Systematic evaluation of signal-to-noise ratio in variant detection from single cell genome multiple displacement amplification and exome sequencing

ABSTRACTWe determined a significant fraction of the genome sequence of a representative ofThiovulum, the uncultivated genus of colorless sulfurEpsilonproteobacteria, by analyzing the genome sequences of four individual cells collected from phototrophic mats from Elkhorn Slough, California. These cells were isolated utilizing a microfluidic laser-tweezing system, and their genomes were amplified by multiple-displacement amplification prior to sequencing.Thiovulumis a gradient bacterium found at oxic-anoxic marine interfaces and noted for its distinctive morphology and rapid swimming motility. The genomic sequences of the four individual cells were assembled into a composite genome consisting of 221 contigs covering 2.083 Mb including 2,162 genes. This single-cell genome represents a genomic view of the physiological capabilities of isolatedThiovulumcells.Thiovulumis the second-fastest bacterium ever observed, swimming at 615 μm/s, and this genome shows that this rapid swimming motility is a result of a standard flagellar machinery that has been extensively characterized in other bacteria. This suggests that standard flagella are capable of propelling bacterial cells at speeds much faster than typically thought. Analysis of the genome suggests that naturally occurringThiovulumpopulations are more diverse than previously recognized and that studies performed in the past probably address a wide range of unrecognized genotypic and phenotypic diversities ofThiovulum. The genome presented in this article provides a basis for future isolation-independent studies ofThiovulum, where single-cell and metagenomic tools can be used to differentiate between differentThiovulumgenotypes.

Download Full-text

A modified exponential amplification reaction (EXPAR) with an improved signal-to-noise ratio for ultrasensitive detection of polynucleotide kinase

Chemical Communications ◽

10.1039/c9cc03568k ◽

2019 ◽

Vol 55 (53) ◽

pp. 7611-7614 ◽

Cited By ~ 8

Author(s):

Yu-Peng Zhang ◽

Yun-Xi Cui ◽

Xiao-Yu Li ◽

Yi-Chen Du ◽

An-Na Tang ◽

...

Keyword(s):

Single Cell ◽

Kinase Activity ◽

Signal To Noise Ratio ◽

Ultrasensitive Detection ◽

Single Cell Level ◽

Signal To Noise ◽

Cell Level ◽

Polynucleotide Kinase ◽

Noise Ratio ◽

Amplification Reaction

We reported a modified exponential amplification reaction strategy and applied it to design an ultrasensitive biosensor for the detection of endogenous polynucleotide kinase activity at single-cell level.

Download Full-text

MLG: Multilayer graph clustering for multi-condition scRNA-seq data

10.1101/2021.03.26.437231 ◽

2021 ◽

Author(s):

Shan Lu ◽

Daniel J. Conn ◽

Shuyang Chen ◽

Kirby D Johnson ◽

Emery H. Bresnick ◽

...

Keyword(s):

Data Integration ◽

Dimensionality Reduction ◽

Single Cell ◽

Large Scale ◽

Signal To Noise Ratio ◽

Graph Clustering ◽

Cellular Heterogeneity ◽

Integrative Approach ◽

Signal To Noise ◽

Noise Ratio

Single-cell transcriptome sequencing (scRNA-seq) enabled investigations of cellular heterogeneity at exceedingly higher resolutions. Identification of novel cell types or transient developmental stages across multiple experimental conditions is one of its key applications. Linear and non-linear dimensionality reduction for data integration became a foundational tool in inference from scRNA-seq data. We present Multi Layer Graph Clustering (MLG) as an integrative approach for combining multiple dimensionality reduction of multi-condition scRNA-seq data. MLG generates a multilayer shared nearest neighbor cell graph with higher signal-to-noise ratio and outperforms current best practices in terms of clustering accuracy across large-scale benchmarking experiments. Application of MLG to a wide variety of datasets from multiple conditions highlights how MLG boosts signal-to-noise ratio for fine-grained sub-population identification. MLG is widely applicable to settings with single cell data integration via dimension reduction.

Download Full-text

High-coverage, single-cell genome and exome sequencing at base-pair resolution to aid biomarker identification

Science-Business eXchange ◽

10.1038/scibx.2014.993 ◽

2014 ◽

Vol 7 (33) ◽

pp. 993-993

Keyword(s):

Single Cell ◽

Exome Sequencing ◽

Base Pair ◽

High Coverage ◽

Biomarker Identification ◽

Cell Genome ◽

Single Cell Genome

Download Full-text

Determination of the Best Emulsion for the Microscopy of Crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096886 ◽

1981 ◽

Vol 39 ◽

pp. 32-33

Author(s):

David A. Grano ◽

Kenneth H. Downing

Keyword(s):

Spatial Frequency ◽

Information Transfer ◽

Signal To Noise Ratio ◽

Experimental Situation ◽

Photographic Emulsion ◽

Modulation Transfer ◽

Signal To Noise ◽

Frequency Space ◽

Noise Ratio

The retrieval of high-resolution information from images of biological crystals depends, in part, on the use of the correct photographic emulsion. We have been investigating the information transfer properties of twelve emulsions with a view toward 1) characterizing the emulsions by a few, measurable quantities, and 2) identifying the “best” emulsion of those we have studied for use in any given experimental situation. Because our interests lie in the examination of crystalline specimens, we've chosen to evaluate an emulsion's signal-to-noise ratio (SNR) as a function of spatial frequency and use this as our critereon for determining the best emulsion.The signal-to-noise ratio in frequency space depends on several factors. First, the signal depends on the speed of the emulsion and its modulation transfer function (MTF). By procedures outlined in, MTF's have been found for all the emulsions tested and can be fit by an analytic expression 1/(1+(S/S0)2). Figure 1 shows the experimental data and fitted curve for an emulsion with a better than average MTF. A single parameter, the spatial frequency at which the transfer falls to 50% (S0), characterizes this curve.

