Name: broth microdilution in vitro screening: an easy and fast method to detect new antifungal compounds
Uploaded: 2018-02-14T15:00:00
Description: Watch this Scientific Journal Video about Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds at JoVE.com

We thank CAPES-Brazil, CNPq-Brazil, FAP/DF for financial support. We are grateful to Dr. Hugo Costa Paes for revising the manuscript.

1. Solutions and Media
<ol>
	<li>Prepare 2X Roswell Park Memorial Institute (RPMI) 1640 medium, phosphate buffered saline (PBS), Sabouraud dextrose broth, and Sabouraud dextrose agar as per Table 1.</li>
</ol>
2. Fungal Inoculum Growth Conditions
<ol>
	<li>Store all fungal strains as frozen stocks in 35% glycerol at -80 &#176;C, until needed.</li>
	<li>Perform the following steps before each experiment.
	<ol>
		<li>For Candida albicans strains:
		<ol>
			<li>Thaw a st...

<ol>
	<li>Armstrong-James, D., Meintjes, G., Brown, G. 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+neglected+epidemic:+fungal+infections+in+HIV/AIDS.">A neglected epidemic: fungal infections in HIV/AIDS.</a> Trends Microbiol. 22 (3), 120-127 (2014).</li><li>Romani, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunity+to+fungal+infections.">Immunity to fungal infections.</a> Nat Rev Immunol. 11 (4), 275-288 (2011).</li><li>Pfaller, 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=Antifungal+drug+resistance:+mechanisms,+epidemiology,+and+consequences+for+treatment.">Antifungal drug resistance: mechanisms, epidemiology, and consequences for treatment.</a> Am J Med. 125 (1 Suppl), S3-S13 (2012).</li><li>Hancock, R. E., Diamond, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+cationic+antimicrobial+peptides+in+innate+host+defences.">The role of cationic antimicrobial peptides in innate host defences.</a> Trends Microbiol. 8 (9), 402-410 (2000).</li><li>Wang, Y., 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=Snake+cathelicidin+from+Bungarus+fasciatus+is+a+potent+peptide+antibiotics.">Snake cathelicidin from Bungarus fasciatus is a potent peptide antibiotics.</a> PLoS One. 3 (9), e3217 (2008).</li><li>Du, Q., 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=AaeAP1+and+AaeAP2:+novel+antimicrobial+peptides+from+the+venom+of+the+scorpion,+Androctonus+aeneas:+structural+characterisation,+molecular+cloning+of+biosynthetic+precursor-encoding+cDNAs+and+engineering+of+analogues+with+enhanced+antimicrobial+and+anticancer+activities.">AaeAP1 and AaeAP2: novel antimicrobial peptides from the venom of the scorpion, Androctonus aeneas: structural characterisation, molecular cloning of biosynthetic precursor-encoding cDNAs and engineering of analogues with enhanced antimicrobial and anticancer activities.</a> Toxins (Basel). 7 (2), 219-237 (2015).</li><li>Benincasa, 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=Fungicidal+activity+of+five+cathelicidin+peptides+against+clinically+isolated+yeasts.">Fungicidal activity of five cathelicidin peptides against clinically isolated yeasts.</a> J Antimicrob Chemother. 58 (5), 950-959 (2006).</li><li>CLSI. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Reference Method for Broth Dilution Antifungal Susceptibiliy Testing of Yeasts; Approved Standard -Third Edition. CLSI document M27-A3. , (2008).</li><li>Guilhelmelli, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity+of+Scorpion+Venom-Derived+Antifungal+Peptides+against+Planktonic+Cells+of+Candida+spp.+and+Cryptococcus+neoformans+and+Candida+albicans+Biofilms.">Activity of Scorpion Venom-Derived Antifungal Peptides against Planktonic Cells of Candida spp. and Cryptococcus neoformans and Candida albicans Biofilms.</a> Front Microbiol. 7, 1844 (2016).</li><li>Roongruangsree, U. T., Kjerulf-Jensen, C., Olson, L. W., Lange, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Viability+Tests+for+Thick+Walled+Fungal+Spores+(ex:+Oospores+of+Peronospora+manshurica).">Viability Tests for Thick Walled Fungal Spores (ex: Oospores of Peronospora manshurica).</a> Journal of Phytopathology. 123 (3), 244-252 (1988).</li><li>Boedijn, K. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trypan+blue+as+stain+for+fungi.">Trypan blue as stain for fungi.</a> Stain Technol. 31 (3), 115-116 (1956).</li><li>Goihman-Yahr, 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=Studies+on+plating+efficiency+and+estimation+of+viability+of+suspensions+of+Paracoccidioides+brasiliensis+yeast+cells.">Studies on plating efficiency and estimation of viability of suspensions of Paracoccidioides brasiliensis yeast cells.</a> Mycopathologia. 71 (2), 73-83 (1980).</li><li>Tati, 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=Histatin+5-spermidine+conjugates+have+enhanced+fungicidal+activity+and+efficacy+as+a+topical+therapeutic+for+oral+candidiasis.">Histatin 5-spermidine conjugates have enhanced fungicidal activity and efficacy as a topical therapeutic for oral candidiasis.</a> Antimicrob Agents Chemother. 58 (2), 756-766 (2014).</li><li>Petrou, M. A., Shanson, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Susceptibility+of+Cryptococcus+neoformans+by+the+NCCLS+microdilution+and+Etest+methods+using+five+defined+media.">Susceptibility of Cryptococcus neoformans by the NCCLS microdilution and Etest methods using five defined media.</a> J Antimicrob Chemother. 46 (5), 815-818 (2000).</li><li>Zaragoza, 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=Process+analysis+of+variables+for+standardization+of+antifungal+susceptibility+testing+of+nonfermentative+yeasts.">Process analysis of variables for standardization of antifungal susceptibility testing of nonfermentative yeasts.</a> Antimicrob Agents Chemother. 55 (4), 1563-1570 (2011).</li><li>Rodriguez-Tudela, J. L., 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=Influence+of+shaking+on+antifungal+susceptibility+testing+of+Cryptococcus+neoformans:+a+comparison+of+the+NCCLS+standard+M27A+medium,+buffered+yeast+nitrogen+base,+and+RPMI-2%+glucose.">Influence of shaking on antifungal susceptibility testing of Cryptococcus neoformans: a comparison of the NCCLS standard M27A medium, buffered yeast nitrogen base, and RPMI-2% glucose.</a> Antimicrob Agents Chemother. 44 (2), 400-404 (2000).</li><li>Beggs, W. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+phase+in+relation+to+ketoconazole+and+miconazole+susceptibilities+of+Candida+albicans.">Growth phase in relation to ketoconazole and miconazole susceptibilities of Candida albicans.</a> Antimicrob Agents Chemother. 25 (3), 316-318 (1984).</li><li>Alcouloumre, M. S., Ghannoum, M. A., Ibrahim, A. S., Selsted, M. E., Edwards, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fungicidal+properties+of+defensin+NP-1+and+activity+against+Cryptococcus+neoformans+in+vitro.">Fungicidal properties of defensin NP-1 and activity against Cryptococcus neoformans in vitro.</a> Antimicrob Agents Chemother. 37 (12), 2628-2632 (1993).</li></ol>

