We thank Texas A&#38;M Agrilife Research Insect Vectored Diseases Grant Program for funding. We also thank the Adelman lab members for help on developing this method and suggestions when drafting the manuscript, as well as Kevin Myles lab members. We also thank the reviewers and editors for their help to make this manuscript better.

1. Plate preparation
<ol>
	<li>Drill holes in 24 well tissue culture plate lids (4&#8722;6 holes per well) using a household drill with a ~1.6 mm (1/16 in) bit (Figure 2). 
	NOTE: These holes prevent water condensation from agarose to accumulate on the lid, where mosquitoes may lay eggs. The standard size of female Ae. aegypti (&#34;Liverpool&#34; strain) is ~3.11 mm wingspan. Reducing the size of the holes is recommended when using smaller mosquitoes to avoid escape from the plate.</li>
	<li>On the day prior to the oviposition experiment, wash and rinse the plates thoroughly and soak them in 1&#8722;5% bleach for 30&#8722;60 min at room temperature. Rinse thoroughly under running deionized water and dry them. 
	NOTE: This process reduces the chance of fungi and bacteria growing on agarose.</li>
	<li>Melt agarose at 2% in deionized water and immediately add 500 &#956;L of the molten agarose to each well of the 24 well plates using a 1,000 &#956;L pipette (Figure 3A,B). When the agarose begins to cool and clog the pipette tip, reheat the agarose and use a new pipette tip. 
	NOTE: Avoid touching the walls of the well with the pipette tip because it may leave a piece of agarose on the wall where a female may lay eggs, complicating the imaging and counting process.</li>
	<li>Before use, dry out any condensation on the well walls overnight on a lab bench (Figure 3C,D). 
	NOTE: The timeline of the EAgaL plate assay from blood feeding to larval imaging is depicted in Figure 4, which is for colony mosquitoes (Ae. aegypti &#8220;Liverpool&#8221;&#160;reared under 14 h light:10 h dark light cycle, 27 &#176;C, 80% relative humidity, 500 larvae in a 49.5 cm x 29.2 cm x 9.5 cm tray with 2 L of water), under insectary conditions. It is recommended that each laboratory test the EAgaL plate with the mosquitoes being used, especially when using different strains, different mosquito species, as well as different rearing protocols.</li>
</ol>
2. Mosquito feeding
NOTE: It is critical to use mosquitoes reared under uniform conditions for all treatment groups and control groups, because larval nutrition has an impact on mosquito fitness parameters10,11. Rear larvae under uncrowded conditions with sufficient food. Let female mosquitoes eclose in the presence of males so that mating is ensured, and mature for at least 3 days.
<ol>
	<li>Remove any source of water and/or sugar from the female mosquitoes at least 16 h prior to blood feeding in order to enhance blood feeding.</li>
	<li>Heat a water circulator for artificial feeding at 37 &#176;C and feed female mosquitoes using vertebrate blood placed in artificial feeders for 15&#8722;30 min (Figure 5A).</li>
	<li>Anesthetize mosquitoes with CO2 or on ice, transfer them to a glass dish on ice, and select ones that are engorged with blood (Figure 5B) into a container provided with 30% sucrose water for more than 72 h, when females finish excretion and egg development. 
	NOTE: If the females are provided with a lower concentration of sucrose water, remove the sucrose water and any wet surfaces after 48 h to prevent the females from ovipositing.</li>
</ol>
3. Oviposition
<ol>
	<li>About 1 h prior to transferring mosquitoes to the plates, add 2&#8722;3 drops (~80&#8722;120 &#956;L) of water into each plate well using a transfer pipette.</li>
	<li>At least 72 h after blood feeding, knockdown mosquitoes with CO2 or on ice, transfer them to a glass dish on ice, and individually place each mosquito on an inverted lid of the 24 well plate on ice (Figure 6A). 
	NOTE: This procedure has been applied from Ioshino et al.9.</li>
	<li>Once all 24 mosquitoes have been placed, cover the lid with an inverted plate bottom (Figure 6B), secure the lid and plate with a fresh, new rubber band and place in an environmental chamber (or rearing room) (Figure 6C) until mosquitoes recover (~10&#8722;15 min) and turn the plate right side up (Figure 6D).</li>
	<li>Allow the female mosquitoes to oviposit for 24&#8722;48 h and remove females by releasing them from the plates into a large cage. 
	NOTE: If it is important to keep track on individual females, anesthetize them by chilling the plates and remove them individually on ice. Delayed oviposition and dark excretions that interfere with egg counting were observed when females were transferred to the plates earlier than 72 h post blood meal (PBM) (Figure 7D).</li>
</ol>
4. Egg counting
<ol>
