We thank Dr. R. Howard Berg, Director of the Integrated Microscopy Facility at the Donald Danforth Plant Science Center, for his guidance and help with confocal microscopy. The authors have no conflict of interest to declare.

1. Labeling of Defensins with Fluorophores
<ol>
	<li>Select a fluorophore that has minimum effect on the antimicrobial properties as well as the uptake and localization of defensin inside the living cell. 
	NOTE: Selecting optimal fluorophore depends on specific experimental objectives. The spectral and chemical properties, photostability, size and charge of the fluorophore should also be considered.</li>
	<li>Label defensin with the selected fluorophore using an appropriate peptide labeling kit available from commercial vendors. Alternatively, chemically synthesize fluorophore-labeled defensins. In this study, label MtDef5 defensin with DyLight550 using a commercial labeling kit according to manufacturer&#39;s protocol and tetramethyl rhodamine (TAMRA)-labeled MtDef4 defensin was chemically synthesized commercially. 
	NOTE: It is recommended that chemically synthesized fluorophore tagged peptides (especially for short peptides of 50 amino acids or less) be used since the fluorophore can be attached to the N- or C-terminal residue of the peptide to ensure minimum effect on its antimicrobial activity. Synthesis of long peptides with more than three disulfide bonds is challenging. In this case, it is recommended that peptide be labeled with an optimal fluorophore using a suitable commercially available peptide labeling kit.</li>
	<li>Test in vitro antimicrobial activity of the labeled defensin and determine the minimal inhibitory concentration (MIC) against the fungi to be investigated. 
	NOTE: In this study, the MIC of DyLight550-MtDef5 and TMR-MtDef4 was determined against Neurospora crassa and Fusarium graminearum.</li>
</ol>
2. Fungal Cultures and Growth Medium
<ol>
	<li>Transfer conidia from a N. crassa stock culture to slant tube containing Vogel&#39;s agar medium21 and incubate at room temperature under light for 5 days.</li>
	<li>Culture F. graminearum PH-1 strain on plates containing complete medium (CM)22 at 28 &#186;C for 5 days. For production of conidia, inoculate 4 (10 mm diameter) plugs of 5 day old culture of F. graminearum PH-1 into 50 mL of carboxymethyl cellulose (CMC) medium (15 g carboxymethyl cellulose, 1 g Yeast extract, 0.5 g MgSO4.7 H2O, 1 g NH4NO3, and 1 g KH2PO4) and culture for 4-7 days at 28 &#186;C in a rotary shaker at 180 rpm.</li>
</ol>
3. Preparation of Conidial Suspension
<ol>
	<li>F. graminearum conidial suspension
	<ol>
		<li>Vortex the F. graminearum liquid culture and collect conidia by filtering 1.5 mL fungal culture through two layers of filtration material (such as Miracloth)&#160;into a 2 mL microcentrifuge tube. Centrifuge the conidial suspension at 13,226 x g speed in a microcentrifuge for 2 min.</li>
		<li>Discard the supernatant, and add 1 mL of sterile water to wash the pellet.</li>
		<li>Centrifuge the conidial suspension at 13,226 x g speed in a microcentrifuge for 2 min. Discard the supernatant and resuspend the pellet in 1 mL of 2X SFM (Synthetic Fungal Media)23.</li>
		<li>Count the conidia using a hemocytometer under a light microscope.</li>
		<li>Adjust the conidial suspension to 105 conidia/mL with 2X SFM.</li>
	</ol>
	</li>
	<li>N. crassa conidial suspension
	<ol>
		<li>Transfer a small amount of growing culture (5 day old) of N. crassa using an inoculation loop to a microcentrifuge tube containing 2 mL of Vogel&#39;s liquid medium.</li>
		<li>Vortex the conidial suspension and filter through filtration material into a new microcentrifuge tube.</li>
