Name: experimental protocol for detecting cyanobacteria in liquid and solid samples with an antibody microarray chip
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Description: Watch this Scientific Journal Video about Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip at JoVE.com

We thank Dr. Antonio Quesada from the Universidad Aut&#243;noma de Madrid for providing cyanobacterial strains. This work was funded by the Subdirecci&#243;n General de Proyectos de Investigaci&#243;n of the Spanish Ministerio de Econom&#237;a y Competitividad (MINECO), grants no. AYA2011-24803 and ESP2014-58494-R.

1. Preparation of the Immunogens
<ol>
	<li>Grow each cyanobacterial strain in the corresponding culture medium under conditions described in Table 1. 
	NOTE: Growth medium and culture conditions for each cyanobacteria strain are listed in Table 1. All the cyanobacterial strains, with the exception of K17, belong to Antonio Quesada&#39;s group from Autonoma University (Madrid, Spain). The antibody against Planktothrix rubescens was generated from a natural sample of the monospecific bloom of this cyanobacterium from Vilasouto reservoir (northern Spain).</li>
	<li>Quantify the number of cells using a cell counting chamber by optical microscopy to obtain approximately 108 cells/mL from a late exponential or stationary growth phase culture.</li>
	<li>Harvest cells from 5 mL of culture by centrifugation at 2,000 x g for 5 min.</li>
	<li>Discard the supernatant and resuspend the cells in a 10-mL tube with 5 mL of 1x phosphate-buffered saline (1x PBS) to obtain around 108 cells/mL.</li>
	<li>Homogenize and lyse the cells of the suspension by sonication for 5 cycles, 30 s each, with a 30- to 60-s pause on ice, using a portable, hand-held ultrasonic processor or by dipping the tube into the water bath of a cell disruptor at maximum amplitude (30 kHz).</li>
	<li>Repeat steps 1.3 - 1.5 for each strain of cyanobacterium. 
	NOTE: Sonication produces cell disruption and cellular content release. While proteins and polysaccharides are good immunogens, specific molecules, such as lipids and nucleic acids, do not induce a humoral immunogenic response by themselves. Therefore, they must bind to carriers, such as polysaccharides or proteins, to increase the molecular complexity. In addition, sonication releases intracellular material that can trigger antibody production.</li>
</ol>
2. Production of Polyclonal Antibodies
<ol>
	<li>Prepare the first immunogen dose by mixing 0.5 mL of the ultrasonicated cell lysate obtained in step 1.5 with 0.5 mL of complete Freund&#39;s adjuvant. Deliver it to the operator of an animal facility for polyclonal rabbit antibody production.</li>
	<li>Prepare three more doses as before for further use as memory boosts in the antibody production process by mixing 0.5 mL of the same homogenate/lysate obtained in step 1.5 with 0.5 mL of incomplete Freund&#39;s adjuvant. Give them to the animal facility to fulfill the antibody production process.</li>
	<li>Repeat steps 2.1 and 2.2 for each new antibody production process. 
	NOTE: Normally, antibody production is entrusted to specialized animal facilities or companies, because appropriate licensing and training are required to work with animals. The companies supply a relative enzyme-linked immunosorbent assay (ELISA) measurement of the quantity of antigen-specific antibodies present in the serum sample.</li>
</ol>
3. Antibody Purification
<ol>
	<li>Purify the immunoglobulin G (IgG) fraction from both the immune and the pre-immune serum collected in step 2 by protein-A affinity chromatography. Some commercial purification kits, based on cartridge systems, work well; follow the provider instructions.</li>
	<li>When the purification kit does not provide a desalting system, change the buffer after the elution of the purified antibodies to 0.1x PBS, either by dialysis or by using centrifugal filter devices with a 100-kDa (or lower) membrane pore size.</li>
	<li>Determine the antibody concentration by measuring the absorbance at 280 nm or by using colorimetric methods, such as Bradford23, Lowry24, or Bicinchoninic acid (BCA)25. 
	NOTE: It is important to avoid including amine groups in the elution buffer (e.g., Tris buffers) because they compete with the antibody for binding to solid surfaces activated with epoxy groups. After purification, it is important to test the antibody activity with ELISA.</li>
</ol>
4. Fluorescence Antibody Labeling
<ol>
	<li>Label the purified antibodies obtained in section 3 with a fluorochrome (e.g., a far-red fluorescent dye) by dissolving a commercial vial containing dye for labeling 1 mg of protein into 100 &#181;L of dimethyl sulfoxide (DMSO). Add 2 &#181;L of the dissolved dye to each antibody preparation at a concentration of 2 mg/mL in a final volume of 50 &#181;L in 50 mM phosphate-buffered saline (pH 8.5).</li>
	<li>Maintain the labeling reactions under continuous agitation for 1 h at ambient temperature and 1,200 rpm on a vibrating platform.</li>
	<li>Purify the labeled antibodies by size exclusion chromatography (e.g., using a gel with a fractionation range between 1.5 and 30 kDa trapped into a column), following supplier recommendations.</li>
	<li>Measure the absorbance at 280 nm and at 650 nm in eluates and calculate the labeling efficiencies following supplier recommendations. 
	NOTE: Up to 50 x 50-&#181;L antibody-labeling reactions can be done with a single vial of the fluorescent dye for labeling 1 mg of protein. It is recommended to cover the tubes with aluminum foil or, alternatively, to use opaque 0.5-mL tubes to avoid quenching processes after step 4.3. For IgG antibodies, optimal labeling is achieved with 3-7 mol of the dye per mol of antibody.</li>
</ol>
5. CYANOCHIP Production
<ol>
	<li>Antibodies and controls in printing solution
	<ol>
		<li>Prepare 30 &#181;L of each purified antibody in printing solution by mixing each antibody at 1 mg/mL in a commercial 1x protein printing buffer with 0.01% (v/v) Tween 20 (a non-ionic detergent), all as final concentrations. 
		NOTE: Alternatively, an antibody solution may contain 20% glycerol, 1% (w/v) sucrose (or trehalose, as a preservative), and 0.01% (v/v) Tween 20 in carbonate buffer (pH 8.5).</li>
		<li>Prepare 30 &#181;L of the printing solution as controls: (a) 1x protein printing buffer with 0.01% (v/v) Tween 20, (b) protein-A purified pre-immune serum at 1 mg/mL in 1x protein printing buffer with 0.01% (v/v) Tween 20, and (c) bovine serum albumin (BSA) at 1 mg/mL in 1x protein printing buffer with 0.01% (v/v) Tween 20.</li>
		<li>Prepare 30 &#181;L of a fluorescently labeled, purified pre-immune serum at different concentrations (e.g., from 50 &#181;g/mL to 1 &#181;g/mL) in 1x protein printing buffer with Tween 20, as in step 5.1.1. These samples will be used as fluorescent frame markers and for relative fluorescence quantification after spotting.</li>
		<li>Add 30 &#181;L per well of the printing solutions prepared in steps 5.1.1, 5.1.2, and 5.1.3 to the highest-quality 384-well microplates for microarray manufacturing, such as polypropylene. 
		NOTE: Protein printing buffer increases the quality and stability of the antibodies, and Tween 20 homogenizes spot morphology and builds up protein coupling up. It is recommended to maintain the 384-well microplate at 4 &#176;C before use. Store it at -20 &#176;C for long periods of time. Polypropylene has low DNA, protein, cell extract, and small-molecule intrinsic binding.</li>
	</ol>
	</li>
	<li>Antibody printing onto a microscope slide 
	NOTE: Print the antibodies onto activated microscope slides by using different array platforms, like contact, split-needle, or non-contact devices, such as piezoelectric printers or &#34;ink jet&#34; technologies. In this work, the CYANOCHIP has been routinely printed by contact using a robotic system (arrayer) capable of spotting nL quantities of the antibodies at the &#181;m scale.
	<ol>
		<li>Set the environmental conditions of the printing room to 20 &#176;C and 40 - 50% relative humidity.</li>
		<li>Set up the slide substrates (e.g., 75- x 25-mm epoxy-activated microscope glass slides) to perform several identical antibody arrays on each slide.</li>
		<li>Spot each purified antibody, including controls and the reference frame, in a triplicate spot pattern; under these conditions, the spots are 180 - 200 &#181;m in diameter.</li>