Microdilution tests can analyze the potential antifungal activity of a target compound using small quantities of the compound, and at the same time test it in a range of concentrations. Accordingly, this protocol is recommended as a first step in screening for potential new antifungal compounds. The protocol presented here is based on the M27-A3 protocol, initially designed to aid in the selection of antifungal therapy in clinics, and can be adapted to a variety of new antifungal compounds. Overall, this protocol can foc...

Fungal infections have become an important medical concern in recent decades, having considerably increased mainly due to a rise in the number of immunocompromised individuals such as those undergoing cancer treatment and those living with HIV/AIDS or transplanted organs1,2. However, a very limited array of available antifungal drugs and the increasing number of reports on fungal resistance to them contribute to the major problems regarding the therapeutics of systemic mycoses3.
A potential source of new antifungal compounds are antimicrobial peptides (AMPs), small cationic peptides produced by many organisms as part of their innate immune response to infection4. Nevertheless, the screening method to test these compounds against fungal pathogens is not standardized. Different procedures have been used to assess the antifungal activity of AMPs, sometimes for the same model microorganism5,6,7. These differences and the lack of detail in some protocols complicate comparisons between compounds and hampers reproducibility.
One way to standardize the testing of new drug candidates is to follow guidelines used to define antifungal susceptibility in clinical settings, such as the Clinical and Laboratory Standards Institute (CLSI) M27-A3 guidelines. However, these antifungal sensitivity tests are too restrictive, and do not take into consideration variation in metabolism across species, as they were only established for a few select agents. For example, they do not take into account the metabolic needs of non-fermenting yeasts.
This protocol allows the assessment of activity of prospective antifungal compounds, and is implemented here for the search for antifungal peptides. It is based on the broth microdilution susceptibility test from the CLSI M27-A3 guidelines with modifications that optimize the screening of new compounds8,9. These changes allow for the use of small amounts of compound, variations in temperature or initial inoculum, and different media for optimal pre-test growth, while standardizing the results with the use of reference antifungals as controls. This method, with the use of multi-well culture plates, makes it possible to quickly and reliably screen a large number of compounds.
Due to its inherent flexibility, this protocol can be used with different chemical classes of compounds and against other microorganisms, with few adaptations.