		<li>Centrifuge the conidial suspension at maximum speed in a microcentrifuge for 2 min. Discard the supernatant and resuspend the conidial pellet in 1 mL of Vogel&#39;s liquid medium.</li>
		<li>Count the conidia using a hemocytometer under a light microscope.</li>
		<li>Adjust the conidial suspension to 105 conidia/mL with Vogel&#39;s liquid medium.</li>
	</ol>
	</li>
</ol>
4. Sample Preparation and Confocal Microscopy
<ol>
	<li>Subcellular localization of MtDef4 defensin into fungal cells
	<ol>
		<li>Pipette 50 &#181;L of each conidial suspension (105 conidia/mL) into the 10 mm microwell of 35 mm glass bottom microwell dishes. For the observation of conidia, directly proceed to the next step, or for germlings preparation, pipette 50 &#181;L of N. crassa and F. graminearum conidia into the 35 mm culture dishes and let germinate for 3-6 h at room temperature.</li>
		<li>Add 50 &#181;L of fluorescently labeled defensin at the MIC to each microwell dish and incubate for 2.5 h. The MIC of the fluorophore-labeled defensins used here (step 1.3) is 3 &#181;M for both N. crassa and F. graminearum and the MIC of TMR-MtDef4 for N. crassa and F. graminearum was 1 &#181;M and 12 &#181;M, respectively.</li>
		<li>Add 2 &#181;L of membrane-selective dye FM4-64 (final concentration: 5 &#181;M) in culture dish and incubate for 30 min and mount immediately on the confocal microscope for imaging.</li>
		<li>Select the White Light laser (WLL). Use the two laser sources 488 nm and 550 nm to excite TMR-MtDef4 and FM4-64 dye, respectively. Detect fluorescence of TMR-MtDef4 at 580-700 nm and detect FM4-64 dye at 690-800 nm. 
		NOTE: Perform confocal microscopy in the dark room.</li>
	</ol>
	</li>
	<li>Time lapse imaging of internalization of MtDef5 defensin
	<ol>
		<li>Pipette 50 &#181;L of N. crassa and F. graminearum conidial suspension (105 conidia/mL) into 10 mm microwell of 35 mm glass bottom microwell dishes. The 10 mm microwell is uncoated and has a No. 1.5 cover glass at the bottom. For the observation of conidia, directly proceed to the next step. For observation of germlings, incubate conidia for 3-6 h at room temperature before proceeding with the microscopy.</li>
		<li>Turn on WLL. Select the laser line at 550 nm to excite the fluorophore-labeled defensins used here (step 1.3) and FM4-64 with 1.00% intensity and activate the corresponding detectors. The fluorophore-labeled defensins used here (step 1.3) was detected at 560 - 600 nm and the FM4-64dye was detected at 690 - 800 nm. 
		NOTE: Use low laser intensity for live cell imaging as high laser intensity can cause damage to the live fungal cells.</li>
		<li>Mount the microwell dish on the microscope. Find the cells using 10 x objectives initially, then switch to 100x/1.44 OIL objective for higher magnification. 
		NOTE: Set the scan mode to xyzt (combination of Z-stack and time-lapse modes), Z position, Zoom, frequency of image capture, etc. before proceeding to the next step.</li>
		<li>Add 50 &#181;L of the fluorophore-labeled defensins used here (step 1.3) of at the MIC of 3 &#181;M and 2 &#181;L of membrane-selective dye FM4-64 (final concentration 5 &#181;M) to each microwell dish, and start time-lapse imaging. Place small pieces of wet filter papers in the microwell dishes to prevent evaporation. The frequency of image capture was 3 min 30 s and the total period was 2 h 30 min. 
		NOTE: Adding defensin and fluorophore after mounting microwell dish in the microscope can defocus the region of interest. Therefore, after adding defensin and fluorophore to the microwell, region of interest needs to be refocused which can cause delay in image acquisition.</li>
		<li>Use a confocal microscope for all confocal imaging and carry out the microscopy at room temperature in a dark room.</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

