Name: analysis of the lipid composition of mycobacteria by thin layer chromatography
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Description: Watch this Scientific Journal Video about Analysis of the Lipid Composition of Mycobacteria by Thin Layer Chromatography at JoVE.com

This research was funded by the Spanish Ministry of Science, Innovation and Universities (RTI2018-098777-B-I00), the FEDER Funds, and the Generalitat of Catalunya (2017SGR-229). Sandra Guallar-Garrido is the recipient of a PhD contract (FI) from the Generalitat de Catalunya.

1. Extraction of the total non-covalent-linked lipids from mycobacteria (Figure 1)
<ol>
	<li>Scratch 0.2 g of mycobacteria from a solid media and add to a glass tube with a polytetrafluoroethlene (PTFE) liner screw caps. Add a solution consisting of 5 mL of chloroform and 10 mL of methanol (chloroform:methanol, 1:2). 
	NOTE: When organic solvents are used, only glass recipient should be used. No plastic containers are allowed. Moreover, PTFE liner screw caps for bottles are needed.<br...

<ol>
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T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipidomic+analyses+of+Mycobacterium+tuberculosis+based+on+accurate+mass+measurements+and+the+novel+"Mtb+LipidDB".">Lipidomic analyses of Mycobacterium tuberculosis based on accurate mass measurements and the novel "Mtb LipidDB".</a> Journal of Lipid Research. 52 (5), 861-872 (2011).</li><li>Li, M., Zhou, Z., Nie, H., Bai, Y., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+advances+of+chromatography+and+mass+spectrometry+in+lipidomics.">Recent advances of chromatography and mass spectrometry in lipidomics.</a> Analytical and Bioanalytical Chemistry. 399 (1), 243-249 (2011).</li><li>Nahar, A., Baker, A. L., Nichols, D. S., Bowman, J. P., Britz, M. 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A simple protocol considered as the gold standard method for the extraction of noncovalently linked lipid compounds from the mycobacterial cell wall is presented. Further visualization by one- and two-dimensional TLCs from the extracted lipids of four different mycobacteria is shown.
Two consecutive combined mixtures of chloroform and methanol to recover the lipidic content of mycobacterial cells is the most widely used solvent mixture23,24<...

