide ion channels in the membrane. This was due to increased partitioning of alamethicin monomers into the membrane at pH 4.97, which is below the pKa (~5.3–5.7) of carboxylate groups on the glutamate residues of the peptide, making the monomers more hydrophobic. Neutralization of the negative charges on these residues, under acidic conditions, increased the concentration of peptide monomers inmore »the membrane, shifting the equilibrium concentrations of peptide aggregate assemblies in the membrane to favor greater numbers of larger, increasingly more conductive pores. It also increased the relaxation time constants for pore formation and decay, and enhanced short-term facilitation and depression of the switching characteristics of the device. Modulating these thresholds globally and independently of alamethicin concentration and applied voltage will enable the assembly of neuromorphic computational circuitry with enhanced functionality. Impact statement We describe how to use pH as a modulatory “interneuron” that changes the voltage-dependent memristance of alamethicin ion channels in lipid bilayers by changing the structure and dynamical properties of the bilayer. Having the ability to independently control the threshold levels for pore conduction from voltage or ion channel concentration enables additional levels of programmability in a neuromorphic system. In this article, we note that barriers to conduction from membrane-bound ion channels can be lowered by reducing solution pH, resulting in higher currents, and enhanced short-term learning behavior in the form of paired-pulse facilitation. Tuning threshold values with environmental variables, such as pH, provide additional training and learning algorithms that can be used to elicit complex functionality within spiking neural networks. Graphical abstract« less