The authors wish to thank Dr. Hudson W. P. de Carvalho for the support to develop this work. The authors are also grateful to the Laboratory of Electron Microscopy &#39;&#39;Prof. Elliot Watanabe Kitajima&#39;&#39; for providing the light microscopy facility. The authors thank&#160;Dr. Fl&#225;via Rodrigues Alves Patr&#237;cio for supplying the plant material with lesions.

1. Preparation of the buffering solution and reagents
<ol>
	<li>Prepare 2 M cacodylate buffer by adding 4.28 g of sodium cacodylate to 100 mL of distilled water and adjust the pH to 7.25 with 0.2 N HCl.</li>
	<li>Prepare 100 mL of the Karnovsky fixative solution by mixing 10 mL of 25% aqueous glutaraldehyde, 10 mL of 10% aqueous formaldehyde, 25 mL of 2 M cacodylate buffer, and 0.5 mL of 0.5 M CaCl226. Make up the volume to 100 mL with distilled water. 
	NOTE: The solution can be kept in a refrigerator for 6 months. 
	CAUTION: The cacodylate buffering solution is toxic; therefore, handle the fixative solution in a fume hood or an open area. Avoid inhaling the solution vapors and wear gloves while handling.</li>
	<li>Prepare aqueous Hoagland nutrient solution by mixing the following: 3 mM Ca(NO3)2.4H2O, 2 mM NH4H2PO4, 5 mM KH2PO4, 2 mM MgSO4.7H2O, 9.07 mM MnSO4, 0.765 mM ZnSO4.7H2O, 46.4 mM H3BO3, 0.09 mM Na2MoO4.H2O, 0.01 mM CuSO4, and 36 mM FeSO4.7H2O as iron-EDTA (ethylenediamine tetraacetic acid)27.</li>
</ol>
2. Plant samples and fungus inoculation
NOTE: For experiments on leaves affected by coffee rust, five 2-month-old seedlings of Coffee arabica cv. Catua&#237; were grown and kept in a greenhouse at the Center of Nuclear Energy in Agriculture (CENA) of the University of S&#227;o Paulo, Piracicaba, S&#227;o Paulo State, Brazil.
<ol>
	<li>Grow coffee plants in 500 mL plastic pots filled with aqueous Hoagland nutrient solution (pH of ~5.5) for 4 months in a growth chamber kept at 27 &#177; 3 &#176;C with a 12 h photoperiod created by LED lamps at the photon flux of 250 &#181;mol photons s-1 m-2. Replace the Hoagland nutrient solution every week for 4 months.</li>
	<li>Inoculate four expanded leaves from five plants on their abaxial surfaces with 1 x 103&#160;H. vastatrix uredospores following the method described in reference28. After inoculation, keep the plants for 48 h in the dark by covering them with a black plastic bag. Harvest the lesions 30 days after inoculation.</li>
	<li>Harvest characteristic lesions caused by Cercospora coffeicola from Coffea arabica cv. Obat&#227; plants located (coordinates: -22.906506126269942, -47.015075902025266) at the Biological Institute, Campinas, S&#227;o Paulo State, Brazil. Before processing the sample, analyze the lesions in a stereomicroscope to verify the presence of coffee C. coffeicola conidia. Then, mount some slides with the conidia to confirm the disease etiology22.</li>
</ol>
3. Sample harvesting, fixation, and dehydration
<ol>
	<li>Using a scalpel and tweezer, harvest a ~10 mm2 leaf sample at the middle region of the lesion (yellow spots; Figure 1) and immerse it in 30 mL of Karnovsky fixative solution (Figure 1&#160;and Figure 2A). The fixation step can take place in a refrigerator for 48 h.</li>
	<li>For at least four times, subject the leaf sample to a low vacuum (500-600 mBar) using an oil pump for 15 min each to increase the permeability of the fixative solution in the leaf tissue. Perform this step with sample rotation (Figure 1).</li>
