The authors thank Bryan T. Vinyard of the USDA, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Biometrical Consulting Service, Beltsville, MD for statistical analyses. This work was supported in part by a grant to J.C.D. from the Deployed War Fighter Protection (DWFP) Research Program funded by the Department of Defense through the Armed Forces Pest Management Board (AFPMB).

1.飼育ヨンエ。ネッタイシマカ大人<ol><li>浅いトレイ内の約¾インチの水でハッチの卵。過密状態は、大人のサイズを小さくします。 </li><li> 25°C（12 hLの：12-HD）でリア幼虫と接地魚の餌で飼育。 注：過剰摂取は、生存率を減少させることができる。 </li><li>毎日のパスツールピペットによって個別に蛹を外し、細かいメッシュ蓋で小さな封じ込めバケットの内側にプラスチック皿（5.5センチメートル×9センチ）に移転、このように24時間の年齢グループを確立する。 </li><li>ケージハウジングの画面の壁に置かれた綿球によるフィード大人の蚊10％のショ糖溶液の幼虫と同じ光周期の下で27℃、相対湿度70％の環境チャンバー内の蚊。 </li><li>電気生理学のために、5〜10日齢の動物を使用しています。一般に、大型動物、より良い結果を生む。 RNA単離のために、5〜10日齢の範囲内の単一の24時間の年齢グループ内にある動物を使用しています。 </li></ol><ol><li>選択した感覚ニューロンからの最小限の活動を誘発電解質の適当な濃度（ 例えば 1-10 mm）を決定します。 10 mMのNaClまたは1mMのKClを実験の開始時のベースライン活性を試験するために合理的な電解質である。 </li><li>適切な溶媒中で、各実験化学物質を溶解させる（ない場合は水、エタノールまたはDMSOを使用）単独の電解質に比べてスパイク活性にほとんどまたは全く効果を有している。 10％エタノールまたは1％DMSOの最終濃度は、妥当な出発濃度である。 </li><li>昆虫に送り抑止や覚せい剤を十分に記載されている制御化学物質（甘いのための苦いまたはスクロース例えばキニーネ）適切なを選択します。 </li></ol> 3.電気生理学（先端記録8;図1） <ol><li>機械的にガラスキャピラリーを引いてフォームガラス電極。熱を最適化し、適切な形状のrecordiを形成するために、ガラスを引っ張って設定を引っ張るNG電極。慎重には、ターゲット感覚子を包むのに十分な幅が、隣接する構造体との接触を回避するのに十分に小さい開いた電極チップを作成するために、解剖顕微鏡下でピンセットを使用してガラス電極の端部を断つ。 </li><li>顕微鏡下で、視覚的に形態によって特定し、先端記録の再現性を確保するために、ターゲット感覚器/感覚子を配置。準備は動物電極エントリの角度から感覚器への無料アクセスを許可する。 </li><li> -20℃の冷凍庫に冷たい麻酔大人の昆虫。低温に露出オーバーにより末梢ニューロンへの損傷を避ける。スライドガラス上にカミソリの刃でセロハンテープの狭いストリップをカット。狭いストリップを使用してスライドガラス上に全昆虫を不動。 </li><li>無関心（アース）電極として機能するように背側胸部または眼の中に化学的に尖らタングステン線を挿入します。 </li><li>興味のある刺激溶液とステップ3.1で行われたガラス電極を埋める。挿入された注射器を使用して、キャップを埋めるエンドを鈍らに引か端からillary。プルダウン端部を保持、すべての気泡をはじく。記録と刺激電極として機能するようにステップ3.1で行われたガラス電極に銀線（塩化物化別売）を挿入します。 </li><li>昆虫におけるコンタクト化学受容の感覚器からの​​記録のために設計されてプリアンプに電極を接続します。このプリアンプ（300 HZ-3 kHzの帯域通過フィルタ）が可能なように導入を刺激に近づけ神経活動をキャプチャするセトリング時間を削減します。収集、保存、スパイク記録ソフトウェアを搭載したマイコンを使用して電気信号を解析する。 注記：正しく記録セットアップを接地すると、急激に信号対雑音比を改善することができる。 </li><li>機能性を確保するために、コントロール溶液（電解液のみ）との感覚器を刺激する。すべての準備のための刺激アーチファクト次の200ミリ秒を開始するスパイクをカウントします。 </li><li>用量応答研究を除いて、すべての実験のための試験化学物質の順序をランダム化、バイアスを除去する。