<table>
	<tbody>
		<tr>
			<td>Media and Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI 1640 medium with l-glutamine, without sodium bicarbonate</td>
			<td>Thermo Fisher</td>
			<td>31800-022</td>
			<td></td>
		</tr>
		<tr>
			<td>3-(N-morpholino) propane sulfonic acid (MOPS) (o que a gente usa tem um s&#243;dio, completa o nome dele please)</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td>Use to buffer 2X RPMI medium</td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl)</td>
			<td>Din&#226;mica</td>
			<td>1528-1</td>
			<td>137 mM for Phosphate buffered saline (PBS)</td>
		</tr>
		<tr>
			<td>Potassium chloride (KCl)</td>
			<td>J.T.Baker</td>
			<td>3040-01</td>
			<td>2.7 mM for Phosphate buffered saline (PBS)</td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic (Na2HPO4)</td>
			<td>Sigma-Aldrich</td>
			<td>V000129</td>
			<td>10 mM for Phosphate buffered saline (PBS)</td>
		</tr>
		<tr>
			<td>Potassium dihydrogen phosphate (KH2PO4)</td>
			<td>Sigma-Aldrich</td>
			<td>60230</td>
			<td>2 mM for Phosphate buffered saline (PBS)</td>
		</tr>
		<tr>
			<td>BD Difco Sabouraud dextrose broth</td>
			<td>BD</td>
			<td>238230</td>
			<td></td>
		</tr>
		<tr>
			<td>BD Difco Sabouraud Dextrose Agar</td>
			<td>BD</td>
			<td>210950</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma-Aldrich</td>
			<td>V000123</td>
			<td>35% for (solu&#231;&#227;o de estoque? Criopreserva&#231;&#227;o?)</td>
		</tr>
		<tr>
			<td>Sterile water</td>
			<td></td>
			<td></td>
			<td>Para dilui&#231;&#227;o das drogas na dilui&#231;&#227;o seriada</td>
		</tr>
		<tr>
			<td>Antifungal drugs</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Amphotericin B</td>
			<td>Sigma-Aldrich</td>
			<td>A2942</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluconazole</td>
			<td>Sigma-Aldrich</td>
			<td>F8929</td>
			<td></td>
		</tr>
		<tr>
			<td>Caspofungin</td>
			<td>Sigma-Aldrich</td>
			<td>PHR1160</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastics</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL conical tube</td>
			<td>Sarstedt</td>
			<td>62.547.254</td>
			<td></td>
		</tr>
		<tr>
			<td>Dish petri</td>
			<td>J.Prolab</td>
			<td>0304-5</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well plate</td>
			<td>Corning</td>
			<td>3595</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile Solution Reservoir</td>
			<td>KASVI</td>
			<td>K30-208</td>
			<td>Use to pippet the solutions using the multichannel pippet</td>
		</tr>
		<tr>
			<td>Equipment and other materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Optical microscope</td>
			<td>Nikon</td>
			<td>E200MV</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifugue</td>
			<td>Thermo Fisher</td>
			<td>MegaFuge 16R</td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator</td>
			<td>Ethik Technology</td>
			<td>403-3D</td>
			<td>Set to 37&#176; C</td>
		</tr>
		<tr>
			<td>Shaker</td>
			<td>New Brunswick Scientific</td>
			<td>Excella E25</td>
			<td>Set to 37&#176; C, 200 RPM</td>
		</tr>
		<tr>
			<td>Cell counting chamber, Neubauer</td>
			<td>BOECO Germany</td>
			<td>BOE 13</td>
			<td></td>
		</tr>
		<tr>
			<td>Multichannel pipette</td>
			<td>HTL</td>
			<td>5123</td>
			<td></td>
		</tr>
	</tbody>
</table>

broth microdilution in vitro screening: an easy and fast method to detect new antifungal compounds

