Name: in vivo calcium imaging in c. elegans body wall muscles
Uploaded: 2019-10-20T12:30:00
Description: Watch this Scientific Journal Video about In Vivo Calcium Imaging in C. elegans Body Wall Muscles at JoVE.com

The authors thank Dr. Alexander Gottschalk for ZX1659, the RCaMP and channelrhodopsin containing worm strain, Dr. Hongkyun Kim for the slo-1(eg142) worm strain, and the National Bioresource Project for the sca-1(tm5339) worm strain.

1. Microscope setup
<ol>
	<li>Use a compound microscope with fluorescence capabilities. For this study, data were collected on an upright microscope (Table of Materials) fitted with LEDs for excitation.</li>
	<li>In order to properly visualize fluorescence changes in body wall muscles, use a high magnification objective.
	<ol>
		<li>For dissected preparations, use a 60x NA 1.0 water immersion objective (Table of Materials).</li>
		<li>For preparations using nanobeads, use a 60x NA 1.4 ...

<ol>
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A., Richmond, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+sarco(endo)plasmic+reticulum+calcium+ATPase+SCA-1+regulates+the+Caenorhabditis+elegans+nicotinic+acetylcholine+receptor+ACR-16.">The sarco(endo)plasmic reticulum calcium ATPase SCA-1 regulates the Caenorhabditis elegans nicotinic acetylcholine receptor ACR-16.</a> Cell Calcium. 72, 104-115 (2018).</li><li>Wang, Z., Saifee, O., Nonet, M. L., Salkoff, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SLO-1+Potassium+Channels+Control+Quantal+Content+of+Neurotransmitter+Release+at+the+C.+elegans+Neuromuscular+Junction.">SLO-1 Potassium Channels Control Quantal Content of Neurotransmitter Release at the C. elegans Neuromuscular Junction.</a> Neuron. 32, 867-881 (2001).</li><li>Abraham, L. S., Oh, H. J., Sancar, F., Richmond, J. E., Kim, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+Alpha-Catulin+Homologue+Controls+Neuromuscular+Function+through+Localization+of+the+Dystrophin+Complex+and+BK+Channels+in+Caenorhabditis+elegans.">An Alpha-Catulin Homologue Controls Neuromuscular Function through Localization of the Dystrophin Complex and BK Channels in Caenorhabditis elegans.</a> PLoS Genetics. 6 (8), 1-13 (2010).</li><li>Gourgou, E., Chronis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemically+induced+oxidative+stress+affects+ASH+neuronal+function+and+behavior+in+C.+elegans.">Chemically induced oxidative stress affects ASH neuronal function and behavior in C. elegans.</a> Scientific Reports. 6, 1-9 (2016).</li><li>Zahratka, J. A., Williams, P. D. E., Summers, P. J., Komuniecki, R. W., Bamber, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serotonin+differentially+modulates+Ca2++transients+and+depolarization+in+a+C.+elegans+nociceptor.">Serotonin differentially modulates Ca2+ transients and depolarization in a C. elegans nociceptor.</a> Journal of Neurophysiology. 113 (4), 1041-1050 (2015).</li><li>Kerr, R., 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=Optical+imaging+of+calcium+transients+in+neurons+and+pharyngeal+muscle+of+C.+elegans.">Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans.</a> Neuron. 26 (3), 583-594 (2000).</li><li>Nekimken, A. 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GECIs are a powerful tool in C. elegans neurobiology. Previous work has utilized calcium imaging techniques to examine a wide variety of functions in both neurons and muscle cells, including sensory and behavioral responses, with varied methods of stimulation. Some studies have used chemical stimuli to trigger calcium transients in sensory ASH neurons22,23 or to induce calcium waves in pharyngeal muscles24. Another group utilized ...

