Biosensors

21 pages, 3948 KiB

Open AccessArticle

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach

by Sergiusz Wesolowski, Marc R. Birtwistle and Grzegorz A. Rempala

Biosensors 2013, 3(3), 238-258; https://doi.org/10.3390/bios3030238 - 28 Jun 2013

Cited by 23 | Viewed by 9835

Transcriptome-based biosensors are expected to have a large impact on the future of biotechnology. However, a central aspect of transcriptomics is differential expression analysis, where, currently, deep RNA sequencing (RNA-seq) has the potential to replace the microarray as the standard assay for RNA [...] Read more.

Transcriptome-based biosensors are expected to have a large impact on the future of biotechnology. However, a central aspect of transcriptomics is differential expression analysis, where, currently, deep RNA sequencing (RNA-seq) has the potential to replace the microarray as the standard assay for RNA quantification. Our contributions here to RNA-seq differential expression analysis are two-fold. First, given the high cost of an RNA-seq run, biological replicates are rare, and therefore, information sharing across genes to obtain variance estimates is crucial. To handle such information sharing in a rigorous manner, we propose an hierarchical, empirical Bayes approach (R-EBSeq) that combines the Cufflinks model for generating relative transcript abundance measurements, known as FPKM (fragments per kilobase of transcript length per million mapped reads) with the EBArrays framework, which was previously developed for empirical Bayes analysis of microarray data. A desirable feature of R-EBSeq is easy-to-implement analysis of more than pairwise comparisons, as we illustrate with experimental data. Secondly, we develop the standard RNA-seq test data set, on the level of reads, where 79 transcripts are artificially differentially expressed and, therefore, explicitly known. This test data set allows us to compare the performance, in terms of the true discovery rate, of R-EBSeq to three other widely used RNAseq data analysis packages: Cuffdiff, DEseq and BaySeq. Our analysis indicates that DESeq identifies the first half of the differentially expressed transcripts well, but then is outperformed by Cuffdiff and R-EBSeq. Cuffdiff and R-EBSeq are the two top performers. Thus, R-EBSeq offers good performance, while allowing flexible and rigorous comparison of multiple biological conditions. Full article

(This article belongs to the Special Issue Bio- and Chemo-Sensor Networks and Arrays)

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24 pages, 923 KiB

Open AccessReview

The DosS-DosT/DosR Mycobacterial Sensor System

by Santhosh Sivaramakrishnan and Paul R. Ortiz de Montellano

Biosensors 2013, 3(3), 259-282; https://doi.org/10.3390/bios3030259 - 4 Jul 2013

Cited by 54 | Viewed by 10732

Abstract

DosS/DosR is a two-component regulatory system in which DosS, a heme-containing sensor also known as DevS, under certain conditions undergoes autophosphorylation and then transfers the phosphate to DosR, a DNA-binding protein that controls the entry of Mycobacterium tuberculosis and other mycobacteria into a [...] Read more.

DosS/DosR is a two-component regulatory system in which DosS, a heme-containing sensor also known as DevS, under certain conditions undergoes autophosphorylation and then transfers the phosphate to DosR, a DNA-binding protein that controls the entry of Mycobacterium tuberculosis and other mycobacteria into a latent, dormant state. DosT, a second sensor closely related to DosS, is present in M. tuberculosis and participates in the control of the dormancy response mediated by DosR. The binding of phosphorylated DosR to DNA initiates the expression of approximately fifty dormancy-linked genes. DosT is accepted to be a gas sensor that is activated in the ferrous state by the absence of an oxygen ligand or by the binding of NO or CO. DosS functions in a similar fashion as a gas sensor, but contradictory evidence has led to the suggestion that it also functions as a redox state sensor. This review focuses on the structure, biophysical properties, and function of the DosS/DosT heme sensors. Full article

(This article belongs to the Special Issue Physiological Sensors of Gases, Light, Redox State and Hypoxia)

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3 pages, 87 KiB

Open AccessEditorial

Micro and Nanotechnologies Enhanced Biomolecular Sensing

by Tza-Huei Wang

Biosensors 2013, 3(3), 283-285; https://doi.org/10.3390/bios3030283 - 5 Jul 2013

Cited by 4 | Viewed by 7320

Abstract

This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive [...] Read more.

