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The fast-growing microbe Vibrio natriegens is capable of natural transformation where it draws DNA in from media via an active process under physiological conditions. Using an engineered strain with a genomic copy of the master competence regulator tfoX from Vibrio cholerae in combination with a new minimal competence media (MCM) that uses acetate as an energy source, we demonstrate naturally competent cells which are created, transformed, and recovered entirely in the same media, without exchange or addition of fresh media. Cells are naturally competent to plasmids, recombination with linear DNA, and cotransformation of both to select for scarless and markerless genomic edits. The entire process is simple and inexpensive, requiring no capital equipment for an entirely room temperature process (zero capital protocol, 10 4 cfu/μg), or just an incubator (high-efficiency protocol, 10 5-6 cfu/μg). These cells retain their naturally competent state when frozen and are transformable immediately upon thawing like a typical chemical or electrochemical competent cell. Since the optimized transformation protocol requires only 50 min of hands-on time, and V. natriegens grows quickly even on plates, a transformation started at 9 AM yields abundant culturable single colonies by 5 PM. Further, because all stages of transformation occur in the same media, and the process can be arbitrarily scaled in volume, this natural competence strain and media could be ideal for automated directed evolution applications. As a result, naturally competent V. natriegens could compete with Escherichia coli as an excellent chassis for low-cost and highly scalable synthetic biology., (© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.)

In electromicrobial production (EMP), electricity is used as microbial energy to produce complex molecules starting from simple compounds like CO 2 . The aviation industry requires sustainable fuel alternatives that can meet demands for high-altitude performance and modern emissions standards. EMP of jet fuel components provides a unique opportunity to generate fuel blends compatible with modern engines producing net-neutral emissions. Branched-chain hydrocarbons modulate the boiling and freezing points of liquid fuels at high altitudes. In this study, we analyze the pathways necessary to generate branched-chain hydrocarbons in vivo utilizing extracellular electron uptake (EEU) and H 2 -oxidation for electron delivery, the Calvin cycle for CO 2 -fixation and the aldehyde deformolating oxygenase decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies to be 40.0 - 4.4 + 0.6 % and 39.8 - 4.5 + 0.7 % . For a model blend containing straight-chain, branched-chain, and terpenoid components, increasing the fraction of branched-chain alkanes from zero to 47% only lowers the electrical energy conversion efficiency from 40.1 - 4.5 + 0.7 % to 39.5 - 4.6 + 0.7 % ., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

Rare earth elements (REE) are essential ingredients in many modern technologies, yet their purification remains either environmentally harmful or economically unviable. Adsorption, or biosorption, of REE onto bacterial cell membranes offers a sustainable alternative to traditional solvent extraction methods. But in order for biosorption-based REE purification to compete economically, the capacity and specificity of biosorption sites must be enhanced. Although there have been some recent advances in characterizing the genetics of REE-biosorption, the variety and complexity of bacterial membrane surface sites make targeted genetic engineering difficult. Here, we propose using multiple rounds of in vivo random mutagenesis induced by the MP6 plasmid combined with plate-throughput REE-biosorption screening to improve a microbe's capacity and selectivity for biosorbing REE. We engineered a strain of Vibrio natriegens capable of biosorbing 210% more dysprosium compared to the wild-type and produced selectivity improvements of up to 50% between the lightest (lanthanum) and heaviest (lutetium) REE. We believe that mutations we observed in ABC transporters as well as a nonessential protein in the BAM outer membrane β-barrel protein insertion complex likely contribute to some─but almost certainly not all─of the biosorption changes we observed. Given the ease of finding significant biosorption mutants, these results highlight just how many genes likely contribute to biosorption as well as the power of random mutagenesis in identifying genes of interest and optimizing a biological system for a task.

Microbes which participate in extracellular electron uptake (EEU) or H 2 oxidation have the ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be valuable to efficiently synthesize drop-in jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-fuel conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency is 37.8 -4.3 +1.8 % when using EEU for electron delivery and 40.1 -4.6 +0.7 % when using H 2 oxidation. The production efficiency can be raised to 44.2 -3.7 +0.5 % when using the Formolase formate-assimilation pathway, and to 49.2 -2.1 +0.3 % with the Wood-Ljungdahl pathway. This efficiency can be further raised by swapping the well-known Aldehyde Deformolating Oxygenase (ADO) termination pathway with the recently discovered Fatty Acid Photodecarboxylase (FAP) pathway. If these systems were supplied with electricity from a maximally-efficient silicon solar photovoltaic, even the least efficient pathway exceeds the maximum solar-to-fuel efficiency of all known forms of photosynthesis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Systemic sclerosis, or scleroderma, is a collagen vascular disease characterized by hardening of the skin and involvement of internal organs, most commonly the esophagus. The most frequent cause of death in these patients is lung disease. Esophageal dysfunction has been implicated in the pathogenesis of interstitial lung disease. We previously developed a standard for the esophageal diameter on chest computed tomography (CT) and hypothesized that patients with esophageal dilation would be more likely to have interstitial lung disease than those without. In this study, we test this in 121 systemic sclerosis patients with interstitial lung disease and 48 of those without interstitial lung disease. For controls, we evaluated 121 patients followed at a general pulmonary clinic and the previously studied normal healthy standards. This study demonstrated that esophageal dilation is common in systemic sclerosis patients (66.3% for the maximal esophageal diameter more than or equal to 15 mm), that systemic sclerosis patients with interstitial lung disease have more dilated esophagi than those without interstitial lung disease (median 19.4 mm vs. 14.1 mm), and that esophageal parameters are negatively correlated with pulmonary function. We also found that patients from general pulmonary clinic were more likely to have dilated esophagi than normal controls (median 12.1 mm vs. 9.7 mm). The CT measurement of esophageal diameter may be a useful marker of patients at risk for developing lung disease.

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster.

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice--leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

Objective: This study was designed to quantify and characterize the air-containing thoracic esophagus on CT to help diagnose diseases and facilitate correlation with lung diseases that may be associated with aspiration., Subjects and Methods: The maximal air-containing esophageal lumina on each section of standard CT scans of 110 subjects were measured. These subjects came from a cohort of 10,132 self-reported healthy individuals who underwent CT for measurement of coronary artery calcium. Measurements were interpolated to account for variation in the length of the thoraces., Results: Greater than 60% of the esophageal segments contained no air. On average the maximum air column was 10.5 (SD, 5.0) mm. Only 7.9% of the lumina were > 10 mm. Only 2% were > 15 mm, and only 0.2% were > 20 mm. The average number of lumina > 10 mm as a proportion of the entire esophageal length was 8% (14%). The average size at the carina was 2.6 (4.1) mm. In the upper 30% and from 61% to 75% down the length of the esophagus, < 5% of the lumina were > 10 mm. Less than 3% of subjects had air in the lowest two sections, indicating that the normal lower esophageal sphincter was closed., Conclusion: Esophageal air of > 10 mm should be considered abnormal in all segments except between the cardiac ventricles and lower esophageal sphincter. In this area, > 15 mm should be considered abnormal. An air-fluid level is abnormal.