We thank Dr. Diane Baronas-Lowell for critical reading of the manuscript. This work was supported by an FAU Charles E. Schmidt College of Science Seed Grant and an Aging Scholarship from the Ellison Medical Foundation to K.J.

1. XLD (Xylose Lysine Desoxycholate) Agar Plates
XLD agar is a selective growth medium for Salmonella, which appears as black colonies on XLD agar plates. However, if there are no concerns of contamination, a regular LB plate can be substituted.
<ol>
	<li>Weigh out 5.5 g XLD agar and resuspend in 5 ml deionized water.</li>
	<li>Mix thoroughly until all agar is wet. Add 95 ml deionized water until all lumps are gone and the medium is completely resuspended.</li>
	<li>Boil the medium to dissolve completely (do not autoclave).</li>
	<li>Cool the medium at room temperature to 50 &#176;C.</li>
	<li>Pour 25 ml agar in each 95 x 15 mm (diameter x height) plate (plates sealed with Parafilm can be stored at 4 &#176;C for up to 1&#160;month).</li>
</ol>
2. Nematode Growth Medium (NGM) RNAi Feeding Plates
Preparation of C. elegans NGM plates has been described previously19. Here a procedure is briefly described to add the antibiotic ampicillin and the RNAi chemical inducer isopropyl &#946;-D-1-thiogalactopyranoside (IPTG) into the NGM media to make the RNAi feeding plates.
<ol>
	<li>Dissolve 3 g NaCl and 2.5 g Bacto peptone in 1 L&#160;deionized water.</li>
	<li>Add 17 g Bacto agar into the media.</li>
	<li>Autoclave the media for 45 min&#160;and cool the media to 50 &#176;C in a water bath.</li>
	<li>Add the following solutions: 1 ml cholesterol (5 mg/ml in 95% ethanol), 1 ml 1 M CaCl2, 1 ml 1 M MgSO4, and 25 ml 1 M potassium phosphate buffer (pH 6.0). Mix well.</li>
	<li>Add 1 ml 1 M IPTG and 500 &#181;l ampicillin (100 mg/ml in sterile water).</li>
	<li>Mix the solution well and pour into 60 x 15 mm (diameter x height) petri plates using a Pipet Aid and 25 ml serological pipette following sterile procedures. Fill each plate with 12 ml agar. Plates can be stored at 4 &#176;C for up to 1&#160;month.</li>
</ol>
3. Prepare RNAi-treated Animals for Infection
The essential autophagy gene bec-1 is used as an example to examine the function of a host gene in defense against Salmonella infection. The experimental procedures are illustrated in Figure 1 and Table 1. The protocol for preparing RNAi-treated animals for infection follows, with the day of each experimental step given in parentheses.
<ol>
	<li>Inoculate bec-1 RNAi feeding and control empty vector L4440 RNAi feeding bacteria by placing a flake of -80 &#176;C frozen bacteria into 2 ml LB medium supplemented with 100 mg/ml ampicillin (Day 1). Repeat this step once a week during the entire experiment to have fresh RNAi bacteria. Store the culture in the 4 &#176;C refrigerator when not used.</li>
	<li>Seed 100 ml of overnight RNAi bacterial culture on RNAi plates. Prepare three bec-1 RNAi and three control empty vector RNAi plates. Incubate the plates at 37 &#176;C overnight (Day 2).</li>
	<li>Remove the RNAi plates from the 37 &#176;C incubator and allow them to cool down to room temperature on the bench. Pick up well-fed L4 wild type N2 hermaphrodites and transfer them to bec-1 RNAi and control empty vector RNAi plates. Place three worms per plate, on triplicate plates. On the same day, prepare RNAi plates as described in step 3.2 (Day 3).</li>
	<li>Incubate the RNAi plates with worms in the 20 &#176;C incubator for 36-40 hr&#160;and transfer worms to fresh corresponding RNAi plates prepared in step 3.3. After worms are transferred, incubate the plates in the 20 &#176;C incubator for 64 hr&#160;(Day 4).</li>
</ol>
4. Prepare Salmonella for Infection
<ol>
	<li>Streak Salmonella -80 &#176;C frozen stock on 1&#160;XLD agar plate and incubate the plate at 37 &#176;C overnight (Day 5).</li>
	<li>Pick a well-isolated black Salmonella colony and inoculate it in 2 ml LB medium at 37 &#176;C with shaking overnight (Day 6).</li>
	<li>Seed 80 ml Salmonella overnight culture on 1&#160;C. elegans 60 x 15 mm (diameter x height) NGM agar plate and prepare 6&#160;plates in total. Incubate the plates at room temperature for 6&#160;hr. The bacterial culture should dry and form a lawn on the plate (Day 7).</li>
</ol>
5. Infect RNAi-treated Worms with Salmonella
<ol>
	<li>Transfer bec-1 RNAi-treated and control empty vector RNAi-treated L4 N2 hermaphrodites (progeny of worms set up in Step 3) to Salmonella plates. Place 40 worms per plate on 3&#160;plates for each group. Incubate the worm plates at 20 &#176;C for 48 hr&#160;(Day 7).</li>
	<li>Prepare one set of fresh RNAi plates as described in steps 3.1 and 3.2 (Day 7 and Day 8).</li>
	<li>After 48 hr&#160;infection, transfer Salmonella-infected worms to the corresponding RNAi plates prepared in step 5.2 and incubate at 20 &#176;C (Day 9).</li>
</ol>
6. Survival Assay
<ol>
	<li>Score the survival of worms daily and transfer worms to fresh corresponding RNAi plates during the egg-laying time. Prepare a set of fresh RNAi plates prior to each worm transfer as described in steps 3.1 and 3.2. Touch the worm body (head, middle part and tail) gently with an end-flattened platinum wire. A worm is scored as dead if no movement of the worm body is observed.</li>
	<li>Score the survival of worms daily or every other day, and transfer worms to fresh corresponding RNAi plates twice a week after worms stop laying eggs.</li>
	<li>After all worms die, pool the survival data from triplicate plates as one data set. Input the survival data of each group into appropriate statistical software such as GraphPad Prism to generate survival curves and to perform Kaplan-Meier survival analysis. The entire experiment is repeated at least once to confirm the conclusion.</li>
</ol>