In this study, a reliable live-cell imaging methodology with the use of fluorescently labeled antifungal defensins was described to study the kinetics of the internalization of these peptides into fungal cells and to determine their subcellular targets. This method is a powerful tool to visualize the dynamics of the interaction between defensins and fungal cells temporally and spatially.
Various methods have been used to study the internalization and intracellular localization of plant defensi...

Plants have evolved a sophisticated innate immune system for defense against the microbial plant pathogens1. They express numerous gene-encoded host defense peptides with putative antimicrobial activity2. Indeed, many of these peptides display antimicrobial activity in vitro3. Defensins comprise one of the largest groups of host defense peptides in the plant kingdom4. These cysteine-rich, cationic peptides exhibit potent growth inhibitory activity against fungal and oomycete pathogens at micromolar concentrations and represent one of the first lines of defense against these pathogens5,6. Because of their potent antifungal activity, defensins can be exploited in agribiotechnological applications to generate disease resistant crops. Constitutive overexpression of several plant defensins has been shown to enhance disease resistance in the greenhouse and field tests of transgenic crops6. It is important to unravel the mechanisms of action (MOA) of these antifungal peptides in order to fully harness their potential as effective tools for crop protection. However, the MOA of these plant defensins are poorly understood. Current evidence suggests that they exhibit different MOA5,6,7,8. Some defensins act extracellularly on fungi and target specific cell wall/plasma membrane resident sphingolipids, disrupt membrane integrity and activate cellular toxicity pathways9,10,11. Recently, however, antifungal defensins that translocate into fungal cells have been discovered12,13,14. Some of these defensins bind to membrane-resident bioactive phospholipids, form oligomeric complexes and permeabilize plasma membranes15,16,17. Thus, some aspects of the MOA of plant defensins have been elucidated. However, the MOA of plant defensins likely involve a complex set of events which have not yet been identified and integrated into a comprehensive model. In particular, there remains a major gap in our understanding of the cellular targets of these peptides.
With recent advances in microscopy technologies and the development of new fluorescent probes, live-cell imaging techniques are now frequently used to study the MOA of antimicrobial peptides (AMPs). These techniques complement widely used methods such as immunolocalization, electron microscopy, atomic force microscopy or X-ray tomography18, which have been employed mostly to analyze the effects of antifungal peptides on the morphology and growth of fungal cells including the study of cell wall integrity, alterations in cell growth/branching patterns, as well as plasma membrane permeabilization and killing. Nevertheless, these studies have been limited to imaging cells at a certain time point after treatment with the peptides instead of performing time-lapse imaging on the same cells to monitor their dynamic changes in response to defensin challenge. In recent years, use of fluorescently labeled peptides in conjunction with live cell imaging using confocal microscopy has enabled real-time visualization of the dynamics of AMP&#8211;microbe interactions. Both naturally purified and chemically synthesized antifungal peptides can be tagged with fluorescent labels (e.g., DyLight, rhodamine, BODIPY, or Alexa Fluor based dyes) and directly observed during their interaction with cells by time-lapse live-cell imaging. The use of these labeled peptides has significantly increased our understanding of the different aspects of their MOA including mode of entry, subcellular localization, intracellular trafficking, and sites of antifungal action within living fungal cells18.
Recently, several studies have shown that various antifungal peptides including plant defensins are internalized by living fungal cells12,14,19,20. The MOA of these defensins likely involve interaction with intracellular targets. We have recently reported the antifungal action of a plant defensin MtDef4 in two ascomycete fungi, Neurospora crassa and Fusarium graminearum. MtDef4 was shown to use different pathways for fungal cell entry and subcellular localization in these fungi14. This study used chemically synthesized tetramethyl rhodamine (TAMRA)-labeled MtDef4 in combination with vital fluorescent dyes (the membrane selective dye, FM4-64; membrane-permeant dye, SYTOX Green; the cell death reporter dye, propidium iodide) and metabolic inhibitors. These analyses demonstrated the kinetics of the internalization of MtDef4, its mechanisms of intracellular transportation and its subcellular targets14.
Here, a protocol for live-cell imaging using confocal microscopy is presented. The protocol utilizes fluorescently labeled peptides in combination with vital fluorescent dyes to study plant defensin-fungal interactions, in particular, the pathways of translocation and the intracellular targets of defensins in fungal cells.

<table>
	<tbody>
		<tr>
			<td>FM4-64 Dye</td>
			<td>Life Technologies</td>
			<td>T13320</td>
			<td></td>
		</tr>
		<tr>
			<td>DyLight 550 Antibody Labeling Kit</td>
			<td>Thermo Scientific</td>
			<td>84530</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Bottom Microwell Dishes</td>
			<td>Mat TeK</td>
			<td>P35G-1.5-10-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Mira cloth</td>
			<td>EMD Millipore Corp</td>
			<td>475855-1R</td>
			<td></td>
		</tr>
		<tr>
			<td>SP8-X confocal microscope</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ software</td>
			<td>FiJi</td>
			<td></td>
			<td>For Image analysis</td>
		</tr>
		<tr>
			<td>Imaris software</td>
			<td>Bitplane</td>
			<td></td>
			<td>For Image analysis</td>
		</tr>
	</tbody>
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live-cell imaging of fungal cells to investigate modes of entry and subcellular localization of antifungal plant defensins

