Author Archive

What we know about cancer tumors

Cancer tumors are a lot more complex than we think: besides cancer cells, supportive tissue cells, fat, and even immune cells can be found in a tumor. Combined crosstalk in between these cell groups influences the way the tumor develops or responses to drug treatment. On the other hand, the majority of what we know about cancer tumors has been acquired by studying cell ensembles. Recent strides to improve our understanding of cancer revealed that we have long been missing the stochastic interactions and rare events due to ensemble-average measurements. We can unveil how these cell groups work together and how the rare events change the fate of a tumor thanks to single-cell analysis techniques.

Single cells can be identified by extrinsic and intrinsic markers. Extrinsic markers are definitive of genetic and proteomic states of a cell. Flow cytometry and mass spectrometry have been the workhorse of extrinsic marker analysis, where genetic or proteomic materials are often fluorescently labeled for detection. With these techniques, multiplexed analysis of thousands of cells can be employed simultaneously. Intrinsic markers include size, shape, density, optical, mechanical, and electrical properties which do not require labelling. Microfluidic techniques provide with a plethora of different functionalities to sort the cells based on intrinsic markers. Combination of both extrinsic and intrinsic data advances our understanding of how cell heterogeneity is reflected in cell-to-cell variations in tumor development and drug-response. Although many powerful methods are available for determining extrinsic markers, not many techniques can gather information about a panel of different intrinsic markers.

A recent study from Biological Microtechnology and BioMEMS group at MIT represents an important microfluidic approach for the development of multiparameter intrinsic cytometry tool. The approach includes several different microfluidic modules combined with microscope imaging and image processing by machine learning. Separate modules measuring cell size, deformability, and polarization can be combined and organized within the tool (Figure 1). (i) Size module detects the cell size optically in a flow through system. Cell size module is necessary to separate different cell types that can give important cues about disease state. (ii) In deformability module, cells pass through narrow channels, and their transit time defines the deformability. Cell deformability gives cues about cytoskeletal and nuclear changes associated with cancer progression. (iii) In the polarization module, dielectrophoretic force at a fixed frequency is applied on cells driven by opposing hydrodynamic forces. Cells approach coplanar electrodes with different equilibrium positions depending on their polarizability. Cell polarizability allows for distinguishing subtle changes in biological phenotypes. As a proof-of-concept work, drug-induced structural changes in cells were detected for the first time using five different intrinsic markers, including size, deformability, and polarizability at three frequencies. The authors indicate that this powerful tool can further be equipped with visual readout capabilities, such as deterministic lateral displacement array, inertial microfluidics, acoustophoresis, optical techniques.

Figure 1. Multiparameter intrinsic cytometry combines different microfluidic modules on one substrate along with cell tracking to correlate per-cell information across modules for different intrinsic properties including size, polarizability, and deformability.

 

To download the full article for free* click the link below:

Multiparameter cell-tracking intrinsic cytometry for single-cell characterization
Apichitsopa, A. Jaffe, and J. Voldman
Lab Chip, 2018, Lab on a Chip Recent Hot Articles
DOI: 10.1039/C8LC00240A

*Article free to read until 31st August 2018

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for quantitative analysis of proteins from single-cells, next generation sequencing,compartmentalized organ-on-chip studies, and desalination of water on the microscale.

 

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Microparticles: Good things come in small packages

Microparticles were first described in 1967 by Peter Wolf, a physician, as ‘minute particulate materials’ when he investigated the platelet activity in human plasma. They were initially used as drug delivery agents because their size is as small as pollens, which can easily go into the human body. Not long after the great promise of microparticles has been realized, and today we use microparticles in numerous applications including pharmaceuticals, biomedicine, bioengineering, cosmetics, printing, and food science. The widespread use is not a coincidence, they can be synthesized from a multitude of materials, i.e. metal, polymer, gel etc. Especially, polymer microparticles, conferring a great versatility in size, shape, and chemistry, gained more attention in industry. Just like their usage areas, fabrication techniques of microparticles vary a lot. Polymer microparticle production is typically done in two ways, first microfluidics-assisted techniques including droplet-based fabrication, flow-lithography-based fabrication, and microjetting; second other techniques including centrifugation, electrohydrodynamics, and molding. With a focus on microfluidics-assisted techniques, we bring a few remarkable and commercialized studies on high throughput production of spherical-shaped and irregular-shaped microparticles to your attention.

