Name: colorimetric analysis of alkaline phosphatase activity in s. aureus biofilm
Uploaded: 2019-04-12T15:00:00
Description: Watch this Scientific Journal Video about Colorimetric Analysis of Alkaline Phosphatase Activity in S. aureus Biofilm at JoVE.com

We thank William Rainey Harper College and the University of Illinois at Chicago for the facility to conduct these experiments. We also thank McGraw Hill Foundation for their generous support.

1. Medium Preparation
<ol>
	<li>Prepare 1 L of Tryptic Soy Broth (TSB): Into 1 L of distilled water, add 15 g of pancreatic digest of casein, 5 g of papaic digest of soybean meal, 3 g of sodium chloride, 2.5 g of dextrose, and 2.5 g of dipotassium phosphate. Sterilize before use.</li>
	<li>For Tryptic Soy Agar (TSA), add 15 g of agar to 1 L of TSB, autoclave. Then let it cool down to room temperature. Next, pour at a ratio of 20 mL per Petri dish (100 mm x 15 mm).</li>
	<li>Biofilm culture medium: Add 10 g of glucose t...

<ol>
	<li>Coleman, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+mechanism+of+alkaline+phosphatase.">Structure and mechanism of alkaline phosphatase.</a> Annual Review of Biophysics and Biomolecular Structure. 21, 441-483 (1992).</li><li>Sharma, U., Pal, D., Prasad, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alkaline+Phosphatase:+An+Overview.">Alkaline Phosphatase: An Overview.</a> Indian Journal of Clinical Biochemistry. 29 (3), 269-278 (2014).</li><li>Mitchell, M. 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=High+frequencies+of+elevated+alkaline+phosphatase+activity+and+rickets+exist+in+extremely+low+birth+weight+infants+despite+current+nutritional+support.">High frequencies of elevated alkaline phosphatase activity and rickets exist in extremely low birth weight infants despite current nutritional support.</a> Boston Medical Center Pediatrics. 9, 47 (2009).</li><li>Fawley, J., Gourlay, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+alkaline+phosphatase:+A+summary+of+its+role+in+clinical+disease.">Intestinal alkaline phosphatase: A summary of its role in clinical disease.</a> Journal of Surgical Research. 202 (1), 225-234 (2016).</li><li>Derman, A. I., Beckwith, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Escherichia+coli+Alkaline+Phosphatase+Localized+to+the+Cytoplasm+Slowly+Acquires+Enzymatic+Activity+in+Cells+Whose+Growth+Has+Been+Suspended:+a+Caution+for+Gene+Fusion+Studies.">Escherichia coli Alkaline Phosphatase Localized to the Cytoplasm Slowly Acquires Enzymatic Activity in Cells Whose Growth Has Been Suspended: a Caution for Gene Fusion Studies.</a> Journal of Bacteriology. 177 (13), 3764-3770 (1995).</li><li>Danikowski, K. M., Cheng, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alkaline+Phosphatase+Activity+of+Staphylococcus+aureus+grown+in+Biofilm+and+Suspension+Cultures.">Alkaline Phosphatase Activity of Staphylococcus aureus grown in Biofilm and Suspension Cultures.</a> Current Microbiology. 75, 1226-1230 (2018).</li><li>Okabayashi, K., Futai, M., Mizuno, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Localization+of+Acid+and+Alkaline+Phosphatases+in+Staphylococcus+aureus.">Localization of Acid and Alkaline Phosphatases in Staphylococcus aureus.</a> Japanese Journal of Microbiology. 18 (4), 287-294 (1974).</li><li>Cheng, K. J., Costerton, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alkaline+Phosphatase+Activity+of+Rumen+Bacteria.">Alkaline Phosphatase Activity of Rumen Bacteria.</a> Applied and Environmental Microbiology. , 586-590 (1997).</li><li>Berezhetskyy, A. 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=Phosphatase+conductometric+biosensor+for+heavy-metal+ions+determination.">Phosphatase conductometric biosensor for heavy-metal ions determination.</a> Innovation and Research in Biomedical Engineering. 29 (2-3), 136-140 (2008).</li><li>Park, E. J., Kang, D. H. <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+bacterial+alkaline+phosphatase+assay+for+rapid+monitoring+of+bacterial+counts+on+spinach.">The use of bacterial alkaline phosphatase assay for rapid monitoring of bacterial counts on spinach.</a> Journal of Food Science. 73 (5), M236-M238 (2008).</li><li>Barber, M., Kuper, S. W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+Staphylococcus+pyogenes+by+the+phosphatase+reaction.">Identification of Staphylococcus pyogenes by the phosphatase reaction.