Name: characterization of amyloid structures in aging c. elegans using fluorescence lifetime imaging
Uploaded: 2020-03-27T15:00:00
Description: Watch this Scientific Journal Video about Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging at JoVE.com

The muscle-Q40-mRFP strain provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). The neuronal-Q40-CFP was a kind gift of the Morimoto Lab. We acknowledge the DFG (KI-1988/5-1 to JK, NeuroCure PhD fellowship by the NeuroCure Cluster of Excellence to MLP), EMBO (Short term fellowship to MLP) and the Company of Biologists (travel grants to CG and MLP) for funding. We also acknowledge the Advanced Light Microscopy imaging facility at the Max Delbr&#252;ck Centre for Molecular Medicine, Berlin, for providing the setup to image the YFP constructs.

1. Synchronization of C. elegans
<ol>
	<li>Synchronize C. elegans either via alkaline hypochlorite solution treatment or via simple egg laying for 4 h at 20 &#176;C8.</li>
	<li>Grow and maintain nematodes at 20 &#176;C on nematode growth medium (NGM) plates seeded with OP50 E. coli according to standard procedures9. Age the nematodes until the desired developmental stage or day. 
	NOTE: In this protocol, young adults are imaged on day 4 and...

<ol>
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A., 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=Reducing+INS-IGF1+signaling+protects+against+non-cell+autonomous+vesicle+rupture+caused+by+SNCA+spreading.">Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading.</a> Autophagy. , 1-22 (2019).</li><li>Porta-de-la-Riva, M., Fontrodona, L., Villanueva, A., Cer&#243;n, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Basic+Caenorhabditis+elegans+methods:+Synchronization+and+observation.">Basic Caenorhabditis elegans methods: Synchronization and observation.</a> Journal of Visualized Experiments. 64, e4019 (2012).</li><li>Stiernagle, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maintenance+of+C.+elegans.">Maintenance of C. elegans.</a> WormBook the online review of C. elegans biology. 1999, 1-11 (2006).</li><li>Kamath, R. S., Martinez-Campos, M., Zipperlen, P., Fraser, A. G., Ahringer, J. <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+specific+RNA-mediated+interference+through+ingested+double-stranded+RNA+in+Caenorhabditis+elegans.">Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans.</a> Genome Biology. 2 (1), 1-10 (2001).</li><li>Becker, W., 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=Fluorescence+Lifetime+Imaging+by+Time-Correlated+Single-Photon+Counting.">Fluorescence Lifetime Imaging by Time-Correlated Single-Photon Counting.</a> Microscopy Research and Technique. 63 (1), 58-66 (2004).</li><li>Warren, S. 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=Rapid+global+fitting+of+large+fluorescence+lifetime+imaging+microscopy+datasets.">Rapid global fitting of large fluorescence lifetime imaging microscopy datasets.</a> PloS one. 8 (8), e70687 (2013).</li><li>Moronetti Mazzeo, L. E., Dersh, D., Boccitto, M., Kalb, R. G., Lamitina, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+and+aging+induce+distinct+polyQ+protein+aggregation+states.">Stress and aging induce distinct polyQ protein aggregation states.</a> Proceedings of the National Academy of Sciences of the United States of America. 109 (26), 10587-10592 (2012).</li><li>Ben-Zvi, A., Miller, E. A., Morimoto, R. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collapse+of+proteostasis+represents+an+early+molecular+event+in+Caenorhabditis+elegans+aging.">Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging.</a> Proceedings of the National Academy of Sciences of the United States of America. 106 (35), 14914-14919 (2009).</li><li>Wallrabe, H., Periasamy, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+protein+molecules+using+FRET+and+FLIM+microscopy.">Imaging protein molecules using FRET and FLIM microscopy.</a> Current Opinion in Biotechnology. 16 (1), 19-27 (2005).</li><li>Chan, F. T. S., Pinotsi, D., Kaminski Schierle, G. S., Kaminski, C. 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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=Fast+Fluorescence+Lifetime+Imaging+Reveals+the+Aggregation+Processes+of+&#945;-Synuclein+and+Polyglutamine+in+Aging+Caenorhabditis+elegans.">Fast Fluorescence Lifetime Imaging Reveals the Aggregation Processes of &#945;-Synuclein and Polyglutamine in Aging Caenorhabditis elegans.</a> ACS Chemical Biology. 14 (7), 1628-1636 (2019).</li><li>Kelbauskas, L., Dietel, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Internalization+of+Aggregated+Photosensitizers+by+Tumor+Cells:+Subcellular+Time-resolved+Fluorescence+Spectroscopy+on+Derivatives+of+Pyropheophorbide-a+Ethers+and+Chlorin+e6+under+Femtosecond+One-+and+Two-photon+Excitation.">Internalization of Aggregated Photosensitizers by Tumor Cells: Subcellular Time-resolved Fluorescence Spectroscopy on Derivatives of Pyropheophorbide-a Ethers and Chlorin e6 under Femtosecond One- and Two-photon Excitation.</a> Photochemistry and Photobiology. 76 (6), 686-694 (2002).</li><li>Becker, W., Su, B., Holub, O., Weisshart, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FLIM+and+FCS+detection+in+laser-scanning+microscopes:+Increased+efficiency+by+GaAsP+hybrid+detectors.">FLIM and FCS detection in laser-scanning microscopes: Increased efficiency by GaAsP hybrid detectors.</a> Microscopy Research and Technique. 74 (9), 804-811 (2011).</li><li>Suhling, K., French, M. 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The protocol presented here describes a microscopy-based technique to identify aggregated species in the C. elegans model system. FLIM can accurately characterize the presence of both aggregated and soluble species fused to a fluorophore via measurement of their fluorescence lifetime decays. When a fusion protein starts to aggregate its recorded average lifetime will shift from a higher to a lower value16. The propensity of aggregation can then be deduced by the drop in lifetime: the lowe...

