Authors acknowledge funding from DBT - Biotechnology Teaching Program, DBT - BUILDER Program and FIST. MR thanks fellowship received from SHODH. HP thanks fellowship received from CSIR.

All bacterial isolates of P. aeruginosa were obtained from medical microbiology laboratories from Vadodara and Jaipur, India. All selected clinical isolates were handled in Biosafety Cabinet (BSL2) and utmost care was taken while handling bacterial isolates during the experiments. The commercial details of all the reagents/solutions are provided in the Table of Materials.
1. Preparation of Chrome Azurol Sulfonate (CAS) dye and agar media
<ol>
	<li>Prepare CAS dye (100 mL) with the following composition:
	<ol>
		<li>Dissolve 60 mg of CAS in 50 mL of distilled water (Solution 1).</li>
		<li>Dissolve 2.7 mg of FeCl3&#183;6H2O in 10 mL of 10 mM HCl (Solution 2).</li>
		<li>Dissolve 73 mg of Cetrimonium bromide (HDTMA) in 40 mL of distilled water (Solution 3).</li>
		<li>Carefully mix Solution 1, Solution 2, and Solution 3. Store it in a glass bottle.</li>
	</ol>
	</li>
	<li>Prepare CAS agar following the steps below:
	<ol>
		<li>Add 100 mL of MM9 salt solution to 750 mL of distilled water.</li>
		<li>Dissolve 32.24 g of piperazine-N,N&#39;-bis(2-ethanesulfonic acid) (PIPES) free acid.</li>
		<li>Add 15 g of Agar agar. Autoclave and allow it to cool.</li>
		<li>Add 30 mL of sterile Casamino acid solution and 10 mL of sterile 20% glucose solution to the mixture.</li>
		<li>Add 100 mL of CAS dye, mix, and pour it in aseptic conditions. 
		NOTE: Preparation of MM9 media, Casamino acid solution, and 8-Hydroxyquinoline are provided in Supplementary File 1. PIPES buffer is pH-sensitive. It will not dissolve until pH 5.6 is achieved. Ensure that the pH is constantly monitored because when PIPES starts to dissolve in water, it will further lower the pH. Extract Casamino acid with the same volume of 3% 8-hydroxyquinoline dissolved in chloroform. Leave the immiscible solution at 4 &#176;C for around 20 min and carefully collect the upper phase of the solution without disturbing the lower phase.</li>
	</ol>
	</li>
</ol>
2. Qualitative analysis of siderophores production
<ol>
	<li>Set the OD600 nm to 0.2 for 24 h grown cultures of P. aeruginosa.</li>
	<li>Using a sterile wire loop, streak the bacterial culture on a CAS agar plate.</li>
	<li>Incubate at 30 &#176;C for 24 h. 
	NOTE: Peptone water media or 0.8% normal saline can be used to dilute the bacterial culture. If no bacterial growth is observed at 24 h, incubate CAS plates for 48 to 72 h.</li>
</ol>
3. Quantitative estimation of total siderophores
<ol>
	<li>Re-inoculate 24-h-grown cultures of P. aeruginosa in Peptone water media after adjusting OD600 nm to 0.25, and incubate at 30 &#176;C for 48 h.</li>
	<li>After 48 h, centrifuge the bacterial culture at 4650 x g for 10 min at room temperature.</li>
	<li>After centrifugation, add 100 &#181;L of cell-free supernatant to a 96-well microtiter plate and add 100 &#181;L of CAS dye to it.</li>
	<li>Cover the plate with aluminum foil and incubate at room temperature for 20 min.</li>
	<li>After incubation, take spectrophotometric readings at 630 nm.</li>
	<li>Calculate the results obtained for the quantification of total siderophores as Percent Siderophore Unit (PSU). 
	NOTE: PSU can be calculated as: [(Ar&#160;- As)/Ar] x 100 
	where, Ar = absorbance of the reference at 630 nm, As = absorbance of the cell-free supernatant of the sample. For the reference, CAS dye should be added to uninoculated peptone water media. Fill all glassware, such as test tubes, flasks, etc., with 6 M HCl for 2 h and rinse them twice with distilled water to remove any trace of iron on them.</li>
</ol>
4. Quantitative estimation of pyoverdine
<ol>
	<li>Re-inoculate 24-h-grown cultures of P. aeruginosa in Peptone water media after adjusting OD600 nm to 0.25 and incubate at 30 &#176;C for 48 h.</li>
	<li>After 48 h, measure the OD600 nm of the bacterial growth before proceeding further.</li>
	<li>Centrifuge the bacterial culture at 4650 x g for 10 min at room temperature.</li>
	<li>After centrifugation, add 100 &#181;L of cell-free supernatant to a 96-well microtiter plate and add 100 &#181;L of 50 mM Tris-HCl (pH 8.0) to it.</li>
	<li>Take spectrophotometric readings at OD405 nm.</li>
</ol>
5. Pyochelin extraction and spectrophotometry
<ol>
	<li>Re-inoculate 24-h-grown cultures of P. aeruginosa in King&#39;s B media (Supplementary File 1) after adjusting OD600 nm to 0.25 and incubate at 30 &#176;C for 24 h.</li>
	<li>After 24 h, take 100 mL of culture and centrifuge at 4650 x g for 10 min at room temperature.</li>
	<li>After centrifugation, add 5 mL of 1 M citric acid to the supernatant. Extract twice with 50 mL of Ethyl acetate.</li>
	<li>Filter the organic phase with magnesium sulfate through a syringe filter. Store the filtered organic phase at -20 &#176;C.</li>
	<li>Take spectrophotometric readings at 320 nm. 
	NOTE: As pyochelin is a highly unstable compound at room temperature, perform the extraction process on ice. Use a 50 mL sterile syringe for filter separation. Place cotton at the tip of the syringe and add 1 gm of magnesium sulfate on it. Fix a sterile syringe filter at the tip of the syringe and collect the filtrate in a sterile tube.</li>
</ol>