</a> The Journal of Pathology and Bacteriology. 63, 65-68 (1951).</li><li>Wolf, P. L., Von der Muehll, E., Ludwick, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+test+to+differentiate+Serratia+from+Enterobacter.">A new test to differentiate Serratia from Enterobacter.</a> American Journal of Clinical Pathology. 56, 241-243 (1972).</li><li>Rangam, C. M., Katdare, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phosphatase+activity+of+Staphylococci+as+an+indication+of+their+pathogenicity.">Phosphatase activity of Staphylococci as an indication of their pathogenicity.</a> Indian Journal of Medical Science. 8, 610-613 (1954).</li><li>Flemming, H. -. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilms:+an+emergent+form+of+bacterial+life.">Biofilms: an emergent form of bacterial life.</a> Nature Reviews Microbiology. 14, 563-575 (2016).</li><li>Hoiby, N., Bjarnsholt, T., Givskov, M., Molin, S., Ciofu, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antibiotic+resistance+of+bacterial+biofilms.">Antibiotic resistance of bacterial biofilms.</a> International Journal of Antimicrobial Agents. 35, 322-332 (2010).</li><li>Ito, A., Taniuchi, A., May, T., Kawata, K., Okabe, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+antibiotic+resistance+of+Escherichia+coli+in+mature+biofilms.">Increased antibiotic resistance of Escherichia coli in mature biofilms.</a> Applied and Environmental Microbiology. 75, 4093-4100 (2009).</li><li>Witherow, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Ten-Week+Biochemistry+Lab+Project+Studying+Wild-Type+and+Mutant+Bacterial+Alkaline+Phosphatase.">A Ten-Week Biochemistry Lab Project Studying Wild-Type and Mutant Bacterial Alkaline Phosphatase.</a> Biochemistry and Molecular Biology Education. 44 (6), (2016).</li><li>Henthorn, P., Zervos, P., Raducha, M., Harris, H., Kadesch, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+a+human+placental+alkaline+phosphatase+gene+in+transfected+cells:+Use+as+a+reporter+for+studies+of+gene+expression.">Expression of a human placental alkaline phosphatase gene in transfected cells: Use as a reporter for studies of gene expression.</a> Proceedings of the National Academy of Science USA. 85, 6324-6346 (1988).</li><li>Horney, B. S., Farmer, A. J., Honor, D. J., MacKenzie, A., Burton, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agarose+gel+electrophoresis+of+alkaline+phosphatase+isoenzymes+in+the+serum+of+hyperthyroid+cats.">Agarose gel electrophoresis of alkaline phosphatase isoenzymes in the serum of hyperthyroid cats.</a> Veterinary Clinical Pathology. 23 (3), 98-102 (1994).</li><li>Farley, J. R., 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=Quantification+of+Skeletal+Alkaline+Phosphatase+in+Osteoporotic+Serum+by+Wheat+Germ+Agglutinin+Precipitation,+Heat+Inactivation,+and+a+Two-Site+Immunoradiometric+Assay.">Quantification of Skeletal Alkaline Phosphatase in Osteoporotic Serum by Wheat Germ Agglutinin Precipitation, Heat Inactivation, and a Two-Site Immunoradiometric Assay.</a> Clinical Chemistry. 40 (9), 1749-1756 (1994).</li><li>O&#8217;Toole, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtiter+Dish+Biofilm+Formation+Assay.">Microtiter Dish Biofilm Formation Assay.</a> Journal of Visualized Experience. , (2011).</li><li>Nomoto, M., Ohsawa, M., Wang, H. L., Chen, C. C., Yeh, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+and+Characterization+of+Extracellular+Alkaline+Phosphatase+from+an+Alkalophilic+Bacterium.">Purification and Characterization of Extracellular Alkaline Phosphatase from an Alkalophilic Bacterium.</a> Agricultural and Biological Chemistry. 52 (7), 1643-1647 (1988).</li></ol>

In our assay, we used pNPP as the ALP substrate. This is a working solution designed for ELISA and no dilution is needed. After hydrolysis by ALP, a yellow product develops and can be measured at 405 nm. At the end of the enzymatic reaction, we briefly centrifuged the 96 well plate and transferred the supernatant to a fresh 96 well plate to measure absorbance using the plate reader. We found that this extra centrifugation step is critical, since it increases the consistency of absorbance at 405 nm, probably by eliminatin...

