Peptide Arrays Identify Isoform-Selective Substrates for Profiling Endogenous Lysine Deacetylase Activity

A cetylation of lysine is a post-translational modifi-cation involved inmany eukaryotic cellular pro-cesses (1). Though most commonly associated with histone proteins (2), a recent proteomic study by Mann and colleagues identified nearly 2,000 proteins in acetylated form and showed that this modification is used globally in regulating cell function (3). This recogni-tion hasmotivated a renaming of the histone acetyltrans-ferase (HAT) and histone deacetylase (HDAC) enzymes to reflect their broader roles [now the lysine acetyltrans-ferases (KATs) and the lysine deacetylases (KDACs) (4)] and has highlighted our limited understanding of the functions of the individual enzymes responsible for achieving andmaintaining acetylation states. A significant effort is now directed at understanding the differential roles that the 18 human KDAC isoforms play in regulating cell behavior (5−8). These studies re

A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic Interface-on-a-Chip

The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging a modified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen microchannel is necessary and sufficient to create the steady-state vertical oxygen gradient in the AOI Chip. We confirmed that the created AOI does not compromise the viability, barrier function, mucin production, and the expression and localization of tight junction proteins in the 3D intestinal epithelial layer. Two obligate anaerobic commensal gut microbiome, Bifidobacterium adolescentis and Eubacterium hallii, that exert metabolic cross-feeding in vivo, were independently co-cultured with epithelial cells in the AOI Chip for up to a week without compromising any cell viability. Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells associated with intestinal metabolism, homeostasis, and immune regulation

Profiling the selectivity of DNA ligases in an array format with mass spectrometry

This article describes a method for the global profiling of the substrate specificities of DNA ligases and illustrates examples using the Taq and T4 DNA ligases. The method combines oligonucleotide arrays, which offer the benefits of high throughput and multiplexed assays, with mass spectrometry to permit label-free assays of ligase activity. Arrays were prepared by immobilizing ternary biotin-tagged DNA substrates to a self-assembled monolayer presenting a layer of streptavidin protein. The array represented complexes having all possible matched and mismatched base pairs at the 3′ side of the nick site and also included a number of deletions and insertions at this site. The arrays were treated with ligases and adenosine triphosphate or analogs of the nucleotide triphosphate and then analyzed by matrix-assisted laser desorption-ionization mass spectrometry to determine the yields for both adenylation of the 5′-probe strand and joining of the two probe strands. The resulting activity profiles reveal the basis for specificity of the ligases and also point to strategies that use ATP analogs to improve specificity. This work introduces a method that can be applied to profile a broad range of enzymes that operate on nucleic acid substrates

Development of microdevices for applications to bioanalysis

textThe development of microdevices for applications related to bioanalysis is described. There are two types of microdevices involved in this study: DNA (or RNA) microarrays and bead-based microfluidic devices. First, a new method to fabricate DNA microarrays is developed: replication of DNA microarrays. It was shown that oligonucleotides immobilized on a glass master can hybridize with their biotin-modified complements, and then the complements can be transferred to a streptavidinfunctionalized replica surface. This results in replication of the master DNA array. Several innovative aspects of replication are discussed. First, the zip code approach allows fabrication of replica DNA arrays having any configuration using a single, universal master array. It is demonstrated that this approach can be used to replicate master arrays having three different sequences (spot feature sizes as small as 100 [mu]m) and that master arrays can be used to prepare multiple replicas. Second, it is shown that a surface T4 DNA polymerase reaction improves the DNA microarray replication method by removing the requirement for using presynthesizd oligonucleotides. This in-situ, enzymatic synthesis approach is used to replicate DNA master arrays consisting of 2304 spots and arrays consisting of different oligonucleotide sequences. Importantly, multiple replica arrays prepared from a single master show consistent functionality to hybridization-based application. It is also shown that RNA microarrays can be fabricated utilizing a surface T4 DNA ligase reaction, which eliminates the requirement of modified RNA in conventional fabrication schemes. This aspect of the work shows that the replication approach may be broadly applicable to bioarray technologies. A different but related aspect of this project focuses on biosensors consisting of microfluidic devices packed with microbeads conjugated to DNA capture probes. The focus here is on understanding the parameters affecting the hybridization of DNA onto the probeconjugated microbeads under microfluidic flow conditions. These parameters include the surface concentration of the probe, the flow rate of the solution, and the concentration of the target. The simple microfluidic device packed with probe-conjugated microbeads exhibits efficient target capture resulting from the inherently high surface-area-to-volume ratio of the beads, optimized capture-probe surface density, and good mass-transfer characteristics. Furthermore, the bead-based microchip is integrated with a hydrogel preconcentrator enhancing the local concentration of DNA in a icrochannel. The integration of the preconcentrator into the bead-based capture chip allows significantly lower limit of detection level (~10-fold enhancement in the sensitivity of the microbeadbased DNA detection).Chemistry and BiochemistryChemistr

