Work pertinent to this study was supported in part by National Institutes of Health (NIH) National Heart, Lung, and Blood Institute grants HL082808, HL123984 (R.L.), and F31HL134241 (M.E.Q.). Funding also provided by NIH National Institute of General Medical Sciences grant T32GM008367 (M.E.Q.); and pilot grant funds from Children&#8217;s Healthcare of Atlanta and Emory University Pediatric Flow Cytometry Core. The authors would like to thank Dr. Hans Deckmyn for sharing the 6B4 antibody, and the Emory Children&#39;s Pediatric Research Center Flow Cytometry Core for technical support.

All methods using donor-derived human platelets described herein were approved by the Institutional Review Board of Emory University/Children&#39;s Healthcare of Atlanta.
1. Blood Draw and Platelet Isolation
<ol>
	<li>Draw human blood from consenting healthy adult donors via venipuncture on the day of the experiment into 3.8% trisodium citrate. One 4.5 mL tube of blood is sufficient to yield enough platelet rich plasma (PRP) for 20-25 conditions in donors whose platelet counts are close to 250 x 103 per &#956;L. 
	NOTE: Avoid drawing blood via narrow gauge needles (smaller than 21 G).</li>
	<li>Prepare PRP via centrifugation at 22 &#176;C and 140 x g for 12 min with a long brake. This will result in two distinct layers, with red blood cells at the bottom and the light colored PRP at the top.</li>
	<li>Isolate the top, cloudy, yellow layer of PRP via careful pipetting through a pipette tip cut at a 45&#176; angle and obtain the platelet count via a complete blood count (CBC).</li>
	<li>If necessary, wash platelets in PIPES-buffered saline (150 mM NaCl, 20 mM PIPES) in the presence of prostaglandin E1 (PGE1) and resuspend in Tyrode&#39;s buffer (134 mM NaCl, 0.34 mM Na2HPO4, 2.9 mM KCl, 1 mM MgCl2, 5 mM glucose, 12 mM NaHCO3, 20 mM HEPES, pH 7.35) with 5 mM glucose, otherwise, proceed to step 1.5. The following steps describe the washing in brief.
	<ol>
		<li>Adjust PRP volume to 10 mL with PIPES-buffered saline and add 0.6 &#956;M PGE1.</li>
		<li>Centrifuge for 8 min at 1,900 x g, then discard supernatant and let the platelet pellet sit in 400 &#956;L of Tyrode&#39;s and glucose solution for 5 min.</li>
		<li>Gently resuspend the platelet pellet and keep it undisturbed for 30 min.</li>
	</ol>
	</li>
	<li>Adjust the platelet count to ~250 x 103 platelets per &#956;L with pooled human platelet-poor plasma (PPP) and maintain the suspension at 22 &#176;C undisturbed or under gentle rotation.</li>
</ol>
2. Ligand and uniform shear treatment
NOTE: All steps in section 2 that require pipetting should be done slowly, so as not to introduce any shear.
<ol>
	<li>Add the desired antibody or ligand to the PRP or washed platelets and mix gently by pipetting up and down or stirring with a pipette tip. Leave it undisturbed at room temperature for 5-10 min. Add an equivalent volume of PPP or Tyrode&#39;s buffer to a negative control.</li>
	<li>Turn on the cone-plate viscometer, set the plate temperature to 22 &#176;C and allow time to let the plate reach this temperature.</li>
	<li>Pipette the treated PRP or washed platelets onto the temperature-controlled cone-plate viscometer directly at the center of the plate. Ensure that all of the sample is deposited between the cone and plate at the point of contact, and not on the outside of the cone&#8217;s rim.</li>
	<li>Shear at an appropriate rate and duration.
	<ol>
		<li>Calculate shear as indicated by the viscometer manual, or as previously shown15,16.</li>
		<li>Determine shear rate from viscosity and desired shear stress via Newton&#39;s law of viscosity; <img alt="Equation 1" src="/files/ftp_upload/59704/59704eq1.jpg" />; plasma viscosity is 1.5-1.6 centipoise (cP)17. For example, a normal shear range for human circulation is 5-30 dyn/cm2 and shear should be applied on the single digit minute time scale.</li>
	</ol>
	</li>
	<li>Lift the cone off of the plate slighlty (~2 mm) so that the sample remains in contact with both the plate and cone, and use a gel-loading or other long pipette tip to collect 5-10 &#956;L from the center of the sample volume.</li>
	<li>Incubate the sheared samples with the desired markers for 20 min at room temperature. For markers of phosphatidylserine, &#946;-galactose, and P-selectin exposure use Lactadherin C2 domain (LactC2) at 0.08 &#956;M18, Erythrina cristagalli lectin (ECL) at 6.25 &#956;g/mL, and anti-P-selectin antibody (20 &#181;g/mL), respectively.</li>
	<li>Fix samples in 2% paraformaldehyde for 20 min at RT prior to dilution or cold storage, and proceed to step 3.1 or store samples at 4 &#176;C for no longer than 12 h.</li>
</ol>
3. Detection of surface markers and crosslinking via flow cytometry
<ol>
	<li>Analyze the sample via flow cytometry, collecting at least 20,000 events for each condition.</li>
	<li>Quantitate signal strength of the fluorescent markers using the height value for the intensity of each fluorophore, or the geometric mean fluorescence intensity (MFI).</li>
	<li>If aiming to detect platelet crosslinking following shear treatment, analyze the sample on an imaging-capable flow cytometer and quantitate crosslinking by area and aspect ratio parameters.
	<ol>
		<li>Plot a histogram of area and/or aspect ratio.</li>
		<li>Use a negative control with bovine serum albumin (BSA) or vehicle to draw a gate excluding most fully circular events (this gate is usually drawn at an aspect ratio ~0.819,20) and quantitate the percentage of events inside of this gate. Events with a lower aspect ratio are more likely to be crosslinked.</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