This paper presents methods for in vivo calcium imaging of C. elegans body wall muscles using optogenetic neuronal stimulation. Pairing a muscle expressed genetically encoded calcium indicator (GECI) with blue light triggered neuronal depolarization and provides a system to clearly observe the evoked postsynaptic calcium transients. This avoids the use of electrical stimulation, allowing a non-invasive analysis of mutants affecting the postsynaptic calcium dynamics.
Single-fluorophore GECIs, such as GCaMP, uses a single fluorescent protein molecule fused to the M13 domain of myosin light chain kinase at its N-terminal end and calmodulin (CaM) at the C-terminus. Upon calcium binding, the CaM domain, which has a high affinity for calcium, undergoes a conformational change inducing a subsequent conformational change in the fluorescent protein leading to an increase in fluorescence intensity1. GCaMP fluorescence is excited at 488 nm, making it unsuitable to be used in conjunction with channelrhodopsin, which has a similar excitation wavelength of 473 nm. Thus, in order to couple calcium measurements with channelrhodopsin stimulation, the green fluorescent protein of GCaMP needs to be replaced with a red fluorescent protein, mRuby (RCaMP). Using the muscle expressed RCaMP, in combination with the cholinergic motor neuron expression of channelrhodopsin, permits studies at the worm neuromuscular junction (NMJ) with simultaneous use of optogenetics and functional imaging within the same animal2.
The use of channelrhodopsin bypasses the need for the electrical stimulation to depolarize the neuromuscular junctions of C. elegans, which can only be achieved in dissected preparations, thus making this technique both easier to employ and more precise when targeting specific tissues. For example, channelrhodopsin has been previously used in C. elegans to reversibly activate specific neurons, leading to either robust activation of excitatory or inhibitory neurons3,4. The use of light-stimulated depolarization also circumvents the issue of neuronal damage due to the direct electrical stimulation. This provides an opportunity to examine the effects of many different stimulation protocols, including sustained and repeated stimulations, on postsynaptic calcium dynamics4.
The transparent nature of C. elegans makes it ideal for the fluorescent imaging functional analysis. However, when stimulating the excitatory acetylcholine neurons at the NMJ, animals are expected to respond with an immediate muscle contraction4, making the immobilization of the worms critical in visualizing discrete calcium changes. Traditionally, pharmacological agents have been used to paralyze the animals. One such drug used is levamisole, a cholinergic acetylcholine receptor agonist5,6,7. Since levamisole leads to the persistent activation of a subtype of excitatory muscle receptors, this reagent is unsuitable for the study of the muscle calcium dynamics. The action of levamisole induces postsynaptic depolarization, elevating the cytosolic calcium, and occluding observations following presynaptic stimulation. To avoid the use of paralyzing drugs, we examined two alternative methods to immobilize C. elegans. Animals were either glued down and then dissected open to expose the body wall muscles, similar to the existing C. elegans NMJ electrophysiology method8, or nanobeads were used to immobilize intact animals9. Both procedures allowed for the reproducible measurements of the resting and evoked muscle calcium transients that were easily quantifiable.