Alkaline phosphatase (ALP) is ubiquitously expressed in both prokaryotic and eukaryotic cells1. It can catalyze the hydrolysis of monophosphate from different molecules such as nucleotides, proteins, alkaloids, phosphate esters and anhydrides of phosphoric acid. In humans, eukaryotic ALP is present in many tissues including liver, bone, intestine and placenta2. It plays important roles in protein phosphorylation, cell growth, apoptosis, stem cell processes as well as normal skeletal mineralization. Eukaryotic ALP is also a key serum indicator for the presence of diseases in bone, liver, and other tissues/organs when elevated3,4.
Prokaryotic ALP has been detected in a variety of bacterial cells, including E. coli5, S. aureus6,7 and some common rumen bacteria in the soils8. Bacterial ALP activity has been used as a biosensor in the detection of pesticides, heavy metals9 and bacterial contamination10. The constitutive expression of ALP has been used to identify Staphylococci11 and to differentiate Serratia from Enterobacter12. It is further suggested that constitutive ALP production is correlated with pathogenicity in staphylococci13. Although ALP has been studied in different settings3,4, yet little is reported for its activity and function in biofilms cultures.
A biofilm has been documented to have a differently functioning bacterial life as compared with its free-living bacterial cell counterpart14. In S. aureus, the formation of biofilm has been identified in a variety of clinical conditions and accounts for the antibiotic resistance and chronic inflammation15,16. Many molecules had been reported to be found in a biofilm matrix such as polysaccharides, proteins, nucleic acids, and lipids, but the mechanism of biofilm formation is not fully understood14. To understand the role of ALP in biofilm formation, we cultured S. aureus biofilms in 96 well tissue culture plates and measured the ALP activity using para-nitrophenylphosphate (pNPP).
The molecule pNPP is a ready-to-use substrate for ALP and has been widely used to measure ALP activity6,17,18. This colorimetric assay is based on the conversion of para-nitrophenyl phosphate (pNPP) to para-nitrophenol resulting in a colored product at 405 nm. Compared to other conventional ALP assay, such as agarose gel electrophoresis19, wheat germ agglutinin (WGA) precipitation, and WGA-HPLC20, this assay is highly specific, sensitive, easy to reproduce, and most importantly, allows for high throughput.

<table>
	<tbody>
		<tr>
			<td>Agar</td>
			<td>VWR</td>
			<td>9002-18-0</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Centrifuge</td>
			<td>Thomas Scientific</td>
			<td>5810</td>
			<td></td>
		</tr>
		<tr>
			<td>Gluose</td>
			<td>VWR</td>
			<td>50-99-7</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH pellets</td>
			<td>VWR</td>
			<td>SS0550-500GR</td>
			<td></td>
		</tr>
		<tr>
			<td>Para-nitrophenylphosphate (pNPP)&#160;</td>
			<td>Sigma</td>
			<td>P7998-100ML</td>
			<td>Typical concentrations of pNPP liquid substrates, often used in enzyme-linked immunesorbent assays (ELISA), range between 10 to 50 mM. Similar to most ready-to-use pNPP liquid substrates like the one used here, the exact pNPP concentration is not disclosed due to its proprietary nature.</td>
		</tr>
		<tr>
			<td>10X PBS, pH7.4. 
			173 mM NaCl, 
			2.7 mM KCl, 
			8 mM Na2HPO4, 
			2 mM KH2PO4</td>
			<td>Sigma</td>
			<td>P3288-1VL</td>
			<td></td>
		</tr>
		<tr>
			<td>Plate Reader</td>
			<td>Biotek</td>
			<td>ELx808</td>
			<td></td>
		</tr>
		<tr>
			<td>S. aureus</td>
			<td>ATCC</td>
			<td>ATCC25923</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptic Soy Agar&#160;&#160;&#160;&#160;&#160;&#160; 15g / L TSB</td>
			<td>VWR</td>
			<td>9002-18-0</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptic Soy Broth:&#160;&#160;&#160;&#160;&#160; g/L 
			Pancreatic Digest of Casein............ 15.0 
			Papaic Digest of Soyben Meal.........5.00 
			Sodium chloride.............................. 3.00 
			Dextrose........................................&#160; 2.50 
			Dipotassium phosphate..................2.50</td>
			<td>VWR</td>
			<td>90006-098</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well tissue culture plates</td>
			<td>BD</td>
			<td>6902D09</td>
			<td>U shaped bottom</td>
		</tr>
	</tbody>
</table>

