Name: dosimetry for cell irradiation using orthovoltage (40-300 kv) x-ray facilities
Uploaded: 2021-02-20T14:00:00
Description: Watch this Scientific Journal Video about Dosimetry for Cell Irradiation using Orthovoltage 40-300 kV X-Ray Facilities at JoVE.com

1. Irradiation platform and determination of irradiation parameters
<ol>
	<li>Use an irradiation platform delivering low to medium energy X-rays. Determine the parameters of the experiment to ensure the robustness and the reproducibility of the radiobiological experiment: High voltage, Intensity, Filtration (inherent and additional), Half Value Layer (HVL), Effective energy, Detector used for dosimetry measurements, Source Sample Distance (SSD), Irradiation field (shape, size, geometry), Dosimetry quantity, Dosimetry m...

<ol>
	<li>Zoetelief, J., Broerse, J. J., Davies, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protocol+for+X-ray+dosimetry+EULEP.+Report+No.+Report+EUR+9507.">Protocol for X-ray dosimetry EULEP. Report No. Report EUR 9507.</a> Commission of the European Communities. , (1985).</li><li>Zoetelief, J., 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=Protocol+for+X-ray+dosimetry+in+radiobiology.">Protocol for X-ray dosimetry in radiobiology.</a> International Journal of Radiation Biology. 77 (7), 817-835 (2001).</li><li>Zoetelief, J., Jansen, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calculated+energy+response+correction+factors+for+LiF+thermoluminescent+dosemeters+employed+in+the+seventh+EULEP+dosimetry+intercomparison.">Calculated energy response correction factors for LiF thermoluminescent dosemeters employed in the seventh EULEP dosimetry intercomparison.</a> Physics in Medicine and Biology. 42 (8), 1491-1504 (1997).</li><li>Coleman, C. 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=Education+and+training+for+radiation+scientists:+radiation+research+program+and+American+Society+of+Therapeutic+Radiology+and+Oncology+Workshop,+Bethesda,+Maryland.">Education and training for radiation scientists: radiation research program and American Society of Therapeutic Radiology and Oncology Workshop, Bethesda, Maryland.</a> Radiation Research. 160 (6), 729-737 (2003).</li><li>Desrosiers, M., 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=The+importance+of+dosimetry+standardization+in+radiobiology.">The importance of dosimetry standardization in radiobiology.</a> Journal of Research of National Institute of Standards and Technology. 118, 403-418 (2013).</li><li>DIN. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Klinische+Dosimetrie:+Teil+4.">Klinische Dosimetrie: Teil 4.</a> Anwendung von R&#246;ntgenstrahlen mit R&#246;hrenspannungen von 10 bis 100 kV in der Strahlentherapie und in der Weichteildianostik. , (1988).</li><li>DIN. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Klinische+Dosimetrie:+Teil+5.">Klinische Dosimetrie: Teil 5.</a> Anwendung von R&#246;ntgenstrahlen mit R&#246;hrenspannungen von 100 bis 400 kV in der Strahlentherapie. , (1996).</li><li>NCS. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dosimetry+of+low+and+medium+energy+x-rays:+A+code+of+practice+for+use+in+radiotherapy+and+radiobiology.">Dosimetry of low and medium energy x-rays: A code of practice for use in radiotherapy and radiobiology.</a> NCS. , (1997).</li><li>International Atomic Energy Agency. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Absorbed+Dose+Determination+in+External+Beam+Radiotherapy.">Absorbed Dose Determination in External Beam Radiotherapy.</a> International Atomic Energy Agency. , (2000).</li><li>Ma, C. M., 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=AAPM+protocol+for+40-300+kV+x-ray+beam+dosimetry+in+radiotherapy+and+radiobiology.">AAPM protocol for 40-300 kV x-ray beam dosimetry in radiotherapy and radiobiology.</a> Medical Physics. 28 (6), 868-893 (2001).</li><li>Peixoto, J. G., Andreo, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+absorbed+dose+to+water+in+reference+conditions+for+radiotherapy+kilovoltage+x-rays+between+10+and+300+kV:+a+comparison+of+the+data+in+the+IAEA,+IPEMB,+DIN+and+NCS+dosimetry+protocols.">Determination of absorbed dose to water in reference conditions for radiotherapy kilovoltage x-rays between 10 and 300 kV: a comparison of the data in the IAEA, IPEMB, DIN and NCS dosimetry protocols.</a> Physics in Medicine and Biology. 45 (3), 563-575 (2000).