Fungal infections have become an important medical condition in the last decades, but the number of available antifungal drugs is limited. In this scenario, the search for new antifungal drugs is necessary. The protocol reported here details a method to screen peptides for their antifungal properties. It is based on the broth microdilution susceptibility test from the Clinical and Laboratory Standards Institute (CLSI) M27-A3 guidelines with modifications to suit the research of antimicrobial peptides as potential new antifungals. This protocol describes a functional assay to evaluate the activity of antifungal compounds and may be easily modified to suit any particular class of molecules under investigation. Since the assays are performed in 96-well plates using small volumes, a large-scale screening can be completed in a short amount of time, especially if carried out in an automation setting. This procedure illustrates how a standardized and adjustable clinical protocol can help the bench-work pursuit of new molecules to improve the therapy of fungal diseases.

The MIC is defined as the lowest antimicrobial compound concentration that completely inhibits visible fungal growth at the end of the incubation period. Since the objective of this protocol is to have a fast method to screen potential antifungals, any well with clear media similar to the blank wells is considered a positive result, whereas any well with turbidity analogous to the negative/growth control wells is considered negative. However, if there is an interest in knowing whether a g...

Watch this Scientific Journal Video about Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds at JoVE.com

Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds

An easy and adaptable broth microdilution method for screening antifungal compounds and extracts.

Broth Microdilution In Vitro Screening: An Easy and Fast Method to Detect New Antifungal Compounds

Fungal infections have become an important medical condition in the last decades, but the number of available antifungal drugs is limited. In this ...