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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caenorhabditis+elegans:+an+emerging+genetic+model+for+the+study+of+innate+immunity.">Caenorhabditis elegans: an emerging genetic model for the study of innate immunity.</a> Nat Rev Genet. 4, 380-390 (2003).</li><li>Mylonakis, E., Aballay, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Worms+and+flies+as+genetically+tractable+animal+models+to+study+host-pathogen+interactions.">Worms and flies as genetically tractable animal models to study host-pathogen interactions.</a> Infection and Immunity. 73, 3833-3841 (2005).</li><li>Ford, M. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+descriptive+study+of+human+Salmonella+serotype+typhimurium+infections+reported+in+Ontario+from+1990+to+1997.">A descriptive study of human Salmonella serotype typhimurium infections reported in Ontario from 1990 to 1997.</a> Can J Infect Dis. 14, 267-273 (2003).</li><li>Voetsch, A. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FoodNet+estimate+of+the+burden+of+illness+caused+by+nontyphoidal+Salmonella+infections+in+the+United+States.">FoodNet estimate of the burden of illness caused by nontyphoidal Salmonella infections in the United States.</a> Clin Infect Dis. 38 Suppl 3, (2004).</li><li>Aballay, A., Yorgey, P., Ausubel, F. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Salmonella+typhimurium+proliferates+and+establishes+a+persistent+infection+in+the+intestine+of+Caenorhabditis+elegans.">Salmonella typhimurium proliferates and establishes a persistent infection in the intestine of Caenorhabditis elegans.</a> Curr Biol. 10, 1539-1542 (2000).</li><li>Alegado, R. A., Tan, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resistance+to+antimicrobial+peptides+contributes+to+persistence+of+Salmonella+typhimurium+in+the+C.+elegans+intestine.">Resistance to antimicrobial peptides contributes to persistence of Salmonella typhimurium in the C. elegans intestine.</a> Cell Microbiol. 10, 1259-1273 (2008).</li><li>Jia, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Autophagy+genes+protect+against+Salmonella+typhimurium+infection+and+mediate+insulin+signaling-regulated+pathogen+resistance.">Autophagy genes protect against Salmonella typhimurium infection and mediate insulin signaling-regulated pathogen resistance.</a> Proceedings of the National Academy of Sciences of the United States of America. 106, 14564-14569 (2009).</li><li>Tenor, J. L., McCormick, B. A., Ausubel, F. M., Aballay, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caenorhabditis+elegans-based+screen+identifies+Salmonella+virulence+factors+required+for+conserved+host-pathogen+interactions.">Caenorhabditis elegans-based screen identifies Salmonella virulence factors required for conserved host-pathogen interactions.</a> Curr Biol. 14, 1018-1024 (2004).</li><li>Levine, B., Klionsky, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+by+self-digestion:+molecular+mechanisms+and+biological+functions+of+autophagy.">Development by self-digestion: molecular mechanisms and biological functions of autophagy.</a> Developmental Cell. 6, 463-477 (2004).</li><li>Birmingham, C. L., Smith, A. C., Bakowski, M. A., Yoshimori, T., Brumell, J. 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Genome sequence of the nematode C. elegans: a platform for investigating biology.</a> Science. 282, 2012-2018 (1998).</li><li>Fire, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Potent+and+specific+genetic+interference+by+double-stranded+RNA+in+Caenorhabditis+elegans.">Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.</a> Nature. 391, 806-811 (1998).</li><li>Kamath, R. S., Martinez-Campos, M., Zipperlen, P., Fraser, A. 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The authors declare that they have no competing financial interests.

