Name: assessing transmissible spongiform encephalopathy species barriers with an in vitro prion protein conversion assay
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We thank John Olsen (Wisconsin Department of Natural Resources), Tom Cooley, Daniel O'Brien and Steve Schmitt (Michigan Department of Natural Resources) and Dr. Daniel Walsh (USGS National Wildlife Health Center) for assistance with tissue acquisition. We also thank the Wisconsin State Laboratory of Hygiene for diagnostic testing services, and Dr. Tonie Rocke and her staff (USGS National Wildlife Health Center) for use of equipment. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Animal work conducted at the USGS National Wildlife Health Center was performed in accordance with the NIH Office of Laboratory Animal Welfare guidelines and under institutional animal care and use committee protocol #EP080716. Tissues from hunter-harvested animals were gifts from the Wisconsin or Michigan Departments of Natural Resources.
1. Solution Preparation
NOTE: The solutions listed below are required for preparation of the CER assay substrate in Section 2 below. Prepare each of these solutions from higher concentration stock solutions; recommended concentrations for stock solutions will be given in parentheses after each respective chemical name listed. Prepare all solutions fresh upon substrate preparation and store at 4 &#176;C until used.
<ol>
	<li>For lysis buffer, prepare a solution of the following in 10 mM Tris, pH 7.5 (1 M Tris, pH 7.5 stock solution recommended): 100 mM sodium chloride (NaCl, 1 M stock solution), 10 mM ethylenediaminetetraacetic acid (EDTA, 500 mM EDTA, pH 8.0 stock solution), 0.5% NP-40 (10% stock solution), 0.5% deoxycholate (DOC, 10% stock solution).</li>
	<li>For conversion buffer, prepare a solution of 0.05% sodium dodecyl sulfate (SDS, 10% stock solution) and 0.5% Triton X-100 (10% stock solution) in 1 phosphate buffered saline (PBS, 10, pH 7.4 stock solution).</li>
	<li>For chaotropic solutions, prepare two 3 M solutions of guanidine hydrochloride (GdnHCl, 8 M stock) in 1x PBS (10x stock solution). Adjust the pH of one of the solutions to 3.5 &#177; 0.05 using concentrated hydrochloric acid (HCl). Check that the pH of the second solution remains at pH 7.4 &#177; 0.05 and adjust using concentrated HCl or sodium hydroxide (NaOH) if necessary.</li>
</ol>
2. Prepare CER Assay Substrate Pairs
<ol>
	<li>Obtain healthy, non-TSE-infected brain tissue from species of interest and prepare a 10% weight-per-volume (w/v) homogenate in lysis buffer using any of the following methods: dounce, bead-mill, or mortar and pestle homogenization. Further refine resulting homogenates by subjecting them to syringe-and-needle homogenization, using needles of increasing gauge until substrate can be aspirated and expelled with ease through a 27 G syringe needle.
	<ol>
		<li>For substrates prepared from rodents and other small mammals, homogenize whole brain(s); for substrates prepared from larger mammals, use obex (brainstem) tissue to prepare homogenates. When selecting the quantity of brain homogenate, prepare no more than 50% of the capacity of the centrifuge used for protein precipitation in step 2.6.</li>
		<li>If the quality of acquired brain tissue is questionable, assess PrPC levels by SDS-PAGE16 and immunoblot17 prior to substrate preparation.</li>
	</ol>
	</li>
	<li>Divide brain homogenate into two equal volumes in separate labelled plastic conical tubes. Add GdnHCl (3 M solutions in 1 PBS) at either pH 3.5 or 7.4 to each tube in a 1:1 volume ratio to brain homogenate.</li>
	<li>Check the pH values of the two solutions. Adjust the pH of the pH 3.5 substrate to pH &#177; 0.05 using concentrated HCl. Ensure the pH of the other substrate remains at pH 7.4 &#177; 0.05 and adjust pH if necessary with HCl or NaOH as needed. Avoid overshooting pH values by judicious addition of acid or base.</li>
	<li>Rotate solutions on an end-over-end mixer at room temperature (RT) for 5 hr.</li>
	<li>Precipitate protein by adding four volumes of methanol to the substrate solutions in each conical tube, vortex to mix well, and incubate at -20 &#176;C for 16-18 hr.</li>
	<li>Sediment samples by centrifugation at 13,000 &#215; g for 30 min at 4 &#176;C. Carefully decant and discard the supernatants and allow methanol to evaporate from the pellets. Use cotton-tipped applicators to assist in absorbing methanol clung to the inside of the tube. Do not allow pellets to over-dry and once methanol is no longer visible, proceed to the next step.</li>
	<li>Resuspend protein pellets in conversion buffer. Use a quantity of conversion buffer equal to the amount of brain homogenate starting material dispensed into each tube in step 2.2. 
	NOTE: It is critical that the conversion buffer used to resuspend protein pellets from both pH 3.5 and 7.4-treated substrate preparations is the solution defined in step 1.2 above (which contains low levels of detergents and a physiological pH).</li>
	<li>Briefly sonicate substrate solutions in a cuphorn sonicator (10 sec at ~30% maximal power), aliquot into 0.5 - 1.0 ml volumes in labeled 1.5 ml microcentrifuge tubes. Perform a quality control immunoblot (step 2.9) on an aliquot of each substrate. Store other aliquots at -80 &#176;C until ready to perform CER assay (Section 4).</li>
	<li>Perform quality control on CER substrate pairs prior to use (Figure 2). These steps ensure that CER substrates will provide optimal results in conversion studies.
	<ol>
		<li>Ensure comparable amounts of PrPC in the two substrates. Compare PrP levels in 10-25 &#181;l of each substrate by SDS-PAGE16 and immunoblotting17. If protein levels in the pH 7.4 and 3.5 substrates are within ~10% of each other, the substrate pairs are appropriate for use in CER studies. 
