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Article: Meeting the technical challenges of personalized medicine and companion diagnostics.

Montagna, Richard A

2012 Volume 44, Issue 1, Page(s) 16, 18, 20 passim

MeSH term(s)	Biomarkers/analysis ; Genome, Human ; Humans ; Pharmacogenetics ; Precision Medicine/methods ; United States
Chemical Substances	Biomarkers
Language	English
Publishing date	2012-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	603205-9
ISSN	0580-7247
ISSN	0580-7247
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A modifiable microarray-based universal sensor: providing sample-to-results automation.

Yasmin, Rubina / Zhu, Hui / Chen, Zongyuan / Montagna, Richard A

Heliyon

2016 Volume 2, Issue 10, Page(s) e00179

Abstract: A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a ... ...

Abstract	A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA "universal" probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined "reporter" probes that are complementary at their 3' termini to one or more of the universal probes and complementary to the target amplicons at their 5' termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of
Language	English
Publishing date	2016-10-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2016.e00179
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A modifiable microarray-based universal sensor: providing sample-to-results automation

Yasmin, Rubina / Zhu, Hui / Chen, Zongyuan / Montagna, Richard A

Heliyon. 2016 Oct., v. 2, no. 10

2016

Abstract	A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.
Keywords	DNA ; Mycobacterium ; automation ; hybridization ; microarray technology ; mutants ; polymerase chain reaction
Language	English
Dates of publication	2016-10
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2016.e00179
Database	NAL-Catalogue (AGRICOLA)

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Article: Genomics.

Estabrooks, Laurel / Schmidt, Megan / Montagna, Richard A

MLO: medical laboratory observer

2013 Volume 45, Issue 8, Page(s) 30

MeSH term(s)	Clinical Laboratory Services ; Genetic Testing/utilization ; Genomics ; Humans ; Sequence Analysis, DNA
Language	English
Publishing date	2013-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	603205-9
ISSN	0580-7247
ISSN	0580-7247
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Article ; Online: Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva.

Sabalza, Maite / Yasmin, Rubina / Barber, Cheryl A / Castro, Talita / Malamud, Daniel / Kim, Beum Jun / Zhu, Hui / Montagna, Richard A / Abrams, William R

PloS one

2018 Volume 13, Issue 2, Page(s) e0192398

Abstract: In recent years, there have been increasing numbers of infectious disease outbreaks that spread rapidly to population centers resulting from global travel, population vulnerabilities, environmental factors, and ecological disasters such as floods and ... ...

Abstract	In recent years, there have been increasing numbers of infectious disease outbreaks that spread rapidly to population centers resulting from global travel, population vulnerabilities, environmental factors, and ecological disasters such as floods and earthquakes. Some examples of the recent outbreaks are the Ebola epidemic in West Africa, Middle East respiratory syndrome coronavirus (MERS-Co) in the Middle East, and the Zika outbreak through the Americas. We have created a generic protocol for detection of pathogen RNA and/or DNA using loop-mediated isothermal amplification (LAMP) and reverse dot-blot for detection (RDB) and processed automatically in a microfluidic device. In particular, we describe how a microfluidic assay to detect HIV viral RNA was converted to detect Zika virus (ZIKV) RNA. We first optimized the RT-LAMP assay to detect ZIKV RNA using a benchtop isothermal amplification device. Then we implemented the assay in a microfluidic device that will allow analyzing 24 samples simultaneously and automatically from sample introduction to detection by RDB technique. Preliminary data using saliva samples spiked with ZIKV showed that our diagnostic system detects ZIKV RNA in saliva. These results will be validated in further experiments with well-characterized ZIKV human specimens of saliva. The described strategy and methodology to convert the HIV diagnostic assay and platform to a ZIKV RNA detection assay provides a model that can be readily utilized for detection of the next emerging or re-emerging infectious disease.
MeSH term(s)	Humans ; Nucleic Acid Amplification Techniques/methods ; RNA, Viral/genetics ; Reverse Transcription ; Saliva/virology ; Zika Virus/genetics ; Zika Virus/isolation & purification
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2018
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0192398
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Prion protein detection in serum using micromechanical resonator arrays.