Spherical microparticles

Particle monodispersity has to be compromised for high-througput production when using coaxial microfluidic devices, and both features are highly desired in medical applications and industry. Luckily, as a droplet-based fabrication technique, high-throughput step emulsification of microparticles addresses this fundamental problem. David Weitz’s research group at Harvard University has recently reported a droplet generator microchip with 135 step-emulsifier nozzles that produce monodisperse emulsions of polymers at an exceptional throughput of 10K mL/h (Figure 1a).1 This means, monodisperse microparticle production with this device is thousands times higher than a typical droplet generator microchip with one droplet maker and a throughput of 10 mL/h. The chip is made of PDMS, which is a flexible and inexpensive material. Monodispersity  at high flow rates is maintained using microchannels connected through an array of parallelized nozzles (Figure 1b). Microparticles are formed at the step between each nozzle and the continuous-phase channel. The formation can be explained by the Laplace pressure difference developing between the nozzle and the symmetric polymer bulb, resulting in suction of the dispersed phase into the bulb. The growing polymer bulb increases the pressure gradient and a neck forms between the nozzle and the bulb due to depletion of dispersed phase, resulting in release of a droplet. This geometry can produce spherical-shaped microparticles. The production efficiency scales linearly with droplet diameter (Figure 1c). Weitz demonstrated the production of oil microcapsules in water with the envision of standardizing the process by converting the emulsifier into a pipettor tip. Such a technology can replace the existing pipettor technology tools including multi-well and robots, and this replacement can serve for parallelizing and automation of the encapsulation chemi- and bio-assays. This technology has recently been introduced to the market by a Switzerland-based startup company called Microcaps.

As an alternative concept, in-air microfluidics is based on the idea of producing droplets at higher flow rates without using microfluidic channels. In the research groups of Detlef Lohse and Marcel Karperien at University of Twente, microparticles were generated using two nozzles, and one of the nozzles is mounted on a vibrating piezoelectric element (Figure 1d). The breakup of the liquid jet ejected from the first nozzle leads to formation of monodisperse droplets, which hit onto a continuous liquid jet ejected from the second nozzle. After passing ‘the meeting point’, both liquids react with each other to form physically-encapsulated microparticles. This technique provides with hundreds to thousands times faster microparticle production when compared to coaxial microchip setups. Such constructs can be especially beneficial in tissue engineering, where rapid fabrication of multi-scale materials with multiple cell types is an ongoing challenge. This technology has recently been introduced to the market by a Dutch startup company called IamFluidics.

Figure 1. Up-scaled step-emulsification device producing monodisperse droplets. (a) A schematic of the entire microfluidic chip actively producing oil-in-water droplets. (b) The emulsification process. (c) Maximum production rates per nozzle plotted against drop diameter, scale bars are 400 µm.The image is modified from Stolovicki et al. (see the references below). (d) Chip-based microfluidics comparison with in-air microfluidics.

Irregular-shaped microparticles

Another microfluidics-assisted fabrication concept is stop-flow lithography, introduced by Patrick Doyle’s research group at Massachusetts Institute of Technology.2 In this concept, while two (or more) streams of monomers flow side by side through a microchannel made of PFPE coated PDMS, the streams are exposed to intermittent illumination of ultraviolet light through a photomask, which blocks the light selectively. Due to the chemical reaction initiated by ultraviolet light, the liquid solidifies, and forms an individual microparticle (Figure 2a). Upon polymerization, gel particles do not stick to the PFPE microchannel walls, allowing for the production of free-floating particles by the virtue of oxygen lubrication layers. As the ultraviolet light is projected onto the stream through the photomask, each particle takes on the shape of the mask, making the microparticles customizable (Figure 2b). Microparticles composed of multiple monomers can be fabricated by combining multiple monomer streams. The single-step production is advantageous to reduce the production costs, however the particle shape is limited by the photomask and the microchannel geometry – not allowing for generation of spherical-shaped particles. For a proof-of-concept demonstration, upconverting nanocrystal laden-microparticles were synthesized and emitted homogenous visible spectrum of light. The technique allows for synthesis of striped microparticles without losing their homogeneous emission property. The microparticles were also encoded with multiple dot-patterns (Figure 2c), each specific to a target molecule (such as DNA) reacting with the other ingredients in the particle. Such a reaction leads to the formation of a fluorescent color in the microparticle, so the reaction can be traced by microscopy. This technology has been introduced to the market by Firefly Bioworks (acquired by Abcam in 2015), and Motif Micro (acquired by YPB Systems in 2018) startup companies.

microparticles

Figure 2. Stop Flow Lithography concept. (a) A schematic demonstration the coaxial microchip. (b) Bright-field and fluorescent images show triangle-shaped particles (c) A mask with an array of barcode particle shapes was aligned on three phase laminar flows in the microchip. Bright-field and fluorescent images show the barcoded particles with three distinct compartments with a region coding “2013”. The image is modified from Bong et al. (see the references below).

To download the full articles click the links below:

1Throughput enhancement of parallel step emulsifier devices by shear-free and efficient nozzle clearance
Elad Stolovicki, Roy Ziblat, and David A. Weitz
Lab Chip, 2018.
DOI: 10.1039/C7LC01037K

2Stop flow lithography in perfluoropolyether (PFPE) microfluidic channels
W. Bong, J. Lee, and P. S. Doyle
Lab Chip, 2014.
DOI: 10.1039/C4LC00877D

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for single-cell analysis, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

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Why should we use optofluidics for monitoring marine environment?

