This work was supported by an APART grant of the Austrian Academy of Sciences (CTH), the Technology Agency of the Czech Republic project no. TA04010877 (CTH, VH and JGS), and the Czech Science Foundation (GACR) project no GA16-01246S (to JGS). We thank W. Tecumseh Fitch for his suggestion to use denture fixative cream, and Ing. P. Liska from the Czech Army Forest Service for his help in acquiring the excised deer larynges.

The animal specimens analyzed in this paper were treated in accordance with the standard ethical requirements of the Palacky University in Olomouc, Czech Republic. They stem from red deer living wildly in forests, which were hunted by the Czech Army Forest Service during a regular hunting season.
1. Preparation of the Hemi-larynx Specimen
Note: Only properly prepared specimens should be used, as indicated in4 . Quick freezing of the larynx25 immediately after excision and storage at -80 &#176;C minimizes the potential of tissue degradation and alteration of biomechanical properties, and allows performing the experiments at any convenient time.
<ol>
	<li>Defrosting the larynx
	<ol>
		<li>Insert the frozen larynx into two autoclave bags or any other plastic bags with waterproof sealing. Seal the bags and put them into a water bath heated to 30 &#176;C until the larynx is completely defrosted. The duration required ranges from a few hours to more than a day, depending on larynx size and freezing temperature.</li>
	</ol>
	</li>
	<li>Cleaning the larynx
	<ol>
		<li>After the larynx is defrosted, remove it from the bag and clean it thoroughly with saline solution (0.9% NaCl).</li>
		<li>Carefully remove superfluous tissue as applicable (i.e. external neck muscles, hyoid bone etc.) without damaging the main laryngeal structures, and shorten the trachea to a length adequate for mounting the larynx onto an air supply tube (usually ca. 4-5 cm).</li>
		<li>Check the laryngeal tissue for potential tissue anomalies, such as wounds, organic deformations, or cracks potentially occurring from the freezing process, which could make the larynx unsuitable for the experiment.</li>
	</ol>
	</li>
	<li>Exposure of the thyroid and cricoid cartilages
	<ol>
		<li>Remove parts of the external laryngeal muscle tissue around the thyroid and cricoid cartilage using a scalpel, thus exposing the cartilages in preparation for the mid-sagittal cut creating the hemi-larynx. This preparation stage is depicted in Figure 1A and 1B.</li>
	</ol>
	</li>
	<li>Mid-sagittal cut through the thyroid cartilage
	<ol>
		<li>Make an initial vertical cut through the anterior part of the thyroid cartilage.</li>
		<li>Carefully place the cut slightly more onto the side that is about to be removed, in order not to damage the vocal fold that needs to remain preserved. If possible, use a scalpel for cutting. If the cartilage is ossified, use a small saw.</li>
	</ol>
	</li>
	<li>Cutting the cricoid cartilage
	<ol>
		<li>Lead the cut vertically (inferiorly) from in between the arytenoid cartilages and then through the cricoid cartilage to an approximately horizontal level of the inferior thyroid notch.</li>
	</ol>
	</li>
	<li>Removal of one vocal fold, creating an L-shaped incision in the larynx
	<ol>
		<li>Make a horizontal cut starting from the inferior end of the previously made vertical cut in the cricoid cartilage, and lead the new cut towards the inferior thyroid notch. Anteriorly fold the side of the larynx that is going to be removed.</li>
		<li>Make a vertical cut through the soft tissue on the inner side of the thyroid cartilage - be careful while leading the cut in between the anterior attachment of the vocal folds to the thyroid cartilage, thus avoiding damage to the vocal fold.</li>
	</ol>
	</li>
	<li>Refinement of the cut through the thyroid cartilage
	<ol>
		<li>Use a scalpel, a saw, or a file, in order to apply a precisely straight cut in the thyroid cartilage, and get as close as possible to the anterior part of the previously inspected vocal fold.</li>
		<li>Remove also a small part of the posterior thyroid cartilage, in order to create space for inserting the prong for adducting the arytenoid cartilage and thus the vocal fold (see below). This preparation stage is depicted in Figure 1C and 1D. 
		Note: Depending on the research question, full exposition of the whole vocal fold may be needed to enable its visibility from above. In such a case, the structures above the (true) vocal fold (i.e., the ventricular or vestibular fold, as applicable given the anatomy of the specimen) should be removed. In some specimens the inner soft laryngeal tissue above the vocal folds might lose its connection with the thyroid cartilage and interferes with the vocal fold during vibration, potentially causing spurious (mostly irregular) oscillatory patterns. In such a case careful removal of that tissue is inevitable.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/55303/55303fig1.jpg" /> 
Figure 1: Hemi-larynx preparation and mounting. (A) and (B) Cleaned larynx specimen, medial and posterior view, before removal of left vocal fold; (C) and (D) Prepared hemi-larynx with L-shaped incision (left vocal fold removed), medial and posterior view. <a href="//cloudfront.jove.com/files/ftp_upload/55303/55303fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