Mycobacterium is a genus that comprises pathogenic and non-pathogenic species, characterized by having a highly hydrophobic and impermeable cell wall formed by their peculiar lipids. Specifically, the mycobacterial cell wall contains mycolic acids, which are &#945;-alkyl and &#946;-hydroxy fatty acids, in which the &#945;-branch is constant in all mycolic acids (except for the length) and the &#946;-chain, called the meromycolate chain, is a long aliphatic chain that may contain different functional chemical groups described along with the literature (&#945;-, &#945;&#39;-, methoxy-, &#954;-, epoxy-, carboxy-, and &#969;-1-methoxy- mycolates), therefore producing seven types of mycolic acids (I-VII)1. Moreover, other lipids with unquestionable importance are also present in the cell wall of mycobacteria species. Pathogenic species such as Mycobacterium tuberculosis, the&#160;causative agent of tuberculosis2 produce specific lipid-based virulence factors such as phthiocerol dimycocerosates (PDIMs), phenolic glycolipid (PGL), di-, tri-, and penta-acyltrehaloses (DAT, TAT, and PAT), or sulfolipids, among others3. Their presence on the mycobacterial surface have been associated with the ability to modify the host immune response and therefore, the evolution and persistence of the mycobacterium inside the host4. For instance, the presence of triacylglycerols (TAG) has been associated with the hypervirulent phenotype of Lineage 2-Beijing sub-lineage of M. tuberculosis, possibly due to its capacity to attenuate the host immune response5,6. Other relevant lipids are lipooligosaccharides (LOSs) present in tuberculous and nontuberculous mycobacteria. In the case of Mycobacterium marinum, the presence of LOSs in its cell wall is related to sliding motility and the ability to form biofilms and interferes with recognition by macrophage pattern recognition receptors, affecting uptake and elimination of the bacteria by host phagocytes7,8. Additionally, the absence or presence of some lipids allows members of the same species to be classified into different morphotypes with virulent or attenuate profiles when interacting with host cells. For instance, the absence of glycopeptidolipids (GPL) in the rough morphotype of Mycobacterium abscessus has been associated with the ability to induce intraphagosomal acidification, and consequently cell apoptosis9, unlike the smooth morphotype that possesses GPLs in their surface. Furthermore, the lipid content of the mycobacterial cell wall is related to the ability to modify the immune response in the host. This is relevant in the context of using some mycobacteria to trigger a protective immune profile against different pathologies10,11,12,13.&#160;It has been demonstrated, for example, that Mycolicibacterium vaccae, a saprophytic mycobacterium, which is currently in phase III clinical trials as an immunotherapeutic vaccine for tuberculosis, display two colonial morphotypes. While the smooth phenotype, that contains a polyester in its surface, triggers a Th2 response, the rough phenotype devoid of the polyester can induce a Th1 profile when it interacts with host immune cells14. The repertoire of lipids present in the mycobacterial cell not only depends on mycobacteria species, but also on the conditions of mycobacterial cultures: time of incubation15,16 or composition of the culture medium17,18. In fact, changes in the culture medium composition affect the antitumor and immunostimulatory activity of M. bovis BCG&#160;and Mycolicibacterium brumae in vitro17. Moreover, the protective immune profile triggered by M. bovis BCG against M. tuberculosis challenge in mice models also depends on the culture media in which M. bovis BCG grows17. These could then be related to the lipid composition of the mycobacteria in each culture condition. For all these reasons, the study of the lipid content of mycobacteria is relevant. A visual procedure to extract and analyze the lipid composition of the mycobacterial cell wall is presented.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Acetic Acid</td>
			<td>Merck</td>
			<td>100063</td>
			<td>CAUTION. Anhydrous for analysis EMSURE&#174; ACS,ISO,Reag. Ph Eur</td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Carlo Erba</td>
			<td>400971N</td>
			<td>CAUTION. ACETONE RPE-ACS-ISO FOR ANALYS ml 1000</td>
		</tr>
		<tr>
			<td>Anthrone</td>
			<td>Merck</td>
			<td>8014610010</td>
			<td>Anthrone for synthesis.</td>
		</tr>
		<tr>
			<td>Benzene</td>
			<td>Carlo Erba</td>
			<td>426113</td>
			<td>CAUTION. Benzene RPE - For analysis - ACS 2.5 l</td>
		</tr>
		<tr>
			<td>Capillary glass tube</td>
			<td>Merck</td>
			<td>BR708709</td>
			<td>BRAND&#174;&#160;disposable BLAUBRAND&#174;&#160;micropipettes, intraMark</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Carlo Erba</td>
			<td>412653</td>
			<td>CAUTION. Chloroform RS - For HPLC - Isocratic grade - Stabilized with ethanol 2.5 L</td>
		</tr>
		<tr>
			<td>Dry block heater</td>
			<td>J.P. Selecta</td>
			<td>7471200</td>
			<td></td>
		</tr>
		<tr>
			<td>Dicloromethane</td>
			<td>Carlo Erba</td>
			<td>412622</td>
			<td>CAUTION. Dichloromethane RS - For HPLC - Isocratic grade - Stabilized with amylene 2.5 L</td>
		</tr>
		<tr>
			<td>Diethyl ether</td>
			<td>Carlo Erba</td>
			<td>412672</td>
			<td>CAUTION. Diethyl ether RS - For HPLC - Isocratic grade - Not stabilized 2.5 L</td>
		</tr>
		<tr>
			<td>Ethyl Acetate</td>
			<td>Panreac</td>
			<td>1313181211</td>
			<td>CAUTION. Ethyl acetate (Reag. USP, Ph. Eur.) for analysis, ACS, ISO</td>
		</tr>
		<tr>
			<td>Ethyl Alcohol Absolute</td>
			<td>Carlo Erba</td>
			<td>4146072</td>
			<td>CAUTION. Ethanol absolute anhydrous RPE - For analysis - ACS - Reag. Ph.Eur. - Reag. USP 1 L</td>
		</tr>
		<tr>
			<td>Glass funnel</td>
			<td>VidraFOC</td>
			<td>DURA.2133148 1217/1</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass tube</td>
			<td>VidraFOC</td>
			<td>VFOC.45066A-16125</td>
			<td>Glass tube with PTFE recovered cap</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Carlo Erba</td>
			<td>412722</td>
			<td>CAUTION. Methanol RS - For HPLC - GOLD - Ultragradient grade 2.5 L</td>
		</tr>
		<tr>
			<td>Molybdatophosphoric acid hydrate</td>
			<td>Merck</td>
			<td>51429-74-4</td>
			<td>CAUTION.</td>
		</tr>
		<tr>
			<td>Molybdenum Blue Spray Reagent, 1.3%</td>
			<td>Sigma</td>
			<td>M1942-100ML</td>
			<td>CAUTION.</td>
		</tr>
		<tr>
			<td>n-hexane</td>
			<td>Carlo Erba</td>
			<td>446903</td>
			<td>CAUTION. n-Hexane 99% RS - ATRASOL - For traces analysis 2.5 L</td>
		</tr>
		<tr>
			<td>n-nitroso-n-methylurea</td>
			<td>Sigma</td>
			<td>N4766</td>
			<td>CAUTION</td>
		</tr>
		<tr>
			<td>Orbital shaking platform</td>
			<td>DDBiolab</td>
			<td>995018</td>
			<td>NB-205L benchtop shaking incubator</td>
		</tr>
		<tr>
			<td>Petroleum ether (60-80&#186;C)</td>
			<td>Carlo Erba</td>
			<td>427003</td>
			<td>CAUTION. Petroleum ether 60 - 80&#176;C RPE - For analysis 2.5 L</td>
		</tr>
		<tr>
			<td>Sprayer</td>
			<td>VidraFOC</td>
			<td>712/1</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium sulphate anhydrous</td>
			<td>Merck</td>
			<td>238597</td>
			<td></td>
		</tr>
		<tr>
			<td>Sulfuric acid 95-97%</td>
			<td>Merck</td>
			<td>1007311000</td>
			<td>CAUTION. Sulfuric acid 95-97%</td>
		</tr>
		<tr>
			<td>TLC chamber</td>
			<td>Merck</td>
			<td>Z204226-1EA</td>
			<td>Rectangular TLC developing tanks, complete L &#215; H &#215; W 22 cm &#215; 22 cm &#215; 10 cm</td>
		</tr>
		<tr>
			<td>TLC plate</td>
			<td>Merck</td>
			<td>1057210001</td>
			<td>TLC SilicaGel 60- 20x20 cm x 25 u</td>
		</tr>
		<tr>
			<td>TLC Plate Heater</td>
			<td>CAMAG</td>
			<td>223306</td>
			<td>CAMAG TLC Plat Heater III</td>
		</tr>
		<tr>
			<td>Toluene</td>
			<td>Carlo Erba</td>
			<td>488551</td>
			<td>CAUTION. Toluene RPE - For analysis - ISO - ACS - Reag.Ph.Eur. - Reag.USP 1 L</td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>Fisher Scientific</td>
			<td>10132562</td>
			<td>IKA&#160;Agitador IKA v&#243;rtex 3</td>
		</tr>
		<tr>
			<td>1-naphthol</td>
			<td>Sigma-Aldrich</td>
			<td>102269427</td>
			<td>CAUTION.</td>
		</tr>
	</tbody>
</table>