Phosphorus is found in natural waters and exerts a major influence on the composition and structure of aquatic ecosystems. It is a crucial nutrient for planktons and algae, which feed fish and other marine organisms. However, human activities may result in excess amount of phosphorus, which, in turn, causes harmful algae to bloom in natural waters. The bloom creates a hostile environment to other forms of marine life by consuming the available oxygen in the sea, and producing toxins. Sea organisms such as fish swim away from the blooms, but the ones that cannot swim, such as shellfish, unfortunately die. We do care about this occurrence as it negatively affects natural life and the economy. There is only one way to interpret the effect of continuously changing phosphorus levels on the strength of the biological pump: real-time monitoring of phosphate levels in the marine environment!

Figure 1. The design of the Fabry-Pérot microcavity, consisting of two parallel mirrors (reflectors) fabricated by coating the surface of the optical fibers with a gold layer. The light is reflected by the mirrors multiple times to enhance the signal. Adapted from Zhu et al., 2017.

Conventional vs. optofluidic monitoring instruments

Conventional phosphate monitoring instruments are mostly used for on-site sampling, then the fresh sample is transported to a laboratory for determining the phosphate level. Laboratories complete one round of analysis in 20 min, often using spectrophotometrical measurement tools. Given the conditions, real-time phosphate monitoring easily becomes laborious, time consuming, and costly. To address this challenge, researchers in Chinese Academy of Sciences, Wuhan University, and The First Institute of Oceanography in China collaborated to develop a portable optofluidic phosphate monitoring tool. However, prototyping an optofluidic marine phosphate detection tool is not straightforward because an absorption cell—a component core to the measurement unit—is simply too big to fit in a microchip. Instead of using a bulky absorption cell, researchers considered integrating a Fabry-Pérot cavity in the microsystem. The Fabry-Pérot cavity consists of two parallel optical fibers with a spacing in between. The cross-sectional surface of each optical fiber is coated with a thin layer of gold to create reflector surfaces (Figure 1) in order to enhance the absorption of phosphate. Shortening the spacing between the reflectors decreases the analysis time from minutes to seconds.

 

How it works?

In the microchip, filtered water sample and a chromogenic reagent are injected into a curved microchannel. After the chromogenic reaction, the water-soluble components are transported into the optical section (Figure 2). The probe light is sent into the Fabry-Pérot cavity via one of the fibers, bounces between the reflectors multiple times to increase the optical feedback and then analyzed by the detector. The obtained absorbance value, therefore, increases linearly with increasing phosphate concentration. In this microsystem, phosphate detection range is 0.1-100 µmol per liter (400 times greater than the range of a conventional instrument) and detection time is 4 seconds (300 times shorter than detection time of a conventional instrument). The authors of the paper think that this technology can be applied to detect other nutrient levels as well as pH changes in marine environment.

 

optofluidic phosphate monitoring

Figure 2. A schematic of the optofluidic microchip consisting of two parts: the microfluidics circuit forming the microreactor in the microchannel, and the optical part to provide optical feedback for enhanced absorption analysis. Adapted from Zhu et al., 2017.

To download the full article for free* click the link below:

 

Optofluidic marine phosphate detection with enhanced absorption using a Fabry–Pérot resonator

M. Zhu, Y. Shi, X. Q. Zhu, Y. Yang, F. H. Jiang, C. J. Sun, W. H. Zhaoc, and X. T. Hanc

Lab Chip, 2017, Lab on a Chip Recent Hot Articles

DOI: 10.1039/C7LC01016H

 

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for quantitative analysis of proteins from single-cells, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

*until 16th February 2018

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Spotting cancer: one in a billion cells

The human body consists of tens of trillions cells, all of which theoretically should have the same genome. Depending on genetic and environmental factors, some of these cells experience point mutations. Although most of those mutations are cleaned up by DNA repair enzymes, about 0.01% of them stay. A low percentage of the persistent mutations turn out to be ‘cancer’ while others stay recessive. Several genes, including the ones responsible for cell growth cycle, cause the persistent mutations. Uncontrolled growth of cells leads to formation of tumor, which is now prone to experience more mutations due to continuous proliferation. These mutations create heterogeneity among the cell population of a tumor, and eventually some cells leave their original tumor and start a new one in another organ of the body. When a cell leaves its parent tumor, it starts circulating in blood vessels before settling in. Those cells are called circulating tumor cells (CTCs), and around 1-10 CTC can be found in 1 mL of blood (which contains about 1 billion red blood cells, and 1 million white blood cells). Capturing ultra-rare CTCs has enormous implications in early cancer diagnosis. Often times, analysis of at least 10 mL of blood is necessary to capture sufficient CTCs to confirm their presence. The available technology can achieve CTC capturing in about 10 hours leading to the loss of target cells and decay of detection biomarkers.