		NOTE: The PrP immunoblots should not show evidence of extensive PrPC degradation. The PrP immunoreactivity should be mainly &#62;20 kDa. Bands less than this molecular mass can be degradation products. Banding patterns should be roughly equivalent between substrate pairs.</li>
		<li>As the PrPC in both substrates should be PK sensitive, treat 10-25 &#181;l of each substrate with PK at a final concentration of 100 &#956;g/ml and digest samples at 1,000 rpm at 37 &#176;C for 1 hr in the thermo-shaker. Assess any remaining PrP signal by SDS-PAGE16 and immunoblotting17. Substrates with PrPres are not appropriate for use in CER studies.</li>
	</ol>
	</li>
</ol>
3. Prepare TSE Agent Seeds
<ol>
	<li>Obtain TSE-infected brain tissue from species of interest and prepare a 10% (w/v) homogenate in 1x PBS pH 7.4 using the methods listed in step 2.1 above. 
	NOTE: Seeds could also be produced from other TSE-infected tissues outside the central nervous system, however, efficiency of conversion of brain derived substrates by seeds derived from TSE-infected peripheral tissues has not yet been experimentally assessed in the published literature.</li>
	<li>Aliquot resulting homogenate(s) into 100 - 300 &#181;l volumes in 0.5 ml microcentrifuge tubes and store at -80 &#176;C until ready to perform the CER assay.</li>
</ol>
4. CER Assay
NOTE: The CER assay involves addition of a relatively small amount of PrPTSE (provided in the &#8220;seed&#8221;) from one species into a relative excess of PrPC (provided in the uninfected brain &#8220;substrate&#8221;) from another species that has been partially denatured at either pH 3.5 or 7.4. Following an extended shaking incubation period, template-driven conversion of PrPC by PrPTSE in each reaction is assessed by the densitometric signal of PrPres remaining after PK digestion and immunoblot detection. Comparing PrPres levels in the substrates previously denatured at pH 3.5 vs. 7.4 provides a measure of the species barrier. An experimental overview of this assay procedure is provided in Figure 1.
<ol>
	<li>Slowly thaw uninfected CER substrate pairs (assay requires equal volumes of substrates previously denatured at both pH 3.5 and 7.4) and TSE-infected seed solutions by placing them on top of a bed of ice (approximately 1 hr thaw time).</li>
	<li>Once fully thawed, aspirate and then expel each substrate solution through a 27 G syringe needle several times to re-homogenize it. Briefly sonicate each TSE-infected seed solution for 10 sec at ~30% maximal power. Keep all solutions on ice while preparing conversion reactions.</li>
	<li>Label 5 individual low binding, thin-walled PCR tubes per TSE agent being tested.</li>
	<li>Prepare conversion reactions in these tubes by adding 5 &#956;l of 10% TSE-infected seed solution to 95 &#956;l of (a) CER substrate prepared at pH 7.4 and (b) CER substrate prepared at pH 3.5.
	<ol>
		<li>For each experimental sample, prepare parallel reactions in CER substrate pairs previously denatured at both pH 3.5 and 7.4.</li>
		<li>Optimize ratios of TSE agent seed to uninfected brain substrate through empirical determination. Common seed:substrate ratios employed maintain a total reaction volume of 100 &#956;l and include 1:99 &#956;l, 2:98 &#956;l and 5:95 &#956;l. For most applications, the 5:95 &#956;l seed:substrate volume ratio is appropriate and is what is presented in this protocol.</li>
	</ol>
	</li>
	<li>Prepare three control samples per TSE agent being tested as follows: (a) add 5 &#181;l of 10% TSE-infected seed solution to 95 &#181;l conversion buffer as a control for input PrPres; add 5 &#181;l conversion buffer to 95 &#181;l substrate prepared at (b) pH 3.5 and (c) pH 7.4 as controls for non-specific, non-templated conversion.</li>
	<li>Briefly vortex each sample in its closed PCR tube to mix seed and substrate well. Follow with a momentary pulse in a low-speed bench top mini-centrifuge to remove any volume of the reaction mixture trapped in the PCR tube lid.</li>
	<li>Load samples in individually-labeled PCR tubes into a bench top thermo-shaker equipped to accept PCR tubes. Shake samples at 1,000 rpm at 37 &#176;C for 24 hr.</li>
	<li>Following shaking, add sarkosyl to a final concentration of 2% (w/v) and PK to a final concentration of 100 &#956;g/ml. Digest samples at 1,000 rpm at 37 &#176;C for 1 hr in the thermo-shaker. 
	NOTE: Addition of sarkosyl to samples post-conversion aids in PK digestion of PrPC. False positive signals in unseeded samples (Step 4.5) are virtually eliminated by addition of sarkosyl.</li>
	<li>Add SDS-PAGE sample buffer, heat samples to 95&#176;C for 5 minutes and resolve remaining PrPres in each sample by SDS-PAGE16 followed by immunoblotting17. 
	NOTE: After addition of sample buffer and heating, samples may be immediately processed or samples can be stored at -20 &#176;C or -80 &#176;C prior to immunoblotting. All data presented here were generated using the Novex NuPAGE gel and transfer systems. Individual samples from the CER assay were treated with sample buffer and reducing agent according to manufacturer&#8217;s instructions. Samples were subsequently heated at 95 &#176;C for 5 min and 30 &#181;l of each sample was loaded into a 12% bis-tris precast gels.</li>
	<li>Calculate the conversion efficiency ratio (CER) as a measure of species barrier. Measure levels of PrPres by densitometry17 and divide the total density of the pH 7.4 sample by that of the pH 3.5 sample. Multiply by 100 to produce a percentage.</li>
	<li>Compile data from independent experimental replicates to generate a mean CER &#177; standard deviation for a species with a given TSE agent.</li>
</ol>