Assessment of Siderophore Production from Pseudomonas aeruginosa Isolates

<ol>
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J., Llamas, M. 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H. T., Hamer, K. E., Clark, C. L., Harshman, L. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pyoverdine+production+by+pseudomonas+aeruginosa+exposed+to+metals+or+an+oxidative+stress+agent.">Pyoverdine production by pseudomonas aeruginosa exposed to metals or an oxidative stress agent.</a> Ecological Applications. 9 (2), 441-448 (1999).</li><li>Visca, P., Imperi, F., Lamont, I. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pyoverdine+siderophores:+From+biogenesis+to+biosignificance.">Pyoverdine siderophores: From biogenesis to biosignificance.</a> Trends in Microbiology. 15 (1), 22-30 (2007).</li><li>Ackerley, D. F., Caradoc-Davies, T. T., Lamont, I. 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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=Universal+chemical+assay+for+the+detection+and+determination+of+siderophores.">Universal chemical assay for the detection and determination of siderophores.</a> Analytical Biochemistry. 160 (1), 47-56 (1987).</li><li>Louden, B. C., Haarmann, D., Lynne, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+blue+agar+cas+assay+for+siderophore+detection.">Use of blue agar cas assay for siderophore detection.</a> Journal of Microbiology &amp; Biology Education. 12 (1), 51-53 (2011).</li><li>Arora, N. K., Verma, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modified+microplate+method+for+rapid+and+efficient+estimation+of+siderophore+produced+by+bacteria.">Modified microplate method for rapid and efficient estimation of siderophore produced by bacteria.</a> 3 Biotech. 7 (381), 1-9 (2017).</li><li>Frac, M., Gryta, A., Oszust, K., Kotowicz, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+and+accurate+microplate+method+(biolog+mt2)+for+detection+of+fusarium+fungicides+resistance/sensitivity.">Fast and accurate microplate method (biolog mt2) for detection of fusarium fungicides resistance/sensitivity.</a> Frontiers in Microbiology. 7 (4), 1-16 (2016).</li><li>Cezard, C., Farvacques, N., Sonnet, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemistry+and+biology+of+pyoverdines,+pseudomonas+primary+siderophores.">Chemistry and biology of pyoverdines, pseudomonas primary siderophores.</a> Current Medicinal Chemistry. 22 (2), 165-186 (2015).</li><li>Braud, A., Hoegy, F., Jezequel, K., Lebeau, T., Schalk, I. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+insights+into+the+metal+specificity+of+the+pseudomonas+aeruginosa+pyoverdine-iron+uptake+pathway.">New insights into the metal specificity of the pseudomonas aeruginosa pyoverdine-iron uptake pathway.</a> Environmental Microbiology. 11 (5), 1079-1091 (2009).</li><li>Brandel, J., 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=a+siderophore+of+pseudomonas+aeruginosa:+Physicochemical+characterization+of+the+iron(iii),+copper+(ii)+and+zinc+(ii)+complexes.">a siderophore of pseudomonas aeruginosa: Physicochemical characterization of the iron(iii), copper (ii) and zinc (ii) complexes.</a> Dalton Transactions. 41 (9), 2820-2834 (2012).</li><li>Hoegy, F., Mislin, G. L. A., Schalk, I. 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The authors have nothing to disclose.