	<li>Check each well of the 24 well plate, as sometimes mosquitoes lay eggs on the wall of wells and at the margin of the agarose/plastic surface, where they are difficult to resolve in photographs. Using a wet paint brush, move the eggs laid on the wall and edge of agarose to the flat surface of the agarose so that all eggs are in a uniform plane and do not overlap with each other. 
	NOTE: The edge of the agarose is typically out of the camera&#8217;s focal plane due to the surface tension of the agarose solution.</li>
	<li>Using forceps, remove any broken legs, wings, and other particles in the wells that may interfere with imaging eggs (Figure 7C).</li>
	<li>Insert white paper underneath the plate to increase the contrast with dark mosquito eggs prior to imaging using a stereomicroscope illuminator (Figure 7A).</li>
	<li>Take an image of each well using a compact digital camera in microscope mode, which allows the user to focus on objects as close as 1 cm. This capability allows the camera to be placed directly on the plate to image eggs without a tripod or a stand (Figure 7A). To distinguish individual eggs laid in clumps, use the fine or super-fine mode to capture high-resolution images so that close-up details can be seen. 
	NOTE: Clear the memory card of the camera before use to prevent confusion between new and old images.</li>
	<li>After photographing each well of a plate, take an image of the entire plate with an imaging order label to distinguish each plate later (Figure 7E).</li>
	<li>Add a thin layer ~5 drops of water (~200 &#956;L) with a transfer pipette to each well to prevent its agarose plug and the eggs from drying and to induce embryo development and hatching. Pay attention to the water levels for the first few hours and check every day, because there may be water loss due to absorption by the agarose or evaporation. Add water when its level is too low for larvae to hatch. 
	NOTE: Evaporation of water occurs non-uniformly both within a plate and within a stack of plates. It has been observed that drying occurs in the following order: 1) corner wells (A1, A6, D1, D6) dry the fastest; followed by 2) wells at the outer edge of the plate (A2-A5, B1, B6, C1, C6, D2-D5); and last 3) wells inside. When plates are stacked, the top plate dries the fastest.</li>
	<li>Transfer the images to a computer with ImageJ (Fiji) and rename the files for easier organization such as &#8220;[plate ID]_[well ID].jpg&#8221; (Figure 8A,B).</li>
	<li>Create a spreadsheet file to record egg numbers (i.e., fecundity) and larval numbers and calculate hatch rate (i.e., fertility) (Figure 9E).</li>
	<li>Open the images with ImageJ (Fiji)12 and use the &#8220;multi-point&#8221; tool to mark each egg (Figure 9A&#8722;C); zoom-in or zoom-out using &#8220;+&#8221; or &#8220;&#8211;&#8221; key to count the eggs in&#160;clumps. After marking all the eggs, double-click the multi-point icon to bring up the number of marks (Figure 9D). Record the results in a spreadsheet.</li>
</ol>
5. Fertility assessment
NOTE: In 2 days, first instar larvae may begin to eclose in the wells. Wait for 3&#8722;5 more days before imaging/counting to ensure that all viable eggs hatch.
<ol>
	<li>Prepare larval food by mixing 1/16 tablespoon (~168 mg) of ground fish food (i.e., normal mosquito larval diet) in 20 mL of water and waiting for large solid particles to settle (Figure 10A&#8722;D). Start adding food (the supernatant) to the wells that contain hatched larvae as soon as they appear, because they do not survive for long without food. 
	NOTE: Excess addition of food particles may interfere with imaging and counting of hatched larvae.</li>
	<li>Approximately 5&#8211;8 days after addition of water to the wells, cool the plate by covering with crushed ice for 15&#8722;20 min to anesthetize larvae.</li>
	<li>Take images of each well while keeping the plates on ice as was done with the eggs. For larval images, provide a dark background by inserting a black material underneath the plate to help enhance the contrast. After photographing each well of a plate, take an image of the entire plate with an imaging order label to distinguish each plate later on. 
	NOTE: Images are taken while the plates are on ice because larval movement may compromise the counting. The plates are reusable; freeze and remove the mosquitoes and agarose to clean for the next use. The EAgaL plate is not suitable for rearing larvae to advanced stages.</li>
	<li>Open images with ImageJ (Fiji) and use the &#8220;multi-point&#8221; tool to count by clicking on each larva. Over the 3&#8722;5 days period some larvae may have molted, especially in wells with low numbers of larvae. Therefore, when counting, exclude the shed cuticles (i.e., exuviae), which look like head-only larvae with a little bit of body, or shrunken larvae (Figure 10E). Record the results in the spreadsheet.</li>
</ol>
6. Perform analysis
<ol>
	<li>Having collected all necessary data for the fecundity and fertility analysis, perform appropriate statistical analysis and create graphs using preferred software.</li>
</ol>

