We sincerely thank Dr. Mustafa Khokha, Yale University, for providing the use of his laboratory resources. We are grateful to Mr. Ming-Jie Wu for excellent technical assistance. EF is an HHMI investigator.This work was supported by a gift from the John Monsky and Jennifer Weis Monsky Lyme Disease Research Fund.

1. Preparation of DNA Templates
<ol>
	<li>Download the 16S rRNA sequence specific to each bacterial genera from the NCBI database and design polymerase chain reaction (PCR) compatible forward and reverse primers that will amplify genera-specific regions (~200 - 250 base-pair long) as described earlier19. Also refer to the open source databases SILVA20,21 and probeBase22 online resources for rRNA-targeted oligonucleotide probes and primers, as RNA probes for some bacterial genera may be commercially available. 
	Note: It is important to select gene regions that are specific to specific genera and ensure that designed primers do not amplify related bacterial genera. This is critical to obtain gene/genera-specific probe hybridization.</li>
	<li>Feed ticks for 24, 48 or 72 h on mice, dissect tick guts and prepare RNA and cDNA from tick guts as described earlier23. Use cDNA as template to PCR amplify genera-specific amplicons using a thermocycler. Run an aliquot of the PCR-product/amplicon on a 1.5% agarose gel and confirm that the amplicon corresponds to the expected size by visualization under ultraviolet (UV) light using a gel imaging system.</li>
	<li>Clone the bacterial 16S ribosomal RNA amplicon of interest into a commercially available TA vector (Table of Materials) containing RNA polymerase promoters suitable for bacteriophage polymerases (SP6, T7 or T3). Sequence the clones to confirm the identity of the amplicon and the directionality of the clone with respect to each of the promoters. Based on this, determine the promoter of choice to generate sense or antisense RNA probes (Figure 1).</li>
	<li>Linearize 1 mg of the plasmid with an appropriate restriction enzyme in a reaction volume of up to 30 &#181;Lfor 2 h at temperatures recommended by the manufacturer. Choose restriction enzymes based on the promoter that will be utilized to generate the sense or antisense probe (Figure 1). Verify linearization by visualization of 2 &#181;L of digest reaction on a 1% agarose gel.</li>
	<li>Purify the remaining 28 &#181;L of digested DNA using a commercially available PCR product column purification kit and quantify DNA concentration by spectrophotometer. 
	Note: Some sense probes may cause background staining much higher than the corresponding antisense probe and other options may need to be explored. Alternative negative controls include plasmids encoding sequences not represented in the sample or another probe that yields a distinctive pattern of hybridization.</li>
</ol>
2. Construction of Digoxygenin-UTP RNA Probes
<ol>
	<li>Prepare the nucleotide mix by combining 7.5 &#181;L of 100 mM UTP, 25 &#181;L of 10 mM digoxygenin-UTP, and 10 &#181;L each of 100 mM ATP, GTP, and CTP in a 1.5 mL centrifuge tube.</li>
	<li>Perform in vitro transcription using commercially available T7 or Sp6 RNA polymerase kits, using 1 &#181;L of the nucleotide mix (Step 2.1) and 0.25 - 1 &#181;g of template DNA. Bring the volume up to 20 &#181;L with water. Flick the tube to combine and pulse spin. Incubate at 37 &#176;C for 2.5 - 3 h. 
	Note: Probe construction has been successful with digested plasmid concentrations as low as 7 ng/&#181;L, but typical concentrations at this step range from 15 - 25 ng/&#181;L. The transcription reaction may also be incubated overnight at 37 &#176;C, but this does not significantly increase the RNA yield.</li>
	<li>Add 1 &#181;L of DNase (2,000 units/&#181;L) and incubate at 37 &#176;C for 10 min. Do not exceed 10 min, or the enzyme may begin degrading RNA.</li>
	<li>Add 30 &#181;L of ice-cold 7.5 - 8 M lithium chloride and 30 &#181;L of chilled nuclease-free water to precipitate the RNA. Flick the tube to mix. Allow precipitation of RNA to proceed overnight at -20 &#176;C.</li>
	<li>Collect RNA by centrifugation at 17,000 x g for 20 min at 4 &#176;C. Wash the pellet once with 1 mL of freshly prepared 75% ethanol in Diethyl pyrocarbonate (DEPC) water, then repeat centrifugation.</li>
	<li>Remove and discard the supernatant, invert the tube on a clean paper towel, and allow to dry for 10 min. Resuspend the pellet in nuclease-free water. If the pellet is easily visible, resuspend in 25 &#181;L. If the pellet is very small or not visible, resuspend in 15 - 20 &#181;L. Obtain an estimate of RNA concentration by spectrophotometer. 
	Note: Typical RNA concentrations range from 200 - 500 ng/&#181;L.</li>
</ol>
3. Visualization of RNA Probes by RNA Formaldehyde Gel Electrophoresis to Assess RNA Purity
CAUTION: Formaldehyde poses an inhalation hazard; therefore, generate the solutions required for RNA gel analysis in a fume hood. Ethidium bromide is a suspected carcinogen; handle with care.
<ol>
	<li>Prepare a 1% formaldehyde agarose gel as previously described24 and cast the gel in a gel box free of RNases. Once cool, fill the gel box with 1x running buffer (1x MOPS at pH 7.0, 5% formaldehyde).</li>
	<li>Prepare the Sample Buffer (5 &#181;L 400 mg/mL ethidium bromide, 20 &#181;L 10x MOPS, 35 &#181;L formaldehyde, and 100 &#181;L formamide). Combine 2 &#181;L of RNA probe (Step 2.6) with 8 &#181;L of Sample Buffer. Incubate at 70 &#176;C for 10 min.</li>
	<li>Prepare RNA Loading Buffer by combining 5 mL 50% glycerol, 1 mL 10% formaldehyde, 40 mg bromophenol blue, 40 mg xylene cyanol, and 20 &#181;L of 0.5 M EDTA (pH 7.5). After use, store this buffer at -20 &#176;C.</li>
	<li>Add 3 &#181;L of Loading Buffer to the RNA sample from Step 3.2 and mix. Keep sample tubes on ice.</li>
	<li>Load the entire sample volume from Step 3.4 into the gel. Load an aliquot of single-stranded RNA ladder alongside to verify RNA size. Run the gel at 100 V or lower until the blue dye migrates approximately 75% of the way down the gel. Visualize the RNA under UV light using a gel imaging system. &#160; 
	Note: &#160;A good quality RNA probe should appear as a discrete band with a mobility corresponding to the expected size of the probe (Figure 2, lane 1). If the probe appears as a diffuse and smeary band (Figure 2, lane 2) this should not be used.</li>
</ol>
4. Tick Gut Collection and Fixation
<ol>
	<li>Collect Ixodes scapularis nymphs that have fed on mice for the time points of interest. 
	Note: For the purposes of this technique, ticks fed for 48 or 72 h work best.&#160;</li>
	<li>Dissect the gut from the tick into MEMFA (Table 1) on a glass slide under a dissection microscope, avoiding damage to the organ as much as possible. Place a tick on a clean microscope slide in 20 - 30 &#181;L of MEMFA. Using a pair of sterile high-carbon steel razor blade #11 slice the head region at the scutum of the tick leaving the body of the tick. Gently press the body to push the gut diverticula and salivary glands out the body cuticle. Separate the salivary glands and the gut and scoop the guts on the razor blade.&#160;</li>
	<li>Collect guts into a 1.5 mL tube containing 500 &#181;L MEMFA. Incubate the tube at room temperature with gentle rocking for 1 h or overnight at 4 &#176;C. 
	Note: Tick salivary glands may also be dissected and similarly fixed and stained.</li>
	<li>Dehydrate the tissue by washing gently 3 times with 1 mL ice-cold 100% ethanol. Let the guts sink naturally to the bottom of the tube between each wash, as centrifugation may damage the tissue. For long-term storage, keep the samples in 100% ethanol at -20 &#176;C.</li>
</ol>
5. Construction of Mesh Sample Baskets and 24-well Basket Holder
<ol>
	<li>Cut the bottoms off of 2 mL or 5 mL snap-top centrifuge tubes using a heated single-edged razor blade on a scalpel. 
	CAUTION: The blade may need to be reheated several times before the cut is completed.</li>
	<li>Cut squares of a 110 &#181;m nylon mesh slightly larger than the new tube opening. Bond the mesh to the bottom of the tube by pressing them together lightly onto a hot plate on medium-low heat until a good seal is made. Let cool, ensure there are no gaps between the mesh and the tube, and trim excess mesh around the edges.&#160;</li>
	<li>Cut holes in the cover of a 24-well plate such that the lip of the sample basket made in Step 5.2 will sit at the hole and not fall through, yielding a set-up where the bottoms of the sample baskets will sit all the way in the wells when they are placed in the holes in the cover.</li>