		<li>After printing, leave the slides for at least 30 min at ambient temperature to let them dry, and then store them at 4 &#176;C; for working in the field, the slides can be transported and stored at ambient temperature for several months. 
		NOTE: The CYANOCHIP is printed in a triplicate spot microarray format with 3 x 8 identical microarrays per slide or 9 identical arrays in a 1 x 9 microarray format. Each array size must not be higher than the reaction chamber dimensions for a 24-well gasket (usually 7.5 x 6.5 mm in a 3 x 8 hybridization chamber).</li>
		<li>Before using the microarray to analyze environmental samples, use FSMI to determine the working dilution for each antibody in a titration curve. For each antibody, use a standard concentration of the corresponding immunogen (103 - 104 cells/mL) and serial dilutions of the fluorescent antibody (between 1:500 and 1:32,000). The optimal antibody concentration corresponds to 50% of the maximum signal intensity obtained in the titration curve. Also, the sensitivity and specificity for each antibody must be determined, as described in Blanco et al.22.</li>
	</ol>
	</li>
</ol>
6. Preparation of Environmental Multianalyte Extracts for the Fluorescent Sandwich Microarray Immunoassay (FSMI)
<ol>
	<li>Multianalyte extract from a liquid sample
	<ol>
		<li>Take 1 - 100 mL of the liquid sample with a sterile syringe (e.g., water from the shore of a water reservoir); the amount of sample is greatly dependent upon the potential concentration of the targets.</li>
		<li>Concentrate the cells by passing the water sample through a 3-&#181;m pore size, 47-mm diameter polycarbonate filter; a cellular concentration between 103 - 108 cells/mL is desirable for positive detection, but the actual concentration is unknown.</li>
		<li>Recover the biomass collected in the filter with 1 mL of a modified Tris-buffered saline, Tween 20-reinforced buffer (TBSTRR; 0.4 M Tris-HCl (pH 8), 0.3 M NaCl, and 0.1% Tween 20) by scraping it with a spatula into a 15-mL tube.</li>
		<li>Homogenize and disaggregate by using a hand-held ultrasonic processor, as described in step 1.5, or just by pipetting up and down multiple times; this prepares the sample for analysis by the microarray.</li>
	</ol>
	</li>
	<li>Multianalyte extract from a solid sample
	<ol>
		<li>Weigh up to 0.5 g of the solid sample (e.g., rock, soil, or sediments) into a 10-mL tube and add up to 2 mL of TBSTRR.</li>
		<li>Sonicate by immersing the sonicator probe in the tube, by dipping the tube into the water bath of a powerful sonicator horn, or by using a hand-held sonicator. Perform at least 5 x 30-s cycles at 30 kHz, stopping for 30 s while on ice .</li>
		<li>Filter to remove sand, clay, and other coarse material with a 10-mL syringe coupled to a 10- to 12-mm diameter, 5- to 20-&#181;m pore size nylon filter holder. Push the sample through the filter into a 1.5-mL tube. If the filter saturates, agitate the suspension in the syringe and take it to a new one; this prepares the filtrate material for the immunoassay (step 7). 
		NOTE: The buffering capacity of TBSTRR depends on the type of sample. It is important to carry out the immunoassay immediately after the preparation of the environmental extract to avoid the effect of enzymatic degradation on the analytes. Alternatively, add protease inhibitors into the environmental extract and freeze at -80 &#176;C until the next step.</li>
	</ol>
	</li>
</ol>
7. Fluorescent Sandwich Microarray Immunoassay (FSMI)
<ol>
	<li>Blocking the CYANOCHIP 
	NOTE: Immediately before use, treat the printed slides to block all free epoxy groups on the slide and to remove the excess of non-covalently bound antibodies.
	<ol>
		<li>Immerse the microarray into 0.5 M Tris-HCl (pH 9) with 5% (w/v) BSA solution on a clean surface (e.g., Petri dish or a 50-mL tube) with mild agitation from a rocker platform for 5 min. Alternatively, lay the slide down onto a 100- to 200-&#181;L drop of the above solution with the microarray spots facing it. Leave for 3 - 5 min and then proceed.</li>
		<li>Carefully pick up the slide using plastic-tipped forceps; try to avoid touching microarray zones. Eliminate the excess of liquid by softly knocking the slide onto a paper towel. Immerse it in 0.5 M Tris-HCl (pH 8) with 2% (w/v) BSA solution for 30 min with mild agitation from a rocker platform.</li>
		<li>Dry the slide by performing a short centrifugation (200 - 300 x g for 1 min) using a commercial microcentrifuge adapted for microscope slides. Alternatively, dry the slide by softly knocking onto a paper towel.</li>
	</ol>
	</li>
	<li>Incubation of the multianalyte sample extract with the microarray
	<ol>
		<li>Set up the slide in a commercial microarray hybridization cassette with 24 wells for multiple microarrays; follow the provider instructions.</li>
		<li>After slide and cassette assembly, pipette up to 50 &#181;L of the sample extract or a dilution of it in TBSTRR into each well of the cassette.</li>
		<li>Repeat step 7.2.2 for each sample to be analyzed.</li>
		<li>As a blank control, pipette 50 &#181;L of TBSTRR buffer into at least two separate wells of the cassette.</li>
		<li>Incubate at ambient temperature for 1 h with mixing by pipetting every 15 min or by leaving it under mild shaking. Alternatively, incubate for 12 h at 4 &#176;C. 
		NOTE: Use other incubation gaskets as a function of the microarray pattern. The time and temperature of the incubation in step 7.2.5 are empirical parameters that normally depend on the affinity and binding kinetics of each paired antigen-antibody.</li>
	</ol>
	</li>
	<li>Washing
	<ol>
		<li>Remove the samples by putting the cassette down and carefully knocking it onto a clean, absorbent paper.</li>
		<li>Wash the wells by adding 150 &#181;L of TBSTRR to each one, and eliminate the buffer, as above.</li>
		<li>Repeat step 7.3.2 three more times.</li>
	</ol>
	</li>
	<li>Incubation with fluorescent detector antibodies
	<ol>
		<li>Add 50 &#181;L of an antibody mixture containing the 17 anti-cyanobacterial-strain antibodies, each labeled with the fluorochrome in TBSTRR with 1% (w/v) BSA. Determine the concentration of each fluorescent antibody in the mixture (from 0.7 to 2 &#181;g/mL) by performing titration experiments of each antigen/antibody pair22.</li>
		<li>Incubate for 1 h at ambient temperature, as described in step 7.2.5, or for 12 h at 4 &#176;C.</li>
	</ol>
	</li>
	<li>Washing out the fluorescent antibodies
	<ol>
		<li>Remove the fluorescent unbound antibodies, as in step 7.3.</li>
		<li>Disassemble the cassette and immerse the slide into 0.1x PBS (e.g., in a 50-mL tube) for a quick rinse.</li>
		<li>Dry the slide as in step 7.1.3.</li>
	</ol>
	</li>
</ol>
8. Scanning for Fluorescence
<ol>
	<li>Scan the slide for fluorescence at the maximum emission fluorescence peak for far-red fluorescent dye in a scanner for fluorescence. Take several images of the microarrays at different scanning parameters, generally by lowering the laser gain value. 
	NOTE: Avoid saturated spots (&#62; 65,000 fluorescence counts)&#8212;they are out of scale and may introduce quantification errors.</li>
</ol>
9. Image Processing and Data Analysis
<ol>
	<li>Use a commercial software for image analysis and quantification; the software provides measurements of the fluorescence intensity (FI; median or mean of all pixels from a single spot) for each spot of the whole microarray. Subtract the local background around the spots: FI = FIspot - FIlocal background.</li>
	<li>Save the FI data and open them using a spreadsheet program.</li>
	<li>Use the values obtained for the blank arrays as the negative control to identify and discard the false positives. Apply the following equation to calculate the FI for each antibody spot: FI = (FIsample - FIblank), where FIsample = FIspot - FIlocal background in the microarrays run with sample extracts and FIblank = FIspot - FIlocal background in the blank microarrays.</li>
	<li>Apply an additional cut-off threshold of 2- to 3-fold the average of the FI of the whole microarray to minimize the probability of false positives; this is especially relevant for poor-quality microarray images and low signal-to-noise ratios.</li>
	<li>Create plots and/or perform further analysis as necessary.</li>
</ol>