	<li>After fixation, wash the leaf sample three times in 0.5 M cacodylate buffer (pH 7.2) diluted in distilled water for 5 min each and then transfer it to a graded ethanolic series (30%, 50%, 70%, 90% (2x), and 100% (2x)) for 15 min at each ethanol concentration (Figure 1 and Figure 2B).</li>
</ol>
4. Historesin embedding procedure
<ol>
	<li>Gradually transfer the samples to glycol methacrylate (GMA) in three steps, following the manufacturer&#39;s instructions. First, make Solution A by mixing the GMA powder (1 g) with 100 mL of basic resin (historesin kit; Table of Materials) under magnetic agitation, and then follow the below steps.
	<ol>
		<li>Immerse the samples in 1:2 Solution A: 100% ethanol for 3 h.</li>
		<li>Immerse the samples in 1:1 Solution A: 100% ethanol for 3 h.</li>
		<li>Immerse the samples in a pure basic resin for 2-4 days. During this step, subject the samples to a low vacuum at least four times a day for 15 min followed by rotation.</li>
	</ol>
	</li>
</ol>
5. Polymerization
NOTE: The polymerization process requires 1.2 mL plastic molds, basic resin, and hardener (see Table of Materials for the details of the commercial kit).
<ol>
	<li>Mix 15 mL of Solution A (step 4.1) with 1 mL of the hardener in a beaker with rotation for 2 min to produce the polymerization solution (Solution B).</li>
	<li>Put 1.2 mL of the polymerization solution (Solution B) in plastic molds. Using a wooden pick, transfer the lesioned leaf samples from pure basic resin to Solution B (Figure 2C). Avoid using tweezers as they can cause tissue crushing.</li>
	<li>Ensure to quickly orient leaf samples perpendicular to the plastic molds as solution B quickly becomes viscous within 5 min. More than one lesioned leaf sample can be placed in a single mold. 
	NOTE: It is recommended to practice the above step several times before applying for many samples. When there are many samples, the polymerization time is different among the molds and the perpendicular orientation of the leaf samples may be difficult to achieve.</li>
	<li>When the perpendicular orientation of the leaf samples is achieved, wait for 30 min, and then transfer the plastic mold to a plastic or glass chamber containing silica gel to prevent humidity. Wait for 2-3 h for polymerization.</li>
	<li>Once the resin and the leaf sample are polymerized after the 2-3 h period, detach the resulting block from the plastic mold by sanding the block base with a sanding file. Then, glue the block to a piece of wood (Figure 2D).</li>
</ol>
6. Sectioning
<ol>
	<li>Using a rotative microtome equipped with 8 cm steel blades (Figure 2E), cut the block into 5 &#181;m thick sections. Place the sections onto glass slides covered with distilled water. Transfer the slides with the sections floating over water to a hot plate at 40 &#176;C to dry and promote the adhesion of the sections to the glass slides.</li>
	<li>After drying (Figure 2F), label the glass slides with the block reference name and the slide number.</li>
</ol>
7. Double staining process
<ol>
	<li>Cover the sections with 2 mL of 5% cotton blue in lactophenol (40% glycerol, 20% phenol, and 20% lactic acid in water) and heat them on a hot plate at 45 &#176;C for 5 min (Figure 3A).</li>
	<li>Remove the excess dye by washing the slide three times in a beaker filled with distilled water (Figure 3B-D).</li>
	<li>Stain with 2 mL of 0.01% ruthenium red in water for 1 min (Figure 3E).</li>
	<li>Remove the excess dye by washing the slide three times in a beaker filled with distilled water (Figure 3F,G).</li>
	<li>Put a drop of distilled water over the sections and cover the sections with a 24 mm x 60 mm coverslip for performing light microscopy analysis.</li>
</ol>