Microfluidic devices are well known for precise sorting of microscale materials. Parallelizing microscale sorting in microfluidic devices enables high-throughput sample processing. In the light of this principle, David Issadore, Jina Ko, and their fellow researchers at University of Pennsylvania coined CaTCh FISH, a circulating tumor cell fluorescence in situ hybridization platform for rapid detection of CTCs. David Issadore kindly accepted to talk about this exciting lab-on-a-chip device. According to David, “the main strength of the CaTCh FISH is that it preserves the sensitivity and specificity of microfluidic cell sorting and RNA FISH, but through clever engineering allows these normally very slow laboratory-based operations to be performed rapidly and automatically on a chip.”

RNA FISH, high-throughput cell handling

Figure 1. Overview of the CaTCh FISH platform. Whole blood sample is processed in TEMPO step, where magnetic nano particle based cell separation is followed by single-cell RNA analysis (modified from Ko et al., 2017).

Processing a whole blood sample using CaTCh FISH involves three steps (Figure 1). First, white blood cells are labelled with magnetic nanoparticles. Second, whole blood is passed through a magnetic micropore filter to selectively trap magnetically labelled cells. “Our magnetic micropore device rapidly and precisely removes all of the cells that we know are not CTCs”, says David. The operating principle of magnetic micropore filter is based on strong and highly localized microscale field gradients formed at the edge of micropores to enable application of high flow rates. Third, single cell RNA analysis is performed on isolated cells using rapid in-situ hybridization strategy so that CTCs can be identified within the isolated cell population. In this way, targeted CTCs can be isolated from the rest of the cell population regardless of their physical and molecular properties. Analysis of a 10 mL blood sample takes less than an hour.

As a key novelty, the researchers maintained high-throughput processing and high sensitivity at the same time by integrating the FISH technique (hybridization of 20-50 fluorescently-labelled oligonucleotide probes to the target RNA, and subsequent fluorescence-signal based detection to enhance signal-to-noise ratio) in a microfluidic chip. CaTCh FISH has also been tested in patients with pancreatic cancer and detected CTCs in the real patient samples.

“The CaTCH FISH technology can be easily modified to measure other rare cells, for the diagnosis of other cancers or for stem cell research for example, by modifying the RNA FISH probes”, says David. He considers converting the platform to a high-precision hospital-based diagnostic tool and he collaborates with a company in the Bay area for this process. The CaTCh FISH device is poised to have a big impact on the way cancer is diagnosed.

To download the full article for free* click the link below:

A magnetic micropore chip for rapid (<1 hour) unbiased circulating tumor cell isolation and in situ RNA analysis

Jina Ko, Neha Bhagwat, Stephanie S. Yee, Taylor Black, Colleen Redlinger, Janae Romeo, Mark O’Hara, Arjun Raj, Erica L. Carpenter, Ben Z. Stanger and David Issadore

Lab Chip, 2017, Paper

DOI: 10.1039/C7LC00703E

 

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for quantitative analysis of proteins from single-cells, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

*until 5th January 2018

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Zenith in “artery”

When cutting a finger, thrombocytes and fibrin in the blood make up the blood-clotting mechanism, aka. haemostasis, to stop the blood loss. Another way to trigger this mechanism is having an artery damaged by atherosclerosis, which is often caused by several genetic or acquired factors. In the latter case, thrombosis develops within a vein or artery, obstructing or stopping the blood flow to major organs like the heart and eventually causing heart attack. Considering every year over 14 million lives worldwide are lost to heart attacks, more investigation on this topic is needed without any doubt.

Recently, a research team led by Andries van der Meer published a research article in Lab on a Chip on mimicking arterial thrombosis in 3D vascular structures, representing a major step forward in the development of accurate and faster methods of studying arterial thrombosis without using animals. The authors highlighted the inconvenience of using animal models to predict arterial thrombosis in humans. This is mainly due to fundamental differences between human and animal physiology, the researchers explain. For instance, rodent platelet biology, coagulation dynamics, and shear stress in mice arteries significantly vary between humans and mice.

thrombosis on chip

Figure 1. Three-dimensional models of a healthy and stenotic vessels and thrombosis formation upon blood perfusion through the channels.

The paper uses miniaturized vascular structures mimicking 3D architectures found in both healthy and stenotic blood vessels in-vitro (Figure 1). They combined stereolithography and 3D printing of computed tomography angiography data to construct 3D-printed templates of vessels in PDMS microchips. The 3D printed vessels are then coated with human umbilical vein endothelial cells, forming a monolayer fully covering the surface. In the next step, the artificial vessels are perfused with blood at normal arterial shear rates, allowing a blood clot to form as it would happen in the human body. The 3D printed vessel is clinically more relevant when compared to 2D vessel models, since the realistic flow profiles of blood and even distribution of shear stress across the vessel are of great importance when researching arterial thrombosis. Hugo Albers, the co-first author of the paper explains what led the team to try 3D models: “Other groups have worked on thrombosis-on-a-chip before, but we wanted to incorporate flow profiles that are similar to what one would find in-vivo. So we opt for a round and thus 3D shape. Since the stenotic geometry is an important part of this work, we wanted to find a technique that allowed us to make almost any shape we could come up with. Thus 3D-printing seemed to be the way to go.”

