The authors would like to thank Dr. Steve Withers and Hong-Ming Chen for providing DNP-Cellobioside substrate.

Before starting this protocol, you will need your metagenomic library stored in a 384 well plate format. In our study, we used the pCC1 copy control fosmid vector in combination with phage T1-resistant TransforMax EPI300-T1R E. coli cells as the library host and stored our plates at -80&deg;C 11.
1. Replication of the Metagenomic Library Plates
<ol>
	<li>Defrost the plates containing your library at 37&deg;C for approximately 20 minutes, or until all wells are thawed.</li>
	<li>Use the UV light sterilizing feature on the qPix2 to sterilize the robot for 15 minutes.</li>
	<li>Prepare LB broth with chloramphenicol at a final concentration of 12.5ug/mL and arabinose at 100ug/mL in a 500mL reagent bottle. Each plate will use approximately 20mL, plus make an additional 50mL to allow for dead volume.</li>
	<li>Set up the qFill3 as per manufacturer's instructions with the media bottle attached to the manifold via the sterile tubing. Program it for the appropriate amount of media, and set it to fill a 45uL volume in each well.</li>
	<li>Purge the air from the tubing and manifold using the purge feature of the robot until media is visible coming from each pin of the manifold.</li>
	<li>Fill the desired number of plates with LB media using the qFill3. Each plate takes approximately 20 seconds to fill.</li>
	<li>Load the library plates and the fresh plates into the appropriate areas of the qPix2 robot. Fill the cleaning baths with the appropriate reagents; 2% Micro90 in the rear bath, autoclaved distilled water in the middle bath, 80% ethanol in the front bath.</li>
	<li>Use the "Replicating" program of the qPix2. In the software, select the appropriate head, number and types of source plates and destination plates. Also set up the head to clean between replications, usually 6 cycles in each bath is enough. Capacity of the machine is 10 plates at a time, and it takes approximately 15 minutes to replicate them all with a 384 pin head (or approximately 50 minutes with a 96 pin head). Note: There is an option to "Stir Source" or "Stir Destination". It is recommended to not use these options as problems have previously occurred with our robot using them.</li>
	<li>Once the plates are replicated, grow the plates at 37&deg;C for 24 hours in a humidity box. Because we are inducing a high copy number of fosmid with addition of arabinose, the clones tend to grow slower than non-induced clones. Return the library plates to -80&deg;C. Note: Incubation in a humidity box ensures evaporation of media does not occur in the wells on the edge of the plates, keeping a uniform environment for all wells.</li>
	<li>Clean the qFill3 robot by first purging it with water (~50mL) and then 80% ethanol (~50mL). Disassemble the components, and clean and autoclave the bottle, lid, and tubing wrapped in aluminium foil.</li>
</ol>
2. Measuring the Growth of E. coli Clones
<ol>
	<li>Remove plates from 37&deg;C incubator. Remove and set aside the lids, and place plates onto the magazine loading platform provided with the RapidStak, up to a maximum of 25 plates. Note: The plate at the bottom of the stack will be the first one to be read. Make sure to keep track of the order of the plates, as the software does not record this.</li>
	<li>Remove one magazine from the Rapid Stak, ensure it is empty, and push it onto the stack of plates to be read. Grab it by the handle, and the plates should all be loaded into the magazine. Load the magazine into the RapidStak. Note: The magazine has a small screw in the corner denoting which corner the A1 wells of the plates should go. The magazine will only mount in the RapidStak in one orientation.</li>
	<li>Open the SkanIt RE program on the computer connected to the machines. Select "New Session" and name it appropriately. Choose "Corning Flat Bottom 384-well plate" as the plate type.</li>
	<li>In the "Plate Layout" area, select the "Wizard" button, and choose it to add 384 unknowns to your plate.</li>
	<li>In the "Protocol" area, select the "Well Loop" option, and enter for 384 wells. A "Well Loop" icon will appear in the flow- tree on the left hand side of the screen. Select the icon and click to add "Photometric Measurement". Set it to read at 600nm.</li>
	<li>Save your protocol with a unique name, and close the SkanIt RE program.</li>
	<li>On the computer, open the PolaraRS program.</li>
