This study was supported by grants from Taiwan (Ministry of Science and Technology, MOST 100-2923-B-002-002-MY3 and 106-2313-B-002-011-MY3 to H.J.L.), the Czech Republic (Grant agency of South Bohemia University, GAJU grant 065/2017/P to Y.H.L), and Spain (Spanish Ministry of Economy and Competitiveness, grants CGL2012-36251 and CGL2015-64727-P to X.B., and the Catalan Government, grant 2014 SGR 619 to X.B.); it also received financial support from the European Fund for Economic and Regional Development (FEDER funds to X.B.).

1. Synthesis and Preparation of dsRNA
<ol>
	<li>Identify the dsRNA target sites in the 3&#39; untranslated region of the target genes. The dsTub is used for targeting the &#945;-tubulin (tub) gene (GenBank accession number: KX228233), and dsEGFP as a negative dsRNA control is designed from the sequence of enhanced green fluorescence protein (EGFP; GenBank accession number: LC311024).</li>
	<li>Perform standard PCR amplification to synthesize the dsRNA templates with gene-specific primers containing the T7 promoter sequence (5&#39;-TAATACGACTCACTATAGGG-3&#39;). The PCR amplification conditions and primer information used are those reported by Lin et al. (2017)12 (see Table of Materials).</li>
	<li>Proceed with dsRNA preparation using a T7 Transcription Kit (see Table of Materials), following the manufacturer&#39;s instructions. 
	Note: To yield high quantity dsRNA, mix two reactions in one tube (in total 40 &#181;L), and incubate at 37 &#176;C overnight.</li>
	<li>Add 2 &#181;L of DNase (see Table of Materials) into dsRNA samples for 15 min at 37 &#176;C to digest DNA templates.</li>
	<li>Add 200 &#181;L extraction reagent (see Table of Materials) and 40 &#181;L chloroform, then vortex.</li>
	<li>Centrifuge for 10 min at 13,000 x g at 4 &#176;C, then collect supernatant (150 &#181;L) in a new microcentrifuge tube.</li>
	<li>Precipitate dsRNA by adding 150 &#181;L isopropanol and incubating for 15 min on ice.</li>
	<li>Centrifuge for 15 min at 13,000 x g at 4 &#176;C, then remove supernatant.</li>
	<li>Add 200 &#181;L of the 70% ethanol to wash dsRNA pellets. Centrifuge for 10 min at 13,000 x g at 4 &#176;C.</li>
	<li>Remove the ethanol and repeat the ethanol wash steps.</li>
	<li>Remove the ethanol and dry dsRNA pellet by centrifugal vacuum concentrators for 3 min, then resuspend dsRNA with RNase-free water.</li>
	<li>Determine the quantity of the purified dsRNA using a micro-volume UV-Vis spectrophotometer (see Table of Materials) according to the manufacturer&#39;s instructions and adjust to the desired concentration (e.g., 0.25 &#181;g/&#181;L for preparation of dsRNA lipoplexes).</li>
	<li>Store the dsRNA samples at -20 &#176;C for up to 3 months.</li>
</ol>
2. Preparation of dsRNA Lipoplexes
<ol>
	<li>Dilute 4 &#181;L of the transfection reagent (see Table of Materials) by adding 4 &#181;L of 5% glucose solution. Dilute 4 &#181;L of the dsRNA (1 &#181;g) by adding 4 &#181;L of 5% glucose solution.</li>
	<li>Add the diluted liposome reagent solution immediately into the diluted dsRNA solution all at once. Vortex briefly to mix them, then incubate for 15 min at 25 &#176;C. 
	Note: Do not mix the solutions in the reverse order.</li>
	<li>The dsRNA lipoplexes are ready for use. Use within 1 hour of preparation, and discard after 1 hour. 
	Note: According to the manufacturer&#39;s instructions, the lipoplexes should be used as soon as possible.</li>
</ol>
3. Collection of Extracellular Enzymes from Hemolymph and Midgut Juice
<ol>
	<li>Insect saline buffer (10x&#160;stock)
	<ol>
		<li>Mix 900 mL double distilled water with 109.3 g NaCl, 15.7 g KCl, 6.3 g CaCl2, and 8.3 g MgCl2&#183;6H2O.</li>
		<li>Adjust pH to 6.8, and fill up to 1,000 mL.</li>
	</ol>
	</li>
	<li>Hemolymph collection
	<ol>
		<li>Anesthetize the cockroaches on ice until they do not move for 3 min.</li>
		<li>Hold the cockroach with two fingers (thumb and index finger), and turn the ventral side of the cockroach up.</li>
		<li>Use the dissecting scissor to cut off the tip of a coxa of a hind leg off. 
		Note: Cut the connected intersection between the coxa and trochanter. The excision of the other part of coxa was less efficient to collect hemolymph.</li>
		<li>Squeeze the abdomen gently with middle finger, and collect the hemolymph bleeding from the incision with a 10 &#181;L micropipette.</li>
		<li>Pool the hemolymph from several cockroaches (5 individuals) in a microcentrifuge tube. 
		Note: Keep the microcentrifuge tubes on ice to prevent melanization. The average volume of hemolymph obtained from a male cockroach is 2 - 3 &#181;L.</li>
