The project was supported by NIH grant U01HL098180 from the National Heart, Lung, and Blood Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Heart, Lung, and Blood Institute or the National Institutes of Health.

1. Reagents Setup
1.1 Dissection and Imaging Medium
Leibovitz's L-15 medium (L15) is supplemented with FBS (10%) and Penicillin-Streptomycin (100 units/ml of penicillin G sodium and 100 &mu;g/ml of streptomycin sulfate) is used during both harvest and imaging of trachea samples.
2. Shallow Walled Culture Chamber Assembly
The chamber used to hold trachea tissue is shown in Figure 1. The floor of the chamber is the glass bottomed 35 mm culture dish. The top and side of the chamber is generated by placing a small piece of 0.3 mm thick silicone sheeting over the glass dish. The edge of the sheet is cut to fit the round bottom dish and the center is further trimmed to form a shallow central chamber (see steps 2.1-2.3). On top of this assembly, a 18 mm round glass cover slip is placed to generate an enclosed chamber suitable for imaging.
<ol>
	<li>Completely cover a 18 mm round glass cover slip with a square of 0.3 mm thick silicone sheeting.</li>
	<li>With standard sharp dissection scissors trim off the excess silicone sheeting from around the edge of the cover slip (resulting in a circular layer of silicone sheeting).</li>
	<li>With a sharp scalpel cut out and remove a central square of silicone sheeting (approximately 10 mm square) from the middle of the covered cover slip (thus forming the top and sides of the imaging chamber).</li>
</ol>
3. Trachea Harvest and Preparation
<ol>
	<li>Euthanize mice in accordance with local institutional animal care and use committee and/or governmental guidelines and remove trachea into a standard plastic 35 mm culture dish with enough L15 media to submerge tissue (authors have used mice just before birth at gestation day 16.5, through to newborn, neonatal, and adult animals 2).</li>
	<li>Remove non-trachea associated tissue attached to the outside of the trachea using blunt dissection.</li>
	<li>Remove the larynx with a transverse cut just below the cricoid cartilage using micro dissection scissors (Figure 2A, line 1).</li>
	<li>Remove the left and right primary bronchial branches with a transverse cut just above the carina using micro dissection scissors (Figure 2A, line 2).</li>
	<li>Gently hold the trachea with fine forceps and flush the lumen 2-3 times with ~1 ml of the bathing L15 medium with a P1000 Pipetman and P1000 tip to clear any mucus and blood.</li>
	<li>Cut out a 3-4 ring segment of trachea using a transverse cut with micro dissection scissors (Figure 2B, line 1).</li>
	<li>Cut longitudinally through the middle of the trachealis muscle of this short trachea segment using micro dissection scissors (Figure 2B, line 2).</li>
	<li>Cut longitudinally through the middle of the tracheal cartilage rings using micro dissection scissors (Figure 2C, line), leaving two sections of trachea tissue suitable for imaging (single section shown in Figure 2D).</li>
</ol>
4. Cilia Imaging
<ol>
	<li>Transfer trachea tissue segments, lumen side down, onto the middle of a 35 mm glass bottom culture dish with 100-200 &mu;l of L-15 medium.</li>
	<li>To quantify cilia generated flow add a small amount of fluorescent 0.20 &mu;m microspheres to the L-15 medium bathing the trachea tissue sample (~1 x 1011 particles/ml or 20 &mu;l/ml of the Fluoresbrite 2.5% aqueous microsphere suspension).</li>
	<li>Place the imaging chamber prepared previously (See Procedure 1-3 above) on top of the trachea sample silicone sheet side down, with the trachea sample located in the middle of the shallow walled chamber formed by the window cut into the silicone sheeting (Figure 1).</li>
	<li>Gently push down on the coverslip to secure in place and remove any excess L-15 media from the edges using a P1000 tip and P1000 Pipetman.</li>
	<li>Mount the 35 mm glass bottom culture dish and trachea sample on a inverted microscope with 100X objective and DIC optics.</li>
	<li>Using a high-speed camera and movie acquisition software collect movies of cilia motility at 200+ frames per second along the ciliated tracheal epithelia of the curled up edge of the trachealis muscle (Figure 2D Outlined box, E: example still image from recorded movie)(Supplementary Movie 1).</li>
	<li>Using FITC epifluorescent imaging and a low light CCD camera (See equipment list above), collect movies of fluorescent microsphere movement across the surface of the ciliated tracheal epithelia to allow later quantification of cilia generated flow (Supplementary Movie 2).</li>
</ol>
5. Quantitation of Cilia Motility
<ol>
	<li>Load DIC imaged movies into the ImageJ software package and following the technique described by Iain Drummond 13 use the line tool to draw a raster line crossing the beating cilia. A "reslice" of this line generates a kymograph type image where cilia movement across the line generates a wave pattern. The number of pixels between each wave peak is them measured (one pixel = one movie frame) from which the number of beats per minute (i.e. Hz) can then be calculated.</li>
	<li>To measure cilia generated flow load fluorescent bead movies into the ImageJ software package, and use the MTrackJ plugin 14 to manually track fluorescent beads across the surface of the trachea epithelia and let the software generate bead velocity and directionality for each bead tracked.</li>
</ol>
Care should be taken when using fluorescent beads to quantify flow as the distance from the beating cilia can strongly influence measured flow magnitude. The bead movement in Supplemental Movie 2 is a good example of this. In this example bead movement is fast at the surface of the beating cilia and significantly drops off for beads further away in the bathing media. To control for this, bead tracings should only be collected at a fixed distance above the ciliated epithelia in all samples to allow correct comparisons to be made. Finally, to obtain representative data on fluid flow, beads should be tracked for as long as possible; we prefer to use bead tracks that cover 10+ ciliated cells for calculating fluid flow.