	<li>Use this fitted basket holder to transfer baskets from one plate to another with relative ease for the entirety of the in situ hybridization protocol. Use two 24-well plates so that while one incubation is occurring, the other plate is prepared for the next wash.</li>
</ol>
6. In Situ Hybridization: Day 1 (Timing: 4 - 5 h)
<ol>
	<li>Transfer guts to labeled sample baskets, separated by experimental condition and intended RNA probe. 
	Note: Stain at least 5 guts per condition to account for natural variation among replicates.</li>
	<li>Rehydrate the samples gently to avoid introducing air bubbles into the tissue by gradually increasing the ratio of phosphate-buffered saline with 0.1 % non-ionic surfactant (PTw; Table 1) to ethanol in the washes. 
	Note: Complete all washes in the 24-well basket holder at ambient temperature with gentle agitation unless otherwise noted. Aliquot 500 - 600 &#181;L of wash solutions into each well of the holder such that the guts in each basket are completely submerged. Prepare all solutions with DEPC-treated water to prevent RNA degradation.
	<ol>
		<li>Wash the samples for 5 min in 500 &#181;L 100% ethanol.</li>
		<li>Prepare at least 500 &#181;L per sample basket of 75%, 50%, and 25% ethanol in PTw. Rehydrate the samples by washing for 5 min in each ethanol solution, moving from the highest ethanol concentration to the lowest.</li>
		<li>Wash the samples 4 times for 5 min each in PTw.</li>
	</ol>
	</li>
	<li>Permeabilize the samples with Proteinase K (10 &#181;g/mL) in PTw for 5 min.</li>
	<li>Prepare the tissue for hybridization with the RNA probes.
	<ol>
		<li>Wash the samples twice as described in 6.2 in the 24-well basket holder at ambient temperature with gentle agitation for 5 min each in 500 &#181;L triethanolamine buffer (0.1 M, pH 7.0 - 8.0) (Table 1) to maintain the samples in an amine-free environment.</li>
		<li>Treat the samples twice with 500 &#181;L 0.25% acetic anhydride in triethanolamine buffer (0.1 M, pH 7.0 - 8.0) for 5 min each, then wash the samples twice in PTw for 5 min each. 
		Note: The acetic anhydride acetylates free amines to neutralize positive charge, which is critical to prevent non-specific electrostatic interactions and ensure specific binding of the probe to mRNA.</li>
		<li>Fix the guts for 20 min with 500 &#181;L 4% paraformaldehyde in PTw, then wash 5 times in PTw for 5 min each.</li>
		<li>Prehybridize by incubating the samples in 500 &#181;L hybridization buffer /in the 24-well basket holder in the 24 well plate (Table 1) for 1.5 - 2.5 h at 60 &#176;C with gentle agitation in a shaking water bath. Save the hybridization buffer used for the prehybridization step to reuse in the Day 2 protocol (Step 7.1).</li>
		<li>Prepare probe hybridization solutions by diluting RNA probes in hybridization buffer to a final concentration of 1 &#181;g/mL. &#160;Incubate samples with probe hybridization solutions in the 24-well basket holder at 60 &#176;C with gentle agitation overnight in a shaking water bath (Table 2). Cover the plate carrying the basket holder snugly with aluminum foil to prevent evaporation of the hybridization solution.</li>
	</ol>
	</li>
</ol>
7. In Situ Hybridization: Day 2 (Timing: 4.5 - 5.5 h)
<ol>
	<li>Remove the samples from the probe hybridization solutions and place them into the reserved hybridization buffer from the previous day. Incubate at 60 &#176;C with gentle agitation for 3 min. 
	Note: Probe hybridization solutions may be stored at -20 &#176;C for reuse up to 3 times.</li>
	<li>Prepare 2x saline-sodium citrate buffer (SSC) by diluting 20x SSC in DEPC-treated water (Table 1). Wash the samples twice for 3 min with 2x SSC, then 3 times for 20 min with 2x SSC at 60 &#176;C to remove all traces of probe and hybridization buffer.</li>
	<li>Treat with RNase A (20 &#181;g/mL) and RNase T1 (10 &#181;g/mL) in 2x SSC for 30 min at 37 &#176;C to remove single stranded RNA probe representing free non-hybridized RNA.</li>
	<li>Wash once with 2x SSC for 10 min at room temperature. Prepare 0.2x SSC by diluting 2x SSC in DEPC-treated water, then wash twice with 0.2x&#160;SSC for 30 min at 60 &#176;C to remove excess RNases.</li>
	<li>Wash twice with 500 &#181;L of maleic acid buffer (MAB; Table 1) for 10 min each.</li>
	<li>Incubate samples with blocking solution (2% blocking reagent in MAB) for 1.5 - 2 h. 
	Note: The blocking reagent can be difficult to dissolve; gentle heating aids dissolution.</li>
	<li>Replace the blocking solution with anti-digoxigenin alkaline phosphatase-conjugated 500 &#181;L of antibody at a 1:3,000 dilution in blocking solution and incubate at room temperature for about 4 h or at 4 &#176;C overnight.</li>
</ol>
8. In Situ Hybridization: Day 3 (Timing: 6 h to overnight)
<ol>
	<li>Wash the samples at least 5 times for 30 min each with 500 &#181;L MAB to remove excess antibody. 
	Note: These washes are flexible and may be extended to 1 - 2 h, or 3 - 4 washes may be substituted for one overnight wash at 4 &#176;C with minimal effect on efficacy.</li>
	<li>Wash twice for 5 min with alkaline phosphatase buffer, pH 9.5 (AP buffer; Table 1).</li>
	<li>Begin the color reaction by replacing the last wash with 500 &#181;L of the chromogenic substrate for alkaline phosphatase (Table of Materials). Cover the sample plate with aluminum foil and let the staining proceed at room temperature for 3-&#160; 5 h or overnight at 4 &#176;C. Monitor the staining reaction periodically by viewing the tissue under a dissecting microscope to avoid overstaining. 
	Note: When the staining is complete, a purple tint is detectable by eye in the antisense-probed samples under the microscope, but the tissue should not be allowed to become very dark. Staining proceeds very slowly at 4 &#176;C and may take up to 20 - 24 h.</li>
	<li>Stop the color reaction by washing for 5 min in 500 &#181;L MAB, then fix the tissue overnight in Bouin&#8217;s solution. 
	CAUTION: Handle the Bouin&#8217;s solution in a fume hood; it is a corrosive carcinogen.</li>
</ol>
9. In Situ Hybridization: Day 4 (Timing: 3 - 3.5 h)
<ol>
	<li>Prepare at least 7 mL per sample basket of 1x SSC by diluting 20x SSC in DEPC-treated water. Remove the Bouin&#8217;s solution by washing the samples 4 to 6 times with 70% ethanol in 1x SSC until the tissue is no longer yellow.</li>
	<li>Prepare 500 &#181;L per sample basket of 75%, 50%, and 25% ethanol solutions in 1x SSC. Wash the samples for 5 min in each solution, moving from highest ethanol concentration to lowest to rehydrate the tissue. Wash twice for 5 min each in 1x SSC.</li>
	<li>Incubate the samples in the bleach solution (Table 1) for 90 min on a lightbox in a fume hood. 
	Note: This step allows any pigmentation in the samples or coloration from Bouins solution to be removed and enhances the probe signal for clear visualization.</li>
	<li>Wash the samples twice with 500 &#181;L of 1x SSC for 5 min.</li>
	<li>Relocate the guts with minimal damage by inverting the sample basket into a well of a new 24-well plate and wash with 70% ethanol through the mesh bottom using a transfer pipette. Store at -20 &#176;C if needed.</li>
	<li>To obtain an overview of the staining patterns of multiple samples as shown in Figure 3, maintain the guts in 70% ethanol in the 24 well-plate and view with any bright-field microscope. To examine individual guts under a bright-field microscope as shown in Figure 4, Figure 5, and Figure 6, mount the guts in 100% glycerol under coverslips. Use a plastic spatula to gently manipulate the tissue with minimal damage. 
	Note: The high viscosity of glycerol helps protect the tissue from damage by compression and allows the careful positioning of diverticula such that the tissue can be viewed optimally at higher magnifications.</li>
	<li>Capture images on the microscope using microscope specific image capture software (Table of Materials) and export as Tiff images to a generic image editing software. To quantify the relative staining differences between experimental treatments, download a generic image analysis software (Table of Materials). Open the image within the analysis software and use the instructions within the software to measure pixel intensity of the staining and compute histogram plots of the staining.</li>
</ol>