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Technol. 49 (3), 1611-1620 (2015).</li><li>Bradford, M. 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+Rapid+and+Sensitive+Method+for+the+Quantitation+of+Microgram+Quantities+of+Protein+Utilizing+the+Principle+of+Protein-Dye+Binding.">A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding.</a> Anal. Chem. 72, 248-254 (1976).</li><li>Lowry, O. H., Rosebrough, N. J., Farr, A. L., Randall, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+measurement+with+the+Folin+phenol+reagent.">Protein measurement with the Folin phenol reagent.</a> J. Biol. Chem. 193 (1), 265-275 (1951).</li><li>Smith, P. K., 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=Measurement+of+protein+using+Bicinchoninic+acid.">Measurement of protein using Bicinchoninic acid.</a> Anal. Biochem. 150 (1), 76-85 (1985).</li><li>Rivas, L. A., Aguirre, J., Blanco, Y., Gonz&#225;lez-Toril, E., Parro, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Graph-based+deconvolution+analysis+of+multiplex+sandwich+microarray+immunoassays:+applications+for+environmental+monitoring.">Graph-based deconvolution analysis of multiplex sandwich microarray immunoassays: applications for environmental monitoring.</a> Environ. Microbiol. 13 (6), 1421-1432 (2011).</li><li>Blanco, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deciphering+the+prokaryotic+community+and+metabolisms+in+south+african+deep-mine+biofilms+through+antibody+microarrays+and+graph+theory.">Deciphering the prokaryotic community and metabolisms in south african deep-mine biofilms through antibody microarrays and graph theory.</a> PloS One. 9 (2), e114180 (2014).</li><li>Gas, F., Baus, B., Quer&#233;, J., Chapelle, A., Dreanno, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+detection+and+quantification+of+the+marine+toxic+algae,+Alexandrium+minutum,+using+a+super-paramagnetic+immunochromatographic+strip+test.">Rapid detection and quantification of the marine toxic algae, Alexandrium minutum, using a super-paramagnetic immunochromatographic strip test.</a> Talanta. 147, 581-589 (2016).</li><li>Parro, V., 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=SOLID3:+a+multiplex+antibody+microarray-based+optical+sensor+instrument+for+in+situ+life+detection+in+planetary+exploration.">SOLID3: a multiplex antibody microarray-based optical sensor instrument for in situ life detection in planetary exploration.</a> Astrobiology. 11, 15-28 (2011).</li><li>McKay, C. P., 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=The+Icebreaker+Life+Mission+to+Mars:+a+search+for+biomolecular+evidence+for+life.">The Icebreaker Life Mission to Mars: a search for biomolecular evidence for life.</a> Astrobiology. 13, 334-353 (2013).</li></ol>

The authors have nothing to disclose.

Here, a multiplex fluorescent sandwich immunoassay using the CYANOCHIP, a 17-antibody microarray for the detection and identification of a wide range of cyanobacterial genera, is described22. These cyanobacteria represent the most frequent benthic and planktonic genera in freshwater habitats, some of them being toxin producers. Recently, the fluorescent sandwich immunoassay format has been used to identify microorganisms and/or bioanalytes in environmental applications26...

