This research was supported by the Consortium de Recherche et Innovations en Bioproc&#233;d&#233;s Industriels au Qu&#233;bec (CRIBIQ)(2016-049-C22), Agropur, Groupe Sani Marc, and the Natural Sciences and Engineering Research Council of Canada (NSERC) (RDCPJ516460-17). We thank Teresa Paniconi for the critical review of the manuscript.

<ol>
	<li>Canada's dairy industry at a glance. Canadian Dairy Information Centre Available from: <a target="_blank" href="https://agriculture.canada.ca/en/canadas-agriculture-sectors/animal-industry/canadian-dairy-information-centre/canadas-dairy-industry-glance">https://agriculture.canada.ca/en/canadas-agriculture-sectors/animal-industry/canadian-dairy-information-centre/canadas-dairy-industry-glance</a> (2017)</li><li>Oliver, S. P., Jayarao, B. M., Almeida, R. 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K., McGuire, J., Daeschel, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+adhesion+and+detachment+of+bacteria+and+spores+on+food-contact+surfaces.">The adhesion and detachment of bacteria and spores on food-contact surfaces.</a> Trends in Food Science &amp; Technology. 7 (5), 152-157 (1996).</li><li>Gupta, S., Anand, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+pitting+corrosion+on+stainless+steel+(grades+304+and+316)+used+in+dairy+industry+by+biofilms+of+common+sporeformers.">Induction of pitting corrosion on stainless steel (grades 304 and 316) used in dairy industry by biofilms of common sporeformers.</a> International Journal of Dairy Technology. 71 (2), 519-531 (2018).</li><li>Marchand, S., 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=Biofilm+formation+in+milk+production+and+processing+environments;+Influence+on+milk+quality+and+safety.">Biofilm formation in milk production and processing environments; Influence on milk quality and safety.</a> Comprehensive Reviews in Food Science and Food Safety. 11 (2), 133-147 (2012).</li><li>Silva, H. O., 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=Efficiency+of+different+disinfectants+on+Bacillus+cereus+sensu+stricto+biofilms+on+stainless-steel+surfaces+in+contact+with+milk.">Efficiency of different disinfectants on Bacillus cereus sensu stricto biofilms on stainless-steel surfaces in contact with milk.</a> Frontiers in Microbiology. 9, 2934 (2018).</li><li>Sedlak, D. L., von Gunten, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemistry.+The+chlorine+dilemma.">Chemistry. The chlorine dilemma.</a> Science. 331 (6013), 42-43 (2011).</li><li>vander Veen, S., Abee, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mixed+species+biofilms+of+Listeria+monocytogenes+and+Lactobacillus+plantarum+show+enhanced+resistance+to+benzalkonium+chloride+and+peracetic+acid.">Mixed species biofilms of Listeria monocytogenes and Lactobacillus plantarum show enhanced resistance to benzalkonium chloride and peracetic acid.</a> International Journal of Food Microbiology. 144 (3), 421-431 (2011).</li><li>Saa Ibusquiza, P., Herrera, J. J., Cabo, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resistance+to+benzalkonium+chloride,+peracetic+acid+and+nisin+during+formation+of+mature+biofilms+by+Listeria+monocytogenes.">Resistance to benzalkonium chloride, peracetic acid and nisin during formation of mature biofilms by Listeria monocytogenes.</a> Food Microbiology. 28 (3), 418-425 (2011).</li><li>Goetz, C., Larouche, J., Velez Aristizabal, M., Niboucha, N., Jean, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficacy+of+organic+peroxyacids+for+eliminating+biofilm+preformed+by+microorganisms+isolated+from+dairy+processing+plants.">Efficacy of organic peroxyacids for eliminating biofilm preformed by microorganisms isolated from dairy processing plants.</a> Applied and Environmental Microbiology. 88 (4), 0188921 (2022).</li><li>Vimont, A., Fliss, I., Jean, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Study+of+the+virucidal+potential+of+organic+peroxyacids+against+norovirus+on+food-contact+surfaces.">Study of the virucidal potential of organic peroxyacids against norovirus on food-contact surfaces.