2. Hemi-larynx Experiment
<ol>
	<li>Hemi-laryngeal setup
	<ol>
		<li>Use an air-supply tube which delivers warmed and humidified air into the larynx.</li>
		<li>Construct two perpendicularly arranged transparent plates as a substitution for removed laryngeal parts.</li>
		<li>Use prongs 4 for increasing the stability of the larynx and creating a proper pre-phonatory larynx configuration by adducting the remaining vocal fold to the vertical glass plate (see Figure 2A). 
		Note: Theoretically, the vocal folds might also be adducted by sutures and weights on a pulley-lever system 26 . However, such an approach has, to the best knowledge of these authors, not yet been attempted for a hemilarynx preparation.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/55303/55303fig2.jpg" />
Figure 2: Hemi-larynx setup. (A) Supporting structures: air supply tube, L-shaped glass plate arrangement, adduction prongs. (B) Mounted hemi-larynx preparation with adduction prongs. (C) and (D) Close-ups of hemi-larynx-preparation, viewed from the side and from the top, respectively. <a href="//cloudfront.jove.com/files/ftp_upload/55303/55303fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="2">
	<li>Mounting the hemi-larynx
	<ol>
		<li>Cover the air supply tube with denture fixative cream and mount the larynx using the remaining part of its trachea. The fixative cream works as an adhesive and closes potential gaps, thus creating an air-tight seal.</li>
		<li>Fasten the trachea with a plastic tightening strap or a hose clamp.&#160;</li>
		<li>Also cover the edges of the cut through the thyroid cartilage with the fixative cream, while avoiding spreading fixative cream on the vocal fold or the inner soft laryngeal tissues.</li>
		<li>Attach the transparent plates.</li>
	</ol>
	</li>
	<li>Stabilization of the thyroid cartilage, adduction of the vocal fold using prongs
	<ol>
		<li>Use the prongs to adduct the vocal fold to the plate and stabilize the thyroid cartilage.</li>
		<li>After the fixative cream has set, apply the airflow in order to establish vocal fold oscillation and check for possible leaks between the hemi-larynx and the glass plates.</li>
		<li>Seal eventually occurring gaps by adding more fixative cream.</li>
	</ol>
	</li>
</ol>

The authors have nothing to disclose.

The hemi-larynx preparation shares the advantages of the &#34;conventional&#34; (full) excised larynx setup: In such an experimental approach, physical and physiological boundary conditions and parameters (such as subglottal pressure or vocal fold elongation) can be controlled fairly well. The behavior of the hemilarynx is homologous to that of a full larynx with a perfect lateral symmetry, with the exception that magnitudes of some parameters (e.g., air flow rate, sound pressure) are reduced by approximately 50...