The detection and monitoring of microorganisms in complex natural microbial communities are crucial in many fields, including biomedicine, environmental ecology, and astrobiology. Cyanobacteria are prokaryotic microorganisms well-known for their ability to form blooms (excessive proliferation) of cells in fresh water. They are ubiquitous, and many species are able to produce toxins, leading not only to a potential risk for human health, but also to an ecological impact. In this regard, it is essential to develop rapid and sensitive methods for the early detection of cyanobacteria and/or their toxins in soil and water. For this purpose, a multiplex fluorescent sandwich microarray immunoassay (FSMI) has been developed as a tool for water managers to help them in making decisions and, consequently, in implementing proper water management programs.
A diverse range of methods has been developed to detect and identify cyanobacterial cells and cyanotoxins in soil and water, including optical microscopy, molecular biology, and immunological techniques. These methods can vary greatly in the information they provide. Microscopic techniques are based on cell morphology and the detection of in vivo fluorescence from cyanobacterial pigments, such as phycocyanin or chlorophyll a1. Although they are quick and cheap methods for real-time and frequent monitoring that inform about the type and number of cyanobacteria present in a sample, they do not give information about the potential toxicity. In addition, they require a certain level of expertise, considering that it is often very difficult to distinguish between closely related species2. To overcome these limitations, light microscopy must be accompanied by both biological and biochemical screening assays and physicochemical methods for the identification and quantification of cyanotoxins.
Enzyme-linked immunosorbent assays (ELISA), protein phosphate inhibition assays (PPIA), and neurochemical tests in mice are examples of biochemical screening assays for the detection of cyanotoxins. While the first two are rapid and sensitive methodologies, false positives have been described when using ELISA and PPIA tests are restricted to three types of toxins. The mouse bioassay is a qualitative technique with low sensitivity and precision, and special licensing and training is required. In addition, it does not give information about the type of toxins present in a sample. Cyanotoxins can be identified and quantified by other analytical methods, such as high-performance liquid chromatography (HPLC), liquid chromatography-mass spectrometry (LC-MS), gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), or matrix-assisted laser desorption/ionization time of flight (MALDI-TOF). However, this is only possible if reference standards, which are needed to determine individual toxin concentrations in complex samples, are available3,4. Moreover, these methods are time-consuming; require costly equipment, supplies, and sample preparation; and must be performed by experienced and specialized staff.
Molecular-based methods have been applied for decades to detect, identify, and quantify cyanobacteria and their corresponding cyanotoxins thanks to the sequence information published in the genome databases (e.g., National Center for Biotechnology Information, NCBI). Among these methods are those based on the polymerase chain reaction (PCR), which requires the design of sets of primers for DNA amplification and depend on previous knowledge of DNA sequences of different cyanobacterial species. While gene detection, like the phycocyanin operon, leads to accurate identification at the genus level, some species or strains are undetected with this method. However, toxin-encoding genes, such as those belonging to the microcystin operon, facilitate the identification of toxins in samples where the producers are scarce5. Nonetheless, the detection of toxin markers by PCR does not necessarily imply toxicity in the environment. Furthermore, the set of primers developed to analyze the whole range of species of cyanobacteria and toxin producers present in a sample is still incomplete, and further studies must be done to identify unknown species. Other molecular techniques are non-PCR-based, such as fluorescence in situ hybridization (FISH) and DNA microarrays.
In the last two decades, microarray technology has gained importance in many fields of application, particularly in environmental monitoring. DNA microarrays allow for discrimination between species and analytes4,6,7,8,9,10, but they are considered very laborious and time-consuming tasks that involve multiple steps (e.g., microarray performance, DNA extraction, PCR amplification, and hybridization). For that reason, less time-consuming assays based on antibodies, such as sandwich and competitive immunological microarrays, have become an essential and reliable high-throughput method for the detection of multiple environmental analytes11,12,13. The capability of antibodies to specifically recognize their target compounds and to detect small amounts of analytes and proteins, along with the possibility of producing antibodies against almost any substance, make antibody microarrays a powerful technique for environmental purposes. In addition, the capability of achieving multiple analyses in a single assay, with limits of detection ranging from ppb to ppm, is one of the main advantages of this method14.
Antibody-based biosensors have proved to be sensitive and rapid tools for the detection of a wide range of pathogens and toxins in environmental monitoring15,16,17,18,19,20,21. While DNA methods involve several steps, the antibody-based microarrays only require a small sample preparation that is mainly based on a short lysis step in an appropriate solution buffer. Delehanty and Ligler15 reported the simultaneous detection of proteins and bacterial analytes in complex mixtures based on an antibody sandwich immunoassay capable of detecting a protein concentration of 4 ppb and 104 cfu/mL of cells. Szkola et al.21 have developed a cheap and reliable multiplex microarray for the simultaneous detection of proteotoxins and small toxins, compounds that might be used in biological warfare. They detected concentrations of ricin toxin, with a limit of detection of 3 ppb, in less than 20 min. Recently, the CYANOCHIP, an antibody microarray-based biosensor for the in situ detection of toxic and nontoxic cyanobacteria, has been described22. This microarray allows for the identification of potential cyanobacterial blooms, mostly in aquatic environments, which are difficult to identify microscopically. The limit of detection of the microarray is 102 - 103 cells for most species, turning this biosensor into a cost-effective tool for the multiplex detection and identification of cyanobacteria, even at the species level. All these properties make the antibody microarray technique, and particularly the method presented in this work, a quicker and simpler method compared to the aforementioned techniques.
This work presents two examples of experiments that use an antibody microarray-based biosensor to detect the presence of cyanobacteria in soil and water samples. It is a simple and reliable method based on a sandwich immunoassay format that requires very small sample volumes and very basic sample preparation. The method requires a short time and can be easily performed in the field.

