scholarly journals Massively Parallel Selection of NanoCluster Beacons

2021 ◽  
Author(s):  
Yu-An Kuo ◽  
Cheulhee Jung ◽  
Yu-An Chen ◽  
Hung-Che Kuo ◽  
Oliver S. Zhao ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Silver Cluster ◽  
Machine Learning Algorithms ◽  
Single Nucleotide ◽  
Silver Nanocluster ◽  
The Difference ◽  
Dna Strand ◽  
Polar Opposite ◽  
Next Generation Sequencing Ngs

NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed the polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here we report a high-throughput selection method that takes advantage of repurposed next-generation-sequencing (NGS) chips to screen the activation fluorescence of ∼40,000 activator sequences. We find the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow and red POTs, respectively. Based on these findings, we propose a “zipper bag model” that explains how these hotspots lead to the creation of distinct silver cluster chromophores and contribute to the difference in chromophore chemical yields. Combining high-throughput screening with machine learning algorithms, we establish a pipeline to rationally design bright and multicolor NCBs.

scholarly journals Accelerating organic solar cell material's discovery: high-throughput screening and big data

2021 ◽  
Author(s):  
Xabier Rodríguez-Martínez ◽  
Enrique Pascual-San-José ◽  
Mariano Campoy-Quiles
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
High Throughput ◽  
Organic Solar Cells ◽  
High Throughput Screening ◽  
Organic Solar Cell ◽  
State Of The Art ◽  
Review Article ◽  
Machine Learning Algorithms ◽  
Device Optimization

This review article presents the state-of-the-art in high-throughput computational and experimental screening routines with application in organic solar cells, including materials discovery, device optimization and machine-learning algorithms.

Automated High-Throughput System Combining Small-Scale Synthesis with Bioassays and Reaction Screening

2021 ◽  
pp. 247263032110478
Author(s):  
Nicolás M. Morato ◽  
MyPhuong T. Le ◽  
Dylan T. Holden ◽  
R. Graham Cooks
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Desorption Electrospray Ionization ◽  
Ambient Ionization ◽  
Machine Learning Algorithms ◽  
Small Scale ◽  
Label Free ◽  
Minimal Sample ◽  
Secondary Droplets ◽  
Automated Platform

The Purdue Make It system is a unique automated platform capable of small-scale in situ synthesis, screening small-molecule reactions, and performing direct label-free bioassays. The platform is based on desorption electrospray ionization (DESI), an ambient ionization method that allows for minimal sample workup and is capable of accelerating reactions in secondary droplets, thus conferring unique advantages compared with other high-throughput screening technologies. By combining DESI with liquid handling robotics, the system achieves throughputs of more than 1 sample/s, handling up to 6144 samples in a single run. As little as 100 fmol/spot of analyte is required to perform both initial analysis by mass spectrometry (MS) and further MSn structural characterization. The data obtained are processed using custom software so that results are easily visualized as interactive heatmaps of reaction plates based on the peak intensities of m/ z values of interest. In this paper, we review the system’s capabilities as described in previous publications and demonstrate its utilization in two new high-throughput campaigns: (1) the screening of 188 unique combinatorial reactions (24 reaction types, 188 unique reaction mixtures) to determine reactivity trends and (2) label-free studies of the nicotinamide N-methyltransferase enzyme directly from the bioassay buffer. The system’s versatility holds promise for several future directions, including the collection of secondary droplets containing the products from successful reaction screening measurements, the development of machine learning algorithms using data collected from compound library screening, and the adaption of a variety of relevant bioassays to high-throughput MS.

scholarly journals A Homogeneous, High-Throughput Fluorescence Anisotropy-Based DNA Supercoiling Assay