This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications. Full article

(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)

11 pages, 326 KiB

Open AccessArticle

The Effect of 3-Thiopheneacetic Acid in the Polymerization of a Conductive Electrotextile for Use in Biosensor Development

by Shannon K. McGraw, Evangelyn Alocilja, Andre Senecal and Kris Senecal

Biosensors 2013, 3(3), 286-296; https://doi.org/10.3390/bios3030286 - 29 Jul 2013

Cited by 2 | Viewed by 6481

Abstract

Investigations were conducted to develop an electrotextile using a nonwoven polypropylene fiber platform conformally coated in a conductive, functionalized copolymer of polypyrrole and 3-thiopheneacetic acid (3TAA). The objectives of this study were to determine: (1) if the inclusion of 3TAA in the polymerization [...] Read more.

Investigations were conducted to develop an electrotextile using a nonwoven polypropylene fiber platform conformally coated in a conductive, functionalized copolymer of polypyrrole and 3-thiopheneacetic acid (3TAA). The objectives of this study were to determine: (1) if the inclusion of 3TAA in the polymerization process would have an effect on the availability of binding sites in the high-surface area electrotextile for biorecognition elements and (2) how the increase in the concentration of 3TAA would affect the physical characteristics of the coating, resistivity of the sample and availability of binding sites. It was found that the addition of 3TAA to the polymerization process resulted in an increase in the size of the polypyrrole coating, as well as the material resistivity and available binding sites for biorecognition elements. These factors were used to determine which of the tested concentrations was best for biosensor development. A polymer coated membrane sample containing a concentration within the range of 10–50 mg/mL of 3TAA was selected as the best for future biosensor work. Full article

(This article belongs to the Special Issue Nanomaterials for Biodetection and Drug Delivery)

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15 pages, 606 KiB

Open AccessArticle

Comparison of Surface Plasmon Resonance, Resonant Waveguide Grating Biosensing and Enzyme Linked Immunosorbent Assay (ELISA) in the Evaluation of a Dengue Virus Immunoassay

by Dongmei Hu, Scott R. Fry, Johnny X. Huang, Xixia Ding, Liwen Qiu, Yuxian Pan, Yue Chen, Jing Jin, Catriona McElnea, Joe Buechler, Xiaoyan Che and Matthew A. Cooper

Biosensors 2013, 3(3), 297-311; https://doi.org/10.3390/bios3030297 - 31 Jul 2013

Cited by 30 | Viewed by 10315

Abstract

Two label-free biosensor platforms, Resonance Waveguide Grating (RWG) and Surface Plasmon Resonance (SPR), were used to rank a large panel of anti-dengue virus NS1 antibodies. Dengue non-structural 1 (NS1) protein is an established serological marker for the early detection of dengue infection. A [...] Read more.

Two label-free biosensor platforms, Resonance Waveguide Grating (RWG) and Surface Plasmon Resonance (SPR), were used to rank a large panel of anti-dengue virus NS1 antibodies. Dengue non-structural 1 (NS1) protein is an established serological marker for the early detection of dengue infection. A variety of commercial dengue NS1 antigen capture immunoassays are available in both ELISA and lateral flow format. However, there is a significant scope to improve both the sensitivity and the specificity of those tests. The interactions of antibody (Ab)-antigen (Ag) were profiled, with weak interactions (K_D = 1–0.1 μM) able to be detected under static equilibrium conditions by RWG, but not observed to under more rigorous flow conditions using SPR. There were significant differences in the absolute affinities determined by the two technologies, and there was a poor correlation between antibodies best ranked by RWG and the lower limit of detection (LLOD) found by ELISA. Hence, whilst high-throughput RWG can be useful as preliminary screening for higher affinity antibodies, care should be exercised in the assignation of quantitative values for affinity between different assay formats. Full article