</a> Food and Environmental Virology. 7 (1), 49-57 (2015).</li><li>ASTM E2562-17. Standard Test Method for Quantification of Pseudomonas aeruginosa Biofilm Grown with High Shear and Continuous Flow using CDC Biofilm Reactor. ASTM International Available from: <a target="_blank" href="https://www.astm.org/e2562-17.html">https://www.astm.org/e2562-17.html</a> (2017)</li><li>ASTM E2871-19. Standard Test Method for Evaluating Disinfectant Efficacy Against Pseudomonas aeruginosa Biofilm Grown in CDC Biofilm Reactor Using Single Tube Method. ASTM International Available from: <a target="_blank" href="https://www.astm.org/e2871-19.html">https://www.astm.org/e2871-19.html</a> (2019)</li><li>Niboucha, N., 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=Comparative+study+of+different+sampling+methods+of+biofilm+formed+on+stainless-steel+surfaces+in+a+CDC+biofilm+reactor.">Comparative study of different sampling methods of biofilm formed on stainless-steel surfaces in a CDC biofilm reactor.</a> Frontiers in Microbiology. 13, 892181 (2022).</li><li>ASTM E2799-17. Standard Test Method for Testing Disinfectant Efficacy against Pseudomonas aeruginosa Biofilm using the MBEC Assay. ASTM International Available from: <a target="_blank" href="https://www.astm.org/e2799-17.html">https://www.astm.org/e2799-17.html</a> (2022)</li><li>Parker, A. E., 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=Ruggedness+and+reproducibility+of+the+MBEC+biofilm+disinfectant+efficacy+test.">Ruggedness and reproducibility of the MBEC biofilm disinfectant efficacy test.</a> Journal of Microbiological Methods. 102, 55-64 (2014).</li><li>Stewart, P. S., Parker, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+antimicrobial+efficacy+against+biofilms:+A+meta-analysis.">Measuring antimicrobial efficacy against biofilms: A meta-analysis.</a> Antimicrobial Agents and Chemotherapy. 63 (5), 00020 (2019).</li><li>Lindsay, D. 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M., 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=Statistical+assessment+of+a+laboratory+method+for+growing+biofilms.">Statistical assessment of a laboratory method for growing biofilms.</a> Microbiology (Reading). 151, 757-762 (2005).</li><li>Williams, D. L., Woodbury, K. L., Haymond, B. S., Parker, A. E., Bloebaum, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+modified+CDC+biofilm+reactor+to+produce+mature+biofilms+on+the+surface+of+peek+membranes+for+an+in+vivo+animal+model+application.">A modified CDC biofilm reactor to produce mature biofilms on the surface of peek membranes for an in vivo animal model application.</a> Current Microbiology. 62 (6), 1657-1663 (2011).</li><li>Pieranski, M. K., Rychlowski, M., Grinholc, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+Streptococcus+agalactiae+biofilm+culture+in+a+continuous+flow+system+for+photoinactivation+studies.">Optimization of Streptococcus agalactiae biofilm culture in a continuous flow system for photoinactivation studies.</a> Pathogens. 10 (9), 1212 (2021).</li><li>Mendez, E., Walker, D. K., Vipham, J., Trinetta, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+a+CDC+biofilm+reactor+to+grow+multi-strain+Listeria+monocytogenes+biofilm.">The use of a CDC biofilm reactor to grow multi-strain Listeria monocytogenes biofilm.</a> Food Microbiology. 92, 103592 (2020).</li><li>Salgar-Chaparro, S. J., Lepkova, K., Pojtanabuntoeng, T., Darwin, A., Machuca, L. 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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+formation+during+hexadecane+degradation+and+the+effects+of+flow+field+and+shear+stresses.">Biofilm formation during hexadecane degradation and the effects of flow field and shear stresses.</a> Annual Transactions - The Nordic Rheology Society. 21, 341-346 (2013).</li><li>Gilmore, B. F., Hamill, T. M., Jones, D. S., Gorman, S. 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The authors declare that they have no conflicts of interest.