Voice is typically created by vibrating laryngeal tissue (mainly the vocal folds), which converts a steady airflow, supplied by the lungs, into a sequence of airflow pulses. The acoustic pressure waveform (i.e., the primary sound) emerging from this sequence of flow pulses acoustically excites the vocal tract which filters them, and the resulting sound is radiated from the mouth and (to a certain degree) from the nose1. The spectral composition of the generated sound is largely influenced by the quality of vocal fold vibration, governed by laryngeal biomechanics and interactions with the tracheal airflow2. Both in a clinical and a research context, documentation and assessment of vocal fold vibration is thus of foremost interest when studying voice production.
In humans, direct endoscopic investigation of the larynx during sound production in vivo is challenging, and it is virtually impossible in nonhuman mammals, given current technological means. Therefore, and in order to guarantee carefully controlled physical and/or physiological experimental boundary conditions, the use of excised larynges3,4 is in many cases an adequate substitution for investigation of in vivo voice production mechanisms.
Vocal fold vibration is a complex three-dimensional phenomenon5. While conventional investigation methods like laryngeal endoscopy (in vivo) or excised larynx preparations typically provide only a superior view of the vibrating vocal folds6, they do not allow for complete three-dimensional analysis of vocal fold motion. In particular, in the superior view the lower (caudal) margins of the vocal folds are invisible during a major portion of the vibratory cycle. This is due to the phase delay between the inferior (caudal) and the superior (cranial) edge of the vocal folds, a phenomenon which is typically seen during vocal fold oscillation5. As direct empirical evidence for backing up findings from mathematical and physical models is scarce, knowledge of the geometry and motion of the lower vocal fold edge7, and thus the geometry of the subglottal channel8,9,10 is crucial for better understanding the interaction between laryngeal airflow, vocal fold tissue, and the resulting forces and pressures11,12. Another aspect of vocal fold vibration that is hidden from the customary superior view is the vertical (caudo-cranial) depth of the contact between the two vocal folds. The vertical contact depth is related to the vertical thickness of the vocal folds, which is a potential indicator of the vocal register used in singing (&#34;chest&#34; vs. &#34;falsetto&#34; register)13,14.
In order to overcome the shortcomings of conventional (full) excised larynx preparations, a so-called hemi-larynx setup can be utilized, where one half of the larynx is removed, thus facilitating the assessment of the vibratory characteristics of the remaining vocal fold in three dimensions. Surprisingly, since the introduction of this setup in the 1960s15 and an initial validation of the concept in 199316, not many laboratories have performed experiments with this promising experimental approach17,18,19,20,21,22,23. An explanation for this might be found in the difficulties of creating a viable hemi-larynx preparation. While the conventional excised (full) larynx preparation is well documented4, no such in-depth instructions are as yet available for creating a hemi-larynx setup. It is therefore the purpose of this paper to provide a tutorial for establishing a reliably reproducible hemi-larynx setup, supplemented by experimental results from red deer specimens.
A hemi-larynx setup shares many features with a &#34;conventional&#34; excised larynx setup, such as measurement equipment, high-speed or other imaging technology to adequately document the vibrations of the laryngeal structures during sound generation, or proper supply of heated, humidified air. These general setup considerations are described in detail in both a book chapter4 and a technical report from the National Center of Voice and Speech24. Reiteration of these instructions would be beyond the scope of this manuscript. Here, only the specialized directives for generating a hemi-larynx setup are presented.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >Surgical blades</td>
			<td >Surgeon</td>
			<td >Jai Surgical Ltd., New Delhi, India</td>
			<td ></td>
		</tr>
		<tr >
			<td >Saw</td>
			<td >Hand saw (Lux, 150 mm length)</td>
			<td >Lux, Wermelskirchen, Germany</td>
			<td ></td>
		</tr>
		<tr >
			<td >Thermometer</td>
			<td >Testo 922</td>
			<td >Testo Ltd., Hampshire, UK</td>
			<td >K-type Probe, Operating temperature -20 to +50 &#176;C</td>
		</tr>
		<tr >
			<td >Autoclave bags</td>
			<td >Autoclave bags</td>
			<td >vwr.com, VWR International s.r.o., Stribrna Skalice, Czech republic</td>
			<td ></td>
		</tr>
		<tr >
			<td >Conductive glass plates</td>
			<td >Custom made</td>
			<td >UPOL - Joint laboratory of Optics 
			Trida 17. listopadu 50A, 772 07 Olomouc, the Czech Rep.</td>
			<td ></td>
		</tr>
		<tr >
			<td >Fixative cream</td>
			<td >Denture fixative cream</td>
			<td >Blend-a-dent Natural</td>
			<td ></td>
		</tr>
		<tr >
			<td >Prongs and fastening system</td>
			<td >Customized Kanya Al eloxed profiles</td>
			<td >Distributor: VISIMPEX a.s.. Seifertova 33, 750 02 Prerov, the Czech Rep.;</td>
			<td >&#160;Combination of Kanya RVS and PVS fastening systems (http://www.kanya.cz/) + custom made prongs</td>
		</tr>
		<tr >
			<td >Mounting tube</td>
			<td >Custom made</td>
			<td >UPOL - Joint laboratory of Optics, 
			Trida 17. listopadu 50A, 772 07 Olomouc, the Czech Rep.</td>
			<td ></td>
		</tr>
		<tr >
			<td >LED Light</td>
			<td >Verbatim 52204 LED Lamp</td>
			<td >Mitsubishi Chemical Holdings Corporation, Tokyo, Japan</td>
			<td ></td>
		</tr>
		<tr >
			<td >Camera</td>
			<td >Canon EOS1100D</td>
			<td >Canon Inc.</td>
			<td >18-55 mm lens</td>
		</tr>
		<tr >
			<td >Airpump</td>
			<td >Resun LP100</td>
			<td >Resun</td>
			<td ></td>
		</tr>
		<tr >
			<td >Strobe light</td>
			<td >ELMED Helio-Strob micro2</td>
			<td >ELMED Dr. Ing. Mense GmbH, Heiligenhaus, Germany</td>
			<td ></td>
		</tr>
		<tr >
			<td >Humidifier</td>
			<td >Custom made</td>
			<td >Voice Research Lab, Dept. Biophysics, Faculty of Sciences, Palacky University Olomouc, Czech republic</td>
			<td ></td>
		</tr>
		<tr >
			<td >Subglottic tract</td>
			<td >Custom made adjustable subglottic tract</td>
			<td >Voice Research Lab, Dept. Biophysics, Faculty of Sciences, Palacky University Olomouc, Czech republic</td>
			<td >Hampala, V., Svec, Jan, Schovanek, P., and Mandat, D. Uzitny vzor c. 25585: Model subglotickeho traktu. [Utility model no. 25585: Model of subglottal tract] (In Czech) Soukup, P. 2013-27834(CZ 25505 U1), 1-7. 24-6-2013. Praha, Urad prumysloveho vlastnictvi</td>
		</tr>
	</tbody>
</table>