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N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mouse+model+of+heterotaxy+with+single+ventricle+spectrum+of+cardiac+anomalies.">Mouse model of heterotaxy with single ventricle spectrum of cardiac anomalies.</a> Pediatric Research. 63, 9-14 (2008).</li><li>Tan, S. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heterotaxy+and+complex+structural+heart+defects+in+a+mutant+mouse+model+of+primary+ciliary+dyskinesia.">Heterotaxy and complex structural heart defects in a mutant mouse model of primary ciliary dyskinesia.</a> J. Clin. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Primary+ciliary+dyskinesia:+improving+the+diagnostic+approach.">Primary ciliary dyskinesia: improving the diagnostic approach.</a> Curr. Opin. Pediatr. 21, 320-325 (2009).</li><li>Delmotte, P., Sanderson, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ciliary+beat+frequency+is+maintained+at+a+maximal+rate+in+the+small+airways+of+mouse+lung+slices.">Ciliary beat frequency is maintained at a maximal rate in the small airways of mouse lung slices.</a> Am. J. Respir. Cell Mol. Biol. 35, 110-117 (2006).</li><li>Choe, M. M., Tomei, A. A., Swartz, M. 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Authors have nothing to disclose.

Measurement of cilia beat frequency (CBF) is relatively easy using high power microscope objectives and fast image acquisition hardware 13,15, and explains why CBF measurements form the basis of most studies investigating mucociliary clearance during health and disease. However, while CBF measurement is essential for understanding mucociliary clearance, measurement of CBF alone ignores the underlying importance of both ciliary generated flow and cilia beat waveform, both of which are more difficult to measure,...