<table><tbody><tr><td>0.22 mm pore diameter filters</td><td>Millipore</td><td>GSWP04700</td><td>For preparation of immunogens</td></tr><tr><td>Eppendorf&amp;nbsp; 5424R microcentrifuge</td><td>Fisher Scientific</td><td></td><td>For preparation of immunogens</td></tr><tr><td>Phosphate buffer saline (PBS) pH 7.4 (10x)</td><td>Thermo Fisher Scientific</td><td>70011036</td><td>50 mM potassium phosphate, 150 mM NaCl, pH 7.4</td></tr><tr><td>Ultrasonic processor UP50H</td><td>Hielscher</td><td></td><td>For preparation of immunogens</td></tr><tr><td>Complete Freund&#039;s adjuvant&amp;nbsp;</td><td>Sigma-Aldrich</td><td>F5881</td><td>Immunopotentiator</td></tr><tr><td>Incomplete Freud&#039;s adjuvant</td><td>Sigma-Aldrich&amp;nbsp;</td><td>F5506</td><td>For boost injections</td></tr><tr><td>Protein A antibody purification kit&amp;nbsp;&amp;nbsp;</td><td>Sigma-Aldrich</td><td>PURE1A&amp;nbsp;</td><td>For isolation of IgG</td></tr><tr><td>Centrifugal filter devices MWCO&amp;lt;100 kDa</td><td>Millipore</td><td>UFC510096-96K</td><td>For isolation of IgG</td></tr><tr><td>Dialysis tubings, benzoylated</td><td>Sigma-Aldrich</td><td>D7884-10FT</td><td>For isolation of IgG</td></tr><tr><td>Illustra Microspin G-50 columns&amp;nbsp;</td><td>GE-HealthCare</td><td>GE27-5330-02</td><td>For isolation of IgG</td></tr><tr><td>Bradford reagent</td><td>Sigma-Aldrich</td><td>B6916-500 mL</td><td>To quantify the antibody concentration</td></tr><tr><td>MicroBCA protein assay kit&amp;nbsp;</td><td>Thermo Scientific</td><td>23235</td><td>To quantify the antibody concentration</td></tr><tr><td>Protein arraying buffer 2x</td><td>Whatman (Sigma Aldrich)&amp;nbsp;</td><td>S00537</td><td>Printing buffer; 30 - 40% glycerol in 1x PBS with 0.01% Tween 20</td></tr><tr><td>Tween 20&amp;nbsp;</td><td>Sigma-Aldrich&amp;nbsp;</td><td>P9416</td><td>Non-ionic detergent</td></tr><tr><td>Bovine serum albumin (BSA)</td><td>Sigma-Aldrich&amp;nbsp;</td><td>A9418</td><td>Control&amp;nbsp; for printing; blocking reagent</td></tr><tr><td>384-wells microplate</td><td>Genetix</td><td>X6004</td><td>For antibody printing</td></tr><tr><td>Robot arrayer for multiple slides</td><td>MicroGrid II TAS arrayer from Digilab</td><td></td><td>For antibody printing</td></tr><tr><td>Epoxy substrate glass slides</td><td>Arrayit corporation</td><td>VEPO25C</td><td>Solid support for antibody printing</td></tr><tr><td>Alexa Fluor-647 Succinimidyl-ester&amp;nbsp;</td><td>Molecular probes</td><td>A20006</td><td>Fluorochrome</td></tr><tr><td>DMSO&amp;nbsp;</td><td>Sigma-Aldrich&amp;nbsp;</td><td>D8418</td><td>Fluorochrome dissolvent</td></tr><tr><td>Heidolph Titramax vibrating platform shaker</td><td>Fisher Scientific</td><td></td><td>For antibody labeling&amp;nbsp;</td></tr><tr><td>Illustra Microspin G-50 columns&amp;nbsp;</td><td>Healthcare</td><td>27-5330-01</td><td>For purification of labeled antibodies</td></tr><tr><td>Safe seal brown 0.5 mL tubes</td><td>Sarstedt</td><td>72,704,001</td><td>For labeled antibodies storage&amp;nbsp;</td></tr><tr><td>Nanodrop 1000 spectrophotometer</td><td>Thermo Scientific</td><td></td><td>To quantify antibody concentration and labeling efficiency</td></tr><tr><td>3 &amp;micro;m pore size polycarbonate 47 mm diameter filter</td><td>Millipore</td><td>TMTP04700</td><td>To concentrate cells</td></tr><tr><td>1 M Trizma hydrochloride solution pH 8</td><td>Sigma-Aldrich&amp;nbsp;</td><td>T3038</td><td>For TBSTRR preparation; to block slides</td></tr><tr><td>Sodium chloride</td><td>Sigma-Aldrich&amp;nbsp;</td><td>S7653</td><td>For TBSTRR preparation</td></tr><tr><td>20 &amp;micro;m nylon filters&amp;nbsp;</td><td>Millipore</td><td>NY2004700</td><td>For environmental extract preparation</td></tr><tr><td>10 - 12 mm filter holders</td><td>Millipore</td><td>SX0001300</td><td>For environmental extract preparation</td></tr><tr><td>Protease inhibitor cocktail</td><td>Sigma-Aldrich&amp;nbsp;</td><td>P8340</td><td>For environmental extract storage</td></tr><tr><td>1 M Trizma hydrochloride solution pH 9</td><td>Sigma-Aldrich&amp;nbsp;</td><td>T2819</td><td>To block slides</td></tr><tr><td>Heidolph Duomax 1030 rocking platform shaker</td><td>VWR</td><td></td><td>To block slides; for incubation processes&amp;nbsp;</td></tr><tr><td>VWR Galaxy miniarray microcentrifuge</td><td>VWR</td><td>C1403-VWR</td><td>To dry slides</td></tr><tr><td>Multi-Well microarray hybridization cassette</td><td>Arrayit corporation</td><td>AHC1X24</td><td>Cassette for 24 assays per slide</td></tr><tr><td>GenePix 4100A microarray scanner&amp;nbsp;</td><td>Molecular Devices</td><td></td><td>Scanner for fluorescence</td></tr><tr><td>GenePix Pro Software</td><td>Molecular Devices</td><td></td><td>Software for image analysis and quantification</td></tr></tbody></table>

experimental protocol for detecting cyanobacteria in liquid and solid samples with an antibody microarray chip

Global warming and eutrophication make some aquatic ecosystems behave as true bioreactors that trigger rapid and massive cyanobacterial growth; this has relevant health and economic consequences. Many cyanobacterial strains are toxin producers, and only a few cells are necessary to induce irreparable damage to the environment. Therefore, water-body authorities and administrations require rapid and efficient early-warning systems providing reliable data to support their preventive or curative decisions. This manuscript reports an experimental protocol for the in-field detection of toxin-producing cyanobacterial strains by using an antibody microarray chip with 17 antibodies (Abs) with taxonomic resolution (CYANOCHIP). Here, a multiplex fluorescent sandwich microarray immunoassay (FSMI) for the simultaneous monitoring of 17 cyanobacterial strains frequently found blooming in freshwater ecosystems, some of them toxin producers, is described. A microarray with multiple identical replicates (up to 24) of the CYANOCHIP was printed onto a single microscope slide to simultaneously test a similar number of samples. Liquid samples can be tested either by direct incubation with the antibodies (Abs) or after cell concentration by filtration through a 1- to 3-&#956;m filter. Solid samples, such as sediments and ground rocks, are first homogenized and dispersed by a hand-held ultrasonicator in an incubation buffer. They are then filtered (5 - 20 &#956;m) to remove the coarse material, and the filtrate is incubated with Abs. Immunoreactions are revealed by a final incubation with a mixture of the 17 fluorescence-labeled Abs and are read by a portable fluorescence detector. The whole process takes around 3 h, most of it corresponding to two 1-h periods of incubation. The output is an image, where bright spots correspond to the positive detection of cyanobacterial markers.