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The authors have nothing to disclose.

For successful completion of this protocol, attention should be paid to PrPC levels in uninfected brain tissue used for substrate preparation (step 2.1.2) and the seed to substrate ratio for conversion reactions (step 4.4.2). In our experience, brains can be extracted for use as CER substrate after a substantial period post-mortem, as long as PrPC is present by immunoblotting (Figure 4). In fact, some autolysis was observed in the brains of the bobcats used for CER studies. Nevertheless, incubation of substrates derived from these brains still resulted in the formation of PrPres. We speculate that, in part, the robustness of the CER assay is derived from the denaturation of CER substrates in 1.5 M GdnHCl, which will inactivate many proteases.
Seed to substrate ratios may need to be empirically determined to obtain acceptable PrPres signal by immunoblotting. Too much or too little PrPres to perform densitometry, high background PrPres levels in control samples lacking substrate and inconsistent conversion ratios are all reasons to optimize seed:substrate ratios. Variations maintain a total reaction volume of 100 &#956;l and include 1:99 &#956;l, 2:98 &#956;l and 5:95 &#956;l. On almost all occasions, we have found that 5:95 &#956;l seed:substrate volume ratio is optimal. No matter what ratio is employed, equal amounts of TSE agent are used and the assay is internally consistent. However, seed concentration of the prion-infected brain homogenate used to template reactions likely affects the outcome of the CER assay in that varying seed titers or dilutions could result in varying levels of PrPC-to-PrPres conversion. This effect has been demonstrated in other in vitro prion conversion assays22 and may complicate the comparison of different prion isolates. To address this in the CER assay, seeds could be titrated in each PrPC substrate prepared at pH 3.5 and 7.4 to identify a range of dilutions that template PrPC conversion. Ideal seed dilutions avoid saturating the solution with excess seed prions and yet provide insight into the sensitivity of the conversion reaction. Alternatively, PrPC-to-PrPres conversion in CER assay reactions could be measured at multiple, regular timepoints throughout the duration of the assay and plotted as rate-of-conversion curves, akin to the readouts for real-time polymerase chain reaction (qPCR)23 and real-time quaking induced conversion (RT-QuIC)24 assays. Such readouts could allow more comprehensive interpretations of species barriers and are an interesting focus of future development of this methodology.
In the protocol presented here, we use low binding, thin-walled PCR tubes, but we have also used standard 1.5 ml tubes in a thermo-shaker equipped for this type of tube. No other variations to the protocol are needed to use the larger sized tubes. In our experience, however, we have had more PrPres production and more reproducible results in low-binding PCR tubes compared to 1.5 ml tubes. While explanations for the improved performance of the assay in PCR tubes are only speculative at this time, based on results indicating that the air-water interface is critical for PrP fibrillization25, we hypothesize that the smaller tubes provide a more optimal surface tension for PrP conversion.
Perhaps the chief limitation to use of the CER assay is in understanding what conversion ratios represent in terms of in vivo species barriers determinants, such as disease penetrance or length of incubation period. While currently unknown, translation between in vitro and in vivo species barrier factors should become clearer with continued use of the CER assay in testing additional TSE species barriers that have already been established in vivo and will help to qualify results in species where bioassay data are not available. An advantage of the CER assay compared to PMCA is the presence of an internal control for PrP conversion, namely the pH 3.5 substrate, which can be converted by any TSE agent. This control is of value when it is unclear which, if any, TSE agents should cause misfolding of an exotic host&#8217;s PrPC. The inability of a given host substrate to amplify a specific TSE agent in PMCA could be interpreted as evidence of a species barrier or could be due to technical failings. Disadvantages of the CER assay compared to PMCA include limited amplification of PrPres, additional steps in CER substrate preparation and no known infectivity in the PrPres produced by CER reactions. It is to be noted that in a previous study, however, we found the CER assay resulted in a similar pattern of PrPres formation as that of PMCA15. The results presented here also indicate that the CER assay correctly predicts the species barriers for transmission of various TSEs to laboratory mice (Figure 3) and suggest that bobcats may have susceptibility to CWD (Figure 4), in agreement with reports that domestic cats (Felis catus) can acquire prion disease after experimental CWD challenge26,27. Studies using the CER assay could compliment PrP sequencing efforts to understand wildlife susceptibility to CWD28.
The CER assay enables rapid, low-cost, reliable assessment of TSE species barriers in vitro. While not a complete replacement for the &#8220;gold standard&#8221; of animal bioassay, the CER assay can be used as an initial assessment of the existence of a TSE species barrier that may justify or obviate further studies in living animals. For this reason, and because the assay relies only on brain tissue which can be acquired from non-experimental animals, the CER is in keeping with efforts to replace, reduce and refine animal experimental procedures29. In addition to assessing species barriers, the CER assay can also provide a simplified platform with which to investigate the mechanisms of the fundamental event defining prion disease biology: the conversion of normal, functional PrPC to a misfolded form.

Transmissible spongiform encephalopathies (TSEs, prion diseases) are a group of fatal neurodegenerative diseases with extended incubation periods that affect a variety of animals and humans. The putative etiological agent of TSEs is comprised of a misfolded isomer of the host prion protein (PrP) that is capable of self-propagation by template-driven conversion of the normal cellular form of PrP (PrPC) into an infectious, disease-associated form (PrPTSE) that accumulates in central nervous system tissues of the infected host1. Infectious mammalian prions generally transmit from host-to-host in a species-specific manner, which has given rise to the concept of the &#8220;TSE species barrier&#8221; limiting interspecies transmission events2. The biological determinants of the prion species barrier are not well understood. Amino acid sequence similarity between the infectious PrPTSE and the host PrPC can strongly influence whether conversion takes place3-5, but remains insufficient to explain all prion transmission events observed in vivo6,7.
Thus, characterization of TSE species barriers has largely relied upon animal challenge studies: exposing na&#239;ve animals from a given species to prions from another and measuring the resulting incubation time to disease onset and attack rate as indicators of transmission efficiency. Mice expressing PrPC from heterologous species are also used for this type of study8. The costs associated with transgenic mouse production and protracted prion bioassays, as well as ethical considerations of animal use, are obstacles to experimental investigation of TSE species barriers. Assessment of the human species barrier to TSEs relies on mice engineered to express human PrPC. These mice require long incubation periods to succumb to human TSEs or modifications to the human PrPC molecule for rapid disease onset9. Incubation periods for non-human TSEs in these mice may extend beyond the normal mouse lifespan making interpretation of negative results challenging. Non-human primates have also been used as proxies for studying human species barriers, but these studies are fraught with the same challenges as other types of animal experimentation and non-human primates may not precisely recapitulate disease as it proceeds in the human host.
Animal bioassays remain the &#8220;gold standard&#8221; method for measuring the susceptibility of a species to a TSE, but the obstacles, costs and ethics of these live animal studies have compelled investigation into alternatives. A number of in vitro assays, based on assessing the conversion of host PrPC to a proteinase K (PK)-resistant state (PrPres) when seeded by PrPTSE, have been developed and used to investigate TSE species barriers10-12. Examples of in vitro assays include cell-free conversion assays, protein misfolding cyclic amplification (PMCA), and the conversion efficiency ratio (CER) assay10-14. While none of these assays take into account peripheral factors involved in species barriers after natural infection, all can be useful to identify potentially susceptible hosts for TSEs.
Here we present the protocol for the CER assay, in which two denatured PrPC substrates derived from normal brain homogenates are used in bench top prion conversion reactions (Figure 1)13. PrPC in the substrate denatured at pH 7.4 can only be converted to PrPres by PrPTSE seeded into the reaction in the absence of a species barrier14. In contrast, denaturation of PrPC in the other substrate at pH 3.5 allows it to be converted to PrPres following incubation with PrPTSE from any species and serves as a control for conversion. The ratio of conversion of PrPC to PrPres in pH 7.4 substrate relative to that of the pH 3.5 substrate provides a measure of the species barrier. We have found that the CER assay predicts known species barriers of laboratory mice to various TSEs and have used the assay in efforts to predict the species barrier of numerous mammalian species, including bighorn sheep, to chronic wasting disease (CWD) and other TSEs14,15. Investigators interested in a tool allowing rapid screening of TSE species barriers or assessment of PrPC-to-PrPres conversion will find this methodology useful.