The overall goal of this method is to evaluate the activity of potential antifungal compounds, using a modification of the broth microdilution susceptibility test, used in clinical laboratories. This method is used to evaluate the fungal activity of natural or synthetic compounds, one of the first tests in the development of anti fungal therapies. We provide instructions for an initial screen for new antifungals using small volumes in a short time, especially, if the experiments are carried out with automation.Demonstrating the procedure will be Daniel Zamith-Miranda, a post doctoral fellow in my laboratory. Begin this procedure by growing the fungal strains for the assay as described in the text protocol. On the following day, collect the cells by centrifuging the conical tubes at 1200 G, for five minutes at room temperature.Discard the supernatant, add ten milliliters of PBS to each tube, and resuspend the cells. Centrifuge again at 1200 G for five minutes at room temperature. Repeat the PBS wash and centrifugation two more times.After the third wash, resuspend the cells in five milliliters of double strength RPMI 1640 medium. Depending on the turbidity of the cell suspension, prepare one milliliter of a one to 100, or one to 1000, dilution of each strain, in a microcentrifuge tube. Aliquat ten microliters of this dilution, place it in a hemocytometer chamber, and count the total number of cells in the four corner quadrants under the microscope.After calculating the density of each cell suspension, prepare stock cell suspensions in double strength RPMI 1640 medium. Prepare 4, 000 cells per milliliter for C.albicans strains, and 20, 000 cells per milliliter for C.neoformans strains. The lypholized peptides are stored in aliquats for one time use at minus 20 degrees Celsius, and only dissolved in deionized water before each experiment.The peptide concentration should be twice the highest final concentration tested in the assay. Reference antifungals are also prepared. The antifungal assay is performed in triplicate and 96 well polystyrene microplates.Using a two fold serial dilution of each peptide and control antifungal, and a final volume of 50 microliters per well. The most crucial step in the protocol is the serial dilutions, so be very careful during the next few steps to avoid any error that will compromise your whole analysis. Using a pipette, add 100 microliters of the antifungal peptide in the double strength concentration of the highest desired final concentration in columns one through three in row A.Using a multichannel pipette, add 50 microliters of sterile water to the other wells in rows B to H.Remove 50 microliters of the wells with the highest concentration.Transfer to the corresponding wells of the next concentration, and homogenize by pipetting up and down several times. Repeat the serial dilution until the wells with the lowest concentration are reached, and discard 50 microliters from these wells. Leave columns 11 and 12 of rows A, B, and C with only water for blank controls, or negative growth controls.Add 50 microliters of the double strength adjusted inoculum in RPMI 1640 medium to each well of columns one to three, plus column 11. The final concentration for C.albicans will be 2, 000 cells per milliliter. The final concentration for C.neoformans will be 10, 000 cells per milliliter.Prepare negative growth controls by mixing 50 microliters of water and 50 microliters of adjusted inoculum without the antifungal. Prepare blank controls by combining 50 microliters of water and 50 microliters of medium without cells. Load the controls into the appropriate wells.Observe all wells using an inverted optical microscope, and then incubate the plates at 37 degrees with shaking at 200 rpm. After the incubation period, observe all wells again to verify changes in morphology, as well as to check for signs of contamination. Acquire an image of each plate using a digital camera.In this representative assay, three antimicrobial peptides, or AMPs, with concentrations ranging from 100 micromolar to point seven eight micromolar, were evaluated for antifungal activity against C.neoformans. A growth control and a blank were included. Any well with clear media similar to the blank wells is considered a positive result, whereas any well with turbidity analogous to the negative growth control wells is considered negative.Since the minimum inhibitory concentration, or MIC, is defined as the lowest antimicrobial compound concentration that completely inhibits visible fungal growth at the end of the incubation period, 25 micromolar is considered the MIC for AMP1. And, 12 point five micromolar, the MIC for AMP2. AMP3 will have to be reevaluated, as the fungus grew at all concentrations tested.In the same manner, three distinct peptides tested against C.albicans, indicted 50 micromolar is the MIC for AMP1. Six micromolar is the MIC for AMP2, and 25 micromolar is the MIC for AMP3. An example of a poor result, likely from improper pipetting during the dilution step, is illustrated by columns five to seven of row C in this plate, where differences in C.neoformans growth are present between replicates.Once mastered, this technique can be done in approximately two hours, plus the time of fungal growth, if it's performed properly. Remember to be aware of the physical chemical features of these tested molecules. Then use appropriate solvents as control in case they are needed, and to always use the cells in the same growth phase.Following this procedure, other methods could be performed such as time kill assay, the use of viability dyes, and ST60 assays to answer additional questions, like whether the compound has a fungicidal or fungistatic effect. After it's development, this technique paved the way for researchers in the field of medical micrology to explore several sources of natural or synthetic compounds in the search for antifungal compounds. After watching this video, you should have a good understanding of how to start a fungal culture, prepare cells for the assay, perform the serial dilutions, and read the results after incubating the fungal strains with our tested compounds.Don't forget, that working with fungal pathogens can be extremely hazard. And preparation such as wearing personal protection equipment, working inside a biological safety hood, and using appropriate safety practice should be taken while performing this procedure.

broth-microdilution-vitro-screening-an-easy-fast-method-to-detect-new

Research

JoVE Journal

Biology

Using Laser Tweezers For Manipulating Isolated Neurons In Vitro

In this paper and video, we describe the protocols used in our laboratory to study the targeting preferences of regenerating cell processes of adult retinal neurons in vitro. Procedures for preparing retinal cell cultures start with the dissection, digestion and trituration of the retina, and end with the plating of isolated retinal cells on dishes made especially for use with laser tweezers. These dishes are divided into a cell adhesive half and a cell repellant half. The cell adhesive side is coated with a layer of Sal-1 antibodies, which provide a substrate upon which our cells grow. Other adhesive substrates could be used for other cell types. The cell repellant side is coated with a thin layer of poly-HEMA. The cells plated on the poly-HEMA side of the dish are trapped with the laser tweezers, transported and then placed adjacent to a cell on the Sal-1 side to create a pair. Formation of cell groups of any size should be possible with this technique. "Laser-tweezers-controlled micromanipulation" means that the investigator can choose which cells to move, and the desired distance between the cells can be standardized. Because the laser beam goes through transparent surfaces of the culture dish, cell selection and placement are done in an enclosed, sterile environment. Cells can be monitored by video time-lapse and used with any cell biological technique required. This technique may help investigations of cell-cell interactions.

This video describes the manipulation of cultured neurons using laser tweezers in vitro.

In this paper and video, we describe the protocols used in our laboratory to study the targeting preferences of regenerating cell processes of adult ...