		<li>Spin down the hemolymph briefly with a benchtop centrifuge for 10 s.</li>
		<li>Transfer desired volume of hemolymph (i.e., 10 &#181;L), and mix it with 50 &#181;L of 1x&#160;insect saline buffer.</li>
		<li>Centrifuge for 10 min at 1,000 x g at 4 &#176;C to spin down hemocytes. Transfer the supernatant to a clean microcentrifuge tube.</li>
		<li>Quantify the total protein concentration using a micro-volume UV-Vis spectrophotometer by measuring A28015.</li>
		<li>Adjust each sample to have the same protein concentration (6 mg/&#181;L of total protein).</li>
	</ol>
	</li>
	<li>Midgut juice collection
	<ol>
		<li>Anesthetize the cockroaches on ice. Fix the cockroaches ventral side up on the dissection plate with cold 1x&#160;insect saline buffer using insect pins.</li>
		<li>Dissect the abdomen with fine tweezers. Remove the entire gut (including the front, mid, and hind gut) to a fresh dish with 1x&#160;insect saline buffer.</li>
		<li>Remove the front and hind gut, and quickly transfer the midgut to a microcentrifuge tube that contains 100 &#181;L insect saline buffer.</li>
		<li>Pool the midguts from six cockroaches in the same tube, and vortex for 10 s.</li>
		<li>Centrifuge for 10 min at 1,000 x g at 4 &#176;C to spin down the hemocytes and gut tissues. Transfer the supernatant to a clean microcentrifuge tube.</li>
		<li>Quantify the total protein concentration using a micro-volume UV-Vis spectrophotometer by measuring A28015.</li>
		<li>Adjust each sample to have the same protein concentration (6 mg/&#181;L of total protein).</li>
	</ol>
	</li>
</ol>
4. dsRNA Degradation Assay
<ol>
	<li>Freshly prepare 4 &#181;L of the naked dsRNA or dsRNA lipoplexes (1 &#181;g).</li>
	<li>Mix dsRNA solutions with 10 &#181;L of insect saline buffer (control), extracted enzymes from hemolymph, or midgut juice.</li>
	<li>Add 2 &#181;L of either EGTA (20 mM) or RNase-free water to separate samples as controls for inhibition of enzyme activities.</li>
	<li>Incubate for 1 hour or longer (6, 12, or 24 hours) at 25 &#176;C.</li>
	<li>Add 200 &#181;L extraction reagent and 40 &#181;L chloroform, then vortex.</li>
	<li>Centrifuge for 10 min at 13,000 x g at 4 &#176;C, then collect supernatant (150 &#181;L) in a new microcentrifuge tube.</li>
	<li>Precipitate dsRNA by adding 150 &#181;L isopropanol and incubating for 15 min on ice.</li>
	<li>Centrifuge for 15 min at 13,000 x g at 4 &#176;C, then remove supernatant.</li>
	<li>Add 200 &#181;L of the 70% ethanol to wash dsRNA pellets. Centrifuge for 10 min at 13,000 x g at 4 &#176;C.</li>
	<li>Remove the ethanol and repeat the ethanol wash steps.</li>
	<li>Remove the ethanol and dry dsRNA pellet by centrifugal vacuum concentrators for 3 min. Resuspend dsRNA with 10 &#181;L RNase-free water.</li>
	<li>Check the integrity of treated dsRNA via gel electrophoresis on a 1.5% agarose gel.</li>
</ol>
5. Oral Administration of dsRNA
<ol>
	<li>Maintain cockroaches on an ad libitum diet of dry food (dog chow). Deprive water supply from the cockroaches one day before dsRNA ingestion experiments.</li>
	<li>Hold a cockroach by grabbing its wings with the flexible forceps (Figure 1, step 5). 
	Note: Do not grab the body parts of cockroaches.</li>
	<li>Prepare the dsRNA lipoplexes, as well as naked dsRNA, for feeding, as described in section 2. 
	Note: The dsRNA lipoplexes should be prepared freshly before feeding.</li>
	<li>Feed 4 &#181;L of dsRNA lipoplexes or naked dsRNA (250 ng) with a micropipette.</li>
	<li>Slowly pipet the droplet of the dsRNA solution close to the mouthparts of cockroaches, and let the cockroaches ingest the droplet completely.</li>
	<li>Perform the ingestion experiments twice a day (1 h after lights on and 1 h before lights off) for 8 days or 16 days continuously. 
	Note: All cockroaches acquired water only through manual feeding with dsRNA solution or control reagents (e.g., nuclease free water, glucose solution, and liposome reagent) during ingestion experiments.</li>
	<li>Provide water bottles to the cockroaches after 16 days of ingestion of dsRNA experiments.</li>
</ol>
6. Assess Knockdown
<ol>
	<li>At chosen time points (2, 9, and 17 days after dsRNA ingestion assay), collect the dsEGFP- and dsTub-treated insects and dissect the chosen tissues (e.g., midgut).</li>
	<li>Perform quantitative real-time PCR (qRT-PCR). The qRT-PCR amplification conditions and primer information as reported by Lin et al. (2017)12.</li>
	<li>Assess the control and dsRNA-treated insects daily to check mortality and remove the cockroaches that are no longer moving.</li>
</ol>