<table><tbody><tr><td>12% Bis-Tris SDS-PAGE gels</td><td>Life Technologies</td><td>NP0342</td><td></td></tr><tr><td>0.5 mm Zirconium oxide beads</td><td>Next Advance</td><td>ZROB05</td><td>Other varieties of beads are also effective</td></tr><tr><td>Antibodies</td><td>various suppliers</td><td></td><td>Select appropriate primary and secondary antibodies for immunoblot detection of PrP&lt;sup&gt;res&lt;/sup&gt; from species of interest</td></tr><tr><td>Bead homogenizer</td><td>Next Advance</td><td>BBY24M</td><td></td></tr><tr><td>Centrifuge</td><td>Beckman Coulter</td><td>369434</td><td>High speed with temperature control</td></tr><tr><td>Conical tubes</td><td>any brand</td><td></td><td></td></tr><tr><td>Cotton-tipped applicator</td><td>Uline</td><td>S-18991</td><td></td></tr><tr><td>Cuphorn sonicator</td><td>Heat Systems-Ultrasonics</td><td>W-380</td><td>Heat Systems-Ultrasonics, Inc. is now Qsonica, LLC</td></tr><tr><td>Densitometry software program</td><td>UVP</td><td>Vision Works LS Image Acquisition and Analysis software</td><td>Other programs, such as NIH ImageJ, will also work</td></tr><tr><td>Dounce homogenizer</td><td>Kimble Chase</td><td>885300</td><td></td></tr><tr><td>End-over-end mixer</td><td>Labnet International</td><td>H5600</td><td></td></tr><tr><td>Ethylenediaminetetra acetic acid</td><td>Boston Bioproducts</td><td>P-770</td><td>Hazardous chemical: eye irritation</td></tr><tr><td>Guanidine hydrochloride, 8 M</td><td>Thermo Fisher Scientific</td><td>24115</td><td>Hazardous chemical: acute toxicity, skin irritation, eye irritation</td></tr><tr><td>Heating block</td><td>Fisher Scientific</td><td>11-718</td><td></td></tr><tr><td>Hydrochloric acid</td><td>Sigma-Aldrich</td><td>435570</td><td>Hazardous chemical: strong acid</td></tr><tr><td>Lithium dodecyl sulfate sample buffer, 4x</td><td>Life Technologies</td><td>NP0008</td><td>Hazardous chemical: skin &amp;amp; respiratory irritation, serious eye damage, flammable solid</td></tr><tr><td>Methanol</td><td>Fisher Scientific</td><td>A454-4</td><td>Hazardous chemical: acute toxicity, flammable liquid</td></tr><tr><td>Microcentrifuge tubes</td><td>any brand</td><td></td><td></td></tr><tr><td>Mini-centrifuge</td><td>Labnet International</td><td>C1301</td><td></td></tr><tr><td>N-lauroyl-sarcosine (sarkosyl)</td><td>Sigma-Aldrich&amp;nbsp;</td><td>L-5125</td><td>Hazardous chemical: acute toxicity, skin irritation, eye damage</td></tr><tr><td>Nonidet P-40</td><td>Amresco</td><td>M158</td><td>Hazardous chemical: skin irritation, eye damage</td></tr><tr><td>SDS-PAGE gel system</td><td>Life Technologies</td><td>NuPAGE electrophoresis system</td><td>Other SDS-PAGE systems will also work</td></tr><tr><td>PCR tubes (low-binding)</td><td>Axygen</td><td>PCR-02-L-C</td><td></td></tr><tr><td>Pestle homogenizer</td><td>Fisher Scientific</td><td>03-392-106</td><td></td></tr><tr><td>pH meter</td><td>Sentron</td><td>SI600</td><td></td></tr><tr><td>Polyvinyldifluoride membrane</td><td>Millipore</td><td>IPVH00010</td><td></td></tr><tr><td>Proteinase K</td><td>Promega</td><td>V3021</td><td>Hazardous chemical: skin &amp;amp; eye irritation, respiratory sensitisation, organ toxicity</td></tr><tr><td>Reducing agent for SDS-PAGE samples, 10x</td><td>Life Technologies</td><td>NP0009</td><td></td></tr><tr><td>Sodium chloride</td><td>Fisher Scientific</td><td>7647-14-5</td><td></td></tr><tr><td>Sodium deoxycholate</td><td>Sigma-Aldrich&amp;nbsp;</td><td>D6750</td><td>Hazardous chemical: acute toxicity</td></tr><tr><td>Sodium dodecyl sulfate</td><td>Thermo Fisher Scientific</td><td>28364</td><td>Hazardous chemical: acute toxicity, skin irritation, eye damage, flammable solid</td></tr><tr><td>Sodium hydroxide</td><td>Sigma-Aldrich</td><td>S5881</td><td>Hazardous chemical; strong base</td></tr><tr><td>Syringe</td><td>BD Biosciences</td><td>various</td><td>Use syringe size appropriate to volumes of substrate to be homogenized</td></tr><tr><td>Syringe needles</td><td>BD Biosciences</td><td>various</td><td></td></tr><tr><td>Thermoshaker (PCR tube shaker)</td><td>Hangzhou All Sheng Instruments</td><td>MS-100</td><td></td></tr><tr><td>Tris base</td><td>Bio Basic</td><td>77-86-1</td><td>Hazardous chemical: skin, eye, respiratory irritation</td></tr><tr><td>Triton X-100</td><td>Integra Chemical Company</td><td>T756.30.30</td><td>Hazardous chemical: acute toxicity, eye irritation</td></tr><tr><td>Vortexer</td><td>Fisher Scientific</td><td>12-812</td><td></td></tr></tbody></table>

assessing transmissible spongiform encephalopathy species barriers with an in vitro prion protein conversion assay

Studies to understanding interspecies transmission of transmissible spongiform encephalopathies (TSEs, prion diseases) are challenging in that they typically rely upon lengthy and costly in vivo animal challenge studies. A number of in vitro assays have been developed to aid in measuring prion species barriers, thereby reducing animal use and providing quicker results than animal bioassays. Here, we present the protocol for a rapid in vitro prion conversion assay called the conversion efficiency ratio (CER) assay. In this assay cellular prion protein (PrPC) from an uninfected host brain is denatured at both pH 7.4 and 3.5 to produce two substrates. When the pH 7.4 substrate is incubated with TSE agent, the amount of PrPC that converts to a proteinase K (PK)-resistant state is modulated by the original host&#8217;s species barrier to the TSE agent. In contrast, PrPC in the pH 3.5 substrate is misfolded by any TSE agent. By comparing the amount of PK-resistant prion protein in the two substrates, an assessment of the host&#8217;s species barrier can be made. We show that the CER assay correctly predicts known prion species barriers of laboratory mice and, as an example, show some preliminary results suggesting that bobcats (Lynx rufus) may be susceptible to white-tailed deer (Odocoileus virginianus) chronic wasting disease agent.

