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Xuan Y, Ghatak S, Clark A, Li Z, Khanna S, Pak D, Agarwal M, Roy S, Duda P, Sen CK. Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo. Nat Protoc 2021; 16:5707-5738. [PMID: 34837085 PMCID: PMC9104164 DOI: 10.1038/s41596-021-00631-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/10/2021] [Indexed: 11/09/2022]
Abstract
Tissue nanotransfection (TNT) is an electromotive gene transfer technology that was developed to achieve tissue reprogramming in vivo. This protocol describes how to fabricate the required hardware, commonly referred to as a TNT chip, and use it for in vivo TNT. Silicon hollow-needle arrays for TNT applications are fabricated in a standardized and reproducible way. In <1 s, these silicon hollow-needle arrays can be used to deliver plasmids to a predetermined specific depth in murine skin in response to pulsed nanoporation. Tissue nanotransfection eliminates the need to use viral vectors, minimizing the risk of genomic integration or cell transformation. The TNT chip fabrication process typically takes 5-6 d, and in vivo TNT takes 30 min. This protocol does not require specific expertise beyond a clean room equipped for basic nanofabrication processes.
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Affiliation(s)
- Yi Xuan
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew Clark
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhigang Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Savita Khanna
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dongmin Pak
- Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Mangilal Agarwal
- Integrated Nanosystems Development Institute, IUPUI, Indianapolis, IN, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA
| | - Peter Duda
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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2
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Tadimety A, Wu Z, Molinski JH, Beckerman R, Jin C, Zhang L, Palinski TJ, Zhang JXJ. Rational design of on-chip gold plasmonic nanoparticles towards ctDNA screening. Sci Rep 2021; 11:14185. [PMID: 34244556 PMCID: PMC8270934 DOI: 10.1038/s41598-021-93207-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 11/23/2022] Open
Abstract
This paper demonstrates the design, synthesis, simulation, and testing of three distinct geometries of plasmonic gold nanoparticles for on-chip DNA screening towards liquid biopsy. By employing a seed-mediated growth method, we have synthesized gold nanospheres, nanorods, and nanobipyramids. In parallel, we developed numerical simulations to understand the effects of nanoparticle geometry on the resonance features and refractive index sensitivity. Both experimental and simulation results were compared through a series of studies including in-solution and on-chip tests. We have thoroughly characterized the impact of nanoparticle geometry on the sensitivity to circulating tumor DNA, with immediate implications for liquid biopsy. The results agree well with theoretical predictions and simulations, including both bulk refractive index sensitivity and thin film sensitivity. Importantly, this work quantitatively establishes the link between nanoparticle geometry and efficacy in detecting rare circulating biomarkers. The nanobipyramids provided the highest sensitivity, approximately doubling the sensitivity compared to nanorods. To the best of our knowledge this is the first report carrying through geometric effects of simulation to clinically relevant biosensing. We put forth here synthesis and testing of three nanoparticle geometries, and a framework for both experimental and theoretical validation of plasmonic sensitivities towards liquid biopsy.
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Affiliation(s)
- Amogha Tadimety
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Ziqian Wu
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - John H Molinski
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Russell Beckerman
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Congran Jin
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Lauren Zhang
- The Lawrenceville School, Lawrenceville, 08648, USA
| | | | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA.
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Pikula M, Ali MM, Filipe C, Hoare T. Single-Step Printable Hydrogel Microarray Integrating Long-Chain DNA for the Discriminative and Size-Specific Sensing of Nucleic Acids. ACS Appl Mater Interfaces 2021; 13:2360-2370. [PMID: 33411496 DOI: 10.1021/acsami.0c21061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A simple approach to fabricating hydrogel-based DNA microarrays is reported by physically entrapping the rolling circle amplification (RCA) product inside printable in situ gelling hydrazone cross-linked poly(oligoethylene glycol methacrylate) hydrogels. The hydrogel-printed RCA microarray facilitates improved RCA immobilization (>65% even after vigorous washing) and resistance to denaturation relative to RCA-only printed microarrays in addition to size-discriminative sensing of DNA probes (herein, 27 or fewer nucleotides) depending on the internal porosity of the hydrogel. Furthermore, the high number of sequence repeats in the concatemeric RCA product enables high-sensitivity detection of complementary DNA probes without the need for signal amplification, with signal/noise ratios of 10 or more achieved over a short 30 min assay time followed by minimal washing. The inherent antifouling properties of the hydrogel enable discriminative hybridization in complex biological samples, particularly for short (∼10 nt) oligonucleotides whose hybridization in other assays tends to be transient and of low affinity. The scalable manufacturability and efficient performance of these hydrogel-printed RCA microarrays thus offer potential for rapid, parallel, and inexpensive sensing of short DNA/RNA biomarkers and ligands, a critical current challenge in diagnostic and affinity screening assays.
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Affiliation(s)
- Milana Pikula
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - M Monsur Ali
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Carlos Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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4
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Al Hajri Q, Dash S, Feng WC, Garner HR, Anandakrishnan R. Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU. Sci Rep 2020; 10:2022. [PMID: 32029803 PMCID: PMC7005272 DOI: 10.1038/s41598-020-58785-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/20/2020] [Indexed: 01/16/2023] Open
Abstract
Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Therefore, treatments that may be effective in some cases are not effective in others. We previously developed an algorithm for identifying combinations of carcinogenic genes with mutations (multi-hit combinations), which could suggest a likely cause for individual instances of cancer. Most cancers are estimated to require three or more hits. However, the computational complexity of the algorithm scales exponentially with the number of hits, making it impractical for identifying combinations of more than two hits. To identify combinations of greater than two hits, we used a compressed binary matrix representation, and optimized the algorithm for parallel execution on an NVIDIA V100 graphics processing unit (GPU). With these enhancements, the optimized GPU implementation was on average an estimated 12,144 times faster than the original integer matrix based CPU implementation, for the 3-hit algorithm, allowing us to identify 3-hit combinations. The 3-hit combinations identified using a training set were able to differentiate between tumor and normal samples in a separate test set with 90% overall sensitivity and 93% overall specificity. We illustrate how the distribution of mutations in tumor and normal samples in the multi-hit gene combinations can suggest potential driver mutations for further investigation. With experimental validation, these combinations may provide insight into the etiology of cancer and a rational basis for targeted combination therapy.
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Affiliation(s)
- Qais Al Hajri
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Sajal Dash
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Wu-Chun Feng
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, 24060, USA
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Harold R Garner
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, 29303, USA
| | - Ramu Anandakrishnan
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA.
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, 29303, USA.
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Warren S, Danaher P, Mashadi-Hossein A, Skewis L, Wallden B, Ferree S, Cesano A. Development of Gene Expression-Based Biomarkers on the nCounter ® Platform for Immuno-Oncology Applications. Methods Mol Biol 2020; 2055:273-300. [PMID: 31502157 DOI: 10.1007/978-1-4939-9773-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biomarkers based on transcriptional profiling can be useful in the measurement of complex and/or dynamic physiological states where other profiling strategies such as genomic or proteomic characterization are not able to adequately measure the biology. One particular advantage of transcriptional biomarkers is the ease with which they can be measured in the clinical setting using robust platforms such as the NanoString nCounter system. The nCounter platform enables digital quantitation of multiplexed RNA from small amounts of blood, formalin-fixed, paraffin-embedded tumors, or other such biological samples that are readily available from patients, and the chapter uses it as the primary example for diagnostic assay development. However, development of diagnostic assays based on RNA biomarkers on any platform requires careful consideration of all aspects of the final clinical assay a priori, as well as design and execution of the development program in a way that will maximize likelihood of future success. This chapter introduces transcriptional biomarkers and provides an overview of the design and development process that will lead to a locked diagnostic assay that is ready for validation of clinical utility.