<ol>
	<li>Bond, J. G., 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=Optimization+of+irradiation+dose+to+Aedes+aegypti+and+Ae.+albopictus+in+a+sterile+insect+technique+program.">Optimization of irradiation dose to Aedes aegypti and Ae. albopictus in a sterile insect technique program.</a> PLoS One. 14 (2), 0212520 (2019).</li><li>Fernandes, K. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aedes+aegypti+larvae+treated+with+spinosad+produce+adults+with+damaged+midgut+and+reduced+fecundity.">Aedes aegypti larvae treated with spinosad produce adults with damaged midgut and reduced fecundity.</a> Chemosphere. 221, 464-470 (2019).</li><li>Inocente, E. A., 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=Insecticidal+and+Antifeedant+Activities+of+Malagasy+Medicinal+Plant+(Cinnamosma+sp.)+Extracts+and+Drimane-Type+Sesquiterpenes+against+Aedes+aegypti+Mosquitoes.">Insecticidal and Antifeedant Activities of Malagasy Medicinal Plant (Cinnamosma sp.) Extracts and Drimane-Type Sesquiterpenes against Aedes aegypti Mosquitoes.</a> Insects. 10 (11), 373 (2019).</li><li>Marrelli, M. T., Moreira, C. K., Kelly, D., Alphey, L., Jacobs-Lorena, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mosquito+transgenesis:+what+is+the+fitness+cost.">Mosquito transgenesis: what is the fitness cost.</a> Trends in Parasitology. 22 (5), 197-202 (2006).</li><li>da Silva Costa, G., Rodrigues, M. M. S., Silva, A. A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+a+blood-free+diet+for+Anopheles+darlingi+(Diptera:+Culicidae).">Toward a blood-free diet for Anopheles darlingi (Diptera: Culicidae).</a> Journal of Medical Entomology. , 217 (2019).</li><li>Gonzales, K. K., Tsujimoto, H., Hansen, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blood+serum+and+BSA,+but+neither+red+blood+cells+nor+hemoglobin+can+support+vitellogenesis+and+egg+production+in+the+dengue+vector+Aedes+aegypti.">Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti.</a> PeerJ. 3, 938 (2015).</li><li>Gonzales, K. 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=The+Effect+of+SkitoSnack,+an+Artificial+Blood+Meal+Replacement,+on+Aedes+aegypti+Life+History+Traits+and+Gut+Microbiota.">The Effect of SkitoSnack, an Artificial Blood Meal Replacement, on Aedes aegypti Life History Traits and Gut Microbiota.</a> Scientific Reports. 8 (1), 11023 (2018).</li><li>Tsujimoto, H., Anderson, M. A. E., Myles, K. M., Adelman, Z. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+Candidate+Iron+Transporters+From+the+ZIP/ZnT+Gene+Families+in+the+Mosquito+Aedes+aegypti.">Identification of Candidate Iron Transporters From the ZIP/ZnT Gene Families in the Mosquito Aedes aegypti.</a> Frontiers in Physiology. 9, 380 (2018).</li><li>Ioshino, R. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oviplate:+A+Convenient+and+Space-Saving+Method+to+Perform+Individual+Oviposition+Assays+in+Aedes+aegypti.">Oviplate: A Convenient and Space-Saving Method to Perform Individual Oviposition Assays in Aedes aegypti.</a> Insects. 9 (3), 103 (2018).</li><li>Price, D. P., Schilkey, F. D., Ulanov, A., Hansen, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+mosquitoes,+large+implications:+crowding+and+starvation+affects+gene+expression+and+nutrient+accumulation+in+Aedes+aegypti.">Small mosquitoes, large implications: crowding and starvation affects gene expression and nutrient accumulation in Aedes aegypti.</a> Parasites &amp; Vectors. 8, 252 (2015).</li><li>Valerio, L., Matilda Collins, C., Lees, R. S., Benedict, M. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Benchmarking+vector+arthropod+culture:+an+example+using+the+African+malaria+mosquito,+Anopheles+gambiae+(Diptera:+Culicidae).">Benchmarking vector arthropod culture: an example using the African malaria mosquito, Anopheles gambiae (Diptera: Culicidae).</a> Malaria Journal. 15 (1), 262 (2016).</li><li>Rueden, C. T., 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=ImageJ2:+ImageJ+for+the+next+generation+of+scientific+image+data.">ImageJ2: ImageJ for the next generation of scientific image data.</a> BMC Bioinformatics. 18 (1), 529 (2017).</li></ol>

The authors declare no conflicts of interest for this study.

The EAgaL plate drastically reduces labor, time, and space to conduct individual fecundity and fertility assays in Aedes aegypti when compared to the FT method. Preliminary comparison between the FT method and the EAgaL plate resulted in shorter times for all steps (imaging technique was applied to the FT method) (Table 1). As a reference, an estimate of startup and&#160;per assay (one 24 well EAgaL plate versus 24 FTs) costs are provided in Table 2.
<p class="jove_...