Successful use of the CER assay is largely dependent upon the quality of the substrate pairs used in conversion reactions. For this reason, following procedures to prepare CER substrate pairs, a quality control immunoblot should be performed (Figure 2). For both substrates, assay 10-25 &#956;l by immunoblotting. PrPC should be easily detectable in each substrate and PrPC levels must be approximately the same between the two. Immunoreactivity will be mainly visible above 20 kDa, but smaller bands may also be evident. In our experience, the presence of smaller bands is species dependent. If lower molecular weight products are observed, their presence should be confirmed in both substrate pairs.
It is important to ensure that CER substrates are free from endogenous PrPres by treating substrates with PK (Figure 2). If PrPres is present, the animal used for substrate preparation may have been TSE-infected or subclinically-infected. Alternatively, the PrPC in the substrate may have misfolded to a PK-resistant state during denaturation or precipitation procedures. Independent from the reason, CER substrate containing PrPres is not acceptable for use in the conversion assay.
Laboratory mice are one of the most frequently used experimental animals in TSE research; as such, their susceptibility to most TSEs is well-characterized8, providing an in vivo benchmark against which to test the fidelity of the CER assay. Figure 3A presents results of CER assay conversion of PrPC from mouse (CD1 strain) substrate to PrPres by 1) the RML strain of mouse-passaged scrapie, an agent adapted to the mouse host18, 2) domestic sheep classical scrapie, an agent that can transmit to mice following a lengthy incubation period18, and 3) white-tailed deer (Odocoileus virginianus) CWD and 263K strain of hamster-passaged scrapie, agents to which mice are minimally or not susceptible19,20. Resulting PrPres levels were variable across mouse substrates denatured at pH 7.4 and seeded with the various TSE agents while PrPres was found in all substrates denatured at pH 3.5 and seeded with a TSE agent. Conversion ratios comparing the PrPres levels in the pH 7.4 and 3.5 substrates were independently calculated at least three times and means &#177; SD are shown in Figure 3B. For reactions seeded by RML, conversion ratios between pH 7.4 and 3.5 substrates were approximately 100%. For those seeded by scrapie, conversion in the pH 7.4 substrate was approximately 75% of that in the pH 3.5 substrate. CWD or 263K-induced conversion of the pH 7.4 substrate was minimal. A one-way analysis of variance could not distinguish a difference in the conversion ratios of RML and scrapie or CWD and 263K, however conversion ratios of RML and scrapie were significantly different from those of CWD and 263K.
The CER assay can be adapted for use with human tissues or with animal species where bioassays are too challenging or not ethical and transgenic mouse production is not desired. We have been using this assay to characterize the susceptibility of various wildlife species to CWD. As an example of the use of this assay, we present some preliminary results in Figure 4. Brains from hunter-trapped bobcats (Lynx rufus) were found to still contain detectable levels of PrPC and PrP breakdown products were not extensive, suggesting that these tissues could be an acceptable source for CER substrate (Figure 4A). Substrate pairs generated from bobcat brain showed PrP immunoreactivity of an appropriate molecular weight and did not contain endogenous PrPres (Figure 4B). When bobcat CER substrate pairs generated from two separate animals were incubated with the same white-tailed deer CWD agent used in the mouse CER assay described in Figure 3, we found substrates prepared at pH 7.4 had levels of PrPres compared to substrates prepared at pH 3.5 (Figure 4C), indicative of a minimal species barrier of bobcat PrPC to conversion by CWD. The CER for conversion of white-tailed deer PrPC by the same CWD isolate used to convert bobcat PrPC here, as a positive control, was previously reported as 95.2 &#177; 18.4% in Morawski et al. (2013)15.
<img alt="Figure 1" src="/files/ftp_upload/52522/52522fig1.jpg" width="450" /> 
Figure 1: Experimental overview of the CER assay. Two assay substrates are prepared by partially denaturing PrPC in non-prion infected brain tissue with chaotropic solutions at either pH 3.5 or pH 7.4. Substrates are seeded with PrPTSE from prion agent of interest and experimental samples are subjected to 24 hr incubation with shaking to allow PrPC to PrPTSE conversion in both pH 3.5 and 7.4 substrates. Following incubation, conversion is assessed by SDS-PAGE and immunoblotting. Signal densities are read by densitometry and the CER is calculated by the ratio of pH 7.4 to pH 3.5 signal densities for each experimental sample.
<img alt="Figure 2" src="/files/ftp_upload/52522/52522fig2.jpg" /> 
Figure 2: Quality control on CER substrates. (A) Prior to their use in the CER assay, mouse substrates prepared at either pH 7.4 or 3.5 are assayed by immunoblot in the 1) absence of PK treatment to assess PrPC content of each substrate pair (PrPC levels should be equivalent between pH 7.4 and 3.5 substrates for use in CER assay) and 2) presence of PK (100 &#181;g/ml) treatment to test for pre-existing PrPres in tissues used to prepare substrates (any substrates that display pre-existing PrPres are not suitable for use in the CER assay). (B) To test for non-specific PrPres formation during the conversion assay, mouse PrPC substrates prepared at either pH 7.4 or 3.5 are seeded with conversion buffer, shaken for 24 hr at 1,000 rpm, 37 &#176;C, and subsequently PK-treated (100 &#181;g/ml) and assayed for PrPres by immunoblotting (right two lanes). Non-shaken, non-PK treated mouse substrates represent total PrPC content in assay reactions (left two lanes). For (B), irrelevant lanes have been cropped for clarity, but each immunoblot panel derives from the same gel, membrane and exposure. Immunoblots in all panels used monoclonal antibody SAF 83.
<img alt="Figure 3" src="/files/ftp_upload/52522/52522fig3.jpg" /> 
Figure 3: CER assay using laboratory mouse substrate. (A) Mouse CER assay substrate prepared at either pH 7.4 or 3.5 was incubated with RML mouse-adapted scrapie, domestic sheep classical scrapie, white-tailed deer chronic wasting disease (CWD) or 263K strain of hamster-adapted scrapie in the CER assay. Control samples (labeled &#8220;none&#8221;) contained only an equal amount of infectious agent and no mouse substrate. Samples were analyzed for the presence of PK-resistant prion protein (PrPres) by immunoblot with monoclonal antibody SAF 83. Raw densitometric values for each sample are displayed below each lane. (B) Bar graph indicating the average ratios (&#177; standard deviation) between pH 7.4 and 3.5 mouse substrates for each infectious agent based on at least 3 independent assay runs. Lower-case letters refer to statistically homogenous subsets (analysis of variance with Tukey-Kramer minimum significance differences method; p &#60;0.05). This figure has been modified from Morawski et al. 201315.
<img alt="Figure 4" src="/files/ftp_upload/52522/52522fig4.jpg" /> 
Figure 4: Sample use of CER assay to investigate bobcat susceptibility to CWD. Bobcat brain homogenate (A) and CER assay substrate (B) was tested by immunoblotting in the absence and presence of PK (100 &#181;g/ml) to assess existing PrPC levels and the presence of pre-existing PrPres, respectively. (C) Bobcat substrates were seeded with conversion buffer and assayed in the CER assay to assess non-specific PrPres formation (left two lanes). Non-shaken, non-PK treated bobcat substrates represent total PrPC content in assay reactions (right two lanes). (D) Bobcat substrate prepared at either pH 7.4 or 3.5 was incubated with white-tailed deer CWD using the CER assay. The control sample (labeled &#8220;none&#8221;) contained an equal amount of CWD agent but no bobcat substrate. Raw densitometric values for each sample are displayed below each lane. Immunoblots in all panels used monoclonal antibody 3F4, which reacts with the feline prion protein21.