analysis of the lipid composition of mycobacteria by thin layer chromatography

Mycobacteria species can differ from one another in the rate of growth, presence of pigmentation, the colony morphology displayed on solid media, as well as other phenotypic characteristics. However, they all have in common the most relevant character of mycobacteria: its unique and highly hydrophobic cell wall. Mycobacteria species contain a membrane-covalent linked complex that includes arabinogalactan, peptidoglycan, and long-chains of mycolic acids with types that differ between mycobacteria species. Additionally, mycobacteria can also produce lipids that are located, non-covalently linked, on their cell surfaces, such as phthiocerol dimycocerosates (PDIM), phenolic glycolipids (PGL), glycopeptidolipids (GPL), acyltrehaloses (AT), or phosphatidil-inositol mannosides (PIM), among others. Some of them are considered virulence factors in pathogenic mycobacteria, or critical antigenic lipids in host-mycobacteria interaction. For these reasons, there is a significant interest in the study of mycobacterial lipids due to their application in several fields, from understanding their role in the pathogenicity of mycobacteria infections, to a possible implication as immunomodulatory agents for the treatment of infectious diseases and other pathologies such as cancer. Here, a simple approach to extract and analyze the total lipid content and the mycolic acid composition of mycobacteria cells grown in a solid medium using mixtures of organic solvents is presented. Once the lipid extracts are obtained, thin-layer chromatography (TLC) is performed to monitor the extracted compounds. The example experiment is performed with four different mycobacteria: the environmental fast-growing Mycolicibacterium brumae and Mycolicibacterium fortuitum, the attenuated slow-growing Mycobacterium bovis bacillus Calmette-Gu&#233;rin (BCG), and the opportunistic pathogen fast-growing Mycobacterium abscessus, demonstrating that methods shown in the present protocol can be used to a wide range of mycobacteria.