</li><li>Pedersen, K. H., Kunugi, K. A., Hammer, C. G., Culberson, W. S., DeWerd, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Radiation+biology+irradiator+dose+verification+survey.">Radiation biology irradiator dose verification survey.</a> Radiation Research. 185 (2), 163-168 (2016).</li><li>Draeger, E., 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=A+dose+of+reality:+how+20+years+of+incomplete+physics+and+dosimetry+reporting+in+radiobiology+studies+may+have+contributed+to+the+reproducibility+crisis.">A dose of reality: how 20 years of incomplete physics and dosimetry reporting in radiobiology studies may have contributed to the reproducibility crisis.</a> International Journal of Radiation Oncology, Biology, Physics. 106 (2), 243-252 (2020).</li><li>Devic, S., 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=Precise+radiochromic+film+dosimetry+using+a+flat-bed+document+scanner.">Precise radiochromic film dosimetry using a flat-bed document scanner.</a> Medical Physics. 32 (7), 2245-2253 (2005).</li><li>Micke, A., Lewis, D. F., Yu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multichannel+film+dosimetry+with+nonuniformity+correction.">Multichannel film dosimetry with nonuniformity correction.</a> Medical Physics. 38 (5), 2523-2534 (2011).</li><li>Poludniowski, G., Landry, G., DeBlois, F., Evans, P. M., Verhaegen, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SpekCalc:+a+program+to+calculate+photon+spectra+from+tungsten+anode+x-ray+tubes.">SpekCalc: a program to calculate photon spectra from tungsten anode x-ray tubes.</a> Physics in Medicine and Biology. 54 (19), 433-438 (2009).</li><li>Hubbell, J. H., Seltzer, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=X-Ray+mass+attenuation+coefficients+-+Tables+of+X-ray+mass+attenuation+coefficients+and+mass+energy-absorption+coefficients+1+keV+to+20+MeV+for+elements+Z+=+1+to+92+and+48+additional+substances+of+dosimetric+interest+(version+1.4).">X-Ray mass attenuation coefficients - Tables of X-ray mass attenuation coefficients and mass energy-absorption coefficients 1 keV to 20 MeV for elements Z = 1 to 92 and 48 additional substances of dosimetric interest (version 1.4).</a> NIST Standard Reference Database. , 126 (1995).</li><li>Wong, J., 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=High-resolution,+small+animal+radiation+research+platform+with+x-ray+tomographic+guidance+capabilities.">High-resolution, small animal radiation research platform with x-ray tomographic guidance capabilities.</a> International Journal of Radiation Oncology, Biology, Physics. 71 (5), 1591-1599 (2008).</li><li>Trompier, F., 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=Investigation+of+the+influence+of+calibration+practices+on+cytogenetic+laboratory+performance+for+dose+estimation.">Investigation of the influence of calibration practices on cytogenetic laboratory performance for dose estimation.</a> International Journal of Radiation Biology. , 1-9 (2016).</li><li>Dos Santos, M., 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=Importance+of+dosimetry+protocol+for+cell+irradiation+on+a+low+X-rays+facility+and+consequences+for+the+biological+response.">Importance of dosimetry protocol for cell irradiation on a low X-rays facility and consequences for the biological response.</a> International Journal of Radiation Biology. , 1-29 (2018).</li><li>Noblet, C., 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=Underestimation+of+dose+delivery+in+preclinical+irradiation+due+to+scattering+conditions.">Underestimation of dose delivery in preclinical irradiation due to scattering conditions.</a> Physica Medica. 30 (1), 63-68 (2014).</li><li>Paixao, L., 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=Monte+Carlo+derivation+of+filtered+tungsten+anode+X-ray+spectra+for+dose+computation+in+digital+mammography.">Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography.</a> Radiologia Brasileira. 48 (6), 363-367 (2015).</li></ol>

This work presents the protocol used and implemented for cell irradiations using low energy X-ray facility. Nowadays, many radiobiology experiments are performed with this type of irradiator as they are easy to use, cost effective and with very few radioprotection constraints, compared to cobalt source for example. Although these setups have many advantages, as they use a low X-ray energy source, a modification of only one irradiation parameter can significantly impact the dosimetry. Several studies have already highligh...