Protein aggregation occurs both in aging and disease. The pathways that lead to the formation and deposition of large amyloids or amorphous inclusions are difficult to follow and their kinetics are similarly challenging to unravel. Proteins can misfold due to intrinsic mutations within their coding sequences, as in the case of genetic diseases. Proteins also misfold because the proteostasis network (PN) that keeps them soluble and properly folded is impaired, as happens during aging. The PN includes molecular chaperones and degradation machineries and is responsible for the biogenesis, folding, trafficking, and degradation of proteins1.
C. elegans has emerged as a model to study aging and disease due to its short lifespan, isogenic nature, and ease of genetic manipulation. Several C. elegans transgenic strains that express human disease-causing proteins in vulnerable tissues have been created. Importantly, many of the strains containing aggregation-prone proteins recapitulate the hallmark of amyloid disorders, the formation of large inclusions. Thanks to C. elegans&#39; transparent body, these aggregates can be visualized in vivo, noninvasively and nondestructively2. Generating any protein of interest (POI) in fusion with a fluorophore allows to investigate its locations, trafficking, interaction network, and general fate.
We present a protocol to monitor the aggregation of disease-causing proteins in living and aging C. elegans via fluorescence lifetime imaging microscopy (FLIM). FLIM is a powerful technique based on the lifetime of a fluorophore, rather than its emission spectra. The lifetime (tau, &#964;) is defined as the average time required by a photon to decay from its excited state back to its ground state. The lifetime of a given molecule is calculated with the time-domain technique of time-correlated single photon counting (TCSPC). In TCSPC-FLIM, the fluorescent decay function is obtained by exciting the fluorophore with short, high-frequency laser pulses and measuring the emitted photon&#39;s arrival times to a detector in respect to the pulses. When scanning a sample, a three-dimensional data array is created for each pixel: the array includes information on the distribution of the photons in their x,y spatial coordinates and their temporal decay curve. A given sample therefore becomes a map of lifetimes revealing information on the protein&#39;s structure, binding, and environment3,4. Each fluorescent protein possesses an intrinsic and precisely defined lifetime, usually of a few nanoseconds (ns), dependent on its physiochemical properties. Importantly, the lifetime of a fluorophore is independent of its concentration, fluorescent intensity, and of the imaging methodology. However, within a biological system, it can be affected by environmental factors such as pH, temperature, ion concentrations, oxygen saturation, and its interaction partners. Lifetimes are also sensitive to internal structural changes and orientation. Fusing a fluorophore to a POI results in a change in its lifetime and consequently information on the behavior of the fused protein. When a fluorophore is surrounded or encapsulated in a tightly bound environment, such as the antiparallel beta sheets of an amyloid structure, it loses energy non-radiatively, a process known as quenching5. Quenching of the fluorophore results in a shortening of its apparent lifetime. When soluble, a protein&#39;s lifetime will stay closer to its original, higher value. In contrast, when a protein starts to aggregate, its lifetime will inevitably shift to a lower value6,7. Therefore, it becomes possible to monitor the aggregation propensity of any amyloid-forming protein at different ages in living C. elegans.