C. elegans is a simple genetic model organism that eats bacteria as its nutrient source. Thus, it is easy to substitute its normal bacterial food with an intestinal pathogen to investigate the interactions between C. elegans and the chosen pathogen. Herein a protocol is described to combine Salmonella infection and C. elegans RNAi feeding treatment to examine the role of host genes in defense against Salmonella infection. Previous infection protocols expose C. elegans...

The free-living soil nematode Caenorhabditis elegans is a simple and genetically tractable model organism used to study many biological questions. C. elegans dominantly exists as self-fertilizing hermaphrodites. Males are spontaneously generated by non-disjunction of the X chromosome during gametogenesis1,2. In the presence of abundant food, C. elegans continuously develop through four larval stages to adult. Temperature also influences C. elegans development; faster development is observed at higher temperatures. In the laboratory, C. elegans is cultured at a standard temperature of 20 &#176;C on agar plates with seeded bacterium Escherichia coli (strain OP50) as food1,2.
In the last decade, C. elegans has emerged as an invertebrate organism to study host-pathogen interactions3-5. In nature, C. elegans eats bacteria as its nutrient source1,2. Its normal bacterial laboratory food, OP50, can be easily substituted with other pathogens to examine the interactions between C. elegans and any chosen pathogen. Under these conditions, the intestine is the primary site of the infection. Indeed, a wide range of bacterial pathogens has been shown to lethally infect C. elegans3-5.
The gram-negative bacterium Salmonella is a gastrointestinal pathogen that causes human food-borne illness worldwide6,7. C. elegans is a good model host for Salmonella typhimurium as this bacterium replicates and exhibits persistent intestinal infections8-10. C. elegans has been used to identify both novel and previously known Salmonella virulence factors11. Interestingly, the C. elegans immune system successfully limits Salmonella replication. It has been reported previously that inhibition of autophagy genes renders increased Salmonella replication in C. elegans, resulting in early death of infected worms10. Macroautophagy (herein referred to as autophagy) is a dynamic process involving the rearrangement of subcellular membranes to sequester cytoplasm and organelles for delivery to the lysosome for degradation12. Autophagy has been reported to limit the Salmonella replication in C. elegans and in mammals10,13.
The C. elegans genome was the first multicellular eukaryotic genome sequenced; it is responsive to RNAi treatment14-16. Moreover, RNAi can be administrated effectively by subjecting worms to ingest bacteria containing the double-stranded RNA of the target gene, known as RNAi feeding16,17. Whole genome RNAi feeding libraries have been generated for genome-wide RNAi screening16,18. Herein, a Salmonella infection protocol is coupled with RNAi feeding to allow testing C. elegans genes of interest for their ability to protect against Salmonella infection.

