Visualization 1: Asymmetric liquid-core cylindrical lens used to measure liquid diffusion coefficient

The dynamic diffusion process for triethylene glycol diffusing in water. Originally published in Applied Optics on 10 March 2016 (ao-55-8-2011

Stepwise Signal Extraction via Marginal Likelihood

<p>This article studies the estimation of a stepwise signal. To determine the number and locations of change-points of the stepwise signal, we formulate a maximum marginal likelihood estimator, which can be computed with a quadratic cost using dynamic programming. We carry out an extensive investigation on the choice of the prior distribution and study the asymptotic properties of the maximum marginal likelihood estimator. We propose to treat each possible set of change-points equally and adopt an empirical Bayes approach to specify the prior distribution of segment parameters. A detailed simulation study is performed to compare the effectiveness of this method with other existing methods. We demonstrate our method on single-molecule enzyme reaction data and on DNA array comparative genomic hybridization (CGH) data. Our study shows that this method is applicable to a wide range of models and offers appealing results in practice. Supplementary materials for this article are available online.</p

Tuning Ionic Transport in Memristive Devices by Graphene with Engineered Nanopores

Memristors, based on inherent memory effects in simple two-terminal structures, have attracted tremendous interest recently for applications ranging from nonvolatile data storage to neuromorphic computing based on non-von Neumann architectures. In a memristor, the ability to modulate and retain the state of an internal variable leads to experimentally observed resistive switching (RS) effects. Such phenomena originate from internal, microscopic ionic migration and associated electrochemical processes that modify the materials’ electrical and other physical properties. To optimize the device performance for practical applications with large-size arrays, controlling the internal ionic transport and redox reaction processes thus becomes a necessity, ideally at the atomic scale. Here we show that the RS characteristics in tantalum-oxide-based memristors can be systematically tuned by inserting a graphene film with engineered nanopores. Graphene, with its atomic thickness and excellent impermeability and chemical stability, can be effectively integrated into the device stack and can offer unprecedented capabilities for the control of ionic dynamics at the nanoscale. In this device structure, the graphene film effectively blocks ionic transport and redox reactions; thereby the oxygen vacancies required during the RS process are allowed to transport only through the engineered nanosized openings in the graphene layer, leading to effective modulation of the device performance by controlling the nanopore size in graphene. The roles of graphene as an ion-blocking layer in the device structure were further supported by transmission electron microscopy, energy-dispersive X-ray spectroscopy, and atomistic simulations based on first-principles calculations

Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by <i>Streptomyces</i> Species MBT28

Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by <i>Streptomyces</i> sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (<b>1</b>) with antimicrobial activity against <i>Bacillus subtilis</i>. The metabolite-guided genome mining of <i>Streptomyces</i> sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics

Bacterial Surface-Assembled Chitinosome for Dismantling Chitin into <i>N</i>‑Acetyl Glucosamine

The construction of an efficient multienzyme catalyst for dismantling recalcitrant polymers into high-value-added chemicals is appealing in sustainable biomanufacturing. Colocalization of cascade enzymes has been broadly adopted by natural and synthetic multienzyme systems for chemical synthesis, while there has been rare research on the decomposition of polymeric substrates. In this study, we constructed an E. coli surface-assembly (ESA) system to colocalize a synthetic chitinosome composed of two chitin hydrolases, BpChiA and BlNagZ, via the SpyCatcher/SpyTag (SpyC/SpyT) conjugation. In the ESA–chitinosome complexes, the loading efficiency and specific activity of enzymes were improved by tuning the copies of SpyC and the linker lengths between the SpyT and enzymes, respectively. The ratio of BpChiA and BlNagZ was also optimized. The ESA–chitinosome complexes exhibited higher productivity of N-acetyl glucosamine than the mixture of separately assembled enzymes on cell surfaces. This work demonstrates that the enzyme colocalization and the formation of the ternary ESA–chitinosome–chitin complexes are critical for the catalytic synergism of cascade enzymes, providing new insights into the decomposition of recalcitrant polymeric substrates

Experimental Demonstration of a Second-Order Memristor and Its Ability to Biorealistically Implement Synaptic Plasticity

Memristors have been extensively studied for data storage and low-power computation applications. In this study, we show that memristors offer more than simple resistance change. Specifically, the dynamic evolutions of internal state variables allow an oxide-based memristor to exhibit Ca²⁺-like dynamics that natively encode timing information and regulate synaptic weights. Such a device can be modeled as a second-order memristor and allow the implementation of critical synaptic functions realistically using simple spike forms based solely on spike activity

Additional file 4: Table S4. of Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

Annotation of the Hycleus cichorii mitogenome. (DOCX 22 kb

Additional file 12: Table S11. of Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

The best-fit schemes and evolutionary models for two datasets. (DOCX 16 kb

Complete mitochondrial genomes of two blattid cockroaches, <i>Periplaneta australasiae</i> and <i>Neostylopyga rhombifolia</i>, and phylogenetic relationships within the Blattaria

<div><p>Complete mitochondrial genomes (mitogenomes) of two cockroach species, <i>Periplaneta australasiae</i> and <i>Neostylopyga rhombifolia</i>, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus <i>Cryptocercus</i>, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA). Three different types of short tandem repeats in the <i>N</i>. <i>rhombifolia</i> control region (CR) were observed. The homologous alignments of these tandem repeats with other six cockroach mitogenome CRs revealed a low similarity. Three conserved sequence blocks (CSB) were detected in both cockroach mitochondrial CRs. CSB1 was specific for blattinine mitogenomes and was highly conserved with 95% similarity, speculating that this block was a possible molecular synapomorphy for this subfamily. CSB3 located nearby downstream of CSB1 and has more variations within blattinine mitogenomes compared with CSB1. The CSB3 was capable of forming stable stem-loop structure with a small T-stretch in the loop portion. We assessed the influence of four datasets and two inference methods on topology within Orthopteroidea. All genes excluding the third codon positions of PCGs could generate more stable topology, and higher posterior probabilities than bootstrap values were presented at some branch nodes. The phylogenetic analysis with different datasets and analytical methods supported the monophyly of Dictyoptera and supported strongly the proposal that Isoptera should be classified as a family (Termitidae) of the Blattaria. Specifically, <i>Shelfordella lateralis</i> was inserted in the clade <i>Periplaneta</i>. Considering the K2P genetic distance, morphological characters, and the phylogenetic trees, we suggested that <i>S</i>. <i>lateralis</i> should be placed in the genus <i>Periplaneta</i>.</p></div

Computational Aspects of Optional Pólya Tree

<div><p></p><p>Optional Pólya tree (OPT) is a flexible nonparametric Bayesian prior for density estimation. Despite its merits, the computation for OPT inference is challenging. In this paper we present time complexity analysis for OPT inference and propose two algorithmic improvements. The first improvement, named limited-lookahead optional Pólya tree (LL-OPT), aims at accelerating the computation for OPT inference. The second improvement modifies the output of OPT or LL-OPT and produces a continuous piecewise linear density estimate. We demonstrate the performance of these two improvements using simulated and real date examples.</p></div