scholarly journals Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip

2019 ◽  
Vol 73 (5) ◽  
pp. 1075-1082.e4 ◽  
Author(s):  
Curtis J. Layton ◽  
Peter L. McMahon ◽  
William J. Greenleaf
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
High Throughput Dna Sequencing ◽  
Protein Assays

scholarly journals Large-scale, quantitative protein assays on a high-throughput DNA sequencing chip

2018 ◽  
Author(s):  
Curtis J Layton ◽  
Peter L McMahon ◽  
William J Greenleaf
Keyword(s):  
Amino Acid ◽  
Dna Sequencing ◽  
High Throughput ◽  
Protein Function ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Molecular Variants ◽  
Amino Acid Interaction ◽  
High Throughput Dna Sequencing ◽  
Protein Assays

SummaryHigh-throughput DNA sequencing techniques have enabled diverse approaches for linking DNA sequence to biochemical function. In contrast, assays of protein function have substantial limitations in terms of throughput, automation, and widespread availability. We have adapted an Illumina high-throughput sequencing chip to display an immense diversity of ribosomally-translated proteins and peptides, and then carried out fluorescence-based functional assays directly on this flow cell, demonstrating that a single, widely-available high-throughput platform can perform both sequencing-by-synthesis and protein assays. We quantified the binding of the M2 anti-FLAG antibody to a library of 1.3×104 variant FLAG peptides, exploring non-additive effects of combinations of mutations and discovering a “superFLAG” epitope variant. We also measured the enzymatic activity of 1.56×105 molecular variants of full-length of human O6-alkylguanine-DNA alkyltransferase (SNAP-tag). This comprehensive corpus of catalytic rates linked to amino acid sequence perturbations revealed amino acid interaction networks and cooperativity, linked positive cooperativity to structural proximity, and revealed ubiquitous positively-cooperative interactions with histidine residues.

scholarly journals Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions

2019 ◽  
Vol 244 (6) ◽  
pp. 534-542 ◽  
Author(s):  
Ana P Christoff ◽  
Aline FR Sereia ◽  
Camila Hernandes ◽  
Luiz FV de Oliveira
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Epidemiological Surveillance ◽  
Indoor Environments ◽  
Natural Ecosystems ◽  
Direct Dna Sequencing ◽  
New Approaches ◽  
Microbial Profile ◽  
High Throughput Dna Sequencing

Microorganisms are widely distributed all over the Earth, inhabiting very diverse natural ecosystems, from the human body to inanimate indoor environments. Until recently, the methods most commonly used to study microbes have been culture-dependent approaches relying on the phenotypic evaluation of isolates that can grow in laboratory conditions. Given the advances in molecular biology and high-throughput DNA sequencing methodologies, scientists could expand their microbiome knowledge to microorganisms that do not grow well in the laboratory or have been considered too difficult and laborious to be cultivated. Culture-independent methods such as direct DNA sequencing can be performed for many samples at once, revealing the entire microbial profile of the samples and making possible the rapid characterization of the whole environmental microbiome. Investigating the microbiome profile of indoor environments such as hospitals, houses, offices and other buildings is of major concern because it could include a number of opportunistic, pathogenic or nosocomial microbes. Additionally, these environments could serve as reservoirs of virulence or antimicrobial resistance, which could be spread by humans or other vectors. High-throughput DNA sequencing has enabled large-scale microbiome screening for multiple indoor areas in a single analysis. Using this approach, we can easily track microorganisms in the environment and monitor microbiome composition related to hygiene processes or environment quality. Gaining such information and resolution regarding indoor microbiome analysis can lend very important assistance for epidemiological surveillance. Impact statement Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.

scholarly journals Chemiluminiscence sensor for high-throughput DNA sequencing

2009 ◽  
Vol 1 (1) ◽  
pp. 1091-1094
Author(s):  
A R A Rahman ◽  
Shihui Foo ◽  
Sanket Goel
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
High Throughput Dna Sequencing

scholarly journals Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 16 ◽  
Author(s):  
Michael P Mullen ◽  
Christopher J Creevey ◽  
Donagh P Berry ◽  
Matt S McCabe ◽  
David A Magee ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Allele Frequency ◽  
High Throughput ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Polymorphism Discovery ◽  
Pooled Dna ◽  
High Throughput Dna Sequencing

Application of high-throughput DNA sequencing to score population-specific variants for rare disorders

2019 ◽  
Vol 305 ◽  
pp. S25
Author(s):  
M.C. Ergoren ◽  
E. Manara ◽  
S. Paolacci ◽  
S.G. Temel ◽  
G. Mocan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Rare Disorders ◽  
High Throughput Dna Sequencing
Sign in / Sign up

Export Citation Format

Share Document