The protocol described in this manuscript allows quick and versatile assessment of the effect of laminar shear on platelet and cell surface receptors. The specific representative results presented here underscore how the effects of multimeric or bivalent ligands can be affected by shear flow. In addition to this application, a uniform shear assay has broad applications in observing shear-dependent effects. In the absence of a known ligand-receptor pair, a uniform shear assay can also detect the effects of shear on factor...

Mechanoreceptors are proteins that respond to mechanical stimuli, such as pressure or mechanical perturbation/deformation. For some mechanoreceptors, sensing these mechanical perturbations is explicit to the function of the cell types in which they are expressed. Take, for example, the stretch receptors in baroreceptor neurons; these mechanosensitive ion channels regulate blood pressure by sensing vascular &#34;stretch&#34;1,2. In the inner ear, ion channels on hair cells detect mechanical deformations caused by sound waves3, and cutaneous low threshold mechanoreceptors (LTMRs) facilitate the transmission of tactile information4. In other cases, mechanoreceptors provide important information to the cell for the establishment of adhesion or growth. Cells can sense the rigidity of their local environment, and may rely on contractile forces via the actin cytoskeleton and integrins to dictate growth or spreading5,6.
When studying receptor-ligand interactions in cell or tissue-based models, common assays exist which can quickly and accurately report the effects of altering temperature, pH, ligand concentration, tonicity, membrane potential, and many other parameters which can vary in vivo. However, these same assays may fall short when it comes to detecting the contribution of mechanical force to receptor activation. Whether cells are sensing their microenvironment, detecting sound waves, or responding to stretch, one thing the aforementioned mechanoreceptors have in common is that they are participating in interactions where the ligand, receptor, or both, are anchored to a surface. Assays developed to test the effects of mechanical forces on receptor interactions often reflect this paradigm. Microfluidics and flow chambers are used to study the effects of shear flow on cells and receptors7,8. These types of experiments have the advantage of allowing fine-tuning of shear rates via established flow speeds. Other techniques employ fluorescent molecular probes to detect forces applied by cells on ligand-rich surfaces, yielding an accurate readout of the magnitude and orientations of forces involved in the interaction9,10.
In addition to mechanosensation occurring where one or both partners are anchored to a surface, shear stress may affect proteins and cells in solution. This is often observed in blood cells/proteins which are constantly in the circulation, and may manifest via activation of mechanoreceptors that are normally surface-anchored11, or through exposure of target sequences which would be occluded under static conditions12. However, relatively fewer techniques assay the effects of shear force on particles in solution. Some in-solution approaches introduce shear via vortexing cells in fluid suspension with varying speeds and durations, although these approaches may not allow a very precise determination of the shear stress generated. Rotational viscometers measure viscosity by applying a specific shear force to fluids. Herein we describe an applied method for determining the effect of specific laminar shear rates on cells or cell fragments in solution.