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Affiliation(s)
- Sarah Warren
- NanoString Technologies, Inc., Seattle, WA, USA.
| | | | | | | | | | - Sean Ferree
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Alessandra Cesano
- NanoString Technologies, Inc., Seattle, WA, USA
- ESSA Pharma, South San Francisco, CA, USA
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Dhingra R, Kwee LC, Diaz-Sanchez D, Devlin RB, Cascio W, Hauser ER, Gregory S, Shah S, Kraus WE, Olden K, Ward-Caviness CK. Evaluating DNA methylation age on the Illumina MethylationEPIC Bead Chip. PLoS One 2019; 14:e0207834. [PMID: 31002714 PMCID: PMC6474589 DOI: 10.1371/journal.pone.0207834] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/29/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation age (DNAm age) has become a widely utilized epigenetic biomarker for the aging process. The Horvath method for determining DNAm age is perhaps the most widely utilized and validated DNA methylation age assessment measure. Horvath DNAm age is calculated based on methylation measurements at 353 loci, present on Illumina's 450k and 27k DNA methylation microarrays. With increasing use of the more recently developed Illumina MethylationEPIC (850k) microarray, it is worth revisiting this aging measure to evaluate estimation differences due to array design. Of the requisite 353 loci, 17 are missing from the 850k microarray. Similarly, an alternate, 71 loci DNA methylation age assessment measure created by Hannum et al. is missing 6 requisite loci. Using 17 datasets with 27k, 450k, and/or 850k methylation data, we compared each sample's epigenetic age estimated from all 353 loci required by the Horvath DNAm age calculator, and using only the 336 loci available on the 850k array. In 450k/27k data, removing loci not on the 850k array resulted in underestimation of Horvath's DNAm age. Underestimation of Horvath DNAm age increased from ages 0 to ~20, remaining stable thereafter (mean deviation = -3.46 y, SD = 1.13 for individuals ≥20 years). Underestimation of Horvath's DNAm age by the reduced 450k/27k data was similar to the underestimation observed in the 850k data indicating it is driven by missing probes. In analogous examination of Hannum's DNAm age, the magnitude and direction of epigenetic age misestimation varied with chronological age. In conclusion, inter-array deviations in DNAm age estimations may be largely driven by missing probes between arrays, despite default probe imputation procedures. Though correlations and associations based on Horvath's DNAm age may be unaffected, researchers should exercise caution when interpreting results based on absolute differences in DNAm age or when mixing samples assayed on different arrays.
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Affiliation(s)
- Radhika Dhingra
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, United States of America
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC United States of America
- * E-mail:
| | - Lydia Coulter Kwee
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - David Diaz-Sanchez
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Robert B. Devlin
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Wayne Cascio
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States of America
- Cooperative Studies Program Epidemiology Center, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | - Simon Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Svati Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States of America
| | - William E. Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States of America
| | - Kenneth Olden
- National Center for Environmental Assessment, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Cavin K. Ward-Caviness
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
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7
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Wu D, Wu W. Battery Powered Portable Thermal Cycler for Continuous-Flow Polymerase Chain Reaction Diagnosis by Single Thermostatic Thermoelectric Cooler and Open-Loop Controller. Sensors (Basel) 2019; 19:s19071609. [PMID: 30987195 PMCID: PMC6479314 DOI: 10.3390/s19071609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/28/2022]
Abstract
Temperature control is the most important and fundamental part of a polymerase chain reaction (PCR). To date, there have been several methods to realize the periodic heating and cooling of the thermal-cycler system for continuous-flow PCR reactions, and three of them were widely used: the thermo-cycled thermoelectric cooler (TEC), the heating block, and the thermostatic heater. In the present study, a new approach called open-loop controlled single thermostatic TEC was introduced to control the thermal cycle during the amplification process. Differing from the former three methods, the size of this microdevice is much smaller, especially when compared to the microdevice used in the heating block method. Furthermore, the rising and cooling speed of this method is much rapider than that in a traditional TEC cycler, and is nearly 20-30% faster than a single thermostatic heater. Thus, a portable PCR system was made without any external heat source, and only a Teflon tube-wrapped TEC chip was used to achieve the continuous-flow PCR reactions. This provides an efficient way to reduce the size of the system and simplify it. In addition, through further experiments, the microdevice is not only found to be capable of amplification of a PCR product from Human papillomavirus type 49 (Genbank ref: X74480.1) and Rubella virus (RUBV), but also enables clinical diagnostics, such as a test for hepatitis B virus.
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Affiliation(s)
- Di Wu
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130000, China.
| | - Wenming Wu
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130000, China.
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Li H, Huang Y, Wei Z, Wang W, Yang Z, Liang Z, Li Z. An oligonucleotide synthesizer based on a microreactor chip and an inkjet printer. Sci Rep 2019; 9:5058. [PMID: 30911034 PMCID: PMC6434144 DOI: 10.1038/s41598-019-41519-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/06/2019] [Indexed: 11/21/2022] Open
Abstract
Synthetic oligonucleotides (oligos) are important tools in the fields of molecular biology and genetic engineering. For applications requiring a large number of oligos with high concentration, it is critical to perform high throughput oligo synthesis and achieve high yield of each oligo. This study reports a microreactor chip for oligo synthesis. By incorporating silica beads in the microreactors, the surface area of the solid substrate for oligo synthesis increases significantly in each microreactor. These beads are fixed in the microreactors to withstand the flushing step in oligo synthesis. Compared to conventional synthesis methods, this design is able to avoid protocols to hold the beads and integrate more microreactors on a chip. An inkjet printer is utilized to deliver chemical reagents in the microreactors. To evaluate the feasibility of oligo synthesis using this proof-of-concept synthesizer, an oligo with six nucleotide units is successfully synthesized.
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Affiliation(s)
- Hui Li
- Institute of Microelectronics, Peking University, Beijing, China
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, United States
| | - Ye Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Department of New Drug Research and Development, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Zewen Wei
- National Center for Nanoscience and Technology, Beijing, China
| | - Wei Wang
- Institute of Microelectronics, Peking University, Beijing, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Zicai Liang
- Institute of Molecular Medicine, Peking University, Beijing, China.
| | - Zhihong Li
- Institute of Microelectronics, Peking University, Beijing, China.
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Damin F, Galbiati S, Soriani N, Burgio V, Ronzoni M, Ferrari M, Chiari M. Analysis of KRAS, NRAS and BRAF mutational profile by combination of in-tube hybridization and universal tag-microarray in tumor tissue and plasma of colorectal cancer patients. PLoS One 2018; 13:e0207876. [PMID: 30562355 PMCID: PMC6298683 DOI: 10.1371/journal.pone.0207876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/06/2018] [Indexed: 01/05/2023] Open
Abstract
Microarray technology fails in detecting point mutations present in a small fraction of cells from heterogeneous tissue samples or in plasma in a background of wild-type cell-free circulating tumor DNA (ctDNA). The aim of this study is to overcome the lack of sensitivity and specificity of current microarray approaches introducing a rapid and sensitive microarray-based assay for the multiplex detection of minority mutations of oncogenes (KRAS, NRAS and BRAF) with relevant diagnostics implications in tissue biopsies and plasma samples in metastatic colorectal cancer patients. In our approach, either wild-type or mutated PCR fragments are hybridized in solution, in a temperature gradient, with a set of reporters with a 5' domain, complementary to the target sequences and a 3' domain complementary to a surface immobilized probe. Upon specific hybridization in solution, which occurs specifically thanks to the temperature gradients, wild-type and mutated samples are captured at specific location on the surface by hybridization of the 3' reporter domain with its complementary immobilized probe sequence. The most common mutations in KRAS, NRAS and BRAF genes were detected in less than 90 minutes in tissue biopsies and plasma samples of metastatic colorectal cancer patients. Moreover, the method was able to reveal mutant alleles representing less than 0,3% of total DNA. We demonstrated detection limits superior to those provided by many current technologies in the detection of RAS and BRAF gene superfamily mutations, a level of sensitivity compatible with the analysis of cell free circulating tumor DNA in liquid biopsy.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail:
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
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Nikitin M, Deych K, Grevtseva I, Girsova N, Kuznetsova M, Pridannikov M, Dzhavakhiya V, Statsyuk N, Golikov A. Preserved Microarrays for Simultaneous Detection and Identification of Six Fungal Potato Pathogens with the Use of Real-Time PCR in Matrix Format. Biosensors (Basel) 2018; 8:E129. [PMID: 30551630 PMCID: PMC6316111 DOI: 10.3390/bios8040129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 01/11/2023]
Abstract
Fungal diseases of plants are of great economic importance causing 70⁻80% of crop losses associated with microbial plant pathogens. Advanced on-site disease diagnostics is very important to maximize crop productivity. In this study, diagnostic systems have been developed for simultaneous detection and identification of six fungal pathogens using 48-well microarrays (micromatrices) for qPCR. All oligonucleotide sets were tested for their specificity using 59 strains of target and non-target species. Detection limit of the developed test systems varied from 0.6 to 43.5 pg of DNA depending on target species with reproducibility within 0.3-0.7% (standard deviation). Diagnostic efficiency of test systems with stabilized and freeze-dried PCR master-mixes did not significantly differ from that of freshly prepared microarrays, though detection limit increased. Validation of test systems on 30 field samples of potato plants showed perfect correspondence with the results of morphological identification of pathogens. Due to the simplicity of the analysis and the automated data interpretation, the developed microarrays have good potential for on-site use by technician-level personnel, as well as for high-throughput monitoring of fungal potato pathogens.