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level. There are several methods, both in vitro and in vivo, to evaluate protein binding, and at least two methods that complement the shortcomings of each other should be conducted to obtain reliable insights. 
For an in vivo assay, the bimolecular fluorescence complementation (BiFC) assay represents the most popular and least invasive approach that enables to detect protein-protein interaction within living cells, as well as identify the intracellular localization of the interacting proteins 1,2. In this assay, non-fluorescent N- and C-terminal halves of GFP or its variants are fused to tested proteins, and when the two fusion proteins are brought together due to the tested proteins&#x2019; interactions, the fluorescent signal is reconstituted3-6. Because its signal is readily detectable by epifluorescence or confocal microscopy, BiFC has emerged as a powerful tool of choice among cell biologists for studying about protein-protein interactions in living cells 3. This assay, however, can sometimes produce false positive results. For example, the fluorescent signal can be reconstituted by two GFP fragments arranged as far as 7 nm from each other due to close packing in a small subcellular compartment, rather that due to specific interactions7.
Due to these limitations, the results obtained from live cell imaging technologies should be confirmed by an independent approach based on a different principle for detecting protein interactions. Co-immunoprecipitation (Co-IP) or glutathione transferase (GST) pull-down assays represent such alternative methods that are commonly used to analyze protein-protein interactions in vitro. However, iIn these assays, however, the tested proteins must be readily soluble in the buffer that supportsused for the binding reaction. Therefore, specific interactions involving an insoluble protein cannot be assessed by these techniques.
 Here, we illustrate the protocol for the protein membrane overlay binding assay, which circumvents this difficulty. In this technique, interaction between soluble and insoluble proteins can be reliably tested because one of the proteins is immobilized on a membrane matrix. This method, in combination with in vivo experiments, such as BiFC, provides a reliable approach to investigate and characterize interactions faithfully between soluble and insoluble proteins. In this article, binding between Tobacco mosaic virus (TMV) movement protein (MP), which exerts multiple functions during viral cell-to-cell transport8-14, and a recently identified plant cellular interactor, tobacco ankyrin repeat-containing protein (ANK) 15, is demonstrated using this technique.

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level.  There are several ...

Measuring Fast Calcium Fluxes in Cardiomyocytes

Cardiomyocytes have multiple Ca2+ fluxes of varying duration that work together to optimize function 1,2. Changes in Ca2+ activity in response to extracellular agents is predominantly regulated by the phospholipase C&beta;- G&alpha;q pathway localized on the plasma membrane which is stimulated by agents such as acetylcholine 3,4. We have recently found that plasma membrane protein domains called caveolae5,6 can entrap activated G&alpha;q 7. This entrapment has the effect of stabilizing the activated state of G&alpha;q and resulting in prolonged Ca2+ signals in cardiomyocytes and other cell types8. We uncovered this surprising result by measuring dynamic calcium responses on a fast scale in living cardiomyocytes. Briefly, cells are loaded with a fluorescent Ca2+ indicator. In our studies, we used Ca2+ Green (Invitrogen, Inc.) which exhibits an increase in fluorescence emission intensity upon binding of calcium ions. The fluorescence intensity is then recorded for using a line-scan mode of a laser scanning confocal microscope. This method allows rapid acquisition of the time course of fluorescence intensity in pixels along a selected line, producing several hundreds of time traces on the microsecond time scale. These very fast traces are transferred into excel and then into Sigmaplot for analysis, and are compared to traces obtained for electronic noise, free dye, and other controls. To dissect Ca2+ responses of different flux rates, we performed a histogram analysis that binned pixel intensities with time. Binning allows us to group over 500 traces of scans and visualize the compiled results spatially and temporally on a single plot. Thus, the slow Ca2+ waves that are difficult to discern when the scans are overlaid due to different peak placement and noise, can be readily seen in the binned histograms. Very fast fluxes in the time scale of the measurement show a narrow distribution of intensities in the very short time bins whereas longer Ca2+ waves show binned data with a broad distribution over longer time bins. These different time distributions allow us to dissect the timing of Ca2+fluxes in the cells, and to determine their impact on various cellular events.

We present a method to isolate rapid (microsecond) calcium events from slower fluxes in living cells using laser scanning confocal microscopy. The method measures fluorescence intensity fluctuations of calcium indicators by recording line scans of several hundred pixels in a cell. Histogram analysis allows us to isolate the time scales of different calcium fluxes.