When it comes to defining the challenges in 3D organ-on-chip modeling and fabrication, “we needed to replicate the cellular environment using human endothelial cells and human whole blood to fully mimic the nature of vasculature” says Albers. “Incorporating the shape of vasculature to recreate the flow profiles found in-vivo and recreating the shape of vasculature on a small scale was quite challenging, since the resolution of 3D-printing quickly started to be the limiting factor. Furthermore, we ran into problems related to working with whole blood. We had to figure out how to perfuse small channels with blood without instigating thrombosis outside of the microfluidic channel.” The researchers successfully overcame the challenges mentioned by Albers and mimicked the formation of thrombosis in a stenotic vessel model as seen in Figure 1 (bottom).

The researchers note that the next step involves co-culturing arterial endothelial cells and smooth muscle cells with human umbilical vein endothelial cells or moving to different cell lines such as differentiated human induced pluripotent stem cells. “I think we can also apply the 3D-printing technique to create thrombosis-on-a-chip devices with different geometries, e.g. aneurysms or bifurcated geometries”, says Albers.

To download the full article for free* click the link below:

Mimicking arterial thrombosis in a 3D-printed microfluidic in vitro vascular model based on computed tomography angiography data

Pedro F. Costa, Hugo J. Albers, John E. A. Linssen, Heleen H. T. Middelkamp, Linda van der Hout, Robert Passier, Albert van den Berg, Jos Malda and Andries D. van der Meer

Lab Chip, 2017, Paper

DOI: 10.1039/C7LC00202E

This paper is included in our Organ-, Body- and Disease-on-a-Chip Thematic Collection. To read other articles in the collection, visit – rsc.li/organonachip

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for quantitative analysis of proteins from single-cells, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

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How can biosensors provide real-time health monitoring?

Like a ripple spreading outwards on a pond’s surface, a plasmon is a collective oscillation of free electrons in a piece of metal. When the metal interacts with light (in this case k vector of light satisfies the momentum condition), the collective movement of oscillating electrons at the metal’s surface leads to the propagation of the light along the surface, also known as a surface plasmon. This simple physics rule is very helpful for sensor nanotechnology and optical signal processing applications since the offered advantages are significant, providing a smaller foot-print, lower limits of detection, and multiplexing opportunities. However, using sensors for biomolecule detection requires clever use of light. For example, surface plasmon resonance can be observed in nanohole arrays patterned on very thin gold films. Nanohole arrays can transmit light much more strongly than expected for the nanohole apertures at certain wavelengths. This phenomenon is called extraordinary optical transmission (EOT) and opens a new avenue for detection of minute amounts of biomolecules.

A nanoplasmonic biosensor was recently developed for real-time monitoring of proteins from live cells in a label-free configuration, thanks to extraordinary optical transmission. The biosensor is structured in a microfluidic device consisting of a cell module and the biosensor module. Microfluidic cell module design is based on a single zigzag channel for directly delivering the secreted proteins to the adjacent biosensor module via a tubing connection. The biosensor module consists of nanoholes fabricated on freestanding SiNx membranes. Antibodies specific to vascular endothelial growth factor (VEGF) are selectively immobilized on the gold nanohole arrays as biorecognition molecules. When the VEGF are captured on the sensor, a change of refractive index proximate to the surface is induced. This change results in a peak shift of the EOT spectrum (Figure 1). By tracing the spectral shifts continuously, the dynamics of cell secretion can be monitored. In this way, the secretion dynamics from live cancer cells are monitored and quantified for 10 hours. The proposed microfluidic device has unique capabilities for multiplexed and label-free detection in a compact footprint, which are promising for miniaturization and integration into lab-on-a-chip devices.

biosensor, microfluidics, extraordinary transmission phenomena, nanohole arrays

Design and working principle of microfluidic-integrated biosensor. Cancer cells grow in a zigzag channel, and secreted vascular endothelial growth factor are directly delivered to the adjacent detection module. Nanohole structures fabricated in the detection (biosensor) module are shown in SEM image with a scale bar of 1 μm (bottom left). The images on the right show the characteristic resonance peak (solid line) and EOT spectral shift of the peak upon binding (dashed line). Spectral displacements of the resonance peak based on molecular binding accumulation is shown in the sensorgram to reveal the real-time binding dynamics. Adapted from Li et al. (Lab Chip, 2017).

This technology will have a potentially significant impact on medicine. Most of the patients agree that preventive medicine is preferable to reactive medicine. However, preventive medicine requires frequent physical exams, which can only be maintained by spending substantial time and money at physicians’ offices. The need for frequent check-up exams could be reduced or eliminated by real-time monitoring of the health status by portable biosensors in the future. Developing biosensors that allow real-time monitoring of target biomolecules is a big step towards the addressing this future goal.