The control of mosquitoes to protect humans from vector-borne pathogens is an important public health goal, mainly due to the lack of effective vaccines for most of the pathogens carried by mosquitoes. Many studies aim to reduce mosquito fitness in conjunction with a field-applicable population reduction strategy1,2,3. This includes extensive studies to create transgenic mosquitoes and/or CRISPR/Cas9 knockout lines. Such population modification approaches require a detailed assessment of individual fitness parameters4. Conventional laboratory techniques to assess the fitness of female mosquitoes includes the individual containment of mated, blood-fed female mosquitoes in 100 mL containers5, modified 50 mL conical tubes, or tubes for Drosophila rearing modified by providing moist surfaces using damp cotton and filter paper discs for oviposition (i.e., egg papers)1,2,6,7. Such methods require a relatively large space (e.g., 30 cm x 30 cm x 10 cm: W x L x H for up to 100 Drosophila tubes) (Figure 1), and the manipulation of individual egg papers for counting eggs and hatching larvae, which can be labor intensive. This manuscript presents a method to count mosquito eggs and determine hatch rates using 24 well plates and agarose as an oviposition surface to circumvent these issues8.
Concurrently, Ioshino et al.9 described a detailed method using 12 and 24 well plates to perform egg counting obtained from individual females. Their protocol represented a significant improvement from conventional methods in saving time and space9. However, the protocol they described continues to use wet filter paper as a surface for oviposition, which requires unfolding each individual paper to get counts, as eggs are often found underneath or in folds. Their protocol also did not include the use of imaging technologies or a method for larval counting.
Presented is an improved method to perform fitness assays for egg number (i.e., fecundity) and hatch rate (i.e., fertility) using agarose as an oviposition surface in a 24 well tissue culture plate format for Ae. aegypti that oviposit on moist surfaces. These plates were named &#8220;EAgaL&#8221; plates, from Egg, Agarose, and Larva. These 24 well plates provide individual mosquitoes with a minimal surface to lay eggs, thus simplifying and drastically reducing the time and effort needed to count and maintain eggs and hatched larvae for a few days. The EAgaL plate uses translucent agarose for the oviposition surface, which eliminates the need for handling egg papers and finding the eggs and larvae when hatched; photographing each well establishes a long-term archived record of the results and separates the counting process in both time and space from the rearing/handling process, where time is often limited.

<table>
	<tbody>
		<tr>
			<td>1.6 mm &#934; drill bit</td>
			<td></td>
			<td></td>
			<td>alternatively heated nails can be used</td>
		</tr>
		<tr>
			<td>1000 &#956;L pipette tips (long)</td>
			<td>Olympus plastics</td>
			<td>24-165RL</td>
			<td></td>
		</tr>
		<tr>
			<td>24-well tissue culture plate</td>
			<td>Thermo Scientific</td>
			<td>930186</td>
			<td>clear, flat-bottom with ringed lid plates</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>VWR</td>
			<td>0710-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Compact digital camera</td>
			<td>Olympus</td>
			<td>TG-5/TG-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Computer (Windows, Mac or Linux)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Deionized water</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fiji (imageJ) software</td>
			<td></td>
			<td></td>
			<td>download from: https://fiji.sc/</td>
		</tr>
		<tr>
			<td>Forceps</td>
			<td>Dumont</td>
			<td></td>
			<td>sharp forceps may break mosquito&#39;s body</td>
		</tr>
		<tr>
			<td>Glass Petri dishes</td>
			<td>VWR</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Household bleach</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Household electric drill</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>illuminator for stereomicroscope (gooseneck)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>P-1000 pipette</td>
			<td>Gilson</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>paint brushes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Rubber bands</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SD card</td>
			<td></td>
			<td></td>
			<td>to record digital camera images (DSHC, SDXC should be better)</td>
		</tr>
		<tr>
			<td>Spreadsheet software (Microsoft Excel)</td>
			<td>Microsoft</td>
			<td></td>
			<td>Any spreadsheet software works</td>
		</tr>
		<tr>
			<td>TetraMin fish food</td>
			<td>Tetra</td>
			<td></td>
			<td>ground with coffee grinder, blender or morter &#38; pestle</td>
		</tr>
		<tr>
			<td>Transfer pipetts</td>
			<td>VWR</td>
			<td>16011-188</td>
			<td></td>
		</tr>
	</tbody>
</table>

improved fecundity and fertility assay for aedes aegypti using 24 well tissue culture plates (eagal plates)

Mosquitoes represent a significant public health problem as vectors of various pathogens. For those studies that require an assessment of mosquito fitness parameters, in particular egg production and hatch rates at the individual level, conventional methods have put a substantial burden on investigators due to high labor intensity and laboratory space requirements. Described is a simple method using 24 well tissue culture plate with agarose in each well and digital imaging of each well to determine egg numbers and hatch rates at an individual level with substantially reduced time and space requirements.