	<li>On the main page there will be table listing the instruments connected to the RapidStak device. The VarioSkan should be on the left side of this table. Under the VarioSkan heading, there will be two links; "RunSession" and "Incubate". Click the "RunSession" option.</li>
	<li>A new window, the assay window, will appear with a flowchart in the middle. Select the "RunSession" item (it should be the only item present). On the right side of the screen a drop-down menu will appear. Find the name of your saved SkanIt RE run in this menu. Note: There appears to be no rational ordering to this menu. It's not alphabetical, or by date added, or related to where on the computer the protocol is saved. This means you must look through all the protocols before finding your own, which is a pain.</li>
	<li>Once you have selected your protocol, in the upper right corner click "Run this assay".</li>
	<li>A box will pop up, asking you to denote which magazine to use as the source, and which magazine is empty. The lower box on the screen corresponds to the front magazine. [Optional: It asks you to enter the number of plates loaded to determine an estimate for the amount of time it will take. This estimate is normally way off.]</li>
	<li>Ensure both the RapidStak and the VarioSkan are turned on, and press "OK".</li>
	<li>The RapidStak will automatically load your plates into the plate reader, allowing for continuous measurements of plates. To read 25 plates takes approximately 50 minutes. Note: It is recommended to observe the first plate loading into the VarioSkan to ensure proper alignment of the machines. If the RapidStak does not load the plate reader properly, use the "Pause this assay" button in the top right corner of the PolaraRS window.</li>
	<li>Once the VarioSkan is done reading all the plates, remove the full magazine and place it on the magazine loading platform. Lift up the outer rectangle of the platform, and the magazine should slide off, leaving the plates standing in a pile in the middle. Replace the lids to the appropriate plates.</li>
</ol>
3. Addition of the Assay Mix to Each Plate
<ol>
	<li>Prepare assay mix using premade 10x stock of lysis mix (10% Triton X-100, 100mM ris, 10mM EDTA) in 50mM potassium acetate buffer at pH 5.5. Prepare a stock of up to 75mg/mL DNP-cellobioside substrate in DMSO, making sure the substrate is fully dissolved. Add DNP-cellobioside stock solution to assay mix to a final concentration of 0.1mg/mL. Each plate will use approximately 20mL of solution, plus make an additional 50mL to allow for dead volume. Note: DNP-Cellobioside is not readily soluble in water, so dissolving in DMSO increases the solubility. The presence of DMSO in the final assay solution has no observable effects.</li>
	<li>Set up the qFill3 as per manufacturer's instructions with the media bottle attached to the manifold via the sterile tubing. Program it for the appropriate amount of media, and set it to fill a 45uL volume in each well.</li>
	<li>Purge the air from the tubing and manifold using the purge feature of the robot until media is visible coming from each pin of the manifold.</li>
	<li>Add assay mix to each plate using the qFill3. Each plate takes approximately 20 seconds to fill.</li>
	<li>Once assay mix is added, incubate the plates at 37&deg;C in a humidity box for 12-16 hours. Note: Over-incubation of plates once the assay mix is added will cause evaporation in the outer wells of the plate, yielding higher absorbance readings than seen for the inside wells. This can be offset by incubating plates in a humidity chamber.</li>
</ol>
4. Reading Absorbance of Assayed Clones
<ol>
	<li>Remove plates from 37&deg;C incubator. Remove and set aside the lids, and place plates onto the magazine loading platform provided with the RapidStak, up to a maximum of 25 plates. Note: The plate at the bottom of the stack will be the first one to be read. Make sure to keep track of the order of the plates, as the software does not record this.</li>
	<li>Remove one magazine from the Rapid Stak, ensure it is empty, and push it onto the stack of plates to be read. Grab it by the handle, and the plates should all be loaded into the magazine. Load the magazine into the RapidStak. Note: The magazine has a small screw in the corner denoting which corner the A1 wells of the plates should go. The magazine will only mount in the RapidStak in one orientation.</li>