Analysis of motile cilia function in the airway epithelia is experimentally important for elucidating the genetic and environmental factors that can affect mucociliary clearance and pulmonary health 1. The simple protocol developed for imaging the mouse airway epithelia provides an efficient method to interrogate airway cilia motility in mutant and knockout mouse models and require only basic skills in mouse tracheal tissue dissection and ex vivo imaging of airway cilia motility with high resolution videomicroscopy. This protocol was established and refined during a large-scale mouse mutagenesis screen to allow rapid evaluation of motile cilia function (cilia beat frequency, cilia beat shape, cilia generated flow) in mutants with congenital heart disease associated with heterotaxy 2-5.
Current techniques used to study airway cilia motility can be grouped into either the acute ex vivo type or longer term in vitro experimental approaches. Acute experiments include ex vivo visualization of human nasal/airway brush biopsies 6,7 and analysis of simple transverse airway sections 8. The in vitro approaches utilize various cell culture techniques to generate sheets of differentiated ciliated epithelia such as in air liquid interface cultures or airway suspension cultures9-11. However, these airway epithelia reciliation techniques require very significant investment in time and training before any useable ciliated epithelial cells are produced for experimentation (4-6 weeks 9,10). While acute ex vivo analysis of airway epithelial brush biopsies are commonly used for human clinical studies, this method is not usable in mouse studies due to exacerbated mechanical tissue injury 12.
 
The technique outlined in this protocol for analysis of mouse tracheal airway epithelia is not only simple to execute, but it requires no special dissection skills nor any specialized equipment besides those standard for imaging by videomicroscopy. There are many advantages to this simple protocol. First, as the mouse trachea tissue harvest is quick and easy to perform, it allows for rapid assessment of airway cilia function in a large number of mice. This can include acute analysis of the short term effects of different in vitro treatments. Second, being an ex vivo technique, the ciliated airway epithelium remains attached to it underlying supporting tissues and thus retain associated cell signaling pathways. Therefore in comparison to in vitro reciliated airway epithelia, this preparation is a better representation of the natural in vivo tissue environment. Third, this protocol allows the acquisition of a number of different quantitative parameters that can provide the objective assessment of motile cilia function. Finally, in contrast to other current methods for airway cilia visualization, this protocol allows for visualization of the cilia at right angles to the cilia beat direction, allowing profile view of the cilia that is optimal for high resolution imaging of cilia beat and metachronal wave generation.
This protocol can be modified in a number of ways to address a wide range of experimental needs such as the role of pharmacological agents, genetic factors, environmental exposures, and/or mechanical factors such as mucus load on airway cilia function and generation/maintenance of airway cilia beat and metachronal wave propagation.