Cardiomyocytes have multiple Ca2+ fluxes of varying duration that work together to optimize function 1,2. Changes in Ca2+ activity in response to ...

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

Construction of an Affordable and Easy-to-Build Zebrafish Facility

In vivo biomedical research is pivotal to translate in vitro findings into clinical advances. Small academic institutions with limited resources find it virtually impossible to build and maintain typical rodent facilities for research. Zebrafish research has been demonstrated to be a valuable alternative for in vivo research in pharmacology, physiology, development and genetic studies. This article demonstrates that a functional zebrafish facility can be built in an easy and affordable manner. We demonstrate that such a facility could be built in about one working day with minimal tools and expertise. The cost of the 27 1.8 L fish tank zebrafish facility constructed in this study was approximately $1,500. We estimate that the maintenance of an initial working 150 fish colony for 3 months is $1,000. This project involved students, who were introduced to aquaculturing of zebrafish for research proposes.

A Zebrafish facility suitable for breeding and in vivo research is built in an easy and affordable manner. Maintenance is minimal. This facility is ideal for student involvement and independent research.

In vivo biomedical research is pivotal to translate in vitro findings into clinical advances. Small academic institutions with limited resources find it ...

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that involves the construction, cloning and expression of mutant libraries, coupled to high frequency homologous DNA recombination in vivo. Here, we present a protocol to create and screen mutant libraries in yeast based on the example of a fungal aryl-alcohol oxidase (AAO) to enhance its total activity. Two protein segments were subjected to focused-directed evolution by random mutagenesis and in vivo DNA recombination. Overhangs of ~50 bp flanking each segment allowed the correct reassembly of the AAO-fusion gene in a linearized vector giving rise to a full autonomously replicating plasmid. Mutant libraries enriched with functional AAO variants were screened in S. cerevisiae supernatants with a sensitive high-throughput assay based on the Fenton reaction. The general process of library construction in S. cerevisiae described here can be readily applied to evolve many other eukaryotic genes, avoiding extra PCR reactions, in vitro DNA recombination and ligation steps.

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

We present a detailed protocol to construct and screen mutant libraries for directed evolution campaigns in Saccharomyces cerevisiae.

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that ...

An Easy Method for Plant Polysome Profiling

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the analysis of translational regulation. The method described here is an easy and economical way for fractionating polysomes from various plant tissues. A sucrose gradient is made without the need for a gradient maker by sequentially freezing each layer. Cytosolic extracts are then prepared in a buffer containing cycloheximide and chloramphenicol to immobilize the cytosolic and chloroplastic ribosomes to mRNA and are loaded onto the sucrose gradient. After centrifugation, six fractions are directly collected from the bottom to the top of the gradient, without piercing the ultracentrifugation tube. During collection, the absorbance at 260 nm is read continuously to generate a polysome profile that gives a snapshot of global translational activity. Fractions are then pooled to prepare three different mRNA populations: the polysomes, mRNAs bound to several ribosomes; the monosomes, mRNAs bound to one ribosome; and mRNAs that are not bound to ribosomes. mRNAs are then extracted. This protocol has been validated for different plants and tissues including Arabidopsis thaliana seedlings and adult plants, Nicotiana benthamiana, Solanum lycopersicum, and Oryza sativa leaves.

This protocol describes an easy method to extract and fractionate transcripts from plant tissues on the basis of the number of bound ribosomes. It allows a global estimate of translation activity and the determination of the translational status of specific mRNAs.

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the ...

Gap Junctional Intercellular Communication: A Functional Biomarker to Assess Adverse Effects of Toxicants and Toxins, and Health Benefits of Natural Products

This protocol describes a scalpel loading-fluorescent dye transfer (SL-DT) technique that measures intercellular communication through gap junction channels, which is a major intercellular process by which tissue homeostasis is maintained. Interruption of gap junctional intercellular communication (GJIC) by toxicants, toxins, drugs, etc. has been linked to numerous adverse health effects. Many genetic-based human diseases have been linked to mutations in gap junction genes. The SL-DT technique is a simple functional assay for the simultaneous assessment of GJIC in a large population of cells. The assay involves pre-loading cells with a fluorescent dye by briefly perturbing the cell membrane with a scalpel blade through a population of cells. The fluorescent dye is then allowed to traverse through gap junction channels to neighboring cells for a designated time. The assay is then terminated by the addition of formalin to the cells. The spread of the fluorescent dye through a population of cells is assessed with an epifluorescence microscope and the images are analyzed with any number of morphometric software packages that are available, including free software packages found on the public domain. This assay has also been adapted for in vivo studies using tissue slices from various organs from treated animals. Overall, the SL-DT assay can serve a broad range of in vitro pharmacological and toxicological needs, and can be potentially adapted for high throughput set-up systems with automated fluorescence microscopy imaging and analysis to elucidate more samples in a shorter time.