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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=Techniques+and+probes+for+the+study+of+Xenopus+tropicalis+development.">Techniques and probes for the study of Xenopus tropicalis development.</a> Developmental Dynamics. 225 (4), 499-510 (2002).</li><li>Jowett, T., Lettice, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-mount+in+situ+hybridizations+on+zebrafish+embryos+using+a+mixture+of+digoxigenin-+and+fluorescein-labelled+probes.">Whole-mount in situ hybridizations on zebrafish embryos using a mixture of digoxigenin- and fluorescein-labelled probes.</a> Trends in Genetics. 10 (3), 73-74 (1994).</li><li>Behnam, F., Vilcinskas, A., Wagner, M., Stoecker, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+straightforward+DOPE+(double+labeling+of+oligonucleotide+probes)-FISH+(fluorescence+in+situ+hybridization)+method+for+simultaneous+multicolor+detection+of+six+microbial+populations.">A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations.</a> Applied Environmental Microbiology. 78 (15), 5138-5142 (2012).</li><li>Pai, V. P., 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=HCN4+ion+channel+function+is+required+for+early+events+that+regulate+anatomical+left-right+patterning+in+a+nodal+and+lefty+asymmetric+gene+expression-independent+manner.">HCN4 ion channel function is required for early events that regulate anatomical left-right patterning in a nodal and lefty asymmetric gene expression-independent manner.</a> Biology Open. 6 (10), 1445-1457 (2017).</li><li>Legendre, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole+mount+RNA+fluorescent+in+situ+hybridization+of+Drosophila+embryos.">Whole mount RNA fluorescent in situ hybridization of Drosophila embryos.</a> JoVE. (71), e50057 (2013).</li></ol>

The authors have no conflicts of interest to disclose.