The methods in this paper can be used to measure the baseline cytosolic calcium levels and transients in postsynaptic body wall muscle cells in C. elegans. Examples of data employing the two different immobilization techniques are given. Both techniques take advantage of optogenetics to depolarize the muscle cells without the use of electrical stimulation. These examples demonstrate the feasibility of this method in evaluating mutations that affect postsynaptic calcium handling in the worms and point out the pros and cons of the two immobilization approaches.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>all-trans retinal</td>
			<td>Sigma-Aldrich</td>
			<td>R2500</td>
			<td>Necessary for excitation of channel rhodopsin</td>
		</tr>
		<tr>
			<td>Amber LED</td>
			<td></td>
			<td></td>
			<td>RCaMP illumination</td>
		</tr>
		<tr>
			<td>Arduino UNO</td>
			<td>Mouser</td>
			<td>782-A000066</td>
			<td>Controls fluorescence illumination</td>
		</tr>
		<tr>
			<td>Blue LED</td>
			<td></td>
			<td></td>
			<td>channelrhodopsin illumination</td>
		</tr>
		<tr>
			<td>BX51WI microscope</td>
			<td>Olympus</td>
			<td></td>
			<td>Fixed state compound microscope</td>
		</tr>
		<tr>
			<td>Current controlled low noise linear power supply</td>
			<td>Ametek</td>
			<td>Sorenson</td>
			<td>Controls LED intensity</td>
		</tr>
		<tr>
			<td>Igor Pro</td>
			<td>Wavemetrics</td>
			<td>Wavemetrics.com</td>
			<td>Graphing software</td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>NIH</td>
			<td>imagej.nih.gov</td>
			<td>Image processing software</td>
		</tr>
		<tr>
			<td>LUMFLN 60x water NA 1.4</td>
			<td>Olympus</td>
			<td></td>
			<td>Water immersion objective for dissected preparation</td>
		</tr>
		<tr>
			<td>Master-8 Stimulator</td>
			<td>A.M.P.I</td>
			<td></td>
			<td>Master timer for image acquisition and LED illumination</td>
		</tr>
		<tr>
			<td>Micro-Manager</td>
			<td></td>
			<td>micro-manager.org</td>
			<td>Controls camera acquisition and LED excitiation</td>
		</tr>
		<tr>
			<td>Microsoft Excel</td>
			<td>Microsoft</td>
			<td></td>
			<td>Spreadsheet software</td>
		</tr>
		<tr>
			<td>pco.edge 4.2 CMOS camera</td>
			<td>pco.</td>
			<td>4.2</td>
			<td>High-speed camera</td>
		</tr>
		<tr>
			<td>PlanApo N 60x oil NA 1.4</td>
			<td>Olympus</td>
			<td></td>
			<td>Oil immersion objective for nanobead preparation</td>
		</tr>
		<tr>
			<td>Polybead microspheres</td>
			<td>Polysciences, Inc.</td>
			<td>00876-15</td>
			<td>For worm immobilization</td>
		</tr>
		<tr>
			<td>solid state switches</td>
			<td>Sensata Technologies</td>
			<td>Crydom CMX100D6</td>
			<td>Controls timing of LED illumination</td>
		</tr>
		<tr>
			<td>Transgenic strain, sca-1(tm5339); [zxIs6{Punc17::chop-2 
			(h134R)::yfp,lin-15(+)}; 
			Pmyo3::RCaMP35]</td>
			<td>Richmond Lab</td>
			<td>SY1627</td>
			<td>Excitatory neuronal channelrhodopsin and body wall muscle RCaMP expressing worm line with SERCA mutant allele</td>
		</tr>
		<tr>
			<td>Transgenic strain, slo-1 (eg142); [zxIs6{Punc17::chop-2 
			(h134R)::yfp,lin-15(+)}; 
			Pmyo3::RCaMP35]</td>
			<td>Richmond Lab</td>
			<td></td>
			<td>Excitatory neuronal channelrhodopsin and body wall muscle RCaMP expressing worm line with calcium-activated BK potassium channel mutant allele</td>
		</tr>
		<tr>
			<td>Transgeneic strain, [zxIs6{Punc17::chop-2 
			(h134R)::yfp,lin-15(+)}; 
			Pmyo3::RCaMP35]</td>
			<td>Gottschalk Lab</td>
			<td>ZX1659</td>
			<td>Excitatory neuronal channelrhodopsin and body wall muscle RCaMP expressing worm line</td>
		</tr>
	</tbody>
</table>