This protocol describes a scalpel loading-fluorescent dye transfer technique that measures intercellular communication through gap junction channels. Gap junctional intercellular communication is a major cellular process by which tissue homeostasis is maintained and disruption of this cell signaling has adverse health effects.

This protocol describes a scalpel loading-fluorescent dye transfer (SL-DT) technique that measures intercellular communication through gap junction ...

An Efficient In Vitro Transposition Method by a Transcriptionally Regulated Sleeping Beauty System Packaged into an Integration Defective Lentiviral Vector

The Sleeping Beauty (SB) transposon is a non-viral integrating system with proven efficacy for gene transfer and functional genomics. To optimize the SB transposon machinery, a transcriptionally regulated hyperactive transposase (SB100X) and T2-based transposon are employed. Typically, the transposase and transposon are provided transiently by plasmid transfection and SB100X expression is driven by a constitutive promoter. Here, we describe an efficient method to deliver the SB components to human cells that are resistant to several physical and chemical transfection methods, to control SB100X expression and stably integrate a gene of interest (GOI) through a &#34;cut and paste&#34; SB mechanism. The expression of hyperactive transposase is tightly controlled by the Tet-ON system, widely used to control gene expression since 1992. The gene of interest is flanked by inverted repeats (IR) of the T2 transposon. Both SB components are packaged in integration defective lentiviral vectors transiently produced in HEK293T cells. Human cells, either cell lines or primary cells from human tissue, are in vitro transiently transduced with viral vectors. Upon addition of doxycycline (dox, tetracycline analog) into the culture medium, a fine-tuning of transposase expression is measured and results in a long-lasting integration of the gene of interest in the genome of the treated cells. This method is efficient and applicable to the cell line (e.g., HeLa cells) and primary cells (e.g., human primary keratinocytes), and thus represents a valuable tool for genetic engineering and therapeutic gene transfer.

An Efficient In Vitro Transposition Method by a Transcriptionally Regulated Sleeping Beauty System Packaged into an Integration Defective Lentiviral Vector

This protocol describes a method to achieve stable integration of a gene of interest into the human genome by the transcriptionally regulated Sleeping Beauty system. Preparation of the integration of defective lentiviral vectors, the in vitro transduction of human cells, and the molecular assay on transduced cells are reported.

The Sleeping Beauty (SB) transposon is a non-viral integrating system with proven efficacy for gene transfer and functional genomics. To optimize the SB ...

An Easy and Flexible Inoculation Method for Accurately Assessing Powdery Mildew-Infection Phenotypes of Arabidopsis and Other Plants

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in turn requires accurate determination of disease phenotypes of plants upon infection with a particular fungal pathogen. However, accurate disease phenotyping with unculturable biotrophic fungal pathogens such as powdery mildew is not easy to achieve and can be a rate-limiting step of a research project. Here, we have developed a safe, efficient, and easy-to-operate disease phenotyping system using the Arabidopsis-powdery mildew interaction as an example. This system mainly consists of three components: (i) a wooden inoculation box fitted with a removable lid mounted with a stainless steel or nylon mesh of ~50 &#181;m pores for inoculating a flat of plants with fungal spores, (ii) a transparent plastic chamber with a small front opening for minimizing spore escape while conducting inoculation inside, and (iii) a spore-dislodging and distribution method for even and effective inoculation. The protocols described here include the steps and parameters for making the inoculation box and the plastic chamber at a low cost, and a video demonstration of how to use the system to enable even inoculation with powdery mildew spores, thereby improving accuracy and reproducibility of disease phenotyping.

We present a protocol for constructing a simple spore-distribution system consisting of an inoculation box with a ~50 &#181;m mesh and a transparent plastic chamber. This can be used to evenly inoculate plants with powdery mildew spores, thereby enabling accurate and reproducible assessment of disease phenotypes of plants under study.

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in ...