 

To download the full article for free* click the link below:

Plasmonic nanohole array biosensor for label-free and real-time analysis of live cell secretion

Xiaokang Li, Maria Soler, Cenk I. Özdemir, Alexander Belushkin, Filiz Yesilköy and Hatice Altug

Lab Chip, 2017

DOI: 10.1039/C7LC00277G

 

*Free to access until 7th August 2017.


About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in Herr Lab at UC Berkeley in the United States. Her research interests include development of microfluidic devices for quantitative analysis of proteins from single-cells, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

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The future of bioensors

St. Paul’s Cathedral in London has its own unique acoustics. The architecture of the dome allows a whisper to be heard from anywhere within the circular gallery, so-called the whispering gallery. The invention of whispering-gallery-mode (WGM) biosensors is indeed derived by this special gallery in St. Paul’s: just like a sound wave travelling within the dome, a light beam traveling within a glass sphere (in this case, a biosensor) circles multiple paths so that any molecule on the surface can be detected. Thanks to this powerful technique, interactions of unlabeled molecules can be analyzed with high sensitivity in real-time.

In early March of 2017, researchers from Max Planck Institute and University of Exeter published a comprehensive review paper in Lab on a Chip, explaining the advances of WGM sensors as scientific laboratory instruments, their development into lab on a chip devices, major challenges on the way towards real-world applications, and potential future applications.

WGM sensors probe the interaction between molecules and electromagnetic waves during a biomolecular reaction, and convert this information to a measurable signal. The probing is made possible thanks to the electromagnetic modes formed inside a resonator with axial symmetry. However, the electromagnetic waves slightly extend into the surrounding medium. Any changes in the surrounding medium, and therefore in the evanescent field, cause a shift of the resonance frequency—this is the basis of the sensing mechanism. WGMs are capable of sensing this shift in three ways: (1) Resonance frequency shift based sensing: measurable signal is the magnitude of the frequency shift, and the sensitivity of the sensor, which scale with the evanescent field strength at the distortion’s position, i.e. interaction of a single atomic ion with a plasmonic nanoparticle (Figure 1a). (2) Loss based sensing: it is based on the resonator’s energy loss per light wave oscillation, i.e. binding of polystyrene nanoparticles (Figure 1b). (3) Mode-splitting based sensing: a scattering molecule/particle couples clock-wise and counter clock-wise propagating WGMs, resulting in the formation of two different standing wave modes, i.e. deposition of multiple nanoparticles on a surface (Figure 1c).

Whishering gallery mode biosensors

Figure 1. Three different sensing mechanisms of whispering-gallery-mode biosensors. (a) Resonance frequency shift based sensing, (b) loss based sensing, (c) mode-splitting based sensing (from Kim et al., Lab Chip, 2017).

The review also focuses on several performance criteria of WGM sensors, such as single molecule sensitivity, time resolution, stability and specificity. Single molecule sensitivity of WGM sensors depends on the resonator’s size, the surrounding medium and excitation wavelength. Despite the fact that these parameters seem to limit the sensitivity, increasing the electric field inside a nanoscale volume significantly can circumvent this problem. Apart from that, WGM sensors can detect events happening in milliseconds to seconds whereas these detection speeds are mostly limited by the equipment, for example, the laser’s maximum scanning speed. When it comes to stability of WGM sensors, one common problem is reported to be the environmental noise sources, affecting the reliability of the measurements. A variety of methods to reduce those negative effects are further discussed in the review. One another notable functionality is that WGM sensors can be as specific as probing a surface-immobilized receptor molecule reacting with an analyte of interest.

microring resonator based on-chip sensor, pillar-supported high Q cavities

Figure 2. Lab on a chip WGMs. Left and middle images show a microring resonator based on-chip sensor with zoom-in images of different components, and right image shows a pillar-supported high Q cavities (from Kim et al., Lab Chip, 2017).

Lab on a chip applications of WGMs are discussed in two categories in the review (Figure 2): Planar resonators let the light to be coupled into multiple ring-resonators that are connected to channels containing different analytes. This type of resonators is low-cost and allows for in-parallel probing of samples. Pillar-supported high Q cavities is the second type, featuring a high Q factor owing to the air-gap between the substrate and the cavities. Pillar-supported resonators are high-cost due to several fabrication difficulties. Apart from those, droplet-based in vivo sensing via WGM sensors is also addressed as an alternative approach with the possibility of using the analyte medium itself as a resonator. Over the past decade, WGM sensors have been widely exploited to study molecular interactions with high sensitivity and seem to gain more and more attention.

 

To download the full article for free* click the link below:

Towards next-generation label-free biosensors: recent advances in whispering gallery mode sensors

Eugene Kim, Martin D. Baaske and Frank Vollmer

Lab Chip, 2017, Critical Review

DOI: 10.1039/C6LC01595F

*Free to access until 12th July 2017.