<ol>
	<li>Hammond, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dicing+and+slicing:+The+core+machinery+of+the+RNA+interference+pathway.">Dicing and slicing: The core machinery of the RNA interference pathway.</a> FEBS Lett. 579, 5822-5829 (2005).</li><li>Bell&#233;s, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Beyond+drosophila:+RNAi+in+vivo+and+functional+genomics+in+insects.">Beyond drosophila: RNAi in vivo and functional genomics in insects.</a> Annu. Rev. Entomol. 55, 111-128 (2010).</li><li>Wynant, N., Santos, D., Vanden Broeck, J., Jeon, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+Five+-+Biological+Mechanisms+Determining+the+Success+of+RNA+Interference+in+Insects.">Chapter Five - Biological Mechanisms Determining the Success of RNA Interference in Insects.</a> International Review of Cell and Molecular Biology. 312, 139-167 (2014).</li><li>San Miguel, K., Scott, J. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+next+generation+of+insecticides:+dsRNA+is+stable+as+a+foliar-applied+insecticide.">The next generation of insecticides: dsRNA is stable as a foliar-applied insecticide.</a> Pest Manag. Sci. 72, 801-809 (2016).</li><li>Scott, 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=Towards+the+elements+of+successful+insect+RNAi.">Towards the elements of successful insect RNAi.</a> J. Insect Physiol. 59, 1212-1221 (2013).</li><li>Joga, M. R., Zotti, M. J., Smagghe, G., Christiaens, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNAi+efficiency,+systemic+properties,+and+novel+delivery+methods+for+pest+insect+control:+What+we+know+so+far.">RNAi efficiency, systemic properties, and novel delivery methods for pest insect control: What we know so far.</a> Front. Physiol. 7, (2016).</li><li>Garbutt, J. S., Bell&#233;s, X., Richards, E. H., Reynolds, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Persistence+of+double-stranded+RNA+in+insect+hemolymph+as+a+potential+determiner+of+RNA+interference+success:+Evidence+from+Manduca+sexta+and+Blattella+germanica.">Persistence of double-stranded RNA in insect hemolymph as a potential determiner of RNA interference success: Evidence from Manduca sexta and Blattella germanica.</a> J. Insect Physiol. 59, 171-178 (2013).</li><li>Arimatsu, Y., Kotani, E., Sugimura, Y., Furusawa, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+characterization+of+a+cDNA+encoding+extracellular+dsRNase+and+its+expression+in+the+silkworm,+Bombyx+mori.">Molecular characterization of a cDNA encoding extracellular dsRNase and its expression in the silkworm, Bombyx mori.</a> Insect Biochem. Mol. Biol. 37, 176-183 (2007).</li><li>Wang, 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=Variation+in+RNAi+efficacy+among+insect+species+is+attributable+to+dsRNA+degradation+in+vivo.">Variation in RNAi efficacy among insect species is attributable to dsRNA degradation in vivo.</a> Insect Biochem. Mol. Biol. 77, 1-9 (2016).</li><li>Wynant, N., 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=Identification,+functional+characterization+and+phylogenetic+analysis+of+double+stranded+RNA+degrading+enzymes+present+in+the+gut+of+the+desert+locust,+Schistocerca+gregaria.">Identification, functional characterization and phylogenetic analysis of double stranded RNA degrading enzymes present in the gut of the desert locust, Schistocerca gregaria.</a> Insect Biochem. Mol. Biol. 46, 1-8 (2014).</li><li>Huang, J. -. H., Belles, X., Lee, H. -. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+characterization+of+hypertrehalosemic+hormone+receptor+in+relation+to+hemolymph+trehalose+and+to+oxidative+stress+in+the+cockroach+Blattella+germanica.">Functional characterization of hypertrehalosemic hormone receptor in relation to hemolymph trehalose and to oxidative stress in the cockroach Blattella germanica.</a> Exp. Endocrinol. 2, 114 (2012).</li><li>Lin, Y. -. H., Lee, C. -. M., Huang, J. -. H., Lee, H. -. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Circadian+regulation+of+permethrin+susceptibility+by+glutathione+S-transferase+(BgGSTD1)+in+the+German+cockroach+(Blattella+germanica).">Circadian regulation of permethrin susceptibility by glutathione S-transferase (BgGSTD1) in the German cockroach (Blattella germanica).</a> J. Insect Physiol. 65, 45-50 (2014).</li><li>Lozano, J., Kayukawa, T., Shinoda, T., Belles, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+role+for+taiman+in+insect+metamorphosis.">A role for taiman in insect metamorphosis.</a> PLOS Genet. 10, 1004769 (2014).</li><li>Lozano, J., Monta&#241;ez, R., Belles, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MiR-2+family+regulates+insect+metamorphosis+by+controlling+the+juvenile+hormone+signaling+pathway.">MiR-2 family regulates insect metamorphosis by controlling the juvenile hormone signaling pathway.</a> Proc. Natl. Acad. Sci. 112, 3740-3745 (2015).</li><li>Lin, Y. -. H., Huang, J. -. H., Liu, Y., Belles, X., Lee, H. -. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oral+delivery+of+dsRNA+lipoplexes+to+German+cockroach+protects+dsRNA+from+degradation+and+induces+RNAi+response.">Oral delivery of dsRNA lipoplexes to German cockroach protects dsRNA from degradation and induces RNAi response.</a> Pest Manag. Sci. 73, 960-966 (2017).</li><li>Gharavi, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chiral+cationic+polyamines+for+chiral+microcapsules+and+siRNA+delivery.">Chiral cationic polyamines for chiral microcapsules and siRNA delivery.</a> Bioorg. Med. Chem. Lett. 23, 5919-5922 (2013).</li><li>Whyard, S., Singh, A. D., Wong, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ingested+double-stranded+RNAs+can+act+as+species-specific+insecticides.">Ingested double-stranded RNAs can act as species-specific insecticides.</a> Insect Biochem. Mol. Biol. 39, 824-832 (2009).</li><li>Luo, 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=Differential+responses+of+migratory+locusts+to+systemic+RNA+interference+via+double-stranded+RNA+injection+and+feeding.">Differential responses of migratory locusts to systemic RNA interference via double-stranded RNA injection and feeding.</a> Insect Mol. Biol. 22, 574-583 (2013).</li><li>Liu, J., Smagghe, G., Swevers, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+response+of+BmToll9-1+and+RNAi+machinery+genes+to+exogenous+dsRNA+in+the+midgut+of+Bombyx+mori.">Transcriptional response of BmToll9-1 and RNAi machinery genes to exogenous dsRNA in the midgut of Bombyx mori.</a> J. Insect Physiol. 59, 646-654 (2013).</li><li>Airs, P. M., Bartholomay, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+interference+for+mosquito+and+mosquito-borne+disease+control.">RNA interference for mosquito and mosquito-borne disease control.</a> Insects. 8, 4 (2017).</li><li>Taning, C. N. 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=Oral+RNAi+to+control+Drosophila+suzukii:+Laboratory+testing+against+larval+and+adult+stages.">Oral RNAi to control Drosophila suzukii: Laboratory testing against larval and adult stages.</a> J. Pest Sci. 89, 803-814 (2016).</li><li>Wu, S. Y., McMillan, N. A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipidic+systems+for+in+vivo+siRNA+delivery.">Lipidic systems for in vivo siRNA delivery.</a> AAPS J. 11, 639-652 (2009).</li><li>Tam, Y. Y. C., Chen, S., Cullis, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+lipid+nanoparticles+for+siRNA+delivery.">Advances in lipid nanoparticles for siRNA delivery.</a> Pharmaceutics. 5, 498-507 (2013).</li><li>Xia, Y., Tian, J., Chen, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+surface+properties+on+liposomal+siRNA+delivery.">Effect of surface properties on liposomal siRNA delivery.</a> Biomaterials. 79, 56-68 (2016).</li></ol>

