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Design-driven optimization of low-cost reagent formulations for reproducible and high-yielding cell-free gene expression
Access to recombinant proteins is vital in basic science and biotechnology research. Cell-free gene expression systems provide one approach to address this need, but widespread utilization remains limited by the cost, complexity, and inconsistency of current platforms. To address these limitations, we carry out a multi-dimensional definitive screening design to reduce the number of reagent components and remove costly secondary energy substrates. From 1,231 different reagent formulations, we discover a simple and reproducible system based on 12 components. The optimized reagent formulation can produce 2.4 ± 0.3 g/L of protein product at the 15-µL scale (~$\$60$/gprotein) and 3.7 ± 0.2 g/L (~$\$39$/gprotein) at the 4-mL scale with oxygen supplementation. This provides an average 95% reduction in cost over previous cell-free reagent formulations. We further show that the optimized reagent formulation can produce nucleoside triphosphates from nitrogenous bases and ribose and that it is robust to failure across batches of cell lysates, users/locations, and in the synthesis of more than 20 different proteins. For example, we demonstrate the production of fifteen therapeutically relevant products, including full-length aglycosylated monoclonal antibodies. We anticipate that our optimized reagent formulation will democratize the use of cell-free systems for protein manufacturing and synthetic biology applications.
The chlorination and separation of aluminum using low-temperature sulfur chloride reagents
There is currently no strategy for the permanent waste disposal or recycling for used nuclear fuelsfrom research reactors. For this reason, low-temperature reactions have been developed for thechlorination of the Al alloys and subsequent separation from used nuclear fuels to reducethe volume of high-level waste in storage. Three sulfur chloride reagents – S 2 Cl 2 , SOCl 2 , and SO 2 Cl 2 —were tested, and two were found to quantitatively chlorinate Al metal and Al alloys undermild conditions. Further, these low-temperature reactions proceed between 298 and 411 K, and up to 5 gof metal is chlorinated in 1–3 h. Preliminary results indicate that the reactivity and exothermicity ofthe reaction between the Al and sulfur chloride reagents is highly dependent on the surface area-to-volume ratio of the metal and the volume of solvent. Elemental S is produced as a by-productduring the chlorination with S 2 Cl 2 but can be quantitatively rechlorinated under mild conditions toregenerate the initial chlorination reagent. Therefore, in this case, chlorine is the only elementconsumed in the reaction, thus minimizing the waste generated during the chlorination process.The AlCl 3 may then be separated from other materials present in Al 6061 or Al 8001 because of itshigh solubility in the sulfur chloride reagents. This process may also be extended to chlorinate Alfrom research reactor fuels.
Pyridine Polyaminocarboxylate Ligands for Use as Actinide-selective Holdback Reagents in Simplified TALSPEAK-like Extraction Systems
Three pyridine-based aqueous complexants have been synthesized and used in an unbuffered TALSPEAK (Trivalent Actinide Lanthanide Separation by Phosphorus-reagent from Aqueous Komplexes) separation system as minor actinide-selective holdback reagents. The selectivity was established based on distribution studies using radiotracer 152/154Eu, 241Am, stable Ln, Y and Th. In this system, these ligands selectively sequester Am from the lanthanides without the need for a secondary pH buffer. Am-lanthanide separation factors for Eu were found to be > 70 for all three ligands and > 15 for Nd. Aqueous pyridine based ligands represent viable alternatives for traditional actinide-selective holdback reagents in TALSPEAK-based systems.
Reagent-free Hyperspectral Diagnosis of SARS-CoV-2 Infection in Saliva Samples
Rapid, reagent-free pathogen-agnostic diagnostics that can be performed at the point of need are vital for preparedness against future outbreaks. Yet, many current strategies are pathogen-specific and require several reagents. We present hyperspectral sensing, using light to non-invasively measure the composition of several molecules to form a spectral signature, to overcome these barriers. To generate these spectral signatures, we present the ProSpectral TM V1, a novel, miniaturized hyperspectral platform with high spectral resolution with two mini-spectrometers. Furthermore, we developed state-of-the-art ML pipelines for near real-time analysis of spectral signatures in saliva samples. We found that we could accurately identify SARS-CoV-2 infection status in double-blinded saliva samples and demonstrate 100% accuracy on a hold out test dataset. To our knowledge, this establishes the fastest hyperspectral diagnostic platform and in a small form factor, and executable with liquid samples, without ligands or reagents, all while maintaining PCR level specificity and sensitivity.