Here we describe a protocol to analyze the aggregation of a fusion protein comprising different polyglutamine (CAG, Q) stretches (Q40, Q44, and Q85). We illustrate how the technique can be applied equally to different fluorophores, such as cyan fluorescent protein (CFP), yellow fluorescent protein (YFP) and monomeric red fluorescent protein (mRFP); and in all tissues of C. elegans, including the neurons, muscles, and the intestine. Moreover, in the context of proteostasis, FLIM is a very useful tool to observe changes upon depletion of molecular chaperones. Knocking down one of the key molecular chaperones, heat shock protein 1 (hsp-1), via RNA interference produces premature misfolding of proteins. The increase in aggregation load as a result of aging, disease, or deficient chaperones, is then measured as a decrease in fluorescence lifetime.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Agar-Agar Kobe I</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>5210.2</td>
			<td>NGM component</td>
		</tr>
		<tr>
			<td>Ahringer Library hsp-1 siRNA</td>
			<td>Source BioScience UK Limited</td>
			<td>F26D10.3</td>
			<td></td>
		</tr>
		<tr>
			<td>Ampicillin</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>K029.3</td>
			<td>Antibiotic</td>
		</tr>
		<tr>
			<td>B&#38;H DCS-120 SPC-150</td>
			<td>Becker &#38; Hickl GmbH</td>
			<td></td>
			<td>FLIM Aquisition software</td>
		</tr>
		<tr>
			<td>B&#38;H SPC830-SPC Image</td>
			<td>Becker &#38; Hickl GmbH</td>
			<td></td>
			<td>FLIM Aquisition software</td>
		</tr>
		<tr>
			<td>BD Bacto Peptone</td>
			<td>BD-Bionsciences</td>
			<td>211677</td>
			<td>NGM component</td>
		</tr>
		<tr>
			<td>C. elegans iQ44-YFP</td>
			<td>CAENORHABDITIS GENETICS CENTER (CGC)</td>
			<td>OG412</td>
			<td></td>
		</tr>
		<tr>
			<td>C. elegans iQ85-YFP</td>
			<td></td>
			<td></td>
			<td>Kind gift from Morimoto Lab</td>
		</tr>
		<tr>
			<td>C. elegans mQ40-RFP</td>
			<td></td>
			<td></td>
			<td>Kind gift from Morimoto Lab</td>
		</tr>
		<tr>
			<td>C. elegans nQ40-CFP</td>
			<td></td>
			<td></td>
			<td>Kind gift from Morimoto Lab</td>
		</tr>
		<tr>
			<td>Deckgl&#228;ser-18x18mm</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>0657.2</td>
			<td>Cover slips</td>
		</tr>
		<tr>
			<td>Isopropyl-&#946;-D-thiogalactopyranosid (IPTG)</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>2316.4</td>
			<td></td>
		</tr>
		<tr>
			<td>Leica M165 FC</td>
			<td>Leica Camera AG</td>
			<td></td>
			<td>Mounting Stereomicroscope</td>
		</tr>
		<tr>
			<td>Leica TCS SP5</td>
			<td>Leica Camera AG</td>
			<td></td>
			<td>Confocal Microscope</td>
		</tr>
		<tr>
			<td>Levamisole Hydrochloride</td>
			<td>AppliChem GmbH</td>
			<td>A4341</td>
			<td>Anesthetic</td>
		</tr>
		<tr>
			<td>OP50 Escherichia coli</td>
			<td>CAENORHABDITIS GENETICS CENTER (CGC)</td>
			<td>OP50</td>
			<td></td>
		</tr>
		<tr>
			<td>PicoQuant PicoHarp300</td>
			<td>PicoQuant GmbH</td>
			<td></td>
			<td>FLIM Aquisition software</td>
		</tr>
		<tr>
			<td>Sodium Azide</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>K305.1</td>
			<td>Anesthetic</td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>3957.2</td>
			<td>NGM component</td>
		</tr>
		<tr>
			<td>Standard-Objekttr&#228;ger</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>0656.1</td>
			<td>Glass slides</td>
		</tr>
		<tr>
			<td>Universal Agarose</td>
			<td>Bio &#38; Sell GmbH</td>
			<td>BS20.46.500</td>
			<td></td>
		</tr>
		<tr>
			<td>Zeiss AxioObserver.Z1</td>
			<td>Carl Zeiss AG</td>
			<td></td>
			<td>Confocal Microscope</td>
		</tr>
		<tr>
			<td>Zeiss LSM510-Meta NLO</td>
			<td>Carl Zeiss AG</td>
			<td></td>
			<td>Confocal Microscope</td>
		</tr>
	</tbody>
</table>

