Colorimetric detection of oxalate in aqueous solution by a pyrogallol red‐based Cu2+ complex

The pyrogallol red (PR)‐based Cu²⁺ complex was proven to be an effective and selective colorimetric chemosensing ensemble for recognition of oxalate over other anions in a perfect aqueous solution. The addition of oxalate to the PR–Cu²⁺ complex resulted in a colour change from purple to orange colour due to the regeneration of PR by the chelation of oxalate with Cu²⁺, while other anions did not induce any significant colour change. Moreover, it was revealed that no obvious interference was observed during the titrations with oxalate into each other anion. Therefore, the PR–Cu²⁺ complex can be used as a simple and practical colorimetric chemosensor for detecting oxalate.     

Kilogrid: a novel experimental environment for the Kilobot robot

We present the Kilogrid, an open-source virtualization environment and data logging manager for the Kilobot robot, Kilobot for short. The Kilogrid has been designed to extend the sensory-motor abilities of the Kilobot, to simplify the task of collecting data during experiments, and to provide researchers with a tool to fine-control the experimental setup and its parameters. Based on the design of the Kilobot and compatible with existing hardware, the Kilogrid is a modular system composed of a grid of computing nodes, or modules that provides a bidirectional communication channel between the Kilobots and a remote workstation. In this paper, we describe the hardware and software architecture of the Kilogrid system as well as its functioning to accompany its release as a new open hardware tool for the swarm robotics community. We demonstrate the capabilities of the Kilogrid using a 200-module Kilogrid, swarms of up to 100 Kilobots, and four different case studies: exploration and obstacle avoidance, site selection based on multiple gradients, plant watering, and pheromone-based foraging. Through this set of case studies, we show how the Kilogrid allows the experimenter to virtualize sensors and actuators not available to the Kilobot and to automatize the collection of data essential for the analysis of the experiments.     

A DNA-scaffold platform enhances a multi-enzymatic cycling reaction

Objective

We explored the co-localization of multiple enzymes on a DNA backbone via a DNA-binding protein, Gene-A* (A*-tag) to increase the efficiency of cascade enzymatic reactions.

Results

Firefly luciferase (FLuc) and pyruvate orthophosphate dikinase (PPDK) were genetically fused with A*-tag and modified with single-stranded (ss) DNA via A*-tag. The components were assembled on ssDNA by hybridization, thereby enhancing the efficiency of the cascading bioluminescent reaction producing light emission from pyrophosphate. The activity of A*-tag in each enzyme was investigated with dye-labeled DNA. Co-localization of the enzymes via hybridization was examined using a gel shift assay. The multi-enzyme complex showed significant improvement in the overall efficiency of the cascading reaction in comparison to a mixture of free enzymes.

Conclusion

A*-tag is highly convenient for ssDNA modification of versatile enzymes, and it can be used for construction of functional DNA–enzyme complexes.

     

Initiation of DNA interstrand cross-link repair in humans: the nucleotide excision repair system makes dual incisions 5' to the cross-linked base and removes a 22- to 28-nucleotide-long damage-free strand.

Most DNA repair mechanisms rely on the redundant information inherent to the duplex to remove damaged nucleotides and replace them with normal ones, using the complementary strand as a template. Interstrand cross-links pose a unique challenge to the DNA repair machinery because both strands are damaged. To study the repair of interstrand cross-links by mammalian cells, we tested the activities of cell extracts of wild-type or excision repair-defective rodent cell lines and of purified human excision nuclease on a duplex with a site-specific cross-link. We found that in contrast to monoadducts, which are removed by dual incisions bracketing the lesion, the cross-link causes dual incisions, both 5' to the cross-link in one of the two strands. The net result is the generation of a 22- to 28-nucleotide-long gap immediately 5' to the cross-link. This gap may act as a recombinogenic signal to initiate cross-link removal.     

Locally oscillatory motion of RNA helix derived from linear relationships of backbone torsion angles

A linear relationship in each of the torsion angle pairs, α-β, β-?, ?-ζ, and α-γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNA^Phe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6 , 223–242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.     

Fine structure of the lateral-line organ of the common eel,Anguilla japonica

Summary The sensory epithelium of the lateral line organ of the common eel consists of two types of cells, (sensory and supporting). The sensory cell bears a kinocilium together with about 40 to 60 stereocilia on its surface. The kinocilium is situated either at rostral or at caudal margin of this cilial group. Such polarity of the cilial group of one cell is inverse to that of an adjacent cell.Two types of crystal-like inclusions exist in the sensory cells, consisting of granules 100 Å in diameter. Granules in one type are arranged regularly whereas those in the other rather irregularly.Two types of nerve endings exist at the base of sensory cells: one is predominant in number and contains few vesicles, accompanied by a dense spherical body surrounded by small vesicles in the sensory cell and the other is rare in number and contains many vesicles, accompanied by a small flat sac just beneath the plasma membrane of the sensory cell.The supporting cells contain numerous mitochondria, a well developed Golgi apparatus and rough-surfaced endoplasmic reticulum, and surround a sensory cell completely. Physiologic significance of some of these components is discussed.     

