| 1. |
- Akbari, Elham, et al.
(författare)
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SEPARATION OF CLUSTERS OF GROUP A STREPTOCOCCI USING DETERMINISTIC LATERAL DISPLACEMENT
- 2021
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Ingår i: MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419031 ; , s. 1201-1202
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Konferensbidrag (refereegranskat)abstract
- Differences in morphologies of bacteria and bacteria clusters are known to influence their pathogenicity. However, it is difficult to separate cells and cell clusters based on morphology using standard cell biological methods, making studies of the underlying mechanisms difficult. Here we report a simple label-free method for the continuous separation of clusters of group A streptococci, based on cluster size and morphology, using Deterministic Lateral Displacement (DLD). In general, this opens up for the generation of cell populations with heterogenicity in cluster size and physical properties.
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| 2. |
- Akbari, Elham, et al.
(författare)
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SEPARATION OF SINGLETS AND CLUSTERS OF GROUP A STREPTOCOCCI USING DETERMINISTIC LATERAL DISPLACEMENT AND FILTER SONICATION
- 2022
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Ingår i: MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419048 ; , s. 306-307
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Konferensbidrag (refereegranskat)abstract
- Differences in morphologies of bacteria and bacteria clusters are thought to contribute to their virulence and colonization. However, the conventional standard cell biological methods cannot separate bacteria and bacteria clusters based on their morphologies and sizes, making studies of the underlying mechanisms difficult. Here we report a simple label-free method for the continuous separation of singlets and clusters, of group A streptococci, based on their size and morphology, using Deterministic Lateral Displacement and filter-sonication. In general, this opens up for the generation of cell populations with heterogenicity in cluster size and physical properties.
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| 3. |
- Al-Fandi, M, et al.
(författare)
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Nano-engineered living bacterial motors for active microfluidic mixing.
- 2010
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Ingår i: IET Nanobiotechnology. - : Institution of Engineering and Technology (IET). - 1751-875X .- 1751-8741. ; 4:3, s. 61-71
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Tidskriftsartikel (refereegranskat)abstract
- Active micromixers with rotating elements are attractive microfluidic actuators in many applications because of their mixing ability at a short distance. However, miniaturising the impeller design poses technical challenges including the fabrication and driving means. As a possible solution inspired by macro magnetic bar-stirrers, this study proposes the use of tethered, rotating bacteria as mixing elements. A tethered cell is a genetically engineered, harmless Escherichia coli (E. coli) attached to a surface by a single, shortened flagellum. The tethered flagellum acts as a pivot around which the entire cell body smoothly rotates. Videomicroscopy, image analysis and computational fluid dynamics (CFD) are utilised to demonstrate a proof-of-concept for the micro mixing process. Flow visualisation experiments show that a approximately 3 [micro sign]m long tethered E. coli rotating at approximately 240 rpm can circulate a 1 [micro sign]m polystyrene bead in the adjacent area at an average speed of nearly 4 [micro sign]m/s. The Peclet (Pe(b)) number for the stirred bead is evaluated to approximately 4. CFD simulations show that the rotary motion of a tethered E. coli rotating at 240 rpm can generate fluid velocities, up to 37 [micro sign]m/s bordering the cell envelop. Based on these simulations, the Strouhal number (St) is calculated to about 2. This hybrid bio-inorganic micromxer could be used as a local, disposable mixer.
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| 4. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Habitat complexity affects microbial growth in fractal maze
- 2023
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Ingår i: Current biology : CB. - : Elsevier BV. - 1879-0445 .- 0960-9822. ; 33:8, s. 4-1458
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Tidskriftsartikel (refereegranskat)abstract
- The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
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| 5. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation
- 2021
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
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| 6. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models
- 2024
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Ingår i: STAR Protocols. - 2666-1667. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1
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| 7. |
- Barrett, Michael P., et al.