Mosquitoes were injected with dsRNA targeting a candidate iron transporter (FeT) or control gene (EGFP), blood-fed, and measured for fecundity and fertility output using the EAgaL plate method, following the procedure described above.
Mosquitoes in which FeT expression was silenced following dsRNA injection exhibited a significant reduction in both egg number and hatch rate (Figure 11A&#8722;C). All control and treatment mosquitoes were placed in ...

Watch this Scientific Journal Video about Improved Fecundity and Fertility Assay for Aedes aegypti using 24 Well Tissue Culture Plates EAgaL Plates at JoVE.com

Improved Fecundity and Fertility Assay for Aedes aegypti using 24 Well Tissue Culture Plates EAgaL Plates

Described is a time and space-saving method to count eggs and determine hatch rates of individual mosquitoes using 24 well tissue culture plates, which can substantially increase the scale and speed of fecundity and fertility assays.

Improved Fecundity and Fertility Assay for Aedes aegypti using 24 Well Tissue Culture Plates (EAgaL Plates)

Mosquitoes represent a significant public health problem as vectors of various pathogens. For those studies that require an assessment of mosquito fitness ...

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4.9K Views.  Texas A&M University. Described is a time and space-saving method to count eggs and determine hatch rates of individual mosquitoes using 24 well tissue culture plates, which can substantially increase the scale and speed of fecundity and fertility assays.

Video: Improved Fecundity and Fertility Assay for Aedes aegypti using 24 Well Tissue Culture Plates EAgaL Plates

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping project is to collect a tissue sample from each individual plant. The traditional approach to this task is to sample plants one-at-a-time. If one wishes to genotype hundreds or thousands of individuals, however, using this strategy results in a significant bottleneck in the genotyping pipeline. The Ice-Cap method that we describe here provides a high-throughput solution to this challenge by allowing one scientist to collect tissue from several thousand seedlings in a single day 1,2. This level of throughput is made possible by the fact that tissue is harvested from plants 96-at-a-time, rather than one-at-a-time.
The Ice-Cap method provides an integrated platform for performing seedling growth, tissue harvest, and DNA extraction. The basis for Ice-Cap is the growth of seedlings in a stacked pair of 96-well plates. The wells of the upper plate contain plugs of agar growth media on which individual seedlings germinate. The roots grow down through the agar media, exit the upper plate through a hole, and pass into a lower plate containing water. To harvest tissue for DNA extraction, the water in the lower plate containing root tissue is rapidly frozen while the seedlings in the upper plate remain at room temperature. The upper plate is then peeled away from the lower plate, yielding one plate with 96 root tissue samples frozen in ice and one plate with 96 viable seedlings. The technique is named "Ice-Cap" because it uses ice to capture the root tissue. The 96-well plate containing the seedlings can then wrapped in foil and transferred to low temperature. This process suspends further growth of the seedlings, but does not affect their viability. Once genotype analysis has been completed, seedlings with the desired genotype can be transferred from the 96-well plate to soil for further propagation. We have demonstrated the utility of the Ice-Cap method using Arabidopsis thaliana, tomato, and rice seedlings. We expect that the method should also be applicable to other species of plants with seeds small enough to fit into the wells of 96-well plates.

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

The Ice-Cap method allows one to grow plants in 96-well plates and non-destructively harvest root tissue from each seedling. DNA extracted from this root tissue can be used for genotyping reactions. We have found that Ice-Cap works well for Arabidopsis thaliana, tomato, and rice seedlings.

It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping ...

RNAi-mediated Gene Knockdown and In Vivo Diuresis Assay in Adult Female Aedes aegypti Mosquitoes

This video protocol demonstrates an effective technique to knockdown a particular gene in an insect and conduct a novel bioassay to measure excretion rate. This method can be used to obtain a better understanding of the process of diuresis in insects and is especially useful in the study of diuresis in blood-feeding arthropods that are able to take up huge amounts of liquid in a single blood meal. 
This RNAi-mediated gene knockdown combined with an in vivo diuresis assay was developed by the Hansen lab to study the effects of RNAi-mediated knockdown of aquaporin genes on Aedes aegypti mosquito diuresis1. 
The protocol is setup in two parts: the first demonstration illustrates how to construct a simple mosquito injection device and how to prepare and inject dsRNA into the thorax of mosquitoes for RNAi-mediated gene knockdown. The second demonstration illustrates how to determine excretion rates in mosquitoes using an in vivo bioassay.

