Gene/Protein Disease Symptom Drug Enzyme Compound
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The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.
ACS Synth Biol 2012 Apr 20
PMID:MAP(2.0)3D: a sequence/structure based server for protein engineering. 2365 Nov 15

The optical and optoelectronic properties of colloidal quantum dots strongly depend on the passivation of their surface. Surface states are however difficult to quantify using optical spectroscopy and techniques based on back gated field effect transistors are limited in the range of carrier density that can be probed, usually significantly below one charge carrier per particle. Here we show that electrolyte gating can be used to quantitatively analyze the increase of defects in a population of nanoparticles with increasing surface irregularities. We illustrate this method using CdSe nanoplatelets that are grown in their thickness using low temperature layer-by-layer method. Spectroscopic analysis of the samples confirm that the nanoplatelet thickness is controlled, on average, with atomic precision, but structural analysis with transmission electron microscopy shows that the number of surface defects increases with the nanoplatelet thickness. The amount of charge defects is probed quantitatively using electrolyte-gated field effect transistor (EFET). We observe that the threshold voltage of the EFET increases with the NPL thickness, in agreement with the structural analysis. All samples displayed n-type conduction with strong current modulation (subthreshold swing slope of 100 mV/decade and on/off ratio close to 10(7)). We also point out that an efficient electrolyte gating of the film requires a fine control of the nanoparticle film morphology.
ACS Nano 2014 Apr 22
PMID:Electrolyte-gated field effect transistor to probe the surface defects and morphology in films of thick CdSe colloidal nanoplatelets. 2460 78

Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.
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PMID:Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater. 3061 9

Interest in developing a rapid and robust DNA sequencing platform has surged over the past decade. Various next-/third-generation sequencing mechanisms have been employed to replace the traditional Sanger sequencing method. In sequencing by synthesis, a signal is monitored by a scanning charge-coupled device (CCD) to identify thousands to millions of incorporated dNTPs with distinctive fluorophores on a chip. Because one reaction site usually occupies dozens of pixels on a CCD detector, a bottleneck related to the bandwidth of CCD imaging limits the throughputs of the sequencing performance and causes trade-offs among speed, accuracy, read length, and the numbers of reaction sites in parallel. Thus, current research aims to align one reaction site to a few pixels by directly stacking nanophotonic layers onto a CMOS detector to minimize the size of the sequencing platforms and accelerate the processing procedures. This article reports a custom integrated optoelectronic device based on a triple-junction photodiode (TPD) CMOS sensor in conjunction with NPL integration for real-time illumination and detection of fluorescent molecules.
ACS Nano 2019 04 23
PMID:Triple-Junction Optoelectronic Sensor with Nanophotonic Layer Integration for Single-Molecule Level Decoding. 3085 19

Nanocarbonaceous materials with specific geometries and physicochemical properties allow the development of high-performance polymer-based smart composite materials. Among them, chemical treatments of graphene allow tailoring its electrical conductivity and, therefore, tuning functional response of materials for sensing applications. Polymer-based nanocomposites have been developed from styrene-ethylene-butylene-styrene (SEBS), a high deformation thermoplastic elastomer, and different graphene-based fillers, including graphene oxide (GO), reduced graphene oxide (rGO), and graphene nanoplatelets (G-NPLs). It is shown that the electrical conductivity shows a percolation threshold around 2 wt % for GO and rGO, remaining nearly independent of the filler content for G-NPL filler contents up to 6 wt %. Furthermore, GO/SEBS and rGO/SEBS composites show high piezoresistive sensibility with gauge factors ranging from 15 up to 120 for strains up to 10%. Thus, GO/SEBS and rGO/SEBS composites can represent a new generation of materials for strain sensor applications, as demonstrated in their implementation in a hand glove prototype with finger movement monitoring.
ACS Appl Mater Interfaces 2019 Dec 11
PMID:Highly Sensitive Piezoresistive Graphene-Based Stretchable Composites for Sensing Applications. 3172 62