<table border="0" cellpadding="0" cellspacing="0" width="621">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">LB Broth</td>
			<td style="width:119px;">Fisher</td>
			<td style="width:119px;">BP9723-500</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">XLD agar</td>
			<td>EMD Chemicals</td>
			<td>1.05287.0500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bacto Agar</td>
			<td>Fisher</td>
			<td>DF0140-01-0</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Peptone</td>
			<td>Fisher</td>
			<td>BP1420-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium Chloride</td>
			<td>Fisher</td>
			<td>S671-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calcium Chloride</td>
			<td>Fisher</td>
			<td>C69-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Magnesium Sulfate</td>
			<td>Fisher</td>
			<td>M65-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">IPTG</td>
			<td>Gold Biotechnology</td>
			<td>12481C50</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cholesterol</td>
			<td>Sigma</td>
			<td>C8667-25G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ampicillin</td>
			<td>Fisher&#160;</td>
			<td>BP1760-25</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Salmonella typhimurium</td>
			<td>ATCC</td>
			<td>ATCC14028</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Petri Dish 95 x 15mm</td>
			<td>Fisher</td>
			<td>FB0875714G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Petri Dish 60 x 15mm&#160;</td>
			<td>Fisher</td>
			<td>08-757-13A&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Serological pipet</td>
			<td>Fisher</td>
			<td>13-668-2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Express Pipet-Aid</td>
			<td>Fisher</td>
			<td>13-675-42</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">MaxQ6000 shaking incubator&#160;</td>
			<td>Thermo Scientific</td>
			<td>SHKE6000-7</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Incubator</td>
			<td>Percival</td>
			<td>I-36DL</td>
			<td></td>
		</tr>
	</tbody>
</table>

a protocol to infect caenorhabditis elegans with salmonella typhimurium

In the last decade, C. elegans has emerged as an invertebrate organism to study interactions between hosts and pathogens, including the host defense against gram-negative bacterium Salmonella typhimurium. Salmonella establishes persistent infection in the intestine of C. elegans and results in early death of infected animals. A number of immunity mechanisms have been identified in C. elegans to defend against Salmonella infections. Autophagy, an evolutionarily conserved lysosomal degradation pathway, has been shown to limit the Salmonella replication in C. elegans and in mammals. Here, a protocol is described to infect C. elegans with Salmonella typhimurium, in which the worms are exposed to Salmonella for a limited time, similar to Salmonella infection in humans. Salmonella infection significantly shortens the lifespan of C. elegans. Using the essential autophagy gene bec-1 as an example, we combined this infection method with C. elegans RNAi feeding approach and showed this protocol can be used to examine the function of C. elegans host genes in defense against Salmonella infection. Since C. elegans whole genome RNAi libraries are available, this protocol makes it possible to comprehensively screen for C. elegans genes that protect against Salmonella and other intestinal pathogens using genome-wide RNAi libraries.

At 20 &#176;C, the median lifespan of wild type N2 worms is 17 days (Figure 2A and Table 2). Salmonella infection significantly decreases the median lifespan of N2 worms to 10.5 days (p = 0.0002, log-rank test) (Figure 2A).
If a C. elegans gene plays an important role in defense against Salmonella infection, it is predicted that its inhibition will impart susceptibility to Salmonella infection. In fact, comp...

Watch this Scientific Journal Video about A Protocol to Infect Caenorhabditis elegans with Salmonella typhimurium at JoVE.com

A Protocol to Infect Caenorhabditis elegans with Salmonella typhimurium

C. elegans has emerged as a new genetic model to study host-pathogen interactions. Here we describe a protocol to infect C. elegans with Salmonella typhimurium coupled with the double-strand RNAi interference technique to examine the role of host genes in defense against Salmonella infection.

A Protocol to Infect Caenorhabditis elegans with Salmonella typhimurium

In the last decade, C. elegans has emerged as an invertebrate organism to study interactions between hosts and pathogens, including the host defense ...