	<li>Open the SkanIt RE program on the computer connected to the machines. Select "New Session" and name it appropriately. Choose "Corning Flat Bottom 384-well plate" as the plate type.</li>
	<li>In the "Plate Layout" area, select the "Wizard" button, and choose it to add 384 unknowns to your plate.</li>
	<li>In the "Protocol" area, select the "Well Loop" option, and enter for 384 wells. A "Well Loop" icon will appear in the flow- tree on the left hand side of the screen. Select the icon and click to add "Photometric Measurement". Set it to read at 400nm.</li>
	<li>Save your protocol with a unique name, and close the SkanIt RE program.</li>
	<li>On the computer, open the PolaraRS program.</li>
	<li>On the main page there will be table listing the instruments connected to the RapidStak device. The VarioSkan should be on the left side of this table. Under the VarioSkan heading, there will be two links; "RunSession" and "Incubate". Click the "RunSession" option.</li>
	<li>A new window, the assay window, will appear with a flowchart in the middle. Select the "RunSession" item (it should be the only item present). On the right side of the screen a drop-down menu will appear. Find the name of your saved SkanIt RE run in this menu.</li>
	<li>Once you have selected your protocol, in the upper right corner click "Run this assay".</li>
	<li>A box will pop up, asking you to denote which magazine to use as the source, and which magazine is empty. The lower box on the screen corresponds to the front magazine. [Optional: It asks you to enter the number of plates loaded to determine an estimate for the amount of time it will take. This estimate is normally way off.]</li>
	<li>Ensure both the RapidStak and the VarioSkan are turned on, and press "OK"</li>
	<li>The RapidStak will automatically load your plates into the plate reader, allowing for continuous measurements of plates. Note: It is recommended to observe the first plate loading into the VarioSkan to ensure proper alignment of the machines. If the RapidStak does not load the plate reader properly, use the "Pause this assay" button in the top right corner of the PolaraRS window.</li>
	<li>Once the VarioSkan is done reading all the plates, remove the full magazine and place it on the magazine loading platform. Lift up the outer rectangle of the platform, and the magazine should slide off, leaving the plates standing in a pile in the middle. The plates can be disposed of according to your lab procedures.</li>
	<li>To export the absorbance readings, open SkanIt RE software, and choose "Open an existing file".</li>
	<li>Select the directory where you saved your session, hit the "+" icon to expand the list and under the title heading will be options labeled "Container 1" to "Container N" depending on the number of plates. Select the first plate to be analyzed.</li>
	<li>In the menu bar at the top of the page, select "Data Processing &gt; Report/Export"</li>
	<li>Choose the options desired for export. Note: I typically select "Plate Layout" and "Photometric" data for export.</li>
	<li>Click "View Report" and then "File &gt; Save". Choose the desired directory. The output format is a Microsoft Excel spreadsheet</li>
</ol>
5. Representative Results
An example of absorbance readings from a single 384 well plate containing a positive clone is shown in Figure 2. Positive clones show a marked increase in absorbance over those not expressing cellulase activity. Differences in assay time, well location on the plate, or DNP concentration (may be introduced by filtering out un-dissolved DNP) can affect absolute absorbance readings. Relative absorbance readings, such as the difference in absorbance above the plate average or column average, are a more robust method of identifying cellulase positive clones.
Following identification of positive clones from the library plates, it is recommended to replicate all positive clones into a new plate for secondary screening. This eliminates effects arising from well location or plate variation and allows for more direct comparison between positive clones.
<img src="/files/ftp_upload/2461/2461fig1.jpg" alt="Figure 1" /> Figure 1. Flow chart of the high-throughput assay for a metagenomic library cloned into E. coli and stored at -80&deg;C.
<img src="/files/ftp_upload/2461/2461fig2.jpg" alt="Figure 2" /> Figure 2. Absorbance readings from one 384-well plate containing a positive clone. Cellulase positive clones can be identified by significantly increased absorbance over negative clones.