Watch this Scientific Journal Video about Assessing Transmissible Spongiform Encephalopathy Species Barriers with an In Vitro Prion Protein Conversion Assay at JoVE.com

Assessing Transmissible Spongiform Encephalopathy Species Barriers with an In Vitro Prion Protein Conversion Assay

Measuring the barrier to the interspecies transmission of prion diseases is challenging and typically involves animal challenges or biochemical assays. Here, we present an in vitro prion protein conversion assay with the ability to predict species barriers.

Assessing Transmissible Spongiform Encephalopathy Species Barriers with an In Vitro Prion Protein Conversion Assay

Studies to understanding interspecies transmission of transmissible spongiform encephalopathies (TSEs, prion diseases) are challenging in that they ...

assessing-transmissible-spongiform-encephalopathy-species-barriers

Universidad San Sebastian

Research

JoVE Journal

Medicine

7.7K Views.  USGS National Wildlife Health Center. Measuring the barrier to the interspecies transmission of prion diseases is challenging and typically involves animal challenges or biochemical assays. Here, we present an in vitro prion protein conversion assay with the ability to predict species barriers.

Video: Assessing Transmissible Spongiform Encephalopathy Species Barriers with an In Vitro Prion Protein Conversion Assay

Monitoring Immune Cells Trafficking Fluorescent Prion Rods Hours after Intraperitoneal Infection

Presence of an abnormal form a host-encoded prion protein (PrPC) that is protease resistant, pathologic and infectious characterizes prion diseases such as Chronic Wasting Disease (CWD) of cervids and scrapie in sheep. The Prion hypothesis asserts that this abnormal conformer constitutes most or all of the infectious prion. The role of the immune system in early events in peripheral prion pathogenesis has been convincingly demonstrated for CWD and scrapie 1-3. Transgenic and pharmacologic studies in mice revealed an important role of the Complement system in retaining and replicating prions early after infection 4-6. In vitro and in vivo studies have also observed prion retention by dendritic cells 7-10, although their role in trafficking remains unclear 11-16. Macrophages have similarly been implicated in early prion pathogenesis, but these studies have focused on events occurring weeks after infection 3,11,17. These prior studies also suffer from the problem of differentiating between endogenous PrPC and infectious prions. Here we describe a semiquantitative, unbiased approach for assessing prion uptake and trafficking from the inoculation site by immune cells recruited there. Aggregated prion rods were purified from infected brain homogenate by detergent solubilization of non-aggregated proteins and ultracentrifugation through a sucrose cushion. Polyacrylamide gel electrophoresis, coomassie blue staining and western blotting confirmed recovery of highly enriched prion rods in the pelleted fraction. Prion rods were fluorochrome-labeled then injected intraperitoneally into mice. Two hours later immune cells from peritoneal lavage fluid, spleen and mediastinal and mesenteric lymph nodes were assayed for prion rod retention and cell subsets identified by multicolor flow cytometry using markers for monocytes, neutrophils, dendritic cells, macrophages and B and T cells. This assay allows for the first time direct monitoring of immune cells acquiring and trafficking prions in vivo within hours after infection. This assay also clearly differentiates infectious, aggregated prions from PrPC normally expressed on host cells, which can be difficult and lead to data interpretation problems in other assay systems. This protocol can be adapted to other inoculation routes (oral, intravenous, intranervous and subcutaneous, e.g.) and antigens (conjugated beads, bacterial, viral and parasitic pathogens and proteins, egg) as well.

Here we describe a novel assay for monitoring prion uptake and trafficking by immune cells immediately following intraperitoneal inoculation by purifying and fluorescently labeling aggregated prion rods from infected brain material then monitoring their uptake and movement from the injection site and characterizing the cells mediating these events.

Presence of an abnormal form a host-encoded prion protein (PrPC) that is protease resistant, pathologic and infectious characterizes prion diseases such ...

Immunology and Infection

Isolation of Soluble and Insoluble PrP Oligomers in the Normal Human Brain

The central event in the pathogenesis of prion diseases involves a conversion of the host-encoded cellular prion protein PrPC into its pathogenic isoform PrPSc 1. PrPC is detergent-soluble and sensitive to proteinase K (PK)-digestion, whereas PrPSc forms detergent-insoluble aggregates and is partially resistant to PK2-6. The conversion of PrPC to PrPSc is known to involve a conformational transition of &alpha;-helical to &beta;-sheet structures of the protein. However, the in vivo pathway is still poorly understood. A tentative endogenous PrPSc, intermediate PrP* or "silent prion", has yet to be identified in the uninfected brain7.
Using a combination of biophysical and biochemical approaches, we identified insoluble PrPC aggregates (designated iPrPC) from uninfected mammalian brains and cultured neuronal cells8, 9. Here, we describe detailed procedures of these methods, including ultracentrifugation in detergent buffer, sucrose step gradient sedimentation, size exclusion chromatography, iPrP enrichment by gene 5 protein (g5p) that specifically bind to structurally altered PrP forms10, and PK-treatment. The combination of these approaches isolates not only insoluble PrPSc and PrPC aggregates but also soluble PrPC oligomers from the normal human brain. Since the protocols described here have been used to isolate both PrPSc from infected brains and iPrPC from uninfected brains, they provide us with an opportunity to compare differences in physicochemical features, neurotoxicity, and infectivity between the two isoforms. Such a study will greatly improve our understanding of the infectious proteinaceous pathogens. The physiology and pathophysiology of iPrPC are unclear at present. Notably, in a newly-identified human prion disease termed variably protease-sensitive prionopathy, we found a new PrPSc that shares the immunoreactive behavior and fragmentation with iPrPC 11, 12. Moreover, we recently demonstrated that iPrPC is the main species that interacts with amyloid-&beta; protein in Alzheimer disease13. In the same study, these methods were used to isolate Abeta aggregates and oligomers in Alzheimer's disease13, suggesting their application to non-prion protein aggregates involved in other neurodegenerative disorders.

A new species of cellular prion protein (PrPC) has recently been identified in uninfected human brains using the methods described here. These methods can be used to isolate various PrP species, while some of them are also useful in isolating other misfolded protein aggregates from human brains.