Small cysteine-rich defensins are one of the largest groups of host defense peptides present in all plants. Many plant defensins exhibit potent in vitro antifungal activity against a broad-spectrum of fungal pathogens and therefore have the potential to be used as antifungal agents in transgenic crops. In order to harness the full potential of plant defensins for diseases control, it is crucial to elucidate their mechanisms of action (MOA). With the advent of advanced microscopy techniques, live-cell imaging has become a powerful tool for understanding the dynamics of the antifungal MOA of plant defensins. Here, a confocal microscopy based live-cell imaging method is described using two fluorescently labeled plant defensins (MtDef4 and MtDef5) in combination with vital fluorescent dyes. This technique enables real-time visualization and analysis of the dynamic events of MtDef4 and MtDef5 internalization into fungal cells. Importantly, this assay generates a wealth of information including internalization kinetics, mode of entry and subcellular localization of these peptides. Along with other cell biological tools, these methods have provided critical insights into the dynamics and complexity of the MOA of these peptides. These tools can also be used to compare the MOA of these peptides against different fungi.

Live cell imaging was carried out to track and compare the internalization and subcellular localization of two defensins, MtDef4 and MtDef5, from Medicago truncatula; in fungal cells. TMR-MtDef4 was chemically synthesized while MtDef5 was labeled with Dylight550 (Dylight550-MtDef5). Conidia were incubated with either defensin in combination with the membrane selective dye FM4-64. Figure 1 shows that TMR-MtDef4 has different trafficking pathways in <e...

Watch this Scientific Journal Video about Live-cell Imaging of Fungal Cells to Investigate Modes of Entry and Subcellular Localization of Antifungal Plant Defensins at JoVE.com

Live-cell Imaging of Fungal Cells to Investigate Modes of Entry and Subcellular Localization of Antifungal Plant Defensins

Plant defensins play an important role in plant defense against pathogens. For effective use of these antifungal peptides as antifungal agents, understanding their modes of action (MOA) is critical. Here, a live-cell imaging method is described to study critical aspects of the MOA of these peptides.

Small cysteine-rich defensins are one of the largest groups of host defense peptides present in all plants. Many plant defensins exhibit potent in vitro ...

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JoVE Journal

Biology

6.6K Views.  Donald Danforth Plant Science Center. Plant defensins play an important role in plant defense against pathogens. For effective use of these antifungal peptides as antifungal agents, understanding their modes of action (MOA) is critical. Here, a live-cell imaging method is described to study critical aspects of the MOA of these peptides.

Video: Live-cell Imaging of Fungal Cells to Investigate Modes of Entry and Subcellular Localization of Antifungal Plant Defensins

Live-cell Imaging and Quantitative Analysis of Embryonic Epithelial Cells in Xenopus laevis

Embryonic epithelial cells serve as an ideal model to study morphogenesis where multi-cellular tissues undergo changes in their geometry, such as changes in cell surface area and cell height, and where cells undergo mitosis and migrate. Furthermore, epithelial cells can also regulate morphogenetic movements in adjacent tissues1. A traditional method to study epithelial cells and tissues involve chemical fixation and histological methods to determine cell morphology or localization of particular proteins of interest. These approaches continue to be useful and provide "snapshots" of cell shapes and tissue architecture, however, much remains to be understood about how cells acquire specific shapes, how various proteins move or localize to specific positions, and what paths cells follow toward their final differentiated fate. High resolution live imaging complements traditional methods and also allows more direct investigation into the dynamic cellular processes involved in the formation, maintenance, and morphogenesis of multicellular epithelial sheets. Here we demonstrate experimental methods from the isolation of animal cap tissues from Xenopus laevis embryos to confocal imaging of epithelial cells and simple measurement approaches that together can augment molecular and cellular studies of epithelial morphogenesis.

Live-cell Imaging and Quantitative Analysis of Embryonic Epithelial Cells in Xenopus laevis

Xenopus embryonic epithelia are an ideal model system to study cell behaviors such as polarity development and shape change during epithelial morphogenesis. Traditional histology of fixed samples is increasingly being complemented by live-cell confocal imaging. Here we demonstrate methods to isolate frog tissues and visualize live epithelial cells and their cytoskeleton using live-cell confocal microscopy.

Embryonic epithelial cells serve as an ideal model to study morphogenesis where multi-cellular tissues undergo changes in their geometry, such as changes ...