The aim of radiobiology is to establish links between the delivered dose and the biological effects; dosimetry is a crucial aspect in the design of radiobiological experiments. For over 30 years, the importance of dosimetry standards and the harmonization of practices have been highlighted1,2,3,4,5. To establish a dose rate reference, several protocols exist6,7,8,9,10; however, as shown by Peixoto and Andreo11 , there can be differences of up to 7% depending on the dosimetric quantity used for the dose rate determination. Moreover, even if protocols exist, it is sometimes difficult to know which protocol is the most suitable for a particular application, if any, because the dose rate for the cells depends on parameters such as the cell container, quantity of cell culture media or beam quality, for example. The scattering and the backscattering for this type of irradiation is also a very important parameter to take into account. Indeed, for low and medium energy X-rays, in the AAPM TG-61 reference protocol10, the absorbed dose in water is measured at the surface of a water phantom. Taking into account the very specific cell irradiation conditions, the small volume of cell culture media surrounded by air is closer to kerma conditions than those defined for an absorbed dose with a large water equivalent phantom as in the TG-61 protocol. Therefore, we have chosen to use the kerma in water as a dosimetric quantity for reference rather than the absorbed dose in water. Thus, we are proposing a new approach to provide a better determination of the actual dose delivered to cells.
Moreover, another crucial aspect for radiobiological studies is the complete reporting of the methods and protocols used for irradiation in order to be able to reproduce, interpret and compare experimental results. In 2016, Pedersen et al.12 highlighted the inadequate reporting of dosimetry in preclinical radiobiological studies. A larger recent study from Draeger et al.13 highlighted that even though some dosimetry parameters such as the dose, energy, or source type are reported, a large part of the physics and dosimetry parameters that are essential to properly replicate the irradiation conditions are missing. This large scale review, of more than 1,000 publications covering the past 20 years, shows a significant lack of the reporting of the physics and dosimetry conditions in radiobiological studies. Thus, a complete description of the protocol and the method utilized in radiobiological studies is mandatory in order to have robust and reproducible experiments.
Taking into account these different aspects, for the radiobiological experiments carried out at IRSN (Institute of Radiation Protection and Nuclear Safety), a stringent protocol was implemented for cell irradiations in an orthovoltage facility. This dosimetry protocol was designed in order to simulate the real cell irradiation conditions as much as possible and thus, to determine the actual dose delivered to cells. To this end, all the irradiation parameters are listed, and the beam quality index was evaluated by measuring the half value layer (HVL) for which some adaptations have been made as the standard recommendations from the AAPM protocol10 cannot be followed. The absolute dose rate measurement was then performed with the ionization chamber inside the cell container used for cell irradiations, and the attenuation and the scattering of the cell culture media was also quantified with EBT3 radiochromic films. As the modification of only one single parameter of the protocol can significantly impact the dose estimation, a dedicated dosimetry is performed for each cell irradiation configuration. Moreover, the HVL value must be calculated for each voltage-filter combination. In this present work, a voltage of 220 kV, an intensity of 3 mA, and an inherent and an additional filtration of 0.8 mm and 0.15 mm of beryllium and copper, respectively, are used. The cell irradiation configuration chosen is on a T25 flask, where cells were irradiated with 5 mL of cell culture media.

<table>
	<tbody>
		<tr>
			<td>31010 ionization chamber</td>
			<td>PTW</td>
			<td>ionization Radiation, Detectors including code of practice, catalog 2019/2020, page 14</td>
			<td>https://www.ptwdosimetry.com/fileadmin/user_upload/DETECTORS_Cat_en_16522900_12/blaetterkatalog/index.html?startpage=1#page_14</td>
		</tr>
		<tr>
			<td>EBT3 radiochromic films</td>
			<td>Meditest</td>
			<td>quote request</td>
			<td>https://www.meditest.fr/produit/ebt3-8x10/</td>
		</tr>
		<tr>
			<td>electrometer UNIDOSEwebline</td>
			<td>PTW</td>
			<td>online catalog, quote request</td>
			<td>https://www.ptwdosimetry.com/en/products/unidos-webline/?type=3451&#38;downloadfile=1593&#38; cHash= 6096ddc2949f8bafe5d556e931e6c865</td>
		</tr>
		<tr>
			<td>HVL material (filter, diaphragm)</td>
			<td>PTW</td>
			<td>online catalog, page 70, quote request</td>
			<td>thickness foils: 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5 and 10 mm of copper, https://www.ptwdosimetry.com/fileadmin/user_upload/Online_Catalog/Radiation_Medicine_Cat_en_ 58721100_11/blaetterkatalog/index.html#page_70</td>
		</tr>
		<tr>
			<td>scanner for radiochromic films</td>
			<td>Epson</td>
			<td>quote request</td>
			<td>Epson V700, seiko Epson corporation, Suwa, Japan</td>
		</tr>
		<tr>
			<td>temperature and pressure measurements, Lufft OPUS20</td>
			<td>lufft</td>
			<td>quote request</td>
			<td>https://www.lufft.com/products/in-room-measurements-291/opus-20-thip-1983/</td>
		</tr>
	</tbody>
</table>