The authors have nothing to disclose.

This protocol presents a method for effective RNAi through oral delivery of dsRNA lipoplexes, involving protection against ribonuclease digestion in the midgut juice of the German cockroach. As shown in other studies in various insect species, the poor RNAi effect through oral delivery of dsRNA is mostly accounted for by the degradation of dsRNA8,9,10. This protocol produces liposomes that serve as protective vehicles in oral de...

RNAi has been demonstrated as an effective method to knockdown gene expression through a mechanism of a post-transcriptional silencing pathway triggered by dsRNA molecules in many eukaryotes1. Over the past decade of study, RNAi has become a useful tool to study the functions of genes from development to behavior by depleting the expression of specific genes via injection and/or feeding of dsRNA in various taxa of insects2,3. Due to the specificity and robustness of the depleting effect, the application of RNAi is currently being considered as a potential strategy for pest control management4,5. However, the efficiency of RNAi varies widely between insect species, depending on the different genes being targeted and the delivery methods. A growing body of evidence suggests that the instability of dsRNA, which is degraded by ribonucleases, is a critical factor in the limited efficacy of RNAi5,6. For instance, the low RNAi sensitivity in Manduca sexta has been explained by the fact that the dsRNA mixed with hemolymph was quickly degraded within 1 hour7. Similarly, the presence of alkaline nucleases in the midgut, which efficiently degrade ingested dsRNA, is strongly correlated with low RNAi efficiency in different insect orders8,9,10.
The oral delivery of dsRNA is particularly interesting for the application of RNAi in a pest control strategy, but a method to retard the degradation of dsRNA by the nucleases in the midgut has not yet been developed, which would have the potential to ensure effective RNAi through feeding. However, the unresponsiveness of RNAi to oral delivery of dsRNA has been reported by feeding large amount of dsRNA, e.g. 50 &#181;g in Bombyx mori, or continuously feeding for 8 days (8 &#181;g dsRNA in total) in the locust species. The German cockroach, Blattella germinica, is highly sensitive to RNAi by the injection of dsRNA11,12,13,14, but is not responsive to dsRNA through feeding. Recently, Lin et al. (2017) have demonstrated that the dsRNA encapsulated with liposome carriers results in successful RNAi to knockdown the &#945;-tubulin gene expression in the midgut and trigger significant mortality of the German cockroach15. As the degradation of dsRNA in the midgut is the limiting factor for oral RNAi, the liposome carriers serve as a vehicle to protect dsRNA from degradation, which is readily applicable in other insects with strong nuclease activities in the gut. Of note, the reason for choosing the particular transfection reagent (see Table of Materials) we used as liposome carrier in the current protocol is that it has been tested for insect cell line transfection with less toxicity, according to the manufacturer&#39;s instructions. According to the comparison of different liposome transfection systems in Gharavi et al. (2013)16, the efficiency of transfecting small interfering RNA (siRNA) is approximately the same between this and other commercially available systems that have been used for dsRNA delivery systems in other insects17,18.Furthermore, our feeding method is careful enough to ensure the proper amount of dsRNA is ingested by each cockroach, and that the results are robust and confirmed. In summary, the present protocol and results demonstrate that using dsRNA lipoplexes improves dsRNA stability and opens the door to the design of the strategy oral delivery of RNAi, which is a promising approach for pest control in the future.