With the aim of showing a wide range of lipids present in different mycobacteria species, M. bovis BCG was selected as it is rough and slow-growing mycobacteria. The rough and fast-growing M. fortuitum and M. brumae were added in the procedure and, finally, the smooth morphotype of M. abscessus was also included. These four species permit us to visualize a broad spectrum of mycobacteria-derived lipids such as acyltrehaloses (AT), GPLs, PDIM, PGL, PIM, TDM, and TMM. Moreover, all four s...

Watch this Scientific Journal Video about Analysis of the Lipid Composition of Mycobacteria by Thin Layer Chromatography at JoVE.com

Analysis of the Lipid Composition of Mycobacteria by Thin Layer Chromatography

A protocol is presented to extract the total lipid content of the cell wall of a wide range of mycobacteria. Moreover, extraction and analytical protocols of the different types of mycolic acids are shown. A thin-layer chromatographic protocol to monitor these mycobacterial compounds is also provided.

Mycobacteria species can differ from one another in the rate of growth, presence of pigmentation, the colony morphology displayed on solid media, as well ...

Mycobacteria Lipids are an important characteristic of the genus and are critical in host Mycobacteria interactions. Speed and versatility are the main advantages of this procedure. This method can be used to understand the role of lipids and the pathogenicity of mycobacteria and their immunostimulatory effect.For the non-covalent linked lipids extraction, add 15 milliliters of one to two chloroform to methanol solution to a glass tube with a PTFE liner screw cap under a laminar flow hood. Then, scratch 200 milligrams of mycobacteria from a solid medium, and add the mycobacteria to the glass tube. Incubate the tube overnight with constant stirring.On the next day, filter the organic solvents through a glass funnel lined with filter paper into a glass tube. After using nitrogen gas flux, to evaporate the liquid phase in the tube, fill the tube with nitrogen gas, to store the tube at four degrees Celsius. Then, add 15 milliliters of a two to one chloroform to methanol solution to the cellular debris and incubate the tube overnight with constant stirring.On the next morning, allow the mixture to rest for one hour, before using a Pasteur pipette to transfer the organic solvents into a filter paper lined glass funnel into the same glass collection tube. Then, evaporate the liquid phase as demonstrated, before refilling the tube with nitrogen gas for four degrees Celsius storage. For mycolic acid extraction, add two to five milliliters of a stirifying solution and 200 milligrams of mycobacteria biomass to a hermetic glass tube with a PTFE liner screw cap, and to mix the contents by vortexing.Incubate the mixture inside a dry bath at 80 degrees Celsius overnight. The next day, when the tube has cooled room temperature, add two milliliters of N hexane, and to mix the contents for 30 seconds by vortexing. Allow the tube to settle until two clear phases appear and transfer the upper N hexane phase to a new tube.Mix two additional milliliters of N hexane with the tube contents and collect the upper layer again. Then, evaporate the tube contents by nitrogen flow and store the sample covered in nitrogen at four degrees Celsius as demonstrated. To analyze the samples by TLC cover one wall of the TLC chamber with a piece of filter paper, add Vaseline on the chamber corners to seal the chamber, to can the solvent mixture over the filter paper and add the remaining volume of the solvent to the bottom of the TLC chamber.Close the TLC chamber for at least 20 minutes to saturated. Meanwhile, dissolve the lipids in the glass tube in 200 to 1000 microliters of chloroform and use a capillary glass tube to apply 10 microliters of the lipid chloroform suspension directly onto the TLC plate. After allowing the sample to dry for five minutes, insert the plate into the saturated TLC chamber and allow the mobile phase to run through the TLC.When the solvent reaches one centimeter from the upper end of the plate, place the plate under laminar flux until the silica is completely dry. Then, spray the dried plate with 15 to 20 milliliters of 10%molar data phosphoric acid hydrate in ethanol until the plate is bright yellow, and heat the plate for two to five minutes at 120 degrees Celsius. In this representative analysis, the mycolic acid extracted from various mycobacteria species, were analyzed through one dimensional TLC using two different elution systems and two dimensional TLC.Two types of methylation procedures were also performed to confirm the presence of type five mycolic acid. In both elution systems, the mycolic acids were located approximately in the middle of the plate, although, the spot corresponding to type five mycolic acid, was observed only after saponification. Two dimensional TLC also allows the identification of individual mycolic acid types.For example, mycobacterium brumae expresses only type one mycolic acids, mycobacterium bovis BCG expresses type one and four, mycobacterium fortuitum expresses type one and five, and mycobacterium abcessus expresses type one and two mycolic acid profiles. The total lipid extracts from various mycobacteria species were analyzed in function of their polarity and size. It reveals that most A polar lipids, such as PDIMs, are present in mycobacterium bovis BCG, but not in mycobacterium fortuitum, mycobacterium brumae and the smooth morphotype of M abcessus.Phenolic GlycoLipids are present only in mycobacterium bovis BCG, while GlycoPeptidoLipids are observed only in samples from mycobacterium abcessus. Similar to mycolic acids, Acylglycerols and PDIMs, PIMs, can also be easily visualized through one dimensional TLC or 2D TLC analysis. Two types of stains were used to reveal PIMs in one dimensional TLC.The most important thing to remember when attempting this protocol is to not use any plastic instruments throughout the procedure.