The MBEC assay (biofilm microplate assay) was the first method to be recognized as a standard biofilm eradication test by the ASTM17. Our study and others have shown that there are two critical steps when using this assay: the sonication step (time and power) and the disinfectant treatment time18. Stewart and Parker also suggested other parameters that could influence the outcome of the assay, such as the microbial species, biofilm age, surface area/volume ratio, etc.<sup c...

The dairy industry is a major industrial sector worldwide, including in Canada, where there are more than 10,500 dairy farms producing nearly 90 million hL of milk each year1. Despite the strict hygiene requirements imposed in the dairy industry, including in processing plants, milk constitutes a great culture medium for microorganisms, and thus, dairy products are likely to contain microorganisms, including spoilage or pathogenic microorganisms. These pathogens can cause various diseases; for example, Salmonella sp. and Listeria monocytogenes can cause gastroenteritis and meningitis, respectively2. Spoilage microorganisms can affect the quality and organoleptic properties of dairy products by producing gases, extracellular enzymes, or acids3. The appearance and color of the milk may also be altered, for example by Pseudomonas spp.4.
Some of these microorganisms can form biofilms on different surfaces, including stainless steel. Such biofilms enable the persistence and multiplication of microorganisms on the surface of the equipment and, thus, the contamination of the dairy products5. Biofilms are also problematic because of their ability to impede heat transfer and accelerate the corrosion of the equipment, leading to premature replacement of the equipment and, thus, to economic losses6.
Clean-in-place (CIP) procedures allow the food industry to control the growth of microorganisms. These procedures involve the sequential use of sodium hydroxide, nitric acid, and, sometimes, sanitizers containing hypochlorous acid and peracetic acid7,8. Although hypochlorous acid is highly effective against microorganisms, it also reacts with natural organic matter, causing the formation of toxic by-products9. Peracetic acid does not generate harmful by-products10; however, its effectiveness against biofilms in the food industry is highly variable10,11. Recently, other peroxyacids, including perpropionic and perlactic acids, have been studied for their antimicrobial activity, and they appear to be a good alternative for the control of microbial growth in biofilms12,13.
Therefore, this study aimed to evaluate the efficacy of organic peroxyacids (peracetic, perpropionic, and perlactic acids and a peracetic acid-based disinfectant) for eradicating dairy biofilms using an approach combining the minimum biofilm eradication concentration (MBEC) assay, a static high-throughput screening method, and the Center for Disease Control (CDC) biofilm reactor, a dynamic method that mimics in situ conditions. The MBEC assay is hereafter referred to as "biofilm microtiter plates" in the protocol. The protocol presented here and the representative results demonstrate the efficacy of organic peroxyacids and their potential application for controlling microbial biofilms in the dairy industry.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >0.2 &#181;m filters&#160;</td>
			<td >Corning</td>
			<td >09-754-28</td>
			<td >diameter: 50 mm, PTFE- Membrane</td>
		</tr>
		<tr >
			<td >316 stainless-steel disc coupon</td>
			<td >Biosurface Technologies Corporation</td>
			<td >RD128-316</td>
			<td></td>
		</tr>
		<tr >
			<td >316 stainless-steel slide coupon</td>
			<td >Biosurface Technologies Corporation</td>
			<td >CBR 2128-316</td>
			<td></td>
		</tr>
		<tr >
			<td >96-microtiter plate</td>
			<td >Corning</td>
			<td >07-200-89</td>
			<td>cell Culture-Treated, flat-Bottom Microplate&#160;</td>
		</tr>
		<tr >
			<td >Acetic acid</td>
			<td >Sigma Aldrich</td>
			<td >27225</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Aluminium stubs</td>
			<td >Electron Microscopy Science</td>
			<td >75830-10</td>
			<td>32x5mm</td>
		</tr>
		<tr >
			<td >Aqueous glutaraldehyde EM Grade 25%</td>
			<td >Electron Microscopy Sciences</td>
			<td >16220</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr >
			<td >AB204-S/FACT Analytical balance</td>
			<td >Mettler Toledo</td>
			<td >AB204-S</td>
			<td></td>
		</tr>
		<tr >
			<td >Bacterial Vent Filter (0.45 &#181;m)</td>
			<td >Biosurface Technologies Corporation</td>
			<td >BST 02915</td>
			<td></td>
		</tr>
		<tr >
			<td >BioDestroy</td>
			<td >Groupe Sani Marc</td>
			<td >09-10215</td>
			<td>commercial peracetic acid-based disinfectant, store at RT</td>
		</tr>
		<tr >
			<td >Carboy LDPE 20 L</td>
			<td >Cole Parmer</td>
			<td >06031-52</td>
			<td></td>
		</tr>
		<tr >