colorimetric analysis of alkaline phosphatase activity in s. aureus biofilm

Alkaline phosphatase (ALP) is a common enzyme expressed in both prokaryotic and eukaryotic cells. It catalyzes the hydrolysis of phosphate monoesters from many molecules at basic pH and plays an indispensable role in phosphate metabolism. In humans, eukaryotic ALP is one of the most frequently used enzymatic signals in diagnosing various diseases, such as cholestasis and rickets. In S. aureus, ALP is detected exclusively on the cell membrane; it is also expressed as a secretory form as well. Yet, little is known about its function in biofilm formation.
The purpose of this manuscript is to develop a quick and reliable assay to measure ALP activity in S. aureus biofilm that does not require protein isolation. Using p-nitrophenyl phosphate (pNPP) as a substrate, we measured ALP activity in S. aureus biofilm formed in 96-well tissue culture plates. Activity was based on the formation of the soluble reaction product measured by 405 nm absorbance. The high throughput nature of the 96 well tissue culture plate method provides a sensitive and reproducible method for ALP activity assays. The same experimental set up can also be extended to measure other extracellular molecular markers related to biofilm formation.

Figure 1 shows a representative result of ALP activity from biofilm cultures of S. aureus in 96 well tissue culture plates. 75 &#956;L of commercially available pNPP solution was added to each well and incubated at room temperature. After incubation for different times (0 min, 15 min, 30 min, 45 min, 60 min, and 75 min, respectively) 75 &#956;L of 5 M NaOH was added to stop the reaction. The product was then measured in a 96 well plate reader at 405 ...

Watch this Scientific Journal Video about Colorimetric Analysis of Alkaline Phosphatase Activity in S. aureus Biofilm at JoVE.com

Colorimetric Analysis of Alkaline Phosphatase Activity in S. aureus Biofilm

In this manuscript, we established a high throughput method to quantify alkaline phosphatase activity in S. aureus biofilm culture from 96-well tissue culture plate

Colorimetric Analysis of Alkaline Phosphatase Activity in S. aureus Biofilm

Alkaline phosphatase (ALP) is a common enzyme expressed in both prokaryotic and eukaryotic cells. It catalyzes the hydrolysis of phosphate monoesters from ...

This protocol presented an easy and reliable method to measure alkalized phosphatase activity in S.aureus biofilm culture. It will help us to understand the function of ALP in biofilm formation. The major advantage of this technique is high throughput.It is very sensitive and easy to perform. Demonstrating the procedure will be Kevin Danikowski, a former student from Harper College. To prepare TSB, add pancreatic digest of casein, papaic digest of soybean meal, sodium chloride, dextrose, and dipotassium phosphate into distilled water.Cover the flask with aluminum foil and put it in an autoclave to sterilize before use. To prepare a TSA, add agar to TSB and put it in the autoclave for sterilization. Then let it cool to room temperature.Next, pour it into the Petri dish at a ratio of 20 milliliters per dish. To prepare a biofilm culture medium, add glucose to autoclaved TSB to achieve the concentration of 10 grams per liter. Using a vacuum filtration kit, filtrate the solution with a 0.2 micrometer pore sized filter.To inoculate, use a sterilized inoculation loop to pick one individual colony of Staph aureus from the Petri dish and place it in the culture tube filled with 10 milliliters of TSB. Put the tube in the incubator to grow overnight at 37 degrees Celsius. With a micropipette, draw 100 microliters of overnight culture and transfer it to a culture tube filled with 10 milliliters of TSB with glucose for a 1:100 volume ratio dilution.Vortex gently to mix for a consistent concentration. Use a micropipette to transfer 200 microliters of diluted culture into a total of 18 wells from one 96 well plate. Incubate the 96 well plate at 37 degrees Celsius for 24 hours for biofilm formation.For the best biofilm formation of S.aureus, it is better to pick a flat or round bottom 96 well plate. After that, slightly tilt the plate to decant the supernatant by aspiration from the edge of each well. Wash each well with 1X PBS.Put the plate in the centrifuge to spin for five minutes at 8, 000 revolutions per minute and decant the supernatant by aspiration. Add 75 microliters of buffered ALP substrate consisting of commercially available PNPP to each well and use a timer to record each time point in triplicate. After each incubation time point, add 75 microliters of five molar sodium hydroxide to each of three wells to stop the reaction.Centrifuge the plate for five minutes at 800 revolutions per minute. Use a pipette to transfer 100 microliters of supernatant into a new 96 well plate for calorimetric measurement. Use a 96 well plate reader to measure the absorbance of each well at 405 nanometers.Use the 30-minute time point wells to control for background noise. Repeat the entire experiment in three 96 well plates. This protocol develops a quick and reliable assay to measure ALP activity in S.aureus biofilm that does not require protein isolation.The representative result of ALP activity shows an increased trend for up to 75 minutes. After 75 minutes, no increase of the ALP activity was observed. It is very important to establish a good biofilm culture and it may take quite a few trials to master.You can confirm biofilm formation by performing crystal violet assay as previously reported by us and others or you can pre-treat the plate with human plasma to facilitate biofilm formation. After its development, you can screen potential ALP inhibitors that might interfere biofilm formation. The result will provide important information toward biofilm management in medical field.Five molar sodium hydroxide might be hazardous in case of contact. Be sure to wear personal protective equipment when handling.