<ol>
	<li>Rubin, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genomics+of+cellulosic+biofuels.">Genomics of cellulosic biofuels.</a> Nature. 454, 841-845 (2008).</li><li>Voget, S., Steele, H. L., Streit, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+a+metagenome+derived+halotolerant+cellulase.">Characterization of a metagenome derived halotolerant cellulase.</a> J. Biotechnol. 126, 26-36 (2006).</li><li>Duan, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+partial+characterization+of+novel+genes+encoding+acidic+cellulases+from+metagenomes+of+buffalo+rumens.">Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens.</a> J. Appl. Microbiol. 107, 245-256 (2009).</li><li>Zhang, Y. H. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Outlook+for+cellulase+improvement:+Screening+and+selection+strategies.">Outlook for cellulase improvement: Screening and selection strategies.</a> Biotech. Advances. 24, 452-481 (2006).</li><li>Teather, R. M., Wood, P. J. <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+congo+red-polysaccharide+interactions+in+enumeration+and+characterization+of+cellulolytic+bacteria+from+the+bovine+rumen.">Use of congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen.</a> Appl. And Environ. Microbiol. 43, 777-780 (1982).</li><li>Sharrock, K. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellulase+assay+methods:+a+review.">Cellulase assay methods: a review.</a> J. Biochem and Biophys Methods. 17, 81-106 (1988).</li><li>Kasana, R. C., Salwan, R., Dhar, H., Dutt, S., Gulati, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+and+easy+method+for+detection+of+microbial+cellulases+on+agar+plates+using+Gram's+Iodine.">A rapid and easy method for detection of microbial cellulases on agar plates using Gram's Iodine.</a> Curr. Microbiology. 57, 503-507 (2008).</li><li>Huang, J. S., Tang, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitive+assay+for+cellulase+and+dextranase.">Sensitive assay for cellulase and dextranase.</a> Anal. Biochem. 73, 369-377 (1976).</li><li>Tull, D., Withers, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+cellulases+and+xylanases:+A+detailed+kinetic+study+of+the+exo-beta-1,4-glycanase+from+Cellulomonas+fimi.">Mechanisms of cellulases and xylanases: A detailed kinetic study of the exo-beta-1,4-glycanase from Cellulomonas fimi.</a> Biochemistry. 33, 6363-6370 (1994).</li><li>Martinez, A., Bradley, A. S., Waldbauer, J. R., Summons, R. E., DeLong, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteorhodopsin+photosystem+gene+expression+enables+photophosphorylation+in+a+heterologous+host.">Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.</a> PNAS. 104, 5590-5595 (2007).</li><li>Taupp, M., Lee, S., Hawley, A., Yang, J., Hallam, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large+Insert+Environmental+Genomic+Library+Production.">Large Insert Environmental Genomic Library Production.</a> J Vis Exp. , (2009).</li><li>Martinez, A., Tyson, G. W., DeLong, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Widespread+known+and+novel+phosphonate+utilization+pathways+in+marine+bacteria+revealed+by+functional+screening+and+metagenomic+analyses.">Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses.</a> Environ Microbiol. 12, 222-238 (2010).</li><li>Wild, J., Hradecna, Z., Szybalski, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conditionally+amplifiable+BACs:+Switching+from+single-copy+to+high-copy+vectors+and+genomic+clones.">Conditionally amplifiable BACs: Switching from single-copy to high-copy vectors and genomic clones.</a> Genome Research. 12, 1434-1444 (2002).</li><li>Johnson, E. 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No conflicts of interest declared.