in vivo calcium imaging in c. elegans body wall muscles

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for the targeted expression of genetically encoded calcium sensors. This protocol outlines the use of these sensors for the in vivo imaging of calcium dynamics in targeted cells, specifically the body wall muscles of the worms. By utilizing the co-expression of presynaptic channelrhodopsin, stimulation of acetylcholine release from excitatory motor neurons can be induced using blue light pulses, resulting in muscle depolarization and reproducible changes in cytoplasmic calcium levels. Two worm immobilization techniques are discussed with varying levels of difficulty. Comparison of these techniques demonstrates that both approaches preserve the physiology of the neuromuscular junction and allow for the reproducible quantification of calcium transients. By pairing optogenetics and functional calcium imaging, changes in postsynaptic calcium handling and homeostasis can be evaluated in a variety of mutant backgrounds. Data presented validates both immobilization techniques and specifically examines the roles of the C. elegans sarco(endo)plasmic reticular calcium ATPase and the calcium-activated BK potassium channel in the body wall muscle calcium regulation.

This technique evaluated changes in mutants thought to affect the calcium handling or muscle depolarization. Baseline fluorescence levels and fluorescent transients were visualized and resting cytosolic calcium and calcium kinetics within the muscle were evaluated. It is important that the animals were grown on all-trans retinal for at least three days to ensure the successful incorporation of retinal, thereby subsequently activating the channelrhodopsin (Figure 2</st...

Watch this Scientific Journal Video about In Vivo Calcium Imaging in C. elegans Body Wall Muscles at JoVE.com

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

This method provides a way to couple optogenetics and genetically encoded calcium sensors to image baseline cytosolic calcium levels and changes in evoked calcium transients in the body wall muscles of the model organism C. elegans.

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for ...

This protocol provides two methods to mobilize C.Elegans to perform in vivo calcium imaging of body wall muscles. This method can help answer questions related to calcium homeostasis and calcium handling, and an accessible synapse in genetically tractable organism. This technique can provide a better understanding of the mechanisms regulating muscle calcium homeostasis, and can, therefore, be important in identifying conditions or molecular pathways that impact excitation contraction coupling through the misregulation of calcium cycling.These methods can provide insight into areas of research including, but not limited too, neurobiology, developmental biology, and cell biology. These techniques could be adapted to study a variety of cell types and C.elegans, other related nematodes as well as filsafat larvae. Visual demonstration of this method is critical so the experimenter can understand the dissection technique, and be able to accurately assess calcium transients from properly immobilized animals.Start by setting up the microscope for fluorescent imaging. Use a scientific CMOS camera capable of full frame imaging at 100 hertz in order to track rapid changes in calcium levels. Control camera acquisition and LED fluorescent excitation with a micromanager software running in ImageJ.Use an opensource electronic platform plug-in which connects to an external opensource microcontroller board to manage the external timing pulses that control fluorescent excitations. To control the timing logic, activate the micromanager acquisition protocol in the software according to manufacturers instructions. Use two LEDs to stimulate channel rhodopsin with blue light and record RCaMP changes.Activate channel rhodopsin with am LED with the peak admission wavelength of 470 nanometers and a bandpass filter, and excite RCaMP with an LED with a peak admission wavelength of 594 nanometers and a bandpass filter. Co-illuminate both LEDs and transmit the light to the same optical path using a dichroic beam combiner. Control the timing of the LED illumination with a solid state switches controlled by TTL signals according to manuscript directions, and set the LED intensity with the current controlled load noise linear power supplies, then program the blue light simulation protocol into a simulator.In this experiment turn on the blue light simulation after two seconds of capturing RCaMP fluorescence only and use a train of five, two millisecond blue light pulses with 50 millisecond intervals to activate channel rhodopsin. If using the dissection preparation, perform C.elegans dissection in low light. Place the animals in the dissection dish with the silicone coated coverslip base that is filled with a one millimole of calcium extracellular solution prepared according to manuscript directions.Glue down the animals using the liquid topical skin adhesive with blue coloring along the dorsal side of the worm. And make a lateral cuticle incision along the glue and worm interface using glass needles. Use a mouth pipette to clear the internal viscera from the worm cavity, then glue down the cuticle flap of the animal to expose the ventral medial body wall muscles for imaging.If using the nano-bead preparation, make a molten 5%Agra solution using distilled water to a final volume of 100 milliliters. Use a Pasteur pipette to place a drop of molten-Agra solution onto a glass slide and immediately place a second glass slide over the top using gently pressure to create an even Agra's pad. Remove the top slide and at approximately four microliters of polystyrene nano-beads to the middle of the pad.In low light add four to six C.elegans into the nano-beads solution, making sure that the animals do not lay on top of each other, and carefully place a coverslip on top. When when ready to image, place the prepared slide or dissection dish on the microscope and find and focus on a worm using 10 times magnification and dim bright field illumination. Switch to 60 times magnification in RCaMP fluorescent excitation to identify a ventrum medial body wall muscle that is anterior to the vulva and in the correct vocal plane.Then change the image pathway from the eyepiece to the camera by pulling out the toggle and clicking live within the data acquisition software. Click the ORI button in the data acquisition software, and create a box around the muscle that is being focused on. On the stimulator, switch on the previously programmed blue light stimulation pathway, then click Acquire on the imaging software to capture the image.When C.elegans are grown on all-trans retinal, successfully incorporating retinal and activating the channel rhodopsin, a calcium transient can be evoked. If animals are not exposed to all-trans retinal no muscle calcium transient is triggered. This protocol was used to investigate loss of function sca-1 mutants, which impact the sarcoplasmic reticulum calcium pump encoded by the sca-1 gene.But, the dissection preparation increases in baseline levels of RCaMP fluorescence were observed in the mutant compared to the control, suggesting that the mutation needs the elevated levels of resting cytoplasmic calcium. There was a significant decrease in peak calcium levels in the sca-1 mutants as compared to the control. However, no change was seen in the rised peak time or the half decay time.Importantly, similar results can be observed using the less technically challenging nano-bead preparation. Loss of function slo-mutants, which disrupt the calcium activated big potassium channels were evaluated in order to investigate mutants that indirectly impact calcium handling in C.elegans. When baseline levels of RCaMP were measured the mutants displayed increased fluorescence compared to the controls.When evaluating the kinetics of the calcium transient no changes in peak calcium levels were seen. The slo-1(eg142)mutants, however, exhibited a significantly increased rise to peak time. The most important step to remember when completing the procedure is to ready experimental animals in all-trans retinal.Without this step the channel rhodopsin will be inactive, preventing light induced calcium transients from being triggered. Following this procedure, electrophysiology and behavioral analysis can be done to evaluate the functional impact of any observed changes in calcium homeostasis. Using the immobilization methods outlined here, paves the way for further exploration of calcium dynamics and demonstrates that comparable results can be observed in response to optogenetic neuronal stimulation and capture of muscle calcium transients using the far less challenging bead immobilization technique.