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Bioengineering

Quantification of Global Diastolic Function by Kinematic Modeling-based Analysis of Transmitral Flow via the Parametrized Diastolic Filling Formalism

Quantitative cardiac function assessment remains a challenge for physiologists and clinicians.&#160;Although historically invasive methods have comprised the only means available, the development of noninvasive imaging modalities (echocardiography, MRI, CT) having high temporal and spatial resolution provide a new window for quantitative diastolic function assessment. Echocardiography is the agreed upon standard for diastolic function assessment, but indexes in current clinical use merely utilize selected features of chamber dimension (M-mode) or blood/tissue motion (Doppler) waveforms without incorporating the physiologic causal determinants of the motion itself.&#160;The recognition that all left ventricles (LV) initiate filling by serving as mechanical suction pumps allows global diastolic function to be assessed based on laws of motion that apply to all chambers. What differentiates one heart from another are the parameters of the equation of motion that governs filling. Accordingly, development of the Parametrized Diastolic Filling (PDF) formalism&#160;has shown that the entire range of clinically observed early transmitral flow (Doppler E-wave) patterns are extremely well fit by the laws of damped oscillatory motion.&#160;This permits analysis of individual E-waves in accordance with a causal mechanism (recoil-initiated suction) that yields three (numerically) unique lumped parameters whose physiologic analogues are chamber stiffness (k), viscoelasticity/relaxation (c), and load (xo).&#160;The recording of transmitral flow (Doppler E-waves) is standard practice in clinical cardiology and, therefore, the echocardiographic recording method is only briefly reviewed. Our focus is on determination of the PDF parameters from routinely recorded E-wave data.&#160;As the highlighted results indicate, once the PDF parameters have been obtained from a suitable number of load varying E-waves, the investigator is free to use the parameters or construct indexes from the parameters (such as stored energy 1/2kxo2, maximum A-V pressure gradient kxo, load independent index of diastolic function, etc.) and select the aspect of physiology or pathophysiology to be quantified.

Accurate, causality-based quantification of global diastolic function has been achieved by kinematic modeling-based analysis of transmitral flow via the Parametrized Diastolic Filling (PDF) formalism. PDF generates unique stiffness, relaxation,&#160;and load parameters and elucidates &#39;new&#39; physiology while providing sensitive and specific indexes of dysfunction.

Quantitative cardiac function assessment remains a challenge for physiologists and clinicians.&#160;Although historically invasive methods have comprised ...

Protocol for Biofilm Streamer Formation in a Microfluidic Device with Micro-pillars

Several bacterial species possess the ability to attach to surfaces and colonize them in the form of thin films called biofilms. Biofilms that grow in porous media are relevant to several industrial and environmental processes such as wastewater treatment and CO2 sequestration. We used Pseudomonas fluorescens, a Gram-negative aerobic bacterium, to investigate biofilm formation in a microfluidic device that mimics porous media. The microfluidic device consists of an array of micro-posts, which were fabricated using soft-lithography. Subsequently, biofilm formation in these devices with flow was investigated and we demonstrate the formation of filamentous biofilms known as streamers in our device. The detailed protocols for fabrication and assembly of microfluidic device are provided here along with the bacterial culture protocols. Detailed procedures for experimentation with the microfluidic device are also presented along with representative results.

Protocols for the study of biofilm formation in a microfluidic device that mimics porous media are discussed. The microfluidic device consists of an array of micro-pillars and biofilm formation by Pseudomonas fluorescens in this device is investigated.

Several bacterial species possess the ability to attach to surfaces and colonize them in the form of thin films called biofilms. Biofilms that grow in ...

Real-time Visualization and Analysis of Chondrocyte Injury Due to Mechanical Loading in Fully Intact Murine Cartilage Explants