dosimetry for cell irradiation using orthovoltage (40-300 kv) x-ray facilities

The importance of dosimetry protocols and standards for radiobiological studies is self-evident. Several protocols have been proposed for dose determination using low energy X-ray facilities, but depending on the irradiation configurations, samples, materials or beam quality, it is sometimes difficult to know which protocol is the most appropriate to employ. We, therefore, propose a dosimetry protocol for cell irradiations using low energy X-ray facility. The aim of this method is to perform the dose estimation at the level of the cell monolayer to make it as close as possible to real cell irradiation conditions. The different steps of the protocol are as follows: determination of the irradiation parameters (high voltage, intensity, cell container etc.), determination of the beam quality index (high voltage-half value layer couple), dose rate measurement with ionization chamber calibrated in air kerma conditions, quantification of the attenuation and scattering of the cell culture medium with EBT3 radiochromic films, and determination of the dose rate at the cellular level. This methodology must be performed for each new cell irradiation configuration as the modification of only one parameter can strongly impact the real dose deposition at the level of the cell monolayer, particularly involving low energy X-rays.

In this work, we used a platform dedicated to small animal irradiation19; however, this platform can be used to irradiate other types of samples such as cells. The irradiation source is a Varian X-ray tube (NDI-225-22) having an inherent filtration of 0.8 mm of beryllium, a large focal sport size of 3 mm, a high voltage range of about 30 to 225 kV and a maximal intensity of 30 mA.
The parameters used for this study are reported in Table 1. We have chose...

Watch this Scientific Journal Video about Dosimetry for Cell Irradiation using Orthovoltage 40-300 kV X-Ray Facilities at JoVE.com

Dosimetry for Cell Irradiation using Orthovoltage 40-300 kV X-Ray Facilities

This document describes a new dosimetry protocol for cell irradiations using low energy X-ray equipment. Measurements are performed in conditions simulating real cell irradiation conditions as much as possible.

Dosimetry for Cell Irradiation using Orthovoltage (40-300 kV) X-Ray Facilities

The importance of dosimetry protocols and standards for radiobiological studies is self-evident. Several protocols have been proposed for dose ...

This protocol was developed to allow dosimetry measurements to be performed as close as possible to real cell irradiation conditions for radiobiological studies. With this protocol, we can determine the exact dose received by cells making it applicable to many x-ray facilities and can take into account all of the parameters and translate to dosimetry. All irradiation parameters must be set upstream to allow an optimal acquisition of the dosimetry measurement requiring a close collaboration between physicists and radiobiologist.To perform an irradiation field evaluation, place a self-developing dosimetry film onto the support used for irradiation and irradiate the film with at least two grays to obtain a well-marked irradiation field. Scan the self-developing dosimetry film using a dedicated scanner and use analyze and plot profile to plot the dose profile in ImageJ. Then, mark the irradiation support surface to ensure that the cell container will be placed in the correct position.To perform a dose rate measurement, place a modified cell container into the irradiation support enclosure and place the ionization chamber into the container in the correct position according to the marks made on the support surface. Confirm that all of the irradiation parameters have been appropriately set and pre-irradiate the ionization chamber for five minutes. Zero the electrometer and obtain 10 one-minute measurements.Then, use the formula to determine the average dose rate in air kerma. Number all of the films for their downstream identification. At least 24 hours before the irradiation, cut pieces of self-developing dosimetry film according to the size of the cell container.To construct a calibration curve, set aside three pieces of film for the non-irradiated controls and place the first film inside the cell container. Then, irradiate the film to obtain the first dose point. When all of the films have been irradiated in triplicate at the appropriate selected doses, a calibration curve can be generated.To measure the cell culture medium attenuation and scattering, select the same irradiation time for all of the irradiations and irradiate three pieces of self-developing dosimetry films in the container without water. Next, place a single piece of film into the container and fill the container with the same volume of water as the volume of medium that will be irradiated. Using small pieces of tape as necessary, position the container within the enclosure.When the irradiation is complete, dry the films with absorbent paper and store the films protected from light. 24 hours after their irradiation, on the scanner, set the TIFF format to 48-bit red green blue and the transmission mode to 150 dots per inch and select no image correction. To warm up the scanner, place a non-irradiated film on the scanner and launch a preview of the scan.At the end of the preview, start a timer and wait 30 seconds before starting the scan. At the end of the scan, start a 90-second timer. At the same time, register the scan and open the image in ImageJ.Trace a square region of interest within the scan and measure the average red pixel level of the area. At the end of the 90 seconds, repeat the scan preview at least 30 times to warm up and stabilize the scanner. Once the scanner has been stabilized, place a film into the center of the scanner bed and launch a preview of the scan.Wait 30 seconds before starting the scan. At the end of the scan, wait 90 seconds before starting the next scan. Measurements to estimate the attenuator thickness were then performed and the different attenuator thicknesses were tested to find the thickness that decreased the beam intensity by a factor of two.When this thickness was determined, five measurements were taken to evaluate the average mRAW value corrected by the temperature and pressure correction factor. For this configuration, a half-value layer of 0.667 millimeter of copper was found. In this representative analysis, a self-developing dosimetry film was irradiated to determine the surface on which the irradiation field is homogeneous, allowing correct placement of the cell container.To determine the exact dose for the cells, the measured air kerma dose rate was converted to water karma using the ratio of the mean mass energy absorption coefficient for water to air evaluated over the photon fluence spectrum, which for this analysis was determined to be 0.659 grays per minute. In this cell culture medium attenuation and scattering analysis, the self-developing dosimetry radiochromic films were first calibrated between zero and three grays with 0.25 gray steps between zero and one gray and 0.5 gray steps between one and three grays. The dose points were then fitted with a fourth-degree polynomial curve.Here, a representative table used for the daily measurement can be observed. Make sure that all of the configuration parameters are respected, that the does rate is measured inside the right cell container, and that the influence of cell culture medium is evaluated. Several protocols exist to establish a dose reference measurement.The key point is to select the appropriate protocol for a specific application, especially when using low x-ray facilities.

dosimetry-for-cell-irradiation-using-orthovoltage-40-300-kv-x-ray

Research

JoVE Journal

Biology

Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard cuticle which makes it difficult to use protocols of classical histology. In addition, histological sectioning destroys the sample and can therefore not be used for unique material. Hence, a non-destructive method is desirable which allows to view inside small samples without the need of sectioning.
We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows us to reconstruct the internal organization in its natural state without the artefacts produced by histological sectioning. These date can be used for quantitative morphology, landmarks, or for the visualization of animated movies to understand the structure of hidden body parts and to follow complete organ systems or tissues through the samples.

We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows the reconstruction of internal structures in their natural state without the artefacts produced by histological sectioning.

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard ...

Protein Crystallization for X-ray Crystallography

Using the three-dimensional structure of biological macromolecules to infer how they function is one of the most important fields of modern biology. The availability of atomic resolution structures provides a deep and unique understanding of protein function, and helps to unravel the inner workings of the living cell. To date, 86% of the Protein Data Bank (rcsb-PDB) entries are macromolecular structures that were determined using X-ray crystallography.
To obtain crystals suitable for crystallographic studies, the macromolecule (e.g. protein, nucleic acid, protein-protein complex or protein-nucleic acid complex) must be purified to homogeneity, or as close as possible to homogeneity. The homogeneity of the preparation is a key factor in obtaining crystals that diffract to high resolution (Bergfors, 1999; McPherson, 1999).
Crystallization requires bringing the macromolecule to supersaturation. The sample should therefore be concentrated to the highest possible concentration without causing aggregation or precipitation of the macromolecule (usually 2-50 mg/ mL). Introducing the sample to precipitating agent can promote the nucleation of protein crystals in the solution, which can result in large three-dimensional crystals growing from the solution. There are two main techniques to obtain crystals: vapor diffusion and batch crystallization. In vapor diffusion, a drop containing a mixture of precipitant and protein solutions is sealed in a chamber with pure precipitant. Water vapor then diffuses out of the drop until the osmolarity of the drop and the precipitant are equal (Figure 1A). The dehydration of the drop causes a slow concentration of both protein and precipitant until equilibrium is achieved, ideally in the crystal nucleation zone of the phase diagram. The batch method relies on bringing the protein directly into the nucleation zone by mixing protein with the appropriate amount of precipitant (Figure 1B). This method is usually performed under a paraffin/mineral oil mixture to prevent the diffusion of water out of the drop.
Here we will demonstrate two kinds of experimental setup for vapor diffusion, hanging drop and sitting drop, in addition to batch crystallization under oil.

The 3-D structure of a molecule provides a unique understanding of how the molecule functions. The principal method for structure determination at near-atomic resolution is X-ray crystallography. Here, we demonstrate the current methods for obtaining three-dimensional crystals of any given macromolecule that are suitable for structure determination by X-ray crystallography.

Using the three-dimensional structure of biological macromolecules to infer how they function is one of the most important fields of modern biology. The ...

Planarian Immobilization, Partial Irradiation, and Tissue Transplantation

The planarian, a freshwater flatworm, has proven to be a powerful system for dissecting metazoan regeneration and stem cell biology1,2. Planarian regeneration of any missing or damaged tissues is made possible by adult stem cells termed neoblasts3. Although these stem cells have been definitively shown to be pluripotent and singularly capable of reconstituting an entire animal4, the heterogeneity within the stem cell population and the dynamics of their cellular behaviors remain largely unresolved. Due to the large number and wide distribution of stem cells throughout the planarian body plan, advanced methods for manipulating subpopulations of stem cells for molecular and functional study in vivo are needed.
Tissue transplantation and partial irradiation are two methods by which a subpopulation of planarian stem cells can be isolated for further study. Each technique has distinct advantages. Tissue transplantation allows for the introduction of stem cells, into a na&iuml;ve host, that are either inherently genetically distinct or have been previously treated pharmacologically. Alternatively, partial irradiation allows for the isolation of stem cells within a host, juxtaposed to tissue devoid of stem cells, without the introduction of a wound or any breech in tissue integrity. Using these two methods, one can investigate the cell autonomous and non-autonomous factors that control stem cell functions, such as proliferation, differentiation, and migration.
Both tissue transplantation5,6 and partial irradiation7 have been used historically in defining many of the questions about planarian regeneration that remain under study today. However, these techniques have remained underused due to the laborious and inconsistent nature of previous methods. The protocols presented here represent a large step forward in decreasing the time and effort necessary to reproducibly generate large numbers of grafted or partially irradiated animals with efficacies approaching 100 percent. We cover the culture of large animals, immobilization, preparation for partial irradiation, tissue transplantation, and the optimization of animal recovery. Furthermore, the work described here demonstrates the first application of the partial irradiation method for use with the most widely studied planarian, Schmidtea mediterranea. Additionally, efficient tissue grafting in planaria opens the door for the functional testing of subpopulations of na&iuml;ve or treated stem cells in repopulation assays, which has long been the gold-standard method of assaying adult stem cell potential in mammals8. Broad adoption of these techniques will no doubt lead to a better understanding of the cellular behaviors of adult stem cells during tissue homeostasis and regeneration.

An effective method for grafting tissue of defined and consistent size between planaria is described. Also included is a description of how the immobilization technique used for transplantation can be adapted, in conjunction with lead shields, for the partial irradiation of live animals.

The planarian, a freshwater flatworm, has proven to be a powerful system for dissecting metazoan regeneration and stem cell biology1,2. Planarian ...

Cell Tracking Using Photoconvertible Proteins During Zebrafish Development

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of genetically-encoded fluorescent proteins has proven a valuable strategy for elucidating dynamic morphogenetic processes as they occur in the intact organism. During the past decade, the development of photoactivatable and photoconvertible fluorescent proteins has opened the possibility to investigate the fate of discrete subpopulations of tagged proteins1. Unlike photoactivatable proteins, photoconvertible fluorescent proteins (PCFPs) are readily tracked and imaged in their native emission state prior to photoconversion, making it easier to identify and select regions by optical inspection. PCFPs, such as Kaede2, KikGR3, Dendra4 and EosFP5, can be shifted from green to red upon exposure to UV or blue light due to a His-Tyr-Gly tripeptide sequence which forms a green chromophore that can be photoconverted to a red one by a light-catalyzed &beta;-elimination and subsequent extension of a &pi;-conjugated system3. PCFPs and their monomeric variants are useful tools for tracking cells6-10 and studying protein dynamics11-14, respectively. During recent years, PCFPs have been expressed in different animal model, such as zebrafish6, chicken7,8 and mouse9,10 for cell fate tracking. Here we report a protocol for cell-specific photoconversion of PCFPs in the living zebrafish embryo and further tracking of photoconverted proteins at later developmental stages. This methodology allows studying, in a tissue-specific manner, cell biological events underlying morphogenesis in the zebrafish animal model.

Here, we present a method for the photoactivated switch of photoconvertible fluorescent proteins (PCFPs) in the living zebrafish embryo and further tracking of photoconverted protein at specific time points during development. This methodology allows monitoring of cell biological events underlying different developmental processes in a live vertebrate organism.

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of ...

Isolation and Kv Channel Recordings in Murine Atrial and Ventricular Cardiomyocytes

KCNE genes encode for a small family of Kv channel ancillary subunits that form heteromeric complexes with Kv channel alpha subunits to modify their functional properties. Mutations in KCNE genes have been found in patients with cardiac arrhythmias such as the long QT syndrome and/or atrial fibrillation. However, the precise molecular pathophysiology that leads to these diseases remains elusive. In previous studies the electrophysiological properties of the disease causing mutations in these genes have mostly been studied in heterologous expression systems and we cannot be sure if the reported effects can directly be translated into native cardiomyocytes. In our laboratory we therefore use a different approach. We directly study the effects of KCNE gene deletion in isolated cardiomyocytes from knockout mice by cellular electrophysiology - a unique technique that we describe in this issue of the Journal of Visualized Experiments. The hearts from genetically engineered KCNE mice are rapidly excised and mounted onto a Langendorff apparatus by aortic cannulation. Free Ca2+ in the myocardium is bound by EGTA, and dissociation of cardiac myocytes is then achieved by retrograde perfusion of the coronary arteries with a specialized low Ca2+ buffer containing collagenase. Atria, free right ventricular wall and the left ventricle can then be separated by microsurgical techniques. Calcium is then slowly added back to isolated cardiomyocytes in a multiple step comprising washing procedure. Atrial and ventricular cardiomyocytes of healthy appearance with no spontaneous contractions are then immediately subjected to electrophysiological analyses by patch clamp technique or other biochemical analyses within the first 6 hours following isolation.

Kv channel dysfunction is associated with cardiac arrhythmias. In order to study the molecular mechanisms that lead to such arrhythmias we utilize a systematic protocol for isolation of atrial and ventricular cardiomyocytes from Kv channel ancillary subunit knockout mice. Isolated cardiomyocytes can then immediately be used for cellular electrophysiological studies, biochemical or immunofluorescence (IF) assays.

KCNE genes encode for a small family of Kv channel ancillary subunits that form heteromeric complexes with Kv channel alpha subunits to modify their ...

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.1 However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.2 These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. 3, 4 The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages.

Using modern plastic extrusion and printing technologies, it is now possible to quickly and inexpensively produce physical models of X-ray CT data taken in a laboratory. The three -dimensional printing of tomographic data is a powerful visualization, research, and educational tool that may now be accessed by the preclinical imaging community.

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing.  Traditional, ...

Reconstitution of a Kv Channel into Lipid Membranes for Structural and Functional Studies

To study the lipid-protein interaction in a reductionistic fashion, it is necessary to incorporate the membrane proteins into membranes of well-defined lipid composition. We are studying the lipid-dependent gating effects in a prototype voltage-gated potassium (Kv) channel, and have worked out detailed procedures to reconstitute the channels into different membrane systems. Our reconstitution procedures take consideration of both detergent-induced fusion of vesicles and the fusion of protein/detergent micelles with the lipid/detergent mixed micelles as well as the importance of reaching an equilibrium distribution of lipids among the protein/detergent/lipid and the detergent/lipid mixed micelles. Our data suggested that the insertion of the channels in the lipid vesicles is relatively random in orientations, and the reconstitution efficiency is so high that no detectable protein aggregates were seen in fractionation experiments. We have utilized the reconstituted channels to determine the conformational states of the channels in different lipids, record electrical activities of a small number of channels incorporated in planar lipid bilayers, screen for conformation-specific ligands from a phage-displayed peptide library, and support the growth of 2D crystals of the channels in membranes. The reconstitution procedures described here may be adapted for studying other membrane proteins in lipid bilayers, especially for the investigation of the lipid effects on the eukaryotic voltage-gated ion channels.

Procedures for complete reconstitution of a prototype voltage-gated potassium channel into lipid membranes are described. The reconstituted channels are suitable for biochemical assays, electrical recordings, ligand screening and electron crystallographic studies. These methods may have general applications to the structural and functional studies of other membrane proteins.