A high throughput screen for the rapid detection of cellulolytic activity from a large insert genomic DNA metagenomic library expressed in E. coli is described in this protocol. This method is an improvement over the CMC/Congo Red assay commonly used in the literature. It is solution based, and allows for one-pot chemistry screening in 384-well plates, with the final output as absorbance readings from a plate reader allowing for quantitative analysis. The automation of each step of this process allows for the un...

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>qPix2</td>
<td>&nbsp;</td>
<td>Genetix</td>
<td>&nbsp;</td>
<td>With 384-pin gridding head</td>
</tr>
<tr>
<td>qFill3</td>
<td>&nbsp;</td>
<td>Genetix</td>
<td>&nbsp;</td>
<td>With 384-well manifold</td>
</tr>
<tr>
<td>Varioskan</td>
<td>&nbsp;</td>
<td>Thermo-Fisher</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>RapidStak</td>
<td>&nbsp;</td>
<td>Thermo-Fisher</td>
<td>&nbsp;</td>
<td>Connected to Varioskan</td>
</tr>
<tr>
<td>Micro90 Detergent</td>
<td>&nbsp;</td>
<td>Cole-Parmer</td>
<td>18100-00</td>
<td>Diluted to 2% in water</td>
</tr>
<tr>
<td>Ethanol</td>
<td>&nbsp;</td>
<td>Major Lab Supplier</td>
<td>&nbsp;</td>
<td>Diluted to 80% in water</td>
</tr>
<tr>
<td>Chloramphenicol</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>C0378</td>
<td>12.5mg/mL in ethanol</td>
</tr>
<tr>
<td>LB broth, Miller</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP1426-2</td>
<td>25g/L, autoclaved</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>384-well flat bottom plates</td>
<td>&nbsp;</td>
<td>Corning</td>
<td>3680</td>
<td>&nbsp;</td>
<tr>
<td>L-(+)-Arabinose</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>A3256</td>
<td>100mg/mL in water</td>
</tr>
<tr>
<td>Potassium Acetate</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>P171</td>
<td>50mM in water, autoclaved, adjusted to pH 5.5 with HCl</td>
</tr>
<tr>
<td>Triton X-100</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP151</td>
<td>&nbsp;</td>
<tr>
<td>Trizma hydrochloride</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>T3253</td>
<td>In TE buffer solution, 100mM</td>
</tr>
<tr>
<td>EDTA disodium salt</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>E5134</td>
<td>In TE buffer solution, 10mM</td>
</tr>
<tr>
<td>2,4-dinitrophenyl cellobioside</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>Provided by Dr. Steve Withers, UBC</td>
</tr>
<tr>
<td>Dimethyl Sulfoxide</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>D8418</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

a high throughput screen for biomining cellulase activity from metagenomic libraries

Cellulose, the most abundant source of organic carbon on the planet, has wide-ranging industrial applications with increasing emphasis on biofuel production 1. Chemical methods to modify or degrade cellulose typically require strong acids and high temperatures. As such, enzymatic methods have become prominent in the bioconversion process. While the identification of active cellulases from bacterial and fungal isolates has been somewhat effective, the vast majority of microbes in nature resist laboratory cultivation. Environmental genomic, also known as metagenomic, screening approaches have great promise in bridging the cultivation gap in the search for novel bioconversion enzymes. Metagenomic screening approaches have successfully recovered novel cellulases from environments as varied as soils 2, buffalo rumen 3 and the termite hind-gut 4 using carboxymethylcellulose (CMC) agar plates stained with congo red dye (based on the method of Teather and Wood 5). However, the CMC method is limited in throughput, is not quantitative and manifests a low signal to noise ratio 6. Other methods have been reported 7,8 but each use an agar plate-based assay, which is undesirable for high-throughput screening of large insert genomic libraries. Here we present a solution-based screen for cellulase activity using a chromogenic dinitrophenol (DNP)-cellobioside substrate 9. Our library was cloned into the pCC1 copy control fosmid to increase assay sensitivity through copy number induction 10. The method uses one-pot chemistry in 384-well microplates with the final readout provided as an absorbance measurement. This readout is quantitative, sensitive and automated with a throughput of up to 100X 384-well plates per day using a liquid handler and plate reader with attached stacking system.

Watch this Scientific Journal Video about A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries at JoVE.com

A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries

This protocol describes a high throughput screen for cellulolytic activity from a metagenomic library expressed in Escherichia coli. The screen is solution based and highly automated, and uses one-pot chemistry in 384 well microplates with the final readout as an absorbance measurement.

Cellulose, the most abundant source of organic carbon on the planet, has wide-ranging industrial applications with increasing emphasis on biofuel ...

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15.0K Views.  University of British Columbia - UBC. This protocol describes a high throughput screen for cellulolytic activity from a metagenomic library expressed in Escherichia coli. The screen is solution based and highly automated, and uses one-pot chemistry in 384 well microplates with the final readout as an absorbance measurement.

Video: A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries

Large-Scale Screens of Metagenomic Libraries

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation. Generating a streamlined procedure for creating and screening metagenomic libraries is therefore useful for efficient high-throughput investigations into the genetic and metabolic properties of uncultured microbial assemblages. Here, key protocols are presented on video, which we propose is the most useful format for accurately describing a long process that alternately depends on robotic instrumentation and (human) manual interventions. First, we employed robotics to spot library clones onto high-density macroarray membranes, each of which can contain duplicate colonies from twenty-four 384-well library plates. Automation is essential for this procedure not only for accuracy and speed, but also due to the miniaturization of scale required to fit the large number of library clones into highly dense spatial arrangements. Once generated, we next demonstrated how the macroarray membranes can be screened for genes of interest using modified versions of standard protocols for probe labeling, membrane hybridization, and signal detection. We complemented the visual demonstration of these procedures with detailed written descriptions of the steps involved and the materials required, all of which are available online alongside the video.