This work describes a multiplex immunoassay test for the simultaneous identification of the most relevant freshwater cyanobacterial species (Table 1) using the CYANOCHIP antibody microarray. The microarray can be a 3 x 8 microarray format printed onto microscope slides. Each microarray is made up of a set of 17 antibodies printed in a triplicate spot pattern, their corresponding pre-immune antibodies and BSA as negative controls. The microarrays also include a fluorescent...

Watch this Scientific Journal Video about Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip at JoVE.com

Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

The presence of cyanobacterial toxins in fresh water reservoirs for human consumption is a major concern for water management authorities. To evaluate the risk of water contamination, this article describes an protocol for the in-field detection of cyanobacterial strains in liquid and solid samples by using an antibody microarray chip.

Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

Global warming and eutrophication make some aquatic ecosystems behave as true bioreactors that trigger rapid and massive cyanobacterial growth; this has ...

experimental-protocol-for-detecting-cyanobacteria-liquid-solid

Universidad San Sebastian

Research

JoVE Journal

Environment

9.0K Views.  Centro de Astrobiología (CAB, INTA-CSIC). The presence of cyanobacterial toxins in fresh water reservoirs for human consumption is a major concern for water management authorities. To evaluate the risk of water contamination, this article describes an protocol for the in-field detection of cyanobacterial strains in liquid and solid samples by using an antibody microarray chip.

Video: Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Often cellular behavior and cellular responses are analyzed at the population level where the responses of many cells are pooled together as an average result masking the rich single cell behavior within a complex population. Single cell protein detection and quantification technologies have made a remarkable impact in recent years. Here we describe a practical and flexible single cell analysis platform based on addressable droplet microarrays. This study describes how the absolute copy numbers of target proteins may be measured with single cell resolution. The tumor suppressor p53 is the most commonly mutated gene in human cancer, with more than 50% of total cancer cases exhibiting a non-healthy p53 expression pattern. The protocol describes steps to create 10 nL droplets within which single human cancer cells are isolated and the copy number of p53 protein is measured with single molecule resolution to precisely determine the variability in expression. The method may be applied to any cell type including primary material to determine the absolute copy number of any target proteins of interest.

Here we present addressable droplet microarrays (ADMs), a droplet array based method able to determine absolute protein abundance in single cells. We demonstrate the capability of ADMs to characterize the heterogeneity in expression of the tumor suppressor protein p53 in a human cancer cell line.

Often cellular behavior and cellular responses are analyzed at the population level where the responses of many cells are pooled together as an average ...

Cancer Research

Bacterial Detection &amp; Identification Using Electrochemical Sensors

Electrochemical sensors are widely used for rapid and accurate measurement of blood glucose and can be adapted for detection of a wide variety of analytes. Electrochemical sensors operate by transducing a biological recognition event into a useful electrical signal. Signal transduction occurs by coupling the activity of a redox enzyme to an amperometric electrode. Sensor specificity is either an inherent characteristic of the enzyme, glucose oxidase in the case of a glucose sensor, or a product of linkage between the enzyme and an antibody or probe.
Here, we describe an electrochemical sensor assay method to directly detect and identify bacteria. In every case, the probes described here are DNA oligonucleotides. This method is based on sandwich hybridization of capture and detector probes with target ribosomal RNA (rRNA). The capture probe is anchored to the sensor surface, while the detector probe is linked to horseradish peroxidase (HRP). When a substrate such as 3,3',5,5'-tetramethylbenzidine (TMB) is added to an electrode with capture-target-detector complexes bound to its surface, the substrate is oxidized by HRP and reduced by the working electrode. This redox cycle results in shuttling of electrons by the substrate from the electrode to HRP, producing current flow in the electrode.

Bacterial Detection & Identification Using Electrochemical Sensors

We describe an electrochemical sensor assay method for rapid bacterial detection and identification. The assay involves a sensor array functionalized with DNA oligonucleotide capture probes for ribosomal RNA (rRNA) species-specific sequences. Sandwich hybridization of target rRNA with the capture probe and a horseradish peroxidase-linked DNA oligonucleotide detector probe produces a measurable amperometric current.

Electrochemical  sensors are widely used for rapid and accurate measurement of blood glucose and  can be adapted for detection of a wide variety of ...

Bioengineering

A Microfluidic Chip for the Versatile Chemical Analysis of Single Cells

We present a microfluidic device that enables the quantitative determination of intracellular biomolecules in multiple single cells in parallel. For this purpose, the cells are passively trapped in the middle of a microchamber. Upon activation of the control layer, the cell is isolated from the surrounding volume in a small chamber. The surrounding volume can then be exchanged without affecting the isolated cell. However, upon short opening and closing of the chamber, the solution in the chamber can be replaced within a few hundred milliseconds. Due to the reversibility of the chambers, the cells can be exposed to different solutions sequentially in a highly controllable fashion, e.g. for incubation, washing, and finally, cell lysis. The tightly sealed microchambers enable the retention of the lysate, minimize and control the dilution after cell lysis. Since lysis and analysis occur at the same location, high sensitivity is retained because no further dilution or loss of the analytes occurs during transport. The microchamber design therefore enables the reliable and reproducible analysis of very small copy numbers of intracellular molecules (attomoles, zeptomoles) released from individual cells. Furthermore, many microchambers can be arranged in an array format, allowing the analysis of many cells at once, given that suitable optical instruments are used for monitoring. We have already used the platform for proof-of-concept studies to analyze intracellular proteins, enzymes, cofactors and second messengers in either relative or absolute quantifiable manner.

In this article we present a microfluidic chip for single cell analysis. It allows the quantification of intracellular proteins, enzymes, cofactors, and second messengers by means of fluorescent assays or immunoassays.&#160;

We present a microfluidic device that enables the quantitative determination of intracellular biomolecules in multiple single cells in parallel. For this ...