(författare)
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Microfluidics-based approaches to the isolation of African trypanosomes
- 2017
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Ingår i: Pathogens. - : MDPI AG. - 2076-0817. ; 6:4
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Forskningsöversikt (refereegranskat)abstract
- African trypanosomes are responsible for significant levels of disease in both humans and animals. The protozoan parasites are free-living flagellates, usually transmitted by arthropod vectors, including the tsetse fly. In the mammalian host they live in the bloodstream and, in the case of human-infectious species, later invade the central nervous system. Diagnosis of the disease requires the positive identification of parasites in the bloodstream. This can be particularly challenging where parasite numbers are low, as is often the case in peripheral blood. Enriching parasites from body fluids is an important part of the diagnostic pathway. As more is learned about the physicochemical properties of trypanosomes, this information can be exploited through use of different microfluidic-based approaches to isolate the parasites from blood or other fluids. Here, we discuss recent advances in the use of microfluidics to separate trypanosomes from blood and to isolate single trypanosomes for analyses including drug screening.
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| 8. |
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| 9. |
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| 10. |
- Beech, Jason
(författare)
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Microfluidics Separation and Analysis of Biological Particles
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the last decade, powerful communication and information technology in the form of the mobile phone has been put into the hands of more than 50% of the global population. In stark contrast, a lack of access to medical diagnostic technology with which to diagnose both communicable and non-communicable diseases will mean that many of these people will die of easily treatable conditions. Small, portable, effective and affordable devices able to give relevant information about the health of an individual, even in resource poor environments, could potentially help to change this. And the developing world is not the only resource poor environment; areas struck by natural disaster or by outbreaks of infectious disease or on the battlefield or even at the frontiers of exploration we find environments in which a mobile phone-sized laboratory would have a profound impact, not only on medical, but environmental diagnostics. There are also less dramatic examples. Compared to a well-equipped hospital most environments are resource poor, including the home. Blood sugar measuring devices for example put important information immediately into the hands of the diabetes sufferer in their own home, allowing them to make informed, life-saving decisions about food intake and medication without recourse to medical doctors. These diagnostic devices will be based on technologies that go under the collective names of micro-total-analysis systems, µTAS, or Lab-on-a-Chip. One of the uniting, integral features of all these technologies is the need to manipulate small volumes of fluids, often containing cells or other particles, from which the diagnostic information is to be wrung. The manipulation of such small volumes of fluids is known as microfluidics. This doctoral thesis is concerned with particle separation science. More specifically it is concerned with the development of tools for the separation of biologically relevant particles, an important step in almost any analysis, using techniques that have been made possible through the advent of microfluidics. A technique based on the flow of fluid through arrays of micrometre-sized obstacles, Deterministic Lateral Displacement (DLD), is promising because of its exceptional resolution, its suitability for biological separations, the wide range of sizes across which it works and not least because of the promise it holds as a candidate for integration within a lab-on-a-chip. The first devices utilizing the principle were limited to use in the separation of particles by size only. However, there are many physical properties other than size holding a wealth of information about particles, for example cancer and infection with malaria or HIV have been shown to change the deformability of cells and so measuring deformability could provide a means of diagnosing these conditions. The central tenet of this work is that DLD can be used to separate particles by highly relevant physical properties other than size, for example shape, deformability or electrical properties and that devices that can do this in a cheap and simple way will constitute powerful particle separation tools, useful for diagnostic applications and well suited for integration in a Lab-on-a-Chip. The aim of this thesis is to present four research papers, documenting the development of new methods that improve the existing DLD technique. Paper I describes how the elastomeric properties of polydimethylsiloxane can be utilized to achieve tuneable separation in DLD devices, making it easier to take advantage of the high resolution inherent in the method. Paper II presents the use of dielectrophoresis to achieve tuneability, improve dynamic range and open up for the separation of particles with regard to factors other than size. Paper III describes how control of particle orientation can be used to separate particles based on their shape and how this can be used to separate blood-borne parasites from blood. Finally Paper IV deals with the size, shape and deformability of cells and how DLD devices can be used, both to measure these properties, and to perform separations based on them. The hope is that these methods might ultimately play a small part in helping diagnostics technology to become as ubiquitous as information technology has become in the last ten years and that this will have a profound impact on global health.