RNAi-mediated Gene Knockdown and In Vivo Diuresis Assay in Adult Female Aedes aegypti Mosquitoes

In this protocol we combine RNAi-mediated gene silencing with an in vivo diuresis assay to study the effects knockdown of genes of interest has on mosquito fluid excretion.

This video protocol demonstrates an effective technique to knockdown a particular gene in an insect and conduct a novel bioassay to measure excretion ...

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Fluorescence in situ hybridization (FISH) is a technique that allows specific DNA sequences to be detected on metaphase or interphase chromosomes in cell nuclei1. The technique uses DNA probes with unique sequences that hybridize to whole chromosomes or specific chromosomal regions, and serves as a powerful adjunct to classic cytogenetics. For instance, many earlier studies reported the frequent detection of increased chromosome aberrations in leukemia patients related with benzene exposure, benzene-poisoning patients, and healthy workers exposed to benzene, using classic cytogenetic analysis2. Using FISH, leukemia-specific chromosomal alterations have been observed to be elevated in apparently healthy workers exposed to benzene3-6, indicating the critical roles of cytogentic changes in benzene-induced leukemogenesis. 
Generally, a single FISH assay examines only one or a few whole chromosomes or specific loci per slide, so multiple hybridizations need to be conducted on multiple slides to cover all of the human chromosomes. Spectral karyotyping (SKY) allows visualization of the whole genome simultaneously, but the requirement for special software and equipment limits its application7. Here, we describe a novel FISH assay, OctoChrome-FISH, which can be applied for Chromosomics, which we define here as the simultaneous analysis of all 24 human chromosomes on one slide in human studies, such as chromosome-wide aneuploidy study (CWAS)8. The basis of the method, marketed by Cytocell as the Chromoprobe Multiprobe System, is an OctoChrome device that is divided into 8 squares, each of which carries three different whole chromosome painting probes (Figure 1). Each of the three probes is directly labeled with a different colored fluorophore, green (FITC), red (Texas Red), and blue (Coumarin). The arrangement of chromosome combinations on the OctoChrome device has been designed to facilitate the identification of the non-random structural chromosome alterations (translocations) found in the most common leukemias and lymphomas, for instance t(9;22), t(15;17), t(8;21), t(14;18)9. Moreover, numerical changes (aneuploidy) in chromosomes can be detected concurrently. The corresponding template slide is also divided into 8 squares onto which metaphase spreads are bound (Figure 2), and is positioned over the OctoChrome device. The probes and target DNA are denatured at high-temperature and hybridized in a humid chamber, and then all 24 human chromosomes can be visualized simultaneously. 
OctoChrome FISH is a promising technique for the clinical diagnosis of leukemia and lymphoma and for detection of aneuploidies in all chromosomes. We have applied this new Chromosomic approach in a CWAS study of benzene-exposed Chinese workers8,10.

A novel fluorescence in situ hybridization (FISH) method that simultaneously examines both numerical and structural chromosome alterations, particularly the specific chromosomal translocations associated with leukemia and lymphoma, of all 24 human chromosomes on a single device in one hybridization, is described.

Fluorescence in situ hybridization (FISH) is a technique that allows specific DNA sequences to be detected on metaphase or interphase chromosomes in cell ...

Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti

Electrophysiological recording of action potentials from sensory neurons of mosquitoes provides investigators a glimpse into the chemical perception of these disease vectors. We have recently identified a bitter sensing neuron in the labellum of female Aedes aegypti that responds to DEET and other repellents, as well as bitter quinine, through direct electrophysiological investigation. These gustatory receptor neuron responses prompted our sequencing of total mRNA from both male and female labella and tarsi samples to elucidate the putative chemoreception genes expressed in these contact chemoreception tissues. Samples of tarsi were divided into pro-, meso- and metathoracic subtypes for both sexes. We then validated our dataset by conducting qRT-PCR on the same tissue samples and used statistical methods to compare results between the two methods. Studies addressing molecular function may now target specific genes to determine those involved in repellent perception by mosquitoes. These receptor pathways may be used to screen novel repellents towards disruption of host-seeking behavior to curb the spread of harmful viruses.

Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti

Using two methods to estimate gene expression in the major gustatory appendages of Aedes aegypti, we have identified the set of genes putatively underlying the neuronal responses to bitter and repulsive compounds, as determined by electrophysiological examination.

Electrophysiological recording of action potentials from sensory neurons of mosquitoes provides investigators a glimpse into the chemical perception of ...