Varshney, Madhukar / Waggoner, Philip S / Montagna, Richard A / Craighead, Harold G

Talanta

2009 Volume 80, Issue 2, Page(s) 593–599

Abstract: Prion proteins that have transformed from their normal cellular counterparts (PrP(c)) into infectious form (PrP(res)) are responsible for causing progressive neurodegenerative diseases in numerous species, such as bovine spongiform encephalopathy (BSE) ... ...

Abstract	Prion proteins that have transformed from their normal cellular counterparts (PrP(c)) into infectious form (PrP(res)) are responsible for causing progressive neurodegenerative diseases in numerous species, such as bovine spongiform encephalopathy (BSE) in cattle (also known as mad cow disease), scrapie in sheep, and Creutzfeldt-Jakob disease (CJD) in humans. Due to a possible link between BSE and CJD it is highly desirable to develop non-invasive and ante mortem tests for the detection of prion proteins in bovine samples. Such ante mortem tests of all cows prior to slaughter will help to prevent the introduction of PrP(res) into the human food supply. Furthermore, detection of PrP(res) in donated blood will also help to prevent the transmission of CJD among humans through blood transfusion. In this study, we have continued development of a micromechanical resonator array that is capable of detecting PrP(c) in bovine blood serum. The sensitivity of the resonators for the detection of PrP(c) is further enhanced by the use of secondary mass labels. A pair of antibodies is used in a sandwich immunoassay format to immobilize PrP(c) on the surface of resonators and attach nanoparticles as secondary mass labels to PrP(c). Secondary mass labeling is optimized in terms of incubation time to maximize the frequency shifts that correspond to the presence of PrP(c) on the surface of resonators. Our results show that a minimum of 200 pg mL(-1) of PrP(c) in blood serum can be detected using micromechanical resonator arrays.
MeSH term(s)	Animals ; Cattle ; Chemistry Techniques, Analytical/instrumentation ; Chemistry Techniques, Analytical/methods ; Creutzfeldt-Jakob Syndrome/blood ; Creutzfeldt-Jakob Syndrome/prevention & control ; Encephalopathy, Bovine Spongiform/blood ; Encephalopathy, Bovine Spongiform/diagnosis ; Humans ; Immunoassay/methods ; Limit of Detection ; Prions/blood ; Reproducibility of Results
Chemical Substances	Prions
Language	English
Publishing date	2009-12-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2009.07.032
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Article: Microfluidic biosensor for the serotype-specific detection of dengue virus RNA.

Zaytseva, Natalya V / Montagna, Richard A / Baeumner, Antje J

Analytical chemistry

2005 Volume 77, Issue 23, Page(s) 7520–7527

Abstract: The development of a microfluidic biosensor with fluorescence detection for the rapid, sensitive, and serotype-specific detection of Dengue virus is presented. The biosensor chip consists of poly(dimethylsiloxane) (PDMS) substrate with fabricated ... ...