			<td >CDC biofilm reactor</td>
			<td >Biosurface Technologies Corporation</td>
			<td >CRB 90</td>
			<td>bioreactor</td>
		</tr>
		<tr >
			<td >Cerium (IV) sulphate</td>
			<td >Thermo Scientific</td>
			<td >35650-K2</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Confocal laser scanning microscope&#160; LSM 700</td>
			<td >Zeiss</td>
			<td >LSM 700</td>
			<td></td>
		</tr>
		<tr >
			<td >Dey-Engley neutralizing broth</td>
			<td >Millipore</td>
			<td >D3435-500G</td>
			<td>store at 4 &#176;C</td>
		</tr>
		<tr >
			<td >EMS950x + 350s gold sputter&#160;</td>
			<td >Electron Microscopy Sciences</td>
			<td ></td>
			<td></td>
		</tr>
		<tr >
			<td >Epoxy resin</td>
			<td >Electron Microscopy Sciences</td>
			<td >14121</td>
			<td>with BDMA</td>
		</tr>
		<tr >
			<td >Ethyl alcohol 95%, USP</td>
			<td >Greenfield global</td>
			<td >P016EA95</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Ferroin indicator solution</td>
			<td >Sigma Aldrich</td>
			<td >318922-100ML</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Filling/venting cap</td>
			<td >Cole Parmer</td>
			<td >RK-06258-00</td>
			<td></td>
		</tr>
		<tr >
			<td >FilmTracer LIVE/DEAD Biofilm Viability Kit</td>
			<td >Invitrogen</td>
			<td >L10316</td>
			<td >fluorescent cell viability kit (SYTO 9: green fluorescent stain, Propidium iodide: red fluorescent stain), store at - 20 &#176;C</td>
		</tr>
		<tr >
			<td >Glass flow break</td>
			<td >Biosurface Technologies Corporation</td>
			<td >FB 50</td>
			<td></td>
		</tr>
		<tr >
			<td >Gold with silver paint&#160;</td>
			<td >Electron Microscopy Sciences</td>
			<td >12684-15</td>
			<td></td>
		</tr>
		<tr >
			<td >Heating plate set</td>
			<td >Biosurface Technologies Corporation</td>
			<td >110V Stir Plate</td>
			<td></td>
		</tr>
		<tr >
			<td >Hex screwdriver</td>
			<td >Biosurface Technologies Corporation</td>
			<td >CBR 5497</td>
			<td></td>
		</tr>
		<tr >
			<td >Hydrogen peroxide</td>
			<td >Sigma</td>
			<td >216763</td>
			<td>store at 4 &#176;C</td>
		</tr>
		<tr >
			<td >Inoculating loops</td>
			<td >VWR</td>
			<td >12000-812</td>
			<td>sterile, 10 &#181;l</td>
		</tr>
		<tr >
			<td >Lactic acid</td>
			<td >Laboratoire MAT</td>
			<td >LU-0200</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >MASTERFLEX L/S 7557-04 W/ 7557-02 with EASY-LOAD II peristaltic pump and 77200-50 Head</td>
			<td >Cole Parmer</td>
			<td >77200-60</td>
			<td></td>
		</tr>
		<tr >
			<td >MBEC (Minimum Biofilm Eradication Concentration) assay biofilm inoculator with a 96-well base</td>
			<td >Innovotech</td>
			<td >19111</td>
			<td>Biofilm microtiter plate</td>
		</tr>
		<tr >
			<td >Oxford agar base</td>
			<td >Thermo Scientific</td>
			<td >OXCM0856B</td>
			<td>store at 4 &#176;C</td>
		</tr>
		<tr >
			<td >Plastic coupon holder</td>
			<td >Biosurface Technologies Corporation</td>
			<td >CBR 2203</td>
			<td></td>
		</tr>
		<tr >
			<td >Plastic slide holder rod</td>
			<td >Biosurface Technologies Corporation</td>
			<td >CBR 2203-GL</td>
			<td></td>
		</tr>
		<tr >
			<td >Potassium iodide</td>
			<td >Fisher Chemical</td>
			<td >P410-500</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Precision slotted screwdriver (1.5 mm x 40 mm)</td>
			<td >Wiha</td>
			<td >26015</td>
			<td></td>
		</tr>
		<tr >
			<td >Propionic acid</td>
			<td >Laboratoire MAT</td>
			<td >PF-0221</td>
			<td>store at RT</td>
		</tr>
		<tr >
			<td >Sartorius BCE822-1S Entris&#174; II Basic Essential Toploading Balance</td>
			<td >Cole Parmer</td>
			<td>&#160;UZ-11976-3</td>
			<td></td>
		</tr>
		<tr >
			<td >Scanning electron microscope JSM-6360LV model</td>
			<td >JEOL</td>
			<td >JSM-6360LV</td>
			<td>SEM and user control interface</td>
		</tr>
		<tr >
			<td >Screw cap tube, 15 mL</td>
			<td >Sarstedt</td>
			<td >62.554.205</td>
			<td>(Lx&#216;): 120 x 17 mm, material: PP, conical base, transparent, HD-PE</td>
		</tr>
		<tr >
			<td >Screw cap tube, 50 mL</td>
			<td >Sarstedt</td>
			<td >62.547.205</td>
			<td>(Lx&#216;): 114 x 28 mm, material: PP, conical base, transparent, HD-PE</td>
		</tr>
		<tr >
			<td >Sodium Cacodylate Trihydrate</td>
			<td >Electron Microscopy Sciences</td>
			<td>&#160;12300</td>
			<td>store at -20 &#176;C</td>
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			<td >Tubing Masterflex L/S 18 25&#39;</td>
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			<td >Tygon SPT-3350 silicon tubing&#160;</td>
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			<td>IDx OD: 1/4 in.x 7/16 in.</td>
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			<td >Zen software</td>
			<td >Zeiss</td>
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evaluation of the efficacy of organic peroxyacids for eradicating dairy biofilms using an approach combining static and dynamic methods