A Microfluidic-based Electrochemical Biochip for Label-free DNA Hybridization Analysis

Miniaturization of analytical benchtop procedures into the micro-scale provides significant advantages in regards to reaction time, cost, and integration of pre-processing steps. Utilizing these devices towards the analysis of DNA hybridization events is important because it offers a technology for real time assessment of biomarkers at the point-of-care for various diseases. However, when the device footprint decreases the dominance of various physical phenomena increases. These phenomena influence the fabrication precision and operation reliability of the device. Therefore, there is a great need to accurately fabricate and operate these devices in a reproducible manner in order to improve the overall performance. Here, we describe the protocols and the methods used for the fabrication and the operation of a microfluidic-based electrochemical biochip for accurate analysis of DNA hybridization events. The biochip is composed of two parts: a microfluidic chip with three parallel micro-channels made of polydimethylsiloxane (PDMS), and a 3 x 3 arrayed electrochemical micro-chip. The DNA hybridization events are detected using electrochemical impedance spectroscopy (EIS) analysis. The EIS analysis enables monitoring variations of the properties of the electrochemical system that are dominant at these length scales. With the ability to monitor changes of both charge transfer and diffusional resistance with the biosensor, we demonstrate the selectivity to complementary ssDNA targets, a calculated detection limit of 3.8 nM, and a 13% cross-reactivity with other non-complementary ssDNA following 20 min&#160;of incubation. This methodology can improve the performance of miniaturized devices by elucidating on the behavior of diffusion at the micro-scale regime and by enabling the study of DNA hybridization events.

We present a microfluidic-based electrochemical biochip for DNA hybridization detection. Following ssDNA probe functionalization, the specificity, sensitivity, and detection limit are studied with complementary and non-complementary ssDNA targets. Results illustrate the influence of the DNA hybridization events on the electrochemical system, with a detection limit of 3.8 nM.

Miniaturization of analytical benchtop procedures into the micro-scale provides significant advantages in regards to reaction time, cost, and integration ...

Early Detection of Cyanobacterial Blooms and Associated Cyanotoxins using Fast Detection Strategy

Fast detection of cyanobacteria and cyanotoxins is achieved using a Fast Detection Strategy (FDS). Only 24 h are needed to unravel the presence of cyanobacteria and related cyanotoxins in water samples and in an organic matrix, such as bivalve extracts. FDS combines remote/proximal sensing techniques with analytical/bioinformatics analyses. Sampling spots are chosen through multi-disciplinary, multi-scale, and multi-parametric monitoring in a three-dimensional physical space, including remote sensing. Microscopic observation and taxonomic analysis of the samples are performed in the laboratory setting, which allows for the identification of cyanobacterial species. Samples are then extracted with organic solvents and processed with LC-MS/MS. Data obtained by MS/MS are analyzed using a bioinformatic approach using the online platform Global Natural Products Social (GNPS) to create a network of molecules. These networks are analyzed to detect and identify toxins, comparing data of the fragmentation spectra obtained by mass spectrometry with the GNPS library. This allows for the detection of known toxins and unknown analogues that appear related in the same molecular network.

A fast-multidisciplinarystrategy for early detection of cyanobacterial blooms and associated cyanotoxins is described here. It allows for the detection of cyanobacteria and related cyanotoxins in water samples and in organic matrices, such as bivalve samples, in 24 h.

Fast detection of cyanobacteria and cyanotoxins is achieved using a Fast Detection Strategy (FDS). Only 24 h are needed to unravel the presence of ...

Chemistry

Electrowetting-based Digital Microfluidics Platform for Automated Enzyme-linked Immunosorbent Assay

Electrowetting is the effect by which the contact angle of a droplet exposed to a surface charge is modified. Electrowetting-on-dielectric (EWOD) exploits the dielectric properties of thin insulator films to enhance the charge density and hence boost the electrowetting effect. The presence of charges results in an electrically induced spreading of the droplet which permits purposeful manipulation across a hydrophobic surface. Here, we demonstrate EWOD-based protocol for sample processing and detection of four categories of antigens, using an automated surface actuation platform, via two variations of an Enzyme-Linked Immunosorbent Assay (ELISA) methods. The ELISA is performed on magnetic beads with immobilized primary antibodies which can be selected to target a specific antigen. An antibody conjugated to HRP binds to the antigen and is mixed with H2O2/Luminol for quantification of the captured pathogens. Assay completion times of between 6 and 10 min were achieved, whilst minuscule volumes of reagents were utilized.

Electrowetting-based digital microfluidic is a technique that utilizes a voltage-driven change in the apparent contact angle of a microliter-volume droplet to facilitate its manipulation. Combining this with functionalized magnetic beads enables the integration of multiple laboratory unit operations for sample preparation and identification of pathogens using Enzyme-linked Immunosorbent Assay (ELISA).

Electrowetting is the effect by which the contact angle of a droplet exposed to a surface charge is modified. Electrowetting-on-dielectric (EWOD) exploits ...

Chemically-blocked Antibody Microarray for Multiplexed High-throughput Profiling of Specific Protein Glycosylation in Complex Samples

In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that allows for the glycosylation profiling of specific proteins. Glycosylation of proteins is the most prevalent post-translational modification found on proteins, and leads diversified modifications of the physical, chemical, and biological properties of proteins. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases. However, current methods to study protein glycosylation typically are too complicated or expensive for use in most normal laboratory or clinical settings and a more practical method to study protein glycosylation is needed. The new protocol described in this study makes use of a chemically blocked antibody microarray with glycan-binding protein (GBP) detection and significantly reduces the time, cost, and lab equipment requirements needed to study protein glycosylation. In this method, multiple immobilized glycoprotein-specific antibodies are printed directly onto the microarray slides and the N-glycans on the antibodies are blocked. The blocked, immobilized glycoprotein-specific antibodies are able to capture and isolate glycoproteins from a complex sample that is applied directly onto the microarray slides. Glycan detection then can be performed by the application of biotinylated lectins and other GBPs to the microarray slide, while binding levels can be determined using Dylight 549-Streptavidin. Through the use of an antibody panel and probing with multiple biotinylated lectins, this method allows for an effective glycosylation profile of the different proteins found in a given human or animal sample to be developed.
Introduction
Glycosylation of protein, which is the most ubiquitous post-translational modification on proteins, modifies the physical, chemical, and biological properties of a protein, and plays a fundamental role in various biological processes1-6. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases 7-12. In fact, most current cancer biomarkers, such as the L3 fraction of &alpha;-1 fetoprotein (AFP) for hepatocellular carcinoma 13-15, and CA199 for pancreatic cancer 16, 17 are all aberrant glycan moieties on glycoproteins. However, methods to study protein glycosylation have been complicated, and not suitable for routine laboratory and clinical settings. Chen et al. has recently invented a chemically blocked antibody microarray with a glycan-binding protein (GBP) detection method for high-throughput and multiplexed profile glycosylation of native glycoproteins in a complex sample 18. In this affinity based microarray method, multiple immobilized glycoprotein-specific antibodies capture and isolate glycoproteins from the complex mixture directly on the microarray slide, and the glycans on each individual captured protein are measured by GBPs. Because all normal antibodies contain N-glycans which could be recognized by most GBPs, the critical step of this method is to chemically block the glycans on the antibodies from binding to GBP. In the procedure, the cis-diol groups of the glycans on the antibodies were first oxidized to aldehyde groups by using NaIO4 in sodium acetate buffer avoiding light. The aldehyde groups were then conjugated to the hydrazide group of a cross-linker, 4-(4-N-MaleimidoPhenyl)butyric acid Hydrazide HCl (MPBH), followed by the conjugation of a dipeptide, Cys-Gly, to the maleimide group of the MPBH. Thus, the cis-diol groups on glycans of antibodies were converted into bulky none hydroxyl groups, which hindered the lectins and other GBPs bindings to the capture antibodies. This blocking procedure makes the GBPs and lectins bind only to the glycans of captured proteins. After this chemically blocking, serum samples were incubated with the antibody microarray, followed by the glycans detection by using different biotinylated lectins and GBPs, and visualized with Cy3-streptavidin. The parallel use of an antibody panel and multiple lectin probing provides discrete glycosylation profiles of multiple proteins in a given sample 18-20. This method has been used successfully in multiple different labs 1, 7, 13, 19-31. However, stability of MPBH and Cys-Gly, complicated and extended procedure in this method affect the reproducibility, effectiveness and efficiency of the method. In this new protocol, we replaced both MPBH and Cys-Gly with one much more stable reagent glutamic acid hydrazide (Glu-hydrazide), which significantly improved the reproducibility of the method, simplified and shorten the whole procedure so that the it can be completed within one working day. In this new protocol, we describe the detailed procedure of the protocol which can be readily adopted by normal labs for routine protein glycosylation study and techniques which are necessary to obtain reproducible and repeatable results.