The central event in the pathogenesis of prion diseases involves a conversion of the host-encoded cellular prion protein PrPC into its pathogenic isoform ...

Protein Misfolding Cyclic Amplification of Prions

Prions are infectious agents that cause the inevitably fatal transmissible spongiform encephalopathy (TSE) in animals and humans9,18. The prion protein has two distinct isoforms, the non-infectious host-encoded protein (PrPC) and the infectious protein (PrPSc), an abnormally-folded isoform of PrPC 8.
One of the challenges of working with prion agents is the long incubation period prior to the development of clinical signs following host inoculation13. This traditionally mandated long and expensive animal bioassay studies. Furthermore, the biochemical and biophysical properties of PrPSc are poorly characterized due to their unusual conformation and aggregation states.
PrPSc can seed the conversion of PrPC to PrPSc in vitro14. PMCA is an in vitro technique that takes advantage of this ability using sonication and incubation cycles to produce large amounts of PrPSc, at an accelerated rate, from a system containing excess amounts of PrPC and minute amounts of the PrPSc seed19. This technique has proven to effectively recapitulate the species and strain specificity of PrPSc conversion from PrPC, to emulate prion strain interference, and to amplify very low levels of PrPSc from infected tissues, fluids, and environmental samples6,7,16,23 .
This paper details the PMCA protocol, including recommendations for minimizing contamination, generating consistent results, and quantifying those results. We also discuss several PMCA applications, including generation and characterization of infectious prion strains, prion strain interference, and the detection of prions in the environment.

Protein misfolding cyclic amplification (PMCA) is an in vitro assay for the study of prion conversion and strain and species barriers. It can also be used as a prion detection assay.

Prions  are infectious agents that cause the inevitably fatal transmissible spongiform  encephalopathy (TSE) in animals and humans9,18. The prion protein ...

Procedures for Identifying Infectious Prions After Passage Through the Digestive System of an Avian Species

Infectious prion (PrPRes) material is likely the cause of fatal, neurodegenerative transmissible spongiform encephalopathy (TSE) diseases1. Transmission of TSE diseases, such as chronic wasting disease (CWD), is presumed to be from animal to animal2,3 as well as from environmental sources4-6. Scavengers and carnivores have potential to translocate PrPRes material through consumption and excretion of CWD-contaminated carrion. Recent work has documented passage of PrPRes material through the digestive system of American crows (Corvus brachyrhynchos), a common North American scavenger7.
We describe procedures used to document passage of PrPRes material through American crows. Crows were gavaged with RML-strain mouse-adapted scrapie and their feces were collected 4 hr post gavage. Crow feces were then pooled and injected intraperitoneally into C57BL/6 mice. Mice were monitored daily until they expressed clinical signs of mouse scrapie and were thereafter euthanized. Asymptomatic mice were monitored until 365 days post inoculation. Western blot analysis was conducted to confirm disease status. Results revealed that prions remain infectious after traveling through the digestive system of crows and are present in the feces, causing disease in test mice.

Scavengers have potential to translocate infectious transmissible spongiform encephalopathy prions in their feces to disease-free areas. We detail methods used to determine if mouse-adapted scrapie prions remain infectious after passage though the digestive tract of American crows (Corvus brachyrhynchos), a common consumer of dead animals.

Infectious prion (PrPRes) material is likely the cause of fatal, neurodegenerative transmissible spongiform encephalopathy (TSE) diseases1. Transmission ...

Clinical Examination Protocol to Detect Atypical and Classical Scrapie in Sheep

The diagnosis of scrapie, a transmissible spongiform encephalopathy (TSEs) of sheep and goats, is currently based on the detection of disease-associated prion protein by post mortem tests. Unless a random sample of the sheep or goat population is actively monitored for scrapie, identification of scrapie cases relies on the reporting of clinical suspects, which is dependent on the individual&#39;s familiarization with the disease and ability to recognize clinical signs associated with scrapie. Scrapie may not be considered in the differential diagnosis of neurological diseases in small ruminants, particularly in countries with low scrapie prevalence, or not recognized&#160;if it presents as nonpruritic form like atypical scrapie. To aid in the identification of clinical suspects, a short examination protocol is presented to assess the display of specific clinical signs associated with pruritic and nonpruritic forms of TSEs in sheep, which could also be applied to goats. This includes assessment of behavior, vision (by testing of the menace response), pruritus (by testing the response to scratching), and movement (with and without blindfolding). This may lead to a more detailed neurologic examination&#160;of reporting animals as scrapie suspects. It&#160;could also be used in experimental TSE studies of sheep or goats to evaluate disease progression or to identify clinical end-point.

A short clinical examination protocol is presented to aid in the detection of classical and atypical scrapie in sheep and goats.

The diagnosis of scrapie, a transmissible spongiform encephalopathy (TSEs) of sheep and goats, is currently based on the detection of disease-associated ...

Real-time Quaking-induced Conversion Assay for Detection of CWD Prions in Fecal Material

The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant prion protein (PrP) substrate using prion seeds as a template for the conversion. RT-QuIC is a novel high-throughput technique which is analogous to real-time polymerase chain reaction (PCR). Detection of amyloid fibril growth is based on the dye Thioflavin T, which fluoresces upon specific interaction with &#7526;-sheet rich proteins. Thus, amyloid formation can be detected in real time. We attempted to develop a reliable non-invasive screening test to detect chronic wasting disease (CWD) prions in fecal extract. Here, we have specifically adapted the RT-QuIC technique to reveal PrPSc seeding activity in feces of CWD infected cervids. Initially, the seeding activity of the fecal extracts we prepared was relatively low in RT-QuIC, possibly due to potential assay inhibitors in the fecal material. To improve seeding activity of feces extracts and remove potential assay inhibitors, we homogenized the fecal samples in a buffer containing detergents and protease inhibitors. We also submitted the samples to different methodologies to concentrate PrPSc on the basis of protein precipitation using sodium phosphotungstic acid, and centrifugal force. Finally, the feces extracts were tested by optimized RT-QuIC which included substrate replacement in the protocol to improve the sensitivity of detection. Thus, we established a protocol for sensitive detection of CWD prion seeding activity in feces of pre-clinical and clinical cervids by RT-QuIC, which can be a practical tool for non-invasive CWD diagnosis.

Here, we present a protocol to describe a simple, fast and efficient prion amplification technique, the real-time quaking-induced conversion (RT-QuIC) method.

The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant ...