The presence of biofilms in the dairy industry is of major concern, as they may lead to the production of unsafe and altered dairy products due to their high resistance to most clean-in-place (CIP) procedures frequently used in processing plants. Therefore, it is imperative to develop new biofilm control strategies for the dairy industry. This protocol is aimed at evaluating the efficacy of organic peroxyacids (peracetic, perpropionic, and perlactic acids and a commercial peracetic acid-based disinfectant) for eradicating dairy biofilms using a combination of static and dynamic methods. All the disinfectants were tested on the strongest biofilm-producing bacteria in either a single or a mixed biofilm using the minimum biofilm eradication concentration (MBEC) assay, a static high-throughput screening method. A contact time of 5 min with the disinfectants at the recommended concentrations successfully eradicated both the single and mixed biofilms. Studies are currently ongoing to confirm these observations using the Center for Disease Control (CDC) biofilm reactor, a dynamic method to mimic in situ conditions. This type of bioreactor enables the use of a stainless-steel surface, which constitutes most industrial equipment and surfaces. The preliminary results from the reactor appear to confirm the efficacy of organic peroxyacids against biofilms. The combined approach described in this study may be used to develop and test new biological or chemical formulations for controlling biofilms and eradicating microorganisms.

The SEM analysis shows the presence of biofilms produced by P. azotoformans PFl1A on the biofilm microplate pegs (Figure 2A). A three-dimensional biofilm structure can be observed. The P. azotoformans PFl1A was previously identified as a strong biofilm producer (A570 &#62; 1.5) using 96-well microtiter plates12.
In addition, the P. azotoformans PFl1A biofilm that formed on a stainless-steel slide using ...

Watch this Scientific Journal Video about Evaluation of the Efficacy of Organic Peroxyacids for Eradicating Dairy Biofilms Using an Approach Combining Static and Dynamic Methods at JoVE.com

Evaluation of the Efficacy of Organic Peroxyacids for Eradicating Dairy Biofilms Using an Approach Combining Static and Dynamic Methods

This protocol describes an approach combining static and dynamic methods to evaluate the efficacy of organic peroxyacids for eradicating biofilms in the dairy industry. This approach may also be used to test the effectiveness of new biological or chemical formulations for controlling biofilms.

The presence of biofilms in the dairy industry is of major concern, as they may lead to the production of unsafe and altered dairy products due to their ...

evaluation-efficacy-organic-peroxyacids-for-eradicating-dairy

Research

JoVE Journal

Biology

1.5K Views.  Université Laval. This protocol describes an approach combining static and dynamic methods to evaluate the efficacy of organic peroxyacids for eradicating biofilms in the dairy industry. This approach may also be used to test the effectiveness of new biological or chemical formulations for controlling biofilms.