Abstract	The development of a microfluidic biosensor with fluorescence detection for the rapid, sensitive, and serotype-specific detection of Dengue virus is presented. The biosensor chip consists of poly(dimethylsiloxane) (PDMS) substrate with fabricated microchannels and a glass substrate used to seal the microchannels. These two substrates are packaged within a pressure-closed Plexiglas housing to provide a watertight reversible sealing at the PDMS-glass interface. The ability to reversibly seal the device permits easy disassembly and quick interchange of the device parts, which is ideal for developmental purposes. The biosensor employs a magnetic bead-based sandwich hybridization system in conjugation with liposome amplification for the specific detection of nucleic acids. The concentrations of the various biosensor components were optimized using a synthesized fragment of Dengue virus RNA. To evaluate the sensitivity of the assay, two detection systems, based on fluorescence measurements of intact and lysed liposomes, were analyzed. The entire analysis was complete within 20 min (including incubation time) with RNA detection limits of 0.125 nM and 50 pM for intact and lysed liposome detection systems, respectively. Subsequently, the biosensor was applied to the analysis of actual RNA obtained from Dengue virus serotypes 1-4. The resulting signals were compared to those obtained using standard electrochemiluminescence detection and shown to correspond perfectly with respect to serotype identification.
MeSH term(s)	Base Sequence ; Biosensing Techniques/instrumentation ; Biosensing Techniques/methods ; Dengue Virus/classification ; Dengue Virus/genetics ; Dextran Sulfate ; Liposomes ; Microfluidics/instrumentation ; Microfluidics/methods ; Nucleic Acid Hybridization ; RNA, Viral/blood ; RNA, Viral/genetics ; Serotyping
Chemical Substances	Liposomes ; RNA, Viral ; Dextran Sulfate (9042-14-2)
Language	English
Publishing date	2005-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac0509206
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Article: A Rapid, Self-confirming Assay for HIV: Simultaneous Detection of Anti-HIV Antibodies and Viral RNA.

Chen, Zongyuan / Zhu, Hui / Malamud, Daniel / Barber, Cheryl / Ongagna, Yhombi Yvon Serge / Yasmin, Rubina / Modak, Sayli / Janal, Malvin N / Abrams, William R / Montagna, Richard A

Journal of AIDS & clinical research

2016 Volume 7, Issue 1

Abstract: Objective: We developed a microfluidic system to simultaneously detect host anti-HIV antibodies and viral RNA in the same specimen in order to satisfy two important diagnostic criteria, especially within resource-limited settings. First, the system can ... ...

Abstract	Objective: We developed a microfluidic system to simultaneously detect host anti-HIV antibodies and viral RNA in the same specimen in order to satisfy two important diagnostic criteria, especially within resource-limited settings. First, the system can detect acute HIV infection and allow immediate confirmation of a seropositive screening result by detection of HIV RNA. It also addresses the well-known "seroconversion window" during early HIV infection when antibodies are not yet detectable and viral loads are at their highest. Methods: We first developed and optimized two separate manual assays for the detection of host anti-HIV antibodies and viral RNA and then converted them to the microfluidic system. We optimized a commercially available serologic assay to run within the microfluidic device while we incorporated the isothermal LAMP assay to detect the presence of viral RNA. The microfluidic device and instrumentation were developed to simultaneously perform both assays without any user intervention. Results: The finalized system consists of a disposable injection molded and film-laminated microfluidic CARD disposable device and a portable, software controlled instrument, which together can automatically perform all steps of both assays without any user intervention after the initial loading of samples and reagents. The microfluidic CARD cartridge has multiple microchannels, valves, pumps and reservoirs, which perform the immunoassay, isolates viral RNA for detection by magnetic bead based purification, and Reverse Transcriptase loop-mediated isothermal amplification (RT-LAMP). The microfluidic system was able to detect host anti-HIV antibodies and viral RNA in either a blood or saliva sample. Conclusion: The ability to detect antibodies and simultaneously confirm a seropositive HIV-RNA result provides healthcare workers with a complete and accurate appraisal of a patient's infection status in the earliest stages of the disease and represents an important tool for the "Test and Treat" and "Treatment as Prevention" approaches for controlling the HIV epidemic.
Language	English
Publishing date	2016-01-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2601227-3
ISSN	2155-6113
ISSN	2155-6113
DOI	10.4172/2155-6113.1000540
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Article: Development of a microfluidic biosensor module for pathogen detection.