One of the most highly expressed proteins on the platelet surface is the glycoprotein (GP) Ib-IX complex. GPIb-IX is the primary receptor for the plasma protein von Willebrand Factor (VWF). Together, this receptor-ligand pair has long been recognized as the foundation of the platelet response to shear stress13. In the event of vascular damage, VWF binds to exposed collagen in the sub-endothelial matrix14, thus recruiting platelets to the site of injury via the VWF-GPIb-IX interaction. VWF engagement to its binding site in the GPIb&#945; subunit if GPIb-IX under physiological shear stress induces unfolding of a membrane-proximal mechanosensory domain (MSD) which in turn activates GPIb-IX15. In a recent study, we have shown that antibodies against GPIb&#945;, like those generated in many immune thrombocytopenia (ITP) patients, are also capable of inducing platelet signaling via MSD unfolding under shear stress11. However, unlike VWF, which facilitates shear-induced GPIb-IX activation by immobilizing the complex under normal circulation, the bivalent antibodies are able to crosslink platelets via GPIb-IX and unfold the MSD in circulation. In this way, a mechanoreceptor which is normally activated by surface immobilization under shear can be activated in solution. In the present report, we will demonstrate how a viscometer-based uniform shear assay was leveraged to detect the effects of specific levels of shear stress on receptor activation in solution.

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	<colgroup>
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		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="34">
			<td height="34" style="height:35px;width:413px;">APC anti-human CD62P (P-Selectin)</td>
			<td style="width:128px;">BioLegend</td>
			<td style="width:135px;">304910</td>
			<td style="width:88px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:413px;">Brookfield Cap 2000+ Viscometer</td>
			<td style="width:128px;">Brookfield</td>
			<td style="width:135px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:413px;">FITC-conjugated Erythrina cristagalli lectin (ECL)</td>
			<td style="width:128px;">Vector Labs</td>
			<td style="width:135px;">FL-1141</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pooled Normal Human Plasma</td>
			<td>Precision Biologic</td>
			<td>CCN-10</td>
			<td></td>
		</tr>
		<tr height="52">
			<td height="52" style="height:52px;width:413px;">Vacutainer Light Blue Blood Collection Tube (Sodium Citrate)</td>
			<td style="width:128px;">BD</td>
			<td style="width:135px;">369714</td>
			<td></td>
		</tr>
		<tr height="53">
			<td height="53" style="height:53px;width:413px;">Vacutainer Blood Collection Set, 21G x &#190;&#34; Needle</td>
			<td style="width:128px;">BD</td>
			<td style="width:135px;">367287</td>
			<td></td>
		</tr>
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a uniform shear assay for human platelet and cell surface receptors via cone-plate viscometry

Many biological cells/tissues sense the mechanical properties of their local environments via mechanoreceptors, proteins that can respond to forces like pressure or mechanical perturbations. Mechanoreceptors detect their stimuli and transmit signals via a great diversity of mechanisms. Some of the most common roles for mechanoreceptors are in neuronal responses, like touch and pain, or hair cells which function in balance and hearing. Mechanosensation is also important for cell types which are regularly exposed to shear stress such as endothelial cells, which line blood vessels, or blood cells which experience shear in normal circulation. Viscometers are devices that detect the viscosity of fluids. Rotational viscometers may also be used to apply a known shear force to fluids. The ability of these instruments to introduce uniform shear to fluids has been exploited to study many biological fluids including blood and plasma. Viscometry may also be used to apply shear to the cells in a solution, and to test the effects of shear on specific ligand-receptor pairs. Here, we utilize cone-plate viscometry to test the effects of endogenous levels of shear stress on platelets treated with antibodies against the platelet mechanosensory receptor complex GPIb-IX.