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Immunology and Infection

11.5K Views.  Florida Atlantic University.  C. Элеганс стала новой генетической модели для изучения хост-патогенных взаимодействий. Здесь мы опишем протокол заразить C. Элеганс с Salmonella Typhimurium в сочетании с техникой помех РНК-интерференции двухцепочечной изучить роль генов хозяина в защит...

Video: A Protocol to Infect Caenorhabditis elegans with Salmonella typhimurium

An Allelotyping PCR for Identifying Salmonella enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium

Current commercial PCRs tests for identifying Salmonella target genes unique to this genus. However, there are two species, six subspecies, and over 2,500 different Salmonella serovars, and not all are equal in their significance to public health. For example, finding S. enterica subspecies IIIa Arizona on a table egg layer farm is insignificant compared to the isolation of S. enterica subspecies I serovar Enteritidis, the leading cause of salmonellosis linked to the consumption of table eggs. Serovars are identified based on antigenic differences in lipopolysaccharide (LPS)(O antigen) and flagellin (H1 and H2 antigens). These antigenic differences are the outward appearance of the diversity of genes and gene alleles associated with this phenotype.
We have developed an allelotyping, multiplex PCR that keys on genetic differences between four major S. enterica subspecies I serovars found in poultry and associated with significant human disease in the US. The PCR primer pairs were targeted to key genes or sequences unique to a specific Salmonella serovar and designed to produce an amplicon with size specific for that gene or allele. Salmonella serovar is assigned to an isolate based on the combination of PCR test results for specific LPS and flagellin gene alleles. The multiplex PCRs described in this article are specific for the detection of S. enterica subspecies I serovars Enteritidis, Hadar, Heidelberg, and Typhimurium.
Here we demonstrate how to use the multiplex PCRs to identify serovar for a Salmonella isolate.

An Allelotyping PCR for Identifying Salmonella enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium

We describe a multiplex PCR for the rapid detection of Salmonella enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium. Specific Salmonella serovars can be identified by targeting a multiplex PCR to genes and sequences unique to the O-antigen biosynthesis cluster and flagellin of a given serovar. Serovar is assigned then to a Salmonella isolate based on the appearance of specific, size amplicons (PCR product) corresponding to the target allele.

Current commercial PCRs tests for identifying Salmonella target genes unique to this genus.  However, there are two species, six subspecies, and over ...

High-throughput Assay to Phenotype Salmonella enterica Typhimurium Association, Invasion, and Replication in Macrophages

Salmonella species are zoonotic pathogens and leading causes of food borne illnesses in humans and livestock1. Understanding the mechanisms underlying Salmonella-host interactions are&#160;important to elucidate the molecular pathogenesis of Salmonella infection. The Gentamicin protection assay to phenotype Salmonella association, invasion and replication in phagocytic cells was adapted to allow high-throughput screening to define the roles of deletion mutants of Salmonella enterica serotype Typhimurium in host interactions using RAW 264.7 murine macrophages. Under this protocol, the variance in measurements is significantly reduced compared to the standard protocol, because wild-type and multiple mutant strains can be tested in the same culture dish and at the same time. The use of multichannel pipettes increases the throughput and enhances precision. Furthermore, concerns related to using less host cells per well in 96-well culture dish were addressed. Here, the protocol of the modified in vitro Salmonella invasion assay using phagocytic cells was successfully employed to phenotype 38 individual Salmonella deletion mutants for association, invasion and intracellular replication. The in vitro phenotypes are presented, some of which were subsequently confirmed to have in vivo phenotypes in an animal model. Thus, the modified, standardized assay to phenotype Salmonella association, invasion and replication in macrophages with high-throughput capacity could be utilized more broadly to study bacterial-host interactions.

High-throughput Assay to Phenotype Salmonella enterica Typhimurium Association, Invasion, and Replication in Macrophages

A high-throughput assay to in vitro phenotype Salmonella or other bacterial association, invasion, and replication in phagocytic cells with high-throughput capacity was developed. The method was employed to evaluate Salmonella gene knockout mutant strains for their involvements in host-pathogen interactions.

Salmonella species are zoonotic pathogens and leading causes of food borne illnesses in humans and livestock1. Understanding the mechanisms underlying ...