<table border="1">
 <tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 <td>Comments (optional)</td>
 </tr>
 <tr>
 <td>Leibovitz's L-15 Medium </td>
 <td>Invitrogen </td>
 <td>21083-027 </td>
 <td>No phenol red </td>
 </tr>
 <tr>
 <td>Fetal bovine serum </td>
 <td>Hyclone </td>
 <td>SH30088.03 </td>
 <td></td>
 </tr>
 <tr>
 <td>Penicillin-Streptomycin </td>
 <td>Invitrogen </td>
 <td>15140-122 </td>
 <td></td>
 </tr>
 <tr>
 <td>2x fine forceps </td>
 <td>Roboz </td>
 <td>RS-4976 </td>
 <td></td>
 </tr>
 <tr>
 <td>Dissection scissors </td>
 <td>Roboz </td>
 <td>RS-5676 </td>
 <td></td>
 </tr>
 <tr>
 <td>Micro dissection scissors </td>
 <td>Roboz </td>
 <td>RS-5620 </td>
 <td></td>
 </tr>
 <tr>
 <td>Scalpel </td>
 <td>Roboz </td>
 <td>RS-9801-15 </td>
 <td></td>
 </tr>
 <tr>
 <td>P1000 pipetman </td>
 <td>Gilson, Inc </td>
 <td>F123602 </td>
 <td></td>
 </tr>
 <tr>
 <td>P1000 tips </td>
 <td>Molecular BioProducts </td>
 <td>2079E </td>
 <td></td>
 </tr>
 <tr>
 <td>18 mm round glass cover slips </td>
 <td>Fisher Scientific </td>
 <td>430588 </td>
 <td></td>
 </tr>
 <tr>
 <td>Plastic 35 mm culture dishes </td>
 <td>Corning </td>
 <td>430588 </td>
 <td></td>
 </tr>
 <tr>
 <td>Glass bottom 35 mm culture dishes </td>
 <td>Warner Instruments </td>
 <td>W3 64-0758 </td>
 <td></td>
 </tr>
 <tr>
 <td>Silicone sheet 0.012" (0.3 mm) thick </td>
 <td>AAA Acme Rubber Co </td>
 <td>CASS-.012X36-63908 </td>
 <td></td>
 </tr>
 <tr>
 <td>0.20 &mu;m diameter Fluoresbrite YG Carboxylate Microspheres </td>
 <td>Polysciences </td>
 <td>09834-10 </td>
 <td></td>
 </tr>
 <tr>
 <td>Inverted microscope, with 100x oil objective and DIC filters </td>
 <td>Lecia</td>
 <td>DMIRE2 </td>
 <td>Brand is not critical. </td>
 </tr>
 <tr>
 <td>100-watt mercury lamp, epifluorescent FITC excitation/emission filters</td>
 <td>Lecia </td>
 <td></td>
 <td>Brand is not critical.</td>
 </tr>
 <tr>
 <td>Microscope stage Incubator</td>
 <td>Lecia </td>
 <td>11521749 </td>
 <td>Not required if imaging cilia at room temperature</td>
 </tr>
 <tr>
 <td>High-speed camera bright field </td>
 <td>Vision Research </td>
 <td>Phantom v4.2 </td>
 <td>Brand is not critical. Must be faster than 125 fps</td>
 </tr>
 <tr>
 <td>High-speed fluorescent camera </td>
 <td>Hamamatsu </td>
 <td>C9100-12 </td>
 <td>Brand is not critical. Must be faster than 10 fps</td>
 </tr>
 <tr>
 <td>Movie analysis software</td>
 <td>National Institutes of Health</td>
 <td>ImageJ with MtrackJ plugin</td>
 <td></td>
 </tr>
 </tbody>
</table>

ex vivo method for high resolution imaging of cilia motility in rodent airway epithelia

An ex vivo technique for imaging mouse airway epithelia for quantitative analysis of motile cilia function important for insight into mucociliary clearance function has been established. Freshly harvested mouse trachea is cut longitudinally through the trachealis muscle and mounted in a shallow walled chamber on a glass-bottomed dish. The trachea sample is positioned along its long axis to take advantage of the trachealis muscle to curl longitudinally. This allows imaging of ciliary motion in the profile view along the entire tracheal length. Videos at 200 frames/sec are obtained using differential interference contrast microscopy and a high speed digital camera to allow quantitative analysis of cilia beat frequency and ciliary waveform. With the addition of fluorescent beads during imaging, cilia generated fluid flow also can be determined. The protocol time spans approximately 30 min, with 5 min for chamber preparation, 5-10 min for sample mounting, and 10-15 min for videomicroscopy.

Control airway cilia should be clearly visible and seen to beat in a coordinated manner (Supplemental Movie 1; movie playback is slowed to 15% real time), with noticeable flow in the direction of cilia beat (Supplemental Movie 2; movie playback is 100% real time). Quantitation of cilia movies should yield results similar to that seen in Figure 3. Collection of high-speed DIC movies makes possible the quantification of cilia beat frequency (Figure 3C) and...

Watch this Scientific Journal Video about Ex vivo Method for High Resolution Imaging of Cilia Motility in Rodent Airway Epithelia at JoVE.com

Ex vivo Method for High Resolution Imaging of Cilia Motility in Rodent Airway Epithelia

An easy and reliable technique for visualizing and quantifying airway cilia motility and cilia generated flow using mouse trachea is described. This technique can be modified to determine how a wide range of factors influence cilia motility, including pharmacological agents, genetic factors, environmental exposures, and/or mechanical factors such as mucus load.

Ex vivo Method for High Resolution Imaging of Cilia Motility in Rodent Airway Epithelia

An ex vivo technique for imaging mouse airway epithelia for quantitative  analysis of motile cilia function important for insight into mucociliary  ...