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Affiliation(s)
- Maksim Nikitin
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | - Ksenia Deych
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | | | - Natalya Girsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Maria Kuznetsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Mikhail Pridannikov
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
- Centre of Parasitology, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia.
| | - Vitaly Dzhavakhiya
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Natalia Statsyuk
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
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Abstract
While high-density DNA microarrays have been available for over three decades, the synthesis of equivalent RNA microarrays has proven intractable until now. Herein we describe the first in situ synthesis of mixed-based, high-density RNA microarrays using photolithography and light-sensitive RNA phosphoramidites. With coupling efficiencies comparable to those of DNA monomers, RNA oligonucleotides at least 30 nucleotides long can now efficiently be prepared using modified phosphoramidite chemistry. A two-step deprotection route unmasks the phosphodiester, the exocyclic amines and the 2' hydroxyl. Hybridization and enzymatic assays validate the quality and the identity of the surface-bound RNA. We show that high-density is feasible by synthesizing a complex RNA permutation library with 262144 unique sequences. We also introduce DNA/RNA chimeric microarrays and explore their applications by mapping the sequence specificity of RNase HII.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Dominik Ameur
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Rue Sherbrooke OMontréalQC H3A 0B8Canada
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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McEwen LM, Jones MJ, Lin DTS, Edgar RD, Husquin LT, MacIsaac JL, Ramadori KE, Morin AM, Rider CF, Carlsten C, Quintana-Murci L, Horvath S, Kobor MS. Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array. Clin Epigenetics 2018; 10:123. [PMID: 30326963 PMCID: PMC6192219 DOI: 10.1186/s13148-018-0556-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/01/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The capacity of technologies measuring DNA methylation (DNAm) is rapidly evolving, as are the options for applicable bioinformatics methods. The most commonly used DNAm microarray, the Illumina Infinium HumanMethylation450 (450K array), has recently been replaced by the Illumina Infinium HumanMethylationEPIC (EPIC array), nearly doubling the number of targeted CpG sites. Given that a subset of 450K CpG sites is absent on the EPIC array and that several tools for both data normalization and analyses were developed on the 450K array, it is important to assess their utility when applied to EPIC array data. One of the most commonly used 450K tools is the pan-tissue epigenetic clock, a multivariate predictor of biological age based on DNAm at 353 CpG sites. Of these CpGs, 19 are missing from the EPIC array, thus raising the question of whether EPIC data can be used to accurately estimate DNAm age. We also investigated a 71-CpG epigenetic age predictor, referred to as the Hannum method, which lacks 6 probes on the EPIC array. To evaluate these epigenetic clocks in EPIC data properly, a prior assessment of the effects of data preprocessing methods on DNAm age is also required. METHODS DNAm was quantified, on both the 450K and EPIC platforms, from human primary monocytes derived from 172 individuals. We calculated DNAm age from raw, and three different preprocessed data forms to assess the effects of different processing methods on the DNAm age estimate. Using an additional cohort, we also investigated DNAm age of peripheral blood mononuclear cells, bronchoalveolar lavage, and bronchial brushing samples using the EPIC array. RESULTS Using monocyte-derived data from subjects on both the 450K and EPIC, we found that DNAm age was highly correlated across both raw and preprocessing methods (r > 0.91). Thus, the correlation between chronological age and the DNAm age estimate is largely unaffected by platform differences and normalization methods. However, we found that the choice of normalization method and measurement platform can lead to a systematic offset in the age estimate which in turn leads to an increase in the median error. Comparing the 450K and EPIC DNAm age estimates, we observed that the median absolute difference was 1.44-3.10 years across preprocessing methods. CONCLUSIONS Here, we have provided evidence that the epigenetic clock is resistant to the lack of 19 CpG sites missing from the EPIC array as well as highlighted the importance of considering the technical variance of the epigenetic when interpreting group differences below the reported error. Furthermore, our study highlights the utility of epigenetic age acceleration measure, the residuals from a linear regression of DNAm age on chronological age, as the resulting values are robust with respect to normalization methods and measurement platforms.
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Affiliation(s)
- Lisa M McEwen
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Meaghan J Jones
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - David Tse Shen Lin
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Rachel D Edgar
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Lucas T Husquin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Julia L MacIsaac
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Katia E Ramadori
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Alexander M Morin
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Christopher F Rider
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Chris Carlsten
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Lluís Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Michael S Kobor
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
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Hufnagel K, Lueong S, Willhauck-Fleckenstein M, Hotz-Wagenblatt A, Miao B, Bauer A, Michel A, Butt J, Pawlita M, Hoheisel JD, Waterboer T. Immunoprofiling of Chlamydia trachomatis using whole-proteome microarrays generated by on-chip in situ expression. Sci Rep 2018; 8:7503. [PMID: 29760479 PMCID: PMC5951824 DOI: 10.1038/s41598-018-25918-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 04/25/2018] [Indexed: 11/09/2022] Open
Abstract
Using Chlamydia trachomatis (Ct) as a complex model organism, we describe a method to generate bacterial whole-proteome microarrays using cell-free, on-chip protein expression. Expression constructs were generated by two successive PCRs directly from bacterial genomic DNA. Bacterial proteins expressed on microarrays display antigenic epitopes, thereby providing an efficient method for immunoprofiling of patients and allowing de novo identification of disease-related serum antibodies. Through comparison of antibody reactivity patterns, we newly identified antigens recognized by known Ct-seropositive samples, and antigens reacting only with samples from cervical cancer (CxCa) patients. Large-scale validation experiments using high-throughput suspension bead array serology confirmed their significance as markers for either general Ct infection or CxCa, supporting an association of Ct infection with CxCa. In conclusion, we introduce a method for generation of fast and efficient proteome immunoassays which can be easily adapted for other microorganisms in all areas of infection research.
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Affiliation(s)
- Katrin Hufnagel
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Smiths Lueong
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Willhauck-Fleckenstein
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beiping Miao
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Bauer
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Michel
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Butt
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Moser N, Rodriguez-Manzano J, Lande TS, Georgiou P. A Scalable ISFET Sensing and Memory Array With Sensor Auto-Calibration for On-Chip Real-Time DNA Detection. IEEE Trans Biomed Circuits Syst 2018; 12:390-401. [PMID: 29570065 DOI: 10.1109/tbcas.2017.2789161] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper presents a novel CMOS-based system-on-chip with a 78 56 ion-sensitive field-effect transistor array using in-pixel quantization and compensation of sensor nonidealities. The pixel integrates sensing circuitry and memory cells to encode the ion concentration in time and store a calibration value per pixel. Temperature sensing pixels spread throughout the array allow temperature monitoring during the reaction. We describe the integration of the array as part of a lab-on-chip cartridge that plugs into a motherboard for power management, biasing, data acquisition, and temperature regulation. This forms a robust ion detection platform, which is demonstrated as a pH sensing system. We show that our calibration is able to perform readout with a linear spread of 0.3% and that the system exhibits a high pH sensitivity of 3.2 /pH. The complete system is shown to perform on-chip real-time DNA amplification and detection of lambda phage DNA by loop-mediated isothermal amplification.