This is the first use of a whole-mount in situ hybridization (WMISH) technique to study the microbiota of an arthropod vector of pathogens. Our protocol was adapted from one used to study development in Drosophila and in frog embryos25,26. Whole-mount RNA in situ hybridization has been routinely used to localize gene transcripts spatially and temporally27 and visualization of transcripts can be done by bright-field or by fluorescent microscopy. We have adopted the former towards detection of microbiota in tick guts. It is important to note that attempts to perform whole-mount in situ hybridization using whole ticks in which the head region was removed to allow penetration of fixative and hybridization solutions was not successful. The protocol described here utilizes dissected guts and has been implemented to study the effects of specific tick proteins on bacterial colonization in the midgut23. Information obtained from WMISH is comparable to immunohistochemistry but has the advantage of not requiring the generation of protein and antibodies to the gene or protein of interest. Genomic information is sufficient to generate the reagents for WMISH. Both WMISH and FISH (fluorescence in situ hybridization) can detect the gene expression. However, due to it being an enzymatic and chromogen-based assay, WMISH has the advantage that color development can be actively monitored, and the reaction is allowed to proceed until desired signal and sensitivity is achieved. It is fully amenable to automation and is easily scalable to high-throughput format. Unlike FISH and immunohistochemistry, no sectioning is required. The disadvantage of WMISH over FISH is that only 2 different mRNAs or genes can be addressed simultaneously and would require that probes be labeled with different nucleotide analogs such as digoxigenin-UTP and fluorescein-UTP28. With FISH, up to 6 different mRNAs can be examined in one assay29. While both assays require comparable time, the cost of fluorescence dyes are higher than that of chromogenic substrates. FISH assays would also require a fluorescence microscope for image visualization, while WMISH image visualization can be performed with any light microscope.
It is crucial that the protocol is followed closely; however, there are some steps that require particular care. Dissection of the midgut from the tick without damaging the tissue requires some dexterity. It may be prudent to collect extra ticks to practice the dissections and gain proficiency. Due to the heterogeneity of staining in the different diverticula of individual guts (Figure 3), it is important to examine all the diverticula of each gut to derive conclusive evidence of bacterial abundance. It is also important to process several guts (at least 5) for each experimental condition in order to obtain conclusive information on the presence, spatial distribution, and abundance of specific bacteria within different diverticula. Production of high-quality RNA probes is also critical to effective tissue staining. It is crucial to also confirm the sequence of the probe template in the cloning vector to ensure that antisense and sense probes are appropriately generated. A productive in vitro transcription reaction requires sufficient template DNA; a minimum of 100 ng may be used, but 0.5 - 1 &#181;g is recommended for optimal probe generation.
The use of sample baskets and 24-well plates in this protocol avoids direct manipulation of the tissue at every wash step, which minimizes damage during the staining process. However, samples are still occasionally lost or damaged; guts from unfed or 24h-fed ticks, in particular, are difficult to see and easy to lose when transferring from the sample baskets to a long-term storage container. Additional care should be taken while handling these samples. Due to this limitation, we have mainly used 48 and 72 h-fed tick guts. The presence of large amounts of blood meal in the guts at these time-points (longer than 72 h) interferes with the staining and visualization due to non-specific background from the blood-meal and also presents a limitation of this technique. It is likely that the use of fluorescently-labeled probes might circumvent this issue.
The most important aspect of the staining procedure is to establish the balance between robust staining and low background signal. The timing of ideal color development can vary depending on the experimental conditions. Thus, it is best to perform the color reaction at room temperature and monitor color development approximately every 30 min. The reaction may also be set up to proceed overnight at 4 &#176;C to slow color development. However, it is extremely critical not to let this reaction proceed for long. The staining reaction can be difficult to monitor by eye, so the samples should be examined under a dissection microscope. A purple tint should be visible on samples probed with antisense RNA, while the samples probed with sense RNA should retain minimal color. If the sense RNA-probed samples stain brightly, troubleshooting steps should begin with reducing the incubation time with BM purple and increasing the blocking time. Sometimes sense probes can cause anomalously high background compared to the antisense probes; in these cases, different regions of the gene might have to be considered for generating RNA probes. DNA sequences not represented in a given sample may also be considered as templates to generate negative control probes. For example, a DNA template encoding a region of the green fluorescent protein, not represented in the tick genome or its microbiome, can be utilized.
One limitation of this technique is that the analysis is largely qualitative; however, image analysis software (Table of Materials) could be used to measure the amount of staining signal in each sample. This would allow a semi-quantitative comparison of the abundance of various bacterial species under different experimental conditions. While this is a time-consuming protocol that takes 3 - 4 days to complete, it is not laborious; each day hands-on time is only about 3 - 5 h on average. However, the ability to process many samples in parallel with the use of the sample baskets and holders allows for high-throughput analysis. Further, this process can be automated using commercially available instruments (Table of Materials) if this protocol is expected to be an essential and routine component of the research laboratory by using commercially available automation-compatible platforms (Table of Materials) to further reduce hands-on time.
The described protocol makes use of digoxygenin-labeled probes that allow the production of a colorimetric signal that can be imaged using bright field microscopy. While we have utilized one chromogenic substrate to detect hybridized RNA probes specific to individual targets, it is also possible to detect multiple targets simultaneously by labeling probes with different nucleotide analogs, such as digoxigenin-UTP and fluorescein-UTP and different chromogenic substrates30. The tissue samples can then be incubated sequentially with alkaline-phosphatase-coupled antibodies against digoxigenin and fluorescein, with different chromogenic reactions for the two steps. This technique could also be adapted for fluorescently-labeled probes, which may facilitate higher-resolution imaging using confocal microscopy31 and provide the option of using multiple probes of different colors in parallel. This technique can only specifically assess a few microorganisms at one time in one sample. However, several samples can be assessed in high-throughput assays to address multiple microorganisms that may be represented in tick microbiota.
Finally, this technique is not limited to the investigation of the interactions between ticks and their associated microbiota. Probes complementary to any gene of interest within the tick genome may be generated and used to examine the abundance and localization of specific genes in different tissues. The salivary glands of the tick can also be processed and analyzed similarly to the gut. Overall, this technique has broad potential for adaptation to studies on the dynamics of microbial communities within other arthropod disease vectors of interest.