Zaytseva, Natalya V / Goral, Vasiliy N / Montagna, Richard A / Baeumner, Antje J

Lab on a chip

2005 Volume 5, Issue 8, Page(s) 805–811

Abstract: The development of a microfluidic biosensor module with fluorescence detection for the identification of pathogenic organisms and viruses is presented in this article. The microfluidic biosensor consists of a network of microchannels fabricated in ... ...

Abstract	The development of a microfluidic biosensor module with fluorescence detection for the identification of pathogenic organisms and viruses is presented in this article. The microfluidic biosensor consists of a network of microchannels fabricated in polydimethylsiloxane (PDMS) substrate. The microchannels are sealed with a glass substrate and packed in a Plexiglas housing to provide connection to the macro-world and ensure leakage-free flow operation. Reversible sealing permits easy disassembly for cleaning and replacing the microfluidic channels. The fluidic flow is generated by an applied positive pressure gradient, and the module can be operated under continuous solution flow of up to 80 microL min(-1). The biosensor recognition principle is based on DNA/RNA hybridization and liposome signal amplification. Superparamagnetic beads are incorporated into the system as a mobile solid support and are an essential part of the analysis scheme. In this study, the design, fabrication and the optimization of concentrations and amounts of the different biosensor components are carried out. The total time required for an assay is only 15 min including sample incubation time. The biosensor module is designed so that it can be easily integrated with a micro total analysis system, which will combine sample preparation and detection steps onto a single chip.
MeSH term(s)	Bacteria/isolation & purification ; Biosensing Techniques/instrumentation ; Biosensing Techniques/methods ; DNA Probes ; Fluorescence ; Liposomes ; Microfluidic Analytical Techniques/instrumentation ; Microfluidic Analytical Techniques/methods ; RNA, Bacterial/analysis ; RNA, Messenger/analysis ; RNA, Ribosomal/analysis ; RNA, Viral/analysis ; Viruses/isolation & purification
Chemical Substances	DNA Probes ; Liposomes ; RNA, Bacterial ; RNA, Messenger ; RNA, Ribosomal ; RNA, Viral
Language	English
Publishing date	2005-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2056646-3
ISSN	1473-0189 ; 1473-0197
ISSN (online)	1473-0189
ISSN	1473-0197
DOI	10.1039/b503856a
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Article: Prion protein detection using nanomechanical resonator arrays and secondary mass labeling.

Varshney, Madhukar / Waggoner, Philip S / Tan, Christine P / Aubin, Keith / Montagna, Richard A / Craighead, Harold G

Analytical chemistry

2008 Volume 80, Issue 6, Page(s) 2141–2148

Abstract: Nanomechanical resonators have shown potential application for mass sensing and have been used to detect a variety of biomolecules. In this study, a dynamic resonance-based technique was used to detect prion proteins (PrP), which in conformationally ... ...

Abstract	Nanomechanical resonators have shown potential application for mass sensing and have been used to detect a variety of biomolecules. In this study, a dynamic resonance-based technique was used to detect prion proteins (PrP), which in conformationally altered forms are known to cause neurodegenerative diseases in animals as well as humans. Antibodies and nanoparticles were used as mass labels to increase the mass shift and thus amplify the frequency shift signal used in PrP detection. A sandwich assay was used to immobilize PrP between two monoclonal antibodies, one of which was conjugated to the resonator's surface while the other was either used alone or linked to the nanoparticles as a mass label. Without additional mass labeling, PrP was not detected at concentrations below 20 microg/mL. In the presence of secondary antibodies the analytical sensitivity was improved to 2 microg/mL. With the use of functionalized nanoparticles, the sensitivity improved an additional 3 orders of magnitude to 2 ng/mL.
MeSH term(s)	Animals ; Antibodies, Monoclonal/immunology ; Humans ; Nanotechnology/instrumentation ; Prions/analysis ; Prions/immunology
Chemical Substances	Antibodies, Monoclonal ; Prions
Language	English
Publishing date	2008-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac702153p
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