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15
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Li R, Zhou M, Yue C, Zhang W, Ma Y, Peng H, Hu Z, Wei Z. Multiple single cell screening and DNA MDA amplification chip for oncogenic mutation profiling. Lab Chip 2018; 18:723-734. [PMID: 29360118 DOI: 10.1039/c7lc00924k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The oncogenic mutation heterogeneity of the cancer cell population has been proven to be essential for predicting both drug-response and drug-resistance of targeted therapies, such as tyrosine kinase inhibitors. It is necessary to accurately evaluate the mutation heterogeneity, oncogenic mutation and resistant mutation profiling at a single cell level. However, there are two major hurdles in the process. First, majority of the cells in tumor tissue are non-cancer cells, which cause background noise. Second, the work load and cost of next generation sequencing on dozens of single cells are prohibitive. To address both these issues, we developed a microfluidic chip for profiling of dozens of selected cells. With the help of a novel tri-states valve structure, which performs precise controlling of the cell/reagent movement, as well as active mixing of different reagents, trapping/identification/lysis and in situ MDA amplification was achieved at a single cell level on the same chip. Using a proof-of-concept assay mimicking EGFR targeting drug Gefitinib treatment of lung cancer cells, the new method was validated as capable of not only detecting the existence of multiple mutations, but also providing complete information of the mutation scenario at the single cell level by using cost-effective Sanger's sequencing.
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Affiliation(s)
- Ren Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
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Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNAs that have been emerging as novel regulators in esophageal adenocarcinoma. Their role has been established in various aspects of esophageal adenocarcinoma including carcinogenesis, progression, treatment, and prognosis. Therefore, miRNA detection, profiling, and quantification have become extremely important for scientists and clinicians. As miRNAs are small, their detection can be challenging. There have been various methods developed to detect and/or quantify miRNAs. This chapter aims to introduce the fundamentals and methods of the most commonly used approaches including miRNA microarrays and quantitative real-time polymerase chain reaction (RT-qPCR) to detect and quantify miRNAs in esophageal adenocarcinoma.
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Affiliation(s)
- Moein Amin
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Farhadul Islam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia.
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Yasui T, Yanagida T, Ito S, Konakade Y, Takeshita D, Naganawa T, Nagashima K, Shimada T, Kaji N, Nakamura Y, Thiodorus IA, He Y, Rahong S, Kanai M, Yukawa H, Ochiya T, Kawai T, Baba Y. Unveiling massive numbers of cancer-related urinary-microRNA candidates via nanowires. Sci Adv 2017; 3:e1701133. [PMID: 29291244 PMCID: PMC5744465 DOI: 10.1126/sciadv.1701133] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/16/2017] [Indexed: 05/06/2023]
Abstract
Analyzing microRNAs (miRNAs) within urine extracellular vesicles (EVs) is important for realizing miRNA-based, simple, and noninvasive early disease diagnoses and timely medical checkups. However, the inherent difficulty in collecting dilute concentrations of EVs (<0.01 volume %) from urine has hindered the development of these diagnoses and medical checkups. We propose a device composed of nanowires anchored into a microfluidic substrate. This device enables EV collections at high efficiency and in situ extractions of various miRNAs of different sequences (around 1000 types) that significantly exceed the number of species being extracted by the conventional ultracentrifugation method. The mechanical stability of nanowires anchored into substrates during buffer flow and the electrostatic collection of EVs onto the nanowires are the two key mechanisms that ensure the success of the proposed device. In addition, we use our methodology to identify urinary miRNAs that could potentially serve as biomarkers for cancer not only for urologic malignancies (bladder and prostate) but also for nonurologic ones (lung, pancreas, and liver). The present device concept will provide a foundation for work toward the long-term goal of urine-based early diagnoses and medical checkups for cancer.
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Affiliation(s)
- Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Corresponding author. (T. Yasui); (T. Yanagida); (T.K.); (Y.B.)
| | - Takeshi Yanagida
- Institute of Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka-cho, Ibaraki, Osaka 567-0047, Japan
- Corresponding author. (T. Yasui); (T. Yanagida); (T.K.); (Y.B.)
| | - Satoru Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuki Konakade
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Daiki Takeshita
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tsuyoshi Naganawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kazuki Nagashima
- Institute of Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Taisuke Shimada
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Noritada Kaji
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuta Nakamura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Ivan Adiyasa Thiodorus
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yong He
- Institute of Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Sakon Rahong
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- College of Nanotechnology, King Mongkut’s Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Masaki Kanai
- Institute of Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Hiroshi Yukawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Tomoji Kawai
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka-cho, Ibaraki, Osaka 567-0047, Japan
- Corresponding author. (T. Yasui); (T. Yanagida); (T.K.); (Y.B.)
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, Takamatsu 761-0395, Japan
- College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan, Republic of China
- Corresponding author. (T. Yasui); (T. Yanagida); (T.K.); (Y.B.)
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Dou M, Sanjay ST, Dominguez DC, Zhan S, Li X. A paper/polymer hybrid CD-like microfluidic SpinChip integrated with DNA-functionalized graphene oxide nanosensors for multiplex qLAMP detection. Chem Commun (Camb) 2017; 53:10886-10889. [PMID: 28703226 PMCID: PMC5626606 DOI: 10.1039/c7cc03246c] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A paper/poly(methyl methacrylate) (PMMA) hybrid CD-like microfluidic SpinChip integrated with DNA probe-functionalized graphene oxide (GO) nanosensors was developed for multiplex quantitative LAMP detection (mqLAMP). This approach can simply and effectively address a major challenging problem of multiplexing in current LAMP methods.
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Affiliation(s)
- Maowei Dou
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, Texas 79968, USA
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Zanardo ÉA, Dutra RL, Piazzon FB, Dias AT, Novo-Filho GM, Nascimento AM, Montenegro MM, Damasceno JG, Madia FAR, da Costa TVMM, Melaragno MI, Kim CA, Kulikowski LD. Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience. Clinics (Sao Paulo) 2017; 72:526-537. [PMID: 29069255 PMCID: PMC5629705 DOI: 10.6061/clinics/2017(09)02] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/04/2017] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients. METHODS We analyzed 93 patients with developmental delay and multiple congenital abnormalities using multiplex ligation-dependent probe amplifications and arrays. RESULTS Multiplex ligation-dependent probe amplification using different kits revealed several changes in approximately 33.3% of patients. The use of arrays with different platforms showed an approximately 53.75% detection rate for at least one pathogenic change and a 46.25% detection rate for patients with benign changes. A concomitant assessment of the two techniques showed an approximately 97.8% rate of concordance, although the results were not the same in all cases. In contrast with the array results, the MLPA technique detected ∼70.6% of pathogenic changes. CONCLUSION The obtained results corroborated data reported in the literature, but the overall detection rate was higher than the rates previously reported, due in part to the criteria used to select patients. Although arrays are the most efficient tool for diagnosis, they are not always suitable as a first-line diagnostic approach because of their high cost for large-scale use in developing countries. Thus, clinical and laboratory interactions with skilled technicians are required to target patients for the most effective and beneficial molecular diagnosis.
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Affiliation(s)
- Évelin Aline Zanardo
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | - Roberta Lelis Dutra
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Flavia Balbo Piazzon
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Alexandre Torchio Dias
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Gil Monteiro Novo-Filho
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Amom Mendes Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Marília Moreira Montenegro
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Jullian Gabriel Damasceno
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Fabrícia Andreia Rosa Madia
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Maria Isabel Melaragno
- Departamento de Morfologia e Genetica, Universidade Federal de Sao Paulo, Sao Paulo, SP, BR
| | - Chong Ae Kim
- Unidade de Genetica, Departamento de Pediatria, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Leslie Domenici Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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Rizzi G, Lee JR, Dahl C, Guldberg P, Dufva M, Wang SX, Hansen MF. Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array. ACS Nano 2017; 11:8864-8870. [PMID: 28832112 PMCID: PMC5810360 DOI: 10.1021/acsnano.7b03053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.