用量応答研究のために、実験的な化学物質の濃度を増加する感覚器を公開。十分な回復を確実にするために刺激間の3分の最小値を許可します。 注：この要件は、昆虫や感覚器によって異なる場合があります。閾値は、標準誤差は試験した最低濃度の標準誤差と重ならないためにその濃度として定義される。 </li></ol> 4. RNA単離および配列決定（図2） <ol><li>しっかりとスナップキャップチューブに合わせて組織disruption.Prepare伴うRNaseフリー乳棒前にドライアイス上でそれらを冷却することによりしっかりとフィット無RNAse乳棒を準備します。積極的に過剰結露を避けるために、解剖しない限り、閉じたコレクションチューブを保管してください。 </li><li>性別によるコールドステージとソートに（-20℃の冷凍庫15秒）で濾過吸引器を使用して、30から40の冷麻酔をかけた蚊を置く。置き動物は味の付属を損傷しないように翼を把握し、ダウンサイド背側。</li><li>細かい鉗子の二組を使用して、解剖顕微鏡下で男性または女性からペアのlabellaまたはtarsiを解剖し、隣接する組織を含めることを制限する。 注：500ペアlabellaは全mRNAの約800〜ナノグラムが得られます。 400個々のtarsi（5セグメント毎に）全mRNAの1,200-1,800ナノグラムをもたらす。 </li><li>あえぎ-鉗子の1対の、軽く内側のスタイレットを公開するlabellaのすぐ近位蚊口吻を把握する。コレクション-鉗子の他のペアを使用して、labellaを削除し、冷たい収集チューブの側に組織を追加します。 </li><li>鉗子の1対の、軽く脛骨と第一足根セグメントの接合部に蚊の足を把握する。鉗子の他のペアを使用して、tarsiを除去し、冷収集チューブの側面に組織を加える。 注：希望と望ましくない組織の界面において考慮細胞型を取る。それは、組織を隣接の混入を制限することが重要であるが、所望の組織の一部を省略しないことも重要である。 FiのNALサンプルを正確に関心のある器官全体を表している必要があります。コレクション鉗子を正確に掻きのみ所望の組織をつかんことで解放することができるように、把持鉗子との正確な境界を作成します。 </li><li>定期的に、チューブの底に組織を維持するために9000×gで簡潔に0℃の遠心機でコレクションチューブをスピンダウン。水分が解剖時に採取管に蓄積する場合、採取した組織をカバーするために冷たいTrizol試薬50μlのを追加します。 </li><li>防汚ラボマーカーを使用して、明らかに1 RNaseフリー1.5ミリリットルコレクションの各組織型用キャップチューブスナップラベルを付けます。 1.5ミリリットルチューブラックと液体窒素を用いて、（トリゾールであれば細かい個）の微粉末に組織を挽く後、凍結。一回繰り返します。 1ミリリットルにトリゾールの全量を、ボルテックスで地面組織を懸濁します。 </li><li>クロロホルム200μlのを追加し、完全に混合する。室温で5分後、4℃、15分間11000×gで遠心分離器でスピンダウン。慎重にゲノムDNAフィルターカラムに直接水層を追加します。 5分間11000×gでスピンダウン。スルー流れ、ピペットで混合するRNaseフリーの70％エタノールを等量加える。 RNAのコレクション列に液体を移し、提供の指示に従ってRNA抽出を続ける。 </li><li>定量化し、精密分光光度計で全RNAの純度を評価し、任意の標準RNA配列決定法を進める。 </li></ol> 5.定量的RT-PCR RNAの配列決定の検証（図3） <ol><li>予測された配列の存在量と推定される化学感覚遺伝子機能の両方で、ダイナミックレンジの相対的な遺伝子発現レベルを比較するために、できるだけ多くの遺伝子を選択する。 </li><li>各標的遺伝子のための設計プライマー対は、特定の100-180塩基対のPCR産物を増幅した。セットごとに少なくとも1つのプライマーは、イントロン境界にまたがる確実にすることによって、非特異的なgDNAの増幅を除外する。あるいは、ゲノム汚染を低減するためにDNase処理を使用しています。 </li><li>集める前のセクションで説明したように昆虫組織。すべてのqRT-PCR反応を完了するのに十分なRNAを提供するために必要な組織を計算する。 注：生物学的三連と技術的三連の反応は、結果の最大の自信を提供します。 </li><li> 、生物学的および技術的の両方をそれぞれの各標的遺伝子の平均のために（Ctは[対象] -Ct [参照]）を複製- X ターゲットとして相対的な遺伝子定量化を計算します。生物学的反復の間のCt値を正規化し、相対的発現の比較でY軸スケールを根絶するために、ハウスキーピング遺伝子を使用する。 </li><li> RNA-seqのと回帰ベース、ブートストラップ同値手順9、反復的に各組織からのデータに、適用を使用して定量RT-PCRデータセットの類似性を評価する。 注：この手順は、観察されたRNA-seqの及び定量RT-PCRデータの周りに構築することができる最小の「類似性の領域」を特定し、QRT-によって測定される相対的な遺伝子発現を可能にするPCRは、RNA-seqのにより相対的遺伝子発現の測定と統計的に同等であると考えられる。 </li></ol>