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Chemistry, purification, methods of use for electron microscopy and mechanism of action.</a> The Anatomical Record. 171 (3), 347-368 (1971).</li><li>Buckeridge, M. S., Cavalari, A. A., Silva, G. B. D. A., Kerbauy, G. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+Wall.">Cell Wall.</a> Plant Physiology. , 165-181 (2013).</li></ol>

The authors declare no conflicts of interest.

The present work introduces an alternative double-staining histochemical test to investigate the pectin composition of cell walls that encapsulates haustoria in a biotrophic pathosystem. The aim is also to demonstrate the efficacy of the method to detect necrotrophic fungus and cell wall changes induced by it. Here, pectin of coffee parenchyma cell walls can encapsulate both the neck and the haustorium of the rust fungus Hemileia vastatrix. Silva et al. have also described encapsulation by cellulose and callose ...

Cell wall defense mechanisms in plants are crucial to restrain fungal infection. Studies have reported changes in cell wall thickness and composition since the 19th century1,2. These changes can be induced by a fungal pathogen that stimulates the formation of a papilla, which prevents fungi from entering the cell or could be used to encapsulate the hyphae to isolate the host cell protoplast from the fungal haustoria. The production of a dynamic cell wall barrier (i.e., papillae and a fully encased haustorium) is important to promote plant resistance3. Histopathological studies on fungus-related diseases have investigated the occurrence of these mechanisms and have described the cell wall polymers, cellulose, hemicellulose (arabinoxylans), and callose as resistance mechanisms to fungal attack4,5,6,7.
The cell wall is the first barrier against microorganismal attack, impairing the plant-fungal interaction. Pectic polysaccharides compose the cell wall and account for about 30% of the cell wall composition in primary cells of eudicot plants in which homogalacturonans are the most abundant polymer (roughly 60%)8. The Golgi secretes complex pectin compounds that comprise the galacturonic acid chains, which may or may not be methylated8,9. Since 2012, the literature has pointed out that the degree of pectin methyl esterification is critical to determining the compatibility during infection by microbial pectic enzymes10,11,12. Thus, protocols are required to verify the presence and distribution of pectic compounds in plant-fungal pathosystems.
Various techniques have been used to detect the encapsulation of papillae or haustoria. The reference methods used are transmission electron microscopy (TEM) of fixed tissue and light microscopy of living and fixed tissues. Regarding TEM, several studies have demonstrated the structural role of cell wall appositions in fungal resistance13,14,15,16, and that the use of lectins and antibodies is an intricate method to locate carbohydrate polymers16. However, studies show that light microscopy is an important approach and that the histochemical and immunohistochemical tools allow a better understanding of the composition of papillae and haustorium encasement6,7.
Pathogenic fungi show two main types of lifestyles: biotrophic and necrotrophic. Biotrophic fungi depend on living cells for their nutrition whereas necrotrophic fungi kill the host cells, and then live in the dead tissues17. In Latin America, coffee leaf rust, caused by the fungus Hemileia vastatrix, is an important disease in coffee crops18,19. Hemileia vastatrix presents a biotrophic behavior and, among the structural changes observed in resistant coffee species or cultivars, a hypersensitivity response, deposition of callose, cellulose, and lignin on the cell walls, as well as cell hypertrophy14&#160;have been reported. To the authors&#39; knowledge, the literature does not report information on the importance of pectin in coffee rust resistance. On the other hand, necrotrophic fungi that cause cercosporiosis target pectin via a set of enzymes associated with cell wall degradation, such as pectinases and polygalacturonase20. Cercosporiosis in coffee, caused by the fungus Cercospora coffeicola is also a major threat to coffee crops21,22. This fungus causes necrotic lesions in both leaves and berries. After penetration, C. coffeicola colonizes plant tissues through intracellular and intercellular pathways23,24,25.
The present protocol investigates the presence of fungal structures and pectin on cell walls. This protocol is useful to identify the plant response associated with pectin (stained with ruthenium red dye, which is specific to acidic groups of polyuronic acids of pectin), induced by the host in a biotrophic interaction with fungus. It also helps to verify the effect of necrotrophic fungi on the degradation of pectic cell walls. The present results indicate that the double staining method is effective to discriminate structures and the reproductive phase of fungi.

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			<td>Microtome (Leica RM 2540)</td>
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			<td>Staining</td>
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			<td>Ruthenium red</td>
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			<td>#006004</td>
			<td>Staining</td>
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			<td>Software Axion Vision</td>
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			<td>#410130-0909-000</td>
			<td>Image capture</td>
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			<td>Vaccum pump</td>
			<td>Prismatec</td>
			<td>131 TIPO 2 V.C.</td>
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double-staining method to detect pectin in plant-fungus interaction

Plant cells use different structural mechanisms, either constitutive or inducible, to defend themselves from fungal infection. Encapsulation is an efficient inducible mechanism to isolate the fungal haustoria from the plant cell protoplast. Conversely, pectin, one of the polymeric components of the cell wall, is a target of several pectolytic enzymes in necrotrophic interactions. Here, a protocol to detect pectin and fungal hyphae through optical microscopy is presented. The pectin-rich encapsulation in the cells of coffee leaves infected by the rust fungus Hemileia vastatrix and the mesophyll cell wall modification induced by Cercospora coffeicola are investigated. Lesioned leaf samples were fixed with the Karnovsky solution, dehydrated, and embedded in glycol methacrylate for 2-4 days. All steps were followed by vacuum-pumping to remove air in the intercellular spaces and improve the embedding process. The embedded blocks were sectioned into 5-7 &#181;m thick sections, which were deposited on a glass slide covered with water and subsequently heated at 40 &#176;C for 30 min. Next, the slides were double-stained with 5% cotton blue in lactophenol to detect the fungus and 0.05% ruthenium red in water to detect pectin (acidic groups of polyuronic acids of pectin). Fungal haustoria of Hemileia vastatrix were found to be encapsulated by pectin. In coffee cercosporiosis, mesophyll cells exhibited dissolution of cell walls, and intercellular hyphae and conidiophores were observed. The method presented here is effective to detect a pectin-associated response in the plant-fungi interaction.

The cotton blue lactophenol staining on the GMA-embedded section revealed the presence of several fungal structures between and inside coffee mesophyll cells in both biotrophic and necrotrophic fungal interactions.
In the biotrophic pathosystem, when stained using the double-staining method, Hemileia vastatrix hyphae containing cell walls and the dense protoplast content appear in dark blue in both spongy and palisade parenchyma (Figure 4A,B</stro...

Watch this Scientific Journal Video about Double-Staining Method to Detect Pectin in Plant-Fungus Interaction at JoVE.com

Double-Staining Method to Detect Pectin in Plant-Fungus Interaction

This protocol describes a microscopical method to detect pectin in coffee-fungus interaction.

Plant cells use different structural mechanisms, either constitutive or inducible, to defend themselves from fungal infection. Encapsulation is an ...

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4.3K Views.  University of São Paulo. This protocol describes a microscopical method to detect pectin in coffee-fungus interaction.

Video: Double-Staining Method to Detect Pectin in Plant-Fungus Interaction

Pyrosequencing: A Simple Method for Accurate Genotyping

Pharmacogenetic research benefits first-hand from the abundance of information provided by the completion of the Human Genome Project. With such a tremendous amount of data available comes an explosion of genotyping methods. Pyrosequencing(R) is one of the most thorough yet simple methods to date used to analyze polymorphisms. It also has the ability to identify tri-allelic, indels, short-repeat polymorphisms, along with determining allele percentages for methylation or pooled sample assessment. In addition, there is a standardized control sequence that provides internal quality control. This method has led to rapid and efficient single-nucleotide polymorphism evaluation including many clinically relevant polymorphisms. The technique and methodology of Pyrosequencing is explained.


Pyrosequencing(R) is one of the most thorough yet simple methods to date used to analyze polymorphisms. This method has led to rapid and efficient single-nucleotide polymorphism evaluation including many clinically relevant polymorphisms. The technique and methodology of Pyrosequencing is explained.

Pharmacogenetic research benefits first-hand from the abundance of information provided by the completion of the Human Genome Project. With such a ...

Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting (LIMACS): a Novel Method to Analyze Protein-lipid Interaction

The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification procedures. As an alternative, lipids can be coated on flat surfaces as used for lipid ELISA and Plasmon resonance spectroscopy. However, surface coating lipids do not form microdomain structures, which may be important for the lipid binding properties. Further, these methods do not allow for the purification of larger amounts of proteins binding to their target lipids.
 To overcome these limitations of testing lipid protein interaction and to purify lipid binding proteins we developed a novel method termed lipid vesicle-mediated affinity chromatography using magnetic-activated cell sorting (LIMACS). In this method, lipid vesicles are prepared with the target lipid and phosphatidylserine as the anchor lipid for Annexin V MACS. Phosphatidylserine is a ubiquitous cell membrane phospholipid that shows high affinity to the protein Annexin V. Using magnetic beads conjugated to Annexin V the phosphatidylserine-containing lipid vesicles will bind to the magnetic beads. When the lipid vesicles are incubated with a cell lysate the protein binding to the target lipid will also be bound to the beads and can be co-purified using MACS. This method can also be used to test if recombinant proteins reconstitute a protein complex binding to the target lipid. 
 We have used this method to show the interaction of atypical PKC (aPKC) with the sphingolipid ceramide and to co-purify prostate apoptosis response 4 (PAR-4), a protein binding to ceramide-associated aPKC. We have also used this method for the reconstitution of a ceramide-associated complex of recombinant aPKC with the cell polarity-related proteins Par6 and Cdc42. Since lipid vesicles can be prepared with a variety of sphingo- or phospholipids, LIMACS offers a versatile test for lipid-protein interaction in a lipid environment that resembles closely that of the cell membrane. Additional lipid protein complexes can be identified using proteomics analysis of lipid binding protein co-purified with the lipid vesicles.

Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting LIMACS: a Novel Method to Analyze Protein-lipid Interaction

To test the interaction of a protein with its target lipid we used MACS and Annexin V-conjugated magnetic beads and lipid vesicles synthesized from the target lipid and Annexin V-binding phosphatidylserine. Proteins bound to the target lipid are co-purified and analyzed after elution from the beads.

The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification ...

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level. There are several methods, both in vitro and in vivo, to evaluate protein binding, and at least two methods that complement the shortcomings of each other should be conducted to obtain reliable insights. 
For an in vivo assay, the bimolecular fluorescence complementation (BiFC) assay represents the most popular and least invasive approach that enables to detect protein-protein interaction within living cells, as well as identify the intracellular localization of the interacting proteins 1,2. In this assay, non-fluorescent N- and C-terminal halves of GFP or its variants are fused to tested proteins, and when the two fusion proteins are brought together due to the tested proteins&#x2019; interactions, the fluorescent signal is reconstituted3-6. Because its signal is readily detectable by epifluorescence or confocal microscopy, BiFC has emerged as a powerful tool of choice among cell biologists for studying about protein-protein interactions in living cells 3. This assay, however, can sometimes produce false positive results. For example, the fluorescent signal can be reconstituted by two GFP fragments arranged as far as 7 nm from each other due to close packing in a small subcellular compartment, rather that due to specific interactions7.
Due to these limitations, the results obtained from live cell imaging technologies should be confirmed by an independent approach based on a different principle for detecting protein interactions. Co-immunoprecipitation (Co-IP) or glutathione transferase (GST) pull-down assays represent such alternative methods that are commonly used to analyze protein-protein interactions in vitro. However, iIn these assays, however, the tested proteins must be readily soluble in the buffer that supportsused for the binding reaction. Therefore, specific interactions involving an insoluble protein cannot be assessed by these techniques.
 Here, we illustrate the protocol for the protein membrane overlay binding assay, which circumvents this difficulty. In this technique, interaction between soluble and insoluble proteins can be reliably tested because one of the proteins is immobilized on a membrane matrix. This method, in combination with in vivo experiments, such as BiFC, provides a reliable approach to investigate and characterize interactions faithfully between soluble and insoluble proteins. In this article, binding between Tobacco mosaic virus (TMV) movement protein (MP), which exerts multiple functions during viral cell-to-cell transport8-14, and a recently identified plant cellular interactor, tobacco ankyrin repeat-containing protein (ANK) 15, is demonstrated using this technique.

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level.  There are several ...

Use of LysoTracker to Detect Programmed Cell Death in Embryos and Differentiating Embryonic Stem Cells

Programmed cell death (PCD) occurs in adults to maintain normal tissue homeostasis and during embryological development to shape tissues and organs1,2,6,7. During development, toxic chemicals or genetic alterations can cause an increase in PCD or change PCD patterns resulting in developmental abnormalities and birth defects3-5. To understand the etiology of these defects, the study of embryos can be complemented with in vitro assays that use differentiating embryonic stem (ES) cells.
Apoptosis is a well-studied form of PCD that involves both intrinsic and extrinsic signaling to activate the caspase enzyme cascade. Characteristic cell changes include membrane blebbing, nuclear shrinking, and DNA fragmentation. Other forms of PCD do not involve caspase activation and may be the end-result of prolonged autophagy. Regardless of the PCD pathway, dying cells need to be removed. In adults, the immune cells perform this function, while in embryos, where the immune system has not yet developed, removal occurs by an alternative mechanism. This mechanism involves neighboring cells (called "non-professional phagocytes") taking on a phagocytic role-they recognize the 'eat me' signal on the surface of the dying cell and engulf it8-10. After engulfment, the debris is brought to the lysosome for degradation. Thus regardless of PCD mechanism, an increase in lysosomal activity can be correlated with increased cell death.
To study PCD, a simple assay to visualize lysosomes in thick tissues and multilayer differentiating cultures can be useful. LysoTracker dye is a highly soluble small molecule that is retained in acidic subcellular compartments such as the lysosome11-13. The dye is taken up by diffusion and through the circulation. Since penetration is not a hindrance, visualization of PCD in thick tissues and multi-layer cultures is possible12,13. In contrast, TUNEL (Terminal deoxynucleotidyl transferase dUTP nick end labeling) analysis14, is limited to small samples, histological sections, and monolayer cultures because the procedure requires the entry/permeability of a terminal transferase.
In contrast to Aniline blue, which diffuses and is dissolved by solvents, LysoTracker Red DND-99 is fixable, bright, and stable. Staining can be visualized with standard fluorescent or confocal microscopy in whole-mount or section using aqueous or solvent-based mounting media12,13. Here we describe protocols using this dye to look at PCD in normal and sonic hedgehog null mouse embryos. In addition, we demonstrate analysis of PCD in differentiating ES cell cultures and present a simple quantification method. In summary, LysoTracker staining can be a great complement to other methods of detecting PCD.

We present a simple protocol to visualize regions of programmed cell death (PCD) in mouse embryos and differentiating embryonic stem (ES) cell cultures using a highly soluble dye called LysoTracker.

Programmed cell death (PCD) occurs in adults to maintain normal tissue homeostasis and during embryological development to shape tissues and ...

Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells.
BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction.

Flow cytometric analysis of Bimolecular Fluorescence Complementation provides a high throughput quantitative method to study protein-protein interaction. This methodology can be applied to mapping protein binding sites and for screening factors that regulate protein-protein interaction.

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC ...

Using Coculture to Detect Chemically Mediated Interspecies Interactions

In nature, bacteria rarely exist in isolation; they are instead surrounded by a diverse array of other microorganisms that alter the local environment by secreting metabolites. These metabolites have the potential to modulate the physiology and differentiation of their microbial neighbors and are likely important factors in the establishment and maintenance of complex microbial communities. We have developed a fluorescence-based coculture screen to identify such chemically mediated microbial interactions. The screen involves combining a fluorescent transcriptional reporter strain with environmental microbes on solid media and allowing the colonies to grow in coculture. The fluorescent transcriptional reporter is designed so that the chosen bacterial strain fluoresces when it is expressing a particular phenotype of interest (i.e. biofilm formation, sporulation, virulence factor production, etc.) Screening is performed under growth conditions where this phenotype is not expressed (and therefore the reporter strain is typically nonfluorescent). When an environmental microbe secretes a metabolite that activates this phenotype, it diffuses through the agar and activates the fluorescent reporter construct. This allows the inducing-metabolite-producing microbe to be detected: they are the nonfluorescent colonies most proximal to the fluorescent colonies. Thus, this screen allows the identification of environmental microbes that produce diffusible metabolites that activate a particular physiological response in a reporter strain. This publication discusses how to: a) select appropriate coculture screening conditions, b) prepare the reporter and environmental microbes for screening, c) perform the coculture screen, d) isolate putative inducing organisms, and e) confirm their activity in a secondary screen. We developed this method to screen for soil organisms that activate biofilm matrix-production in Bacillus subtilis; however, we also discuss considerations for applying this approach to other genetically tractable bacteria.

Bacteria produce secreted compounds that have the potential to affect the physiology of their microbial neighbors. Here we describe a coculture screen that allows detection of such chemically mediated interspecies interactions by mixing soil microbes with fluorescent transcriptional reporter strains of Bacillus subtilis on solid media.

In nature, bacteria rarely exist in isolation; they are instead surrounded by a diverse array of other microorganisms that alter the local environment by ...

Analysis of Apoptosis in Zebrafish Embryos by Whole-mount Immunofluorescence to Detect Activated Caspase 3

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis in zebrafish embryos. The whole-mount analysis provides spatial information in regard to tissue specificity of apoptosing cells, although sectioning and/or colabeling is ultimately required to pinpoint the exact cell types undergoing apoptosis. The whole-mount Casp3 assay is optimized for analysis of fixed embryos between the 4-cell stage and 32 hr-post-fertilization and is useful for a number of applications, including analysis of zebrafish mutants and morphants, overexpression of mutant and wild-type mRNAs, and exposure to chemicals. Compared to acridine orange staining, which can identify apoptotic cells in live embryos in a matter of hours, Casp3 and TUNEL assays take considerably longer to complete (2-4 days). However, because of the dynamic nature of apoptotic cell formation and clearance, analysis of fixed embryos ensures accurate comparison of apoptotic cells across multiple samples at specific time points. We have also found the Casp3 assay to be superior to analysis of apoptotic cells by the whole-mount TUNEL assay in regard to cost and reliability. Overall, the Casp3 assay represents a robust, highly reproducible assay in which to analyze apoptotic cells in early zebrafish embryos.