Homeostasis of articular cartilage depends on the viability of resident cells (chondrocytes). Unfortunately, mechanical trauma can induce widespread chondrocyte death, potentially leading to irreversible breakdown of the joint and the onset of osteoarthritis. Additionally, maintenance of chondrocyte viability is important in osteochondral graft procedures for optimal surgical outcomes. We present a method to assess the spatial extent of cell injury/death on the articular surface of intact murine synovial joints after application of controlled mechanical loads or impacts. This method can be used in comparative studies to investigate the effects of different mechanical loading regimens, different environmental conditions or genetic manipulations, as well as different stages of cartilage degeneration on short- and/or long-term vulnerability of in situ articular chondrocytes. The goal of the protocol introduced in the manuscript is to assess the spatial extent of cell injury/death on the articular surface of murine synovial joints. Importantly, this method enables testing on fully intact cartilage without compromising native boundary conditions. Moreover, it allows for real-time visualization of vitally stained articular chondrocytes and single image-based analysis of cell injury induced by application of controlled static and impact loading regimens. Our representative results demonstrate that in healthy cartilage explants, the spatial extent of cell injury depends sensitively on load magnitude and impact intensity. Our method can be easily adapted to investigate the effects of different mechanical loading regimens, different environmental conditions or different genetic manipulations on the mechanical vulnerability of in situ articular chondrocytes.

We present a method to assess the spatial extent of cell injury/death on the articular surface of intact murine joints after application of controlled mechanical loads or impacts. This method can be used to investigate how osteoarthritis, genetic factors and/or different loading regimens affect the vulnerability of in situ chondrocytes.

Homeostasis of articular cartilage depends on the viability of resident cells (chondrocytes). Unfortunately, mechanical trauma can induce widespread ...

A Zebrafish Embryo Model for In Vivo Visualization and Intravital Analysis of Biomaterial-associated Staphylococcus aureus Infection

Biomaterial-associated infection (BAI) is a major cause of the failure of biomaterials/medical devices. Staphylococcus aureus is one of the major pathogens in BAI. Current experimental BAI mammalian animal models such as mouse models are costly and time-consuming, and therefore not suitable for high throughput analysis. Thus, novel animal models as complementary systems for investigating BAI in vivo are desired. In the present study, we aimed to develop a zebrafish embryo model for in vivo visualization and intravital analysis of bacterial infection in the presence of biomaterials based on fluorescence microscopy. In addition, the provoked macrophage response was studied. To this end, we used fluorescent protein-expressing S. aureus and transgenic zebrafish embryos expressing fluorescent proteins in their macrophages and developed a procedure to inject bacteria alone or together with microspheres into the muscle tissue of embryos. To monitor bacterial infection progression in live embryos over time, we devised a simple but reliable method of microscopic scoring of fluorescent bacteria. The results from microscopic scoring showed that all embryos with more than 20 colony-forming units (CFU) of bacteria yielded a positive fluorescent signal of bacteria. To study the potential effects of biomaterials on infection, we determined the CFU numbers of S. aureus with and without 10 &#181;m polystyrene microspheres (PS10) as model biomaterials in the embryos. Moreover, we used the ObjectJ project file &#34;Zebrafish-Immunotest&#34; operating in ImageJ to quantify the fluorescence intensity of S. aureus infection with and without PS10 over time. Results from both methods showed higher numbers of S. aureus in infected embryos with microspheres than in embryos without microspheres, indicating an increased infection susceptibility in the presence of the biomaterial. Thus, the present study shows the potential of the zebrafish embryo model to study BAI with the methods developed here.

A Zebrafish Embryo Model for In Vivo Visualization and Intravital Analysis of Biomaterial-associated Staphylococcus aureus Infection

The present study describes a zebrafish embryo model for in vivo visualization and intravital analysis of biomaterial-associated infection over time based on fluorescence microscopy. This model is a promising system complementing mammalian animal models such as mouse models for studying biomaterial-associated infections in vivo.

Biomaterial-associated infection (BAI) is a major cause of the failure of biomaterials/medical devices. Staphylococcus aureus is one of the major ...

High-resolution Patterned Biofilm Deposition Using pDawn-Ag43

Spatial structure and patterning play an important role in bacterial biofilms. Here we demonstrate an accessible method for culturing E. coli biofilms into arbitrary spatial patterns at high spatial resolution. The technique uses a genetically encoded optogenetic construct&#8212;pDawn-Ag43&#8212;that couples biofilm formation in E. coli to optical stimulation by blue light. We detail the process for transforming E. coli with&#160;pDawn-Ag43, preparing the required optical set-up, and the protocol for culturing patterned biofilms using pDawn-Ag43 bacteria. Using this protocol, biofilms with a spatial resolution below 25 &#956;m can be patterned on various surfaces and environments, including enclosed chambers, without requiring microfabrication, clean-room facilities, or surface pretreatment. The technique is convenient and appropriate for use in applications that investigate the effect of biofilm structure, providing tunable control over biofilm patterning. More broadly, it also has potential applications in biomaterials, education, and bio-art.

We demonstrate a method for depositing Escherichia coli bacterial biofilms in arbitrary spatial patterns with a high resolution using optical stimulation of a genetically encoded surface-adhesion construct.