Figure 1 outlines how the trigger model of GPIb-IX activation, initially introduced to explain shear-dependent receptor activation when anchored to the vessel wall, may also support activation of platelets crosslinked by a multivalent ligand. Figure 2 shows readouts of human platelet activation treated by two antibodies targeting the N-terminal domain of GPIb-IX (6B4 and 11A8), and one control antibody (normal IgG) under sheared and static conditions. In <strong...

Watch this Scientific Journal Video about A Uniform Shear Assay for Human Platelet and Cell Surface Receptors via Cone-plate Viscometry at JoVE.com

A Uniform Shear Assay for Human Platelet and Cell Surface Receptors via Cone-plate Viscometry

We describe an in-solution method to apply uniform shear to platelet surface receptors using cone-plate viscometry. This method may also be used more broadly to apply shear to other cell types and cell-fragments and need not target a specific ligand-receptor pair.

Many biological cells/tissues sense the mechanical properties of their local environments via mechanoreceptors, proteins that can respond to forces like ...

a-uniform-shear-assay-for-human-platelet-cell-surface-receptors-via

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7.6K Views.  Children's Healthcare of Atlanta. We describe an in-solution method to apply uniform shear to platelet surface receptors using cone-plate viscometry. This method may also be used more broadly to apply shear to other cell types and cell-fragments and need not target a specific ligand-receptor pair.

Video: A Uniform Shear Assay for Human Platelet and Cell Surface Receptors via Cone-plate Viscometry

A Chromatin Assay for Human Brain Tissue

Chronic neuropsychiatric illnesses such as schizophrenia, bipolar disease and autism are thought to result from a combination of genetic and environmental factors that might result in epigenetic alterations of gene expression and other molecular pathology. Traditionally, however, expression studies in postmortem brain were confined to quantification of mRNA or protein. The limitations encountered in postmortem brain research   such as variabilities in autolysis time and tissue integrities   are also likely to impact any studies of higher order chromatin structures. However, the nucleosomal organization of genomic DNA   including DNA:core histone binding - appears to be largely preserved in representative samples provided by various brain banks. Therefore, it is possible to study the methylation pattern and other covalent modifications of the core histones at defined genomic loci in postmortem brain. Here, we present a simplified native chromatin immunoprecipitation (NChIP) protocol for frozen (never-fixed) human brain specimens. Starting with micrococcal nuclease digestion of brain homogenates, NChIP followed by qPCR can be completed within three days. The methodology presented here should be useful to elucidate epigenetic mechanisms of gene expression in normal and diseased human brain.

Until recently, expression studies on human brain were limited to quantification of RNA or protein. With the chromatin immunoprecipitation techniques described in this paper, it will be possible to map histone methylation and other epigenetic regulators of gene expression in postmortem brain.

Chronic neuropsychiatric illnesses such as schizophrenia, bipolar disease and autism are thought to result from a combination of genetic and environmental ...

The Microfluidic Probe: Operation and Use for Localized Surface Processing

Microfluidic devices allow assays to be performed using minute amounts of sample and have recently been used to control the microenvironment of cells. Microfluidics is commonly associated with closed microchannels which limit their use to samples that can be introduced, and cultured in the case of cells, within a confined volume. On the other hand, micropipetting system have been used to locally perfuse cells and surfaces, notably using push-pull setups where one pipette acts as source and the other one as sink, but the confinement of the flow is difficult in three dimensions. Furthermore, pipettes are fragile and difficult to position and hence are used in static configuration only. 
The microfluidic probe (MFP) circumvents the constraints imposed by the construction of closed microfluidic channels and instead of enclosing the sample into the microfluidic system, the microfluidic flow can be directly delivered onto the sample, and scanned across the sample, using the MFP. . The injection and aspiration openings are located within a few tens of micrometers of one another so that a microjet injected into the gap is confined by the hydrodynamic forces of the surrounding liquid and entirely aspirated back into the other opening. The microjet can be flushed across the substrate surface and provides a precise tool for localized deposition/delivery of reagents which can be used over large areas by scanning the probe across the surface. 
In this video we present the microfluidic probe1 (MFP). We explain in detail how to assemble the MFP, mount it atop an inverted microscope, and align it relative to the substrate surface, and finally show how to use it to process a substrate surface immersed in a buffer.