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.

The protocol shows how to accurately monitor the formation of aggregated species in living C. elegans, both during its natural aging and when subjected to stress. We selected four different strains of transgenic nematodes expressing polyglutamine proteins of either 40Q, 44Q, or 85Q repeats. These proteins are synthesized in different tissues and were fused to different fluorophores. The C. elegans strains either expressed Q40-mRFP in the body wall muscles (mQ40-RFP), Q40...

Watch this Scientific Journal Video about Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging at JoVE.com

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.

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 ...

The method allow us to clearly distinguish integrated amyloid protein structures from the soluble and even accumulated counterparts. The technique is performed in vivo in a noninvasive manner with little or no toxic side effects. As it depends on the fluorescent properties of the fluorophore itself, it is highly robust and reproducible over time.FLIM has been utilized in the field of cancer diagnosis. However, we employ it to study the basic mechanisms of protein aggregation which are indeed relevant to neurodegenerative diseases. The methodology can be used in the field of protein aggregation.As long as the disease associated protein is tagged with a fluorescent probe, it can be tracked and monitored over time. Compounds and strategies that either promote or prevent aggregation can be successfully studied. Any biological system that allows to be visualized by light microscopy is suitable for FLIM either in vivo or ex vivo, for example in cell culture, in fixated or permeabilized samples and in any medium necessary.Make sure to test the properties of your selected fluorophore within the nematode before obtaining experimental data and to test that the setup is fully functional before acquiring measurements. To begin, grow and maintain nematodes at 20 degrees Celsius on NGM plates. Age the nematodes until day four of life as the young adults and day eight of life as the old adults.On the day of imaging, start by preparing the imaging slides. Place agarose and double distilled water at a concentration of 3%weight by volume. Transfer it into a microwave to melt and then let it cool slightly.Cut the tip of a one milliliter pipette tip and take roughly 200 microliters of the melted agarose. Pipette the agarose onto a clean glass slide and immediately place a second one on top avoiding the formation of any bubbles. Leave the slides to dry and gently remove the top glass slide.The result is a glass slide with an even agarose surface where the nematodes will be positioned. Once the imaging setup is ready to use, working under a stereo microscope, place a 10 microliter drop of anesthetic compound onto an agarose pad and gently transfer five to 10 nematodes into it. Use an eyelash tip to separate the nematodes.Keep them close together but not touching to allow for easier localization of the nematodes during image acquisition. Carefully overlay the nematodes with a coverslip. Within one hour after mounting, take measurements.Make sure the nematodes are completely immobile. Open the FLIM acquisition software. Locate the tab button and press enable outputs.Place the slide with the mounted C.elegans on the stage and using a 10X magnification lens in transmission mode, localize the position of the nematodes on the slide. Remove the slide, switch the objective to a 63X magnification lens, and apply the required immersion medium. Place the slide on the stage and localize the nematodes.Start scanning the sample. Select a region of interest and focus on its maximum projection plane. On the interface of the FLIM software, preview the number of photons detected.The ADC value should be between one times 10 to the fourth and one times 10 to the fifth. If necessary, shift the focus on a different plane or increase the laser power to collect more photons. Ensure that you avoid photon pileup but collect a sufficient amount of photons to create a good lifetime fit and measurement.In the menu bar, select the tab to set the acquisition parameters. Select scan sync in to allow for single photon detection. Set the acquisition to a fixed amount of time or a fixed number of photons.Press start to begin acquisition. Open the software and import FLIM data files via file, load FLIM data. Load all the samples from one condition even if obtained in different sessions and from different biological repeats.If necessary, segment to signal nematode for many FLIM picture via segmentation, segmentation manager. Drag the cropping tool around the area of interest until it is highlighted. Once completed, press OK.Select a small region where the intensity-based image of a C.elegans appears.The decay curve of that region appears in the large decay window on the right side of the interface. To extrapolate the lifetime, on the data tab, set an arbitrary integrated minimum value between 40 to 300 to exclude any pixels that are too dim to produce a good fit. Select