Fluorescence-based Measurement of Store-operated Calcium Entry in Live Cells: from Cultured Cancer Cell to Skeletal Muscle Fiber

Store operated Ca2+ entry (SOCE), earlier termed capacitative Ca2+ entry, is a tightly regulated mechanism for influx of extracellular Ca2+ into cells to replenish depleted endoplasmic reticulum (ER) or sarcoplasmic reticulum (SR) Ca2+ stores1,2. Since Ca2+ is a ubiquitous second messenger, it is not surprising to see that SOCE plays important roles in a variety of cellular processes, including proliferation, apoptosis, gene transcription and motility. Due to its wide occurrence in nearly all cell types, including epithelial cells and skeletal muscles, this pathway has received great interest3,4. However, the heterogeneity of SOCE characteristics in different cell types and the physiological function are still not clear5-7.
The functional channel properties of SOCE can be revealed by patch-clamp studies, whereas a large body of knowledge about this pathway has been gained by fluorescence-based intracellular Ca2+ measurements because of its convenience and feasibility for high-throughput screening. The objective of this report is to summarize a few fluorescence-based methods to measure the activation of SOCE in monolayer cells, suspended cells and muscle fibers5,8-10. The most commonly used of these fluorescence methods is to directly monitor the dynamics of intracellular Ca2+ using the ratio of F340nm and F380nm (510 nm for emission wavelength) of the ratiometric Ca2+ indicator Fura-2. To isolate the activity of unidirectional SOCE from intracellular Ca2+ release and Ca2+ extrusion, a Mn2+ quenching assay is frequently used. Mn2+ is known to be able to permeate into cells via SOCE while it is impervious to the surface membrane extrusion processes or to ER uptake by Ca2+ pumps due to its very high affinity with Fura-2. As a result, the quenching of Fura-2 fluorescence induced by the entry of extracellular Mn2+ into the cells represents a measurement of activity of SOCE9. Ratiometric measurement and the Mn+2 quenching assays can be performed on a cuvette-based spectrofluorometer in a cell population mode or in a microscope-based system to visualize single cells. The advantage of single cell measurements is that individual cells subjected to gene manipulations can be selected using GFP or RFP reporters, allowing studies in genetically modified or mutated cells. The spatiotemporal characteristics of SOCE in structurally specialized skeletal muscle can be achieved in skinned muscle fibers by simultaneously monitoring the fluorescence of two low affinity Ca2+ indicators targeted to specific compartments of the muscle fiber, such as Fluo-5N in the SR and Rhod-5N in the transverse tubules9,11,12.

The extent of store-operated Ca2+ entry (SOCE) can be monitored using fluorescent Ca2+ indicators. Mn2+ quenching of such indicators assays SOCE in cultured cells and skeletal muscle fibers. A technique allowing spatial and temporal resolution of SOCE by confocal imaging of mechanically skinned muscle fibers is also described.

Store operated Ca2+ entry (SOCE), earlier termed capacitative Ca2+ entry, is a tightly regulated mechanism for influx of extracellular Ca2+ into cells to ...

Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins

Double-strand breaks (DSBs) are the most deleterious DNA lesions a cell can encounter. If left unrepaired, DSBs harbor great potential to generate mutations and chromosomal aberrations1. To prevent this trauma from catalyzing genomic instability, it is crucial for cells to detect DSBs, activate the DNA damage response (DDR), and repair the DNA. When stimulated, the DDR works to preserve genomic integrity by triggering cell cycle arrest to allow for repair to take place or force the cell to undergo apoptosis. The predominant mechanisms of DSB repair occur through nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR) (reviewed in2). There are many proteins whose activities must be precisely orchestrated for the DDR to function properly. Herein, we describe a method for 2- and 3-dimensional (D) visualization of one of these proteins, 53BP1.
The p53-binding protein 1 (53BP1) localizes to areas of DSBs by binding to modified histones3,4, forming foci within 5-15 minutes5. The histone modifications and recruitment of 53BP1 and other DDR proteins to DSB sites are believed to facilitate the structural rearrangement of chromatin around areas of damage and contribute to DNA repair6. Beyond direct participation in repair, additional roles have been described for 53BP1 in the DDR, such as regulating an intra-S checkpoint, a G2/M checkpoint, and activating downstream DDR proteins7-9. Recently, it was discovered that 53BP1 does not form foci in response to DNA damage induced during mitosis, instead waiting for cells to enter G1 before localizing to the vicinity of DSBs6. DDR proteins such as 53BP1 have been found to associate with mitotic structures (such as kinetochores) during the progression through mitosis10.
In this protocol we describe the use of 2- and 3-D live cell imaging to visualize the formation of 53BP1 foci in response to the DNA damaging agent camptothecin (CPT), as well as 53BP1's behavior during mitosis. Camptothecin is a topoisomerase I inhibitor that primarily causes DSBs during DNA replication. To accomplish this, we used a previously described 53BP1-mCherry fluorescent fusion protein construct consisting of a 53BP1 protein domain able to bind DSBs11. In addition, we used a histone H2B-GFP fluorescent fusion protein construct able to monitor chromatin dynamics throughout the cell cycle but in particular during mitosis12. Live cell imaging in multiple dimensions is an excellent tool to deepen our understanding of the function of DDR proteins in eukaryotic cells.

