Pathway engineering for the discovery and optimized production of phosphonic acids

Natural products have been a great benefit to mankind, especially in modern times. With approximately half of all drugs used today being derived from small molecules observed in nature, the impact of these compounds is immeasurable. In the mid-twentieth century, a period known as the Golden Age of Antibacterials, the natural product field experienced a wave of discovery that has yet to be replicated. Even with the increased focus on using synthetic chemistry to discover potential pharmaceuticals, there has been a steady decline in discovery rates over the past decades. While traditional natural product discovery methods are limited to what is detectable in nature, advances in DNA sequencing technology, bioinformatics, and molecular biology have given researchers the ability to mine genomes for new compounds. By combing the abundant wealth of available genomic data, biosynthetic gene clusters can be readily identified for exploitation. However, two bottlenecks impede the transition from identified gene cluster to useful drug. The first hurdle is identifying the molecule linked to a set of biosynthetic genes. This step is well beyond any computational approach and must rely on empirical substantiation. The second hurdle is to produce enough of the compound in an economically feasible manner. In this work we implement pathway engineering strategies to further lower these barriers, with a focus on the class of natural products called phosphonic acids. These compounds have a stable carbon-phosphorus bond, which allow them to mimic phosphate esters and carboxylic acids, making them potential enzyme inhibitors. For the antimalarial phosphonate FR900098, a novel pathway engineering strategy, called enriched library screening, was developed that allows one to home in on top pathways in combinatorial libraries. When applied to the FR900098 pathway, a strain with a significant increase in production was found. This method can also be applied to other natural product pathways to rapidly find expression configurations that give higher yields. Additional strain engineering was also undertaken on the FR900098 strain; however, improvements were not seen despite a number of gene knockouts and knockdowns tested. To discover new phosphonic acids, biosynthetic pathways from two actinobacteria, Streptomyces species NRRL F-525 and Kibdelosporangium aridum largum NRRL B-24462, were fully engineered for production in the expression host Streptomyces lividans. This was done by placing the individual biosynthetic genes downstream of promoters characterized in S. lividans. Phosphonate production was seen in both hosts, with a novel phosphonate being identified in the Streptomyces species NRRL F-525 cluster. This approach can also be extended to discover other natural product gene clusters

NASA's Robotic Lunar Lander Development Program

NASA Marshall Space Flight Center and the Johns Hopkins University Applied Physics Laboratory have developed several mission concepts to place scientific and exploration payloads ranging from 10 kg to more than 200 kg on the surface of the moon. The mission concepts all use a small versatile lander that is capable of precision landing. The results to date of the lunar lander development risk reduction activities including high pressure propulsion system testing, structure and mechanism development and testing, and long cycle time battery testing will be addressed. The most visible elements of the risk reduction program are two fully autonomous lander flight test vehicles. The first utilized a high pressure cold gas system (Cold Gas Test Article) with limited flight durations while the subsequent test vehicle, known as the Warm Gas Test Article, utilizes hydrogen peroxide propellant resulting in significantly longer flight times and the ability to more fully exercise flight sensors and algorithms. The development of the Warm Gas Test Article is a system demonstration and was designed with similarity to an actual lunar lander including energy absorbing landing legs, pulsing thrusters, and flight-like software implementation. A set of outdoor flight tests to demonstrate the initial objectives of the WGTA program was completed in Nov. 2011, and will be discussed

Atrial high-rate episodes and stroke prevention.

While the benefit of oral anticoagulants (OACs) for stroke prevention in patients with atrial fibrillation (AF) is well established, it is not known whether oral anticoagulation is indicated in patients with atrial high-rate episodes (AHRE) recorded on a cardiac implantable electronic device, sometimes also called subclinical AF, and lasting for at least 6 min in the absence of clinically diagnosed AF. Clinical evidence has shown that short episodes of rapid atrial tachycarrhythmias are often detected in patients presenting with stroke and transient ischaemic attack. Patients with AHRE have a higher likelihood of suffering from subsequent strokes, but their stroke rate seems lower than in patients with diagnosed AF, and not all AHRE episodes correspond to AF. The prognostic and pathological significance of AHRE is not yet fully understood. Clinical trials of OAC therapy are being conducted to determine whether therapeutic intervention would be beneficial to patients experiencing AHRE in terms of reducing the risk of stroke

Peptides as quorum sensing molecules : measurement techniques and obtained levels in vitro and in vivo

The expression of certain bacterial genes is regulated in a cell-density dependent way, a phenomenon called quorum sensing. Both Gram-negative and Gram-positive bacteria use this type of communication, though the signal molecules (auto-inducers) used by them differ between both groups: Gram-negative bacteria use predominantly N-acyl homoserine lacton (AHL) molecules (autoinducer-1, AI-1) while Gram-positive bacteria use mainly peptides (autoinducer peptides, AIP or quorum sensing peptides). These quorum sensing molecules are not only involved in the inter-microbial communication, but can also possibly cross-talk directly or indirectly with their host. This review summarizes the currently applied analytical approaches for quorum sensing identification and quantification with additionally summarizing the experimentally found in vivo concentrations of these molecules in humans

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach

Prospects for Beyond the Standard Model Physics Searches at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach

Prospects for Beyond the Standard Model Physics Searches at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.Comment: 55 pages, 40 figures, paper based on the DUNE Technical Design Report (arXiv:2002.03005

The DUNE Far Detector Interim Design Report, Volume 3: Dual-Phase Module

The DUNE IDR describes the proposed physics program and technical designs of the DUNE far detector modules in preparation for the full TDR to be published in 2019. It is intended as an intermediate milestone on the path to a full TDR, justifying the technical choices that flow down from the high-level physics goals through requirements at all levels of the Project. These design choices will enable the DUNE experiment to make the ground-breaking discoveries that will help to answer fundamental physics questions. Volume 3 describes the dual-phase module's subsystems, the technical coordination required for its design, construction, installation, and integration, and its organizational structure

Design, construction and operation of the ProtoDUNE-SP Liquid Argon TPC

The ProtoDUNE-SP detector is a single-phase liquid argon time projection chamber (LArTPC) that was constructed and operated in the CERN North Area at the end of the H4 beamline. This detector is a prototype for the first far detector module of the Deep Underground Neutrino Experiment (DUNE), which will be constructed at the Sandford Underground Research Facility (SURF) in Lead, South Dakota, USA. The ProtoDUNE-SP detector incorporates full-size components as designed for DUNE and has an active volume of $7\times 6\times 7.2$~m$^3$. The H4 beam delivers incident particles with well-measured momenta and high-purity particle identification. ProtoDUNE-SP's successful operation between 2018 and 2020 demonstrates the effectiveness of the single-phase far detector design. This paper describes the design, construction, assembly and operation of the detector components