scholarly journals Instrument for Label-Free Detection of Noncoding RNAs

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Peter Noy ◽  
Roger Steiner ◽  
Joerg Voelkle ◽  
Martin Hegner ◽  
Christof Fattinger
Keyword(s):  
Noncoding Rnas ◽  
Analysis Tool ◽  
Label Free ◽  
Cantilever Arrays ◽  
Label Free Detection ◽  
Before And After ◽  
Direct Binding ◽  
Experimental Protocols ◽  
Set Up ◽  
User Friendly

We set up a label-free direct binding assay for the detection of noncoding RNAs. The assay is based on nanomechanical cantilever arrays for the detection of surface stress induced by immobilized biomolecules and their interaction partners. We used various means to significantly reduce the drift of the cantilever readout that was a prominent feature in experiments with readout in stationary fluid before and after sample injection. Major improvements were achieved by focusing on a faster system equilibration (for instance temperature control and diffusion independence). Experimental protocols were improved to provide user-friendly and less time-consuming measurements. Further enhancements were achieved by, for example, using pre-gold-coated cantilever array wafers compared to individually prepared ones and a directly implemented data analysis tool as real-time feature of the measurement software. We have demonstrated picomolar specific biomarker target detection and can easily distinguish modified targets with single-nucleotide mismatches that hybridize with lower affinity.

scholarly journals Strong binding and fluorescence sensing of bisphosphonates by guanidinium-modified calix[5]arene

2018 ◽  
Vol 14 ◽  
pp. 1840-1845 ◽  
Author(s):  
Jie Gao ◽  
Zhe Zheng ◽  
Lin Shi ◽  
Si-Qi Wu ◽  
Hongwei Sun ◽  
...  
Keyword(s):  
Salt Bridge ◽  
Quantitative Detection ◽  
Label Free ◽  
Fluorescence Sensing ◽  
Buffer Solution ◽  
Biologically Relevant ◽  
Strong Binding ◽  
Label Free Detection ◽  
Artificial Urine ◽  
Set Up

Based on the indicator displacement assay (IDA) approach, we herein report the fluorescence “switch-on” sensing and quantitative detection of bisphosphonates (BPs), a class of drugs extensively used in the treatment of patients with various skeletal diseases. Guanidinium-modified calix[5]arene (GC5A) affords strong binding on the micromolar to nanomolar level towards BPs dominantly via multiple salt bridge interactions, which was evaluated by fluorescence competitive titrations. Fluorescent IDA enables the highly sensitive and label-free detection of BPs in buffer solution, and more importantly, in artificial urine. Calibration lines were therefore set up in untreated artificial urine, allowing for quantifying the concentrations of BPs in the biologically relevant low range.

Gold nanodome SERS platform for label-free detection of protease activity

2017 ◽  
Vol 205 ◽  
pp. 345-361 ◽  
Author(s):  
Pieter C. Wuytens ◽  
Hans Demol ◽  
Nina Turk ◽  
Kris Gevaert ◽  
Andre G. Skirtach ◽  
...  
Keyword(s):  
Protease Activity ◽  
Aromatic Amino Acids ◽  
Label Free ◽  
Peptide Cleavage ◽  
Substrate Peptide ◽  
Label Free Detection ◽  
Surface Enhanced ◽  
Before And After ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering

Surface-enhanced Raman scattering provides a promising technology for sensitive and selective detection of protease activity by monitoring peptide cleavage. Not only are peptides and plasmonic hotspots similarly sized, Raman fingerprints also hold large potential for spectral multiplexing. Here, we use a gold-nanodome platform for real-time detection of trypsin activity on a CALNNYGGGGVRGNF substrate peptide. First, we investigate the spectral changes upon cleavage through the SERS signal of liquid-chromatography separated products. Next, we show that similar patterns are detected upon digesting surface-bound peptides. We demonstrate that the relative intensity of the fingerprints from aromatic amino acids before and after the cleavage site provides a robust figure of merit for the turnover rate. The presented method offers a generic approach for measuring protease activity, which is illustrated by developing an analogous substrate for endoproteinase Glu-C.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

2019 ◽  
Vol 14 (7) ◽  
pp. 621-627 ◽  
Author(s):  
Youhuang Bai ◽  
Xiaozhuan Dai ◽  
Tiantian Ye ◽  
Peijing Zhang ◽  
Xu Yan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Populus Trichocarpa ◽  
Noncoding Rnas ◽  
Reference Database ◽  
Protein Coding ◽  
Arabidopsis Lyrata ◽  
User Friendly

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

scholarly journals The Role of Surface Chemistry in the Efficacy of Protein and DNA Microarrays for Label-Free Detection: An Overview

Polymers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1026
Author(s):  
Elisa Chiodi ◽  
Allison M. Marn ◽  
Matthew T. Geib ◽  
M. Selim Ünlü
Keyword(s):  
Surface Chemistry ◽  
Surface Functionalization ◽  
Dna Microarrays ◽  
Label Free ◽  
Polymeric Coatings ◽  
Label Free Detection ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
The Impact

The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules’ functionalities is critically analyzed.