In this video we present the microfluidic probe1 (MFP). We explain in detail how to assemble the MFP, mount it atop an inverted microscope, and align it relative to the substrate surface, and finally show how to use it to process a substrate surface immersed in a buffer solution.

Microfluidic devices allow assays to be performed using minute amounts of sample and have recently been used to control the microenvironment of cells. ...

Preparation of Pooled Human Platelet Lysate (pHPL) as an Efficient Supplement for Animal Serum-Free Human Stem Cell Cultures

Platelet derived growth factors have been shown to stimulate cell proliferation efficiently in vivo1,2 and in vitro. This effect has been reported for mesenchymal stromal cells (MSCs), fibroblasts and endothelial colony-forming cells with platelets activated by thrombin3-5 or lysed by freeze/thaw cycles6-14 before the platelet releasate is added to the cell culture medium. The trophic effect of platelet derived growth factors has already been tested in several trials for tissue engineering and regenerative therapy.1,15-17 Varying efficiency is considered to be at least in part due to individually divergent concentrations of growth factors18,19 and a current lack of standardized protocols for platelet preparation.15,16 This protocol presents a practicable procedure to generate a pool of human platelet lysate (pHPL) derived from routinely produced platelet rich plasma (PRP) of forty to fifty single blood donations. By several freeze/thaw cycles the platelet membranes are damaged and growth factors are efficiently released into the plasma. Finally, the platelet fragments are removed by centrifugation to avoid extensive aggregate formation and deplete potential antigens. The implementation of pHPL into standard culture protocols represents a promising tool for further development of cell therapeutics propagated in an animal protein-free system.

Preparation of Pooled Human Platelet Lysate pHPL as an Efficient Supplement for Animal Serum-Free Human Stem Cell Cultures

Human platelet lysate is a rich source of growth factors and a potent supplement in cell culture. This protocol presents the process of preparing a large pool of human platelet lysate by starting from platelet rich plasma, performing several freeze-thaw cycles and depleting the platelet fragments.

Platelet derived growth factors have been shown to stimulate cell proliferation efficiently in vivo1,2 and in vitro. This effect has been reported for ...

A &#946;-glucuronidase (GUS) Based Cell Death Assay

We have developed a novel transient plant expression system that simultaneously expresses the reporter gene, &beta;-glucuronidase (GUS), with putative positive or negative regulators of cell death. In this system, N. benthamiana leaves are co-infiltrated with a 35S driven expression cassette containing the gene to be analyzed, and the GUS vector pCAMBIA 2301 using Agrobacterium strain LBA4404 as a vehicle. Because live cells are required for GUS expression to occur, loss of GUS activity is expected when this marker gene is co-expressed with positive regulators of cell death. Equally, increased GUS activity is observed when anti-apoptotic genes are used compared to the vector control. As shown below, we have successfully used this system in our lab to analyze both pro- and anti-death players. These include the plant anti-apoptotic Bcl-2 Associated athanoGene (BAG) family, as well as, known mammalian inducers of cell death, such as BAX. Additionally, we have used this system to analyze the death function of specific truncations within proteins, which could provide clues on the possible post-translational modification/activation of these proteins. Here, we present a rapid and sensitive plant based method, as an initial step in investigating the death function of specific genes.

A &#946;-glucuronidase GUS Based Cell Death Assay

Programmed cell death assays commonly used in mammalian systems such as DNA laddering or TUNEL assays, are often difficult to reproduce in plants. In combination with a GUS reporter system, we propose a rapid, plant based transient assay to analyze the potential death properties of specific genes.

We have developed a novel transient plant expression system that simultaneously expresses the reporter gene, &beta;-glucuronidase (GUS), with putative ...

Avidity-based Extracellular Interaction Screening (AVEXIS) for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ensuring cohesion within multicellular organisms. Proteins predicted to form extracellular interactions are encoded by approximately a quarter of human genes1, but despite their importance and abundance, the majority of these proteins have no documented binding partner. Primarily, this is due to their biochemical intractability: membrane-embedded proteins are difficult to solubilise in their native conformation and contain structurally-important posttranslational modifications. Also, the interaction affinities between receptor proteins are often characterised by extremely low interaction strengths (half-lives &lt; 1 second) precluding their detection with many commonly-used high throughput methods2. 
Here, we describe an assay, AVEXIS (AVidity-based EXtracellular Interaction Screen) that overcomes these technical challenges enabling the detection of very weak protein interactions (t1/2 &le; 0.1 sec) with a low false positive rate3. The assay is usually implemented in a high throughput format to enable the systematic screening of many thousands of interactions in a convenient microtitre plate format (Fig. 1). It relies on the production of soluble recombinant protein libraries that contain the ectodomain fragments of cell surface receptors or secreted proteins within which to screen for interactions; therefore, this approach is suitable for type I, type II, GPI-linked cell surface receptors and secreted proteins but not for multipass membrane proteins such as ion channels or transporters.
The recombinant protein libraries are produced using a convenient and high-level mammalian expression system4, to ensure that important posttranslational modifications such as glycosylation and disulphide bonds are added. Expressed recombinant proteins are secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (&beta;-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA (Fig. 1). The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, we have shown that interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates3.

Avidity-based Extracellular Interaction Screening AVEXIS for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

AVEXIS is a high throughput protein interaction assay developed to systematically screen for novel extracellular receptor-ligand pairs involved in cellular recognition processes. It is specifically designed to detect transient protein interactions that are difficult to identify using other high throughput approaches.

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ...

Glycopeptide Capture for Cell Surface Proteomics

Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, differentiation, and proliferation. A comprehensive characterization of these proteins provides rich information for biomarker discovery, cell-type identification, and drug-target selection, as well as helping to advance our understanding of cellular biology and physiology. Surface proteins, however, pose significant analytical challenges, because of their inherently low abundance, high hydrophobicity, and heavy post-translational modifications. Taking advantage of the prevalent glycosylation on surface proteins, we introduce here a high-throughput glycopeptide-capture approach that integrates the advantages of several existing N-glycoproteomics means. Our method can enrich the glycopeptides derived from surface proteins and remove their glycans for facile proteomics using LC-MS. The resolved N-glycoproteome comprises the information of protein identity and quantity as well as their sites of glycosylation. This method has been applied to a series of studies in areas including cancer, stem cells, and drug toxicity. The limitation of the method lies in the low abundance of surface membrane proteins, such that a relatively large quantity of samples is required for this analysis compared to studies centered on cytosolic proteins.

Cell surface proteins are biologically important and widely glycosylated. We introduce here a glycopeptide-capture approach to solubilize, enrich, and deglycosylate these proteins for facile LC-MS based proteomic analyses.

Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, ...

Visualizing Clathrin-mediated Endocytosis of G Protein-coupled Receptors at Single-event Resolution via TIRF Microscopy

Many important signaling receptors are internalized through the well-studied process of clathrin-mediated endocytosis (CME). Traditional cell biological assays, measuring global changes in endocytosis, have identified over 30 known components participating in CME, and biochemical studies have generated an interaction map of many of these components. It is becoming increasingly clear, however, that CME is a highly dynamic process whose regulation is complex and delicate. In this manuscript, we describe the use of Total Internal Reflection Fluorescence (TIRF) microscopy to directly visualize the dynamics of components of the clathrin-mediated endocytic machinery, in real time in living cells, at the level of individual events that mediate this process. This approach is essential to elucidate the subtle changes that can alter endocytosis without globally blocking it, as is seen with physiological regulation. We will focus on using this technique to analyze an area of emerging interest, the role of cargo composition in modulating the dynamics of distinct clathrin-coated pits (CCPs). This protocol is compatible with a variety of widely available fluorescence probes, and may be applied to visualizing the dynamics of many cargo molecules that are internalized from the cell surface.

Clathrin-mediated endocytosis, a rapid and highly dynamic process internalizes many proteins, including signaling receptors. The protocol described here directly visualizes the kinetics of individual endocytic events. This is essential for understanding how core members of the endocytic machinery coordinate with each other, and how protein cargo influence this process.

Many important signaling receptors are internalized through the well-studied process of clathrin-mediated endocytosis (CME). Traditional cell biological ...

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.

A protocol is provided to select structure-switching aptamers for small molecule targets based on a tunable stringency magnetic bead selection method. Aptamers selected with structure-switching properties are beneficial for assays that require a conformational change to signal the presence of a target, such as the described gold nanoparticle assay.

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health ...

The Assembly and Application of 'Shear Rings': A Novel Endothelial Model for Orbital, Unidirectional and Periodic Fluid Flow and Shear Stress

Deviations from normal levels and patterns of vascular fluid shear play important roles in vascular physiology and pathophysiology by inducing adaptive as well as pathological changes in endothelial phenotype and gene expression. In particular, maladaptive effects of periodic, unidirectional flow induced shear stress can trigger a variety of effects on several vascular cell types, particularly endothelial cells. While by now endothelial cells from diverse anatomic origins have been cultured, in-depth analyses of their responses to fluid shear have been hampered by the relative complexity of shear models (e.g., parallel plate flow chamber, cone and plate flow model). While these all represent excellent approaches, such models are technically complicated and suffer from drawbacks including relatively lengthy and complex setup time, low surface areas, requirements for pumps and pressurization often requiring sealants and gaskets, creating challenges to both maintenance of sterility and an inability to run multiple experiments. However, if higher throughput models of flow and shear were available, greater progress on vascular endothelial shear responses, particularly periodic shear research at the molecular level, might be more rapidly advanced. Here, we describe the construction and use of shear rings: a novel, simple-to-assemble, and inexpensive tissue culture model with a relatively large surface area that easily allows for a high number of experimental replicates in unidirectional, periodic shear stress studies on endothelial cells.

Different levels and patterns of fluid shear are known to modulate endothelial gene expression, phenotype and susceptibility to disease. We discuss the assembly and use of 'shear rings': a model that produces unidirectional, periodic shear stress patterns. Shear rings are simple to assemble, economical and can produce high cell yields.

Deviations from normal levels and patterns of vascular fluid shear play important roles in vascular physiology and pathophysiology by inducing adaptive as ...

Live-cell Imaging of Platelet Degranulation and Secretion Under Flow

Blood platelets are essential players in hemostasis, the formation of thrombi to seal vascular breaches. They are also involved in thrombosis, the formation of thrombi that occlude the vasculature and injure organs, with life-threatening consequences. This motivates scientific research on platelet function and the development of methods to track cell-biological processes as they occur under flow conditions.
A variety of flow models are available for the study of platelet adhesion and aggregation, two key phenomena in platelet biology. This work describes a method to study real-time platelet degranulation under flow during activation. The method makes use of a flow chamber coupled to a syringe-pump setup that is placed under a wide-field, inverted, LED-based fluorescence microscope. The setup described here allows for the simultaneous excitation of multiple fluorophores that are delivered by fluorescently labeled antibodies or fluorescent dyes. After live-cell imaging experiments, the cover glasses can be further processed and analyzed using static microscopy (i.e., confocal microscopy or scanning electron microscopy).

This work describes a fluorescence microscopy-based method for the study of platelet adhesion, spreading, and secretion under flow. This versatile platform enables the investigation of platelet function for mechanistic research on thrombosis and hemostasis.