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. typhimurium bacteria are quickly detected and phagocytized by macrophages, and contained in vesicles known as phagosomes in order to be degraded. Isolation of S. typhimurium-containing phagosomes have been widely used to study how S. typhimurium infection alters the process of phagosome maturation to prevent bacterial degradation. Classically, the isolation of bacteria-containing phagosomes has been performed by sucrose gradient centrifugation. However, this process is time-consuming, and requires specialized equipment and a certain degree of dexterity. Described here is a simple and quick method for the isolation of S. typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin-streptavidin-conjugated magnetic beads. Phagosomes obtained by this method can be suspended in any buffer of choice, allowing the utilization of isolated phagosomes for a broad range of assays, such as protein, metabolite, and lipid analysis. In summary, this method for the isolation of S. typhimurium-containing phagosomes is specific, efficient, rapid, requires minimum equipment, and is more versatile than the classical method of isolation by sucrose gradient-ultracentrifugation.

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

We describe here a simple and quick method for the isolation of Salmonella typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin and streptavidin.

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. ...

A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli

Post-translational modifications that occur at specific positions of proteins have been shown to play important roles in a variety of cellular processes. Among them, reversible lysine acetylation is one of the most widely distributed in all domains of life. Although numerous mass spectrometry-based acetylome studies have been performed, further characterization of these putative acetylation targets has been limited. One possible reason is that it is difficult to generate purely acetylated proteins at desired positions by most classic biochemical approaches. To overcome this challenge, the genetic code expansion technique has been applied to use the pair of an engineered pyrrolysyl-tRNA synthetase variant, and its cognate tRNA from Methanosarcinaceae species, to direct the cotranslational incorporation of acetyllysine at the specific site in the protein of interest. After first application in the study of histone acetylation, this approach has facilitated acetylation studies on a variety of proteins. In this work, we demonstrated a facile protocol to produce site-specifically acetylated proteins by using the model bacterium Escherichia coli as the host. Malate dehydrogenase was used as a demonstration example in this work.

A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli

Genetic code expansion serves as a powerful tool to study a wide range of biological processes, including protein acetylation. Here we demonstrate a facile protocol to exploit this technique for generating homogeneously acetylated proteins at specific sites in Escherichia coli cells.

Post-translational modifications that occur at specific positions of proteins have been shown to play important roles in a variety of cellular processes. ...

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella spp./Shigella spp. The gold standard method for the detection of Salmonella spp./Shigella spp. is direct culture but this is labor-intensive and time-consuming. Here, we describe a high-throughput platform for Salmonella spp./Shigella spp. screening, using real-time polymerase chain reaction (PCR) combined with guided culture. There are two major stages: real-time PCR and the guided culture. For the first stage (real-time PCR), we explain each step of the method: sample collection, pre-enrichment, DNA extraction and real-time PCR. If the real-time PCR result is positive, then the second stage (guided culture) is performed: selective culture, biochemical identification and serological characterization. We also illustrate representative results generated from it. The protocol described here would be a valuable platform for the rapid, specific, sensitive and high-throughput screening of Salmonella spp./Shigella spp.

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Salmonella spp./Shigella spp. are common pathogens attributed to diarrhea. Here, we describe a high-throughput platform for the screening of Salmonella spp./Shigella spp. using real-time PCR combined with guided culture.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella ...

Evaluating Virulence and Pathogenesis of Aeromonas Infection in a Caenorhabditis elegans Model

The human pathogen Aeromonas has been clinically shown to cause gastroenteritis, wound infections, septicemia, and urinary tract infections. Most human diseases have been reported to be associated with four species of bacteria: Aeromonas dhakensis, Aeromonas hydrophila, Aeromonas veronii, and Aeromonas caviae. The model organism Caenorhabditis elegans is a bacterivore that provides an excellent infection model by which to study the bacterial pathogenesis of Aeromonas. Here, we introduce three different experiments to study Aeromonas infection using a C. elegans model, including survival, liquid toxicity, and muscle necrosis assays. The results of the three methods determining the virulence of Aeromonas were consistent. A. dhakensis was shown to be the most toxic among the 4 major Aeromonas species causing clinical infections. These methods are shown to be a convenient way to evaluate the toxicity among and within Aeromonas species and contribute to our understanding of the pathogenesis of Aeromonas infection.