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Affiliation(s)
- Giovanni Rizzi
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, South Korea
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
| | - Christina Dahl
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 93405, United States
- Corresponding Authors:.
| | - Mikkel F. Hansen
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
- Corresponding Authors:.
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Abstract
Controlled alignment of long DNA nanofibers is challenging. This communication reports a method to align human genomic DNA with nearly unlimited length using lithographically produced micro-patterns of self-assembled monolayers (SAMs) with positively charged terminal groups. The micro-patterns act as local DNA reservoirs to supply DNAs for nanofiber formation, and can also stretch and align DNA nanofibers to form an ordered array by controlling the dewetting profile. By reducing the size and inter-patch distance of a micro-patch, a nearly uniform array of long DNA nanofibers can be patterned over a large area. A controlled motion of a DNA containing droplet allows for free patterning of DNA nanofibers and production of complex structures without a transfer process. Bending of DNA nanofibers due to local distortion of the contact line bridges more adjacent micro-patches and increases the chance of producing continuous nanofibers. The interplay between surface tension and electrostatic attraction of positively charged micro-patterns allows the production of long DNA nanofibers in a simple yet powerful way.
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Affiliation(s)
- J Xia
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, USA.
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Michael Dunne W, Pouseele H, Monecke S, Ehricht R, van Belkum A. Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools. Infect Genet Evol 2017; 63:332-345. [PMID: 28943408 DOI: 10.1016/j.meegid.2017.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 02/05/2023]
Abstract
The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.
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Affiliation(s)
- W Michael Dunne
- Data Analytics Unit, bioMerieux, 100 Rodolphe Street, Durham, NC 27712, USA.
| | - Hannes Pouseele
- Data Analytics Unit, bioMerieux, 100 Rodolphe Street, Durham, NC 27712, USA; Applied Maths NV, Keistraat 120, 9830 Sint-Martens-Latem, Belgium.
| | - Stefan Monecke
- Alere Technologies GmbH, Jena, Germany; InfectoGnostics Research Campus, Jena, Germany; Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Jena, Germany; InfectoGnostics Research Campus, Jena, Germany.
| | - Alex van Belkum
- Data Analytics Unit, bioMérieux, 3, Route de Port Michaud, 38390 La Balme Les Grottes, France.
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Kober C, Niessner R, Seidel M. Quantification of viable and non-viable Legionella spp. by heterogeneous asymmetric recombinase polymerase amplification (haRPA) on a flow-based chemiluminescence microarray. Biosens Bioelectron 2017; 100:49-55. [PMID: 28863324 DOI: 10.1016/j.bios.2017.08.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/01/2017] [Accepted: 08/23/2017] [Indexed: 11/19/2022]
Abstract
Increasing numbers of legionellosis outbreaks within the last years have shown that Legionella are a growing challenge for public health. Molecular biological detection methods capable of rapidly identifying viable Legionella are important for the control of engineered water systems. The current gold standard based on culture methods takes up to 10 days to show positive results. For this reason, a flow-based chemiluminescence (CL) DNA microarray was developed that is able to quantify viable and non-viable Legionella spp. as well as Legionella pneumophila in one hour. An isothermal heterogeneous asymmetric recombinase polymerase amplification (haRPA) was carried out on flow-based CL DNA microarrays. Detection limits of 87 genomic units (GU) µL-1 and 26GUµL-1 for Legionella spp. and Legionella pneumophila, respectively, were achieved. In this work, it was shown for the first time that the combination of a propidium monoazide (PMA) treatment with haRPA, the so-called viability haRPA, is able to identify viable Legionella on DNA microarrays. Different proportions of viable and non-viable Legionella, shown with the example of L. pneumophila, ranging in a total concentration between 101 to 105GUµL-1 were analyzed on the microarray analysis platform MCR 3. Recovery values for viable Legionella spp. were found between 81% and 133%. With the combination of these two methods, there is a chance to replace culture-based methods in the future for the monitoring of engineered water systems like condensation recooling plants.
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Affiliation(s)
- Catharina Kober
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany
| | - Reinhard Niessner
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany.
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24
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Yan D, Xiang G, Chai X, Qing J, Shang H, Zou B, Mittal R, Shen J, Smith RJH, Fan YS, Blanton SH, Tekin M, Morton C, Xing W, Cheng J, Liu XZ. Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach. PLoS One 2017; 12:e0169219. [PMID: 28273078 PMCID: PMC5342170 DOI: 10.1371/journal.pone.0169219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/04/2016] [Indexed: 12/12/2022] Open
Abstract
The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Guangxin Xiang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xingping Chai
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jie Qing
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Haiqiong Shang
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Bing Zou
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts, United States of America
| | - Richard J. H. Smith
- Department of Otolaryngology - Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yao-Shan Fan
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Susan H. Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Cynthia Morton
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Center, University of Manchester, United Kingdom
| | - Wanli Xing
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Tsinghua University School of Medicine, Beijing, China
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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25
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Wang X, Ying S, Han R, Yuan J. [Development of multiplex oligonucleotide ligation-PCR-universal DNA microarrays for detection of foodborne pathogens]. Wei Sheng Yan Jiu 2017; 46:225-231. [PMID: 29903098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To develop a multiplex oligonucleotide ligation-polymerase chain reaction( MOL-PCR) based universal microarray assay for multiplexed detection of foodborne pathogens. METHODS Eight common foodborne pathogens causing bacterial food poisoning were selected as detection models. An upstream and downstream adjacent detection probes were designed within specific primer pair for each of eight pathogens. Target fragments of the eight pathogens were enriched by multiplex PCR and used as ligation templates. Abundant fluorescently labeled single-stranded amplicons containing anti-tag sequences were gained by multiplex ligase detection reaction and asymmetric PCR labeling with universal primers. The products could be detected by hybridization with corresponding tag sequences immobilized on DNA microarrays. RESULTS The results indicated that the assay could specifically identify all eight pathogens in single and multiple infections. The detection limits were( 1. 1- 8. 5) × 10~2 CFU /mL of pure bacterial cultures. The microarray results for 96 food poisoning and clinical diarrheal samples were consistent with that of traditional culture, biochemical identification and real-time PCR. CONCLUSION The assay provides a novel platform for rapid, accurate, sensitive and high-throughput detection of pathogenic bacteria of foodborne diseases.
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Affiliation(s)
- Xiaoqiang Wang
- Xi'an Center for Disease Control and Prevention, Xi'an 710054, China
| | - Sisi Ying
- Xi'an Center for Disease Control and Prevention, Xi'an 710054, China
| | - Ruijun Han
- Xi'an Center for Disease Control and Prevention, Xi'an 710054, China
| | - Jun Yuan
- Xi'an Center for Disease Control and Prevention, Xi'an 710054, China
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26
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Shim TS, Estephan ZG, Qian Z, Prosser JH, Lee SY, Chenoweth DM, Lee D, Park SJ, Crocker JC. Shape changing thin films powered by DNA hybridization. Nat Nanotechnol 2017; 12:41-47. [PMID: 27775726 DOI: 10.1038/nnano.2016.192] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Active materials that respond to physical and chemical stimuli can be used to build dynamic micromachines that lie at the interface between biological systems and engineered devices. In principle, the specific hybridization of DNA can be used to form a library of independent, chemically driven actuators for use in such microrobotic applications and could lead to device capabilities that are not possible with polymer- or metal-layer-based approaches. Here, we report shape changing films that are powered by DNA strand exchange reactions with two different domains that can respond to distinct chemical signals. The films are formed from DNA-grafted gold nanoparticles using a layer-by-layer deposition process. Films consisting of an active and a passive layer show rapid, reversible curling in response to stimulus DNA strands added to solution. Films consisting of two independently addressable active layers display a complex suite of repeatable transformations, involving eight mechanochemical states and incorporating self-righting behaviour.