in-vivo-calcium-imaging-in-c-elegans-body-wall-muscles

Research

JoVE Journal

Biochemistry

Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo

Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many of these conditions cause protein unfolding in the cell and have detrimental impact on the survival of the organism. A group of unrelated, stress-specific molecular chaperones have been shown to play essential roles in the survival of these stress conditions. While fully folded and chaperone-inactive before stress, these proteins rapidly unfold and become chaperone-active under specific stress conditions. Once activated, these conditionally disordered chaperones bind to a large number of different aggregation-prone proteins, prevent their aggregation and either directly or indirectly facilitate protein refolding upon return to non-stress conditions. The primary approach for gaining a more detailed understanding about the mechanism of their activation and client recognition involves the purification and subsequent characterization of these proteins using in vitro chaperone assays. Follow-up in vivo stress assays are absolutely essential to independently confirm the obtained in vitro results.
This protocol describes in vitro and in vivo methods to characterize the chaperone activity of E. coli HdeB, an acid-activated chaperone. Light scattering measurements were used as a convenient read-out for HdeB&#39;s capacity to prevent acid-induced aggregation of an established model client protein, MDH, in vitro. Analytical ultracentrifugation experiments were applied to reveal complex formation between HdeB and its client protein LDH, to shed light into the fate of client proteins upon their return to non-stress conditions. Enzymatic activity assays of the client proteins were conducted to monitor the effects of HdeB on pH-induced client inactivation and reactivation. Finally, survival studies were used to monitor the influence of HdeB&#39;s chaperone function in vivo.

Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo

This study describes biophysical, biochemical and molecular techniques to characterize the chaperone activity of Escherichia coli HdeB under acidic pH conditions. These methods have been successfully applied for other acid-protective chaperones such as HdeA and can be modified to work for other chaperones and stress conditions.

Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many ...

Combining Raman Imaging and Multivariate Analysis to Visualize Lignin, Cellulose, and Hemicellulose in the Plant Cell Wall

The application of Raman imaging to plant biomass is increasing because it can offer spatial and compositional information on aqueous solutions. The analysis does not usually require extensive sample preparation; structural and chemical information can be obtained without labeling. However, each Raman image contains thousands of spectra; this raises difficulties when extracting hidden information, especially for components with similar chemical structures. This work introduces a multivariate analysis to address this issue. The protocol establishes a general method to visualize the main components, including lignin, cellulose, and hemicellulose within the plant cell wall. In this protocol, procedures for sample preparation, spectral acquisition, and data processing are described. It is highly dependent upon operator skill at sample preparation and data analysis. By using this approach, a Raman investigation can be performed by a non-specialist user to acquire high-quality data and meaningful results for plant cell wall analysis.

This protocol aims to present a general method to visualize lignin, cellulose, and hemicellulose in plant cell walls using Raman imaging and multivariate analysis.

The application of Raman imaging to plant biomass is increasing because it can offer spatial and compositional information on aqueous solutions. The ...

Preparation of Keratin Hydrolysate from Chicken Feathers and Its Application in Cosmetics

Keratin hydrolysates (KHs) are established standard components in hair cosmetics. Understanding the moisturizing effects of KH is advantageous for skin-care cosmetics. The goals of the protocol are: (1) to process chicken feathers into KH by alkaline-enzymatic hydrolysis and purify it by dialysis, and (2) to test if adding KH into an ointment base (OB) increases hydration of the skin and improves skin barrier function by diminishing transepidermal water loss (TEWL). During alkaline-enzymatic hydrolysis feathers are first incubated at a higher temperature in an alkaline environment and then, under mild conditions, hydrolyzed with proteolytic enzyme. The solution of KH is dialyzed, vacuum dried, and milled to a fine powder. Cosmetic formulations comprising from oil in water emulsion (O/W) containing 2, 4, and 6 weight% of KH (based on the weight of the OB) are prepared. Testing the moisturizing properties of KH is carried out on 10 men and 10 women at time intervals of 1, 2, 3, 4, 24, and 48 h. Tested formulations are spread at degreased volar forearm sites. The skin hydration of stratum corneum (SC) is assessed by measuring capacitance of the skin, which is one of the most world-wide used and simple methods. TEWL is based on measuring the quantity of water transported per a defined area and period of time from the skin. Both methods are fully non-invasive. KH makes for an excellent occlusive; depending on the addition of KH into OB, it brings about a 30% reduction in TEWL after application. KH also functions as a humectant, as it binds water from the lower layers of the epidermis to the SC; at the optimum KH addition in the OB, up to 19% rise in hydration in men and 22% rise in women occurs.

The goal of the protocol is to prepare keratin hydrolysate from chicken feathers by alkaline-enzymatic hydrolysis and to test whether adding keratin hydrolysate into a cosmetics ointment base improves skin barrier function (heightening hydration and diminishing transepidermal water loss). Tests are conducted on men and woman volunteers.

Keratin hydrolysates (KHs) are established standard components in hair cosmetics. Understanding the moisturizing effects of KH is advantageous for ...

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

A protocol for the structural analysis of polysaccharides by gel electrophoresis (PACE), using mannan as an example, is described.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts ...

Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering

The automated crystallization device is a patented technique1 especially developed for monitoring protein crystallization experiments with the aim to precisely maneuver the nucleation and crystal growth towards desired sizes of protein crystals. The controlled crystallization is based on sample investigation with in situ Dynamic Light Scattering (DLS) while all visual changes in the droplet are monitored online with the help of a microscope coupled to a CCD camera, thus enabling a full investigation of the protein droplet during all stages of crystallization. The use of in situ DLS measurements throughout the entire experiment allows a precise identification of the highly supersaturated protein solution transitioning to a new phase &#8211; the formation of crystal nuclei. By identifying the protein nucleation stage, the crystallization can be optimized from large protein crystals to the production of protein microcrystals. The experimental protocol shows an interactive crystallization approach based on precise automated steps such as precipitant addition, water evaporation for inducing high supersaturation, and sample dilution for slowing induced homogeneous nucleation or reversing phase transitions.

Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering

Here we present a protocol for controlled production of protein microcrystals. The process uses an automated device allowing controlled manipulation of several crystallization parameters. The protein crystallization is carried-out by controlled and automated addition of crystallization solutions while monitoring and investigating the radius distribution of particles in the crystallization droplet.

The automated crystallization device is a patented technique1 especially developed for monitoring protein crystallization experiments with the aim to ...

A Colorimetric Method for Measuring Iron Content in Plants

Iron, one of the most important micronutrients in living organisms, is involved in basic processes, such as respiration and photosynthesis. Iron content is rather low in all organisms, amounting in plants to about 0.009% of dry weight. To date, one of the most accurate methods for measuring iron concentration in plant tissues is flame absorption atomic spectroscopy. However, this approach is time-consuming and expensive and requires specific equipment not commonly found in plant laboratories. Therefore, a simpler, yet accurate method that can be routinely used is needed. The colorimetric Prussian Blue method is regularly used for qualitative iron staining in animal and plant histological sections. In this study, we adapted the Prussian Blue method for quantitative measurements of iron in tobacco leaves. We validated the accuracy of this method using both atomic spectroscopy and Prussian Blue staining to measure iron content in the same samples and found a linear regression (R2 = 0.988) between the two procedures. We conclude that the Prussian Blue method for quantitative iron measurement in plant tissues is precise, simple, and inexpensive. However, the linear regression presented here may not be appropriate for other plant species, due to potential interactions between the sample and the reagent. Establishment of a regression curve is thus needed for different plant species.

We present a simple and reliable protocol for measuring iron content in plant tissues using the colorimetric Prussian Blue method.

Iron, one of the most important micronutrients in living organisms, is involved in basic processes, such as respiration and photosynthesis. Iron content ...

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be employed using a conventional confocal microscope equipped with digital detectors. A protocol for the use of the technique in vitro is shown by means of a use case where number and brightness can be seen to accurately quantify the oligomeric state of mVenus-labelled FKBP12F36V before and after the addition of the dimerizing drug AP20187. The importance of using the correct microscope acquisition parameters and the correct data preprocessing and analysis methods are discussed. In particular, the importance of the choice of photobleaching correction is stressed. This inexpensive method can be employed to study protein-protein interactions in many biological contexts.

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

This protocol describes a calibration-free approach for quantifying protein homo-oligomerization in vitro based on fluorescence fluctuation spectroscopy using commercial light scanning microscopy. The correct acquisition settings and analysis methods are shown.

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be ...

In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans

Fast oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting (HRPF) method used to study protein structure, protein-ligand interactions, and protein-protein interactions. FPOP utilizes a KrF excimer laser at 248 nm for photolysis of hydrogen peroxide to generate hydroxyl radicals which in turn oxidatively modify solvent-accessible amino acid side chains. Recently, we expanded the use of FPOP of in vivo oxidative labeling in Caenorhabditis elegans (C. elegans), entitled IV-FPOP. The transparent nematodes have been used as model systems for many human diseases. Structural studies in C. elegans by IV-FPOP is feasible because of the animal&#8217;s ability to uptake hydrogen peroxide, their transparency to laser irradiation at 248 nm, and the irreversible nature of the modification. The assembly of a microfluidic flow system for IV-FPOP labeling, IV-FPOP parameters, protein extraction, and LC-MS/MS optimized parameters are described herein.