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation.  Generating a ...

High-throughput Yeast Plasmid Overexpression Screen

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, including those with direct relevance to human disease. Because of its short generation time and well-characterized genome, a major experimental advantage of the yeast model system is the ability to perform genetic screens to identify genes and pathways that are involved in a given process. Over the last thirty years such genetic screens have been used to elucidate the cell cycle, secretory pathway, and many more highly conserved aspects of eukaryotic cell biology 1-5. In the last few years, several genomewide libraries of yeast strains and plasmids have been generated 6-10. These collections now allow for the systematic interrogation of gene function using gain- and loss-of-function approaches 11-16. Here we provide a detailed protocol for the use of a high-throughput yeast transformation protocol with a liquid handling robot to perform a plasmid overexpression screen, using an arrayed library of 5,500 yeast plasmids. We have been using these screens to identify genetic modifiers of toxicity associated with the accumulation of aggregation-prone human neurodegenerative disease proteins. The methods presented here are readily adaptable to the study of other cellular phenotypes of interest.

Here we describe a plasmid overexpression screen in Saccharomyces cerevisiae, using an arrayed plasmid library and a high-throughput yeast transformation protocol with a liquid handling robot.

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, ...

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted into fuel alcohols1. The potential for enzymatic hydrolysis of cellulosic biomass to provide renewable energy has intensified efforts to engineer cellulases for economical fuel production2. Of particular interest are fungal cellulases3-8, which are already being used industrially for foods and textiles processing.
Identifying active variants among a library of mutant cellulases is critical to the engineering process; active mutants can be further tested for improved properties and/or subjected to additional mutagenesis. Efficient engineering of fungal cellulases has been hampered by a lack of genetic tools for native organisms and by difficulties in expressing the enzymes in heterologous hosts. Recently, Morikawa and coworkers developed a method for expressing in E. coli the catalytic domains of endoglucanases from H. jecorina3,9, an important industrial fungus with the capacity to secrete cellulases in large quantities. Functional E. coli expression has also been reported for cellulases from other fungi, including Macrophomina phaseolina10 and Phanerochaete chrysosporium11-12. 
We present a method for high throughput screening of fungal endoglucanase activity in E. coli. (Fig 1) This method uses the common microbial dye Congo Red (CR) to visualize enzymatic degradation of carboxymethyl cellulose (CMC) by cells growing on solid medium. The activity assay requires inexpensive reagents, minimal manipulation, and gives unambiguous results as zones of degradation (&#x201C;halos&#x201D;) at the colony site. Although a quantitative measure of enzymatic activity cannot be determined by this method, we have found that halo size correlates with total enzymatic activity in the cell. Further characterization of individual positive clones will determine , relative protein fitness. 
Traditional bacterial whole cell CMC/CR activity assays13 involve pouring agar containing CMC onto colonies, which is subject to cross-contamination, or incubating cultures in CMC agar wells, which is less amenable to large-scale experimentation. Here we report an improved protocol that modifies existing wash methods14 for cellulase activity: cells grown on CMC agar plates are removed prior to CR staining. Our protocol significantly reduces cross-contamination and is highly scalable, allowing the rapid screening of thousands of clones. In addition to H. jecorina enzymes, we have expressed and screened endoglucanase variants from the Thermoascus aurantiacus and Penicillium decumbens (shown in Figure 2), suggesting that this protocol is applicable to enzymes from a range of organisms.

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

We describe a low cost, high throughput method to screen for fungal endoglucanase activity in E. coli. The method relies on a simple visual readout of substrate degradation, does not require enzyme purification, and is highly scalable. This allows for the rapid screening of large libraries of enzyme variants.

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted ...