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Affiliation(s)
- Tae Soup Shim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemical Engineering, Ajou University, Suwon 16499, Korea
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Zaki G Estephan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Zhaoxia Qian
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jacob H Prosser
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Su Yeon Lee
- Division of Advanced Materials, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - So-Jung Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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27
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Abstract
Digital PCR (dPCR) is an innovative approach for detection and quantification of nucleic acid that offers an alternative method to conventional real-time quantitative PCR for absolute quantification. dPCR is a highly precise and sensitive technique that does not require a standard reference, making it a suitable method for the detection of microRNAs. The potential of these small noncoding RNA as biomarkers is on the rise, especially due to their presence in body fluids, making them easily accessible. Nevertheless, the problem of lack of consensus regarding an optimal method for miRNAs normalization compromises their use. Here, we describe an innovative method for the absolute quantification of miRNAs across different types of biological samples using a chip-based platform, the QuantStudio 3D digital PCR.
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Affiliation(s)
- Cristina Borzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Linda Calzolari
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Davide Conte
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Orazio Fortunato
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
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28
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Abstract
To study photorespiration and to characterize related components, gene expression analysis is a central approach. An overview of the experimental setup, protocols, and methods we use to investigate photorespiration-associated gene expression is presented. Within this chapter, we describe simple procedures to experimentally alter the photorespiratory flux and provide protocols for transcriptomic analysis with a focus on genes encoding photorespiratory proteins as well as those induced by photorespiratory hydrogen peroxide (H2O2). Examples of typical results are presented and their significance to understanding redox signaling is discussed.
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Affiliation(s)
- Amna Mhamdi
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Pavel I Kerchev
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Patrick Willems
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Medical Biotechnology Center, VIB, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000, Ghent, Belgium
| | - Graham Noctor
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405, Orsay cedex, France.
- Unité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France.
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
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29
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Hsieh HB, Fitch J, White D, Torres F, Roy J, Matusiak R, Krivacic B, Kowalski B, Bruce R, Elrod S. Ultra-High-Throughput Microarray Generation and Liquid Dispensing Using Multiple Disposable Piezoelectric Ejectors. ACTA ACUST UNITED AC 2016; 9:85-94. [PMID: 15006131 DOI: 10.1177/1087057103260943] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The authors have constructed an array of 12 piezoelectric ejectors for printing biological materials. A single-ejector footprint is 8 mm in diameter, standing 4 mm high with 2 reservoirs totaling 76 µL. These ejectors have been tested by dispensing various fluids in several environmental conditions. Reliable drop ejection can be expected in both humidity-controlled and ambient environments over extended periods of time and in hot and cold room temperatures. In a prototype system, 12 ejectors are arranged in a rack, together with an X - Y stage, to allow printing any pattern desired. Printed arrays of features are created with a biological solution containing bovine serum albumin conjugated oligonucleotides, dye, and salty buffer. This ejector system is designed for the ultra-high-throughput generation of arrays on a variety of surfaces. These single or racked ejectors could be used as long-term storage vessels for materials such as small molecules, nucleic acids, proteins, or cell libraries, which would allow for efficient preprogrammed selection of individual clones and greatly reduce the chance of cross-contamination and loss due to transfer. A new generation of design ideas includes plastic injection molded ejectors that are inexpensive and disposable and handheld personal pipettes for liquid transfer in the nanoliter regime. ( Journal of Biomolecular Screening 2004:85-94)
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30
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Abstract
DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics- or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results. Here, we employ a nano-disk model to quantitatively analyze the sequencing process by examining the variations of ionic current when a DNA strand translocates a nanopore. Our focus is placed on signal-boosting and noise-suppressing strategies in order to attain the single-nucleotide resolution. Apart from decreasing pore diameter and thickness, it is crucial to also reduce the translocation speed and facilitate a stepwise translocation. Our best-case scenario analysis points to severe challenges with employing plain nanopore technology, i.e., without recourse to any signal amplification strategy, in achieving sequencing with the desired single-nucleotide resolution. A conceptual approach based on strand synthesis in the nanopore of the translocating DNA from single-stranded to double-stranded is shown to yield a 10-fold signal amplification. Although it involves no advanced physics and is very simple in mathematics, this simple model captures the essence of nanopore sequencing and is useful in guiding the design and operation of nanopore sequencing.
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Affiliation(s)
- Chenyu Wen
- Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
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31
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Hernández-Cabronero M, Blanes I, Pinho AJ, Marcellin MW, Serra-Sagristà J. Analysis-Driven Lossy Compression of DNA Microarray Images. IEEE Trans Med Imaging 2016; 35:654-664. [PMID: 26462084 DOI: 10.1109/tmi.2015.2489262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA microarrays are one of the fastest-growing new technologies in the field of genetic research, and DNA microarray images continue to grow in number and size. Since analysis techniques are under active and ongoing development, storage, transmission and sharing of DNA microarray images need be addressed, with compression playing a significant role. However, existing lossless coding algorithms yield only limited compression performance (compression ratios below 2:1), whereas lossy coding methods may introduce unacceptable distortions in the analysis process. This work introduces a novel Relative Quantizer (RQ), which employs non-uniform quantization intervals designed for improved compression while bounding the impact on the DNA microarray analysis. This quantizer constrains the maximum relative error introduced into quantized imagery, devoting higher precision to pixels critical to the analysis process. For suitable parameter choices, the resulting variations in the DNA microarray analysis are less than half of those inherent to the experimental variability. Experimental results reveal that appropriate analysis can still be performed for average compression ratios exceeding 4.5:1.
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32
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Abstract
Here, we describe detection of single nucleotide polymorphism (SNP) in genomic DNA samples using a NanoBioArray (NBA) chip. Fast DNA hybridization is achieved in the chip when target DNAs are introduced to the surface-arrayed probes using centrifugal force. Gold nanoparticles (AuNPs) are used to assist SNP detection at room temperature. The parallel setting of sample introduction in the spiral channels of the NBA chip enables multiple analyses on many samples, resulting in a technique appropriate for high-throughput SNP detection. The experimental procedure, including chip fabrication, probe array printing, DNA amplification, hybridization, signal detection, and data analysis, is described in detail.
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Affiliation(s)
- Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6.
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33
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Abstract
Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. The abnormal expression of lncRNAs has been implicated in a range of many human diseases, including cancer. But only a small number of functional lncRNAs have been well characterized to date. lncRNA expression profiling may help to identify useful molecular biomarkers and targets for novel therapeutic approaches in the future. In this chapter, we describe a highly efficient lncRNA expression profiling method using a custom-designed microarray.
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Affiliation(s)
- Xinna Zhang
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gabriel Lopez-Berestein
- Center for RNA Interference andNon-coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - George A Calin
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of GynecologicOncology and ReproductiveMedicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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34
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Holden MT, Carter MCD, Wu CH, Wolfer J, Codner E, Sussman MR, Lynn DM, Smith LM. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates. Anal Chem 2015; 87:11420-8. [PMID: 26494264 PMCID: PMC4945104 DOI: 10.1021/acs.analchem.5b02893] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.
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Affiliation(s)
- Matthew T. Holden
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | | | - Cheng-Hsien Wu
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | - Jamison Wolfer
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - Eric Codner
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - David M. Lynn
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
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35
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Zhang J, Fu R, Xie L, Li Q, Zhou W, Wang R, Ye J, Wang D, Xue N, Lin X, Lu Y, Huang G. A smart device for label-free and real-time detection of gene point mutations based on the high dark phase contrast of vapor condensation. Lab Chip 2015; 15:3891-3896. [PMID: 26266399 DOI: 10.1039/c5lc00488h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A smart device for label-free and real-time detection of gene point mutation-related diseases was developed based on the high dark phase contrast of vapor condensation. The main components of the device included a Peltier cooler and a mini PC board for image processing. Heat from the hot side of the Peltier cooler causes the fluid in a copper chamber to evaporate, and the vapor condenses on the surface of a microarray chip placed on the cold side of the cooler. The high dark phase contrast of vapor condensation relative to the analytes on the microarray chip was explored. Combined with rolling circle amplification, the device visualizes less-to-more hydrophilic transitions caused by gene trapping and DNA amplification. A lung cancer gene point mutation was analysed, proving the high selectivity and multiplex analysis capability of this low-cost device.