Prion Safety Laboratory Swipe Test

Transmission of iatrogenic prion disease has occurred from contaminated neurosurgical tools, transplant materials, and occupational exposure to prion-contaminated laboratory tools. Prions cause disease by the templated misfolding of the normal cellular form of the prion protein, PrPC, into the misfolded and pathogenic form PrPSc and are invariably fatal. Reducing iatrogenic and occupational prion transmission is challenging. First, prions can bind to and persist on surfaces for long periods of time. Second, prions are highly resistant to inactivation. Given this, surfaces can retain infectivity for long periods of time following ineffective decontamination. Not only can this pose a potential occupational risk for prion laboratory workers, but it could potentially cross-contaminate laboratory experiments utilizing sensitive prion amplification techniques. The protocol described here for a prion safety laboratory swipe test includes steps for the identification and documentation of high-traffic laboratory areas, recommended swabbing controls to ensure the validity of results, steps to identify proper responses to positive surface swabbing sites, representative results from prion swipe testing, as well as potential artifactual results. Overall, the prion safety laboratory swipe test can be implemented as part of a broader prion safety program to assess decontamination of surfaces, monitor common spaces for prion contamination, and implement the documentation of prion decontamination status.

A method to assess commonly used areas in laboratory settings for prion contamination and effective decontamination is lacking. The protocol described here provides key fundamentals for implementing a laboratory prion safety swipe test that can easily be modified to meet the individual needs of specific laboratories.

Transmission of iatrogenic prion disease has occurred from contaminated neurosurgical tools, transplant materials, and occupational exposure to ...

Detection of Abnormal Prion Protein by Immunohistochemistry

Abnormal prion proteins (PrPSc) are the disease-associated isoform of cellular prion protein and diagnostic markers of transmissible spongiform encephalopathies (TSEs). These neurodegenerative diseases affect humans and several animal species and include scrapie, zoonotic bovine spongiform encephalopathy (BSE), chronic wasting disease of cervids (CWD), and the newly identified camel prion disease (CPD). Diagnosis of TSEs relies on immunodetection of PrPSc by application of both immunohistochemistry (IHC) and western immunoblot methods (WB) on encephalon tissues, namely, the brainstem (obex level). IHC is a widely used method that uses&#160;primary antibodies (monoclonal or polyclonal) against antigens of interest in cells of a tissue section. The antibody-antigen binding can be visualized by a color reaction that remains localized in the area of the tissue or cell where the antibody was targeted. As such, in prion diseases, as in other fields of research, the immunohistochemistry techniques are not solely used for diagnostic purposes but also in pathogenesis studies. Such studies involve detecting the PrPSc patterns and types from those previously described to identify the new prion strains. As BSE can infect humans, it is recommended that biosafety laboratory level-3 (BSL-3) facilities and/or practices are used to handle cattle, small ruminants, and cervid samples included in the TSE surveillance. Additionally, containment and prion-dedicated equipment are recommended, whenever possible, to limit contamination. The PrPSc IHC procedure consists of a formic acid epitope-demasking step also acting as a prion inactivation measure, as formalin-fixed and paraffin-embedded tissues used in this technique remain infectious. When interpreting the results, care must be taken to distinguish non-specific immunolabeling from target labeling. For this purpose, it is important to recognize artifacts of immunolabeling obtained in known TSE-negative control animals to differentiate those from specific PrPSc immunolabeling types, which can vary between TSE strains, host species, and prnp genotype, further described herein.

Immunolabeling abnormal prion protein using immunohistochemistry protocols requires specific sample and anti-PrP antibody preparation methodologies. The present protocol describes the key steps in epitope demasking to ensure proper PrP immunolabeling and to minimize non-specific background staining. Also, this approach considers biosafety measures when conducting immunohistochemistry studies with the prion-infected tissues.

Abnormal prion proteins (PrPSc) are the disease-associated isoform of cellular prion protein and diagnostic markers of transmissible spongiform ...

Neuroscience

High-throughput Screening for Protein-based Inheritance in S. cerevisiae

The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived inheritance encoded in protein conformation (rather than sequence) has long been viewed as paradigm-shifting but rare. The best characterized examples of such epigenetic elements are prions, which possess a self-assembling behavior that can drive the heritable manifestation of new phenotypes. Many archetypal prions display a striking N/Q-rich sequence bias and assemble into an amyloid fold. These unusual features have informed most screening efforts to identify new prion proteins. However, at least three known prions (including the founding prion, PrPSc) do not harbor these biochemical characteristics. We therefore developed an alternative method to probe the scope of protein-based inheritance based on a property of mass action: the transient overexpression of prion proteins increases the frequency at which they acquire a self-templating conformation. This paper describes a method for analyzing the capacity of the yeast ORFeome to elicit protein-based inheritance. Using this strategy, we previously found that &gt;1% of yeast proteins could fuel the emergence of biological traits that were long-lived, stable, and arose more frequently than genetic mutation. This approach can be employed in high throughput across entire ORFeomes or as a targeted screening paradigm for specific genetic networks or environmental stimuli. Just as forward genetic screens define numerous developmental and signaling pathways, these techniques provide a methodology to investigate the influence of protein-based inheritance in biological processes.

High-throughput Screening for Protein-based Inheritance in S. cerevisiae

This protocol describes a high-throughput methodology to functionally screen for protein-based inheritance in S. cerevisiae.

The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived ...

Biology

Detection of Misfolded Prion Protein Aggregates in Mouse Brain Tissue Using Western Blotting

Take tissue homogenate from a mammalian brain that contains both normal prion proteins and misfolded prion aggregates responsible for neurodegenerative diseases.
Incubate with a proteolytic enzyme to digest the normal prions, leaving the resistant aggregates intact.
Treat the aggregates with a denaturing buffer at a high temperature to linearize the proteins and impart a uniform negative charge.
Load the sample onto an electrophoresis gel and separate the proteins into bands, which confirms the presence of aggregates.
Using an electric field, transfer the separated proteins onto a membrane.
Incubate the membrane in a blocking solution to mask non-specific binding sites.
Incubate with peroxidase enzyme-tagged antibodies, which bind specifically to the prion aggregates.
Wash the membrane to remove unbound antibodies, minimizing non-specific signals.
Add a chemiluminescent substrate and an oxidizing agent, enabling the peroxidase to oxidize the substrate and produce light.
Measure the light intensity to quantify misfolded prions in the homogenate.

Assessing Transmissible Spongiform Encephalopathy Species Barriers with an In Vitro Prion Protein Conversion Assay

Summary

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Isolation of Soluble and Insoluble PrP Oligomers in the Normal Human Brain

Protein Misfolding Cyclic Amplification of Prions

Procedures for Identifying Infectious Prions After Passage Through the Digestive System of an Avian Species

Clinical Examination Protocol to Detect Atypical and Classical Scrapie in Sheep

Real-time Quaking-induced Conversion Assay for Detection of CWD Prions in Fecal Material

Prion Safety Laboratory Swipe Test

Detection of Abnormal Prion Protein by Immunohistochemistry

High-throughput Screening for Protein-based Inheritance in S. cerevisiae

Detection of Misfolded Prion Protein Aggregates in Mouse Brain Tissue Using Western Blotting