<table border="0" cellpadding="0" cellspacing="0" style="width:1124px;" width="1123">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">GenJe Plus DNA in vitro Transfection reagent</td>
			<td style="width:133px;">SignaGen</td>
			<td style="width:157px;">SL100499</td>
			<td style="width:481px;">for lipoplexes preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Blend Taq plus</td>
			<td style="width:133px;">TOYOBO&#160;</td>
			<td style="width:157px;">BTQ-201</td>
			<td>for PCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fast SYBR Green Master Mix</td>
			<td style="width:133px;">ABI&#160;</td>
			<td style="width:157px;">4385612</td>
			<td>for qPCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">FirstChoice RLM-RACE Kit</td>
			<td style="width:133px;">Invitrogen</td>
			<td style="width:157px;">AM1700</td>
			<td>for 3&#39; UTR identification&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">MEGAscript T7 Transcription Kit</td>
			<td style="width:133px;">Invitrogen</td>
			<td style="width:157px;">AMB13345</td>
			<td>for dsRNA synthesis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TURBO DNase</td>
			<td style="width:133px;">Invitrogen</td>
			<td style="width:157px;">AM2239</td>
			<td>remove DNA template from dsRNA</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TRIzol</td>
			<td style="width:133px;">Invitrogen</td>
			<td style="width:157px;">15596018</td>
			<td>for dsRNA or total RNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RQ1 RNase-Free Dnase</td>
			<td style="width:133px;">Promega</td>
			<td style="width:157px;">M6101</td>
			<td>remove DNA template from total RNA&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">chloroform&#160;</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">C2432</td>
			<td>for dsRNA or total RNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">2-Propanol</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">I9516</td>
			<td>for dsRNA or total RNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ethanol</td>
			<td>Sigma-Aldrich</td>
			<td>24102</td>
			<td>for dsRNA or total RNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">Diethyl pyrocarbonate, DEPC</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">D5758</td>
			<td>for RNase free water preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">glucose solution</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">G3285</td>
			<td>for lipoplexes preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium chloride, NaCl</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">S7653</td>
			<td>insect saline buffer formula</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">Potassium chloride, KCl</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">P9333</td>
			<td>insect saline buffer formula</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:352px;">Calcium chloride, CaCl2</td>
			<td>Sigma-Aldrich</td>
			<td>C1016</td>
			<td>insect saline buffer formula</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">Magnesium chloride hexahydrate, MgCl2.6H2O</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">M2670</td>
			<td>insect saline buffer formula</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">EGTA&#160;</td>
			<td>Sigma-Aldrich</td>
			<td style="width:157px;">E3889</td>
			<td>enzyme inhibitor&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">dissecting scissor</td>
			<td style="width:133px;">F.S.T.</td>
			<td style="width:157px;"></td>
			<td>cockroach dissection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">fine tweezers</td>
			<td style="width:133px;">F.S.T.</td>
			<td style="width:157px;"></td>
			<td>cockroach dissection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">flexible tweezer</td>
			<td style="width:133px;">F.S.T.</td>
			<td style="width:157px;"></td>
			<td>cockroach holding&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pipetman</td>
			<td style="width:133px;">RAININ</td>
			<td style="width:157px;">P10</td>
			<td>sample preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">microcentrifuge tube</td>
			<td style="width:133px;">Axygen</td>
			<td>MCT175C, PCR02C</td>
			<td>sample preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">pipette tip&#160;</td>
			<td style="width:133px;">Axygen</td>
			<td></td>
			<td>sample preparation</td>
		</tr>
		<tr height="23">
			<td height="23" style="height:23px;">vortexter</td>
			<td style="width:133px;">Digisystem</td>
			<td style="width:157px;">vm1000</td>
			<td>sample preparation</td>
		</tr>
		<tr height="23">
			<td height="23" style="height:23px;">Minispin centrifuge</td>
			<td style="width:133px;">The Gruffin Group</td>
			<td style="width:157px;">GMC 206</td>
			<td>for liquid spin down&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Centrifuge</td>
			<td style="width:133px;">ALC</td>
			<td style="width:157px;">PK121R</td>
			<td>sample preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pH meter&#160;</td>
			<td style="width:133px;">JENCO</td>
			<td style="width:157px;">6071</td>
			<td>for pH adjust</td>
		</tr>
		<tr height="23">
			<td height="23" style="height:23px;">micro-volume spectrophotometer</td>
			<td style="width:133px;">Quawell</td>
			<td style="width:157px;">Q3000</td>
			<td>nucleic acid quantitative</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">PCR Thermal cycler</td>
			<td style="width:133px;">ABI&#160;</td>
			<td style="width:157px;">2720</td>
			<td>for template PCR or&#160; dsRNA synthesis incubation&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">quantitative real-time PCR</td>
			<td style="width:133px;">ABI&#160;</td>
			<td style="width:157px;">StepOne plus</td>
			<td>gene expression quantitative</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Centrifugal Vacuum Concentrators</td>
			<td style="width:133px;">eppendorf</td>
			<td style="width:157px;">5301</td>
			<td>for dsRNA or total RNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Multipette&#160;</td>
			<td style="width:133px;">eppendorf</td>
			<td style="width:157px;">xstream</td>
			<td>for real-time PCR sample loading&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agarose I</td>
			<td style="width:133px;">amresco</td>
			<td style="width:157px;">0710</td>
			<td>for nucleic acid electrophoresis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">tub gene specfifc forward preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>GGG ACA AGC CGG AGT GCA GA</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">tub gene specfifc reverse preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>TCC TGC TCC TGT CTC GCT GA</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">dsTub template forward primer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>TAA TAC GAC TCA CTA TAG GGA CAA GCC GGA GTG CAG&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">dsTub template reverse primer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>TAA TAC GAC TCA CTA TAG GGT CCT GCT CCT GTC TCG CTG&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">dsEGFP template forward preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>TAA TAC GAC TCA CTA TAG GGT ATG GTG AGC AAG GGC GAG GAG</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">dsEGFP template reverse preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>TAA TAC GAC TCA CTA TAG GGT GGC GGA TCT TGA AGT TCA CC</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">tub qPCR forward primer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>GGA CCG CAT CAG GAA ACT GGC</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">tub qPCR reverse preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>CCA CAG ACA GCC TCT CCA TGA GC</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">ef1 qPCR forward primer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>CGC TTG AGG AAA TCA AGA AGG A</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">ef1 qPCRreverse preimer</td>
			<td style="width:133px;">tri-I biotech</td>
			<td style="width:157px;"></td>
			<td>CCT GCA GAG GAA GAC GAA G</td>
		</tr>
	</tbody>
</table>