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Whole transcriptome sequencing by mRNA-Seq is now used extensively to perform global gene expression, mutation, allele-specific expression and other genome-wide analyses. mRNA-Seq even opens the gate for gene expression analysis of non-sequenced genomes. mRNA-Seq offers high sensitivity, a large dynamic range and allows measurement of transcript copy numbers in a sample. Illumina&#x2019;s genome analyzer performs sequencing of a large number (&gt; 107) of relatively short sequence reads (&lt; 150 bp).The &quot;paired end&quot; approach, wherein a single long read is sequenced at both its ends, allows for tracking alternate splice junctions, insertions and deletions, and is useful for de novo transcriptome assembly.
One of the major challenges faced by researchers is a limited amount of starting material. For example, in experiments where cells are harvested by laser micro-dissection, available starting total RNA may measure in nanograms. Preparation of mRNA-Seq libraries from such samples have been described1, 2 but involves significant PCR amplification that may introduce bias. Other RNA-Seq library construction procedures with minimal PCR amplification have been published3, 4 but require microgram amounts of starting total RNA.
Here we describe a protocol for the Illumina Genome Analyzer II platform for mRNA-Seq sequencing for library preparation that avoids significant PCR amplification and requires only 10 nanograms of total RNA. While this protocol has been described previously and validated for single-end sequencing5, where it was shown to produce directional libraries without introducing significant amplification bias, here we validate it further for use as a paired end protocol. We selectively amplify polyadenylated messenger RNAs from starting total RNA using the T7 based Eberwine linear amplification method, coined &quot;T7LA&quot; (T7 linear amplification). The amplified poly-A mRNAs are fragmented, reverse transcribed and adapter ligated to produce the final sequencing library. For both single read and paired end runs, sequences are mapped to the human transcriptome6 and normalized so that data from multiple runs can be compared. We report the gene expression measurement in units of transcripts per million (TPM), which is a superior measure to RPKM when comparing samples7.

Here we describe a method for preparation of both single read and paired end Illumina mRNA-Seq sequencing libraries for gene expression analysis based on T7 linear RNA amplification. This protocol requires only 10 nanograms of starting total RNA and generates highly consistent libraries representing whole transcripts.

Whole transcriptome sequencing by mRNA-Seq is now used extensively to perform global gene expression, mutation, allele-specific expression and other ...

High Throughput Microinjections of Sea Urchin Zygotes

Microinjection into cells and embryos is a common technique that is used to study a wide range of biological processes. In this method a small amount of treatment solution is loaded into a microinjection needle that is used to physically inject individual immobilized cells or embryos. Despite the need for initial training to perform this procedure for high-throughput delivery, microinjection offers maximum efficiency and reproducible delivery of a wide variety of treatment solutions (including complex mixtures of samples) into cells, eggs or embryos. Applications to microinjections include delivery of DNA constructs, mRNAs, recombinant proteins, gain of function, and loss of function reagents. Fluorescent or colorimetric dye is added to the injected solution to enable instant visualization of efficient delivery as well as a tool for reliable normalization of the amount of the delivered solution. The described method enables microinjection of 100-400 sea urchin zygotes within 10-15 min.

Microinjection is a common technique used to deliver DNA constructs, mRNAs, morpholino antisense oligonucleotides or other treatments into eggs, embryos, and cells of various species.

Microinjection into cells and embryos is a common technique that is used to study a wide range of biological processes. In this method a small amount of ...

A Manual Small Molecule Screen Approaching High-throughput Using Zebrafish Embryos

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology due to their considerable degree of genetic conservation with humans. Chemical genetics entails testing the effect that small molecules have on a biological process and is becoming a popular translational research method to identify therapeutic compounds. Zebrafish are specifically appealing to use for chemical genetics because of their ability to produce large clutches of transparent embryos, which are externally fertilized. Furthermore, zebrafish embryos can be easily drug treated by the simple addition of a compound to the embryo media. Using whole-mount in situ hybridization (WISH), mRNA expression can be clearly visualized within zebrafish embryos. Together, using chemical genetics and WISH, the zebrafish becomes a potent whole organism context in which to determine the cellular and physiological effects of small molecules. Innovative advances have been made in technologies that utilize machine-based screening procedures, however for many labs such options are not accessible or remain cost-prohibitive. The protocol described here explains how to execute a manual high-throughput chemical genetic screen that requires basic resources and can be accomplished by a single individual or small team in an efficient period of time. Thus, this protocol provides a feasible strategy that can be implemented by research groups to perform chemical genetics in zebrafish, which can be useful for gaining fundamental insights into developmental processes, disease mechanisms, and to identify novel compounds and signaling pathways that have medically relevant applications.