Measuring Oxidative Stress Resistance of Caenorhabditis elegans in 96-well Microtiter Plates

Oxidative stress, which is the result of an imbalance between production and detoxification of reactive oxygen species, is a major contributor to chronic human disorders, including cardiovascular and neurodegenerative diseases, diabetes, aging, and cancer. Therefore, it is important to study oxidative stress not only in cell systems but also using whole organisms. C. elegans is an attractive model organism to study the genetics of oxidative stress signal transduction pathways, which are highly evolutionarily conserved.
Here, we provide a protocol to measure oxidative stress resistance in C. elegans in liquid. Briefly, ROS-inducing reagents such as paraquat (PQ) and H2O2 are dissolved in M9 buffer, and solutions are aliquoted in the wells of a 96 well microtiter plate. Synchronized L4/young adult C. elegans animals are transferred to the wells (5-8 animals/well) and survival is measured every hour until most worms are dead. When performing an oxidative stress resistance assay using a low concentration of stressors in plates, aging might influence the behavior of animals upon oxidative stress, which could lead to an incorrect interpretation of the data. However, in the assay described herein, this problem is unlikely to occur since only L4/young adult animals are being used. Moreover, this protocol is inexpensive and results are obtained in one day, which renders this technique attractive for genetic screens. Overall, this will help to understand oxidative stress signal transduction pathways, which could be translated into better characterization of oxidative stress-associated human disorders.

Measuring Oxidative Stress Resistance of Caenorhabditis elegans in 96-well Microtiter Plates

C. elegans is an attractive model organism to study signal transduction pathways involved in oxidative stress resistance. Here we provide a protocol to measure oxidative stress resistance of C. elegans animals in liquid phase, using several oxidizing agents in 96 well plates.

Oxidative stress, which is the result of an imbalance between production and detoxification of reactive oxygen species, is a major contributor to chronic ...

Improved Swiss-rolling Technique for Intestinal Tissue Preparation for Immunohistochemical and Immunofluorescent Analyses

Understanding the role of factors that regulate intestinal epithelial homeostasis and response to injury and regeneration is important. The current literature describes several different methodological approaches to obtain images of intestinal tissues for data validation. In this paper, we delineate a common protocol relating to the derivation and processing of mouse intestinal tissues. Proper fixation of intestinal tissues and Swiss-roll techniques that enhance intestinal epithelial morphology are discussed. Postresection processing and reorientation of embedded intestinal tissues are critical in obtaining paraffin-embedded blocks that display intact intestinal structural features after sectioning. The Swiss-rolling technique helps in histological assessment of the complete intestinal or colonic sections examined. An ability to differentiate intestinal structural features can be vital in quantitative measurements of intestinal inflammation and tumorigenesis along the entire length. Finally, paraffin-embedded sections are ideal for robust processing using both immunohistochemical and immunofluorescent detection methods. Nonfluorescent immunohistochemical sections provide a vibrant image of the tissue detailing different cellular structural features but do not provide flexibility for intracellular co-localization experiments. Multiple fluorescent channels can be appropriately utilized with immunofluorescent detection for co-localization experiments, lending support to mechanistic studies.

Accurate identification and location of epithelial cells along the intestinal mucosal lining are essential to define different cell lineages. Proper imaging of intestinal tissues is crucial for identification of protein expression patterns with maximum resolution. This study aims to delineate the optimal methods and conditions for processing mouse intestinal tissues.

Understanding the role of factors that regulate intestinal epithelial homeostasis and response to injury and regeneration is important. The current ...

Fat Body Organ Culture System in Aedes Aegypti, a Vector of Zika Virus

The insect fat body plays a central role in insect metabolism and nutrient storage, mirroring functions of the liver and fat tissue in vertebrates. Insect fat body tissue is usually distributed throughout the insect body. However, it is often concentrated in the abdomen and attached to the abdominal body wall.
The mosquito fat body is the sole source of yolk proteins, which are critical for egg production. Therefore, the in vitro culture of mosquito fat body tissues represents an important system for the study of mosquito physiology, metabolism, and, ultimately, egg production. The fat body culture process begins with the preparation of solutions and reagents, including amino acid stock solutions, Aedes physiological saline salt stock solution (APS), calcium stock solution, and fat body culture medium. The process continues with fat body dissection, followed by an experimental treatment. After treatment, a variety of different analyses can be performed, including RNA sequencing (RNA-Seq), qPCR, Western blots, proteomics, and metabolomics.
In our example experiment, we demonstrate the protocol through the excision and culture of fat bodies from the yellow fever mosquito, Aedes aegypti, a principal vector of arboviruses including dengue, chikungunya, and Zika. RNA from fat bodies cultured under a physiological condition known to upregulate yolk proteins versus the control were subject to RNA-Seq analysis to demonstrate the potential utility of this procedure for investigations of gene expression.

Fat Body Organ Culture System in Aedes Aegypti, a Vector of Zika Virus

The fat body is the central metabolic organ in insects. We present a live organ culture system that enables the user to study the responses of isolated fat body tissue to various stimuli.

The insect fat body plays a central role in insect metabolism and nutrient storage, mirroring functions of the liver and fat tissue in vertebrates. Insect ...