Download Full-text

Experiments in Bright-Field Imaging with Hollow-Cone Illumination

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100097703 ◽

1981 ◽

Vol 39 ◽

pp. 226-227

Author(s):

W. Kunath ◽

K. Weiss ◽

E. Zeitler

Keyword(s):

Signal To Noise Ratio ◽

Carbon Support ◽

Electronic System ◽

Optic Axis ◽

Hollow Cone ◽

Signal To Noise ◽

Bright Field ◽

Noise Ratio ◽

Single Field ◽

Field Imaging

Bright-field images taken with axial illumination show spurious high contrast patterns which obscure details smaller than 15 ° Hollow-cone illumination (HCI), however, reduces this disturbing granulation by statistical superposition and thus improves the signal-to-noise ratio. In this presentation we report on experiments aimed at selecting the proper amount of tilt and defocus for improvement of the signal-to-noise ratio by means of direct observation of the electron images on a TV monitor.Hollow-cone illumination is implemented in our microscope (single field condenser objective, Cs = .5 mm) by an electronic system which rotates the tilted beam about the optic axis. At low rates of revolution (one turn per second or so) a circular motion of the usual granulation in the image of a carbon support film can be observed on the TV monitor. The size of the granular structures and the radius of their orbits depend on both the conical tilt and defocus.

Download Full-text

Information capacity and bandwidth limitations in the SEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152392 ◽

1989 ◽

Vol 47 ◽

pp. 84-85

Author(s):

D. C. Joy ◽

R. D. Bunn

Keyword(s):

Signal To Noise Ratio ◽

Critical Dimension ◽

Information Capacity ◽

Acquisition Time ◽

Signal To Noise ◽

Sem Image ◽

Probe Size ◽

Minimum Number ◽

Noise Ratio ◽

Signal Channel

The information available from an SEM image is limited both by the inherent signal to noise ratio that characterizes the image and as a result of the transformations that it may undergo as it is passed through the amplifying circuits of the instrument. In applications such as Critical Dimension Metrology it is necessary to be able to quantify these limitations in order to be able to assess the likely precision of any measurement made with the microscope.The information capacity of an SEM signal, defined as the minimum number of bits needed to encode the output signal, depends on the signal to noise ratio of the image - which in turn depends on the probe size and source brightness and acquisition time per pixel - and on the efficiency of the specimen in producing the signal that is being observed. A detailed analysis of the secondary electron case shows that the information capacity C (bits/pixel) of the SEM signal channel could be written as :

Download Full-text

Speech Reception in the Presence of Classroom Noise

Language Speech and Hearing Services in Schools ◽

10.1044/0161-1461.1004.221 ◽

1979 ◽

Vol 10 (4) ◽

pp. 221-230 ◽

Cited By ~ 2

Author(s):

Veronica Smyth

Keyword(s):

Signal To Noise Ratio ◽

Learning Processes ◽

Speech Discrimination ◽

Signal To Noise ◽

Speech Reception ◽

Monosyllabic Words ◽

Noise Ratio

Three hundred children from five to 12 years of age were required to discriminate simple, familiar, monosyllabic words under two conditions: 1) quiet, and 2) in the presence of background classroom noise. Of the sample, 45.3% made errors in speech discrimination in the presence of background classroom noise. The effect was most marked in children younger than seven years six months. The results are discussed considering the signal-to-noise ratio and the possible effects of unwanted classroom noise on learning processes.

Download Full-text

Quantifying the Effects of Background Speech Babble on Preschool Children's Novel Word Learning in a Multisession Paradigm: A Preliminary Study

Journal of Speech Language and Hearing Research ◽

10.1044/2019_jslhr-h-19-0083 ◽

2020 ◽

Vol 63 (1) ◽

pp. 345-356

Author(s):

Meital Avivi-Reich ◽

Megan Y. Roberts ◽

Tina M. Grieco-Calub

Keyword(s):

Word Learning ◽

Signal To Noise Ratio ◽

Preschool Age ◽

Exposure Condition ◽

Signal To Noise ◽

Verbal Recall ◽

Referent Selection ◽

Main Effect ◽

Noise Ratio ◽

Novel Word Learning

Purpose This study tested the effects of background speech babble on novel word learning in preschool children with a multisession paradigm. Method Eight 3-year-old children were exposed to a total of 8 novel word–object pairs across 2 story books presented digitally. Each story contained 4 novel consonant–vowel–consonant nonwords. Children were exposed to both stories, one in quiet and one in the presence of 4-talker babble presented at 0-dB signal-to-noise ratio. After each story, children's learning was tested with a referent selection task and a verbal recall (naming) task. Children were exposed to and tested on the novel word–object pairs on 5 separate days within a 2-week span. Results A significant main effect of session was found for both referent selection and verbal recall. There was also a significant main effect of exposure condition on referent selection performance, with more referents correctly selected for word–object pairs that were presented in quiet compared to pairs presented in speech babble. Finally, children's verbal recall of novel words was statistically better than baseline performance (i.e., 0%) on Sessions 3–5 for words exposed in quiet, but only on Session 5 for words exposed in speech babble. Conclusions These findings suggest that background speech babble at 0-dB signal-to-noise ratio disrupts novel word learning in preschool-age children. As a result, children may need more time and more exposures of a novel word before they can recognize or verbally recall it.

Download Full-text