The zebrafish is an excellent experimental organism to study vertebrate developmental processes and model human disease. Here, we describe a protocol on how to perform a manual high-throughput chemical screen in zebrafish embryos with a whole-mount in situ hybridization (WISH) read-out.

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology ...

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays focus on transcriptional regulation, being essentially aimed at the identification of promoter-targeting molecules. As a result, post-transcriptional mechanisms are largely uncovered by gene expression targeted drug development. Here we describe a cell-based assay aimed at investigating the role of the 3&#39; untranslated region (3&#8217; UTR) in the modulation of the fate of its mRNA, and at identifying compounds able to modify it. The assay is based on the use of a luciferase reporter construct containing the 3&#8217; UTR of a gene of interest stably integrated into a disease-relevant cell line. The protocol is divided into two parts, with the initial focus on the primary screening aimed at the identification of molecules affecting luciferase activity after 24 hr of treatment. The second part of the protocol describes the counter-screening necessary to discriminate compounds modulating luciferase activity specifically through the 3&#8217; UTR. In addition to the detailed protocol and representative results, we provide important considerations about the assay development and the validation of the hit(s) on the endogenous target. The described cell-based reporter gene assay will allow scientists to identify molecules modulating protein levels via post-transcriptional mechanisms dependent on a 3&#8217; UTR.

Here we describe a cell-based reporter gene assay as a valuable tool to screen chemical libraries for compounds modulating post-transcriptional control mechanisms exerted through 3&#8217; UTR.

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays ...

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII1, and one synthetic chromosome arm, synIXR2, have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis. However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

Designer chromosomes of the Synthetic Yeast Genome project, Sc2.0, can be distinguished from their native counterparts using a PCR-based genotyping assay called PCRTagging, which has a presence/absence endpoint. Here we describe a high-throughput real time PCR detection method for PCRTag genotyping.

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic ...

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Site-directed mutagenesis has long been used as a method to interrogate protein structure, function and evolution. Recent advances in massively-parallel sequencing technology have opened up the possibility of assessing the functional or fitness effects of large numbers of mutations simultaneously. Here, we present a protocol for experimentally determining the effects of all possible single amino acid mutations in a protein of interest utilizing high-throughput sequencing technology, using the 263 amino acid antibiotic resistance enzyme TEM-1 &#946;-lactamase as an example. In this approach, a whole-protein saturation mutagenesis library is constructed by site-directed mutagenic PCR, randomizing each position individually to all possible amino acids. The library is then transformed into bacteria, and selected for the ability to confer resistance to &#946;-lactam antibiotics. The fitness effect of each mutation is then determined by deep sequencing of the library before and after selection. Importantly, this protocol introduces methods which maximize sequencing read depth and permit the simultaneous selection of the entire mutation library, by mixing adjacent positions into groups of length accommodated by high-throughput sequencing read length and utilizing orthogonal primers to barcode each group. Representative results using this protocol are provided by assessing the fitness effects of all single amino acid mutations in TEM-1 at a clinically relevant dosage of ampicillin. The method should be easily extendable to other proteins for which a high-throughput selection assay is in place.

We present a protocol for the functional assessment of comprehensive single-site saturation mutagenesis libraries of proteins utilizing high-throughput sequencing. Importantly, this approach uses orthogonal primer pairs to multiplex library construction and sequencing. Representative results using TEM-1 &#946;-lactamase selected at a clinically relevant dosage of ampicillin are provided.

Site-directed mutagenesis has long been used as a method to interrogate protein structure, function and evolution. Recent advances in massively-parallel ...

Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples

Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4&#8211;24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.

Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples

Here, we present a protocol to prepare DNA samples from food and environmental microbiomes for concerted detection and subtyping of Salmonella through quasimetagenomic sequencing. The combined use of culture enrichment, immunomagnetic separation (IMS), and multiple displacement amplification (MDA) allows effective concentration of Salmonella genomic DNA from food and environmental samples.&#160;