Nucleotide excision repair 3' endonuclease XPG stimulates the activity of base excision repairenzyme thymine glycol DNA glycosylase.

An ionizing radiation-induced DNA lesion, thymine glycol, is removed from DNA by a thymine glycol DNA glycosylase with an apurinic/apyrimidinic (AP) lyase activity encoded by the Escherichia coli endonuclease III ( nth ) gene and its homolog in humans. Cells from Cockayne syndrome patients with mutations in the XPG gene show approximately 2-fold reduced global repair of thymine glycol. Hence, I decided to investigate the molecular mechanism of the effect of XPG protein observed in vivo on thymine glycol removal by studying the interactions of XPG protein and human endonuclease III (HsNTH) protein in vitro and the effect of XPG protein on the activity of HsNTH protein on a substrate containing thymine glycol. The XPG protein stimulates the binding of HsNTH protein to its substrate and increases its glycosylase/AP lyase activity by a factor of approximately 2 through direct interaction between the two proteins. These results provide in vitro evidence for a second function of XPG protein in DNA repair and a mechanistic basis for its stimulatory activity on HsNTH protein.     

Protoporphyrin IX regulates peripheral benzodiazepine receptor associated protein 7 (PAP7) and divalent metal transporter 1 (DMT1) in K562 cells

BackgroundProtoporphyrin IX (PP IX), the immediate precursor to heme, combines with ferrous iron to make this product. The effects of exogenous PP IX on iron metabolism remain to be elucidated. Peripheral-type benzodiazepine receptor (PBR) is implicated in the transport of coproporphyrinogen into the mitochondria for conversion to PP IX. We have demonstrated that PBR-Associated Protein 7 (PAP7) bound to the Iron Responsive Element (IRE) isoform of divalent metal transporter 1 (DMT1). PP IX and PAP7 are ligands for PBR, thus, we hypothesized that PAP7 interact with PP IX via PBR.MethodsWe have examined in K562 cells, which can be induced to undergo erythroid differentiation by PP IX and hemin, the effects of PP IX on the expression of PAP7 and other proteins involved in cellular iron metabolism, transferrin receptor 1 (TfR1), DMT1, ferritin heavy chain (FTH), c-Myc and C/EBPα by western blot and quantitative real time PCR analyses.ResultsPP IX significantly decreased mRNA levels of DMT1 (IRE) and (non-IRE) from 4 h. PP IX markedly decreased protein levels of C/EBPα, PAP7 and DMT1. In contrast, hemin, which like PP IX also induces K562 cell differentiation, had no effect on PAP7 or DMT1 expression.ConclusionWe hypothesize that PP IX binds to PBR displacing PAP7 protein, which is then degraded, decreasing the interaction of PAP7 with DMT1 (IRE) and resulting in increased turnover of DMT1.General significanceThese results suggest that exogenous PP IX disrupts iron metabolism by decreasing the protein expression levels of PAP7, DMT1 and C/EBPα.     

Sensitive detection of EGFR mutations using a competitive probe to suppress background in the SMart Amplification Process.

In a previous study, a single nucleotide polymorphism (SNP) diagnostic system named the SMart Amplification Process version 2 (SMAP 2) was reported, which enabled rapid gene diagnostics from crude samples such as whole blood. The asymmetric primer design and use of Taq MutS were reported as innovative background suppression technologies employed by SMAP 2, but Taq MutS is known to display differential affinities for various mismatch combinations, and hence may not be entirely effective for all possible applications. To address this issue we developed another approach using a competitive probe (CP) to enhance background suppression technology instead of Taq MutS. CP is a 3'-end aminated oligonucleotide that competes with 3'-end of a discrimination primer or the self-priming elongation site on intermediate product 2 (IM2) for non-target sequences, such as the alternative allele. The preferred hybridization kinetics for the full-match CP on the non-target sequence results in effective background suppression in SMAP 2 assays. By using a CP, we demonstrated the sensitive detection of EGFR gene mutations in purified genomic DNA from mixed cell populations. The CP approach is another tool enhancing the effectiveness and versatility of SMAP 2 assays, expanding its potential applications, and reinforcing its position as a highly effective technology for molecular diagnostics.