practical use of rna interference: oral delivery of double-stranded rna in liposome carriers for cockroaches

RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool operating by disruption of essential gene expression. Although different methods, such as injection, feeding, and soaking, have been reported for successful delivery of double-stranded RNA (dsRNA), the efficiency of RNAi through oral delivery of dsRNA is highly variable among different insect groups. The German cockroach, Blattella germanica, is highly sensitive to the injection of dsRNA, as shown by many studies published previously. The present study describes a method to demonstrate that the dsRNA encapsulated with liposome carriers is sufficient to retard the degradation of dsRNA by midgut juice. Notably, the continuous feeding of dsRNA encapsulated by liposomes significantly reduces the tubulin expression in the midgut, and led to the death of cockroaches. In conclusion, the formulation and utilization of dsRNA lipoplexes, which protect dsRNA against nucleases, could be a practical use of RNAi for insect pest control in the future.

A simplified scheme of the protocol for the oral delivery of dsRNA is presented in Figure 1, where the key steps for preparation of dsRNA lipoplexes are shown.
In order to investigate the protection given by liposome carriers upon dsRNA degradation in the midgut juice of B. germanica, an ex vivo assay where dsTub lipoplexes were incubated with midgut juice was conducted, and the in...

Watch this Scientific Journal Video about Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches at JoVE.com

Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches

This manuscript demonstrates the depletion of gene expression in the midgut of the German cockroach through oral ingestion of double-stranded RNA encapsulated in liposomes.

RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool ...

practical-use-rna-interference-oral-delivery-double-stranded-rna

Research

JoVE Journal

Biology

9.3K Views.  National Taiwan University. This manuscript demonstrates the depletion of gene expression in the midgut of the German cockroach through oral ingestion of double-stranded RNA encapsulated in liposomes.

Video: Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13.
Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.

Chromatin Isolation by RNA Purification ChIRP

ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites.

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental ...