In this study, we describe an improved protocol for a multiplexed high-throughput antibody microarray with lectin detection method that can be used in glycosylation profiling of specific proteins. This protocol features new reliable reagents and significantly reduces the time, cost, and lab equipment requirements as compared to the previous procedure.

 In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that ...

Biology

Human Serum Anti-aquaporin-4 Immunoglobulin G Detection by Cell-based Assay

Anti-aquaporin-4 (AQP4) immunoglobulin G (IgG) is the core diagnostic biomarker for neuromyelitis optica spectrum disorders (NMOSD). The cell-based assay (CBA) is a widely used method to detect anti-AQP4 IgG in human serum with high sensitivity and specificity. Briefly, serum anti-AQP4 IgG is captured by AQP4-transfected cell that is fixed on the biochip then detected by a fluorescein-labelled secondary antibody. Fluorescence microscopy is utilized to visualize the fluorescence, and the intensity of fluorescence is evaluated by at least two experienced clinicians. A final diagnosis of NMOSD can be made based on the combination of anti-AQP4 IgG detection results, clinical manifestations, and neuroradiological findings. According to previous studies, CBA is more sensitive and specific than other anti-AQP4 IgG detection methods, and it can be applied to both clinical diagnosis and studies of NMOSD. The method has limitations; for example, an international scale to evaluate serum anti-AQP4 IgG titers is still lacking. Here, a detailed protocol for human serum anti-AQP4 IgG detection using CBA is described.

Cell-based assay is a widely used method to detect serum anti-aquaporin-4 immunoglobulin G. This method could be applied to clinical diagnosis and scientific researches of neuromyelitis optical spectrum disorders.

Anti-aquaporin-4 (AQP4) immunoglobulin G (IgG) is the core diagnostic biomarker for neuromyelitis optica spectrum disorders (NMOSD). The cell-based assay ...

Immunology and Infection

Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes

The influenza virus remains a significant cause of mortality worldwide due to the limited effectiveness of currently available vaccines. A key challenge to the development of universal influenza vaccines is high antigenic diversity resulting from antigenic drift. Overcoming this challenge requires novel research tools to measure the breadth of serum antibodies directed against many virus strains across different antigenic subtypes. Here, we present a protocol for analyzing the breadth of serum antibodies against diverse influenza virus strains using a protein microarray of influenza antigens.
This influenza antigen microarray is constructed by printing purified hemagglutinin and neuraminidase antigens onto a nitrocellulose-coated membrane using a microarray printer. Human sera are incubated on the microarray to bind antibodies against the influenza antigens. Quantum-dot-conjugated secondary antibodies are used to simultaneously detect IgG and IgA antibodies binding to each antigen on the microarray. Quantitative antibody binding is measured as fluorescence intensity using a portable imager. Representative results are shown to demonstrate assay reproducibility in measuring subtype-specific and cross-reactive influenza antibodies in human sera.
Compared to traditional methods such as ELISA, the influenza antigen microarray provides a high throughput multiplexed approach capable of testing hundreds of sera for multiple antibody isotypes against hundreds of antigens in a short time frame, and thus has applications in sero-surveillance and vaccine development. A limitation is the inability to distinguish binding antibodies from neutralizing antibodies.

We present a protocol for using a protein microarray constructed by printing influenza antigens onto nitrocellulose-coated slides to simultaneously probe serum for multiple antibody isotypes against over 250 antigens from different virus strains, thus allowing measurement of the breadth of serum antibodies across virus subtypes.

The influenza virus remains a significant cause of mortality worldwide due to the limited effectiveness of currently available vaccines. A key challenge ...

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators. This DNA-affinity-purified-chip method may be used for any purified regulator in any organism with a sequenced genome. The protocol involves allowing the purified tagged protein to bind to sheared genomic DNA and then affinity purifying the protein-bound DNA, followed by fluorescent labeling of the DNA and hybridization to a custom tiling array. Preceding steps that may be used to optimize the assay for specific regulators are also described. The peaks generated by the array data analysis are used to predict binding site motifs, which are then experimentally validated. The motif predictions can be further used to determine gene targets of orthologous response regulators in closely related species. We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the function for a sigma54-dependent response regulator DVU3023 in the environmental bacterium Desulfovibrio vulgaris Hildenborough.

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

This video article describes an in vitro microarray based method to determine the gene targets and binding sites for two component system response regulators.

In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of ...

Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

Summary

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Bacterial Detection & Identification Using Electrochemical Sensors

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A Microfluidic-based Electrochemical Biochip for Label-free DNA Hybridization Analysis

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Chemically-blocked Antibody Microarray for Multiplexed High-throughput Profiling of Specific Protein Glycosylation in Complex Samples

Human Serum Anti-aquaporin-4 Immunoglobulin G Detection by Cell-based Assay

Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems