Name: a rapid laser probing method facilitates the non-invasive and contact-free determination of leaf thermal properties
Uploaded: 2017-01-07T17:00:00
Description: Watch this Scientific Journal Video about A Rapid Laser Probing Method Facilitates the Non-invasive and Contact-free Determination of Leaf Thermal Properties at JoVE.com

The authors are grateful to Dr. Thomas Rademacher and Ibrahim Al Amedi for cultivating the plants used in this study. We would like to thank Dr. Richard M. Twyman for his assistance with editing the manuscript. This work was in part funded by the European Research Council Advanced Grant "Future-Pharma", proposal number 269110, the Fraunhofer Zukunftsstiftung (Future Foundation), the Fraunhofer-Gesellschaft Internal Programs under Grant No. Attract 125-600164.

1. Plant Cultivation and Sample Preparation
<ol>
	<li>Flush each mineral wool block with 1-2 L of deionized water and subsequently with 1 L of 0.1% [m/v] fertilizer solution. Place one tobacco (Nicotiana tabacum or N. benthamiana) seed in each block and gently flush with 0.25 L of fertilizer solution without washing away the seed.</li>
	<li>Cultivate the plants for 7 weeks in a greenhouse or phytotron with 70% relative humidity, a 16-h photoperiod (180 &#181;mol s&#8722;1 m&...

<ol>
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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=Effectiveness+of+cuticular+transpiration+barriers+in+a+desert+plant+at+controlling+water+loss+at+high+temperatures.">Effectiveness of cuticular transpiration barriers in a desert plant at controlling water loss at high temperatures.</a> AoB PLANTS. 8, (2016).</li><li>Parker, W. J., Jenkins, R. J., Abbott, G. L., Butler, C. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flash+Method+of+Determining+Thermal+Diffusivity,+Heat+Capacity,+and+Thermal+Conductivity.">Flash Method of Determining Thermal Diffusivity, Heat Capacity, and Thermal Conductivity.</a> J Appl Phys. 32, 1679-1684 (1961).</li><li>Hays, R. 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The contact-free, non-destructive measurement method described above can be used to determine cp,s and &#654; in a simultaneous and reproducible manner. The calculation of &#654; in particular depends on several parameters that are sensitive to errors. Nevertheless, the impact of these errors was either linear or sub-proportional, and the coefficient of variation for all parameters was found to be less than 10%. Even though the method can thus be regarded as robust, some technical improvements can be ...

The large-scale processing of biological materials often requires heat-treatment steps such as pasteurization. The equipment for such processes can be designed more precisely if the thermal properties of the biological materials are well characterized, including the specific heat capacity (cp,s) and thermal conductivity (&#955;). These parameters can be determined easily for liquids, suspensions and homogenates by calorimetry 1. However, measuring such parameters in solid samples can be labor intensive, and often requires direct contact with the sample or even its destruction 2. For example, photothermal techniques require direct contact between the sample and detector 3. Such limitations are acceptable during food processing, but are incompatible with highly regulated processes such as the production of biopharmaceutical proteins in plants in the context of good manufacturing practice 4. In such a context, repeated (e.g., weekly) monitoring of thermal properties may be required during a seven-week growth period for individual plants as a quality control tool. If such a monitoring would require and consume a leaf for each measurement, there would be no biomass left to process at the time of harvest.
Additionally, using only leaf parts instead would cause wounding to the plant and increase the risk of necrosis or pathogen infection, again diminishing the process yield. The likelihood of pathogen infection may also increase if a method with direct contact to the sample would be used, inducing the risk that an entire batch of plants can be infected through contact with a contaminated sensor device. Similar aspects have to be considered for the monitoring of plant stresses like drought, e.g., in an ecophysiological context. For example, water loss is often monitored by a change in the fresh biomass, which requires an invasive treatment of the plants under investigation 5, e.g., dissecting a leaf. Instead, determining the specific heat capacity, which depends on the water content of a sample, in a non-invasive manner as describe here, can be used as a surrogate parameter for the hydration status of plants. In both scenarios (pharmaceutical production and ecophysiology), artificial stresses induced by destructive or invasive measurement techniques would be deleterious as they can distort the experimental data. Therefore, previously reported flash methods 6 or the placement of samples between silver plates 7 are unsuitable for such processes and experiments because they either require direct contact to the sample or are destructive. The parameters cp,s and &#955; must be determined in order to design the process equipment for a blanching step that can simplify product purification and thus reduce manufacturing costs 8-10. Both cp,s and &#955; can now be rapidly determined by contact-free non-destructive near infrared (NIR) laser probing in a consistent and reproducible manner 11 and this new method will be explained in detail below. The results obtained with this method were successfully used to simulate heat transfer in tobacco leaves 12, allowing the design of appropriate processing equipment and the selection of corresponding parameters such as the blanching temperature.
The method is easy to set up (Figure 1) and has two phases, measurement and analysis, each of which comprises two major steps. In the measurement phase, a leaf sample is first locally heated by a short laser pulse and the maximum sample temperature is recorded. The temperature profile of the sample is then recorded for a duration of 50 s. In the analysis phase, leaf properties such as density (easily and accurately determined by pycnometric measurement) are combined with the maximum sample temperature to calculate cp,s. In the second step, the leaf temperature profile is used as the input for an energy balance equation, taking conduction, convection and radiation into account, to calculate &#955;.
Detailed step-by-step instructions are provided in the protocol section, expanding on the contents of the accompanying video. Typical measurements are then shown in the results section. Finally, the benefits and limitations of the method are highlighted in the discussion section along with potential improvements and further applications.
<img alt="Figure 1" src="/files/ftp_upload/54835/54835fig1.jpg" /> 
Figure 1: Apparatus used to determine leaf thermal properties. A. Photograph of the measurement apparatus used to determine the specific heat capacity and thermal conductivity of leaves. The peripheral devices (computers, oscilloscope) are not shown. B. Schematic representation of the measurement apparatus. The laser and connected equipment are highlighted in red, the NIR detector for temperature measurement is shown in purple, the leaf sample is green and the photodiode power sensor is blue. C. Drawing of the elements of the measurement setup with the same color code as in B. The size bar indicates 0.1 m. D. Screenshot illustrating the typical elements of the laser control software. <a href="http://cloudflare.jove.com/files/ftp_upload/54835/54835fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="0" cellpadding="0" cellspacing="0" width="1207">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">1&#34; tube</td>
			<td style="width:259px;">Thorlabs</td>
			<td style="width:136px;">SM1L10E</td>
			<td style="width:403px;">Tube for fiber holder</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Agarose</td>
			<td style="width:259px;">Sigma Aldrich</td>
			<td>A0701</td>
			<td>Agarose</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Bi-Convex lense f=25.4</td>
			<td style="width:259px;">Thorlabs</td>
			<td>LB1761</td>
			<td>Lense</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:411px;">Digital Handheld Optical&#160;Power and Energy Meter Console</td>
			<td style="width:259px;">Thorlabs</td>
			<td style="width:136px;">PM100D</td>
			<td>Console for thermal surface absorber sensor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Digital Phosphor Oscilloscope&#160;</td>
			<td style="width:259px;">Tektronix</td>
			<td style="width:136px;">DPO7104</td>
			<td>Oscilloscope</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">DMR light microscope</td>
			<td style="width:259px;">Leica</td>
			<td style="width:136px;">n.a.</td>
			<td>Light microscope</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Falcon 50mL Conical Centrifuge Tubes</td>
			<td style="width:259px;">Fisher Scientific</td>
			<td style="width:136px;">14-432-2</td>
			<td>Pycnometer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Ferty 2 Mega</td>
			<td style="width:259px;">Kammlott</td>
			<td style="width:136px;">5.220072</td>
			<td>Fertilizer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Fiber holder</td>
			<td style="width:259px;">Thorlabs</td>
			<td style="width:136px;"></td>
			<td>Fiber holder</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Forma -86C ULT freezer</td>
			<td style="width:259px;">ThermoFisher</td>
			<td style="width:136px;">88400</td>
			<td>Freezer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Greenhouse</td>
			<td style="width:259px;">n.a.</td>
			<td style="width:136px;">n.a.</td>
			<td>For plant cultivation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Grodan Rockwool Cubes 10x10cm</td>
			<td style="width:259px;">Grodan</td>
			<td style="width:136px;">102446</td>
			<td>Rockwool block</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Infrared Detector Optris CT</td>
			<td style="width:259px;">Optris</td>
			<td style="width:136px;">OPTCTLT15</td>
			<td>Infrared detector</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Infrared Detector Software Compact Connect</td>
			<td style="width:259px;">Optris</td>
			<td style="width:136px;">n.a.</td>
			<td>Control software for infrared detector</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Lambda 1050 UV/Vis spectrophotometer</td>
			<td style="width:259px;">PerkinElmer</td>
			<td>L1050</td>
			<td>UV/VIS Spectrophotometer</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:411px;">Laser 400&#956;m, 1550nm Conduction Cooled Single Bar Fiber Coupled Module</td>
			<td style="width:259px;">DILAS</td>
			<td style="width:136px;">M1F-SS2.1</td>
			<td>Laser</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Laser cover&#160;</td>
			<td style="width:259px;">Amtron</td>
			<td style="width:136px;">LM200</td>
			<td>Laser Cover</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Laser Driver&#160;</td>
			<td style="width:259px;">Amtron</td>
			<td style="width:136px;">CS 408</td>
			<td>Laser Driver</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Osram cool white 36 W</td>
			<td style="width:259px;">Osram</td>
			<td style="width:136px;">4930440</td>
			<td>Light source</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Photodiode sensor&#160;</td>
			<td style="width:259px;">Thorlabs</td>
			<td style="width:136px;">PDA20H-EC</td>
			<td>Power sensor for transmission measurements</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Precision weight Ohaus Analytical Plus</td>
			<td style="width:259px;">Ohaus</td>
			<td style="width:136px;">80251552</td>
			<td>Precision weight</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Sample frame</td>
			<td style="width:259px;">Fraunhofer ILT</td>
			<td style="width:136px;">n.a.</td>
			<td>Fixation of the leaf sample</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Software Pyro Control</td>
			<td style="width:259px;">Amtron</td>
			<td style="width:136px;">n.a.</td>
			<td>Laser Power Control Software</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Stainless-steel-holder</td>
			<td style="width:259px;">n.a.</td>
			<td style="width:136px;">n.a.</td>
			<td>Holder for measurement set-up</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Teflon plates 2cm</td>
			<td style="width:259px;">Fraunhofer ILT</td>
			<td style="width:136px;">n.a.</td>
			<td>Teflon attenuation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Thermal surface absorber Power sensor</td>
			<td style="width:259px;">Thorlabs</td>
			<td style="width:136px;">S314C</td>
			<td>Sensor for laser power measurements</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Vibratome</td>
			<td style="width:259px;">Leica</td>
			<td style="width:136px;">1491200S001</td>
			<td>Vibratome</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:411px;">Zoc/Pro 6.51&#160;</td>
			<td style="width:259px;">EmTec Innovative Software</td>
			<td style="width:136px;">n.a.</td>
			<td>Laser Control Software&#160;</td>
		</tr>
	</tbody>
</table>

a rapid laser probing method facilitates the non-invasive and contact-free determination of leaf thermal properties

Plants can produce valuable substances such as secondary metabolites and recombinant proteins. The purification of the latter from plant biomass can be streamlined by heat treatment (blanching). A blanching apparatus can be designed more precisely if the thermal properties of the leaves are known in detail, i.e., the specific heat capacity and thermal conductivity. The measurement of these properties is time consuming and labor intensive, and usually requires invasive methods that contact the sample directly. This can reduce the product yield and may be incompatible with containment requirements, e.g., in the context of good manufacturing practice. To address these issues, a non-invasive, contact-free method was developed that determines the specific heat capacity and thermal conductivity of an intact plant leaf in about one minute. The method involves the application of a short laser pulse of defined length and intensity to a small area of the leaf sample, causing a temperature increase that is measured using a near infrared sensor. The temperature increase is combined with known leaf properties (thickness and density) to determine the specific heat capacity. The thermal conductivity is then calculated based on the profile of the subsequent temperature decline, taking thermal radiation and convective heat transfer into account. The associated calculations and critical aspects of sample handling are discussed.

Measurement of Leaf Properties
Using the above microscopic method, a leaf thickness of 0.22-0.29 &#215; 10&#8722;3 m was determined for both N. tabacum (0.25&#177;0.04 &#215; 10&#8722;3 m, n=33) and N. benthamiana (0.26&#177;0.02 &#215; 10&#8722;3 m, n=24), which is well within the 0.20-0.33 &#215; 10&#8722;3</sup...

Watch this Scientific Journal Video about A Rapid Laser Probing Method Facilitates the Non-invasive and Contact-free Determination of Leaf Thermal Properties at JoVE.com

A Rapid Laser Probing Method Facilitates the Non-invasive and Contact-free Determination of Leaf Thermal Properties

A method was developed to determine the specific heat capacity and thermal conductivity of leaf tissue by non-invasive, contact-free near infrared laser probing, which requires less than 1 min per sample.

Plants can produce valuable substances such as secondary metabolites and recombinant proteins. The purification of the latter from plant biomass can be ...

The overall goal of this procedure is to determine the thermal properties of leaves in a contact-free manner. This method can help answer key questions in the field of molecular farming about in-process control of plant growth and health. The main advantages of this technique are that it is contact-free, fast, and does not damage the sample.The implications of this technique extend toward automated inspection of plantations with a mobile detector to define feeding and nutrition on a plant-by-plant basis. To begin plant cultivation, flush mineral wool blocks with one to two liters of deionized water each, then flush each block with one liter of a 0.1%fertilizer solution. Place one tobacco seed in each block and flush with 250 milliliters of fertilizer solution, ensuring that the seed is not washed away.Cultivate the plants for seven weeks in a greenhouse or phytotron. Once the plants have grown, either harvest intact, undamaged single leaves for plant characterization or use intact plants. To begin leaf thickness determination, prepare in autoclave 50 milliliters of a 2%mass by volume agarose solution and phosphate-buffered saline.Allow the solution to cool to 40 degrees celsius and then add the solution to a Petri dish containing a single leaf sample. Cool the sample at four degrees celsius for 30 minutes to solidify the agarose and embed the leaf. Then use a vibratome to cut the agarose block into 200 micrometer slices.Mount five transversal leaf sections on a glass slide with cyanoacrylate. Use a microscope or dial gauge to determine the thickness of vein-free areas of the leaf sample. Use another single leaf sample in water to determine leaf density with a pycnometer.Next, clamp another single leaf in front of the detector in a UV vis spectrophotometer sample chamber. In the spectrophotometer software, select a spectrum of 900 to 1, 600 nanometers. Perform the scan and record the transmission value based on the spectral curve.Then, clamp the leaf behind the detector and repeat the scan. Determine the reflection value from the spectral curve. Obtain transmission and reflection measurements from at least three leaf samples.To begin, mount a 1, 550 nanometer fiber coupled single bar near-IR diode laser in the cone. Then secure a biconvex lens with a 25.4 millimeter focal length at the end of the cone. Clamp a 25.4 millimeter diameter cone with a stainless steel holder to a laboratory stand.Place a neutral density filter with an optical density of 1.0 in a 22 millimeter thick ceramic plate above the censor to attenuate the laser beam. Mount a photo diode power sensor 354 millimeters below the bottom of the lens. Connect the photo diode power sensor to an oscilloscope.Affix a 10 centimeter by 10 centimeter frame with a six centimeter by six centimeter sample exposure area 308 millimeters below the lens. Mount the detector 135 millimeters above the ceramic attenuator. Connect a near-IR detector to a computer and prepare the software.Put an absorber plate on the leaf and turn on the laser. Adjust the detector angle to 45 degrees relative to the laser beam. Continue adjusting the detector angle and height until the maximum temperature reading is observed.In the laser control software, select power control. Set the output laser power to five watts and the pulse duration to 0.5 seconds. To begin the measurements, either bring a whole plant to the measurement apparatus or harvest whole, undamaged single leaves.Immediately mount the leaf sample in the frame, taking care not to damage the leaf. Do not allow the leaf to contact the ceramic attenuator. In the near-IR software, start a new 60 second measurement.Record the baseline temperature profile for 10 seconds before activating a single 0.5 second laser pulse. Continue recording data for the remaining 49.5 seconds. When the measurement is complete, click on the stop button above the thermal profile and then save the profile.Export the raw time and temperature data as a dot dat file for further analysis. Then in the oscilloscope software, determine the flank heights in the voltage profile, which were automatically collected during the laser pulse. Repeat the temperature profile measurement with a single 0.5 second laser pulse for each sample.Then repeat the laser signal measurement without a leaf sample as a reference. Determine the flank heights from this voltage profile and calculate the transmission values for each sample. Use spreadsheet software to calculate and graph the specific heat capacity and thermal conductivity of the samples.Single leaf samples of the plant species Nicotiana tabacum, known as tobacco, and Nicotiana benthamiana were analyzed with this method. Both species showed a rapid increase to maximum temperature in less than one second in response to the laser pulse, followed by an exponential decrease to ambient temperature. The specific heat capacity and thermal conductivity values were calculated for both species from leaves collected at the bottom, middle, and top of the plant.An increase in thermal conductivity for leaves further up the plant was observed for both species, however Nicotiana tabacum showed an inverse trend in specific heat capacity. No correlation between cultivation duration and thermal conductivity was observed in Nicotiana tabacum. Further, no correlation between cultivation conditions and thermal properties were observed in Nicotiana benthamiana.The effect of individual variables on specific heat capacity and thermal conductivity was examined. The thermal conductivity of Nicotiana benthamiana was highly sensitive to ambient temperature. Specific heat capacity was not significantly sensitive to any of the parameters involved in its calculation.Once mastered, this technique can be done in a few minutes per sample if it is performed properly. While attempting this procedure, it is important to remember to correctly mount the leaf at the given precision to ensure high quality measurements and reproducible results. Following this procedure, other methods like fluorescence measurements can be performed in order to answer additional questions like recombinant protein expression.After its development, this technique paved the way for researchers in the field of plant biotechnology to explore plant growth in Nicotiana species. After watching this video, you should have a good understanding of how to determine the specific heat capacity and thermal conductivity of leaves in a contact-free and non-destructive manner. Don't forget that working with lasers can be hazardous to your eyes and precautions such as wearing the appropriate safety glasses should always be taken while performing this procedure.

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Research

JoVE Journal

Biochemistry

Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development

Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not detected or are not identified as differentially expressed (DE) in transcriptomic analyses of whole plant organs. Laser Microdissection RNA-Seq (LM RNA-Seq) is a powerful tool to identify genes that are DE in specific developmental domains. However, the choice of cellular domains to microdissect and compare, and the accuracy of the microdissections are crucial to the success of the experiments. Here, two examples illustrate design considerations for transcriptomics experiments; a LM RNA-seq analysis to identify genes that are DE along the maize leaf proximal-distal axis, and a second experiment to identify genes that are DE in liguleless1-R (lg1-R) mutants compared to wild-type. Key elements that contributed to the success of these experiments were detailed histological and in situ hybridization analyses of the region to be analyzed, selection of leaf primordia at equivalent developmental stages, the use of morphological landmarks to select regions for microdissection, and microdissection of precisely measured domains. This paper provides a detailed protocol for the analysis of developmental domains by LM RNA-Seq. The data presented here illustrate how the region selected for microdissection will affect the results obtained.

Many developmentally important genes have cell- or tissue-specific expression patterns. This paper describes LM RNA-seq experiments to identify genes that are differentially expressed at the maize leaf blade-sheath boundary and in lg1-R mutants compared to wild-type. The experimental considerations discussed here apply to transcriptomic analyses of other developmental phenomena.

Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not ...

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a target for future development of inhibitors to decrease the virulence of the pathogen. To perform biophysical and structural characterization as well as inhibitor screening, large amounts of pure and active protein will be needed. We have developed a protocol for efficient production and purification of PPEP-1 by the use of E. coli as the expression host yielding sufficient amounts and purity of protein for crystallization and structure determination. Additionally, using microseeding, highly intergrown crystals of PPEP-1 can be grown to well-ordered crystals suitable for X-ray diffraction analysis. The methods could also be used to produce other recombinant proteins and to study the structures of other proteins producing intergrown crystals.

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Proline-proline endopeptidase-1 (PPEP-1) is a secreted metalloprotease and promising drug-target from the human pathogen Clostridium difficile. Here we describe all methods necessary for the production and structure determination of this protein.

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a ...

Differential Scanning Calorimetry &#8212; A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural &#8220;fingerprint&#8221; that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; &#8710;H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

Differential Scanning Calorimetry &amp;#8212; A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Differential scanning calorimetry measures the thermal transition temperature(s) and total heat energy required to denature a protein. Results obtained are used to assess the thermal stability of protein antigens in vaccine formulations.

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the ...