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| 11. |
- Beech, Jason P., et al.
(författare)
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Active Posts in Deterministic Lateral Displacement Devices
- 2019
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Ingår i: Advanced Materials Technologies. - : Wiley. - 2365-709X. ; 4:9
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Tidskriftsartikel (refereegranskat)abstract
- Using electrically connected metal-coated posts in a deterministic lateral displacement (DLD) device and applying electric fields, electrokinetics is used to tune separations, significantly decrease the critical size for separation, and increase the dynamic range with switching times on the order of seconds. The strength of DLD stems from its binary behavior. To first approximation, particles move in one out of two trajectories based on their effective size. For particles that are close to the threshold size, a small external force is sufficient to nudge the particles from one trajectory to another. The devices consist of arrays of cylindrical metal-coated SU-8 posts connected by an underlying metal layer. This allows the application of voltages at the post surfaces and the generation of electric field gradients between neighboring posts, causing polarizable particles to experience a dielectrophoretic (DEP) force. This force, which depends on the volume and polarizability of the particle, can be made sufficient to push particles from one trajectory into another. In this way, the critical size in a device, normally fixed by the geometry, can be tuned. What's more, adding DEP in this way allows for the simultaneous creation of multiple size fractions.
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| 12. |
- Beech, Jason P., et al.
(författare)
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Capillary driven separation on patterned surfaces
- 2009
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Ingår i: Proceedings of Conference, MicroTAS 2009 - The 13th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9780979806421 ; , s. 785-787
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Konferensbidrag (refereegranskat)abstract
- Deterministic lateral displacement (DLD) is a powerful bimodal separation scheme [1] based on fluid flow through regular obstacle arrays that in its basic embodiment sends suspended particles in two different directions as a function of size. We show that without the need to seal devices and without the need for fluidic connections or pumps, particle separation can be achieved by the passive flow of a sample over a patterned surface. Risk of clogging is minimized by the movement of large particles above the obstacle array. Suitable application areas include blood fractionation and analysis of drinking water. 0
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| 13. |
- Beech, Jason P., et al.
(författare)
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Cell morphology and deformability in deterministic lateral displacement devices
- 2011
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Ingår i: 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011. - 9781618395955 ; 2, s. 1355-1357
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Konferensbidrag (refereegranskat)abstract
- Deterministic Lateral Displacement (DLD) devices have been used to separate particles based on size [1] and shape [2]. Here we show how DLD devices can also be used to separate particles based on their ability to deform under shear forces. Varying experimental conditions allows us to vary the relative contributions of size, morphology and deformability. The ability to distinguish between cells based on deformability with high resolution and throughput, in cheap and simple devices, could find highly interesting and relevant applications, for example in the detection of circulating tumor cells or malaria-infected blood cells.
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| 14. |
- Beech, Jason P., et al.
(författare)
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Electrokinetic wall effect mechanisms and applications
- 2020
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Ingår i: MicroTAS 2020 - 24th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419017 ; , s. 42-43
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Konferensbidrag (refereegranskat)abstract
- Under the application of longitudinal electric fields in microchannels, microparticles experience lift forces that push them away from the channel walls and affect their trajectories. At high frequencies (>100KHz) the dielectrophoretic forces dominate and are well understood but at lower frequencies there is little agreement as to the exact nature of the forces, how they are generated and how they vary due to the many different experimental conditions that are used in microfluidics devices. Here we present an experimental study of these mechanisms.
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| 15. |
- Beech, Jason P., et al.