Human and livestock pathogens transmitted by arthropod vectors are found worldwide and account for about 20% of infectious diseases globally1, but effective and safe vaccines against most of these pathogens are not available. Our understanding of the important role of commensal, symbiotic and pathogenic microorganisms, collectively known as the microbiome2, in modulating and shaping the health of almost all metazoans3 is expanding. It is now evident that arthropod vectors of pathogens also harbor gut microbiota and these vector-associated microbiota have been shown to influence diverse vector-borne pathogens4,5. The arthropod microbiome is composed of eubacteria, archaea, viruses, and eukaryotic microbes such as protozoa, nematodes, and fungi6. However, the predominant research focus has been on eubacteria due, in part, to the availability of marker genes and reference databases to identify specific bacterial members.
With a focus on Ixodes scapularis, the tick vector of multiple human pathogens including Borrelia burgdorferi7, the causative agent of Lyme disease, the optimization of a microbial visualization technique was aimed at improving our understanding of tick gut microbiota in the context of vector-pathogen interactions. Several questions remain to be answered in the tick microbiome field. The gut is the site of the first extended encounter between the tick and the incoming pathogen in the context of horizontally transferred pathogens; therefore, understanding the role of vector gut microbiota in modulating vector-pathogen interactions will reveal meaningful insights. Ticks have a unique mode of blood meal digestion, where processing of blood meal components takes place intracellularly8. The gut lumen seemingly serves as a vessel to contain the blood meal as the tick feeds, and nutrient digestion and assimilation ensue throughout the several days of feeding and continue post-repletion. The pathogens acquired by the tick during feeding enter the gut lumen along with the bloodmeal and thus the lumen becomes a primary site of interactions among the tick, pathogen, and resident microbiota. As digestion proceeds through the repletion and Ixodid tick molting, the gut undergoes structural and functional changes9. The composition and the spatial organization of gut bacteria is also likely to vary in concert with the changing gut milieu. It is, therefore, important to understand the architecture of resident bacteria in the tick gut to fully understand the interplay of tick, pathogen, and gut microbiota.
Molecular techniques to describe host-associated microbiota routinely utilize high-throughput parallel sequencing strategies10 to amplify and sequence bacterial 16S ribosomal DNA (rDNA). These sequencing strategies circumvent the need to obtain axenic cultures of specific bacteria and provide an in-depth description of all bacterial members represented in the sample. Nevertheless, such strategies are confounded by the inability to distinguish environmental contaminations from bona fide residents. Further, when assessing samples, such as ticks, that are small in size and hence contain low microbiota-specific DNA yields, the likelihood of amplification of environmental contaminants is increased11 and results in the ambiguous interpretation of microbiome composition. Functional characterization in conjunction with the visualization of specific viable bacteria will, therefore, be critical to define and discern the microbiome of the tick temporally and spatially. Towards this goal, we took advantage of the whole-mount RNA in situ hybridization. This technique is routinely used to assess gene expression patterns in organs and embryos12,13,14 and allows semiquantitative analysis of expression over the entire sample of interest. This differs from traditional in situ hybridization techniques which utilize tissue sections and often require extensive analysis of sectioned material with a computational assembly to predict expression in whole organs15. While whole-mount generally refers to whole organisms12, here whole-mount refers to whole guts or organs. The advantages of using the whole-mount RNA in situ hybridization approach to assess the architecture of tick gut microbiota are multifold. The tick gut is composed of 7 pairs of diverticula, each pair varying in size16. The functional differences, if any, among these diverticula, are not understood in the context of tick biology, tick microbiota or tick-pathogen interactions. Manipulations of the gut that rupture the gut diverticula would displace microbiota present in the gut lumen or those associated loosely with the gut and result in misinterpretation of the spatial localization of microbiota. Fluorescence-labeled RNA in situ hybridization has been utilized earlier to examine tick gut transcripts17 by fixing and opening individual gut diverticula to ensure probe hybridization and to localize B. burgdorferi transcripts by sectioning paraffin-embedded whole ticks18. Both these approaches require manipulations of the tick tissues prior to hybridization that would affect the gut microbiota architecture.
In this report, we describe in detail the protocol to examine viable tick gut microbiota using whole-mount in situ hybridization (WMISH). The use of whole-mount RNA in situ hybridization enables a global understanding of the presence and abundance of specific gut bacteria in the different regions of the gut and may spur new insights into tick gut biology in the context of pathogen colonization and transmission. Further, the use of RNA probes directed against specific bacterial RNA allows detection of viable bacteria in the tick gut.

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		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Image capture software</td>
			<td style="width:220px;">Zeiss</td>
			<td style="width:348px;">Zen lite</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Image editing software&#160;</td>
			<td style="width:220px;">Adobe&#160;</td>
			<td style="width:348px;">Adobe Photoshop CS4 version 11.0</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:320px;">Image analysis software</td>
			<td style="width:220px;">National Institutes of Health</td>
			<td>ImageJ-NIH /imagej.nih.gov/ij/</td>
			<td></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;">Automation compatible instrumentation</td>
			<td style="width:220px;">Intavis Bioanalytical Instruments, Tubingen, Germany).&#160;</td>
			<td style="width:348px;">Intavis, Biolane HT1.16v</td>
			<td></td>
		</tr>
	</tbody>
</table>

visualization of microbiota in tick guts by whole-mount in situ hybridization

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these diseases, do not exist in isolation when they colonize the vector; rather, they likely engage in interactions with resident microorganisms in the gut lumen. The vector microbiota has been demonstrated to play an important role in pathogen transmission for several vector-borne diseases. Whether resident bacteria in the gut of the Ixodes scapularis tick, the vector of several human pathogens including Borrelia burgdorferi, influence tick transmission of pathogens is not determined. We require methods for characterizing the composition of the bacteria associated with the tick gut to facilitate a better understanding of potential interspecies interactions in the tick gut. Using whole-mount in situ hybridization to visualize RNA transcripts associated with particular bacterial species allows for the collection of qualitative data regarding the abundance and distribution of the microbiota in intact tissue. This technique can be used to examine changes in the gut microbiota milieu over the course of tick feeding and can also be applied to analyze expression of tick genes. Staining of whole tick guts yield information about the gross spatial distribution of target RNA in the tissue without the need for three-dimensional reconstruction and is less affected by environmental contamination, which often confounds the sequencing-based methods frequently used to study complex microbial communities. Overall, this technique is a valuable tool that can be used to better understand vector-pathogen-microbiota interactions and their role in disease transmission.