2010 ◽  
Vol 15 (9) ◽  
pp. 1088-1098 ◽  
Author(s):  
Adam Shapiro ◽  
Haris Jahic ◽  
Swati Prasad ◽  
David Ehmann ◽  
Jason Thresher ◽  
...  
Keyword(s):  
High Throughput ◽  
Fluorescence Anisotropy ◽  
High Throughput Screening ◽  
Topoisomerase I ◽  
Dna Supercoiling ◽  
New Drugs ◽  
E Coli ◽  
Cellular Processes ◽  
The Difference ◽  
Cellular Replication

The degree of supercoiling of DNA is vital for cellular processes, such as replication and transcription. DNA topology is controlled by the action of DNA topoisomerase enzymes. Topoisomerases, because of their importance in cellular replication, are the targets of several anticancer and antibacterial drugs. In the search for new drugs targeting topoisomerases, a biochemical assay compatible with automated high-throughput screening (HTS) would be valuable. Gel electrophoresis is the standard method for measuring changes in the extent of supercoiling of plasmid DNA when acted upon by topoisomerases, but this is a low-throughput and laborious method. A medium-throughput method was described previously that quantitatively distinguishes relaxed and supercoiled plasmids by the difference in their abilities to form triplex structures with an immobilized oligonucleotide. In this article, the authors describe a homogeneous supercoiling assay based on triplex formation in which the oligonucleotide strand is labeled with a fluorescent dye and the readout is fluorescence anisotropy. The new assay requires no immobilization, filtration, or plate washing steps and is therefore well suited to HTS for inhibitors of topoisomerases. The utility of this assay is demonstrated with relaxation of supercoiled plasmid by Escherichia coli topoisomerase I, supercoiling of relaxed plasmid by E. coli DNA gyrase, and inhibition of gyrase by fluoroquinolones and nalidixic acid.

scholarly journals Novel Multiplex Single Nucleotide Polymorphism-Based Method for Identifying Epidemic Clones of Listeria monocytogenes

2011 ◽  
Vol 77 (17) ◽  
pp. 6290-6294 ◽  
Author(s):  
Sara Lomonaco ◽  
Stephen J. Knabel ◽  
Alessandra Dalmasso ◽  
Tiziana Civera ◽  
Maria Teresa Bottero
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
High Throughput Screening ◽  
Virulence Genes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACTA novel primer extension-based, multiplex minisequencing assay targeting six highly informative single nucleotide polymorphisms (SNPs) in four virulence genes correctly identified and differentiated all four epidemic clones (ECs) ofListeria monocytogenesand 9 other strains initially misclassified as non-ECs. This assay allows rapid, accurate, and high-throughput screening for all known ECs ofL. monocytogenes.

Large-Scale Zygosity Testing Using Single Nucleotide Polymorphisms

2007 ◽  
Vol 10 (4) ◽  
pp. 604-625 ◽  
Author(s):  
Ulf Hannelius ◽  
Loreana Gherman ◽  
Ville-Veikko Mäkelä ◽  
Astrid Lindstedt ◽  
Marco Zucchelli ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
Tandem Repeats ◽  
Snp Markers ◽  
Quality Data ◽  
Genotyping Error ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

AbstractA requirement for performing robust genetic and statistical analyses on twins is correctly assigned zygosities. In order to increase the power to detect small risk factors of disease, zygosity testing should also be amenable for high throughput screening. In this study we validate and implement the use of a panel of 50 single nucleotide polymorphisms (SNPs) for reliable high throughput zygosity testing and compare it to a panel of 16 short tandem repeats (STRs). We genotyped both genomic (gDNA) and whole genome amplified DNA (WGA DNA), ending up with 47 SNP and 11 STR markers fulfilling our quality criteria. Out of 99 studied twin pairs, 2 were assigned a different zygosity using SNP and STR data as compared to self reported zygosity in a questionnaire. We also performed a sensitivity analysis based on simulated data where we evaluated the effects of genotyping error, shifts in allele frequencies and missing data on the qualitative zygosity assignments. The frequency of false positives was less than 0.01 when assuming a 1% genotyping error, a decrease of 10% of the observed minor allele frequency compared to the actual values and up to 10 missing markers. The SNP markers were also successfully genotyped on both gDNA and WGA DNA from whole blood, saliva and filter paper. In conclusion, we validate a robust panel of 47 highly multiplexed SNPs that provide reliable and high quality data on a range of different DNA templates.