Substrate Generation for Endonucleases of CRISPR/Cas Systems

The interaction of viruses and their prokaryotic hosts shaped the evolution of bacterial and archaeal life. Prokaryotes developed several strategies to evade viral attacks that include restriction modification, abortive infection and CRISPR/Cas systems. These adaptive immune systems found in many Bacteria and most Archaea consist of clustered regularly interspaced short palindromic repeat (CRISPR) sequences and a number of CRISPR associated (Cas) genes (Fig. 1) 1-3. Different sets of Cas proteins and repeats define at least three major divergent types of CRISPR/Cas systems 4. The universal proteins Cas1 and Cas2 are proposed to be involved in the uptake of viral DNA that will generate a new spacer element between two repeats at the 5' terminus of an extending CRISPR cluster 5. The entire cluster is transcribed into a precursor-crRNA containing all spacer and repeat sequences and is subsequently processed by an enzyme of the diverse Cas6 family into smaller crRNAs 6-8. These crRNAs consist of the spacer sequence flanked by a 5' terminal (8 nucleotides) and a 3' terminal tag derived from the repeat sequence 9. A repeated infection of the virus can now be blocked as the new crRNA will be directed by a Cas protein complex (Cascade) to the viral DNA and identify it as such via base complementarity10. Finally, for CRISPR/Cas type 1 systems, the nuclease Cas3 will destroy the detected invader DNA 11,12 .
These processes define CRISPR/Cas as an adaptive immune system of prokaryotes and opened a fascinating research field for the study of the involved Cas proteins. The function of many Cas proteins is still elusive and the causes for the apparent diversity of the CRISPR/Cas systems remain to be illuminated. Potential activities of most Cas proteins were predicted via detailed computational analyses. A major fraction of Cas proteins are either shown or proposed to function as endonucleases 4.
Here, we present methods to generate crRNAs and precursor-cRNAs for the study of Cas endoribonucleases. Different endonuclease assays require either short repeat sequences that can directly be synthesized as RNA oligonucleotides or longer crRNA and pre-crRNA sequences that are generated via in vitro T7 RNA polymerase run-off transcription. This methodology allows the incorporation of radioactive nucleotides for the generation of internally labeled endonuclease substrates and the creation of synthetic or mutant crRNAs. Cas6 endonuclease activity is utilized to mature pre-crRNAs into crRNAs with 5'-hydroxyl and a 2',3'-cyclic phosphate termini.

CRISPR/Cas systems mediate adaptive immunity in Bacteria and Archaea. Many Cas proteins are proposed to act as endoribonucleases acting on crRNA precursors of varying length. Here we illustrate three different approaches to generate pre-crRNA substrates for the biochemical analysis of Cas endonuclease activity.

The  interaction of viruses and their prokaryotic hosts shaped the evolution of  bacterial and archaeal life. Prokaryotes developed several strategies to ...

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems including plants, invertebrates and vertebrates. There are various methods to achieve RNAi in vivo4,5. For example, the target gene may be transformed into an RNAi vector, and then either permanently or transiently transformed into cell lines or primary cells to achieve gene knockdown effects; alternatively synthesized double-strand oligonucleotides from specific target genes (RNAi oligos) may be transiently transformed into cell lines or primary cells to silence target genes; or synthesized double-strand RNA molecules may be microinjected into an organism. Since the nematode C. elegans uses bacteria as a food source, feeding the animals with bacteria expressing double-strand RNA against target genes provides a viable strategy6. Here we present an RNAi feeding method to score body size phenotype. Body size in C. elegans is regulated primarily by the TGF- &beta; - like ligand DBL-1, so this assay is appropriate for identification of TGF-&beta; signaling components7. We used different strains including two RNAi hypersensitive strains to repeat the RNAi feeding experiments. Our results showed that rrf-3 strain gave us the best expected RNAi phenotype. The method is easy to perform, reproducible, and easily quantified. Furthermore, our protocol minimizes the use of specialized equipment, so it is suitable for smaller laboratories or those at predominantly undergraduate institutions.

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

We demonstrate how to use the RNAi feeding technique to knock down target genes and score body size phenotype in C. elegans. This method could be used for a large scale screen to identify potential genetic components of interest, such as those involved in body size regulation by DBL-1/TGF-&beta; signaling.

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems ...

Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. Metagenomic RNA-Seq has become an important tool to analyze transcriptomes from various microbes present in a microbial community. Messenger RNA usually comprises only 1-3% of total RNA, while rRNA constitutes approximately 90%. It is challenging to enrich messenger RNA from a metagenomic microbial RNA sample because most prokaryotic mRNA species lack stable poly(A) tails. This prevents oligo d(T) mediated mRNA isolation. Here, we describe a protocol that employs sample derived rRNA capture probes to remove rRNA from a metagenomic total RNA sample. To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. Then, the community specific biotinylated antisense ribosomal RNA probes are synthesized in vitro using T7 RNA polymerase. The biotinylated rRNA probes are hybridized to the total RNA. The hybrids are captured by streptavidin-coated beads and removed from the total RNA. This subtraction-based protocol efficiently removes both mosquito and microbial rRNA from the total RNA sample. The mRNA enriched sample is further processed for RNA amplification and RNA-Seq.

A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity ...

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based &#8220;mix and measure&#8221; hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.

A highly sensitive ribozyme-based assay, applicable to high-throughput screening of chemicals targeting the unique process of RNA editing in trypanosomatid pathogens, is described in this paper. Inhibitors can be used as tools for hypothesis-driven analysis of the RNA editing process and ultimately as therapeutics.

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been ...

Larval RNA Interference in the Red Flour Beetle, Tribolium castaneum

The red flour beetle, Tribolium&#160;castaneum, offers a repertoire of experimental tools for genetic and developmental studies, including a fully annotated genome sequence, transposon-based transgenesis, and effective RNA interference (RNAi). Among these advantages, RNAi-based gene knockdown techniques are at the core of Tribolium research. T. castaneum show a robust systemic RNAi response, making it possible to perform RNAi at any life stage by simply injecting double-stranded RNA (dsRNA) into the beetle&#8217;s body cavity.
In this report, we provide an overview of our larval RNAi technique in T. castaneum. The protocol includes (i) isolation of the proper stage of T. castaneum larvae for injection, (ii) preparation for the injection setting, and (iii) dsRNA injection. Larval RNAi is a simple, but powerful technique that provides us with quick access to loss-of-function phenotypes, including multiple gene knockdown phenotypes as well as a series of hypomorphic phenotypes. Since virtually all T. castaneum tissues are susceptible to extracellular dsRNA, the larval RNAi technique allows researchers to study a wide variety of tissues in diverse contexts, including the genetic basis of organismal responses to the outside environment. In addition, the simplicity of this technique stimulates more student involvement in research, making T. castaneum an ideal genetic system for use in a classroom setting.