The measurement and estimation of the quality of the RNA probes are critical prior to beginning the staining. In vitro transcription efficiency depends highly on the amount and quality of the DNA template. We routinely visualized the RNA probes on a formaldehyde gel to verify the purity and amount of probe generated by the transcription reactions. The probes should appear as bright, discrete bands (Figure 2). Spectrophotometric measurements of RNA concentration were highly indicative of probe quality and correlated well with the appearance of the bands on the gel. Thus, the gel visualization step may be skipped if desired once familiarity with the protocol has been attained. Either way, it is important to ensure that sufficient RNA of high quality is produced, as all downstream steps depend upon the robustness of the probes.
The strength of this technique is in facilitating broad observations about the tick microbiota, including presence or absence of bacterial species, changes in abundance of bacteria over time as the tick feeds, and localization of species within the whole tissue. Some variation in staining amount and distribution is normal among biological replicates as well as among the 7 pairs of diverticula of individual guts (Figure 3), therefore, it is best to stain at least five guts per condition to get an idea of average staining pattern. The overall success of the protocol is best gauged by comparing the staining of the sense and antisense samples for each condition. The sense samples, important negative controls for this type of analysis, should have minimal to no purple color (Figure 4). Conversely, antisense samples should display robust staining with minimal background, the intensity of which will depend on the abundance of the specific bacterial transcripts being targeted. The staining pattern within the tissue will also vary based on these parameters. Importantly, the sense and antisense samples must be developed for the same amount of time in order to be able to directly compare them, so these samples should be processed in parallel. Overdevelopment of the color reaction can result in a high amount of background staining, where the sense samples begin to look similar to the antisense (Figure 5). Particular care should be taken at this step in the protocol to avoid overstaining, as there is no way to reverse the reaction once it occurs.
It is critical to make sure all guts are fully submerged in each reagent during every step; an increase in the variation across samples may be due to uneven exposure to reagents. The amount of time that the ticks are fed before the guts are collected also has a significant effect on the results. Ticks that were unfed or only fed for 24 h were difficult to work with; the guts were also more easily damaged and did not stain well (Figure 6) and is a limitation of this approach at this time. Ticks fed for 48 - 72 h were easiest to work with, due to the larger size of these guts when compared to guts from ticks fed for 24 h. Guts from later time points also stained better than 24 h-fed ticks, possibly due to increases in bacterial burden during the later stages of feeding. The 72-h tissue often had a slight background of brown tint from blood, but the purple staining was clearly visible over the tint (Figure 4). The guts are best viewed at low magnification (5X or 10X) to be able to view the staining patterns across the entire tissue using a bright-field microscope. Viewing whole-mount tissue at higher magnification, such as with a 63X oil objective, runs the risk of damaging the tissue as the objective would press against the slide and compress the tissue due to the thickness of the samples. If higher resolution imaging is desired, the potential for tissue sectioning should be examined.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/57758/57758fig1.jpg" /> 
Figure 1. Schematic of template preparation for probe generation. Clone the 16S rRNA amplicon into a TA cloning vector containing T7 and Sp6 promoters. Linearize the construct using restriction enzymes to cut at sites a or b for in vitro transcription using T7 or Sp6 promoter to generate sense or antisense probes respectively. <a href="/files/ftp_upload/57758/57758fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/57758/57758fig2.jpg" /> 
Figure 2. Visualization of the RNA probe by gel electrophoresis. RNA probes (~700 ng) were electrophoresed on a formaldehyde agarose gel, visualized under UV light, and imaged using a commercial gel imaging system. A representative good quality, lane 1; and poor-quality RNA probe, lane 2.
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/57758/57758fig3.jpg" /> 
Figure 3. A representative overview of whole-mount in situ hybridization of 48 h-fed guts. Guts from ticks fed for 48 h stained with antisense RNA complementary to a conserved 16S ribosomal RNA sequence shows differential staining of gut diverticula. Scale bar represents 200 &#181;m. <a href="/files/ftp_upload/57758/57758fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/57758/57758fig4.jpg" /> 
Figure 4. Representative images of successful whole-mount in situ hybridization in Ixodes scapularis guts. Guts from ticks fed for the indicated amount of time were stained using either sense (negative control) or antisense RNA probes. Antisense probes were complementary to a conserved 16S ribosomal RNA sequence (Universal 16S) or a 16S RNA sequence specific to a particular bacterial genus (as indicated). Enterococcus did not yield robust staining at 48 h. Scale bars represent 140 &#181;m. <a href="/files/ftp_upload/57758/57758fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/57758/57758fig5.jpg" /> 
Figure 5. Prolonged chromogenic reaction time leads to non-specific staining. Guts from ticks fed for 48 h were probed with a sense RNA probe or an antisense probe complementary to a conserved 16S RNA sequence. The tissue was incubated with the alkaline phosphatase substrate BM purple overnight at 4 &#176;C and then at room temperature for about 4 h before stopping the reaction. Scale bars represent 140 &#181;m. <a href="/files/ftp_upload/57758/57758fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/57758/57758fig6.jpg" /> 
Figure 6. Whole-mount in situ hybridization using unfed or 24h fed tick guts. Guts from unfed or 24 h-fed ticks were stained using sense RNA probes or antisense probes complementary to a conserved 16S RNA sequence or a sequence specific to the genus Rickettsia. Staining in the antisense samples is less robust than observed at later time points and the guts are also more easily damaged. Scale bars represent 60 &#181;m. <a href="/files/ftp_upload/57758/57758fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Name</td>
			<td>Final Concentrations</td>
			<td>Final pH</td>
			<td>Storage notes</td>
		</tr>
		<tr>
			<td>MEMFA</td>
			<td>0.1 M MOPS</td>
			<td>-</td>
			<td>Room temperature</td>
		</tr>
		<tr>
			<td></td>
			<td>2 mM EGTA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>1 mM magnesium sulfate</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>3.7% formaldehyde</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PBS-Tween (PTw)</td>
			<td>1x PBS, 0.1% Tween-20</td>
			<td>7.0</td>
			<td>Room temperature</td>
		</tr>
		<tr>
			<td></td>
			<td>0.1% Tween-20</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Triethanolamine buffer</td>
			<td>1x PBS</td>
			<td>7.0 - 8.0</td>
			<td>Room temperature</td>
		</tr>
		<tr>
			<td></td>
			<td>0.1 M triethanolamine</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hybridization buffer</td>
			<td>50% formamide</td>
			<td>-</td>
			<td>-20 &#176;C</td>
		</tr>
		<tr>
			<td></td>
			<td>5x SSC</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>1 mg/mL Torula RNA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>100 &#181;g/mL heparin</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>1x Denhart&#39;s solution</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>0.1% Tween-20</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>0.1% CHAPS</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>10 mM EDTA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Maleic acid buffer (MAB)</td>
			<td>100 mM maleic acid</td>
			<td>7.0</td>
			<td>Room temperature</td>
		</tr>
		<tr>
			<td></td>
			<td>150 mM sodium chloride</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Alkaline phosphatase (AP) buffer</td>
			<td>100 mM Tris</td>
			<td>9.5</td>
			<td>-20 &#176;C</td>
		</tr>
		<tr>
			<td></td>
			<td>50 mM magnesium chloride</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>100 mM sodium chloride</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>0.1% Tween-20</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>5 mM levamisol</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bleach solution</td>
			<td>1% hydrogen peroxide</td>
			<td>-</td>
			<td>Prepare fresh</td>
		</tr>
		<tr>
			<td></td>
			<td>5% formamide</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>0.5x SSC</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>
Table 1. Recipes of solutions used in the protocol.

Watch this Scientific Journal Video about Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization at JoVE.com

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

Here, we present a protocol to spatially and temporally assess the presence of viable microbiota in tick guts using a modified whole-mount in situ hybridization approach.

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these ...

visualization-microbiota-tick-guts-whole-mount-situ

Nanyang Technological University

Research

JoVE Journal

Genetics

9.5K Views.  Yale University School of Medicine. Here, we present a protocol to spatially and temporally assess the presence of viable microbiota in tick guts using a modified whole-mount in situ hybridization approach.

Video: Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

In Situ Labeling of Mitochondrial DNA Replication in Drosophila Adult Ovaries by EdU Staining

The mitochondrial genome is inherited exclusively through the maternal line. Understanding of how the mitochondrion and its genome are proliferated and transmitted from one generation to the next through the female oocyte is of fundamental importance. Because of the genetic tractability, and the elegant, ordered simplicity by which oocyte development proceeds, Drosophila oogenesis has become an invaluable system for mitochondrial study. An EdU (5-ethynyl-2&#180;-deoxyuridine) labeling method was utilized to detect mitochondrial DNA (mtDNA) replication in Drosophila ovaries. This method is superior to the BrdU (5-bromo-2'-deoxyuridine) labeling method in that it allows for good structural preservation and efficient fluorescent dye penetration of whole-mount tissues.
Here we describe a detailed protocol for labeling replicating mitochondrial DNA in Drosophila adult ovaries with EdU. Some technical solutions are offered to improve the viability of the ovaries, maintain their health during preparation, and ensure high-quality imaging. Visualization of newly synthesized mtDNA in the ovaries not only reveals the striking temporal and spatial pattern of mtDNA replication through oogenesis, but also allows for simple quantification of mtDNA replication under various genetic and pharmacological perturbations.