Evaluating Virulence and Pathogenesis of Aeromonas Infection in a Caenorhabditis elegans Model

Here, we introduce three different experiments to study Aeromonas infection in C. elegans. Using these convenient methods, it is easy to evaluate the toxicity among and within Aeromonas species.

The human pathogen Aeromonas has been clinically shown to cause gastroenteritis, wound infections, septicemia, and urinary tract infections. Most human ...

Application of Consistent Massage-Like Perturbations on Mouse Calves and Monitoring the Resulting Intramuscular Pressure Changes

Massage is generally recognized to be beneficial for relieving pain and inflammation. Although previous studies have reported anti-inflammatory effects of massage on skeletal muscles, the molecular mechanisms behind are poorly understood. We have recently developed a simple device to apply local cyclical compression (LCC), which can generate intramuscular pressure waves with varying amplitudes. Using this device, we have demonstrated that LCC modulates inflammatory responses of macrophages in situ and alleviates immobilization-induced muscle atrophy. Here, we describe protocols for the optimization and application of LCC as a massage-like intervention against immobilization-induced inflammation and atrophy of skeletal muscles of mouse hindlimbs. The protocol that we have developed can be useful for investigating the mechanism underlying beneficial effects of physical exercise and massage. Our experimental system provides a prototype of the analytical approach to elucidate the mechanical regulation of muscle homeostasis, although further development needs to be made for more comprehensive studies.

Here we describe the protocols for applying defined mechanical loads to mouse calves and for monitoring the concomitant intramuscular pressure changes. The experimental systems that we have developed can be useful for investigating the mechanism behind the beneficial effects of physical exercise and massage.

Massage is generally recognized to be beneficial for relieving pain and inflammation. Although previous studies have reported anti-inflammatory effects of ...

Using Human Induced Pluripotent Stem Cell-derived Intestinal Organoids to Study and Modify Epithelial Cell Protection Against Salmonella and Other Pathogens

The intestinal &#8216;organoid&#8217; (iHO) system, wherein 3-D structures representative of the epithelial lining of the human gut can be produced from human induced pluripotent stem cells (hiPSCs) and maintained in culture, provides an exciting opportunity to facilitate the modeling of the epithelial response to enteric infections. In vivo, intestinal epithelial cells (IECs) play a key role in regulating intestinal homeostasis and may directly inhibit pathogens, although the mechanisms by which this occurs are not fully elucidated. The cytokine interleukin-22 (IL-22) has been shown to play a role in the maintenance and defense of the gut epithelial barrier, including inducing a release of antimicrobial peptides and chemokines in response to infection.
We describe the differentiation of healthy control hiPSCs into iHOs via the addition of specific cytokine combinations to their culture medium before embedding them into a basement membrane matrix-based prointestinal culture system. Once embedded, the iHOs are grown in media supplemented with Noggin, R-spondin-1, epidermal growth factor (EGF), CHIR99021, prostaglandin E2, and Y-27632 dihydrochloride monohydrate. Weekly passages by manual disruption of the iHO ultrastructure lead to the formation of budded iHOs, with some exhibiting a crypt/villus structure. All iHOs demonstrate a differentiated epithelium consisting of goblet cells, enteroendocrine cells, Paneth cells, and polarized enterocytes, which can be confirmed via immunostaining for specific markers of each cell subset, transmission electron microscopy (TEM), and quantitative PCR (qPCR). To model infection, Salmonella enterica serovar Typhimurium SL1344 are microinjected into the lumen of the iHOs and incubated for 90 min at 37 &#176;C, and a modified gentamicin protection assay is performed to identify the levels of intracellular bacterial invasion. Some iHOs are also pretreated with recombinant human IL-22 (rhIL-22) prior to infection to establish whether this cytokine is protective against Salmonella infection.

Using Human Induced Pluripotent Stem Cell-derived Intestinal Organoids to Study and Modify Epithelial Cell Protection Against Salmonella and Other Pathogens

Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids offer exciting opportunities to model enteric diseases in vitro. We demonstrate the differentiation of hiPSCs into intestinal organoids (iHOs), the stimulation of these iHOs with cytokines, and the microinjection of Salmonella Typhimurium into the iHO lumen, enabling the study of an epithelial invasion by this pathogen.