Rise of Nationalism in China and Japan: the Consequences on Domestic Politics and Sino-Japanese Relations

Nationalism is once again gaining momentum in East Asia. Not only do the political leaders of China, Korea, and Japan explicitly claim their own nations legitimate rights based on nationalist sentiments, but also the mass citizens of each nations seem to give zealous support to the leaders that do make a nationalist stance. Today we are aware of the anti-Japanese, popular nationalism rising in China; nationalism based on Pro-Japanese stance and its history gaining force in Japan as well. Public mass protests, internet forum discussions, and political positions based on the rising nationalism are day by day prevailing in China and Japan. But then in order to correctly understand its political implications, we must ask ourselves the question: precisely what is the nationalism in China and Japan, and how does this popular social phenomenon affect political policies? For political scientists, it is never sufficient to just know that nationalism is a social trend present within a state system, but what is critical is to offer insights by trying to analyze and understand these phenomena scientifically. I wish to offer a scientific analysis and insight on the rise of nationalism in China and Japan, and how it transfers to the political domain in terms of political actions including governmental stance and policies.Ope

Mass-Production of Visible Metalenses via Wafer-Scale Printing

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Post-Synthesis Modification of Photoluminescent and Electrochemiluminescent Au Nanoclusters with Dopamine

Here, we report a post-synthesis functionalization of the shell of Au nanoclusters (NCs) synthesized using glutathione as a thiolate ligand. The as-synthesized Au NCs are subjected to the post-synthesis functionalization via amidic coupling of dopamine on the cluster shell to tailor photoluminescence (PL) and electrochemiluminescence (ECL) features of the Au NCs. Because the NCs’ PL at ca. 610 nm is primarily ascribed to the Au(I)-thiolate (SG) motifs on the cluster shell of the NCs, the post-synthesis functionalization of the cluster shell enhanced the PL intensity of the Au NCs via rigidification of the cluster shell. In contrast to the PL enhancement, the post-synthesis modification of the cluster shell does not enhance the near-infrared (NIR) ECL of the NCs because the NIR ECL at ca. 800 nm is ascribed to the Au(0)-SG motifs in the metallic core of the NCs

Modification of Indium Tin Oxide with Dendrimer-Encapsulated Nanoparticles To Provide Enhanced Stable Electrochemiluminescence of Ru(bpy)₃²⁺/Tripropylamine While Preserving Optical Transparency of Indium Tin Oxide for Sensitive Electrochemiluminescence-Based Analyses

Here, we report highly enhanced stable electrogenerated chemiluminescence (ECL) of Ru­(bpy)₃²⁺ (bpy = 2,2′-bipyridyl) with tripropylamine (TPrA) coreactant on indium tin oxide (ITO) electrodes modified with amine-terminated dendrimers encapsulating catalytic nanoparticles while maintaining optical transparency of ITO and feasibility of the modified ITOs to sensitive ECL-based assays. As model systems, we prepared Pt and Au dendrimer-encapsulated nanoparticles (DENs) using amine-terminated sixth-generation poly­(amido amine) dendrimers and subsequently immobilized the DENs onto ITO surfaces via electrooxidative grafting of the terminal amines of dendrimers to the surfaces. The resulting DEN-modified ITOs preserved good optical transparency of ITO and exhibited highly catalyzed electrochemical oxidation of Ru­(bpy)₃²⁺/TPrA, leading to significantly increased ECL emission. Especially, the Pt DEN-modified ITO electrode provides negligible transmittance drop, i.e., only ∼1.99% over the entire visible region, and exhibited not only much enhanced (i.e., ∼213-fold increase compared to ECL obtained from bare ITO) but also stable ECL emission under consecutive potential scans from 0.00 to 1.10 V for 10 cycles, which allowed ∼329 times more sensitive ECL-based analysis of nicotine using the Pt DEN-modified ITO compared with the use of bare ITO

Photonic encryption platform using dual-band UV vectorial hologram

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