 

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in BIOS Lab on a Chip Group at University of Twente in The Netherlands. Her research interests include development of microfluidic devices for quantitative analysis of proteins of a single-cell, next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

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Optical DNA maps

Just like Google maps, DNA maps can tell us the distance between two genes, and allow us to zoom in on the region of interest. DNA mapping started with human genome project, where DNA sequencing techniques opened a way to unveil the genetic information. However, determining the unique places and repetitions of four “chemical letters” found in our DNA—together known as the genes—is a difficult mission due to temperature, pH, and pressure sensitivity of the molecule.  DNA mapping technology allows for easy identification of large structural variations in DNA and therefore provides long-range information of the genome and can more.

Optical DNA mapping has emerged in the past decade as a powerful alternative to other DNA sequencing techniques since it can easily be applied with reduced risk of DNA damage. Over 100000 basepairs of DNA molecules, which are quite difficult to handle with other techniques, are labeled, stretched, and rendered in a single image. The stretching part is done using nanochannels (and therefore lab-on-a-chip technology), while the labeling part can be done by either enzymatic or affinity-based techniques (Figure 1). The concept and applications of optical DNA mapping has recently been very well explained in a tutorial review written by Vilhelm Müller and Fredrik Westerlund from Chalmers University of Technology in Sweden.

In enzymatic labelling nucleotides at particular regions on a single DNA strand are replaced by new ones using a DNA polymerase. The replacement nucleotides are then utilized to incorporate fluorophores into the DNA strand and allow for visualization. Nicking enzymes and methyl-transferases present two different approaches to employ enzymatic labelling process. While the use of differently colored fluorophores extends the applicability of this technique, the final resolution depends on the degree of stretching and the density of fluorophores on the region.

Affinity-based labelling is based on non-covalent interactions which can be enabled by either denaturation mapping or competitive binding. In denaturation mapping, DNA is heated to discriminate between the bases by their different bond energies. While G-C-basepairs still hold both strands of DNA—due to 3 hydrogen bonds holding them—, A-T-basepairs will melt—due to 2 hydrogen bonds holding them—. At this stage, an intercalating fluorescent dye can be linked to G-C-basepairs, allowing for imaging. Competitive binding relies on the usage of a fluorescent intercalating dye and a molecule selective for either A-T or G-C regions. Therefore, fluorescent dye cannot bind where the selective molecules have already bound. An optical map of DNA molecules can be obtained in this way. Affinity-based labelling is also highly dependent on the degree of stretching.


Optical DNA mapping techniques are useful tools for a wide range of applications from assembly of complex genomes to bacterial plasmid epidemiology. The concept opens up exciting research directions as it allows for automation of whole analysis using lab-on-a-chip systems and observation of the results using smartphones.

optical DNA mapping

Figure 1. Schematic illustration of DNA labelling techniques used in optical DNA mapping. Enzyme-based labelling involves nicking enzymes and methyl-transferases techniques, while affinity-based labelling can be employed by denaturation mapping or competitive binding methods. This figure is adapted from “Optical DNA mapping in nanofluidic devices: principles and applications” paper.

To download the full article for free* click the link below:

Optical DNA mapping in nanofluidic devices: principles and applications

Vilhelm Müller and Fredrik Westerlund

Lab Chip, 2017, Articles

DOI: 10.1039/C6LC01439A

 

*Free to access until 5th May 2017.


About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in BIOS Lab on a Chip Group at University of Twente in The Netherlands. Her research interests include development of microfluidic devices for next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

 

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Sample-in-answer-out

You have worked hard all year and wanted to treat yourself with something different for the summer. You decided to arrange a journey to South-Africa to enjoy the beautiful natural scenery. Discovering the range of wildlife in immense national parks, hiking in mountains, and meeting with warm locals made your journey unforgettable. You arrived at one of the best photography spots in a national park just before the sunset. While focussing on capturing the best image from the picturesque scenery, you got bitten by a Marsh mosquito, perhaps infected with a Plasmodium falciparum parasite. This parasite is known for causing malaria, the most significant parasitic disease of humans. You are not the only one: approximately 30,000 travellers from industrialized countries contract malaria each year. During the next 14 days, this parasite will differentiate and proliferate in the body. It will invade and destroy the red blood cells, eventually affecting the liver, spleen, and brain functionality. A few days after the bite, you found a small-scale laboratory for the malaria diagnosis test, but there was a problem: this laboratory can detect malaria only if you have 50-100 parasites per microliter of blood, occurring when the patient carries the parasite for weeks. You, then, had to find a larger laboratory equipped with a benchtop loop-mediated isothermal DNA amplification (LAMP) system, which can detect 1 malaria parasite per microlitre of blood. You wished there was a highly sensitive device for malaria diagnosis at the point of need. Well, we might have some good news for you.