In Situ Labeling of Mitochondrial DNA Replication in Drosophila Adult Ovaries by EdU Staining

Drosophila oogenesis continues to be exceptionally useful in the study of mitochondrial proliferation and inheritance. This manuscript describes a detailed protocol used to label the replicating mitochondrial DNA (mtDNA) in Drosophila adult ovaries with 5-ethynyl-2&#180;-deoxyuridine (EdU), which facilitates uncovering mechanisms associated with mitochondrial inheritance that were previously debatable.

The mitochondrial genome is inherited exclusively through the maternal line. Understanding of how the mitochondrion and its genome are proliferated and ...

Optogenetic Random Mutagenesis Using Histone-miniSOG in C. elegans

Forward genetic screening in model organisms is the workhorse to discover functionally important genes and pathways in many biological processes. In most mutagenesis-based screens, researchers have relied on the use of toxic chemicals, carcinogens, or irradiation, which requires designated equipment, safety setup, and/or disposal of hazardous materials. We have developed a simple approach to induce heritable mutations in C. elegans using germline-expressed histone-miniSOG, a light-inducible potent generator of reactive oxygen species. This mutagenesis method is free of toxic chemicals and requires minimal laboratory safety and waste management. The induced DNA modifications include single-nucleotide changes and small deletions, and complement those caused by classical chemical mutagenesis. This methodology can also be used to induce integration of extrachromosomal transgenes. Here, we provide the details of the LED setup and protocols for standard mutagenesis and transgene integration.

Optogenetic Random Mutagenesis Using Histone-miniSOG in C. elegans

Genetically-encoded histone-miniSOG induces genome-wide heritable mutations in a blue&#160;light-dependent manner. This mutagenesis method is simple, fast, free of toxic chemicals, and well-suited for forward genetic screening and transgene integration.

Forward genetic screening in model organisms is the workhorse to discover functionally important genes and pathways in many biological processes. In most ...

Detection of Inter-chromosomal Stable Aberrations by Multiple Fluorescence In Situ Hybridization (mFISH) and Spectral Karyotyping (SKY) in Irradiated Mice

Ionizing radiation (IR) induces numerous stable and unstable chromosomal aberrations. Unstable aberrations, where chromosome morphology is substantially compromised, can easily be identified by conventional chromosome staining techniques. However, detection of stable aberrations, which involve exchange or translocation of genetic materials without considerable modification in the chromosome morphology, requires sophisticated chromosome painting techniques that rely on in situ hybridization of fluorescently labeled DNA probes, a chromosome painting technique popularly known as fluorescence in situ hybridization (FISH). FISH probes can be specific for whole chromosome/s or precise sub-region on chromosome/s. The method not only allows visualization of stable aberrations, but it can also allow detection of the chromosome/s or specific DNA sequence/s involved in a particular aberration formation. A variety of chromosome painting techniques are available in cytogenetics; here two highly sensitive methods, multiple fluorescence in situ hybridization (mFISH) and spectral karyotyping (SKY), are discussed to identify inter-chromosomal stable aberrations that form in the bone marrow cells of mice after exposure to total body irradiation. Although both techniques rely on fluorescent labeled DNA probes, the method of detection and the process of image acquisition of the fluorescent signals are different. These two techniques have been used in various research areas, such as radiation biology, cancer cytogenetics, retrospective radiation biodosimetry, clinical cytogenetics, evolutionary cytogenetics, and comparative cytogenetics.

Detection of Inter-chromosomal Stable Aberrations by Multiple Fluorescence In Situ Hybridization mFISH and Spectral Karyotyping SKY in Irradiated Mice

The present protocol describes the usefulness of multiple fluorescence in situ hybridization (mFISH) and spectral karyotyping (SKY) in identifying inter-chromosomal stable aberrations in the bone marrow cells of mice after exposure to total body irradiation.

Ionizing radiation (IR) induces numerous stable and unstable chromosomal aberrations. Unstable aberrations, where chromosome morphology is substantially ...

Targeted in Situ Mutagenesis of Histone Genes in Budding Yeast

We describe a PCR- and homologous recombination-based system for generating targeted mutations in histone genes in budding yeast cells. The resulting mutant alleles reside at their endogenous genomic sites and no exogenous DNA sequences are left in the genome following the procedure. Since in haploid yeast cells each of the four core histone proteins is encoded by two non-allelic genes with highly homologous open reading frames (ORFs), targeting mutagenesis specifically to one of two genes encoding a particular histone protein can be problematic. The strategy we describe here bypasses this problem by utilizing sequences outside, rather than within, the ORF of the target genes for the homologous recombination step. Another feature of this system is that the regions of DNA driving the homologous recombination steps can be made to be very extensive, thus increasing the likelihood of successful integration events. These features make this strategy particularly well-suited for histone gene mutagenesis, but can also be adapted for mutagenesis of other genes in the yeast genome.

Targeted in Situ Mutagenesis of Histone Genes in Budding Yeast

A strategy for generating mutations in histone genes at their endogenous location in Saccharomyces cerevisiae is presented.

We describe a PCR- and homologous recombination-based system for generating targeted mutations in histone genes in budding yeast cells. The resulting ...

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of tissues, we have developed numerous modifications and improvements to our original fluorescent in situ hybridization (FISH) protocol. To facilitate throughput and cost effectiveness, all steps, from probe generation to signal detection, are performed using exon 96-well microtiter plates. Digoxygenin (DIG)-labelled antisense RNA probes are produced using either cDNA clones or genomic DNA as templates. After tissue fixation and permeabilization, probes are hybridized to transcripts of interest and then detected using a succession of anti-DIG antibody conjugated to biotin, streptavidin conjugated to horseradish peroxidase (HRP) and fluorescently conjugated tyramide, which in the presence of HRP, produces a highly reactive intermediate that binds to electron dense regions of immediately adjacent proteins. These amplification and localization steps produce a robust and highly localized signal that facilitates both cellular and subcellular transcript localization. The protocols provided have been optimized to produce highly specific signals in a variety of tissues and developmental stages. References are also provided for additional variations that allow the simultaneous detection of multiple transcripts, or transcripts and proteins, at the same time.

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

The described RNA in situ hybridization protocol allows the detection of RNA in whole Drosophila embryos or dissected tissues. Using 96-well microtiter plates and tyramide signal amplification, transcripts can be detected at high resolution, sensitivity, and throughput, and at a relatively low cost.

In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of ...