Video: Evaluation of the Efficacy of Organic Peroxyacids for Eradicating Dairy Biofilms Using an Approach Combining Static and Dynamic Methods

Application of Light-cured Dental Adhesive Resin for Mounting Electrodes or Microdialysis Probes in Chronic Experiments

In chronic recording experiments, self-curing dental acrylic resins have been used as a mounting base of electrodes or microdialysis-probes. Since these acrylics do not bond to the bone, screws have been used as anchors. However, in small experimental animals like finches or mouse, their craniums are very fragile and can not successfully hold the anchors. In this report, we propose a new application of light-curing dental resins for mounting base of electrodes or microdialysis probes in chronic experiments. This material allows direct bonding to the cranium. Therefore, anchor screws are not required and surgical field can be reduced considerably. Past experiences show that the bonding effect maintains more than 2 months. Conventional resin's window of time when the materials are pliable and workable is a few minutes. However, the window of working time for these dental adhesives is significantly wider and adjustable.

In this report, we propose a new application of light-curing dental resins for mounting base of electrodes or microdialysis probes in chronic experiments. This material allows direct bonding to the cranium.

In chronic recording experiments, self-curing dental acrylic resins have been used as a mounting base of electrodes or microdialysis-probes. Since these ...

Robotics and Dynamic Image Analysis for Studies of Gene Expression in Plant Tissues

Gene expression in plant tissues is typically studied by destructive extraction of compounds from plant tissues for in vitro analyses. The methods presented here utilize the green fluorescent protein (gfp) gene for continual monitoring of gene expression in the same pieces of tissues, over time. The gfp gene was placed under regulatory control of different promoters and introduced into lima bean cotyledonary tissues via particle bombardment. Cotyledons were then placed on a robotic image collection system, which consisted of a fluorescence dissecting microscope with a digital camera and a 2-dimensional robotics platform custom-designed to allow secure attachment of culture dishes. Images were collected from cotyledonary tissues every hour for 100 hours to generate expression profiles for each promoter. Each collected series of 100 images was first subjected to manual image alignment using ImageReady to make certain that GFP-expressing foci were consistently retained within selected fields of analysis. Specific regions of the series measuring 300 x 400 pixels, were then selected for further analysis to provide GFP Intensity measurements using ImageJ software. Batch images were separated into the red, green and blue channels and GFP-expressing areas were identified using the threshold feature of ImageJ. After subtracting the background fluorescence (subtraction of gray values of non-expressing pixels from every pixel) in the respective red and green channels, GFP intensity was calculated by multiplying the mean grayscale value per pixel by the total number of GFP-expressing pixels in each channel, and then adding those values for both the red and green channels. GFP Intensity values were collected for all 100 time points to yield expression profiles. Variations in GFP expression profiles resulted from differences in factors such as promoter strength, presence of a silencing suppressor, or nature of the promoter. In addition to quantification of GFP intensity, the image series were also used to generate time-lapse animations using ImageReady. Time-lapse animations revealed that the clear majority of cells displayed a relatively rapid increase in GFP expression, followed by a slow decline. Some cells occasionally displayed a sudden loss of fluorescence, which may be associated with rapid cell death. Apparent transport of GFP across the membrane and cell wall to adjacent cells was also observed. Time lapse animations provided additional information that could not otherwise be obtained using GFP Intensity profiles or single time point image collections.

We report a method for introduction, tracking and quantitative analysis of GFP expression in plant cells. This method utilizes a custom-designed robotics system for semi-continuous image collection from large numbers of samples, over time. We also demonstrate the use of ImageJ and ImageReady for analysis of image series.

Gene expression in plant tissues is typically studied by destructive extraction of compounds from plant tissues for in vitro analyses. The methods ...

A Chemical Screening Procedure for Glucocorticoid Signaling with a Zebrafish Larva Luciferase Reporter System

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids can lead to severe side effects. Test systems are needed to search for novel compounds influencing glucocorticoid signaling in vivo or to determine unwanted effects of compounds on the glucocorticoid signaling pathway. We have established a transgenic zebrafish assay which allows the measurement of glucocorticoid signaling activity in vivo and in real-time, the GRIZLY assay (Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY). The luciferase-based assay detects effects on glucocorticoid signaling with high sensitivity and specificity, including effects by compounds that require metabolization or affect endogenous glucocorticoid production. We present here a detailed protocol for conducting chemical screens with this assay. We describe data acquisition, normalization, and analysis, placing a focus on quality control and data visualization. The assay provides a simple, time-resolved, and quantitative readout. It can be operated as a stand-alone platform, but is also easily integrated into high-throughput screening workflows. It furthermore allows for many applications beyond chemical screening, such as environmental monitoring of endocrine disruptors or stress research.