Certain genetic perturbations or exposure to toxins can disrupt normal developmental processes leading to death of specific cell types. The analysis of activated Caspase 3 by whole-mount immunofluorescence in zebrafish embryos reveals stage- and tissue-specific localization of cells specifically undergoing apoptosis.

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis ...

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an affinity purified yeast kinase fusion protein containing a V5-epitope tag for read-out. Purified kinase is obtained through culture of a yeast strain optimized for high copy protein production harboring a plasmid containing a Kinase-V5 fusion construct under a GAL inducible promoter. The yeast is grown in restrictive media with a neutral carbon source for 6 hr followed by induction with 2% galactose. Next, the culture is harvested and kinase is purified using standard affinity chromatographic techniques to obtain a highly purified protein kinase for use in the assay. The purified kinase is diluted with kinase buffer to an appropriate range for the assay and the protein microarrays are blocked prior to hybridization with the protein microarray. After the hybridization, the arrays are probed with monoclonal V5 antibody to identify proteins bound by the kinase-V5 protein. Finally, the arrays are scanned using a standard microarray scanner, and data is extracted for downstream informatics analysis1,2 to determine a high confidence set of protein interactions for downstream validation in vivo.

Using protein microarrays containing nearly the entire S. cerevisiae proteome is probed for rapid unbiased interrogation of thousands of protein-protein interactions in parallel. This method can be utilized for protein-small molecule, posttranslational modification, and other assays in high-throughput.

High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an ...

Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds

Fungal infections have become an important medical condition in the last decades, but the number of available antifungal drugs is limited. In this scenario, the search for new antifungal drugs is necessary. The protocol reported here details a method to screen peptides for their antifungal properties. It is based on the broth microdilution susceptibility test from the Clinical and Laboratory Standards Institute (CLSI) M27-A3 guidelines with modifications to suit the research of antimicrobial peptides as potential new antifungals. This protocol describes a functional assay to evaluate the activity of antifungal compounds and may be easily modified to suit any particular class of molecules under investigation. Since the assays are performed in 96-well plates using small volumes, a large-scale screening can be completed in a short amount of time, especially if carried out in an automation setting. This procedure illustrates how a standardized and adjustable clinical protocol can help the bench-work pursuit of new molecules to improve the therapy of fungal diseases.

Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds

An easy and adaptable broth microdilution method for screening antifungal compounds and extracts.

Fungal infections have become an important medical condition in the last decades, but the number of available antifungal drugs is limited. In this ...

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates

Beneficial plant-associated bacteria play an important role in promoting growth and preventing disease in plants. The application of plant growth-promoting rhizobacteria (PGPR) as biofertilizers or biocontrol agents has become an effective alternative to the use of conventional fertilizers and can increase crop productivity at low cost. Plant-microbe interactions depend upon host plant-secreted signals and a reaction hereon by their associated bacteria. However, the molecular mechanisms of how beneficial bacteria respond to their associated plant-derived signals are not fully understood. Assessing the transcriptomic response of bacteria to root exudates is a powerful approach to determine the bacterial gene expression and regulation under rhizospheric conditions. Such knowledge is necessary to understand the underlying mechanisms involved in plant-microbe interactions. This paper describes a detailed protocol to study the transcriptomic response of B. mycoides EC18, a strain isolated from the potato endosphere, to potato root exudates. With the help of recent high-throughput sequencing technology, this protocol can be performed in several weeks and produce massive datasets. First, we collect the root exudates under sterile conditions, after which they are added to B. mycoides cultures. The RNA from these cultures is isolated using a phenol/chloroform method combined with a commercial kit and subjected to quality control by an automated electrophoresis instrument. After sequencing, data analysis is performed with the web-based T-REx pipeline and a group of differentially expressed genes is identified. This method is a useful tool to facilitate new discoveries on the bacterial genes involved in plant-microbe interactions.

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates

The goal of the protocol presented here is to study the transcriptomic response of endosphere-isolated Bacillus mycoides to potato root exudates. This method facilitates the identification of important bacterial genes involved in plant-microbe interactions and is in principle applicable to other endophytes and plants, with minor adjustments.