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Affiliation(s)
- Junqi Zhang
- Department of Biomedical Engineering, Tsinghua University School of Medicine, Beijing 100084, China. tshgl@ tsinghua.edu.cn
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36
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Misra S, Pamnany K, Aluru S. Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel® Xeon Phi™ Coprocessor. IEEE/ACM Trans Comput Biol Bioinform 2015; 12:1008-1020. [PMID: 26451815 DOI: 10.1109/tcbb.2015.2415931] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Construction of whole-genome networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, most cannot handle network reconstruction at the whole-genome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel Xeon Phi coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We also present a solution on the Intel® Xeon® processor. Our solution is based on TINGe, a fast parallel network reconstruction technique that uses mutual information and permutation testing for assessing statistical significance. We demonstrate the first ever inference of a plant whole genome regulatory network on a single chip by constructing a 15,575 gene network of the plant Arabidopsis thaliana from 3,137 microarray experiments in only 22 minutes. In addition, our optimization for parallelizing mutual information computation on the Intel Xeon Phi coprocessor holds out lessons that are applicable to other domains.
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37
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Zhirnov IV, Ryabinin VA, Sinyakov AN, Ternovoy VA, Shikov AN. [A prototype of oligonucleotide microarray for detection of pathogens relating to arena- and Filoviridae families]. Bioorg Khim 2015; 41:54-66. [PMID: 26050472 DOI: 10.1134/s1068162014050136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A prototype of oligonucleotide microarray for detection of Lassa, Junin, Machupo, Guanarito viruses (Arenaviridae family), Ebola and Marburg viruses (Filoviridae family) was presented. An original approach founded on virus proteins (nucleocapsid protein for Junin, Guanarito, Machupo viruses and RNA-dependent RNA-polymerase for Lassa, Ebola and Marburg viruses) amino acid sequences analysis with subsequent transform of revealed unique peptides into due sets of oligonucleotides was used to design probes for hybridization and primers.
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38
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Fernández A, Gómez J, Alonso B, Iglesias S, Coto E. A Next-Generation Sequencing of the NOTCH3 and HTRA1 Genes in CADASIL Patients. J Mol Neurosci 2015; 56:613-6. [PMID: 25929831 DOI: 10.1007/s12031-015-0560-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/30/2015] [Indexed: 12/28/2022]
Abstract
Our purpose was to develop a next-generation sequencing procedure to search for NOTCH3 and HTRA1 mutations in patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) features. A total of 70 patients were sequenced with semiconductor chips in an Ion Torrent Personal Genome Machine. The putative mutations were confirmed through Sanger sequencing of the corresponding patient. Six patients had a typical cysteine-involving NOTCH3 mutation. A new non-reported NOTCH3 variant (p.Pro2178Ser) was found in two patients. One patient was heterozygous for a non-reported HTRA1 variant, likely non-pathogenic (p.Ser139Ala). We found a typical NOTCH3 mutation in 9 % of the patients. None of the patients had HTRA1 variants with likely pathogenic effect. The next-generation sequencing (NGS) procedure here described would facilitate the rapid and cost-effective screening of large cohorts of CADASIL patients.
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Affiliation(s)
- Angela Fernández
- Genética-Laboratorio de Medicina, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain
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39
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Hung TQ, Sun Y, Poulsen CE, Linh-Quyen T, Chin WH, Bang DD, Wolff A. Miniaturization of a micro-optics array for highly sensitive and parallel detection on an injection moulded lab-on-a-chip. Lab Chip 2015; 15:2445-2451. [PMID: 25912610 DOI: 10.1039/c5lc00176e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A miniaturised array of supercritical angle fluorescence (SAF) micro-optics embedded in a microfluidic chamber was fabricated by injection moulding. The fabricated chip could enhance the fluorescence signal around 46 times compared to a conventional microscope. Collection of the fluorescence signal from the SAF array is almost independent of the numerical aperture, and the limit of detection was improved 36-fold using a simple and inexpensive optical detection system.
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Affiliation(s)
- Tran Quang Hung
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark.
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40
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Chen Y, Abrams ES, Boles TC, Pedersen JN, Flyvbjerg H, Austin RH, Sturm JC. Concentrating genomic length DNA in a microfabricated array. Phys Rev Lett 2015; 114:198303. [PMID: 26024203 DOI: 10.1103/physrevlett.114.198303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Indexed: 05/19/2023]
Abstract
We demonstrate that a microfabricated bump array can concentrate genomic-length DNA molecules efficiently at continuous, high flow velocities, up to 40 μm/s, if the single-molecule DNA globule has a sufficiently large shear modulus. Increase in the shear modulus is accomplished by compacting the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions for next-generation DNA-sequencing libraries will be an important application of this development.
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Affiliation(s)
- Yu Chen
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ezra S Abrams
- Sage Science, Inc., Beverly, Massachusetts 01915, USA
| | | | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Robert H Austin
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - James C Sturm
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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Wang C, Huang N, Zhuang H, Jiang X. Enhanced performance of nanocrystalline ZnO DNA biosensor via introducing electrochemical covalent biolinkers. ACS Appl Mater Interfaces 2015; 7:7605-7612. [PMID: 25799179 DOI: 10.1021/acsami.5b00040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Zinc oxide (ZnO) is considered to be one of the most promising candidates for the third-generation DNA biosensor because of its good chemical stability, wonderful biocompatibility, easy surface modification, and numerous kinds of nanostructures. In this work, we report a new and simple method to modify ZnO surface for the immobilization of oligonucleotides by electrochemical covalent grafting of diazonium salts. The atomic force microscope, X-ray photoelectron spectroscopy, surface contact angle system, and electrochemical workstation were employed to characterize the functionalization process. Fluorescence results show that this kind of DNA biosensor from covalently linking strategy has an enhanced performance compared to that based on an electrostatic adsorption route. The functionalized ZnO biosensor has the capability to distinguish four-base mismatched, one-base mismatched, and complementary DNA sequences. Moreover, a linear relationship has been observed between the fluorescence intensity and the concentration of the complementary DNA in the solution within the range from 10(-6) to 10(-9) M, offering us a possibility in the qualitative determination of the level of target DNA.
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Affiliation(s)
- Chun Wang
- †Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Wenhua Road 72, 110016 Shenyang, China
| | - Nan Huang
- †Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Wenhua Road 72, 110016 Shenyang, China
| | - Hao Zhuang
- ‡Institute of Materials Engineering, University of Siegen, Paul-Bonatz-Str. 9-11, 57076 Siegen, Germany
| | - Xin Jiang
- †Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Wenhua Road 72, 110016 Shenyang, China
- ‡Institute of Materials Engineering, University of Siegen, Paul-Bonatz-Str. 9-11, 57076 Siegen, Germany
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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43
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Valavanis I, Sifakis EG, Georgiadis P, Kyrtopoulos S, Chatziioannou AA. A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip. IEEE J Biomed Health Inform 2015; 18:817-23. [PMID: 24808224 DOI: 10.1109/jbhi.2014.2298351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic, and analytical pipelines for an efficient systems level analysis and interpretation. In this study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the--established in transcriptomic microarrays--logarithmic ratio of the methylated versus the unmethylated signal intensities, quoted as M-value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures exploiting the coefficient variation of DNA methylation measurements between control and case samples alleviate the impact of technical variation. The results presented here are juxtaposed to those derived by applying classical preprocessing and statistical selection methodologies. Overall, in comparison to traditional approaches, the superior performance of the proposed framework in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies.
