1
|
Kumar S, Eaton SM, Bollani M, Sotillo B, Chiappini A, Ferrari M, Ramponi R, Di Trapani P, Jedrkiewicz O. Laser surface structuring of diamond with ultrashort Bessel beams. Sci Rep 2018; 8:14021. [PMID: 30232362 PMCID: PMC6145940 DOI: 10.1038/s41598-018-32415-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/07/2018] [Indexed: 11/17/2022] Open
Abstract
We investigate the effect of ultrafast laser surface machining on a monocrystalline synthetic diamond sample by means of pulsed Bessel beams. We discuss the differences of the trench-like microstructures generated in various experimental conditions, by varying the beam cone angle, the energy and pulse duration, and we present a brief comparison of the results with those obtained with the same technique on a sapphire sample. In diamond, we obtain V-shaped trenches whose surface width varies with the cone angle, and which are featured by micrometer sized channels having depths in the range of 10-20 μm. By laser writing crossed trenches we are also able to create and tailor on the diamond surface pillar-like or tip-like microstructures potentially interesting for large surface functionalization, cells capturing and biosensing.
Collapse
Affiliation(s)
- Sanjeev Kumar
- Department of Science and High technology, Università dell'Insubria, via Valleggio 11, 22100, Como, Italy
| | - Shane M Eaton
- Institute for Photonics and Nanotechnologies, CNR and Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Monica Bollani
- Institute for Photonics and Nanotechnologies, CNR, L-NESS, Via Anzani 42, 22100, Como, Italy
| | - Belén Sotillo
- Institute for Photonics and Nanotechnologies, CNR and Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Andrea Chiappini
- Institute for Photonics and Nanotechnologies, CNR, CSMFO Lab., Via alla Cascata 56/C, Povo, Trento, 38123, Italy
| | - Maurizio Ferrari
- Institute for Photonics and Nanotechnologies, CNR, CSMFO Lab., Via alla Cascata 56/C, Povo, Trento, 38123, Italy
| | - Roberta Ramponi
- Institute for Photonics and Nanotechnologies, CNR and Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Paolo Di Trapani
- Department of Science and High technology, Università dell'Insubria, via Valleggio 11, 22100, Como, Italy
| | - Ottavia Jedrkiewicz
- Institute for Photonics and Nanotechnologies, CNR, Udr Como, Via Valleggio 11, 22100, Como, Italy.
| |
Collapse
|
2
|
Human genomic DNA isolation from whole blood using a simple microfluidic system with silica- and polymer-based stationary phases. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 74:10-20. [DOI: 10.1016/j.msec.2016.12.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
|
3
|
Tan SJ, Phan H, Gerry BM, Kuhn A, Hong LZ, Min Ong Y, Poon PSY, Unger MA, Jones RC, Quake SR, Burkholder WF. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps. PLoS One 2013; 8:e64084. [PMID: 23894273 PMCID: PMC3722208 DOI: 10.1371/journal.pone.0064084] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/12/2013] [Indexed: 01/23/2023] Open
Abstract
Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.