Spatial structure and patterning play an important role in bacterial biofilms. Here we demonstrate an accessible method for culturing E. coli biofilms ...

Measuring Global Cellular Matrix Metalloproteinase and Metabolic Activity in 3D Hydrogels

Three-dimensional (3D) cell culture systems often more closely recapitulate in vivo cellular responses and functions than traditional two-dimensional (2D) culture systems. However, measurement of cell function in 3D culture is often more challenging. Many biological assays require retrieval of cellular material which can be difficult in 3D cultures. One way to address this challenge is to develop new materials that enable measurement of cell function within the material. Here, a method is presented for measurement of cellular matrix metalloproteinase (MMP) activity in 3D hydrogels in a 96-well format. In this system, a poly(ethylene glycol) (PEG) hydrogel is functionalized with a fluorogenic MMP cleavable sensor. Cellular MMP activity is proportional to fluorescence intensity and can be measured with a standard microplate reader. Miniaturization of this assay to a 96-well format reduced the time required for experimental set up by 50% and reagent usage by 80% per condition as compared to the previous 24-well version of the assay. This assay is also compatible with other measurements of cellular function. For example, a metabolic activity assay is demonstrated here, which can be conducted simultaneously with MMP activity measurements within the same hydrogel. The assay is demonstrated with human melanoma cells encapsulated across a range of cell seeding densities to determine the appropriate encapsulation density for the working range of the assay. After 24 h of cell encapsulation, MMP and metabolic activity readouts were proportional to cell seeding density. While the assay is demonstrated here with one fluorogenic degradable substrate, the assay and methodology could be adapted for a wide variety of hydrogel systems and other fluorescent sensors. Such an assay provides a practical, efficient and easily accessible 3D culturing platform for a wide variety of applications.

Here, a protocol is presented for encapsulating and culturing cells in poly(ethylene glycol) (PEG) hydrogels functionalized with a fluorogenic matrix metalloproteinase (MMP)-degradable peptide. Cellular MMP and metabolic activity are measured directly from the hydrogel cultures using a standard microplate reader.

Three-dimensional (3D) cell culture systems often more closely recapitulate in vivo cellular responses and functions than traditional two-dimensional (2D) ...

Home-Based Monitor for Gait and Activity Analysis

Current outcomes in neuromuscular disorder clinical trials include motor function scales, timed tests, and strength measures performed by trained clinical evaluators. These measures are slightly subjective and are performed during a visit to a clinic or hospital and constitute therefore a point assessment. Point assessments can be influenced by daily patient condition or factors such as fatigue, motivation, and intercurrent illness. To enable home-based monitoring of gait and activity, a wearable magneto-inertial sensor (WMIS) has been developed. This device is a movement monitor composed of two very light watch-like sensors and a docking station. Each sensor contains a tri-axial accelerometer, gyroscope, magnetometer, and a barometer that record linear acceleration, angular velocity, the magnetic field of the movement in all directions, and barometric altitude, respectively. The sensors can be worn on the wrist, ankle, or wheelchair to record the subject&#8217;s movements during the day. The docking station enables data uploading and recharging of sensor batteries during the night. Data are analyzed using proprietary algorithms to compute parameters representative of the type and intensity of the performed movement. This WMIS can record a set of digital biomarkers, including cumulative variables, such as total number of meters walked, and descriptive gait variables, such as the percentage of the most rapid or longest stride that represents the top performance of patient over a predefined period of time.

This innovative device uses magneto-inertial sensors to permit gait and activity analysis in uncontrolled environments. Currently in the qualification process as an outcome measure in the European Medical Agency, one of the applications will be to serve as a clinical endpoint in clinical trials in neuromuscular diseases.

Current outcomes in neuromuscular disorder clinical trials include motor function scales, timed tests, and strength measures performed by trained clinical ...

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images

The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in live-cell imaging and high-throughput microscopy techniques. This led to a constant increase in the amount and complexity of the microscopy data for a single experiment. Because manual analysis of microscopy data is very time consuming, subjective, and prohibits quantitative analyses, automation of bioimage analysis is becoming almost unavoidable. We built an informatics workflow called Substructure Analyzer to fully automate signal analysis in bioimages from fluorescent microscopy. This workflow is developed on the user-friendly open-source platform Icy and is completed by functionalities from ImageJ. It includes the pre-processing of images to improve the signal to noise ratio, the individual segmentation of cells (detection of cell boundaries) and the detection/quantification of cell bodies enriched in specific cell compartments. The main advantage of this workflow is to propose complex bio-imaging functionalities to users without image analysis expertise through a user-friendly interface. Moreover, it is highly modular and adapted to several issues from the characterization of nuclear/cytoplasmic translocation to the comparative analysis of different cell bodies in different cellular sub-structures. The functionality of this workflow is illustrated through the study of the Cajal (coiled) Bodies under oxidative stress (OS) conditions. Data from fluorescence microscopy show that their integrity in human cells is impacted a few hours after the induction of OS. This effect is characterized by a decrease of coilin nucleation into characteristic Cajal Bodies, associated with a nucleoplasmic redistribution of coilin into an increased number of smaller foci. The central role of coilin in the exchange between CB components and the surrounding nucleoplasm suggests that OS induced redistribution of coilin could affect the composition and the functionality of Cajal Bodies.