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Cell Biology

Immunology and Infection

Unit 1

Biochemistry of the Cell

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A Functional Whole Blood Assay to Measure Viability of Mycobacteria, using Reporter-Gene Tagged BCG or M.Tb (BCG lux/M.Tb lux)

Functional assays have long played a key role in measuring of immunogenicity of a given vaccine. This is conventionally expressed as serum bactericidal titers. Studies of serum bactericidal titers in response to childhood vaccines have enabled us to develop and validate cut-off levels for protective immune responses and such cut-offs are in routine use. No such assays have been taken forward into the routine assessment of vaccines that induce primarily cell-mediated immunity in the form of effector T cell responses, such as TB vaccines. In the animal model, the performance of a given vaccine candidate is routinely evaluated in standardized bactericidal assays, and all current novel TB-vaccine candidates have been subjected to this step in their evaluation prior to phase 1 human trials. The assessment of immunogenicity and therefore likelihood of protective efficacy of novel anti-TB vaccines should ideally undergo a similar step-wise evaluation in the human models now, including measurements in bactericidal assays.
Bactericidal assays in the context of tuberculosis vaccine research are already well established in the animal models, where they are applied to screen potentially promising vaccine candidates. Reduction of bacterial load in various organs functions as the main read-out of immunogenicity. However, no such assays have been incorporated into clinical trials for novel anti-TB vaccines to date.
Although there is still uncertainty about the exact mechanisms that lead to killing of mycobacteria inside human macrophages, the interaction of macrophages and T cells with mycobacteria is clearly required. The assay described in this paper represents a novel generation of bactericidal assays that enables studies of such key cellular components with all other cellular and humoral factors present in whole blood without making assumptions about their relative individual contribution. The assay described by our group uses small volumes of whole blood and has already been employed in studies of adults and children in TB-endemic settings. We have shown immunogenicity of the BCG vaccine, increased growth of mycobacteria in HIV-positive patients, as well as the effect of anti-retroviral therapy and Vitamin D on mycobacterial survival in vitro. Here we summarise the methodology, and present our reproducibility data using this relatively simple, low-cost and field-friendly model.
Note: Definitions/Abbreviations
BCG lux = M. bovis BCG, Montreal strain, transformed with shuttle plasmid pSMT1 carrying the luxAB genes from Vibrio harveyi, under the control of the mycobacterial GroEL (hsp60) promoter. 
CFU = Colony Forming Unit (a measure of mycobacterial viability).

A Functional Whole Blood Assay to Measure Viability of Mycobacteria, using Reporter-Gene Tagged BCG or M.Tb BCG lux/M.Tb lux

We describe an alternative approach to the enumeration of mycobacteria in vitro, which uses reporter-gene tagged mycobacteria instead of colony-forming units (CFU). &#x201C;Survival&#x201D; of organisms as well as host response-markers are measured simultaneously, providing a low-cost, versatile and functional system for studies of host/pathogen interactions in the context of tuberculosis.