Determination of the Glycogen Content in Cyanobacteria

Cyanobacteria accumulate glycogen as a major intracellular carbon and energy storage&#160;during photosynthesis. Recent developments in research have highlighted complex mechanisms of glycogen metabolism, including the diel cycle of biosynthesis and catabolism, redox regulation, and the involvement of non-coding RNA. At the same time, efforts are being made to redirect carbon from glycogen to desirable products in genetically engineered cyanobacteria to enhance product yields. Several methods are used to determine the glycogen contents in cyanobacteria, with variable accuracies and technical complexities. Here, we provide a detailed protocol for the reliable determination of the glycogen content in cyanobacteria that can be performed in a standard life science laboratory. The protocol entails the selective precipitation of glycogen from the cell lysate and the enzymatic depolymerization of glycogen to generate glucose monomers, which are detected by a glucose oxidase-peroxidase (GOD-POD) enzyme coupled assay. The method has been applied to Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002, two model cyanobacterial species that are widely used in metabolic engineering. Moreover, the method successfully showed differences in the glycogen contents between the wildtype and mutants defective in regulatory elements or glycogen biosynthetic genes.

Here, we present a reliable and easy assay to measure the glycogen content in cyanobacterial cells. The procedure entails precipitation, selectable depolymerization, and the detection of glucose residues. This method is suitable for both wildtype and genetically engineered strains and can facilitate the metabolic engineering of cyanobacteria.

Cyanobacteria accumulate glycogen as a major intracellular carbon and energy storage&#160;during photosynthesis. Recent developments in research have ...

Rapid Isolation of the Mitoribosome from HEK Cells

The human mitochondria possess a dedicated set of ribosomes (mitoribosomes) that translate 13 essential protein components of the oxidative phosphorylation complexes encoded by the mitochondrial genome. Since all proteins synthesized by human mitoribosomes are integral membrane proteins, human mitoribosomes are tethered to the mitochondrial inner membrane during translation. Compared to the cytosolic ribosome the mitoribosome has a sedimentation coefficient of 55S, half the rRNA content, no 5S rRNA and 36 additional proteins. Therefore, a higher protein-to-RNA ratio and an atypical structure make the human mitoribosome substantially distinct from its cytosolic counterpart.
Despite the central importance of the mitoribosome to life, no protocols were available to purify the intact complex from human cell lines. Traditionally, mitoribosomes were isolated from mitochondria-rich animal tissues that required kilograms of starting material. We reasoned that mitochondria in dividing HEK293-derived human cells grown in nutrient-rich expression medium would have an active mitochondrial translation, and, therefore, could be a suitable source of material for the structural and biochemical studies of the mitoribosome. To investigate its structure, we developed a protocol for large-scale purification of intact mitoribosomes from HEK cells. Herein, we introduce nitrogen cavitation method as a faster, less labor-intensive and more efficient alternative to traditional mechanical shear-based methods for cell lysis. This resulted in preparations of the mitoribosome that allowed for its structural determination to high resolution, revealing the composition of the intact human mitoribosome and its assembly intermediates. Here, we follow up on this work and present an optimized and more cost-effective method requiring only ~1010 cultured HEK cells. The method can be employed to purify human mitoribosomal translating complexes, mutants, quality control assemblies and mitoribosomal subunits intermediates. The purification can be linearly scaled up tenfold if needed, and also applied to other types of cells.

Mitochondria have specialized ribosomes that diverged from their bacterial and cytoplasmic counterparts. Here we show how mitoribosomes can be obtained from their native compartment in HEK cells. The method involves isolation of mitochondria from suspension cells and consequent purification of mitoribosomes.

The human mitochondria possess a dedicated set of ribosomes (mitoribosomes) that translate 13 essential protein components of the oxidative ...

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Plants produce thousands of small molecules that are diverse in their chemical properties. Mass spectrometry (MS) is a powerful technique for analyzing plant metabolites because it provides molecular weights with high sensitivity and specificity. Leaf spray MS is an ambient ionization technique where plant tissue is used for direct chemical analysis via electrospray, eliminating chromatography from the process. This approach to sampling metabolites allows for a wide range of chemical classes to be detected simultaneously from intact plant tissues, minimizing the amount of sample preparation needed. When used with a high-resolution, accurate mass MS, leaf spray MS facilitates the rapid detection of metabolites of interest. It is also possible to collect tandem mass fragmentation data with this technique to facilitate a compound identification. The combination of accurate mass measurements and fragmentation is beneficial in confirming compound identities. The leaf spray MS technique requires only minor modifications to a nanospray ionization source and is a useful tool to further expand the capabilities of a mass spectrometer. Here, fresh leaf tissue from Sceletium tortuosum (Aizoaceae), a traditional medicinal plant from South Africa, is analyzed; numerous mesembrine alkaloids are detected with leaf spray MS.