(författare)
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Gravitationally driven deterministic lateral displacement devices
- 2009
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Ingår i: Proceedings of Conference, MicroTAS 2009 - The 13th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9780979806421 ; , s. 779-781
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Konferensbidrag (refereegranskat)abstract
- Deterministic lateral displacement (DLD) is a powerful bimodal separation scheme [1] based on regular obstacle arrays that in its basic embodiment sends particles in two different directions as a function of size. We add functionality to the technique by including gravitational forces, as a perturbation to particles transported by fluid flow, and as a way of transporting the particles through a stationary fluid.
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| 16. |
- Beech, Jason P., et al.
(författare)
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Morphology-based sorting-blood cells and parasites
- 2010
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Ingår i: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010. - 9781618390622 ; 2, s. 1343-1345
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Konferensbidrag (refereegranskat)abstract
- Morphology represents a hitherto unexploited source of specificity in microfluidic particle separation and may serve as the basis for label-free particle fractionation. There is a wealth of morphological changes in blood cells due to a wide range of clinical conditions, diseases, medication and other factors. Also, blood-borne parasites differ in morphology from blood cells. We present the use of Deterministic Lateral Displacement to create a chip-based, label-free diagnostic tool, capable of harvesting some of the wealth of information locked away in red blood cell morphology. We also use the device to separate the parasites that cause sleeping sickness from blood.
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| 17. |
- Beech, Jason P., et al.
(författare)
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Sample preparation for single-cell whole chromosome analysis
- 2012
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Ingår i: Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012. - 9780979806452 ; , s. 998-999
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Konferensbidrag (refereegranskat)abstract
- In this work we present an integrated system for whole chromosome analysis of single bacterium. Using whole genome barcoding techniques, which offer direct and rapid microscopic visualization of the entire genome in one field-of-view, we aim to rapidly identify individual bacterium. We are developing our device to achieve the crucial, and difficult process of isolating a bacterium, removing the DNA in one piece and transferring it to a nano-channel for visualisation. In order to achieve control over the bacteria we encapsulate them in agarose, using flow focusing. The encapsulated bacteria can then be transported in microchannels to proximity with the nanochannels and then chemically lysis can be performed. Following lysis the intact genome can be extracted and transferred to the meandering nanochannel for analysis. We believe this device holds the potential to significantly decrease analysis times for single cell, whole genome analysis with the potential of opening up for automated, high-throughput genome analysis in microfluidic systems.
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| 18. |
- Beech, Jason P., et al.
(författare)
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Separation of pathogenic bacteria by chain length
- 2018
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Ingår i: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 1000, s. 223-231
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Tidskriftsartikel (refereegranskat)abstract
- Using Deterministic Lateral Displacement devices optimized for sensitivity to particle length, we separate subpopulations of bacteria depending on known properties that affect their capability to cause disease (virulence). For the human bacterial pathogen Streptococcus pneumoniae, bacterial chain length and the presence of a capsule are known virulence factors contributing to its ability to cause severe disease. Separation of cultured pneumococci into subpopulations based on morphological type (single cocci, diplococci and chains) will enable more detailed studies of the role they play in virulence. Moreover, we present separation of mixed populations of almost genetically identical encapsulated and non-encapsulated pneumococcal strains in our device.
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| 19. |
- Beech, Jason P., et al.
(författare)
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Shape-based particle sorting - A new paradigm in microfluidics
- 2009
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Ingår i: Proceedings of Conference, MicroTAS 2009 - The 13th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9780979806421 ; , s. 800-802
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Konferensbidrag (refereegranskat)abstract
- Conventional fractionation techniques fail to fully benefit from the variety in morphology and shape that is found among biological particles. Although light scattering in conventional FACS gives some information on the size and morphology of a particle, it is generally not capable of giving a definite number on specified dimensions of a small object. We demonstrate an approach where we select which dimension of a particular object is used to determine its trajectory through an obstacle course and thereby sort not merely with respect to hydrodynamic radius but rather with respect to e.g. thickness, length or width.