We describe the procedure and data analysis of a chemical screening system for glucocorticoid stress hormone signaling using zebrafish larvae: the Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY (GRIZLY) assay. The assay sensitively and specifically detects effects on glucocorticoid signaling by compounds that require metabolization or affect endogenous glucocorticoid production.

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method offers the opportunity of investigating interactions occurring in solution (thus avoiding problems due to closeby surfaces as in other single molecule methods), controlling the DNA extension and tracking interaction dynamics as a function of both mechanical parameters and DNA sequence. The methods for establishing successful optical trapping and nanometer localization of single molecules are illustrated. We illustrate the experimental conditions allowing the study of interaction of lactose repressor (lacI), labeled with Atto532, with a DNA molecule containing specific target sequences (operators) for LacI binding. The method allows the observation of specific interactions at the operators, as well as one-dimensional diffusion of the protein during the process of target search. The method is broadly applicable to the study of protein-DNA interactions but also to molecular motors, where control of the tension applied to the partner track polymer (for example actin or microtubules) is desirable.

Here we describe the instrumentation and methods for detecting single fluorescently-labeled protein molecules interacting with a single DNA molecule suspended between two optically trapped microspheres.

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase synthesis using standard phosphoramidite chemistry. Oligonucleotides are post-synthetically labeled by two new photostable cyanine dyes using copper-catalyzed click-chemistry. The synthesis of both donor and acceptor dye is described and is performed in three consecutive steps. With the DNA as the surrounding architecture, these two dyes undergo an energy transfer when they are brought into close proximity by hybridization. Therefore, annealing of two single stranded DNA strands is visualized by a change of fluorescence color. This color change is characterized by fluorescence spectroscopy but can also be directly observed by using a handheld ultraviolet (UV) lamp. The concept of a dual fluorescence color readout makes these oligonucleotide probes excellent tools for molecular imaging especially when the described photostable dyes are used. Thereby, photobleaching of the imaging probes is prevented, and biological processes can be observed in real time for a longer time period.

Photostable cyanine dyes are attached to oligonucleotides to monitor hybridization by energy transfer.

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase ...

Methods for the Extraction of Endosymbionts from the Whitefly Bemisia tabaci

Bacterial symbionts form an intimate relationship with their hosts and confer advantages to the hosts in most cases. Genomic information is critical to study the functions and evolution of bacterial symbionts in their host. As most symbionts cannot be cultured in vitro, methods to isolate an adequate quantity of bacteria for genome sequencing are very important. In the whitefly Bemisia tabaci, a number of endosymbionts have been identified and are predicted to be of importance in the development and reproduction of the pests through multiple approaches. However, the mechanism underpinning the associations remains largely unknown. The obstacle partially comes from the fact that the endosymbionts in whitefly, mostly restrained in bacteriocytes, are hard to separate from the host cells. Here we report a step-by-step protocol for the identification, extraction and purification of endosymbionts from the whitefly B. tabaci mainly by dissection and filtration. Endosymbiont samples prepared by this method, although still a mixture of different endosymbiont species, are suitable for subsequent genome sequencing and analysis of the possible roles of endosymbionts in B. tabaci. This method may also be used to isolate endosymbionts from other insects.

Methods for the Extraction of Endosymbionts from the Whitefly Bemisia tabaci

Here, we present a protocol to isolate endosymbionts from the whitefly Bemisia tabaci through dissection and filtration. After amplification, the DNA samples are suitable for subsequent sequencing and study of the mutualism between endosymbionts and whitefly.

Bacterial symbionts form an intimate relationship with their hosts and confer advantages to the hosts in most cases. Genomic information is critical to ...

Methods for Staging Pupal Periods and Measurement of Wing Pigmentation of Drosophila guttifera

Diversified species of Drosophila (fruit fly) provide opportunities to study mechanisms of development and genetic changes responsible for evolutionary changes. In particular, the adult stage is a rich source of morphological traits for interspecific comparison, including wing pigmentation comparison. To study developmental differences among species, detailed observation and appropriate staging are required for precise comparison. Here we describe protocols for staging of pupal periods and quantification of wing pigmentation in a polka-dotted fruit fly, Drosophila guttifera. First, we describe the method for detailed morphological observation and definition of pupal stages based on morphologies. This method includes a technique for removing the puparium, which is the outer chitinous case of the pupa, to enable detailed observation of pupal morphologies. Second, we describe the method for measuring the duration of defined pupal stages. Finally, we describe the method for quantification of wing pigmentation based on image analysis using digital images and ImageJ software. With these methods, we can establish a solid basis for comparing developmental processes of adult traits during pupal stages.