hemi-laryngeal setup for studying vocal fold vibration in three dimensions

The voice of humans and most non-human mammals is generated in the larynx through self-sustaining oscillation of the vocal folds. Direct visual documentation of vocal fold vibration is challenging, particularly in non-human mammals. As an alternative, excised larynx experiments provide the opportunity to investigate vocal fold vibration under controlled physiological and physical conditions. However, the use of a full larynx merely provides a top view of the vocal folds, excluding crucial portions of the oscillating structures from observation during their interaction with aerodynamic forces. This limitation can be overcome by utilizing a hemi-larynx setup where one half of the larynx is mid-sagittally removed, providing both a superior and a lateral view of the remaining vocal fold during self-sustained oscillation.
Here, a step-by-step guide for the anatomical preparation of hemi-laryngeal structures and their mounting on the laboratory bench is given. Exemplary phonation of the hemi-larynx preparation is documented with high-speed video data captured by two synchronized cameras (superior and lateral views), showing three-dimensional vocal fold motion and corresponding time-varying contact area. The documentation of the hemi-larynx setup in this publication will facilitate application and reliable repeatability in experimental research, providing voice scientists with the potential to better understand the biomechanics of voice production.

Illustrations of the hemi-larynx preparation and its mounting on the air supply tube, as referenced in the previous section, are provided in Figure 1 and Figure 2, respectively.
Documentation of vocal fold vibration from two camera angles
Airflow-induced self-sustaining oscillation of the hemi...

Watch this Scientific Journal Video about Hemi-laryngeal Setup for Studying Vocal Fold Vibration in Three Dimensions at JoVE.com

Hemi-laryngeal Setup for Studying Vocal Fold Vibration in Three Dimensions

This paper introduces a protocol for the preparation of hemi-larynx specimens facilitating a multi-dimensional view of vocal fold vibration, in order to investigate various biophysical aspects of voice production in humans and non-human mammals.