This protocol enables researchers to quantitate total siderophores and two different siderophores of P. aeruginosa, namely pyoverdine and pyochelin, from the bacterial cell-free supernatant. In the CAS agar plates assay, CAS dye and Fe3+ ions form a complex. When bacteria produce siderophores, they quench Fe3+ ions from the CAS-Fe3+ complex, leading to a color change around the bacterial growth. This change results in a clear orange halo around the bacterial growth<sup class="xre...

Organisms require iron to perform various vital functions, such as electron transport and DNA replication1. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is known to possess a variety of virulence factors to establish infection in the host, among which one mechanism is siderophore formation2. During iron-depleting conditions, P. aeruginosa releases specialized molecules called siderophores, which quench iron from the surrounding environment. Siderophores chelate iron extracellularly, and the resulting ferric-siderophore complex is actively transported back to the cell3.
P. aeruginosa is known to produce two siderophores, pyoverdine and pyochelin. Pyoverdine is known to have a higher iron chelating affinity (1:1), whereas pyochelin is known to have a lesser iron chelating affinity (2:1)4. Pyochelin is also called a secondary siderophore because it has a lower iron chelating affinity5. The production and regulation of siderophores are actively controlled by Quorum Sensing (QS) systems in P. aeruginosa6.
Besides iron quenching, siderophores are also involved in regulating virulence factors and play an active role in biofilm formation7. Siderophores serve additional crucial roles, including involvement in cell signaling, defense against oxidative stress, and facilitation of interactions between microbial communities8. Siderophores are typically categorized based on the specific functional groups through which they chelate iron. The three primary bidentate ligands in this classification are catecholate, hydroxamate, and &#945;-hydroxycarboxylate3. Pyoverdines are hallmarks of fluorescent Pseudomonas species such as P. aeruginosa and P. fluorescens5. They consist of a mixed green fluorescent chromophore coupled to an oligopeptide containing 6-12 amino acids. Several non-ribosomal peptide synthetases (NRPs) are involved in their synthesis9. Four genes involved in pyoverdine production and regulation are pvdL, pvdI, pvdJ, and pvdD10. Pyoverdine is also responsible for infection and virulence in mammals11. P. aeruginosa is noted to produce pyochelin in moderate iron-limiting conditions, while pyoverdine is produced during severe iron-limiting environments12. Two operons involved in pyochelin production are pchDCBA and pchEFGHI13. It is noted that in the presence of pyocyanin, pyochelin (catecholate) induces oxidative damage and inflammation and generates hydroxyl radicals, which are harmful to host tissues11.
The Chrome Azurol Sulfonate (CAS) assay is widely adopted due to its comprehensiveness, high sensitivity, and greater convenience compared to microbiological assays, which, although sensitive, can be overly specific14. The CAS assay can be conducted on agar surfaces or in a solution. It relies on the color change that occurs when the ferric ion transitions from its intense blue complex to orange. The CAS colorimetric assay quantifies the depletion of iron from a Fe-CAS-surfactant ternary complex. This particular complex, consisting of metal, organic dye, and surfactant, has a blue color and exhibits an absorption peak at 630 nm.