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| 20. |
- Beech, Jason P., et al.
(författare)
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Sorting bacteria by chain length - A factor of virulence?
- 2016
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Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 250-251
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Konferensbidrag (refereegranskat)abstract
- Using Deterministic Lateral Displacement (DLD), we are able to separate bacteria by their size and their chain length. This separation enables the study of these properties as factors of virulence.
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| 21. |
- Beech, Jason P., et al.
(författare)
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The separation and identification of parasite eggs from horse feces
- 2019
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Ingår i: 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019. - 9781733419000 ; , s. 602-603
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Konferensbidrag (refereegranskat)abstract
- Freely grazing horses are at risk of infection by parasites such as Parascaris equorum (roundworm), Strongylus spp. (large bloodworms), Cyathostomes (small bloodworms), and Anoplochephala perfoliata (tapeworms). Mixed infections are common and diagnosis is based on demonstrations of eggs in feces followed by identification of larvae after fecal culture. Drug resistance is a growing problem, not least because treatments tend to be cheaper than diagnosis and “just in case” treatments common. There is a need for improved methods that are easy to use, rapid and cheap. Furthermore, a successful approach may find use with other livestock such as ruminants and pigs.
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| 22. |
- Beech, Jason P., et al.
(författare)
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The separation of nano-sized particles in micro-scaled post arrays
- 2019
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Ingår i: 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019. - 9781733419000 ; , s. 10-11
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Konferensbidrag (refereegranskat)abstract
- The precise separation of nanoscale particles has proven challenging due to diffusion and the need to use nanoscale devices. We show the separation of particles in the 100 nm size range in Deterministic Lateral Displacement (DLD) devices with feature sizes in the 10 µm size range. We achieve this using Dielectrophoretic (DEP) forces, generated between the metal coated posts that act as active electrodes. This opens up for the separation of submicron particles based not only on size but also on electric and dielectric properties.
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| 23. |
- Beech, Jason P., et al.
(författare)
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Throughput through thin-film fluidics
- 2008
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Ingår i: ; , s. 1492-1494
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Konferensbidrag (refereegranskat)abstract
- We demonstrate fluidics realized in thin film plastic foils patterned using roll-toroll nanoimprinting lithography (rrNIL). Realizing fluidics devices in thin plastic foils opens up for parallel operation in stacked devices. It also provides a convenient format for storage and distribution of the devices.
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| 24. |
- Beech, Jason P., et al.
(författare)
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Tipping the balance with dielectrophoretic forces - An electric deterministic lateral displacement device
- 2008
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Ingår i: ; , s. 95-97
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Konferensbidrag (refereegranskat)abstract
- We present experimental results and simulations on a simple method for tunable particle separation based on a combination of Deterministic Lateral Displacement (DLD) and Insulator Based Dielectrophoresis (I-DEP). Rather than deriving its tunability from its elastic properties[1], our present device uses an applied AC field to perturb the particle trajectories in the pressure-driven flow and is thereby capable of scanning the critical size over a range of factor two. Potential benefits include: extended dynamic range, facilitated fabrication and less clogging for given particle sizes, and combination of the precision afforded by DLD with the versatility of DEP.
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| 25. |
- Beech, Jason P., et al.
(författare)
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Tunable separation and DNA manipulation in metal coated pillar arrays
- 2018
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Ingår i: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. - 9781510897571 ; 4, s. 2090-2093
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Konferensbidrag (refereegranskat)abstract
- Implementing electrically connected metal-coated posts in a Deterministic Lateral Displacement (DLD) device and applying electric fields, we use electrokinetics to achieve tunable particle separations and to trap and manipulate DNA. The strength of DLD stems from its typically binary behavior. Particles move in one out of two trajectories based on their effective size. For particles that are close to the threshold size, a minute external force is sufficient to nudge the particles from one trajectory to another. Dielectrophoresis (DEP) provides such a force and also gives specificity based on the dielectric properties of the particles.
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