Leaf spray mass spectrometry is a direct chemical analysis technique that minimizes the sample preparation and eliminates chromatography, allowing for the rapid detection of small molecules from plant tissues.

Plants produce thousands of small molecules that are diverse in their chemical properties. Mass spectrometry (MS) is a powerful technique for analyzing ...

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.

Here, we present a protocol to characterize nucleosome particles at the single-molecule level using static and time-lapse atomic force microscopy (AFM) imaging techniques. The surface functionalization method described allows for the capture of the structure and dynamics of nucleosomes in high-resolution at the nanoscale.

Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription ...

Rapid Collection of Floral Fragrance Volatiles using a Headspace Volatile Collection Technique for GC-MS Thermal Desorption Sampling

Fragrances of many flower families have been sampled and the volatiles analyzed. Knowing the compounds that make up the fragrances can be an important step to conservation of flowers that are threatened or endangered. Because floral fragrance is critical for attracting pollinators, this method could be used to better understand or even enhance pollination. We present a protocol using a portable charcoal air filter and vacuum to collect floral fragrance volatiles, which are then analyzed by a GC-MS. By using this method, fragrance volatiles can be sampled using a non-destructive method with a machine that is easily transported. This methodology uses a rapid sampling procedure, cutting sampling time down from 2-3 hours to approximately 10 minutes. Using GC-MS, the fragrance compounds can be identified individually, based on authentic standards. The steps used for collecting fragrance and control data are presented, from material setup to collecting the data output.

Here, we present a protocol for collecting the floral fragrance volatiles from blooming flowers, using a non-destructive sampling procedure.

Fragrances of many flower families have been sampled and the volatiles analyzed. Knowing the compounds that make up the fragrances can be an important ...

A Planarian Motility Assay to Gauge the Biomodulating Properties of Natural Products

A straightforward, controllable means of using the non-parasitic planarian, Dugesia tigrina, a free-living aquatic flatworm, to study the stimulant and withdrawal properties of natural products is described. Experimental assays benefitting from unique aspects of planarian physiology have been applied to studies on wound healing, regeneration, and tumorigenesis. In addition, because planarians exhibit sensitivity to a variety of environmental stimuli and are capable of learning and developing conditioned responses, they can be used in behavioral studies examining learning and memory. Planarians possess a basic bilateral symmetry and a central nervous system that uses neurotransmitter systems amenable to studies examining the effects of neuromuscular biomodulators. Consequently, experimental systems monitoring planarian movement and motility have been developed to examine substance addiction and withdrawal. Because planarian motility offers the potential for a sensitive, easily standardized motility assay system to monitor the effect of stimuli, the planarian locomotor velocity (pLmV) test was adapted to monitor both stimulation and withdrawal behaviors by planarians through the determination of the number of grid lines crossed by the animals with time. Here, the technique and its application are demonstrated and explained.

Planarian motility is used to gauge the stimulant and withdrawal properties of natural products when compared to the movement of the animals in spring water alone.

A straightforward, controllable means of using the non-parasitic planarian, Dugesia tigrina, a free-living aquatic flatworm, to study the stimulant and ...

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Measurements of the specificity and affinity of antigen-antibody interactions are critically important for medical and research applications. In this protocol, we describe the implementation of a new single-molecule technique, mass photometry (MP), for this purpose. MP is a label- and immobilization-free technique that detects and quantifies molecular masses and populations of antibodies and antigen-antibody complexes on a single-molecule level. MP analyzes the antigen-antibody sample within minutes, allowing for the precise determination of the binding affinity and simultaneously providing information on the stoichiometry and the oligomeric state of the proteins. This is a simple and straightforward technique that requires only picomole quantities of protein and no expensive consumables. The same procedure can be used to study protein-protein binding for proteins with a molecular mass larger than 50 kDa. For multivalent protein interactions, the affinities of multiple binding sites can be obtained in a single measurement. However, the single-molecule mode of measurement and the lack of labeling imposes some experimental limitations. This method gives the best results when applied to measurements of sub-micromolar interaction affinities, antigens with a molecular mass of 20 kDa or larger, and relatively pure protein samples. We also describe the procedure for performing the required fitting and calculation steps using basic data analysis software.

We describe a single-molecule approach to antigen-antibody affinity measurements using mass photometry (MP). The MP-based protocol is fast, accurate, uses a very small amount of material, and does not require protein modification.

Measurements of the specificity and affinity of antigen-antibody interactions are critically important for medical and research applications. In this ...