To study the lipid-protein interaction in a reductionistic fashion, it is necessary to incorporate the membrane proteins into membranes of well-defined ...

Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

The norovirus capsid is composed of a single major structural protein, termed VP1. VP1 is subdivided into a shell (S) domain and a protruding (P) domain. The S domain forms a contiguous scaffold around the viral RNA, whereas the P domain forms viral spikes on the S domain and contains determinants for antigenicity and host-cell interactions. The P domain binds carbohydrate structures, i.e., histo-blood group antigens, which are thought to be important for norovirus infections. In this protocol, we describe a method for producing high quality norovirus P domains in high yields. These proteins can then be used for X-ray crystallography and ELISA in order to study antigenicity and host-cell interactions.
The P domain is firstly cloned into an expression vector and then expressed in bacteria. The protein is purified using three steps that involve immobilized metal-ion affinity chromatography and size exclusion chromatography. In principle, it is possible to clone, express, purify, and crystallize proteins in less than four weeks, which makes this protocol a rapid system for analyzing newly emerging norovirus strains.

Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

Here, we describe a method to express and purify high quality norovirus protruding (P) domains in E. coli for use in X-ray crystallography studies. This method can be applied to other calicivirus P domains, as well as non-structural proteins, i.e., viral protein genome-linked (VPg), protease, and RNA dependent RNA polymerase (RdRp).

The norovirus capsid is composed of a single major structural protein, termed VP1. VP1 is subdivided into a shell (S) domain and a protruding (P) domain. ...

A Rapid Automated Protocol for Muscle Fiber Population Analysis in Rat Muscle Cross Sections Using Myosin Heavy Chain Immunohistochemistry

Quantification of muscle fiber populations provides a deeper insight into the effects of disease, trauma, and various other influences on skeletal muscle composition. Various time-consuming methods have traditionally been used to study fiber populations in many fields of research. However, recently developed immunohistochemical methods based on myosin heavy chain protein expression provide a quick alternative to identify multiple fiber types in a single section. Here, we present a rapid, reliable and reproducible protocol for improved staining quality, allowing automatic acquisition of whole cross sections and automatic quantification of fiber populations with ImageJ. For this purpose, embedded skeletal muscles are cut in cross sections, stained using myosin heavy chains antibodies with secondary fluorescent antibodies and DAPI for cell nuclei staining. Whole cross sections are then scanned automatically using a slide scanner to obtain high-resolution composite pictures of the entire specimen. Fiber population analyses are subsequently performed to quantify slow, intermediate and fast fibers using an automated macro for ImageJ. We have previously shown that this method can identify fiber populations reliably to a degree of &#177;4%. In addition, this method reduces inter-user variability and time per analyses significantly using the open source platform ImageJ.

Here, we present a protocol for rapid muscle fiber analyses, which allows improved staining quality, and thereby automatic acquisition and quantification of fiber populations using the freely available software ImageJ.

Quantification of muscle fiber populations provides a deeper insight into the effects of disease, trauma, and various other influences on skeletal muscle ...

Micron-scale Phenotyping Techniques of Maize Vascular Bundles Based on X-ray Microcomputed Tomography

It is necessary to accurately quantify the anatomical structures of maize materials based on high-throughput image analysis techniques. Here, we provide a 'sample preparation protocol' for maize materials (i.e., stem, leaf, and root) suitable for ordinary microcomputed tomography (micro-CT) scanning. Based on high-resolution CT images of maize stem, leaf, and root, we describe two protocols for the phenotypic analysis of vascular bundles: (1) based on the CT image of maize stem and leaf, we developed a specific image analysis pipeline to automatically extract 31 and 33 phenotypic traits of vascular bundles; (2) based on the CT image series of maize root, we set up an image processing scheme for the three-dimensional (3-D) segmentation of metaxylem vessels, and extracted two-dimensional (2-D) and 3-D phenotypic traits, such as volume, surface area of metaxylem vessels, etc. Compared with traditional manual measurement of vascular bundles of maize materials, the proposed protocols significantly improve the efficiency and accuracy of micron-scale phenotypic quantification.

We provide a novel method to improve the X-ray absorption contrast of maize tissue suitable for ordinary microcomputed tomography scanning. Based on CT images, we introduce a set of image-processing workflows for different maize materials to effectively extract microscopic phenotypes of vascular bundles of maize.

It is necessary to accurately quantify the anatomical structures of maize materials based on high-throughput image analysis techniques. Here, we provide a ...