This report presents a method for the qualitative detection of siderophore production, where one can detect the production of siderophores on an agar plate. A method for the quantitative estimation of total siderophore production in a microtiter plate and the detection and quantitative analysis of two siderophores, pyoverdine and pyochelin, from P. aeruginosa, is also provided.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Agar Agar, Type I</td>
			<td>HIMEDIA</td>
			<td>GRM666</td>
			<td></td>
		</tr>
		<tr>
			<td>8-Hydroxyquinoline</td>
			<td>Loba Chemie</td>
			<td>4151</td>
			<td></td>
		</tr>
		<tr>
			<td>Casamino Acid</td>
			<td>SRL Chemicals</td>
			<td>68806</td>
			<td></td>
		</tr>
		<tr>
			<td>Cetyltrimethyl Ammonium Bromide (CTAB)</td>
			<td>HIMEDIA</td>
			<td>RM4867-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Merck</td>
			<td>1070242521</td>
			<td></td>
		</tr>
		<tr>
			<td>Chrome azurol sulfonate</td>
			<td>HIMEDIA</td>
			<td>RM336-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Citric acid</td>
			<td>Merck</td>
			<td>100241</td>
			<td></td>
		</tr>
		<tr>
			<td>Dextrose monohydrate</td>
			<td>Merck</td>
			<td>108342</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane</td>
			<td>Merck</td>
			<td>107020</td>
			<td></td>
		</tr>
		<tr>
			<td>Ferric chloride hexahydrate</td>
			<td>HIMEDIA</td>
			<td>GRM6353</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Flasks</td>
			<td>Borosil</td>
			<td>5100021</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Test-tubes</td>
			<td>Borosil</td>
			<td>9820U05</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>SDFCL</td>
			<td>20125</td>
			<td></td>
		</tr>
		<tr>
			<td>King&#39;s medium B base</td>
			<td>HIMEDIA</td>
			<td>M1544-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>M9 Minimal Medium Salts</td>
			<td>HIMEDIA</td>
			<td>G013-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Sulphate&#160;</td>
			<td>Qualigens</td>
			<td>10034</td>
			<td></td>
		</tr>
		<tr>
			<td>MultiskanGO UV Spectrophotometer</td>
			<td>Thermo Scientific</td>
			<td>51119200</td>
			<td></td>
		</tr>
		<tr>
			<td>Peptone Type I, Bacteriological</td>
			<td>HIMEDIA</td>
			<td>RM667-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>PIPES free acid</td>
			<td>MP Biomedicals</td>
			<td>190257</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium dihydrogen phosphate</td>
			<td>Merck</td>
			<td>1048731000</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteose peptone</td>
			<td>HIMEDIA</td>
			<td>RM005-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Shimadzu UV-Vis Spectrophotometer</td>
			<td>Shimadzu</td>
			<td>2072310058</td>
			<td></td>
		</tr>
		<tr>
			<td>Sigma Laborzentrifuge</td>
			<td>Sigma-Aldrich</td>
			<td>3-18K</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Qualigens</td>
			<td>15915</td>
			<td></td>
		</tr>
	</tbody>
</table>