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15 pages, 357 KiB

Open AccessArticle

A Self-Referencing Detection of Microorganisms Using Surface Enhanced Raman Scattering Nanoprobes in a Test-in-a-Tube Platform

by Nan Xiao, Chao Wang and Chenxu Yu

Biosensors 2013, 3(3), 312-326; https://doi.org/10.3390/bios3030312 - 13 Sep 2013

Cited by 24 | Viewed by 11179

Abstract

Anisotropic nanoparticles (i.e., silver nanocubes) were functionalized with target-specific antibodies and Raman active tags to serve as nanoprobes for the rapid detection of bacteria in a test-in-a-tube platform. A self-referencing scheme was developed and implemented in which surface enhanced Raman spectroscopic [...] Read more.

Anisotropic nanoparticles (i.e., silver nanocubes) were functionalized with target-specific antibodies and Raman active tags to serve as nanoprobes for the rapid detection of bacteria in a test-in-a-tube platform. A self-referencing scheme was developed and implemented in which surface enhanced Raman spectroscopic (SERS) signatures of the targets were observed superimposed with the SERS signals of the Raman tags. The assessment through the dual signals (superimposed target and tag Raman signatures) supported a specific recognition of the targets in a single step with no washing/separation needed to a sensitivity of 10² CFU/mL, even in the presence of non-target bacteria at a 10 times higher concentration. The self-referencing protocol implemented with a portable Raman spectrometer potentially can become an easy-to-use, field-deployable spectroscopic sensor for onsite detection of pathogenic microorganisms. Full article

(This article belongs to the Special Issue Nanomaterials for Biodetection and Drug Delivery)

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14 pages, 553 KiB

Open AccessReview

Lab-on-a-Chip Magneto-Immunoassays: How to Ensure Contact between Superparamagnetic Beads and the Sensor Surface

by Bernhard Eickenberg, Judith Meyer, Lars Helmich, Daniel Kappe, Alexander Auge, Alexander Weddemann, Frank Wittbracht and Andreas Hütten

Biosensors 2013, 3(3), 327-340; https://doi.org/10.3390/bios3030327 - 17 Sep 2013

Cited by 12 | Viewed by 10679

Abstract

Lab-on-a-chip immuno assays utilizing superparamagnetic beads as labels suffer from the fact that the majority of beads pass the sensing area without contacting the sensor surface. Different solutions, employing magnetic forces, ultrasonic standing waves, or hydrodynamic effects have been found over the past [...] Read more.

Lab-on-a-chip immuno assays utilizing superparamagnetic beads as labels suffer from the fact that the majority of beads pass the sensing area without contacting the sensor surface. Different solutions, employing magnetic forces, ultrasonic standing waves, or hydrodynamic effects have been found over the past decades. The first category uses magnetic forces, created by on-chip conducting lines to attract beads towards the sensor surface. Modifications of the magnetic landscape allow for additional transport and separation of different bead species. The hydrodynamic approach uses changes in the channel geometry to enhance the capture volume. In acoustofluidics, ultrasonic standing waves force µm-sized particles onto a surface through radiation forces. As these approaches have their disadvantages, a new sensor concept that circumvents these problems is suggested. This concept is based on the granular giant magnetoresistance (GMR) effect that can be found in gels containing magnetic nanoparticles. The proposed design could be realized in the shape of paper-based test strips printed with gel-based GMR sensors. Full article

(This article belongs to the Special Issue Nanomaterials for Biodetection and Drug Delivery)

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Biosensors, Volume 3, Issue 3 (September 2013) – 8 articles , Pages 238-359

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