Larval RNA Interference in the Red Flour Beetle, Tribolium castaneum

RNA interference (RNAi)-based gene knockdown techniques are at the core of Tribolium research. Here, we provide an overview of our larval RNAi technique in Tribolium castaneum. Larval RNAi is a simple, but powerful technique that provides quick access to loss-of-function phenotypes, allowing researchers to study gene functions in diverse contexts.

The red flour beetle, Tribolium&#160;castaneum, offers a repertoire of experimental tools for genetic and developmental studies, including a fully ...

Production of Double-stranded DNA Ministrings

We constructed linear covalently closed (LCC) DNA minivectors as a non-viral gene-delivery vector alternative produced via a simple platform in vivo. DNA ministrings possess a heightened safety profile and also efficiently deliver DNA cargo to targeted cells. Conventional DNA vectors carry undesirable prokaryotic sequences, including antibiotic resistance genes, CpG motifs, and bacterial origins of replication, which may lead to the stimulation of host immunological responses. The bioavailability of conventional DNA vectors is also compromised due to their larger molecular size. Their circular nature may also impart chromosomal integration, leading to insertional mutagenesis.
Bacterial sequences are excised from DNA minivectors, leaving only the gene of interest (GOI) and necessary eukaryotic expression elements. Our LCC DNA minivectors, or DNA ministrings, are devoid of immunogenic bacterial sequences; therefore improving their bioavailability and GOI expression. In the event of vector integration into the chromosome, the LCC DNA ministring will lethally disrupt the host chromosome, thereby removing the potentially dangerous mutant from the proliferating cell population. Consequently, DNA ministrings offer the benefits of &#39;minicircle&#39; DNA while eliminating the potential for undesirable vector integration events. In comparison to conventional plasmids and their isogenic circular covalently closed (CCC) counterparts, DNA ministrings demonstrate superior bioavailability, transfection efficiency, and cytoplasmic kinetics - they thus require lower amounts of cationic surfactants for effective transfection of target cells.
We have constructed a one-step inducible in vivo system for the production of DNA ministrings in Escherichia coli that is simple to use, rapid, and scalable.

The linear covalently closed (LCC) DNA minivector (DNA ministring) is a non-viral gene delivery vector offering high transfection efficiency and is relevant to any DNA delivery application. The production system is simple, rapid, and scalable in vivo. The following protocol provides visual step-by-step instructions for the production of DNA ministrings.

We constructed linear covalently closed (LCC) DNA minivectors as a non-viral gene-delivery vector alternative produced via a simple platform in vivo. DNA ...

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

RNA-binding proteins (RBPs) are emerging as a regulatory layer in the development and function of adipose. RBPs play a key role in the gene expression regulation at posttranscriptional levels by affecting the stability and translational efficiency of target mRNAs. RNA pull-down technique has been widely used to study RNA-protein interaction, which is necessary to elucidate the mechanism underlying RBPs&#39; as well as long non-coding RNAs&#39; (lncRNAs) function. However, the high lipid abundance in adipocytes poses a technical challenge in conducting this experiment. Here a detailed RNA pull-down protocol is optimized for primary adipocyte culture. An RNA fragment from androgen receptor&#39;s (AR) 3&#39; untranslated region (3&#39;UTR) containing an adenylate-uridylate-rich elementwas used as an example to demonstrate how to retrieve its RBP partner, HuR protein, from adipocyte lystate. The method described here can be applied to detect the interactions between RBPs and noncoding RNAs, as well as between RBPs and coding RNAs.

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

An RNA pull-down protocol is optimized here for detection of interactions between RNA-binding proteins (RBPs) and noncoding as well as coding RNAs. An RNA fragment from androgen receptor (AR) was used as an example to demonstrate how to retrieve its RBP from lystate of primary brown adipocytes.

RNA-binding proteins (RBPs) are emerging as a regulatory layer in the development and function of adipose. RBPs play a key role in the gene expression ...

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological functions have been extensively studied. Indeed, the advent of next-generation deep sequencing and chromatin immunoprecipitation (ChIP) via specific histone modification antibodies has revolutionized our view of epigenetic regulation across the genome. Conversely, tissues typically consist of diverse cell types, and their complex mixture poses analytic challenges to investigating the epigenome in a particular cell type. To address the cell type-specific chromatin state in a genome-wide manner, we recently developed tandem chromatin immunoprecipitation sequencing (tChIP-Seq), which is based on the selective purification of chromatin by tagged core histone proteins from cell types of interest, followed by ChIP-Seq. The goal of this protocol is the introduction of best practices of tChIP-Seq. This technique provides a versatile tool for tissue-specific epigenome investigation in diverse histone modifications and model organisms.

We describe a step-by-step protocol for tandem chromatin immunoprecipitation sequencing (tChIP-Seq) that enables the analysis of cell-type-specific genome-wide histone modification.

Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological ...