Evolution of Organic Solvent-Resistant DNA Polymerases.

The introduction of thermostable polymerases revolutionized the polymerase chain reaction (PCR) and biotechnology. However, many GC-rich genes cannot be PCR-amplified with high efficiency in water, irrespective of temperature. Although polar organic cosolvents can enhance nucleic acid polymerization and amplification by destabilizing duplex DNA and secondary structures, nature has not selected for the evolution of solvent-tolerant polymerase enzymes. Here, we used ultrahigh-throughput droplet-based selection and deep sequencing along with computational free-energy and binding affinity calculations to evolve Taq polymerase to generate enzymes that are both stable and highly active in the presence of organic cosolvents, resulting in up to 10% solvent resistance and over 100-fold increase in stability at 97.5 °C in the presence of 1,4-butanediol, as well as tolerance to up to 10 times higher concentrations of the potent cosolvents sulfolane and 2-pyrrolidone. Using these polymerases, we successfully amplified a broad spectrum of GC-rich templates containing regions with over 90% GC content, including templates recalcitrant to amplification with existing polymerases, even in the presence of cosolvents. We also demonstrated dramatically reduced GC bias in the amplification of genes with widely varying GC content in quantitative polymerase chain reaction (qPCR). By expanding the scope of solvent systems compatible with nucleic acid polymerization, these organic solvent-resistant polymerases enable a dramatic reduction of sequence bias not achievable through thermal resistance alone, with significant implications for a wide range of applications including sequencing and synthetic biology in mixed aqueous-organic media.

Discovery of novel compounds as potent activators of Sirt3.

Among the sirtuin enzymes, Sirt3 is one of the most important deacetylases as it regulates acetylation levels in mitochondria, which are linked to the metabolism of multiple organs and therefore involved in many types of age-related human diseases such as cancer, heart diseases and metabolic diseases. Given the dearth of direct activators of Sirt3, the identification of new modulators could be a key step in the development of new therapeutics. Here we report the discovery of Sirt3 modulators, including activators, through the use of DNA encoded library technology (DEL) and computational high-throughput screening methodologies. Top hits from both screenings against Sirt3 were evaluated according to their activity and affinity. Our best activator is more potent than the previously reported activator Honokiol. Docking studies suggest that our activators identified from virtual screening interact with Sirt3 at a site similar to Honokiol, whereas the activators identified from DEL selection interact with Sirt3 at an atypical site. Our results establish the attractiveness of these high-throughput screening technologies in identifying novel and potent Sirt3 activators and, therefore, in associated therapeutic applications.

Professional quality of life in nurses on the frontline against COVID-19.

AIMS: This study aimed to investigate professional quality of life (ProQOL) in nurses who were fighting against COVID-19 in Wuhan and its related factors. BACKGROUND: COVID-19 epidemic is a major threat to public health. Frontline nurses have engaged in infection prevention and control, isolation, containment and public health. However, available data on ProQOL in these nurses are limited. METHODS: From 15 to 21 March 2020, the Chinese version of ProQOL was utilized to survey a total of 102 nurses through an electronic questionnaire. The stepwise regression analysis was performed to determine which factors (e.g. demographic and work-related factors) were related to ProQOL. RESULTS: The scores of compassion satisfaction (CS), burnout (BO) and secondary traumatic stress (STS) were 38.09 ± 5.22, 21.77 ± 4.92 and 20.75 ± 6.27, respectively. The STS and CS scores were higher than the critical value. None of the nurses reported a low level of CS or a high level of BO and STS. Nurses' ProQOL was related to working hours, workload, job satisfaction and salary satisfaction. CONCLUSIONS: Nurses who were fighting against COVID-19 had better CS and BO, whereas STS was relatively worse. Nurses who worked for long hours had more severe STS. BO of nurses with heavy workload and dissatisfaction with their salary was more severe. Nurses who were unsatisfied with their job had poor CS. IMPLICATIONS FOR NURSING MANAGEMENT: It is believed that these results may help nurse managers to improve ProQOL of nurses who were fighting against COVID-19 by minimizing working hours, reducing workload and improving job satisfaction and rewards.

Biophysical characterization of hit compounds for mechanism-based enzyme activation.

Across all families of enzymes, only a dozen or so distinct classes of non-natural small molecule activators have been characterized, with only four known modes of activation among them. All of these modes of activation rely on naturally evolved binding sites that trigger global conformational changes. Among the enzymes that are of greatest interest for small molecule activation are the seven sirtuin enzymes, nicotinamide adenine dinucleotide (NAD+)-dependent protein deacylases that play a central role in the regulation of healthspan and lifespan in organisms ranging from yeast to mammals. However, there is currently no understanding of how to design sirtuin-activating compounds beyond allosteric activators of SIRT1-catalyzed reactions that are limited to particular substrates. Here, we introduce a general mode of sirtuin activation that is distinct from the known modes of enzyme activation. Based on the conserved mechanism of sirtuin-catalyzed deacylation reactions, we establish biophysical properties of small molecule modulators that can in principle result in enzyme activation for diverse sirtuins and substrates. Building upon this framework, we propose strategies for the identification, characterization and evolution of hits for mechanism-based enzyme activating compounds.

Molecular system identification for enzyme directed evolution and design.

The rational design of chemical catalysts requires methods for the measurement of free energy differences in the catalytic mechanism for any given catalyst Hamiltonian. The scope of experimental learning algorithms that can be applied to catalyst design would also be expanded by the availability of such methods. Methods for catalyst characterization typically either estimate apparent kinetic parameters that do not necessarily correspond to free energy differences in the catalytic mechanism or measure individual free energy differences that are not sufficient for establishing the relationship between the potential energy surface and catalytic activity. Moreover, in order to enhance the duty cycle of catalyst design, statistically efficient methods for the estimation of the complete set of free energy differences relevant to the catalytic activity based on high-throughput measurements are preferred. In this paper, we present a theoretical and algorithmic system identification framework for the optimal estimation of free energy differences in solution phase catalysts, with a focus on one- and two-substrate enzymes. This framework, which can be automated using programmable logic, prescribes a choice of feasible experimental measurements and manipulated input variables that identify the complete set of free energy differences relevant to the catalytic activity and minimize the uncertainty in these free energy estimates for each successive Hamiltonian design. The framework also employs decision-theoretic logic to determine when model reduction can be applied to improve the duty cycle of high-throughput catalyst design. Automation of the algorithm using fluidic control systems is proposed, and applications of the framework to the problem of enzyme design are discussed.

Mechanism of inhibition of the human sirtuin enzyme SIRT3 by nicotinamide: computational and experimental studies.

Sirtuins are key regulators of many cellular functions including cell growth, apoptosis, metabolism, and genetic control of age-related diseases. Sirtuins are themselves regulated by their cofactor nicotinamide adenine dinucleotide (NAD+) as well as their reaction product nicotinamide (NAM), the physiological concentrations of which vary during the process of aging. Nicotinamide inhibits sirtuins through the so-called base exchange pathway, wherein rebinding of the reaction product to the enzyme accelerates the reverse reaction. We investigated the mechanism of nicotinamide inhibition of human SIRT3, the major mitochondrial sirtuin deacetylase, in vitro and in silico using experimental kinetic analysis and Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB(GB)SA) binding affinity calculations with molecular dynamics sampling. Through experimental kinetic studies, we demonstrate that NAM inhibition of SIRT3 involves apparent competition between the inhibitor and the enzyme cofactor NAD+, contrary to the traditional characterization of base exchange as noncompetitive inhibition. We report a model for base exchange inhibition that relates such kinetic properties to physicochemical properties, including the free energies of enzyme-ligand binding, and estimate the latter through the first reported computational binding affinity calculations for SIRT3:NAD+, SIRT3:NAM, and analogous complexes for Sir2. The computational results support our kinetic model, establishing foundations for quantitative modeling of NAD+/NAM regulation of mammalian sirtuins during aging and the computational design of sirtuin activators that operate through alleviation of base exchange inhibition.

An optimized method for the measurement of acetaldehyde by high-performance liquid chromatography.

BACKGROUND: Acetaldehyde is produced during ethanol metabolism predominantly in the liver by alcohol dehydrogenase and rapidly eliminated by oxidation to acetate via aldehyde dehydrogenase. Assessment of circulating acetaldehyde levels in biological matrices is performed by headspace gas chromatography and reverse phase high-performance liquid chromatography (RP-HPLC). METHODS: We have developed an optimized method for the measurement of acetaldehyde by RP-HPLC in hepatoma cell culture medium, blood, and plasma. After sample deproteinization, acetaldehyde was derivatized with 2,4-dinitrophenylhydrazine (DNPH). The reaction was optimized for pH, amount of derivatization reagent, time, and temperature. Extraction methods of the acetaldehyde-hydrazone (AcH-DNP) stable derivative and product stability studies were carried out. Acetaldehyde was identified by its retention time in comparison with AcH-DNP standard, using a new chromatography gradient program, and quantitated based on external reference standards and standard addition calibration curves in the presence and absence of ethanol. RESULTS: Derivatization of acetaldehyde was performed at pH 4.0 with an 80-fold molar excess of DNPH. The reaction was completed in 40 minutes at ambient temperature, and the product was stable for 2 days. A clear separation of AcH-DNP from DNPH was obtained with a new 11-minute chromatography program. Acetaldehyde detection was linear up to 80 µM. The recovery of acetaldehyde was >88% in culture media and >78% in plasma. We quantitatively determined the ethanol-derived acetaldehyde in hepatoma cells, rat blood and plasma with a detection limit around 3 µM. The accuracy of the method was <9% for intraday and <15% for interday measurements, in small volume (70 µl) plasma sampling. CONCLUSIONS: An optimized method for the quantitative determination of acetaldehyde in biological systems was developed using derivatization with DNPH, followed by a short RP-HPLC separation of AcH-DNP. The method has an extended linear range, is reproducible and applicable to small-volume sampling of culture media and biological fluids.

Phosphorylation of osteopontin is required for inhibition of calcium oxalate crystallization.

Under near-physiological pH, temperature, and ionic strength, a kinetics constant composition (CC) method was used to examine the roles of phosphorylation of a 14 amino acid segment (DDVDDTDDSHQSDE) corresponding to potential crystal binding domains within the osteopontin (OPN) sequence. The phosphorylated 14-mer OPN peptide segment significantly inhibits both the nucleation and growth of calcium oxalate monohydrate (COM), inhibiting nucleation by markedly increasing induction times and delaying subsequent growth by at least 50% at concentrations less than 44 nM. Molecular modeling predicts that the doubly phosphorylated peptide binds much more strongly to both (-101) and (010) faces of COM. The estimated binding energies are, in part, consistent with the CC experimental observations. Circular dichroism spectroscopy indicates that phosphorylation does not result in conformational changes in the secondary peptide structure, suggesting that the local binding of negatively charged phosphate side chains to crystal faces controls growth inhibition. These in vitro results reveal that the interactions between phosphorylated peptide and COM crystal faces are predominantly electrostatic, further supporting the importance of macromolecules rich in anionic side chains in the inhibition of kidney stone formation. In addition, the phosphorylation-deficient form of this segment fails to inhibit COM crystal growth up to concentrations of 1450 nM. However, at sufficiently high concentrations, this nonphosphorylated segment promotes COM nucleation. Dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) results confirm that aggregation of the nonphosphorylated peptide segment takes place in solution above 900 nM when the aggregated peptide particles may exceed a well-defined minimum size to be effective crystallization promoters.

Functionalized PEG-PEI copolymers complexed to exon-skipping oligonucleotides improve dystrophin expression in mdx mice.

Exon-skipping oligonucleotides (ESOs) with 2'-O-methyl modifications are promising compounds for the treatment of Duchenne muscular dystrophy (DMD). However, the usefulness of these compounds is limited by their poor delivery profile to muscle tissue in vivo. We previously established that copolymers made of poly(ethylene imine) (PEI) and poly(ethylene glycol) (PEG) enhanced ESO transfection in skeletal muscle of mdx mice, resulting in widespread distribution of dystrophin-positive fibers, but limited dystrophin expression by Western blot. In an attempt to improve ESO delivery and dystrophin expression, a new formulation of PEG-PEI copolymer was used, along with functionalized derivatives containing either the cell-penetrating peptide TAT (trans-activator of transcription), adsorbed colloidal gold (CG), or both TAT and CG. Tibialis anterior muscles were given three intramuscular injections of various PEG-PEI-ESO polyplexes (3 days apart; 5 microg of ESO per injection) and muscles were harvested 3 weeks after the first injection. Surface modifications of PEG-PEI copolymers with TAT showed the highest level of dystrophin recovery, with a 6-fold increase in dystrophin-positive fibers compared with ESO alone and up to 30% of normal dystrophin expression by Western blot. The adsorption of CG to either PEG-PEI or TAT-PEG-PEI copolymers showed no further improvement in dystrophin expression. Our data indicate that TAT-modified PEG-PEI copolymers are effective carriers for delivery of ESOs to skeletal muscle and are promising compounds for the therapeutic treatment of DMD.

An understanding of renal stone development in a mixed oxalate-phosphate system.

The in vivo formation of calcium oxalate concretions having calcium phosphate nidi is simulated in an in vitro (37 degrees C, pH 6.0) dual constant composition (DCC) system undersaturated (sigma DCPD = -0.330) with respect to brushite (DCPD, CaHPO 4 . 2H 2O) and slightly supersaturated (sigma COM = 0.328) with respect to calcium oxalate monohydrate (COM, CaC2O4 . H2O). The brushite dissolution provides calcium ions that raise the COM supersaturation, which is heterogeneously nucleated either on or near the surface of the dissolving calcium phosphate crystals. The COM crystallites may then aggregate, simulating kidney stone formation. Interestingly, two intermediate phases, anhydrous dicalcium phosphate (monetite, CaHPO4) and calcium oxalate trihydrate (COT), are also detected by X-ray diffraction during this brushite-COM transformation. In support of clinical observations, the results of these studies demonstrate the participation of calcium phosphate phases in COM crystallization providing a possible physical chemical mechanism for kidney stone formation.

Mimicking the Self-Organized Microstructure of Tooth Enamel.

Under near-physiological pH, temperature, and ionic strength, amelogenin (Amel) accelerates hydroxyapatite (HAP) nucleation kinetics, decreasing the induction time in a concentration-dependent manner. Hierarchically organized apatite microstructures are achieved by self-assembly involving nucleated nanocrystallites and Amel oligomers and nanospheres at low supersaturations and protein concentrations in a slow and well-controlled constant composition (CC) system. The CC method allows the capture of an intermediate structure, the nanorod, following the formation of the critical nuclei at the earliest nucleation stages of calcium phosphate crystallization. The nanorod building blocks form spontaneously by synergistic interactions between flexible Amel protein assemblies and rigid calcium phosphate nanocrystallites. These intermediate structures further assemble by a self-epitaxial growth mechanism to form the final hierarchically organized microstructures that are compositionally and morphologically similar to natural enamel. This in vitro observation provides direct evidence that Amel promotes apatite crystallization and organization. We interpret our observations to propose that in vivo Amel may maximally exert an influence on the structural control of developing enamel crystals at the earliest nucleation stages.

Amelogenin Promotes the Formation of Elongated Apatite Microstructures in a Controlled Crystallization System.

The organic matrix in forming enamel consists largely of the amelogenin protein self-assembled into nanospheres that play a pivotal role in controlling the oriented and elongated growth of highly ordered apatitic crystals during enamel biomineralization. However, the mechanisms of amelogenin-mediated mineralization have not yet been fully elucidated. Here we report that amelogenin dramatically accelerates the nucleation kinetics by decreasing the induction time in a dose-dependent manner in a controlled constant composition (CC) in vitro crystallization system. Remarkably, at very low protein concentrations, elongated microstructures which are similar in appearance to apatitic crystals in enamel were formed at relatively low supersaturations, through interfacial structural match/synergy between structured amelogenin assemblies and apatite nanocrystallites. This heterogeneous crystallization study provides experimental evidence to support the concept that templating by amelogenin very early in the crystallization process facilitates the formation of developing enamel crystals.

Modulation of calcium oxalate crystallization by linear aspartic acid-rich peptides.

Calcium oxalate monohydrate (COM) kidney stone formation is prevented in most humans by urinary crystallization inhibitors. Urinary osteopontin (OPN) is a prototype of the aspartic acid-rich proteins (AARP) that modulate biomineralization. Synthetic poly(aspartic acids) that resemble functional domains of AARPs provide surrogate molecules for exploring the role of AARPs in biomineralization. Effects of linear aspartic acid-rich peptides on COM growth kinetics and morphology were evaluated by the combination of constant composition (CC) analysis and atomic force microscopy (AFM). A spacer amino acid (either glycine or serine) was incorporated during synthesis after each group of 3 aspartic acids (DDD) in the 27-mer peptide sequences. Kinetic CC studies revealed that the DDD peptide with serine spacers (DDDS) was more than 30 times more effective in inhibiting COM crystal growth than the DDD peptide with glycine spacers (DDDG). AFM revealed changes in morphology on (010) and (-101) COM faces that were generally similar to those previously described for OPN and citrate, respectively. At comparable peptide levels, the effects of step pinning and reduced growth rate caused by DDDS were remarkably greater. In CC nucleation studies, DDDS caused a greater prolongation of induction periods than DDDG. Thus, nucleation studies link changes in interfacial energy caused by peptide adsorption to COM to the CC growth and AFM results. These studies indicate that, in addition to the number of acidic residues, the contributions of other amino acids to the conformation of DDD peptides are also important determinants of the inhibition of COM nucleation and growth.

The potential calcification of octacalcium phosphate on intraocular lens surfaces.

Recently, calcification was observed on implanted intraocular lens (IOL) surfaces when viscoelastic substances were applied during surgery. To elucidate the mechanisms of mineral formation, the crystallization of calcium phosphates on IOL surfaces was studied in vitro with nanomolar sensitivity using a constant composition method. Three different commercial viscoelastic materials (Viscoat, OcuCoat, and Amvisc Plus) were investigated and it was found that some IOLs treated with Viscoat or Amvisc Plus induced the nucleation and growth of octacalcium phosphate crystallites under biological conditions. After treatments, the IOL surfaces became more hydrophilic probably because of the high viscoelastic phosphate and carboxylate contents. In contrast to Viscoat, the use of OcuCoat during surgery resulted in virtually no octacalcium phosphate nucleations. Calcification studies of IOL surfaces treated with fatty acids, which are present in human aqueous humor, suggest that hydrophobic cyclic silicones adsorbed on the IOL surfaces interact strongly with hydrophobic hydrocarbon chains of the fatty acids, creating a layer of amphiphiles oriented with functional carboxylate groups exposed to the aqueous solution and serving as active calcification sites.

Calcification of intraocular implant lens surfaces.

Calcification of octacalcium phosphate [Ca8H2(PO4)6 x 5H2O, OCP] on differently packaged "Ultem" and "Surefold" intraocular implant lens surfaces has been studied in vitro in solutions supersaturated with respect to OCP at pH = 7.10 and 37 degrees C. No mineral deposition was observed on the lenses packaged in Ultem vials even after treatment with behenic acid, one of the fatty acids identified on explanted lenses. Following treatment with behenic acid, nucleation of OCP occurred on the lenses from Surefold vials, which incorporate silicone gaskets; induction periods preceding calcification were about 6 h. No mineralization was found on the lenses in vials with other gasket materials, including polytetrafluoroethylene, fluorocarbon elastomer, and polypropylene. The results of this study indicate that both silicone and fatty acids such as behenic acid play important roles in inducing the in vivo calcification of OCP on IOL lenses; all of the lens treatment steps were necessary for nucleation induction.