In vitro evolution-enabled selection of affinity reagents against bio/chem-threats [Slides]
Affinity reagent are molecules whose function depends on specific recognition of a target. The function can allow therapeutic and/or diagnostic applications. The support CBDP pillars are--Understand: high accuracy/sensitivity, low cost, deployable detection; Protect: pre-event treatment of soldiers; and Mitigate: post-event treatment of soldiers; help identifying the need for specific decontamination protocols. The Los Alamos affinity reagents team (LA-ART) can can obtain affinity reagents to any target, on demand, using a well-established in vitro evolution platform. Recent success stories are shared.
Teaching an Old Reagent New Tricks: Synthesis, Unusual Reactivity, and Solution Dynamics of Borohydride Grignard Compounds
Grignard reagents of general formula RMgX (X = Cl - , Br - , I - ) have been utilized in various chemistries for over 100 years. Here, we report that replacing the halide in a Grignard reagent with a reactive borohydride anion adds a new synthetic dimension for these influential compounds. Here, we synthesized the series RMgBH 4 (R=Et, n-Bu, Ph, Bn) and characterized the reactivity toward both organic and inorganic molecules. Using butylmagnesium borohydride (BuMgBH 4 ) as an exemplar, we demonstrate that these compounds possess unique reactivity due to the presence of reducing borohydride groups, resulting in tandem reactivity with organic amides/esters to generate secondary and primary alcohols. Molecular dynamics simulations indicate the stability of BuMgBH 4 is comparable to that of Mg(BH 4 ) 2 + MgBu 2 , validating the Schlenk equilibrium in borohydride Grignard compounds. Metadynamics simulations confirm that the equilibrium is kinetically accessible through solvent-mediated processes. BuMgBH 4 also reacts with CO 2 and NH 3 , revealing potential uses for CO 2 utilization and as a mixed-anion metal borohydride/amide precursor.
Rapid Alloy Surface Engineering through Closed-Vessel Reagent Pyrolysis
For rapid surface engineering of Cr-containing alloys by low-temperature nitrocarburization, we introduce a process based on pyrolysis of solid reagents, e.g., urea, performed in an evacuated closed vessel. Upon heating to temperatures high enough for rapid diffusion of interstitial solute, but low enough to avoid second-phase precipitation, the reagent is pyrolyzed to a gas atmosphere containing molecules that (i) activate the alloy surface by stripping away the passivating Cr 2 O 3 -rich surface film (diffusion barrier) and (ii) rapidly infuse carbon and nitrogen into the alloy. We demonstrate quantitatively that this method can generate a subsurface zone with concentrated carbon and nitrogen comparable to what can be accomplished by established (e.g., gas-phase- or plasma-based) methods, but with significantly reduced processing time. As another important difference to established gas-phase processing, the interaction of gas molecules with the alloy surface can have auto-catalytic effects by altering the gas composition in a way that accelerates solute infusion by providing a high activity of HNCO. The new method lends itself to rapid experimentation with a minimum of laboratory equipment.
Use of Fluorescent Protein Reporters for Assessing and Detecting Genome Editing Reagents and Transgene Expression in Plants
Fluorescent protein reporters have been widely used for monitoring the expression of target genes in various engineered organisms. Although a wide range of analytical approaches (e.g., genotyping PCR, digital PCR, DNA sequencing) have been utilized to detect and identify genome editing reagents and transgene expression in genetically modified plants, these methods are usually limited to use in the late stages of plant transformation and can only be used invasively. Here we describe GFP- and eYGFPuv-based strategies and methods for assessing and detecting genome editing reagents and transgene expression in plants, including protoplast transformation, leaf infiltration, and stable transformation. These methods and strategies enable easy, noninvasive screening of genome editing and transgenic events in plants.
Hydrothermal liquefaction of sewage sludge – effect of four reagents on relevant parameters related to biocrude and $\mathrm{PFAS}$
Catalytic hydrothermal liquefaction (HTL) can convert wet biomass into crude-like oil and has potential to degrade pollutants during the thermal depolymerization process. To avoid negative environmental impacts from per- and polyfluoroalkyl substances (PFAS) in sewage sludge after its final disposal, we comprehensively evaluated catalytic destruction of PFAS in sludge through HTL. Here the results showed that adding red mud to HTL was beneficial for the biocrude yield and significantly increased the carbon conversion efficiency and energy recovery of the hydrothermal process. HTL at 300 °C for 2 h degraded > 96% of spiked perfluorooctanoic acid (PFOA). The mass of spiked perfluorobutanesulfonic acid (PFBS) and perfluorooctanesulfonic acid (PFOS) and pre-existing perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), however, increased in the HTL product streams. The remaining PFAS after HTL mainly stayed in the biocrude phase. Our findings indicated that HTL under the studied condition was not able to degrade all PFAS existed in sewage sludge. Although adding red mud could improve the HTL performance with respect to biocrude, this reagent did not improve the removal of perfluoroalkyl acids (PFAAs). As a matter of fact, the hydrothermal process amended with the selected reagents resulted in increased mass of PFBS, PFHxA, and PFHpA in the HTL products due to degradation of PFAA precursors. Thus, other treatment approaches for PFAS removal from sewage sludge need to be identified to prevent possible contamination of environments receiving PFAS-containing sludge.
Characterization of Lactobacilli Phage Endolysins and Their Functional Domains–Potential Live Biotherapeutic Testing Reagents
Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach uses the endolysin cell wall binding domains (CBD) for LBP potency assays and the endolysin killing activity for purity assays. CBDs of the following five lactobacilli phage lysins were characterized: CL1, Jlb1, Lj965, LL-H, and ΦJB. They exhibited different bindings to 27 LAB strains and were found to bind peptidoglycan or surface polymers. Flow cytometry based on CBD binding was used to enumerate viable counts of two strains in the mixture. CL1-lys, jlb1-lys, and ΦJB-lys and their enzymatic domains (EADs) exhibited cell wall digestive activity and lytic activity against LAB. Jlb1-EAD and ΦJB-EAD were more sensitive than their respective hololysins to buffer pH and NaCl changes. The ΦJB-EAD exhibited stronger lytic activity than ΦJB-lys, possibly due to ΦJB-CBD-mediated sequestration of ΦJB-lys by cell debris. CBD multiplex assays indicate that these proteins may be useful LBP potency reagents, and the lytic activity suggests that CL1-lys, jlb1-lys, and ΦJB-lys and their EADs are good candidates for LBP purity reagent development.
Reagent to label proteins via lysine isopeptide bonds
Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction—first, cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate, and second, joining the terminal threonine to the nucleophilic lysine residue residing within the pilin motif of another pilin protomer. Informed by the high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and by developing structural variants of the sortase enzyme whose catalytic pocket has been unmasked by activating mutations, we have developed new reagents capable of forming isopeptide bonds in vitro. The reagents disclosed herein can catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile new platform for protein engineering and bio-conjugation that has major implications for biotechnology.
Influence of ion-pairing reagents on the separation of intact glycoproteins using hydrophilic-interaction liquid chromatography - high-resolution mass spectrometry
Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ~40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.
Comparative Study of Solvatomorphs of Stryker's Reagent Using MicroED and Quantum Mechanics
Abstract The atomic position of hydrogen atoms in metal hydrides has been a long‐standing structural question in inorganic chemistry given that hydride delivery is integral to diverse chemical reactions. Microcrystal electron diffraction (microED), with it's increased sensitivity toward hydrogen atoms relative to X‐ray diffraction, offers a potential path to addressing this challenge. Herein, the first microED study of Stryker's reagent is reported, resulting in the structure of a new benzene solvate. Improved accuracy for hydrogen atom positions was obtained via a quantum crystallography (QCr) approach, Hirshfeld atom refinement (HAR). Structural and topological analysis supports edge bridging hydrides in the microED structure of a THF solvate form, consistent with previous diffraction studies. Interestingly, analysis of a new benzene solvate, discovered in this study, is consistent with mixed edge‐ and face‐bridging hydrides.
Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications
Here, we present an update and revision to our 2010 review on the topic of proton- coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XHn in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H 2 ), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H 2 ) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.
Protonated Tungsten Bronze (H x WO 3 ) Acts as an Easily Regenerable Reagent for PCET Reactions
In this study, protonated tungsten bronze powder (H x WO 3 ) was synthesized by a microwave heating technique from tungsten(VI) chloride in benzyl alcohol. This material facilitates a proton-coupled electron transfer (PCET) reaction with 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) in toluene, an aprotic solvent, to form TEMPOH, evidenced by UV–vis analysis of the organic product and X-ray photoelectron spectroscopy (XPS) analysis showing the oxidation of W 5+ to W 6+ in the remaining powder. Then, under illumination in an acidic aqueous solution, the oxidized WO 3 powder reacts photochromically to regenerate H x WO 3 . The regenerated H x WO 3 reagent remains active for further PCET reactions.
B -Alkyl-borabicyclo[3.3.1]nonane Reagents Promote Closed-Shell Nickel-Catalyzed Alkylarylation Toward Encoded Cyclooctene Monomers
Access to new tailored monomers is essential to explore unprecedented polymer structures and modulate their properties. In previous work, we disclosed an iteroselective diarylation of 1,5-cyclooctadiene as an attractive platform for preparing diverse cyclooctene monomers; however, it was limited to C(sp 2 ) coupling partners. Established difunctionalization methods with C(sp 3 ) fragments rely on carbon-based radical formation, which is incompatible with 1,5-cyclooctadiene. This work describes a two-electron redox manifold for the nickel-catalyzed alkylarylation of 1,5-cyclooctadiene and discloses B -alkyl-borabicyclo[3.3.1]nonane (alkyl-9-BBN) as an effective transmetalating reagent for maintaining a polar reaction mechanism. The method provides 5,6-alkylarylated cyclooctenes suitable for ring-opening metathesis polymerization to obtain new materials. The properties of these polymers are benchmarked and fine-tuned by variation of coupling partners in the nickel catalysis. Density functional theory calculations revealed that destabilization of the pretransmetalation complex promotes the reactivity of alkyl-9-BBN in transmetalation compared to alkylboronic esters.
A Carborane-Derived Proton-Coupled Electron Transfer Reagent
Reagents capable of concerted proton–electron transfer (CPET) reactions can access reaction pathways with lower reaction barriers compared to stepwise pathways involving electron transfer (ET) and proton transfer (PT). To realize reductive multielectron/proton transformations involving CPET, one approach that has shown recent promise involves coupling a cobaltocene ET site with a protonated arylamine Brønsted acid PT site. This strategy colocalizes the electron/proton in a matter compatible with a CPET step and net reductive electrocatalysis. To probe the generality of such an approach a class of C,C'-diaryl-ocarboranes is herein explored as a conceptual substitute for the cobaltocene subunit, with an arylamine linkage still serving as a colocalized Brønsted base suitable for protonation. The featured ocarborane (PhCbPh N ) can be reduced and protonated to generate an N–H bond with a weak effective bond dissociation free energy (BDFE eff ) of 31 kcal/mol, estimated with measured thermodynamic data. This N–H bond is among the lowest measured element–H bonds for analyzed nonmetal compounds. Distinct solid-state crystal structures of the one- and two-electron reduced forms of diaryl-o-carboranes are disclosed to gain insight into their well-behaved redox characteristics. The singly reduced, protonated form of the diaryl-o-carborane can mediate multi-ET/PT reductions of azoarenes, diphenylfumarate, and nitrotoluene. In contrast to the aforementioned cobaltocene system, available mechanistic data disclosed herein support these reactions occurring by a rate-limiting ET step and not a CPET step. A relevant hydrogen evolution reaction (HER) reaction was also studied, with data pointing to a PT/ ET/PT mechanism, where the reduced carborane core is itself highly stable to protonation.