Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster

As sequence databases grow, characterizing diversity across extremely large collections of genomes requires the development of efficient methods that avoid costly all-vs-all comparisons [Marschall et al., 2018]. In addition to exponential increases in the amount of natural genomes being sequenced, improved techniques for the creation of human engineered sequences is ushering in a new wave of synthetic genome sequence databases that grow alongside naturally occurring genome databases. In this paper, we analyze the full diversity of available sequenced natural and synthetic plasmid genome sequences. This diversity can be represented by a data structure that captures all presently available nucleotide sequences, known as a pan-genome. In our case, we construct a single linear pan-genome nucleotide sequence that captures this diversity. To process such a large number of sequences, we introduce the plaster algorithmic pipeline. Using plaster we are able to construct the full synthetic plasmid pan-genome from 51,047 synthetic plasmid sequences as well as a natural pan-genome from 6,642 natural plasmid sequences. We demonstrate the efficacy of plaster by comparing its speed against another pan-genome construction method as well as demonstrating that nearly all plasmids align well to their corresponding pan-genome. Finally, we explore the use of pan-genome sequence alignment to distinguish between naturally occurring and synthetic plasmids. We believe this approach will lead to new techniques for rapid characterization of engineered plasmids. Applications for this work include detection of genome editing, tracking an unknown plasmid back to its lab of origin, and identifying naturally occurring sequences that may be of use to the synthetic biology community. The source code for fully reconstructing the natural and synthetic plasmid pan-genomes as well for plaster are publicly available and can be downloaded at https://gitlab.com/qiwangrice/plaster.git

Synthesis and evaluation of analogues of the glycinocin family of calcium-dependent antibiotics

The glycinocins are a class of calcium-dependent, acidic cyclolipopeptide antibiotics that are structurally related to the clinically approved antibiotic daptomycin. In this article, we describe the synthesis of a small library of glycinocin analogues that differ by variation in the exocyclic fatty acyl substituent. The glycinocin analogues were screened against a panel of Gram-positive bacteria (as well as Gram-negative P. aeruginosa). These analogues exhibited similar calcium-dependent activity to the parent natural products against Gram-positive bacteria but showed no activity against P. aeruginosa. The length of the fatty acid was shown to be important for optimal biological activity, while the hybridisation at the α,β position and branching within the fatty acyl chain had only subtle effects on activity

Nonlinear optical interactions in silicon waveguides

The strong nonlinear response of silicon photonic nanowire waveguides allows for the integration of nonlinear optical functions on a chip. However, the detrimental nonlinear optical absorption in silicon at telecom wavelengths limits the efficiency of many such experiments. In this review, several approaches are proposed and demonstrated to overcome this fundamental issue. By using the proposed methods, we demonstrate amongst others supercontinuum generation, frequency comb generation, a parametric optical amplifier, and a parametric optical oscillator

Rapid Additive-Free Selenocystine–Selenoester Peptide Ligation

We describe an unprecedented reaction between peptide selenoesters and peptide dimers bearing N-terminal selenocystine that proceeds in aqueous buffer to afford native amide bonds without the use of additives. The selenocystine-selenoester ligations are complete in minutes, even at sterically hindered junctions, and can be used in concert with one-pot deselenization chemistry. Various pathways for the transformation are proposed and probed through a combination of experimental and computational studies. Our new reaction manifold is also showcased in the total synthesis of two proteins

Systemwide Clinical Ultrasound Program Development: An Expert Consensus Model.

Clinical ultrasound (CUS) is integral to the practice of an increasing number of medical specialties. Guidelines are needed to ensure effective CUS utilization across health systems. Such guidelines should address all aspects of CUS within a hospital or health system. These include leadership, training, competency, credentialing, quality assurance and improvement, documentation, archiving, workflow, equipment, and infrastructure issues relating to communication and information technology. To meet this need, a group of CUS subject matter experts, who have been involved in institution- and/or systemwide clinical ultrasound (SWCUS) program development convened. The purpose of this paper was to create a model for SWCUS development and implementation

Heat Shock Protein gp96 Is a Master Chaperone for Toll-like Receptors and Is Important in the Innate Function of Macrophages

Summarygp96 is an endoplasmic reticulum chaperone for cell-surface Toll-like receptors (TLRs). Little is known about its roles in chaperoning other TLRs or in the biology of macrophage in vivo. We generated a macrophage-specific gp96-deficient mouse. Despite normal development and activation by interferon-γ, tumor necrosis factor-α, and interleukin-1β, the mutant macrophages failed to respond to ligands of both cell-surface and intracellular TLRs including TLR2, TLR4, TLR5, TLR7, and TLR9. Furthermore, we found that TLR4 and TLR9 preferentially interacted with a super-glycosylated gp96 species. The categorical loss of TLRs in gp96-deficient macrophages operationally created a conditional and cell-specific TLR null mouse. These mice were resistant to endotoxin shock but were highly susceptible to Listeria monocytogenes. Our results demonstrate that gp96 is the master chaperone for TLRs and that macrophages, but not other myeloid cells, are the dominant source of proinflammatory cytokines during endotoxemia and Listeria infections

Strong tunable coupling between two distant superconducting spin qubits

Superconducting (or Andreev) spin qubits have recently emerged as an alternative qubit platform with realizations in semiconductor-superconductor hybrid nanowires. In these qubits, the spin degree of freedom is intrinsically coupled to the supercurrent across a Josephson junction via the spin-orbit interaction, which facilitates fast, high-fidelity spin readout using circuit quantum electrodynamics techniques. Moreover, this spin-supercurrent coupling has been predicted to facilitate inductive multi-qubit coupling. In this work, we demonstrate a strong supercurrent-mediated coupling between two distant Andreev spin qubits. This qubit-qubit interaction is of the longitudinal type and we show that it is both gate- and flux-tunable up to a coupling strength of 178 MHz. Finally, we find that the coupling can be switched off in-situ using a magnetic flux. Our results demonstrate that integrating microscopic spin states into a superconducting qubit architecture can combine the advantages of both semiconductors and superconducting circuits and pave the way to fast two-qubit gates between remote spins.Comment: 26 pages, 27 figure

Electrolyzer Design for Flexible Decoupled Water Splitting and Organic Upgrading with Electron Reservoirs

The Bigger Picture Electrocatalytic water splitting is a green approach to producing clean H2 fuel, especially when it is driven by renewable energy sources. Conventional water electrolysis always produces H2 and O2 simultaneously under corrosive acidic or alkaline conditions with large voltage inputs, posing safety concerns of H2/O2 mixing. Therefore, it is desirable to develop a new electrolyzer design for decoupled water splitting in an eco-friendly neutral solution with small voltage inputs to enable separated H2 and O2 evolution. Herein, we report (ferrocenylmethyl)trimethylammonium chloride and Na4[Fe(CN)6] as proton-independent electron reservoirs for achieving separated H2 and O2 evolution in near-neutral solution driven by electricity or solar cells under sunlight irradiation. Na4[Fe(CN)6] can also integrate H2 evolution with organic oxidation to yield H2 and high-value organic products. This work offers promising economic and safety advantages for sustainable H2 production and organic transformation