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44
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Roy E, Stewart G, Mounier M, Malic L, Peytavi R, Clime L, Madou M, Bossinot M, Bergeron MG, Veres T. From cellular lysis to microarray detection, an integrated thermoplastic elastomer (TPE) point of care Lab on a Disc. Lab Chip 2015; 15:406-416. [PMID: 25385141 DOI: 10.1039/c4lc00947a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an all-thermoplastic integrated sample-to-answer centrifugal microfluidic Lab-on-Disc system (LoD) for nucleic acid analysis. The proposed CD system and engineered platform were employed for analysis of Bacillus atrophaeus subsp. globigii spores. The complete assay comprised cellular lysis, polymerase chain reaction (PCR) amplification, amplicon digestion, and microarray hybridization on a plastic support. The fluidic robustness and operating efficiency of the assay were ensured through analytical optimization of microfluidic tools enabling beneficial implementation of capillary valves and accurate control of all flow timing procedures. The assay reliability was further improved through the development of two novel microfluidic strategies for reagents mixing and flow delay on the CD platform. In order to bridge the gap between the proof-of-concept LoD and production prototype demonstration, low-cost thermoplastic elastomer (TPE) was selected as the material for CD fabrication and assembly, allowing the use of both, high quality hot-embossing and injection molding processes. Additionally, the low-temperature and pressure-free assembly and bonding properties of TPE material offer a pertinent solution for simple and efficient loading and storage of reagents and other on-board components. This feature was demonstrated through integration and conditioning of microbeads, magnetic discs, dried DNA buffer reagents and spotted DNA array inserts. Furthermore, all microfluidic functions and plastic parts were designed according to the current injection mold-making knowledge for industrialization purposes. Therefore, the current work highlights a seamless strategy that promotes a feasible path for the transfer from prototype toward realistic industrialization. This work aims to establish the full potential for TPE-based centrifugal system as a mainstream microfluidic diagnostic platform for clinical diagnosis, water and food safety, and other molecular diagnostic applications.
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Affiliation(s)
- Emmanuel Roy
- Life Sciences Division, National Research Council of Canada, 75 Boul. de Mortagne, Boucherville, J4B 6Y4, Québec, Canada.
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45
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Stewart SK, Morris TJ, Guilhamon P, Bulstrode H, Bachman M, Balasubramanian S, Beck S. oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips. Methods 2015; 72:9-15. [PMID: 25175075 PMCID: PMC4304834 DOI: 10.1016/j.ymeth.2014.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/07/2014] [Accepted: 08/15/2014] [Indexed: 12/14/2022] Open
Abstract
DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However, BeadChip processing relies on traditional bisulfite (BS) based protocols which cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we report the adaptation of the recently developed oxidative bisulfite (oxBS) chemistry to specifically detect both 5mC and 5hmC in a single workflow using 450K BeadChips, termed oxBS-450K. Supported by validation using mass spectrometry and pyrosequencing, we demonstrate reproducible (R(2)>0.99) detection of 5hmC in human brain tissue using the optimised oxBS-450K protocol described here.
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Affiliation(s)
- Sabrina K Stewart
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Tiffany J Morris
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Paul Guilhamon
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Harry Bulstrode
- Scottish Centre for Regenerative Medicine, Edinburgh EH16 4UU, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Stephan Beck
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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46
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Abstract
Human platelet antigen (HPA) typing plays a critical role in the diagnosis of fetal/neonatal alloimmune thrombocytopenia, and the prevention of posttransfusion purpura and refractoriness to platelet transfusions. The recent development of high-throughput genotyping methods, allowing simultaneous genotyping of as many as 17 HPAs, is of utmost interest for saving time and money. Here, we describe a microarray technology named "BeadChip," designed for HPA-1 to -9, -11, and -15 genotyping of up to 96 individuals, in approximately 5 h. This technology was used to study allele frequencies in Brazilian blood donors, considering the heterogeneous ethnic composition.
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Affiliation(s)
- Gerald Bertrand
- Histocompatibilty and Immunogenetics Laboratory, EFS Bretagne, Rue Pierre Jean-Gineste, 35000, Rennes, France,
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47
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Wei J, Liu H, Liu F, Zhu M, Zhou X, Xing D. Miniaturized paper-based gene sensor for rapid and sensitive identification of contagious plant virus. ACS Appl Mater Interfaces 2014; 6:22577-84. [PMID: 25412341 DOI: 10.1021/am506695g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Plant viruses cause significant production and economic losses in the agricultural industry worldwide. Rapid and early identification of contagious plant viruses is an essential prerequisite for the effective control of further spreading of infection. In this work, we describe a miniaturized paper-based gene sensor for the rapid and sensitive identification of a contagious plant virus. Our approach makes use of hybridization-mediated target capture based on a miniaturized lateral flow platform and gold nanoparticle colorimetric probes. The captured colorimetric probes on the test line and control line of the gene sensor produce characteristic red bands, enabling visual detection of the amplified products within minutes without the need for sophisticated instruments or the multiple incubation and washing steps performed in most other assays. Quantitative analysis is realized by recording the optical intensity of the test line. The sensor was used successfully for the identification of banana bunchy top virus (BBTV). The detection limit was 0.13 aM of gene segment, which is 10 times higher than that of electrophoresis and provides confirmation of the amplified products. We believe that this simple, rapid, and sensitive bioactive platform has great promise for warning against plant diseases in agricultural production.
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Affiliation(s)
- Jitao Wei
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
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Gandhiraman RP, Nordlund D, Jayan V, Meyyappan M, Koehne JE. Scalable low-cost fabrication of disposable paper sensors for DNA detection. ACS Appl Mater Interfaces 2014; 6:22751-22760. [PMID: 25423585 PMCID: PMC4278686 DOI: 10.1021/am5069003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Controlled integration of features that enhance the analytical performance of a sensor chip is a challenging task in the development of paper sensors. A critical issue in the fabrication of low-cost biosensor chips is the activation of the device surface in a reliable and controllable manner compatible with large-scale production. Here, we report stable, well-adherent, and repeatable site-selective deposition of bioreactive amine functionalities and biorepellant polyethylene glycol-like (PEG) functionalities on paper sensors by aerosol-assisted, atmospheric-pressure, plasma-enhanced chemical vapor deposition. This approach requires only 20 s of deposition time, compared to previous reports on cellulose functionalization, which takes hours. A detailed analysis of the near-edge X-ray absorption fine structure (NEXAFS) and its sensitivity to the local electronic structure of the carbon and nitrogen functionalities. σ*, π*, and Rydberg transitions in C and N K-edges are presented. Application of the plasma-processed paper sensors in DNA detection is also demonstrated.
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Affiliation(s)
- Ram P. Gandhiraman
- NASA Ames Research Center, Moffett
Field, California 94035, United States
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Vivek Jayan
- NASA Ames Research Center, Moffett
Field, California 94035, United States
| | - M. Meyyappan
- NASA Ames Research Center, Moffett
Field, California 94035, United States
| | - Jessica E. Koehne
- NASA Ames Research Center, Moffett
Field, California 94035, United States
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49
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Nimse SB, Song K, Sonawane MD, Sayyed DR, Kim T. Immobilization techniques for microarray: challenges and applications. Sensors (Basel) 2014; 14:22208-29. [PMID: 25429408 PMCID: PMC4299010 DOI: 10.3390/s141222208] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 02/03/2023]
Abstract
The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keumsoo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea.
| | - Mukesh Digambar Sonawane
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Danishmalik Rafiq Sayyed
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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50
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Handy SM, Chizhikov V, Yakes BJ, Paul SZ, Deeds JR, Mossoba MM. Microarray chip development using infrared imaging for the identification of catfish species. Appl Spectrosc 2014; 68:1365-1373. [PMID: 25356840 DOI: 10.1366/14-07505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Several families of catfish species are extensively aquacultured around the world; however, only those from the family Ictaluridae can be labeled as catfish in the United States. Non-Ictalurid catfish species that are marketed as "catfish" in the USA are considered misbranded. Misbranding in general has led to an increased interest in developing deoxyribonucleic acid (DNA)-based methods such as DNA barcoding, polymerase chain reaction restriction fragment length polymorphism, and DNA microarrays with fluorescence detection for the identification of fish species. In this proof-of-concept study, DNA microarrays coupled with a newly developed mid-infrared imaging detection method were applied to the identification of seven species of catfish for the first time. Species-specific DNA probes targeting three regions per species of the cytochrome c oxidase 1 (barcoding) gene were developed and printed as microarrays on glass slides. Deoxyribonucleic acid targets labeled with biotin were hybridized to their complementary probes using a strategy that allowed the selective formation of a silver layer on hybridized spots needed for detection. Using this three-probe format, the seven species were all identified correctly, even when a limited number of false positive spots were observed. Raman spectroscopy was employed to further characterize the arrays.
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Affiliation(s)
- Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740 USA
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