Collapse
Affiliation(s)
- Swee Jin Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Huan Phan
- Fluidigm Corporation, South San Francisco, California, United States of America
| | | | - Alexandre Kuhn
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Lewis Zuocheng Hong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Yao Min Ong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Polly Suk Yean Poon
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | | | - Robert C. Jones
- Fluidigm Corporation, South San Francisco, California, United States of America
| | - Stephen R. Quake
- Departments of Bioengineering and Applied Physics, Stanford University and Howard Hughes Medical Institute, Stanford, California, United States of America
- Visiting Investigator, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore, Singapore
| | - William F. Burkholder
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
- * E-mail:
| |
Collapse
|
4
|
Zhang R, Gong HQ, Zeng X, Lou C, Sze C. A microfluidic liquid phase nucleic acid purification chip to selectively isolate DNA or RNA from low copy/single bacterial cells in minute sample volume followed by direct on-chip quantitative PCR assay. Anal Chem 2013; 85:1484-91. [PMID: 23272769 DOI: 10.1021/ac3026509] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Purification of nucleic acids from a low quantity of bacterial cells in minute volume is important in many clinical and biological applications. We developed a novel microfluidic liquid phase nucleic acid purification chip to selectively isolate DNA or RNA from bacterial cells in the range of 5000 down to a single cell in the sample volume of 1 μl or 125 nl, which can be directly put through on-chip quantitative PCR assay. The aqueous phase bacterial lysate was isolated in an array of microwells, after which an immiscible organic (phenol-chloroform) phase was introduced in a headspace channel connecting the microwell array. Continuous flow of the organic phase increases the interfacial contact with the aqueous phase to achieve purification of target nucleic acid through phase partitioning. Significantly enhanced nucleic acid recovery yield, up to 10 fold higher, was achieved using the chip-based liquid phase nucleic acid purification technique compared to that obtained by the conventional column-based solid phase nucleic acid extraction method. One step vacuum-driven microfluidics allowed an on-chip quantitative PCR assay to be carried out in the same microwells within which bacterial nucleic acids were isolated, avoiding sample loss during liquid transfer. Using this nucleic acid purification device set in a two-dimensional (2D) array format of 900 microwells, it was demonstrated for the first time that high-throughput extraction of RNA couple with direct on-chip PCR analysis from single bacterial cells could be achieved. Our microfluidic platform offered a simple and effective solution for nucleic acid preparation, which can be integrated for automated bacterial pathogen detection and high throughput transcriptional profiling.
Collapse
Affiliation(s)
- Rui Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | | | | | | | | |
Collapse
|
5
|
Kashkary L, Kemp C, Shaw KJ, Greenway GM, Haswell SJ. Improved DNA extraction efficiency from low level cell numbers using a silica monolith based micro fluidic device. Anal Chim Acta 2012; 750:127-31. [PMID: 23062434 DOI: 10.1016/j.aca.2012.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/10/2012] [Accepted: 05/12/2012] [Indexed: 12/01/2022]
Abstract
The evaluation of a micro fluidic system with an integrated silica monolith for performing DNA extraction from limited biological samples has been carried out. Low DNA target concentrations usually require the addition of carrier RNA to ensure desired extraction efficiencies. Here, we demonstrate a micro fluidic extraction system with increasingly efficient extraction performances for biological samples containing <15 ng of total DNA without the need of adding carrier nucleic acids. All extracted DNA showed successful amplification via the polymerase chain reaction demonstrating both the effectiveness of the proposed system at removing potential inhibitors and yielding good quality DNA. The work presented here beneficially identifies reduced sample volumes/concentrations as suitable for processing with respect to downstream analysis by enabling pre-concentration of the biological sample, particularly important when dealing with clinical or forensic specimens.
Collapse
Affiliation(s)
- Loay Kashkary
- Department of Chemistry, University of Hull, Cottingham Road, Hull HU6 7RX, UK.
| | | | | | | | | |
Collapse
|
6
|
Preston CM, Harris A, Ryan JP, Roman B, Marin R, Jensen S, Everlove C, Birch J, Dzenitis JM, Pargett D, Adachi M, Turk K, Zehr JP, Scholin CA. Underwater application of quantitative PCR on an ocean mooring. PLoS One 2011; 6:e22522. [PMID: 21829630 PMCID: PMC3148215 DOI: 10.1371/journal.pone.0022522] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/22/2011] [Indexed: 11/21/2022] Open
Abstract
The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
Collapse
Affiliation(s)
- Christina M Preston
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Bezuidenhout LW, Nazemifard N, Jemere AB, Harrison DJ, Brett MJ. Microchannels filled with diverse micro- and nanostructures fabricated by glancing angle deposition. LAB ON A CHIP 2011; 11:1671-1678. [PMID: 21445412 DOI: 10.1039/c0lc00721h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The integration of porous structures into microchannels is known to enable unique and useful separations both in electrophoresis and chromatography. Etched pillars and other nanostructures have received considerable interest in recent years as a platform for creating microchannels with pores tailored to specific applications. We present a versatile method for integration of three-dimensionally sculptured nano- and micro-structures into PDMS microchannels. Glancing angle deposition was used to fabricate nanostructures that were subsequently embedded in PDMS microchannels using a sacrificial resist process. With this technique, an assortment of structures made from a wide selection of materials can be integrated in PDMS microchannels; some examples of this versatility, including chiral and chevron nanostructures, are demonstrated. We also present a working device made using this process, separating 6/10/20 kbp and 10/48 kbp DNA mixtures in a DNA fractionator containing GLAD-deposited SiO(2) vertical posts as the separating medium. The separation mechanism was verified to resemble that found in prior fractionation devices, using total internal reflection fluorescence microscopy. GLAD fabrication enables insertion of three-dimensional structures into microchannels that cannot be fabricated with any existing techniques, and this versatility in structural design could facilitate new developments in on-chip separations.