Modern nucleic acid testing methods of malaria detection, such as LAMP, enable high sensitivity, high specificity, robust, and rapid analyses for asymptomatic infections. As performing these methods requires bulky and costly peripheral equipment and trained technicians, access to such equipment in rural areas is unlikely. Fortunately, researchers in Pennsylvania State University recently introduced a stand-alone, portable, and high sensitivity system that can perform “sample-in-answer-out” analyses. The system consists of a compact disc and a reader unit (Figure 1). The compact disc includes valves and microfluidic channels, where the blood sample is processed using magnetic beads. The reader unit can automatically perform all analysis steps including DNA purification, elution, amplification, and real-time detection. For a real demonstration of how the test is performed, the movie included below is well worth the watch. Test results can be displayed on a LCD screen or a smartphone within 40 minutes. The system can detect down to 0.6 parasites per microliter of blood. Each test costs around $1. With these specifications, this technology has the opportunity to create a new paradigm in molecular diagnosis at the point of care.

malaria detection test

Figure 1. Schematic view of an assembled compact disc made of PMMA; AnyMDX reading unit consisting of a magnet, heater plate, optical detection system, and LCD screen; and the illustration of integrated sample processing steps on the compact disc. The technique is based on DNA-carrying magnetic beads actuated against stationary reagent droplets.

To download the full article for free* click the link below:

A field-deployable mobile molecular diagnostic system for malaria at the point of need

Gihoon Choi, Daniel Song, Sony Shrestha, Jun Miao, Liwang Cuic and Weihua Guan

Lab Chip, 2016, Articles

DOI: 10.1039/C6LC01078D

About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in BIOS Lab on a Chip Group at University of Twente in The Netherlands. Her research interests includedevelopment of microfluidic devices for next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale.

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What can a magnet do?

The magic of magnetism can be shown through a simple classroom demonstration of bringing two magnetic pieces together and then trying to pull them apart. The attraction between the opposite poles of the magnets becomes very apparent as you struggle to tear them apart. This simple concept can be applied to lab-on-a-chip devices to eliminate the need for off-device hardware with power requirements, and therefore, enable the use of lab-on-a-chip technology in low-resource settings.

The majority of existing lab-on-a-chip systems use manual pipettes, syringe pumps, or pressure pump systems to manipulate the fluid flow. The dependence on off-chip hardware, however, makes the integration of these systems into low-cost environments rather challenging. Researchers in both, academia and industry think that this challenge can be addressed by “manually operated self-contained microfluidic devices”, which has gained significant attention over the past couple of years. In line with this objective, magnetically-adhesive based valves have for the first time shown to control fluid flow in a microfluidic device in a recent collaboration work by Sandia National Labs and Qorvo Inc. Here, the “magnetic-adhesive based valve” simply consists of a disk magnet seated on a thin ring of adhesive material.

In this study, a microfluidic device is designed to perform bioassays and contains a port connecting two chambers in different planes. The port is closed by an internal magnet located on a pressure-sensitive adhesive tape, and is opened by the help of an external magnet which displaces the internal magnet (figure 1). When the port is open, the reagents can flow in the microchannels, as shown in figure 2. The adhesive tape prevents any leakage within the microchip, while the magnet serves as an actuatable gate for reagents. The microfluidic device, therefore, allows for storage and on-demand transport of different types of reagents (both liquid, solid, and gas) to perform bioassays.

Magnetic-adhesive based valves are fabricated at the millimeter-scale, however, it is possible to manufacture micron-sized valves depending on the resolution of the laser ablation system used to cut the valve layout. Design considerations and characterization of magnetic-adhesive based valves are further addressed in the paper. Apart from this, the self-contained device is made of low-cost materials (such as PMMA and magnetic alloys), resulting in a fabrication cost as low as 0.2 dollars per chip. As portable and low-cost devices start to draw increasing attention in lab-on-a-chip technology, this work might be an important milestone for next generation micro total analysis systems.

Magnetic valves for lab on a chip sytems

Figure 1. Schematic and photos of magnetic-adhesive based valve working mechanism.

Magnetic valves for lab on a chip devices

Figure 2. Controlled transport and reaction of the stored components in a simple, power- and instrument-free manner in a three chambered microfluidic device.

This is a recently published Hot article and you can download it for free* by clicking the link below:

Magnetic-adhesive based valves for microfluidic devices used in low-resource settings

Jason C. Harper, Jenna M. Andrews, Candice Ben, Andrew C. Hunt, Jaclyn K. Murton, Bryan D. Carson, George D. Bachand, Julie A. Lovchik, William D. Arndt, Melissa R. Finley and Thayne L. Edwards

Lab Chip, 2016, Recent HOT Articles

DOI: 10.1039/C6LC00858E


About the Webwriter

Burcu Gumuscu is a postdoctoral fellow in BIOS Lab on a Chip Group at University of Twente in The Netherlands.

Her research interests include development of microfluidic devices for next generation sequencing, compartmentalized organ-on-chip studies, and desalination of water on the microscale .

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