The voice of humans and most non-human mammals is generated in the larynx through self-sustaining oscillation of the vocal folds. Direct visual ...

hemi-laryngeal-setup-for-studying-vocal-fold-vibration-three

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10.9K Views.  Palacky University Olomouc. This paper introduces a protocol for the preparation of hemi-larynx specimens facilitating a multi-dimensional view of vocal fold vibration, in order to investigate various biophysical aspects of voice production in humans and non-human mammals.

Video: Hemi-laryngeal Setup for Studying Vocal Fold Vibration in Three Dimensions

Chip-based Three-dimensional Cell Culture in Perfused Micro-bioreactors

We have developed a chip-based cell culture system for the three-dimensional cultivation of cells. The chip is typically manufactured from non-biodegradable polymers, e.g., polycarbonate or polymethyl methacrylate by micro injection molding, micro hot embossing or micro thermoforming. But, it can also be manufactured from bio-degradable polymers. Its overall dimensions are 0.7 1 x 20 x 20 x 0.7 1 mm (h x w x l). The main features of the chips used are either a grid of up to 1156 cubic micro-containers (cf-chip) each the size of 120-300 x 300 x 300 &mu; (h x w x l) or round recesses with diameters of 300 &mu; and a depth of 300 &mu; (r-chip). The scaffold can house 10 Mio. cells in a three-dimensional configuration. For an optimal nutrient and gas supply, the chip is inserted in a bioreactor housing. The bioreactor is part of a closed steril circulation loop that, in the simplest configuration, is additionaly comprised of a roller pump and a medium reservoir with a gas supply. The bioreactor can be run in perfusion, superfusion, or even a mixed operation mode. We have successfully cultivated cell lines as well as primary cells over periods of several weeks. For rat primary liver cells we could show a preservation of organotypic functions for more than 2 weeks. For hepatocellular carcinoma cell lines we could show the induction of liver specific genes not or only slightly expressed in standard monolayer culture. The system might also be useful as a stem cell cultivation system since first differentiation experiments with stem cell lines were promising.

We describe a chip-based platform for the three-dimensional cultivation of cells in micro-bioreactors. One chip can house up to 10 Mio. cells that can be cultivated under precisely defined conditions with regard to fluid flow, oxygen tension etc. in a sterile, closed circulation loop.

We have developed a chip-based cell culture system for the three-dimensional cultivation of cells. The chip is typically manufactured from ...

Microinjection Techniques for Studying Mitosis in the Drosophila melanogaster Syncytial Embryo

This protocol describes the use of the Drosophila melanogaster syncytial embryo for studying mitosis1. Drosophila has useful genetics with a sequenced genome, and it can be easily maintained and manipulated. Many mitotic mutants exist, and transgenic flies expressing functional fluorescently (e.g. GFP) - tagged mitotic proteins have been and are being generated. Targeted gene expression is possible using the GAL4/UAS system2. 

The Drosophila early embryo carries out multiple mitoses very rapidly (cell cycle duration, &asymp;10 min). It is well suited for imaging mitosis, because during cycles 10-13, nuclei divide rapidly and synchronously without intervening cytokinesis at the surface of the embryo in a single monolayer just underneath the cortex. These rapidly dividing nuclei probably use the same mitotic machinery as other cells, but they are optimized for speed; the checkpoint is generally believed to not be stringent, allowing the study of mitotic proteins whose absence would cause cell cycle arrest in cells with a strong checkpoint. Embryos expressing GFP labeled proteins or microinjected with fluorescently labeled proteins can be easily imaged to follow live dynamics (Fig. 1). In addition, embryos can be microinjected with function-blocking antibodies or inhibitors of specific proteins to study the effect of the loss or perturbation of their function3. These reagents can diffuse throughout the embryo, reaching many spindles to produce a gradient of concentration of inhibitor, which in turn results in a gradient of defects comparable to an allelic series of mutants. Ideally, if the target protein is fluorescently labeled, the gradient of inhibition can be directly visualized4. It is assumed that the strongest phenotype is comparable to the null phenotype, although it is hard to formally exclude the possibility that the antibodies may have dominant effects in rare instances, so rigorous controls and cautious interpretation must be applied. Further away from the injection site, protein function is only partially lost allowing other functions of the target protein to become evident.