In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans

In vivo fast photochemical oxidation of proteins (IV-FPOP) is a hydroxyl radical protein footprinting technique that allows for mapping of protein structure in their native environment. This protocol describes the assembly and set-up of the IV-FPOP microfluidic flow system.

Fast oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting (HRPF) method used to study protein structure, protein-ligand interactions, ...

Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging

Amyloid fibrils are associated with a number of neurodegenerative diseases such as Huntington&#39;s, Parkinson&#39;s, or Alzheimer&#39;s disease. These amyloid fibrils can sequester endogenous metastable proteins as well as components of the proteostasis network (PN) and thereby exacerbate protein misfolding in the cell. There are a limited number of tools available to assess the aggregation process of amyloid proteins within an animal. We present a protocol for fluorescence lifetime microscopy (FLIM) that allows monitoring as well as quantification of the amyloid fibrilization in specific cells, such as neurons, in a noninvasive manner and with the progression of aging and upon perturbation of the PN. FLIM is independent of the expression levels of the fluorophore and enables an analysis of the aggregation process without any further staining or bleaching. Fluorophores are quenched when they are in close vicinity of amyloid structures, which results in a decrease of the fluorescence lifetime. The quenching directly correlates with the aggregation of the amyloid protein. FLIM is a versatile technique that can be applied to compare the fibrilization process of different amyloid proteins, environmental stimuli, or genetic backgrounds in vivo in a non-invasive manner.

Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging

Fluorescence lifetime imaging monitors, quantifies and distinguishes the aggregation tendencies of proteins in living, aging, and stressed C. elegans disease models.

Amyloid fibrils are associated with a number of neurodegenerative diseases such as Huntington&#39;s, Parkinson&#39;s, or Alzheimer&#39;s disease. These ...

Monitoring Protein Aggregation Kinetics In Vivo using Automated Inclusion Counting in Caenorhabditis elegans

Protein aggregation into insoluble inclusions is a hallmark of a variety of human diseases, many of which are age-related. The nematode Caenorhabditis elegans is a well-established model organism that has been widely used in the field to study protein aggregation and toxicity. Its optical transparency enables the direct visualization of protein aggregation by fluorescence microscopy. Moreover, the fast reproductive cycle and short lifespan make the nematode a suitable model to screen for genes and molecules that modulate this process.
However, the quantification of aggregate load in living animals is poorly standardized, typically performed by manual inclusion counting under a fluorescence dissection microscope at a single time point. This approach can result in high variability between observers and limits the understanding of the aggregation process. In contrast, amyloid-like protein aggregation in vitro is routinely monitored by thioflavin T fluorescence in a highly quantitative and time-resolved fashion.
Here, an analogous method is presented for the unbiased analysis of aggregation kinetics in living C. elegans, using a high-throughput confocal microscope combined with custom-made image analysis and data fitting. The applicability of this method is demonstrated by monitoring inclusion formation of a fluorescently labeled polyglutamine (polyQ) protein in the body wall muscle cells. The image analysis workflow allows the determination of the numbers of inclusions at different timepoints, which are fitted to a mathematical model based on independent nucleation events in individual muscle cells. The method described here may prove useful to assess the effects of proteostasis factors and potential therapeutics for protein aggregation diseases in a living animal in a robust and quantitative manner.

Monitoring Protein Aggregation Kinetics In Vivo using Automated Inclusion Counting in Caenorhabditis elegans

Here, a method is presented for the analysis of protein aggregation kinetics in the nematode Caenorhabditis elegans. Animals from an age-synchronized population are imaged at different time points, followed by semiautomated inclusion counting in CellProfiler and fitting to a mathematical model in AmyloFit.

Protein aggregation into insoluble inclusions is a hallmark of a variety of human diseases, many of which are age-related. The nematode Caenorhabditis ...