a time minimum and a time maximum number to limit the FLIM signal to these values.Do not change the preset counts photon of one. Input the repetition rate in megahertz of the laser utilized during acquisition. Input a gate max value to exclude all saturated pixels.On the lifetime tab, select a global fitting to be used. Do not change any other parameter except the number of exponential selection if it is known that the chosen fluorescence decay is multi-exponential and exhibits more than a single lifetime. Upload the IRF via the IRF menu.To estimate the IRF shift, select IRF, estimate IRF shift. A set of values automatically appears on the IRF tab. Once this is established, do not change any other parameters of this tab.Once all parameters are set, press fit data set. The resulting fit highlighted in a blue line should overlap with all the events. A good fit is obtained when all events are aligned along the fit.Click the parameters tab located within the top right menus of the software's interface and select statistic, weighted mean, and check that the chi square value is as close as possible to one. The lifetime value of the selected image is thus revealed as tau one. Export any information of interest through file, export intensity images, fit result table, images, histograms.Representative maps of C.elegans expressing muscular Q40 RFP on day four or day eight of life are shown here. The longer Q stretch of the IQ85 was more prone to aggregation and exhibited a fluorescence lifetime shift in the histogram already at day four of life. In fact, at day four, foci formation was observed for IQ85 while still absent in IQ44.Upon aging, however, IQ44 also exhibited foci formation and thus a reduced fluorescence lifetime. Finally, foci formation was not detected nor was decreased fluorescence lifetime in the NQ40CFP strain. For this strain, there were only subtle non-significant changes to the mean fluorescence lifetime upon aging.Once the nematode model is established, the amount of photon collected is paramount to obtain a good lifetime fit. The method can be further conjoined with different techniques such as Forster resonance energy transfer, FRET, fluorescence recovery after photobleaching, FRAP, or measurement. All of these adaptations provide extra information on the properties of the protein studies and its aggregated form.Within the field of protein aggregation and protein homeostasis, the technique allowed to investigate any perturbation imposed on the system, the distribution of different protein species, and the trafficking and in general the difference and significance of soluble and insoluble protein fractions within the living organism. The anesthetic sodium azide is toxic and should be handled with gloves and goggles and diluted under a fume hood. Because the technique is microscopy-based, it is important to follow all warnings related to work with lasers.

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Research

JoVE Journal

Biochemistry

Imaging Amyloid Tissues Stained with Luminescent Conjugated Oligothiophenes by Hyperspectral Confocal Microscopy and Fluorescence Lifetime Imaging

Proteins that deposit as amyloid in tissues throughout the body can be the cause or consequence of a large number of diseases. Among these we find neurodegenerative diseases such as Alzheimer&#39;s and Parkinson&#39;s disease afflicting primarily the central nervous system, and systemic amyloidosis where serum amyloid A, transthyretin and IgG light chains deposit as amyloid in liver, carpal tunnel, spleen, kidney, heart, and other peripheral tissues. Amyloid has been known and studied for more than a century, often using amyloid specific dyes such as Congo red and Thioflavin T (ThT) or Thioflavin (ThS). In this paper, we present heptamer-formyl thiophene acetic acid (hFTAA) as an example of recently developed complements to these dyes called luminescent conjugated oligothiophenes (LCOs). hFTAA is easy to use and is compatible with co-staining in immunofluorescence or with other cellular markers. Extensive research has proven that hFTAA detects a wider range of disease associated protein aggregates than conventional amyloid dyes. In addition, hFTAA can also be applied for optical assignment of distinct aggregated morphotypes to allow studies of amyloid fibril polymorphism. While the imaging methodology applied is optional, we here demonstrate hyperspectral imaging (HIS), laser scanning confocal microscopy and fluorescence lifetime imaging (FLIM). These examples show some of the imaging techniques where LCOs can be used as tools to gain more detailed knowledge of the formation and structural properties of amyloids. An important limitation to the technique is, as for all conventional optical microscopy techniques, the requirement for microscopic size of aggregates to allow detection. Furthermore, the aggregate should comprise a repetitive &#946;-sheet structure to allow for hFTAA binding. Excessive fixation and/or epitope exposure that modify the aggregate structure or conformation can render poor hFTAA binding and hence pose limitations to accurate imaging.

Amyloid deposition is a hallmark of different diseases and afflicts many different organs. This paper describes the application of luminescent conjugated oligothiophene fluorescence staining in combination with fluorescence microscopy techniques. This staining method represents a powerful tool for detection and exploration of protein aggregates in both clinical and scientific setups.

Proteins that deposit as amyloid in tissues throughout the body can be the cause or consequence of a large number of diseases. Among these we find ...

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 ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Here we describe a simple protocol for rapidly producing hundreds of nematode growth media agar, 96-well culture plates with consistent numbers of Caenorhhabditis elegans per well. These cultures are useful for the phenotypic screening of whole organisms. We focus here on using these cultures to screen chemicals for pro-longevity effects.

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

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 ...

Use of Two Dimensional Semi-denaturing Detergent Agarose Gel Electrophoresis to Confirm Size Heterogeneity of Amyloid or Amyloid-like Fibers

Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. The ability to readily detect the formation of these fibers under various experimental conditions is essential for understanding their potential function. Many methods have been used to detect the fibers, but not without some drawbacks. For example, electron microscopy (EM), or staining with Congo Red or Thioflavin T often requires purification of the fibers. On the other hand, semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) allows detection of the SDS-resistant amyloid-like fibers in the cell extracts without purification. In addition, it allows the comparison of the size difference of the fibers. More importantly, it can be used to identify specific proteins within the fibers by Western blotting. It is less time consuming and more easily accessible to a wider number of labs. SDD-AGE results often show variable degree of heterogeneity. It raises the question whether part of the heterogeneity results from the dissociation of the protein complex during the electrophoresis in the presence of SDS. For this reason, we have employed a second dimension of SDD-AGE to determine if the size heterogeneity seen in SDD-AGE is truly a result of fiber heterogeneity in vivo and not a result of either degradation or dissociation of some of the proteins during electrophoresis. This method allows fast, qualitative confirmation that the amyloid or amyloid-like fibers are not partially dissociating during the SDD-AGE process.

Here we use two-dimensional semi-denaturing agarose gel electrophoresis to confirm the presence of amyloid-like fibers of heterogeneous size and exclude the possibility that the size heterogeneity is due to dissociation of the amyloid fibers during the gel running process.

Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. ...

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 ...

Rapid Fluorescence-based Characterization of Single Extracellular Vesicles in Human Blood with Nanoparticle-tracking Analysis

Extracellular vesicles (EVs), including exosomes, are specialized membranous nano-sized vesicles found in bodily fluids that are constitutively released from many cell types and play a pivotal role in regulating cell-cell communication and a diverse range of biological processes. Many different methods for the characterization of EVs have been described. However, most of these methods have the disadvantage that the preparation and characterization of the samples are very time-consuming, or it is extremely difficult to analyze specific markers of interest due to their small size and due to the lack of discrete populations. While methods for analysis of EVs have been considerably improved over the last decade, there is still no standardized method for characterization of single EVs. Here, we demonstrate a semi-automated method for characterization of single EVs by fluorescence-based nanoparticle-tracking analysis. The protocol that is presented addresses the common problem of many researchers in this field and provides the complete workflow for rapid isolation of EVs and characterization with PKH67, a general cell membrane linker, as well as with specific surface markers such as CD63, CD9, vimentin, and lysosomal-associated membrane protein 1 (LAMP-1). The presented results show a high level of reproducibility, as confirmed by other methods, such as Western blotting. In the conducted experiments, we exclusively used EVs isolated from human serum samples, but this method is also suitable for plasma or other body fluids and can be adjusted for characterization of EVs from cell culture supernatants. Irrespective of the future progress of research on EV biology, the protocol that is presented here provides a rapid and reliable method for rapid characterization of single EVs with specific markers.

In this protocol, we describe the complete workflow for rapid isolation of extracellular vesicles from human whole blood and characterization of specific markers by fluorescence-based nanoparticle-tracking analysis. The presented results show a high level of reproducibility and can be adjusted to cell culture supernatants.

Extracellular vesicles (EVs), including exosomes, are specialized membranous nano-sized vesicles found in bodily fluids that are constitutively released ...

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.

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.

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

Interactions with and Membrane Permeabilization of Brain Mitochondria by Amyloid Fibrils

A growing body of evidence indicates that membrane permeabilization, including internal membranes such as mitochondria, is a common feature and primary mechanism of amyloid aggregate-induced toxicity in neurodegenerative diseases. However, most reports describing the mechanisms of membrane disruption are based on phospholipid model systems, and studies directly targeting events occurring at the level of biological membranes are rare. Described here is a model for studying the mechanisms of amyloid toxicity at the membrane level. For mitochondrial isolation, density gradient medium is used to obtain preparations with minimal myelin contamination. After mitochondrial membrane integrity confirmation, the interaction of amyloid fibrils arising from &#945;-synuclein, bovine insulin, and hen egg white lysozyme (HEWL) with rat brain mitochondria, as an in vitro biological model, is investigated. The results demonstrate that treatment of brain mitochondria with fibrillar assemblies can cause different degrees of membrane permeabilization and ROS content enhancement. This indicates structure-dependent interactions between amyloid fibrils and mitochondrial membrane. It is suggested that biophysical properties of amyloid fibrils and their specific binding to mitochondrial membranes may provide explanations for some of these observations.

Provided here is a protocol for investigating the interactions between native form, prefibrillar, and mature amyloid fibrils of different peptides and proteins with mitochondria isolated from different tissues and various areas of the brain.

A growing body of evidence indicates that membrane permeabilization, including internal membranes such as mitochondria, is a common feature and primary ...

SUMO-Binding Entities (SUBEs) as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer

Post-translational modification is a key mechanism regulating protein homeostasis and function in eukaryotic cells. Among all ubiquitin-like proteins in liver cancer, the modification by SUMO (Small Ubiquitin MOdifier) has been given the most attention. Isolation of endogenous SUMOylated proteins in vivo is challenging due to the presence of active SUMO-specific proteases. Initial studies of SUMOylation in vivo were based on the molecular detection of specific SUMOylated proteins (e.g., by western blot). However, in many cases, antibodies, generally made with non-modified recombinant protein, did not immunoprecipitate SUMOylated forms of the protein of interest.&#160;Nickel chromatography has been the other approach to study SUMOylation by capturing histidine-tagged versions of SUMO molecules. This approach is mainly used in cells stably expressing or transiently transfected with His-SUMO molecules. To overcome these limitations, SUMO-binding entities (SUBEs) were developed to isolate endogenous SUMOylated proteins. Herein, we describe all the steps required for the enrichment, isolation, and identification of SUMOylated substrates from human hepatoma cells and hepatic tissues from a liver cancer mouse model by using SUBEs. Firstly, we describe methods involved in the preparation and lysis of the human hepatoma cells and liver tumor tissue samples. Then, a thorough explanation of the preparation of SUBEs and controls is detailed along with the protocol for the protein pull-down assays. Finally, some examples are provided regarding the options available for the identification and characterization of the SUMOylated proteome, namely the use of western-blot analysis for the detection of a specific SUMOylated substrate from liver tumors or the use of proteomics by mass spectrometry for high-throughput characterization of the SUMOylated proteome and interactome in hepatoma cells.

SUMO-Binding Entities SUBEs as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer

Here, we present a protocol to enrich, isolate, identify, and characterize proteins modified by SUMO in vivo both from human hepatoma cells and liver tumors obtained from mouse models of hepatocellular carcinoma by using SUMO-binding entities (SUBEs).

Post-translational modification is a key mechanism regulating protein homeostasis and function in eukaryotic cells. Among all ubiquitin-like proteins in ...