Microinjection Techniques for Studying Mitosis in the Drosophila melanogaster Syncytial Embryo

This protocol describes the use of microinjection and high resolution imaging in the Drosophila melanogaster syncytial embryo to study mitosis.

This protocol describes the use of the Drosophila melanogaster syncytial embryo  for studying mitosis1.  Drosophila has useful genetics with a sequenced ...

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may also be used to study the structure-function relationship for other ion channels and neurotransmitter receptors1. BK channels are widely expressed in different tissues and have been implicated in many physiological functions, including regulation of smooth muscle contraction, frequency tuning of inner hair cells and regulation of neurotransmitter release2-6. BK channels are activated by membrane depolarization and by intracellular Ca2+ and Mg2+ 6-9. Therefore, the protocol is designed to control both the membrane voltage and the intracellular solution. In this protocol, messenger RNA of BK channels is injected into Xenopus laevis oocytes (stage V-VI) followed by 2-5 days of incubation at 18&deg;C10-13. Membrane patches that contain single or multiple BK channels are excised with the inside-out configuration using patch clamp techniques10-13. The intracellular side of the patch is perfused with desired solutions during recording so that the channel activation under different conditions can be examined. To summarize, the mRNA of BK channels is injected into Xenopus laevis oocytes to express channel proteins on the oocyte membrane; patch clamp techniques are used to record currents flowing through the channels under controlled voltage and intracellular solutions.

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

Ionic current of BK channels is recorded using patch clamp techniques. BK channels are expressed in Xenopus oocytes by injecting messenger RNA. The intracellular solution during patch clamp recordings is controlled by a perfusion system.

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may ...

FRET Imaging in Three-dimensional Hydrogels

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly employ two-dimensional (2D) culture, which does not mimic the three-dimensional (3D) cellular microenvironment. A method to perform quenched emission FRET imaging using conventional widefield epifluorescence microscopy of cells within a 3D hydrogel environment is presented. Here an analysis method for ratiometric FRET probes that yields linear ratios over the probe activation range is described. Measurement of intracellular cyclic adenosine monophosphate (cAMP) levels is demonstrated in chondrocytes under forskolin stimulation using a probe for EPAC1 activation (ICUE1) and the ability to detect differences in cAMP signaling dependent on hydrogel material type, herein a photocrosslinking hydrogel (PC-gel, polyethylene glycol dimethacrylate) and a thermoresponsive hydrogel (TR-gel). Compared with 2D FRET methods, this method requires little additional work. Laboratories already utilizing FRET imaging in 2D can easily adopt this method to perform cellular studies in a 3D microenvironment. It can further be applied to high throughput drug screening in engineered 3D microtissues. Additionally, it is compatible with other forms of FRET imaging, such as anisotropy measurement and fluorescence lifetime imaging (FLIM), and with advanced microscopy platforms using confocal, pulsed, or modulated illumination.

F&#246;rster resonance energy transfer (FRET) imaging is a powerful tool for real-time cell biology studies. Here a method for FRET imaging cells in physiologic three-dimensional (3D) hydrogel microenvironments using conventional epifluorescence microscopy is presented. An analysis for ratiometric FRET probes that yields linear ratios over the activation range is described.

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly ...

An In Vitro Model for Studying Cellular Transformation by Kaposi Sarcoma Herpesvirus