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The authors have nothing to disclose.

味覚感覚器からの​​記録活動電位の最も挑戦的な側面はあるの応答を決定されている「通常」与えられた昆虫種、総数と味覚受容体ニューロンの感度（GRNs）の最初の時間を記録する単一の味覚感覚子チップを採用する場合であるそう不明。多くの予備録音は最初のテストの範囲や化学物質の濃度を決定するために必要とされる。この例では、我々は、単一のGRNはDEETの低濃度（ 図1）<...

DEET、Picaridin、シトロネラールとIR3535のような化合物は、効果的に重要な病気のベクトル1,2 ネッタイシマカヒトスジシマカなどの蚊を、撃退することが示されている。私たちは、蚊の忌避に関与する細胞を決定するために、特定の味覚感覚器に関連した感覚ニューロンからの活動電位を記録します。これらの組織で発現された遺伝子の下流の配列決定と相まって、我々は、改善された撥水性機能のための新規な化合物をスクリーニングするために最も可能性の高いこれらの細胞の応答を媒介する遺伝子を同定することができる。 RNA-seqが迅速に遺伝子発現の時間的·空間的変化を追跡するための標準になりつつ、強力なツールです。昆虫化学感覚付属や臓器のRNA-seqの分析が大幅に遺伝子6により従来のPCRベースの検索遺伝子に改善し、いくつかの昆虫種3-5の分子受容体を発見するために使用されている。昆虫は最も多様な動物のクラスを表す、事前遺伝子とユニークな表現型との間の接続を研究する多くの機会をセンディング。 RNA-seqの技術は、あらゆる生きている昆虫の組織に採用することができる。同様に、uniporous味覚感覚器内の感覚細胞からの電気生理学的記録は、多くの異なる昆虫種で達成することができる。これら2つの技術のペアリングは、研究者が観測された化学感覚表現型に関与セット遺伝子を絞り込むことができます。異なる種は、特定の課題を提示するが、化学感覚受容体遺伝子および化学感覚適応の間の接続を通知することができる。化学感覚感覚器のサイズおよび形態は可変であり、活動電位を記録する際のノイズを低減し、反復可能な信号を識別するために大規模なトラブルシューティングを必要とする場合がある。化学感覚器官の解剖は、昆虫の形態およびサイズ​​に応じて、些細なまたは繊細で時間がかかるかもしれない。高品質なRNAの回収は、そのような中に特定の顔料を避けるように、同様にいくつかのトラブルシューティングが必要な場合があります組織収集。 行動試験によって忌避化合物の効果を実証する直接的で有益であるが、このアプローチは、時間の作用機構に関して集中的かつ広い。 RNA-seqのと相まって電気生理学は、昆虫に回避行動を駆動何のより具体的な分析が可能になります。化学的差別の「キット」は、昆虫種で同定されたならば、既知の忌避剤に改善するためのより具体的な試みが可能である。これらの行動に関与する感覚細胞における受容体および関連タンパク質は、直接的な化学スクリーニングのために、異種発現されてもよい。さらに、分子モデリングは、化学物質は、これらの受容体7からの強い応答を誘発するかを予測することができます。 化学感覚組織の狭いセット内のすべてのアクティブな遺伝子のスナップショットは、他の種における類似の遺伝子を同定するのに有用であり得る。配列相同性および発現シを使用してmilarities、研究者は、最も可能性の昆虫に広く有効である忌避剤に対する応答を媒介する受容体分子の集合を形成することができる。私たちは、昆虫の化学感覚経路を解体の研究者を支援する非モデルと経済的に重要な昆虫のneuroethology掘り下げるために多くを説得するために以下のプロトコルを提示する。

<table border="0" cellpadding="0" cellspacing="0" width="1272">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Name of Material/ Equipment</td>
			<td style="width:367px;">Company</td>
			<td style="width:189px;">Catalog Number</td>
			<td style="width:467px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Glass capillary</td>
			<td style="width:367px;">A-M Systems</td>