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20.7K 조회수.  University of Pittsburgh. 기도 섬모 운동과 섬모 생성 흐름을 마우스 기관을 사용하여 시각화 및 정량화를위한​​ 쉽고 안정적​​인 방법이 설명되어 있습니다. 이 기술은 요소의 넓은 범위 약리 대리인, 유전 적 요인, 환경 노출 및 / 또는 점액 부하와 같은 기계적 요인 등 섬모 운동성에 영향을 미치는 방법을 결정 수정할 수 있습니다.

비디오: Ex vivo Method for High Resolution Imaging of Cilia Motility in Rodent Airway Epithelia

Neuronal Cell Cultures from Aplysia for High-Resolution Imaging of Growth Cones

Neuronal growth cones are the highly motile structures at the tip of axons that can detect guidance cues in the environment and transduce this information into directional movement towards the appropriate target cell. To fully understand how guidance information is transmitted from the cell surface to the underlying dynamic cytoskeletal networks, one needs a model system suitable for live cell imaging of protein dynamics at high temporal and spatial resolution. Typical vertebrate growth cones are too small to quantitatively analyze F-actin and microtubule dynamics. Neurons from the sea hare Aplysia californica are 5-10 times larger than vertebrate neurons, can easily be kept at room temperature and are very robust cells for micromanipulation and biophysical measurements. Their growth cones have very defined cytoplasmic regions and a well-described cytoskeletal system. The neuronal cell bodies can be microinjected with a variety of probes for studying growth cone motility and guidance. In the present protocol we demonstrate a procedure for dissection of the abdominal ganglion, culture of bag cell neurons and setting up an imaging chamber for live cell imaging of growth cones.

Aplysia californica neurons develop large growth cones in culture that are excellent for high-resolution imaging of growth cone motility and guidance. Here, we present a protocol for dissection and plating of Aplysia bag cell neurons as well as for setting up a chamber for live cell imaging.

Neuronal growth cones are the highly motile structures at the tip of axons that can detect guidance cues in the environment and transduce this information ...

Method for Culture of Early Chick Embryos ex vivo (New Culture)

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  the formation and patterning of brain, neural tube, somite and heart primordia. Applications of chick embryo culture include electroporation of DNA or RNA constructs in order to analyze gene function, grafts of growth factor coated beads such as FGFs and BMPs , as well as whole mount in situ hybridization and immunohistochemistry. This video demonstrates the different steps in chick embryo culture; First, the embryo is explanted in saline. Then, the embryo is centered on a glass ring. The membranes surrounding the embryo are lifted along the walls of the ring. The ring is then placed in a culture dish containing a pool of albumine. The culture dish is sealed and placed in a humid chamber, where the embryo is cultured for up to 24 hrs. Finally, the embryo is removed from the ring, fixed and processed for further applications. A troubleshooting guide is also presented.

Method for Culture of Early Chick Embryos ex vivo New Culture

This video demonstrates New culture, a method by which chick embryos are cultured outside the egg for up to 24 hr. This method enables one to study early development (primitive streak to 14 som.), a period corresponding to E7-9 in mouse. Applications of this technique include electroporation, in situ hybridization and immunohistochemistry.

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

High-Resolution Video Tracking of Locomotion in Adult Drosophila Melanogaster

Flies provide an important model for studying complex behavior due to the plethora of genetic tools available to researchers in this field. Studying locomotor behavior in Drosophila melanogaster relies on the ability to be able to quantify changes in motion during or in response to a given task. For this reason, a high-resolution video tracking system, such as the one we describe in this paper, is a valuable tool for measuring locomotion in real-time. Our protocol involves the use of an initial air pulse to break the flies momentum, followed by a thirty second filming period in a square chamber. A tracking program is then used to calculate the instantaneous speed of each fly within the chamber in 10 msec increments. Analysis software then compiles this data, and outputs a variety of parameters such as average speed, max speed, time spent in motion, acceleration, etc. This protocol will discuss proper feeding and management of flies for behavioral tasks, handling flies without anesthetization or immobilization, setting up a controlled environment, and running the assay from start to finish.