qualitative and quantitative analysis of siderophore production from pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) is known for its production of a diverse range of virulence factors to establish infections in the host. One such mechanism is the scavenging of iron through siderophore production. P. aeruginosa produces two different siderophores: pyochelin, which has lower iron-chelating affinity, and pyoverdine, which has higher iron-chelating affinity. This report demonstrates that pyoverdine can be directly quantified from bacterial supernatants, while pyochelin needs to be extracted from supernatants before quantification.
The primary method for qualitatively analyzing siderophore production is the Chrome Azurol Sulfonate (CAS) agar plate assay. In this assay, the release of CAS dye from the Fe3+-Dye complex leads to a color change from blue to orange, indicating siderophore production. For the quantification of total siderophores, bacterial supernatants were mixed in equal proportions with CAS dye in a microtiter plate, followed by spectrophotometric analysis at 630 nm. Pyoverdine was directly quantified from the bacterial supernatant by mixing it in equal proportions with 50 mM Tris-HCl, followed by spectrophotometric analysis. A peak at 380 nm confirmed the presence of pyoverdine. As for Pyochelin, direct quantification from the bacterial supernatant was not possible, so it had to be extracted first. Subsequent spectrophotometric analysis revealed the presence of pyochelin, with a peak at 313 nm.

Before quantification of siderophores from clinical isolates, a qualitative screening for siderophore production was carried out to ensure siderophores production. Qualitative detection of siderophores from clinical isolates was observed by streaking bacteria on CAS agar plates. Three clinical isolates, namely MR1, TL7, J3, along with PAO1 (the reference strain), were selected for the study. All three clinical isolates and PAO1 showed positive results for siderophore production, where a c...

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Author Spotlight: Quantifying Siderophores and Pyochelin for Infection Control 

This protocol provides both qualitative and quantitative analyses of total siderophores, pyoverdine, and pyochelin from Pseudomonas aeruginosa.

Qualitative and Quantitative Analysis of Siderophore Production from Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) is known for its production of a diverse range of virulence factors to establish infections in the host. One such ...

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3.7K Views.  The Maharaja Sayajirao University of Baroda. This protocol provides both qualitative and quantitative analyses of total siderophores, pyoverdine, and pyochelin from Pseudomonas aeruginosa.

Video: Author Spotlight: Quantifying Siderophores and Pyochelin for Infection Control 

Use of Rotorod as a Method for the Qualitative Analysis of Walking in Rat

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a rotorod, animals remain in approximately the same place making repetitive movements of stepping. Thus the task provides a rich source of information on the details of foot stepping movements. Subjects were hemi-Parkinson analogue rats, produced by injection of 6-hydroxydopamine (6-OHDA) into the right nigrostriatal bundle to deplete nigrostriatal dopamine (DA). The present report provides a video analysis illustration of animals previously were filmed from frontal, lateral, and posterior views as they walked (15). Rating scales and frame-by-frame replay of the video records of stepping behavior indicated that the hemi-Parkinson rats were chronically impaired in posture and limb use contralateral to the DA-depletion. The contralateral limbs participated less in initiating and sustaining propulsion than the ipsilateral limbs. These deficits secondary to unilateral DA-depletion show that the rotorod provides a use task for the analysis of stepping movements.

The rotorod test is used to assess motor status in the walking movement of hemi-Parkinson analogue rats.

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a ...

A Quantitative Fitness Analysis Workflow

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA.
The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking.
QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods5,6. However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases3. For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously1.
Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and imaging. Any of these automated steps can be replaced by an equivalent, manual procedure, with an associated reduction in throughput, and we also present a lower throughput manual protocol. The same QFA software tools can be applied to images captured in either workflow.
We have extensive experience applying QFA to cultures of the budding yeast S. cerevisiae but we expect that QFA will prove equally useful for examining cultures of the fission yeast S. pombe and bacterial cultures.

Quantitative Fitness Analysis (QFA) is a complementary series of experimental and computational methods for estimating microbial culture fitnesses. QFA estimates the effect of genetic mutations, drugs or other applied treatments on microbe growth. Experiments scaling from focussed analysis of single cultures to thousands of parallel cultures can be designed.

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. ...

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine1. This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)1,10. Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)1,2,3. Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation4,5. Although the essential components of this pathway are well-characterized6,7,8,9, many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy11,12.
Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early stages of autophagy induction. With commercially available digital image analysis applications, we can readily obtain statistical information about autophagosome and lysosome number, size, distribution, and degree of colocalization from any imaged cell. This information allows us to precisely track the progress of autophagy in living cells and enables our continued investigation into the role of autophagy in cancer chemotherapy.

Autophagy is a ubiquitous process that enables cells to degrade and recycle proteins and organelles. We apply advanced fluorescence microscopy to visualize and quantify the small, but essential, physical changes associated with the induction of autophagy, including the formation and distribution of autophagosomes and lysosomes, and their fusion into autolysosomes.

Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

In vitro Investigation of the MexAB Efflux Pump From Pseudomonas aeruginosa

There is an emerging scientific need for reliable tools for monitoring membrane protein transport. We present a methodology leading to the reconstitution of efflux pumps from the Gram-negative bacteria Pseudomonas aeruginosa in a biomimetic environment that allows for an accurate investigation of their activity of transport. Three prerequisites are fulfilled: compartmentation in a lipidic environment, use of a relevant index for transport, and generation of a proton gradient. The membrane protein transporter is reconstituted into liposomes together with bacteriorhodopsin, a light-activated proton pump that generates a proton gradient that is robust as well as reversible and tunable. The activity of the protein is deduced from the pH variations occurring within the liposome, using pyranin, a pH-dependent fluorescent probe. We describe a step-by-step procedure where membrane protein purification, liposome formation, protein reconstitution, and transport analysis are addressed. Although they were specifically designed for an RND transporter, the described methods could potentially be adapted for use with any other membrane protein transporter energized by a proton gradient.