Maintaining Aedes aegypti Mosquitoes Infected with Wolbachia

Aedes aegypti mosquitoes experimentally infected with Wolbachia are being utilized in programs to control the spread of arboviruses such as dengue, chikungunya and Zika. Wolbachia-infected mosquitoes can be released into the field to either reduce population sizes through incompatible matings or to transform populations with mosquitoes that are refractory to virus transmission. For these strategies to succeed, the mosquitoes released into the field from the laboratory must be competitive with native mosquitoes. However, maintaining mosquitoes in the laboratory can result in inbreeding, genetic drift and laboratory adaptation which can reduce their fitness in the field and may confound the results of experiments. To test the suitability of different Wolbachia infections for deployment in the field, it is necessary to maintain mosquitoes in a controlled laboratory environment across multiple generations. We describe a simple protocol for maintaining Ae. aegypti mosquitoes in the laboratory, which is suitable for both Wolbachia-infected and wild-type mosquitoes. The methods minimize laboratory adaptation and implement outcrossing to increase the relevance of experiments to field mosquitoes. Additionally, colonies are maintained under optimal conditions to maximize their fitness for open field releases.

Maintaining Aedes aegypti Mosquitoes Infected with Wolbachia

Aedes aegypti mosquitoes infected with Wolbachia are being released into natural populations to suppress the transmission of arboviruses. We describe methods to rear Ae. aegypti with Wolbachia infections in the laboratory for experiments and field release, taking precautions to minimize laboratory adaptation and selection.

Aedes aegypti mosquitoes experimentally infected with Wolbachia are being utilized in programs to control the spread of arboviruses such as dengue, ...

Modified Methods for Loading of High-Throughput DNA Extraction Plates Reduce Potential for Contamination

High-throughput DNA sequencing techniques have contributed substantially to advances in our understanding of relationships among microbial communities, host characteristics, and broader ecosystem functions. With this rapid increase in breadth and depth of sequencing capabilities have come methods to extract, amplify, analyze, and interpret environmental DNA successfully with maximum efficiency. Unfortunately, performing DNA extractions quickly can come at the cost of increasing the risk of contamination among samples. In particular, high-throughput extractions that are based on samples contained in a 96-well plate offer a relatively quick method, compared to single-tube extractions, but also increase opportunities for well-to-well cross-contamination. To minimize the risk of cross-contamination among samples, while retaining the benefits of high-throughput extraction techniques, we developed a new method for loading environmental samples into 96-well plates. We used pierceable PCR sealing films to cover each plate while loading samples and added samples first to PCR tubes before moving them into wells; together, these practices reduce the risk of sample drift and unintended double loading of wells. The method outlined in this paper provides researchers with an approach to maximize available high-throughput extraction techniques while reducing the risk of cross-contamination inherent to 96-well plates. We provide a detailed step by step outline of how to move from sample collection to DNA extraction while minimizing the risk of unwanted cross-contamination.

Current methods for loading 96-well plates for DNA extractions can be prone to contamination. We detail a new method for loading 96-well plates that reduces risk of cross-contamination among wells. Our method will help other researchers capitalize on the efficiency of high-throughput DNA extraction techniques and minimize risk of contamination.

High-throughput DNA sequencing techniques have contributed substantially to advances in our understanding of relationships among microbial communities, ...

Preparing Irradiated and Marked Male Aedes aegypti Mosquitoes for Release in an Operational Sterile Insect Technique Program

The control of such human diseases as dengue, Zika, and chikungunya relies on the control of their vector, the Aedes aegypti mosquito, because there is no prevention. Control of mosquito vectors can rely on chemicals applied to the immature and adult stages, which can contribute to the mortality of non-targets and more importantly, lead to insecticide resistance in the vector. The sterile insect technique (SIT) is a method of controlling populations of pests through the release of sterilized adult males that mate with wild females to produce non-viable offspring. This paper describes the process of producing sterile males for use in an operational SIT program for the control of Aedes aegypti mosquitoes. Outlined here are the steps used in the program including rearing and maintaining a colony, separating male and female pupae, irradiating and marking adult males, and shipping Aedes aegypti males to the release site. Also discussed are procedural caveats, program limitations, and future objectives.

Preparing Irradiated and Marked Male Aedes aegypti Mosquitoes for Release in an Operational Sterile Insect Technique Program

The sterile insect technique (SIT) is used to control specific, medically important mosquito populations that may be resistant to chemical controls. Here, we describe a method of mass rearing and preparation of sterile male mosquitoes for release in an operational SIT program targeting the Aedes aegypti mosquito.

The control of such human diseases as dengue, Zika, and chikungunya relies on the control of their vector, the Aedes aegypti mosquito, because there is no ...