The study of complex locomotor behavior in Drosophila melanogaster is dependent upon the ability to quantify changes in a given fly's movement. This article demonstrates how to do this using a high-resolution tracking system.

Flies provide an important model for studying complex behavior due to the plethora of genetic tools available to researchers in this field.  Studying ...

In vivo Imaging of Intact Drosophila Larvae at Sub-cellular Resolution

Recent improvements in optical imaging, genetically encoded fluorophores and genetic tools allowing efficient establishment of desired transgenic animal lines have enabled biological processes to be studied in the context of a living, and in some instances even behaving, organism. In this protocol we will describe how to anesthetize intact Drosophila larvae, using the volatile anesthetic desflurane, to follow the development and plasticity of synaptic populations at sub-cellular resolution1-3. While other useful methods to anesthetize Drosophila melanogaster larvae have been previously described4,5,6,7,8, the protocol presented herein demonstrates significant improvements due to the following combined key features: (1) A very high degree of anesthetization; even the heart beat is arrested allowing for lateral resolution of up to 150 nm1, (2) a high survival rate of &gt; 90% per anesthetization cycle, permitting the recording of more than five time-points over a period of hours to days2 and (3) a high sensitivity enabling us in 2 instances to study the dynamics of proteins expressed at physiological levels. In detail, we were able to visualize the postsynaptic glutamate receptor subunit GluR-IIA expressed via the endogenous promoter1 in stable transgenic lines and the exon trap line FasII-GFP1. (4) In contrast to other methods4,7 the larvae can be imaged not only alive, but also intact (i.e. non-dissected) allowing observation to occur over a number of days1. The accompanying video details the function of individual parts of the in vivo imaging chamber2,3, the correct mounting of the larvae, the anesthetization procedure, how to re-identify specific positions within a larva and the safe removal of the larvae from the imaging chamber.

In vivo Imaging of Intact Drosophila Larvae at Sub-cellular Resolution

This protocol describes a reliable method for anesthetization and imaging of intact Drosophila melanogaster larvae. We have utilized the volatile anesthetic desflurane to allow for repetitive imaging at sub-cellular resolution and re-identification of structures for up to a few days1.

Recent improvements in optical imaging, genetically encoded fluorophores and genetic tools allowing efficient establishment of desired transgenic animal ...

A Novel Ex vivo Culture Method for the Embryonic Mouse Heart

Developmental studies in the mouse are hampered by the inaccessibility of the embryo during gestation. Thus, protocols to isolate and culture individual organs of interest are essential to provide a method of both visualizing changes in development and allowing novel treatment strategies. To promote the long-term culture of the embryonic heart at late stages of gestation, we developed a protocol in which the excised heart is cultured in a semi-solid, dilute Matrigel. This substrate provides enough support to maintain the three-dimensional structure but is flexible enough to allow continued contraction. In brief, hearts are excised from the embryo and placed in a mixture of cold Matrigel diluted 1:1 with growth medium. After the diluted Matrigel solidifies, growth medium is added to the culture dish. Hearts excised as late as embryonic day 16.5 were viable for four days post-dissection. Analysis of the coronary plexus shows that this method does not disrupt coronary vascular development. Thus, we present a novel method for long-term culture of embryonic hearts.

A Novel Ex vivo Culture Method for the Embryonic Mouse Heart

Developmental studies in the mouse are hampered by the inaccessibility of the embryo during gestation. To promote the long-term culture of the embryonic heart at late stages of gestation, we developed a protocol in which the excised heart is cultured in a semi-solid, dilute Matrigel.

Developmental studies in the mouse are hampered  by the inaccessibility of the embryo during gestation. Thus, protocols to  isolate and culture individual ...

Preparation, Imaging, and Quantification of Bacterial Surface Motility Assays

Bacterial surface motility, such as swarming, is commonly examined in the laboratory using plate assays that necessitate specific concentrations of agar and sometimes inclusion of specific nutrients in the growth medium. The preparation of such explicit media and surface growth conditions serves to provide the favorable conditions that allow not just bacterial growth but coordinated motility of bacteria over these surfaces within thin liquid films. Reproducibility of swarm plate and other surface motility plate assays can be a major challenge. Especially for more &#8220;temperate swarmers&#8221; that exhibit motility only within agar ranges of 0.4%-0.8% (wt/vol), minor changes in protocol or laboratory environment can greatly influence swarm assay results. &#8220;Wettability&#8221;, or water content at the liquid-solid-air interface of these plate assays, is often a key variable to be controlled. An additional challenge in assessing swarming is how to quantify observed differences between any two (or more) experiments. Here we detail a versatile two-phase protocol to prepare and image swarm assays. We include guidelines to circumvent the challenges commonly associated with swarm assay media preparation and quantification of data from these assays. We specifically demonstrate our method using bacteria that express fluorescent or bioluminescent genetic reporters like green fluorescent protein (GFP), luciferase (lux operon), or cellular stains to enable time-lapse optical imaging. We further demonstrate the ability of our method to track competing swarming species in the same experiment.

Swarming motility is influenced by physical and environmental factors. We describe a two-phase protocol and guidelines to circumvent the challenges commonly associated with swarm assay preparation and data collection. A macroscopic imaging technique is employed to obtain detailed information on swarm behavior that is not provided by current analysis techniques.

Bacterial surface motility, such as swarming, is commonly examined in the laboratory using plate assays that necessitate specific concentrations of agar ...

Spatiotemporal Mapping of Motility in Ex Vivo Preparations of the Intestines

Multiple approaches have been used to record and evaluate gastrointestinal motility including: recording changes in muscle tension, intraluminal pressure, and membrane potential. All of these approaches depend on measurement of activity at one or multiple locations along the gut simultaneously which are then interpreted to provide a sense of overall motility patterns. Recently, the development of video recording and spatiotemporal mapping (STmap) techniques have made it possible to observe and analyze complex patterns in ex vivo whole segments of colon and intestine. Once recorded and digitized, video records can be converted to STmaps in which the luminal diameter is converted to grayscale or color [called diameter maps (Dmaps)]. STmaps can provide data on motility direction (i.e., stationary, peristaltic, antiperistaltic), velocity, duration, frequency and strength of contractile motility patterns. Advantages of this approach include: analysis of interaction or simultaneous development of different motility patterns in different regions of the same segment, visualization of motility pattern changes over time, and analysis of how activity in one region influences activity in another region. Video recordings can be replayed with different timescales and analysis parameters so that separate STmaps and motility patterns can be analyzed in more detail. This protocol specifically details the effects of intraluminal fluid distension and intraluminal stimuli that affect motility generation. The use of luminal receptor agonists and antagonists provides mechanistic information on how specific patterns are initiated and how one pattern can be converted into another pattern. The technique is limited by the ability to only measure motility that causes changes in luminal diameter, without providing data on intraluminal pressure changes or muscle tension, and by the generation of artifacts based upon experimental setup; although, analysis methods can account for these issues. When compared to previous techniques the video recording and STmap approach provides a more comprehensive understanding of gastrointestinal motility.

Spatiotemporal Mapping of Motility in Ex Vivo Preparations of the Intestines

Recently available video recording and spatiotemporal mapping (STmap) techniques make it possible to visualize and quantify both propagating and mixing patterns of intestinal motility. The goal of this protocol is to explain the generation and analysis of STmaps using the GastroIntestinal Motility Monitoring (GIMM) system.

Multiple approaches have been used to record and evaluate gastrointestinal motility including: recording changes in muscle tension, intraluminal pressure, ...