This protocol describes a method for visualizing a DNA double-strand break signaling protein activated in response to DNA damage as well as its localization during mitosis.

Double-strand breaks (DSBs) are the most deleterious DNA lesions a cell can encounter. If left unrepaired, DSBs harbor great potential to generate ...

Induction and Analysis of Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) is essential for proper morphogenesis during development. Misregulation of this process has been implicated as a key event in fibrosis and the progression of carcinomas to a metastatic state. Understanding the processes that underlie EMT is imperative for the early diagnosis and clinical control of these disease states. Reliable induction of EMT in vitro is a useful tool for drug discovery as well as to identify common gene expression signatures for diagnostic purposes. Here we demonstrate a straightforward method for the induction of EMT in a variety of cell types. Methods for the analysis of cells pre- and post-EMT induction by immunocytochemistry are also included. Additionally, we demonstrate the effectiveness of this method through antibody-based array analysis and migration/invasion assays.

A straightforward method is described for the induction of epithelial to mesenchymal transition (EMT) in a variety of cell types. Methods for the analysis of cells in EMT states by immunocytochemistry are included.

Epithelial  to mesenchymal transition (EMT) is essential for proper morphogenesis during  development. Misregulation of this  process has been implicated ...

Live Cell Imaging of Early Autophagy Events: Omegasomes and Beyond

Autophagy is a cellular response triggered by the lack of nutrients, especially the absence of amino acids. Autophagy is defined by the formation of double membrane structures, called autophagosomes, that sequester cytoplasm, long-lived proteins and protein aggregates, defective organelles, and even viruses or bacteria. Autophagosomes eventually fuse with lysosomes leading to bulk degradation of their content, with the produced nutrients being recycled back to the cytoplasm. Therefore, autophagy is crucial for cell homeostasis, and dysregulation of autophagy can lead to disease, most notably neurodegeneration, ageing and cancer.	
	Autophagosome formation is a very elaborate process, for which cells have allocated a specific group of proteins, called the core autophagy machinery. The core autophagy machinery is functionally complemented by additional proteins involved in diverse cellular processes, e.g. in membrane trafficking, in mitochondrial and lysosomal biology. Coordination of these proteins for the formation and degradation of autophagosomes constitutes the highly dynamic and sophisticated response of autophagy. Live cell imaging allows one to follow the molecular contribution of each autophagy-related protein down to the level of a single autophagosome formation event and in real time, therefore this technique offers a high temporal and spatial resolution.	
	Here we use a cell line stably expressing GFP-DFCP1, to establish a spatial and temporal context for our analysis. DFCP1 marks omegasomes, which are precursor structures leading to autophagosomes formation. A protein of interest (POI) can be marked with either a red or cyan fluorescent tag. Different organelles, like the ER, mitochondria and lysosomes, are all involved in different steps of autophagosome formation, and can be marked using a specific tracker dye. Time-lapse microscopy of autophagy in this experimental set up, allows information to be extracted about the fourth dimension, i.e. time. Hence we can follow the contribution of the POI to autophagy in space and time.

Time-lapse microscopy of fluorescently labeled autophagy markers allows monitoring of the dynamic autophagy response with high temporal resolution. Using specific autophagy and organelle markers in a combination of 3 different colors, we can follow the contribution of a protein to autophagosome formation in a robust spatial and temporal context.

Autophagy is a  cellular response triggered by the lack of nutrients, especially the absence of  amino acids. Autophagy is defined by the formation of ...