The intestinal &#8216;organoid&#8217; (iHO) system, wherein 3-D structures representative of the epithelial lining of the human gut can be produced from ...

Chronic Salmonella Infection Induced Intestinal Fibrosis

Tissue fibrosis characterized by the pathological accumulation of extracellular matrix such as collagen is the outcome of persistent inflammation and dysregulated repair. In inflammatory bowel disease (IBD), fibrosis leads to recurrent stricture formations for which there is no effective therapy other than surgical resection. Due to its late onset, the processes that drive fibrosis is less studied and largely unknown. Therefore, fibrotic complications represent a major challenge in IBD. In this protocol, a robust in vivo model of intestinal fibrosis is described where streptomycin pre-treatment of C57Bl/6 mice followed by oral gavage with vaccine grade Salmonella Typhimurium &#916;AroA mutant leads to persistent pathogen colonization and fibrosis of the cecum. Methodologies for preparing S. Typhimurium &#916;AroA for inoculation, quantifying pathogen loads in the cecum and spleen, and evaluating collagen deposition in intestinal tissues are explained. This experimental disease model is useful for examining host factors that either enhance or exacerbate CD-like intestinal fibrosis.

This protocol describes a mouse model of Salmonella driven intestinal fibrosis that resembles key pathological hallmarks of Crohn&#8217;s disease including transmural inflammation and fibrosis. This method can be used to evaluate host factors that alter fibrotic outcomes using mutant mice maintained on a C57Bl/6 genetic background.

Tissue fibrosis characterized by the pathological accumulation of extracellular matrix such as collagen is the outcome of persistent inflammation and ...

NF-&#954;B-dependent Luciferase Activation and Quantification of Gene Expression in Salmonella Infected Tissue Culture Cells

The dimeric transcription factor NF-&#954;B regulates many cellular response pathways, including inflammatory pathways by inducing the expression of various cytokines and chemokines. NF-&#954;B is constitutively expressed and is sequestered in the cytosol by the inhibitory protein nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha (I&#954;B&#945;). Activation of NF-&#954;B requires the degradation of I&#954;B&#945;, which then exposes a nuclear localization signal on NF-&#954;B and promotes its trafficking to the nucleus. Once in the nucleus, NF-&#954;B binds to the promotor region of NF-&#954;B target genes such as interleukin 6 (IL-6) and IL-23, to promote their expression.
The activation of NF-&#954;B occurs independently of transcription or translation. Therefore, the activation state of NF-&#954;B must be measured either by quantifying NF-&#954;B specifically in the nucleus, or by quantifying expression of NF-&#954;B target genes. In this protocol, cells stably transfected with an NF-&#954;B::luciferase reporter construct are assayed for NF-&#954;B activation using in vitro tissue culture techniques. These cells are infected with Salmonella Typhimurium to activate NF-&#954;B, which traffics to the nucleus and binds to &#954;B sites in the promoter region of luciferase, inducing its expression. Cells are lysed and analyzed with the luciferase assay system. The amount of luciferase produced by the cells correlates with the intensity of the luminescence signal, which is detected by a plate reader. The luminescence signal generated by this procedure provides a quick and highly sensitive method by which to assess NF-&#954;B activation under a range of conditions. This protocol also utilizes quantitative reverse transcription PCR (RT-qPCR) to detect relative mRNA levels that are indicative of gene expression.

NF-&amp;#954;B-dependent Luciferase Activation and Quantification of Gene Expression in &lt;em&gt;Salmonella&lt;/em&gt; Infected Tissue Culture Cells

Here, we present a protocol to quickly and easily measure nuclear factor kappa-light-chain-enhancer of activated B cells (NF-&#954;B) activation in cell lines expressing NF-&#954;B::luciferase reporter constructs, via measurements of luminescence in the cell lysate. Additionally, gene expression is determined via RT-qPCR isolated from cells infected with Salmonella Typhimurium.

The dimeric transcription factor NF-&#954;B regulates many cellular response pathways, including inflammatory pathways by inducing the expression of ...