Kaposi sarcoma (KS) is an unusual tumor composed of proliferating spindle cells that is initiated by infection of endothelial cells (EC) with KSHV, and develops most often in the setting of immunosuppression. Despite decades of research, optimal treatment of KS remains poorly defined and clinical outcomes are especially unfavorable in resource-limited settings. KS lesions are driven by pathological angiogenesis, chronic inflammation, and oncogenesis, and various in vitro cell culture models have been developed to study these processes. KS arises from KSHV-infected cells of endothelial origin, so EC-lineage cells provide the most appropriate in vitro surrogates of the spindle cell precursor. However, because EC have a limited in vitro lifespan, and as the oncogenic mechanisms employed by KSHV are less efficient than those of other tumorigenic viruses, it has been difficult to assess the processes of transformation in primary or telomerase-immortalized EC. Therefore, a novel EC-based culture model was developed that readily supports transformation following infection with KSHV. Ectopic expression of the E6 and E7 genes of human papillomavirus type 16 allows for extended culture of age- and passage-matched mock- and KSHV-infected EC and supports the development of a truly transformed (i.e., tumorigenic) phenotype in infected cell cultures. This tractable and highly reproducible model of KS has facilitated the discovery of several essential signaling pathways with high potential for translation into clinical settings.

An In Vitro Model for Studying Cellular Transformation by Kaposi Sarcoma Herpesvirus

Kaposi sarcoma (KS) is a tumor induced by infection with the oncogenic virus human herpesvirus-8/KS herpesvirus (HHV-8/KSHV). The endothelial cell culture model described here is uniquely suited for studying the mechanisms by which KSHV transforms host cells.

Kaposi sarcoma (KS) is an unusual tumor composed of proliferating spindle cells that is initiated by infection of endothelial cells (EC) with KSHV, and ...

Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory

The use of genetic model organisms such as Caenorhabditis elegans has led to seminal discoveries in biology over the last five decades. Most of what we know about C. elegans is limited to laboratory cultivation of the nematodes that may not necessarily reflect the environments they normally inhabit in nature. Cultivation of C. elegans in a 3D habitat that is more similar to the 3D matrix that worms encounter in rotten fruits and vegetative compost in nature could reveal novel phenotypes and behaviors not observed in 2D. In addition, experiments in 3D can address how phenotypes we observe in 2D are relevant for the worm in nature. Here, a new method in which C. elegans grows and reproduces normally in three dimensions is presented. Cultivation of C. elegans in Nematode Growth Tube-3D (NGT-3D) can allow us to measure the reproductive fitness of C. elegans strains or different conditions in a 3D environment. We also present a novel method, termed Nematode Growth Bottle-3D (NGB-3D), to cultivate C. elegans in 3D for microscopic analysis. These methods allow scientists to study C. elegans biology in conditions that are more reflective of the environments they encounter in nature. These can help us to understand the overlying evolutionary relevance of the physiology and behavior of C. elegans we observe in the laboratory.

Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory

We present a simple method to construct 3D nematode cultivation systems called NGT-3D and NGB-3D. These can be used to study nematode fitness and behaviors in habitats that are more similar to natural Caenorhabditis elegans habitats than the standard 2D laboratory C. elegans culture plates.

The use of genetic model organisms such as Caenorhabditis elegans has led to seminal discoveries in biology over the last five decades. Most of what we ...

Quantitative Approaches for Studying Cellular Structures and Organelle Morphology in Caenorhabditis elegans

Defining the cellular mechanisms underlying disease is essential for the development of novel therapeutics. A strategy frequently used to unravel these mechanisms is to introduce mutations in candidate genes and qualitatively describe changes in the morphology of tissues and cellular organelles. However, qualitative descriptions may not capture subtle phenotypic differences, might misrepresent phenotypic variations across individuals in a population, and are frequently assessed subjectively. Here, quantitative approaches are described to study the morphology of tissues and organelles in the nematode Caenorhabditis elegans using laser scanning confocal microscopy combined with commercially available bio-image processing software. A quantitative analysis of phenotypes affecting synapse integrity (size and integrated fluorescence levels), muscle development (muscle cell size and myosin filament length), and mitochondrial morphology (circularity and size) was performed to understand the effects of genetic mutations on these cellular structures. These quantitative approaches are not limited to the applications described here, as they could readily be used to quantitatively assess the morphology of other tissues and organelles in the nematode, as well as in other model organisms.

Quantitative Approaches for Studying Cellular Structures and Organelle Morphology in Caenorhabditis elegans

This study outlines quantitative measurements of synaptic size and localization, muscle morphology, and mitochondrial shape in C. elegans using freely available image processing tools. This approach allows future studies in&#160;C. elegans&#160;to quantitatively compare the extent of tissue and organelle structural changes as a result of genetic mutations.