A High Resolution Method to Monitor Phosphorylation-dependent Activation of IRF3

The IRF3 transcription factor is critical for the first line of defense against pathogens mainly through interferon &#946; and antiviral gene expression. A detailed analysis of IRF3 activation is essential to understand how pathogens induce or evade the innate antiviral response. Distinct activated forms of IRF3 can be distinguished based on their phosphorylation and monomer vs dimer status. In vivo discrimination between the different activated species of IRF3 can be achieved through the separation of IRF3 phosphorylated forms based on their mobility shifts on SDS-PAGE. Additionally, the levels of IRF3 monomer and dimer can be monitored using non-denaturing electrophoresis. Here, we detail a procedure to reach the highest resolution to gain the most information regarding IRF3 activation status. This is achieved through the combination of a high resolution SDS-PAGE and a native-PAGE coupled to immunoblots using multiple total and phosphospecific antibodies. This experimental strategy constitutes an affordable and sensitive approach to acquire all the necessary information for a complete analysis of the phosphorylation-mediated activation of IRF3.

Here we describe a procedure allowing a detailed analysis of the phosphorylation-dependent activation of the IRF3 transcription factor. This is achieved through the combination of a high resolution SDS-PAGE and a native-PAGE coupled to immunoblots using multiple phosphospecific antibodies.

The IRF3 transcription factor is critical for the first line of defense against pathogens mainly through interferon &#946; and antiviral gene expression. ...

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes within individual endothelial cells (ECs). These processes are critical for homeostatic maintenance such as wound healing, and are also crucial in promoting tumor growth and metastasis. EC morphology is defined by the organization of the cytoskeleton, a tightly regulated system of actin and microtubule (MT) dynamics that is known to control EC branching, polarity and directional migration, essential components of angiogenesis. To study MT dynamics, we used high-resolution fluorescence microscopy coupled with computational image analysis of fluorescently-labeled MT plus-ends to investigate MT growth dynamics and the regulation of EC branching morphology and directional migration. Time-lapse imaging of living Human Umbilical Vein Endothelial Cells (HUVECs) was performed following transfection with fluorescently-labeled MT End Binding protein 3 (EB3) and Mitotic Centromere Associated Kinesin (MCAK)-specific cDNA constructs to evaluate effects on MT dynamics. PlusTipTracker software was used to track EB3-labeled MT plus ends in order to measure MT growth speeds and MT growth lifetimes in time-lapse images. This methodology allows for the study of MT dynamics and the identification of how localized regulation of MT dynamics within sub-cellular regions contributes to the angiogenic processes of EC branching and migration.

Protocols for Human Umbilical Vein Endothelial Cell (HUVEC) culture, transient transfection of fluorescently-labeled markers of microtubule growth, live-cell imaging and automated analysis of interphase microtubule growth dynamics are detailed.

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes ...

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

Dynamic microtubules are fundamental to many cellular processes, and accurate measurements of microtubule dynamics can provide insight into how cells regulate these processes and how genetic mutations impact regulation. The quantification of microtubule dynamics in metazoan models has a number of associated challenges, including a high microtubule density and limitations on genetic manipulations. In contrast, the budding yeast model offers advantages that overcome these challenges. This protocol describes a method to measure the dynamics of single microtubules in living yeast cells. Cells expressing fluorescently tagged tubulin are adhered to assembled slide chambers, allowing for stable time-lapse image acquisition. A detailed guide for high-speed, four-dimensional image acquisition is also provided, as well as a protocol for quantifying the properties of dynamic microtubules in confocal image stacks. This method, combined with conventional yeast genetics, provides an approach that is uniquely suited for quantitatively assessing the effects of microtubule regulators or mutations that alter the activity of tubulin subunits.

Budding yeast is an advantageous model for studying microtubule dynamics in vivo due to its powerful genetics and the simplicity of its microtubule cytoskeleton. The following protocol describes how to transform and culture yeast cells, acquire confocal microscopy images, and quantitatively analyze microtubule dynamics in living yeast cells.

Dynamic microtubules are fundamental to many cellular processes, and accurate measurements of microtubule dynamics can provide insight into how cells ...