Collapse
Affiliation(s)
- Louis W Bezuidenhout
- Department of Electrical and Computer Engineering, University of Alberta, T6G 2V4, Edmonton, Canada
| | | | | | | | | |
Collapse
|
8
|
Staton SJR, Chen KP, Taylor TJ, Pacheco JR, Hayes MA. Characterization of particle capture in a sawtooth patterned insulating electrokinetic microfluidic device. Electrophoresis 2010; 31:3634-41. [DOI: 10.1002/elps.201000438] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 09/01/2010] [Indexed: 11/07/2022]
|
9
|
Hiraoka M, Fiorini P, Zhang L, De Malsche W, Majeed B, Sabuncuoglu Tezcan D, Desmet G, Yamashita I, Van Hoof C, Op de Beeck M. Integrated fluidic system for bio-molecule separation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2010:6514-6517. [PMID: 21096495 DOI: 10.1109/iembs.2010.5627080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An integrated fluidic system has been fabricated, capable of separating a mixture of different bio-molecules into its components. It is composed of a filter and an actuator; the pressure generated by the actuator sustains the flow of the mixture through the filter. The actuator is made by stacking several layers of conductive polymer. Actuator strain in excess of 10% has been obtained, which corresponds to a fluid flow of 3 microL/min in the fabricated system. The filter consists of an ordered array of Si micro-pillars. A mixture composed of DNA fragments of different length (300 and 400 base-pair) has been effectively separated by using the fabricated filter and chromatographic techniques.
Collapse
Affiliation(s)
- M Hiraoka
- Imec, Kapeldreef 75, 3001 Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Liu L, Yu S, Yang S, Zhou P, Hu J, Zhang Y. Extraction of genomic DNA using a new amino silica monolithic column. J Sep Sci 2009; 32:2752-8. [DOI: 10.1002/jssc.200900208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Chen XW, Chen ML, Chen S, Wang JH. Flow-based analysis: a versatile, powerful platform for DNA assays. Trends Analyt Chem 2008. [DOI: 10.1016/j.trac.2008.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Regan JF, Makarewicz AJ, Hindson BJ, Metz TR, Gutierrez DM, Corzett TH, Hadley DR, Mahnke RC, Henderer BD, Breneman IV JW, Weisgraber TH, Dzenitis JM. Environmental Monitoring for Biological Threat Agents Using the Autonomous Pathogen Detection System with Multiplexed Polymerase Chain Reaction. Anal Chem 2008; 80:7422-9. [DOI: 10.1021/ac801125x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John F. Regan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Anthony J. Makarewicz
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Benjamin J. Hindson
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Thomas R. Metz
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Dora M. Gutierrez
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Todd H. Corzett
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Dean R. Hadley
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Ryan C. Mahnke
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Bruce D. Henderer
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - John W. Breneman IV
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Todd H. Weisgraber
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - John M. Dzenitis
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| |
Collapse
|
13
|
Wen J, Legendre LA, Bienvenue JM, Landers JP. Purification of Nucleic Acids in Microfluidic Devices. Anal Chem 2008; 80:6472-9. [DOI: 10.1021/ac8014998] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Wen
- University of Virginia and University of Virginia Health Sciences Center
| | | | - Joan M. Bienvenue
- University of Virginia and University of Virginia Health Sciences Center
| | - James P. Landers
- University of Virginia and University of Virginia Health Sciences Center
| |
Collapse
|
14
|
Dauriac V, Descroix S, Chen Y, Peltre G, Sénéchal H. Isoelectric focusing in an ordered micropillar array. Electrophoresis 2008; 29:2945-52. [DOI: 10.1002/elps.200800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|