We present a freely available workflow built for rapid exploration and accurate analysis of cellular bodies in specific cell compartments in fluorescence microscopy images. This user-friendly workflow is designed on the open-source software Icy and also uses ImageJ functionalities. The pipeline is affordable without knowledge in image analysis.

The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in ...

Electric and Magnetic Field Devices for Stimulation of Biological Tissues

Electric fields (EFs) and magnetic fields (MFs) have been widely used by tissue engineering to improve cell dynamics such as proliferation, migration, differentiation, morphology, and molecular synthesis. However, variables such stimuli strength and stimulation times need to be considered when stimulating either cells, tissues or scaffolds. Given that EFs and MFs vary according to cellular response, it remains unclear how to build devices that generate adequate biophysical stimuli to stimulate biological samples. In fact, there is a lack of evidence regarding the calculation and distribution when biophysical stimuli are applied. This protocol is focused on the design and manufacture of devices to generate EFs and MFs and implementation of a computational methodology to predict biophysical stimuli distribution inside and outside of biological samples. The EF device was composed of two parallel stainless-steel electrodes located at the top and bottom of biological cultures. Electrodes were connected to an oscillator to generate voltages (50, 100, 150 and 200 Vp-p) at 60 kHz. The MF device was composed of a coil, which was energized with a transformer to generate a current (1 A) and voltage (6 V) at 60 Hz. A polymethyl methacrylate support was built to locate the biological cultures in the middle of the coil. The computational simulation elucidated the homogeneous distribution of EFs and MFs inside and outside of biological tissues. This computational model is a promising tool that can modify parameters such as voltages, frequencies, tissue morphologies, well plate types, electrodes and coil size to estimate the EFs and MFs to achieve a cellular response.

This protocol describes the step-by-step process to build both electrical and magnetic stimulators used to stimulate biological tissues. The protocol includes a guideline to simulate computationally electric and magnetic fields and manufacture of stimulator devices.

Electric fields (EFs) and magnetic fields (MFs) have been widely used by tissue engineering to improve cell dynamics such as proliferation, migration, ...

Large-Scale, Automated Production of Adipose-Derived Stem Cell Spheroids for 3D Bioprinting

Adipose-derived stromal/stem cells (ASCs) are a subpopulation of cells found in the stromal vascular fraction of human subcutaneous adipose tissue recognized as a classical source of mesenchymal stromal/stem cells. Many studies have been published with ASCs for scaffold-based tissue engineering approaches, which mainly explored the behavior of these cells after their seeding on bioactive scaffolds. However, scaffold-free approaches are emerging to engineer tissues in vitro and in vivo, mainly by using spheroids, to overcome the limitations of scaffold-based approaches.
Spheroids are 3D microtissues formed by the self-assembly process. They can better mimic the architecture and microenvironment of native tissues, mainly due to the magnification of cell-to-cell and cell-to-extracellular matrix interactions. Recently, spheroids are mainly being explored as disease models, drug screening studies, and building blocks for 3D bioprinting. However, for 3D bioprinting approaches, numerous spheroids, homogeneous in size and shape, are necessary to biofabricate complex tissue and organ models. In addition, when spheroids are produced automatically, there is little chance for microbiological contamination, increasing the reproducibility of the method.
The large-scale production of spheroids is considered the first mandatory step for developing a biofabrication line, which continues in the 3D bioprinting process and finishes in the full maturation of the tissue construct in bioreactors. However, the number of studies that explored the large-scale ASC spheroid production are still scarce, together with the number of studies that used ASC spheroids as building blocks for 3D bioprinting. Therefore, this article aims to show the large-scale production of ASC spheroids using a non-adhesive micromolded hydrogel technique spreading ASC spheroids as building blocks for 3D bioprinting approaches.

Here, we describe the large-scale production of adipose-derived stromal/stem cell (ASC) spheroids using an automated pipetting system to seed the cell suspension, thus ensuring homogeneity of spheroid size and shape. These ASC spheroids can be used as building blocks for 3D bioprinting approaches.