Research on pull-type multi-AGV system dynamic path optimization based on time window

2021 ◽  
pp. 095440702098271
Author(s):  
Hongying Shan ◽  
Chuang Wang ◽  
Cungang Zou ◽  
Mengyao Qin
Keyword(s):  
Path Planning ◽  
Time Window ◽  
Planning Problem ◽  
Dijkstra Algorithm ◽  
Before And After ◽  
Common Planning ◽  
Planning Algorithm ◽  
Dynamic Path ◽  
Set Up ◽  
Path Planning Algorithm

This paper is a study of the dynamic path planning problem of the pull-type multiple Automated Guided Vehicle (multi-AGV) complex system. First, based on research status at home and abroad, the conflict types, common planning algorithms, and task scheduling methods of different AGV complex systems are compared and analyzed. After comparing the different algorithms, the Dijkstra algorithm was selected as the path planning algorithm. Secondly, a mathematical model is set up for the shortest path of the total driving path, and a general algorithm for multi-AGV collision-free path planning based on a time window is proposed. After a thorough study of the shortcomings of traditional single-car planning and conflict resolution algorithms, a time window improvement algorithm for the planning path and the solution of the path conflict covariance is established. Experiments on VC++ software showed that the improved algorithm reduces the time of path planning and improves the punctual delivery rate of tasks. Finally, the algorithm is applied to material distribution in the OSIS workshop of a C enterprise company. It can be determined that the method is feasible in the actual production and has a certain application value by the improvement of the data before and after the comparison.

scholarly journals Label-Free Electrochemical Sensor for Rapid Bacterial Pathogen Detection Using Vancomycin-Modified Highly Branched Polymers

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1872
Author(s):  
Holger Schulze ◽  
Harry Wilson ◽  
Ines Cara ◽  
Steven Carter ◽  
Edward N. Dyson ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Electrochemical Impedance ◽  
Point Of Care ◽  
Branched Polymers ◽  
Label Free ◽  
Conformation Change ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Staphylococcus Carnosus ◽  
Label Free Detection

Rapid point of care tests for bacterial infection diagnosis are of great importance to reduce the misuse of antibiotics and burden of antimicrobial resistance. Here, we have successfully combined a new class of non-biological binder molecules with electrochemical impedance spectroscopy (EIS)-based sensor detection for direct, label-free detection of Gram-positive bacteria making use of the specific coil-to-globule conformation change of the vancomycin-modified highly branched polymers immobilized on the surface of gold screen-printed electrodes upon binding to Gram-positive bacteria. Staphylococcus carnosus was detected after just 20 min incubation of the sample solution with the polymer-functionalized electrodes. The polymer conformation change was quantified with two simple 1 min EIS tests before and after incubation with the sample. Tests revealed a concentration dependent signal change within an OD600 range of Staphylococcus carnosus from 0.002 to 0.1 and a clear discrimination between Gram-positive Staphylococcus carnosus and Gram-negative Escherichia coli bacteria. This exhibits a clear advancement in terms of simplified test complexity compared to existing bacteria detection tests. In addition, the polymer-functionalized electrodes showed good storage and operational stability.

scholarly journals Wear and Friction Characteristics of 65Mn Steel for Spike-Tooth Harrow

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 319
Author(s):  
Zhiguo Lu ◽  
Chuanyu Du ◽  
Qingcai Chen ◽  
Tianying Niu ◽  
Na Wang ◽  
...  
Keyword(s):  
Friction And Wear ◽  
Working Environment ◽  
Manganese Steel ◽  
Wear Loss ◽  
Variable Parameters ◽  
Wear Characteristics ◽  
Before And After ◽  
Set Up ◽  
Worn Surface ◽  
Friction And Wear Characteristics

The friction and wear characteristics of spike-tooth material (65Mn steel) of Spike-Tooth Harrow in a two-stage peanut harvester were studied in this paper. The friction and wear tests of pin and disc on 65 manganese steel were carried out on the tribometer, then the wear loss and the friction coefficient were studied. The wear loss of the pin was acquired by calculating the mass of the pin before and after the experiment using an electronic balance. According to the actual working environment of peanut spring-finger, four variable parameters are set up: load, speed, soil moisture and soil type. The friction and wear characteristics of pins were studied under different loads, speeds and different soil environments. After wearing, the worn surface of the material was observed by scanning microscope and the wear mechanism was studied. The experimental results show that the wear of the pin increases with the increase of load and decreases with the increase of rotational speed in the same rotation number. Especially in the case of the sandy soil with 20% in moisture, a maximum wear loss of the pin is achieved.

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