In vitro Investigation of the MexAB Efflux Pump From Pseudomonas aeruginosa

We present a protocol for the in vitro investigation of efflux pumps from Pseudomonas aeruginosa. This protocol allows for the generation of a robust, reversible, and tunable proton gradient within the liposome membrane and hence should be adaptable to any membrane protein energized by the protomotive force.

There is an emerging scientific need for reliable tools for monitoring membrane protein transport. We present a methodology leading to the reconstitution ...

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the &#8220;gold standard&#8221; enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.

A novel semi-automated hybrid DNA extraction method for use with environmental poultry production samples was developed and demonstrated improvements over a common mechanical and enzymatic extraction method in terms of the quantitative and qualitative estimates of the total bacterial communities.

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses ...

Measurement and Analysis of Extracellular Acid Production to Determine Glycolytic Rate

Extracellular measurement of oxygen consumption and acid production is a simple and powerful way to monitor rates of respiration and glycolysis1. Both mitochondrial (respiration) and non-mitochondrial (other redox) reactions consume oxygen, but these reactions can be easily distinguished by chemical inhibition of mitochondrial respiration. However, while mitochondrial oxygen consumption is an unambiguous and direct measurement of respiration rate2, the same is not true for extracellular acid production and its relationship to glycolytic rate 3-6. Extracellular acid produced by cells is derived from both lactate, produced by anaerobic glycolysis, and CO2, produced in the citric acid cycle during respiration. For glycolysis, the conversion of glucose to lactate- + H+ and the export of products into the assay medium is the source of glycolytic acidification. For respiration, the export of CO2, hydration to H2CO3 and dissociation to HCO3- + H+ is the source of respiratory acidification. The proportions of glycolytic and respiratory acidification depend on the experimental conditions, including cell type and substrate(s) provided, and can range from nearly 100% glycolytic acidification to nearly 100% respiratory acidification 6. Here, we demonstrate the data collection and calculation methods needed to determine respiratory and glycolytic contributions to total extracellular acidification by whole cells in culture using C2C12 myoblast cells as a model.

Glycolysis is a defining metabolic marker in multiple biological systems. Monitoring glycolysis by measuring the extracellular flux of H+ is common, but requires correction to be quantitative and unambiguous. Here, we demonstrate how to gather and correct extracellular flux data to distinguish between respiratory and glycolytic sources of extracellular acidification.

Extracellular measurement of oxygen consumption and acid production is a simple and powerful way to monitor rates of respiration and glycolysis1. Both ...

Development and Characterization of In Vitro Microvessel Network and Quantitative Measurements of Endothelial [Ca2+]i and Nitric Oxide Production

Endothelial cells (ECs) lining the blood vessel walls in vivo are constantly exposed to flow, but cultured ECs are often grown under static conditions and exhibit a pro-inflammatory phenotype. Although the development of microfluidic devices has been embraced by engineers over two decades, their biological applications remain limited. A more physiologically relevant in vitro microvessel model validated by biological applications is important to advance the field and bridge the gaps between in vivo and in vitro studies. Here, we present detailed procedures for the development of cultured microvessel network using a microfluidic device with a long-term perfusion capability. We also demonstrate its applications for quantitative measurements of agonist-induced changes in EC [Ca2+]i and nitric oxide (NO) production in real time using confocal and conventional fluorescence microscopy. The formed microvessel network with continuous perfusion showed well-developed junctions between ECs. VE-cadherin distribution was closer to that observed in intact microvessels than statically cultured EC monolayers. ATP-induced transient increases in EC [Ca2+]i and NO production were quantitatively measured at individual cell levels, which validated the functionality of the cultured microvessels. This microfluidic device allows ECs to grow under a well-controlled, physiologically relevant flow, which makes the cell culture environment closer to in vivo than that in the conventional, static 2D cultures. The microchannel network design is highly versatile, and the fabrication process is simple and repeatable. The device can be easily integrated to the confocal or conventional microscopic system enabling high resolution imaging. Most importantly, because the cultured microvessel network can be formed by primary human ECs, this approach will serve as a useful tool to investigate how pathologically altered blood components from patient samples affect human ECs and provide insight into clinical issues. It also can be developed as a platform for drug screening.