Defining the cellular mechanisms underlying disease is essential for the development of novel therapeutics. A strategy frequently used to unravel these ...

Quadruple-Checkerboard: A Modification of the Three-Dimensional Checkerboard for Studying Drug Combinations

The concept of drug-combination therapy is becoming very important mainly with the drastic increase in resistance to drugs. The Quadruple&#160;checkerboard, also called the Q-checkerboard, aims at maximizing the number of possible combinations that can be obtained between four drugs in one experiment to minimize the time and work needed to accomplish the same results with other protocols. This protocol is based on the simple micro dilution technique where the drugs are diluted and combined together in several 96-well plates.
In the first set of 96-well plates, Muller-Hinton broth is added followed by the first required drug (e.g., Cefotaxime here) to serially dilute it. After the first step is done, another set of 96-well plates is used to dilute the second drug (e.g., Amikaci), which will be transferred by removing a specific volume of drug 2 and put in the corresponding wells in the first set of 96-well plates that contains drug one. The third step is done by adding the required concentrations of the third drug (e.g., Levofloxacin), to the appropriate plates in the initial set containing combination of drug 1 and 2. The fourth step is done by adding the required concentrations of the fourth drug (e.g., Trimethoprim-sulfamethoxazol) into the appropriate plates in the first set. Then, E. coli ESBL bacterial inoculum will be prepared and added.
This method is important to evaluate all the possible combinations and has a wider range of possibilities to be tested furthermore for in vivo testing. Despite being a tiring technique requiring a lot of focus, the results are remarkable and time saving where a lot of combinations can be tested in a single experiment.

This protocol describes how to study all possible combinations that can be obtained between four drugs in one single experiment. This method is based on the standard 96-well plate micro dilution assay and the calculation of fractional inhibitory concentrations (FICs) to evaluate the results.

The concept of drug-combination therapy is becoming very important mainly with the drastic increase in resistance to drugs. The ...

Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often require indirect methods due to their small diameter (40-250 nm), which is beneath the diffraction limit of typical light microscopy. We have developed a super-resolution microscopy-based visualization of EVs to bypass the diffraction limit in both two and three dimensions. Using this approach, we can resolve the three-dimensional shape of EVs to within +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution along the Z-axis. In conclusion, we propose that super-resolution microscopy be considered as a characterization method of EVs, including exosomes, as well as enveloped viruses.

Direct stochastic optical reconstruction microscopy (dSTORM) is used to bypass the typical diffraction limit of light microscopy and to view exosomes at the nanometer scale. It can be employed in both two and three dimensions to characterize exosomes.

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often ...

Studying Habituation in Stentor coeruleus

Learning is usually associated with a complex nervous system, but there is increasing evidence that life at all levels, down to single cells, can display intelligent behaviors. In both natural and artificial systems, learning is the adaptive updating of system parameters based on new information, and intelligence is a measure of the computational process that facilitates learning. Stentor coeruleus is a unicellular pond-dwelling organism that exhibits habituation, a form of learning in which a behavioral response decreases following a repeated stimulus. Stentor contracts in response to mechanical stimulation, which is an apparent escape response from aquatic predators. However, repeated low-force perturbations induce habituation, demonstrated by a progressive reduction in contraction probability. Here, we introduce a method for quantifying Stentor habituation using a microcontroller board-linked apparatus that can deliver mechanical pulses at a specified force and frequency, including methods for building the apparatus and setting up the experiment in a way that minimizes external perturbations. In contrast to the previously described approaches for mechanically stimulating Stentor, this device allows the force of stimulation to be varied under computer control during the course of a single experiment, thus greatly increasing the variety of input sequences that can be applied. Understanding habituation at the level of a single cell will help characterize learning paradigms that are independent of complex circuitry.

Studying Habituation in Stentor coeruleus

We introduce a method for quantifying Stentor habituation using a microcontroller board-linked apparatus that can deliver mechanical pulses at a specified force and frequency. We also include methods for assembling the apparatus and setting up the experiment in a way that minimizes external perturbations.

Learning is usually associated with a complex nervous system, but there is increasing evidence that life at all levels, down to single cells, can display ...