scholarly journals Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems

2017 ◽  
Author(s):  
Qing Liu ◽  
Chun Wang ◽  
Xiaozhen Jiao ◽  
Huawei Zhang ◽  
Lili Song ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
High Reliability ◽  
Mutation Screening ◽  
Screening Strategy ◽  
Library Construction ◽  
Genetic Modifications ◽  
Parameter Configuration ◽  
Next Generation Sequencing Ngs

AbstractThe CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we describe a cheap, practicable and high-throughput screening strategy that allows parallel screening of 96 × N (N denotes the number of targets) genome-modified sites. The strategy simplified and streamlined the process of next-generation sequencing (NGS) library construction by fixing the bridge sequences and barcoding primers. We also developed Hi-TOM (available at http://www.hi-tom.net/hi-tom/), an online tool to track the mutations with precise percentage. Analysis of the samples from rice, hexaploid wheat and human cells reveals that the Hi-TOM tool has high reliability and sensitivity in tracking various mutations, especially complex chimeric mutations that frequently induced by genome editing. Hi-TOM does not require specially design of barcode primers, cumbersome parameter configuration or additional data analysis. Thus, the streamlined NGS library construction and comprehensive result output make Hi-TOM particularly suitable for high-throughput identification of all types of mutations induced by CRISPR/Cas systems.

scholarly journals Adaptation of nitrate reductase activity assay for high throughput screening of crops

2020 ◽  
Vol 49 (6) ◽  
pp. 23-33
Author(s):  
G I. Karlov ◽  
D. Y. Litvinov ◽  
P. N. Kharchenko ◽  
P. Yu. Krupin ◽  
S. Yu. Shirnin ◽  
...  
Keyword(s):  
Nitrate Reductase ◽  
High Throughput ◽  
Total Protein ◽  
High Throughput Screening ◽  
Reductase Activity ◽  
Potassium Nitrate ◽  
Activity Assay ◽  
Freeze Dried ◽  
The Difference ◽  
Nr Activity

The  possibility of freeze drying of plant material and its grinding in a shaking bead mill to determine the activity of nitrate reductase (NR) was studied. The effectiveness of applying this approach to high throughput mass screening of crops was shown. The assay was carried out on seedlings of common wheat (Triticum aestivum) of the following cultivars: Altigo, Vassa, Grom, Doka, Soberbash, Starshina, Fisht and spring wheat Novosibirskaya 67. The crops were grown during 4-5 weeks on substrate without nitrogen and on substrate supplemented with 50 millimol / l (mM) of potassium nitrate. Nitrate reductase in plants retained its activity after lyophilization and grinding of dried leaves in a mill. The proposed protocol for NR activity assay is suitable for plant lysates with an NR activity suffi cient to form nitrite in the range of 5–120 micromoles / l (μM) in 800 μl of reaction mix (for instance, freeze-dried sample originated from 100 mg of wheat seedling leaves).  Centrifugation of a plant lysate at 20,000 g almost did not change NR activity compared to 12,000 g that is achievable for most lab centrifuges. Lysates from fresh leaves contained signifi cantly more total protein than lysates from lyophilized leaves (with an equal amount of starting wet material). The difference in the nitrate-reducing activity in lysates from fresh and lyophilized leaves was not as high as the difference in protein concentration. Thus, the activity of NR calculated per g of total protein was higher in lyophilized leaves than in fresh leaves. The activity of NR was signifi cantly induced by nitrate for all cultivars. The basal and nitrate-induced NR activity varied widely between the cultivars, and the induction ranged from 2.5 fold for Novosibirskaya 67 variety and 2.7 fold for Vassa to 5.4 for Altigo and 5.7 fold for Grom.

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