Functional assays have long played a key role in measuring of immunogenicity of a given vaccine. This is conventionally expressed as serum bactericidal ...

A Microscopic Phenotypic Assay for the Quantification of Intracellular Mycobacteria Adapted for High-throughput/High-content Screening

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since several decades, the sudden burst of multi- and extensively-drug resistant strains is a serious threat for the control of tuberculosis. Therefore, it is essential to identify new targets and pathways critical for the causative agent of the tuberculosis, Mycobacterium tuberculosis (Mtb) and to search for novel chemicals that could become TB drugs. One approach is to set&#160;up methods suitable for the genetic and chemical screens of large scale libraries enabling the search of a needle in a haystack. To this end, we developed a phenotypic assay relying on the detection of fluorescently labeled Mtb within fluorescently labeled host&#160;cells using automated confocal microscopy. This in vitro assay allows an image based quantification of the colonization process of Mtb&#160;into the host and was optimized for the 384-well microplate format, which is proper for screens of siRNA-, chemical compound- or Mtb mutant-libraries. The images are then processed for multiparametric analysis, which provides read&#160;out inferring on the pathogenesis of Mtb&#160;within host cells.

Here, we describe a phenotypic assay applicable to the High-throughput/High-content screens of small-interfering synthetic RNA (siRNA), chemical compound, and Mycobacterium tuberculosis mutant libraries. This method relies on the detection of fluorescently labeled Mycobacterium tuberculosis within fluorescently labeled host&#160;cell using automated confocal microscopy.

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since ...

Analysis of the Epithelial Damage Produced by Entamoeba histolytica Infection

Entamoeba histolytica is the causative agent of human amoebiasis, a major cause of diarrhea and hepatic abscess in tropical countries. Infection is initiated by interaction of the pathogen with intestinal epithelial cells. This interaction leads to disruption of intercellular structures such as tight junctions (TJ). TJ ensure sealing of the epithelial layer to separate host tissue from gut lumen. Recent studies provide evidence that disruption of TJ by the parasitic protein EhCPADH112 is a prerequisite for E. histolytica invasion that is accompanied by epithelial barrier dysfunction. Thus, the analysis of molecular mechanisms involved in TJ disassembly during E. histolytica invasion is of paramount importance to improve our understanding of amoebiasis pathogenesis. This article presents an easy model that allows the assessment of initial host-pathogen interactions and the parasite invasion potential. Parameters to be analyzed include transepithelial electrical resistance, interaction of EhCPADH112 with epithelial surface receptors, changes in expression and localization of epithelial junctional markers and localization of parasite molecules within epithelial cells.

Analysis of the Epithelial Damage Produced by Entamoeba histolytica Infection

Human infection by Entamoeba histolytica leads to amoebiasis, a major cause of diarrhea in tropical countries. Infection is initiated by pathogen interactions with intestinal epithelial cells, provoking the opening of cell-cell contacts and consequently diarrhea, sometimes followed by liver infection. This article provides a model to assess the early host-pathogen interactions to improve our understanding of amoebiasis pathogenesis.

Entamoeba histolytica is the causative agent of human amoebiasis, a major cause of diarrhea and hepatic abscess in tropical countries. Infection is ...

Rapid Analysis of Chromosome Aberrations in Mouse B Lymphocytes by PNA-FISH

Defective DNA repair leads to increased genomic instability, which is the root cause of mutations that lead to tumorigenesis. Analysis of the frequency and type of chromosome aberrations in different cell types allows defects in DNA repair pathways to be elucidated. Understanding mammalian DNA repair biology has been greatly helped by the production of mice with knockouts in specific genes. The goal of this protocol is to quantify genomic instability in mouse B lymphocytes. Labeling of the telomeres using PNA-FISH probes (peptide nucleic acid - fluorescent in situ hybridization) facilitates the rapid analysis of genomic instability in metaphase chromosome spreads. B cells have specific advantages relative to fibroblasts, because they have normal ploidy and a higher mitotic index. Short-term culture of B cells therefore enables precise measurement of genomic instability in a primary cell population which is likely to have fewer secondary genetic mutations than what is typically found in transformed fibroblasts or patient cell lines.