Single Molecule Fluorescence In Situ Hybridization (smFISH) Analysis in Budding Yeast Vegetative Growth and Meiosis

Single molecule fluorescence in situ hybridization (smFISH) is a powerful technique to study gene expression in single cells due to its ability to detect and count individual RNA molecules. Complementary to deep sequencing-based methods, smFISH provides information about the cell-to-cell variation in transcript abundance and the subcellular localization of a given RNA. Recently, we have used smFISH to study the expression of the gene&#160;NDC80&#160;during meiosis in budding yeast, in which two transcript isoforms exist and the short transcript isoform has its entire sequence shared with the long isoform. To confidently identify each transcript isoform, we optimized known smFISH protocols and obtained high consistency and quality of smFISH data for the samples acquired during budding yeast meiosis. Here, we describe this optimized protocol, the criteria that we use to determine whether high quality of smFISH data is obtained, and some tips for implementing this protocol in&#160;other yeast strains and growth conditions.

Single Molecule Fluorescence In Situ Hybridization smFISH Analysis in Budding Yeast Vegetative Growth and Meiosis

This single molecule fluorescence in situ hybridization protocol is optimized to quantify the number of RNA molecules in budding yeast during vegetative growth and meiosis.

Single molecule fluorescence in situ hybridization (smFISH) is a powerful technique to study gene expression in single cells due to its ability to detect ...

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell type-specific fashion. AS expression patterns are typically analyzed by RT-PCR and RNA-seq using RNA samples isolated from a population of cells. In situ examination of AS expression patterns for a particular biological structure can be carried out by RNA in situ hybridization (ISH) using exon-specific probes. However, this particular use of ISH has been limited because alternative exons are generally too short to design exon-specific probes. In this report, the use of BaseScope, a recently developed technology that employs short antisense oligonucleotides in RNA ISH, is described to analyze AS expression patterns in mouse brain sections. Exon 23a of neurofibromatosis type 1 (Nf1) is used as an example to illustrate that short exon-exon junction probes exhibit robust hybridization signals with high specificity in RNA ISH analysis on mouse brain sections. More importantly, signals detected with exon inclusion- and skipping-specific probes can be used to reliably calculate the percent spliced in values of Nf1 exon 23a expression in different anatomical areas of a mouse brain. The experimental protocol and calculation method for AS analysis are presented. The results indicate that BaseScope provides a powerful new tool to assess AS expression patterns in situ.

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

An in situ hybridization (ISH) protocol that uses short antisense oligonucleotides to detect alternative pre-mRNA splicing patterns in mouse brain sections is described.

Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell ...

Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization

micro-RNAs (miRNAs) are single-stranded RNA transcripts that bind to messenger RNAs (mRNAs) and inhibit their translation or promote their degradation. To date, miRNAs have been implicated in a large number of biological and disease processes, which has signified the need for the reliable detection methods of miRNA transcripts. Here, we describe a detailed protocol for digoxigenin-labeled (DIG) Locked Nucleic Acid (LNA) probe-based miRNA detection, combined with protein immunostaining on mouse heart sections. First, we performed an in situ hybridization technique using the probe to identify miRNA-182 expression in heart sections from control and cardiac hypertrophy mice. Next, we performed immunostaining for cardiac Troponin T (cTnT) protein, on the same sections, to co-localize miRNA-182 with the cardiomyocyte cells. Using this protocol, we were able to detect miRNA-182 through an alkaline phosphatase based colorimetric assay, and cTnT through fluorescent staining. This protocol can be used to detect the expression of any miRNA of interest through DIG-labeled LNA probes, and relevant protein expression on mouse heart tissue sections.

Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization

micro-RNAs (miRNAs) are short and highly homologous RNA sequences, serving as post-transcriptional regulators of messenger RNAs (mRNAs). Current miRNA detection methods vary in sensitivity and specificity. We describe a protocol that combines in situ hybridization and immunostaining for concurrent detection of miRNA and protein molecules on mouse heart tissue sections.

micro-RNAs (miRNAs) are single-stranded RNA transcripts that bind to messenger RNAs (mRNAs) and inhibit their translation or promote their degradation. To ...

Raising the Mexican Tetra Astyanax mexicanus for Analysis of Post-larval Phenotypes and Whole-mount Immunohistochemistry

River and cave-adapted populations of Astyanax mexicanus show differences in morphology, physiology, and behavior. Research focused on comparing adult forms has revealed the genetic basis of some of these differences. Less is known about how the populations differ at post-larval stages (at the onset of feeding). Such studies may provide insight into how cavefish survive through adulthood in their natural environment. Methods for comparing post-larval development in the laboratory require standardized aquaculture and feeding regimes. Here we describe how to raise fish on a diet of nutrient-rich rotifers in non-recirculating water for up to two-weeks post fertilization. We demonstrate how to collect post-larval fish from this nursery system and perform whole-mount immunostaining. Immunostaining is an attractive alternative to transgene expression analysis for investigating development and gene function in A. mexicanus. The nursery method can also be used as a standard protocol for establishing density-matched populations for growth into adults.

Raising the Mexican Tetra Astyanax mexicanus for Analysis of Post-larval Phenotypes and Whole-mount Immunohistochemistry

In this protocol, we demonstrate how to breed Astyanax mexicanus adults, raise the larvae, and perform whole-mount immunohistochemistry on post-larval fish to compare the phenotypes of surface and cave morphotypes.

River and cave-adapted populations of Astyanax mexicanus show differences in morphology, physiology, and behavior. Research focused on comparing adult ...

Characterizing Histone Post-translational Modification Alterations in Yeast Neurodegenerative Proteinopathy Models

Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and Parkinson&#39;s disease (PD), cause the loss of hundreds of thousands of lives each year. Effective treatment options able to halt disease progression are lacking. Despite the extensive sequencing efforts in large patient populations, the majority of ALS and PD cases remain unexplained by genetic mutations alone. Epigenetics mechanisms, such as the post-translational modification of histone proteins, may be involved in neurodegenerative disease etiology and progression and lead to new targets for pharmaceutical intervention. Mammalian in vivo and in vitro models of ALS and PD are costly and often require prolonged and laborious experimental protocols. Here, we outline a practical, fast, and cost-effective approach to determining genome-wide alterations in histone modification levels using Saccharomyces cerevisiae as a model system. This protocol allows for comprehensive investigations into epigenetic changes connected to neurodegenerative proteinopathies that corroborate previous findings in different model systems while significantly expanding our knowledge of the neurodegenerative disease epigenome.

This protocol outlines experimental procedures to characterize genome-wide changes in the levels of histone post-translational modifications (PTM) occurring in connection with the overexpression of proteins associated with ALS and Parkinson&#39;s disease in Saccharomyces cerevisiae models. After SDS-PAGE separation, individual histone PTM levels are detected with modification-specific antibodies via Western blotting.

Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and Parkinson&#39;s disease (PD), cause the loss of hundreds of thousands of lives ...