Development and Characterization of In Vitro Microvessel Network and Quantitative Measurements of Endothelial [Ca2+]i and Nitric Oxide Production

Primary human umbilical vein endothelial cells (HUVECs) were grown to confluence within a microfluidic network device. The endothelial cell junction and F-actin distributions were illustrated and the changes in intracellular calcium concentration and nitric oxide production in response to adenosine triphosphate (ATP) were quantified in real-time at individual cell levels.

Endothelial cells (ECs) lining the blood vessel walls in vivo are constantly exposed to flow, but cultured ECs are often grown under static conditions and ...

Quantitative Analysis of Cell Edge Dynamics during Cell Spreading

Cell spreading is a dynamic process in which a cell suspended in media attaches to a substrate and flattens itself from a rounded to a thin and spread-out shape. Following the cell-substrate attachment, the cell forms a thin sheet of lamellipodia emanating from the cell body. In the lamellipodia, globular actin (G-actin) monomers polymerize into a dense filamentous actin (F-actin) meshwork that pushes against the plasma membrane, thereby providing the mechanical forces required for the cell to spread. Notably, the molecular players that control the actin polymerization in lamellipodia are essential for many other cellular processes, such as cell migration and endocytosis. 
Since spreading cells form continuous lamellipodia that span the entire cell periphery and persistently expand outward, cell spreading assays have become an efficient tool to assess the kinetics of lamellipodial protrusions. Although several technical implementations of the cell spreading assay have been developed, a detailed description of the workflow, which would include both a step-by-step protocol and computational tools for data analysis, is currently lacking. Here, we describe the experimental procedures of the cell spreading assay and present an open-source tool for quantitative and unbiased analysis of cell edge dynamics during spreading. When combined with pharmacological manipulations and/or gene-silencing techniques, this protocol is amenable to a large-scale screen of molecular players regulating lamellipodial protrusions.

In this protocol, we present the experimental procedures of a cell spreading assay that is based on live-cell microscopy. We provide an open-source computational tool for the unbiased segmentation of fluorescently labeled cells and quantitative analysis of lamellipodia dynamics during cell spreading.

Cell spreading is a dynamic process in which a cell suspended in media attaches to a substrate and flattens itself from a rounded to a thin and spread-out ...

Sperm Collection and Computer-Assisted Sperm Analysis in the Teleost Model Japanese Medaka (Oryzias latipes)

Japanese medaka (Oryzias latipes) is a teleost fish and&#160;an emerging vertebrate model for ecotoxicology, developmental, genetics, and physiology research. Medaka is also used extensively to investigate vertebrate reproduction, which is an essential biological function as it allows a species to perpetuate. Sperm quality is an important indicator of male fertility and, thus, reproduction success. Techniques for extracting sperm and sperm analysis are well documented for many species, including teleost fish. Collecting sperm is relatively simple in larger fish but can be more complicated in small model fish as they produce less sperm and are more delicate. This article, therefore, describes two methods of sperm collection in the small model fish, Japanese medaka: testes dissection and abdominal massage. This paper demonstrates that both approaches are feasible for medaka and shows that abdominal massage can be performed a repeated number of times as the fish quickly recover from the procedure. This article also describes a protocol for computer-assisted sperm analysis in medaka to objectively assess several important indicators of medaka sperm quality (motility, progressivity, duration of motility, relative concentration). These procedures, specified for this useful small teleost model, will greatly enhance understanding of the environmental, physiological, and genetic factors influencing fertility in vertebrate males.

Sperm Collection and Computer-Assisted Sperm Analysis in the Teleost Model Japanese Medaka Oryzias latipes

This article describes two quick and efficient methods for collecting sperm from the small model fish medaka (Oryzias latipes), as well as a protocol for reliably assessing sperm quality using computer-assisted sperm analysis (CASA).

Japanese medaka (Oryzias latipes) is a teleost fish and&#160;an emerging vertebrate model for ecotoxicology, developmental, genetics, and physiology ...