DNA repair pathways are essential for maintenance of genomic integrity and preventing mutation and cancer. The goal of this protocol is to quantify genomic instability by direct observation of chromosome aberrations in metaphase spreads from mouse B cells using fluorescent in situ hybridization (FISH) for telomeric DNA repeats.

Defective DNA repair leads to increased genomic instability, which is the root cause of mutations that lead to tumorigenesis. Analysis of the frequency ...

Visualization of the Charcoal Agar Resazurin Assay for Semi-quantitative, Medium-throughput Enumeration of Mycobacteria

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the etiological agent of TB, is refractory to rapid and lasting chemotherapy due to the presence of bacilli exhibiting phenotypic drug resistance. The charcoal agar resazurin assay (CARA) was developed as a tool to characterize active molecules discovered by high-throughput screening campaigns against replicating and non-replicating M. tuberculosis. Inclusion of activated charcoal in bacteriologic agar medium helps mitigate the impact of compound carry-over, and eliminates the requirement to pre-dilute cells prior to spotting on CARA microplates. After a 7-10 day incubation period at 37 &#176;C, the reduction of resazurin by mycobacterial microcolonies growing on the surface of CARA microplate wells permits semi-quantitative assessment of bacterial numbers via fluorometry. The CARA detects approximately a 2-3 log10 difference in bacterial numbers and predicts a minimal bactericidal concentration leading to &#8805;99% bacterial kill (MBC&#8805;99). The CARA helps determine whether a molecule is active on bacilli that are replicating, non-replicating, or both. Pilot experiments using the CARA facilitate the identification of which concentration of test agent and time of compound exposure require further evaluation by colony forming unit (CFU) assays. In addition, the CARA can predict if replicating actives are bactericidal or bacteriostatic.

The charcoal agar resazurin assay (CARA) is a semi-quantitative, medium-throughput method to assess activity of test agents against mycobacteria that are replicating, non-replicating, or both. The CARA permits rapid evaluation of time- and concentration-dependent activity and identifies parameters to pursue by colony forming unit (CFU) assays.

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the ...

Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis

Sectioning via paraffin embedding is a broadly established technique in eukaryotic systems. Here we provide a method for the fixation, embedding, and sectioning of intact microbial colony biofilms using perfused paraffin wax. To adapt this method for use on colony biofilms, we developed techniques for maintaining each sample on its growth substrate and laminating it with an agar overlayer, and added lysine to the fixative solution. These optimizations improve sample retention and preservation of micromorphological features. Samples prepared in this manner are amenable to thin sectioning and imaging by light, fluorescence, and transmission electron microscopy. We have applied this technique to colony biofilms of Pseudomonas aeruginosa, Pseudomonas synxantha, Bacillus subtilis, and Vibrio cholerae. The high level of detail visible in samples generated by this method, combined with reporter strain engineering or the use of specific dyes, can provide exciting insights into the physiology and development of microbial communities.

We describe fixation, paraffin embedding, and thin sectioning techniques for microbial colony biofilms. In prepared samples, biofilm substructure and reporter expression patterns can be visualized by microscopy.

Sectioning via paraffin embedding is a broadly established technique in eukaryotic systems. Here we provide a method for the fixation, embedding, and ...

Characterization of Human Monocyte Subsets by Whole Blood Flow Cytometry Analysis

Monocytes are key contributors in various inflammatory disorders and alterations to these cells, including their subset proportions and functions, can have pathological significance. An ideal method for examining alterations to monocytes is whole blood flow cytometry as the minimal handling of samples by this method limits artifactual cell activation. However, many different approaches are taken to gate the monocyte subsets leading to inconsistent identification of the subsets between studies. Here we demonstrate a method using whole blood flow cytometry to identify and characterize human monocyte subsets (classical, intermediate, and non-classical). We outline how to prepare the blood samples for flow cytometry, gate the subsets (ensure contaminating cells have been removed), and determine monocyte subset expression of surface markers &#8212; in this example M1 and M2 markers. This protocol can be extended to other studies that require a standard gating method for assessing monocyte subset proportions and monocyte subset expression of other functional markers.

Here we present a protocol for characterizing monocyte subsets by whole blood flow cytometry. This includes outlining how to gate the subsets and assess their expression of surface markers and giving an example of the assessment of the expression of M1 (inflammatory) and M2 markers (anti-inflammatory).

Monocytes are key contributors in various inflammatory disorders and alterations to these cells, including their subset proportions and functions, can ...

Optimized Interferon-gamma ELISpot Assay to Measure T Cell Responses in the Guinea Pig Model after Vaccination

The guinea pig has played a pivotal role as a relevant small animal model in the development of vaccines for infectious diseases such as tuberculosis, influenza, diphtheria, and viral hemorrhagic fevers. We have demonstrated that plasmid-DNA (pDNA) vaccine delivery into the skin elicits robust humoral responses in the guinea pig. However, the use of this animal to model immune responses was somewhat limited in the past due to the lack of available reagents and protocols to study T cell responses. T cells play a pivotal role in both immunoprophylactic and immunotherapeutic mechanisms. Understanding T cell responses is crucial for the development of infectious disease and oncology vaccines and accommodating delivery devices. Here we describe an interferon-gamma (IFN-&#947;) enzyme-linked immunospot (ELISpot) assay for guinea pig peripheral blood mononuclear cells (PBMCs). The assay enables researchers to characterize vaccine-specific T-cell responses in this important rodent model. The ability to assay cells isolated from the peripheral blood provides the opportunity to track immunogenicity in individual animals.

The development of the interferon-gamma ELISpot assay for guinea pig PBMCs allows the characterization of T-cell responses in this highly relevant model for studying infectious diseases. We have applied the assay to measure T cell responses associated with intradermal delivery of DNA vaccines.

The guinea pig has played a pivotal role as a relevant small animal model in the development of vaccines for infectious diseases such as tuberculosis, ...

Analysis of Lipid Droplet Content in Fission and Budding Yeasts using Automated Image Processing

Lipid metabolism and its regulation are of interest to both basic and applied life sciences and biotechnology. In this regard, various yeast species are used as models in lipid metabolic research or for industrial lipid production. Lipid droplets are highly dynamic storage bodies and their cellular content represents a convenient readout of the lipid metabolic state. Fluorescence microscopy is a method of choice for quantitative analysis of cellular lipid droplets, as it relies on widely available equipment and allows analysis of individual lipid droplets. Furthermore, microscopic image analysis can be automated, greatly increasing overall analysis throughput. Here, we describe an experimental and analytical workflow for automated detection and quantitative description of individual lipid droplets in three different model yeast species: the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus, and the budding yeast Saccharomyces cerevisiae. Lipid droplets are visualized with BODIPY 493/503, and cell-impermeable fluorescent dextran is added to the culture media to help identify cell boundaries. Cells are subjected to 3D epifluorescence microscopy in green and blue channels and the resulting z-stack images are processed automatically by a MATLAB pipeline. The procedure outputs rich quantitative data on cellular lipid droplet content and individual lipid droplet characteristics in a tabular format suitable for downstream analyses in major spreadsheet or statistical packages. We provide example analyses of lipid droplet content under various conditions that affect cellular lipid metabolism.

Here, we present a MATLAB implementation of automated detection and quantitative description of lipid droplets in fluorescence microscopy images of fission and budding yeast cells.

Lipid metabolism and its regulation are of interest to both basic and applied life sciences and biotechnology. In this regard, various yeast species are ...

Isolation and Characterization of Extracellular Vesicles Produced by Iron-limited Mycobacteria

Mycobacteria, including Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, naturally release extracellular vesicles (EVs) containing immunologically active molecules. Knowledge regarding the molecular mechanisms of vesicle biogenesis, the content of the vesicles, and their functions at the pathogen-host interface is very limited. Addressing these questions requires rigorous procedures for isolation, purification, and validation of EVs. Previously, vesicle production was found to be enhanced when M. tuberculosis was exposed to iron restriction, a condition encountered by Mtb in the host environment. Presented here is a complete and detailed protocol to isolate and purify EVs from iron-deficient mycobacteria. Quantitative and qualitative methods are applied to validate purified EVs.

Mycobacterium tuberculosis shows increased production and release of extracellular vesicles in response to low iron conditions. This work details a protocol for generating low iron conditions and methods for the purification and characterization of mycobacterial extracellular vesicles released in response to iron deficiency.

Mycobacteria, including Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, naturally release extracellular vesicles (EVs) ...