Scanning Electron Microscopy (SEM) Protocols for Problematic Plant, Oomycete, and Fungal Samples

Common problems in the processing of biological samples for observations with the scanning electron microscope (SEM) include cell collapse, treatment of samples from wet microenvironments and cell destruction. Using young floral tissues, oomycete cysts, and fungi spores (Agaricales) as examples, specific protocols to process delicate samples are described here that overcome some of the main challenges in sample treatment for image capture under the SEM.
Floral meristems fixed with FAA (Formalin-Acetic-Alcohol) and processed with the Critical Point Dryer (CPD) did not display collapsed cellular walls or distorted organs. These results are crucial for the reconstruction of floral development. A similar CPD-based treatment of samples from wet microenvironments, such as the glutaraldehyde-fixed oomycete cysts, is optimal to test the differential growth of diagnostic characteristics (e.g., the cyst spines) on different types of substrates. Destruction of nurse cells attached to fungi spores was avoided after rehydration, dehydration, and the CPD treatment, an important step for further functional studies of these cells.
The protocols detailed here represent low-cost and rapid alternatives for the acquisition of good-quality images to reconstruct growth processes and to study diagnostic characteristics.

Scanning Electron Microscopy SEM Protocols for Problematic Plant, Oomycete, and Fungal Samples

Problems in the processing of biological samples for scanning electron microscopy observation include cell collapse, treatment of samples from wet microenvironments and cell destruction. Low-cost and relatively rapid protocols suited for preparing challenging samples such as floral meristems, oomycete cysts, and fungi (Agaricales) are compiled and detailed here.

Common problems in the processing of biological samples for observations with the scanning electron microscope (SEM) include cell collapse, treatment of ...

Utilizing pHluorin-tagged Receptors to Monitor Subcellular Localization and Trafficking

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular organelles and those localized on the plasma membrane. Traditional fluorescence-based measurements lack the capability to distinguish membrane proteins residing in different organelles. Cutting edge methodologies transcend traditional methods by coupling pH-sensitive fluorophores with total internal reflection fluorescence microscopy (TIRFM). TIRF illumination excites the sample up to approximately 150 nm from the glass-sample interface, thus decreasing background, increasing the signal to noise ratio, and enhancing resolution. The excitation volume in TIRFM encompasses the plasma membrane and nearby organelles such as the peripheral ER. Superecliptic pHluorin (SEP) is a pH sensitive version of GFP. Genetically encoding SEP into the extracellular domain of a membrane protein of interest positions the fluorophore on the luminal side of the ER and in the extracellular region of the cell. SEP is fluorescent when the pH is greater than 6, but remains in an off state at lower pH values. Therefore, receptors tagged with SEP fluoresce when residing in the endoplasmic reticulum (ER) or upon insertion in the plasma membrane (PM) but not when confined to a trafficking vesicle or other organelles such as the Golgi. The extracellular pH can be adjusted to dictate the fluorescence of receptors on the plasma membrane. The difference in fluorescence between TIRF images at neutral and acidic extracellular pH for the same cell corresponds to a relative number of receptors on the plasma membrane. This allows a simultaneous measurement of intracellular and plasma membrane resident receptors. Single vesicle insertion events can also be measured when the extracellular pH is neutral, corresponding to a low pH trafficking vesicle fusing with the plasma membrane and transitioning into a fluorescent state. This versatile technique can be exploited to study localization, expression, and trafficking of membrane proteins.

Labeling the extracellular domain of a membrane protein with a pH sensitive fluorophore, superecliptic pHluorin (SEP), allows subcellular localization, expression, and trafficking to be determined. Imaging SEP-labeled proteins with total internal reflection fluorescence microscopy (TIRFM) enables the quantification of protein levels in the peripheral ER and plasma membrane.

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular ...

Live-cell Imaging of Platelet Degranulation and Secretion Under Flow

Blood platelets are essential players in hemostasis, the formation of thrombi to seal vascular breaches. They are also involved in thrombosis, the formation of thrombi that occlude the vasculature and injure organs, with life-threatening consequences. This motivates scientific research on platelet function and the development of methods to track cell-biological processes as they occur under flow conditions.
A variety of flow models are available for the study of platelet adhesion and aggregation, two key phenomena in platelet biology. This work describes a method to study real-time platelet degranulation under flow during activation. The method makes use of a flow chamber coupled to a syringe-pump setup that is placed under a wide-field, inverted, LED-based fluorescence microscope. The setup described here allows for the simultaneous excitation of multiple fluorophores that are delivered by fluorescently labeled antibodies or fluorescent dyes. After live-cell imaging experiments, the cover glasses can be further processed and analyzed using static microscopy (i.e., confocal microscopy or scanning electron microscopy).

This work describes a fluorescence microscopy-based method for the study of platelet adhesion, spreading, and secretion under flow. This versatile platform enables the investigation of platelet function for mechanistic research on thrombosis and hemostasis.

Blood platelets are essential players in hemostasis, the formation of thrombi to seal vascular breaches. They are also involved in thrombosis, the ...

Super-Resolution Live Cell Imaging of Subcellular Structures

There has long been a crucial tradeoff between spatial and temporal resolution in imaging. Imaging beyond the diffraction limit of light has traditionally been restricted to be used only on fixed samples or live cells outside of tissue labeled with strong fluorescent signal. Current super-resolution live cell imaging techniques require the use of special fluorescence probes, high illumination, multiple image acquisitions with post-acquisition processing, or often a combination of these processes. These prerequisites significantly limit the biological samples and contexts that this technique can be applied to.
Here we describe a method to perform super-resolution (~140 nm XY-resolution) time-lapse fluorescence live cell imaging in situ. This technique is also compatible with low fluorescent intensity, for example, EGFP or mCherry endogenously tagged at lowly expressed genes. As a proof-of-principle, we have used this method to visualize multiple subcellular structures in the Drosophila testis. During tissue preparation, both the cellular structure and tissue morphology are maintained within the dissected testis. Here, we use this technique to image microtubule dynamics, the interactions between microtubules and the nuclear membrane, as well as the attachment of microtubules to centromeres.
This technique requires special procedures in sample preparation, sample mounting and immobilizing of specimens. Additionally, the specimens must be maintained for several hours after dissection without compromising cellular function and activity. While we have optimized the conditions for live super-resolution imaging specifically in Drosophila male germline stem cells (GSCs) and progenitor germ cells in dissected testis tissue, this technique is broadly applicable to a variety of different cell types. The ability to observe cells under their physiological conditions without sacrificing either spatial or temporal resolution will serve as an invaluable tool to researchers seeking to address crucial questions in cell biology.

Presented here is a protocol for super-resolution live-cell imaging in intact tissue. We have standardized the conditions for imaging a highly sensitive adult stem cell population in its native tissue environment. This technique involves balancing temporal and spatial resolution to allow for the direct observation of biological phenomena in live tissue.

There has long been a crucial tradeoff between spatial and temporal resolution in imaging. Imaging beyond the diffraction limit of light has traditionally ...

Live-cell Imaging of Single-Cell Arrays (LISCA) - a Versatile Technique to Quantify Cellular Kinetics

Live-cell Imaging of Single-Cell Arrays (LISCA) is a versatile method to collect time courses of fluorescence signals from individual cells in high throughput. In general, the acquisition of single-cell time courses from cultured cells is hampered by cell motility and diversity of cell shapes. Adhesive micro-arrays standardize single-cell conditions and facilitate image analysis. LISCA combines single-cell microarrays with scanning time-lapse microscopy and automated image processing. Here, we describe the experimental steps of taking single-cell fluorescence time courses in a LISCA format. We transfect cells adherent to a micropatterned array using mRNA encoding for enhanced green fluorescent protein (eGFP) and monitor the eGFP expression kinetics of hundreds of cells in parallel via scanning time-lapse microscopy. The image data stacks are automatically processed by newly developed software that integrates fluorescence intensity over selected cell contours to generate single-cell fluorescence time courses. We demonstrate that eGFP expression time courses after mRNA transfection are well described by a simple kinetic translation model that reveals expression and degradation rates of mRNA. Further applications of LISCA for event time correlations of multiple markers in the context of signaling apoptosis are discussed.

Live-cell Imaging of Single-Cell Arrays LISCA - a Versatile Technique to Quantify Cellular Kinetics

We present a method for the acquisition of fluorescence reporter time courses from single cells using micropatterned arrays. The protocol describes the preparation of single-cell arrays, the setup and operation of live-cell scanning time-lapse microscopy and an open-source image analysis tool for automated preselection, visual control and tracking of cell-integrated fluorescence time courses per adhesion site.

Live-cell Imaging of Single-Cell Arrays (LISCA) is a versatile method to collect time courses of fluorescence signals from individual cells in high ...