Methods for Staging Pupal Periods and Measurement of Wing Pigmentation of Drosophila guttifera

Protocols for staging pupal periods and measurement of wing pigmentation of Drosophila guttifera are described. Staging and quantification of pigmentation provide a solid basis for studying developmental mechanisms of adult traits and enable interspecific comparison of trait development.

Diversified species of Drosophila (fruit fly) provide opportunities to study mechanisms of development and genetic changes responsible for evolutionary ...

Visualization of 3D White Adipose Tissue Structure Using Whole-mount Staining

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various techniques have been developed to study the morphology and biology of adipose tissue. However, conventional visualization methods are limited to studying the tissue in 2D sections, failing to capture the 3D architecture of the whole organ. Here we present whole-mount staining, an immunohistochemistry method that preserves intact adipose tissue morphology with minimal processing steps. Hence, the structures of adipocytes and other cellular components are maintained without distortion, achieving the most representative 3D visualization of the tissue. In addition, whole-mount staining can be combined with lineage tracing methods to determine cell fate decisions. However, this technique has some limitations to providing accurate information regarding deeper parts of adipose tissue. To overcome this limitation, whole-mount staining can be further combined with tissue clearing techniques to remove the opaqueness of tissue and allow for complete visualization of entire adipose tissue anatomy using light-sheet fluorescent microscopy. Therefore, a higher resolution and more accurate representation of adipose tissue structures can be captured with the combination of these techniques.

The focus of the present study is to demonstrate the whole-mount immunostaining and visualization technique as an ideal method for 3D imaging of adipose tissue architecture and cellular component.

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various ...

Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach

Here, we developed an individual-tree model of 5-year basal area increments based on a dataset including 21898 Picea asperata trees from 779 sample plots located in Xinjiang Province, northwest China. To prevent high correlations among observations from the same sampling unit, we developed the model using a linear mixed-effects approach with random plot effect to account for stochastic variability. Various tree- and stand-level variables, such as indices for tree size, competition, and site condition, were included as fixed effects to explain the residual variability. In addition, heteroscedasticity and autocorrelation were described by introducing variance functions and autocorrelation structures. The optimal linear mixed-effects model was determined by several fit statistics: Akaike&#8217;s information criterion, Bayesian information criterion, logarithm likelihood, and a likelihood ratio test. The results indicated that significant variables of individual-tree basal area increment were the inverse transformation of diameter at breast height, the basal area of trees larger than the subject tree, the number of trees per hectare, and elevation. Furthermore, errors in variance structure were most successfully modeled by the exponential function, and the autocorrelation was significantly corrected by first-order autoregressive structure (AR(1)). The performance of the linear mixed-effects model was significantly improved relative to the model using ordinary least squares regression.

Mixed-effects models are flexible and useful tools for analyzing data with a hierarchical stochastic structure in forestry and could also be used to significantly improve the performance of forest growth models. Here, a protocol is presented that synthesizes information relating to linear mixed-effects models.

Here, we developed an individual-tree model of 5-year basal area increments based on a dataset including 21898 Picea asperata trees from 779 sample plots ...

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization

Traditionally used for bulk biochemical assays, Xenopus laevis egg extracts have emerged as a powerful imaging-based tool for studying cytoplasmic phenomena, such as cytokinesis, mitotic spindle formation and assembly of the nucleus. Building upon early methods that imaged fixed extracts sampled at sparse time points, recent approaches image live extracts using time-lapse microscopy, revealing more dynamical features with enhanced temporal resolution. These methods usually require sophisticated surface treatments of the imaging vessel. Here we introduce an alternative method for live imaging of egg extracts that require no chemical surface treatment. It is simple to implement and utilizes mass-produced laboratory consumables for imaging. We describe a system that can be used for both wide-field and confocal microscopy. It is designed for imaging extracts in a 2-dimensional (2D) field, but can be easily extended to imaging in 3D. It is well-suited for studying spatial pattern formation within the cytoplasm. With representative data, we demonstrate the typical dynamic organization of microtubules, nuclei and mitochondria in interphase extracts prepared using this method. These image data can provide quantitative information on cytoplasmic dynamics and spatial organization.

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization

We describe a method for the preparation and live imaging of undiluted cytoplasmic extracts from Xenopus laevis eggs.