			<td style="width:189px;">628000</td>
			<td>Standard, 1.5mm X 0.86mm, 4&#34;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Silver wire</td>
			<td style="width:367px;">A-M Systems</td>
			<td style="width:189px;">7875</td>
			<td>.015&#34; bare</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Tungsten wire</td>
			<td style="width:367px;">Alfa Products</td>
			<td style="width:189px;">369</td>
			<td>0.127mm diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Fine forceps</td>
			<td style="width:367px;">Fine Science Tools</td>
			<td style="width:189px;">11252</td>
			<td>#5SF Inox</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Refridgerated stage</td>
			<td style="width:367px;">BioQuip Products</td>
			<td style="width:189px;">1429</td>
			<td>Chill Table</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Preamplifier</td>
			<td style="width:367px;">Syntech</td>
			<td style="width:189px;">Taste Probe</td>
			<td style="width:467px;">preamplifier</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Software for electrophysiology</td>
			<td style="width:367px;">Syntech</td>
			<td style="width:189px;">Autospike</td>
			<td style="width:467px;">software for electrophysiology</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;">TetraMin fish food</td>
			<td style="width:367px;">Tetra</td>
			<td style="width:189px;">Tropical fish food granules</td>
			<td>fish food ground to fine powder</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TRIzol</td>
			<td>Life Technologies</td>
			<td>15596-026</td>
			<td>RNA isolation reagent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RNeasy Plus Mini Kit</td>
			<td>Qiagen</td>
			<td style="width:189px;">74136</td>
			<td style="width:467px;">includes gDNA eliminator and RNeasy spin columns</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nanodrop spectrophotometer</td>
			<td>Nano Drop Products</td>
			<td style="width:189px;">ND-1000</td>
			<td>tabletop spectrometer</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:251px;">R statistics</td>
			<td style="width:367px;">freeware (created by Robert Gentleman and Ross Ihaka)</td>
			<td>www.r-project.org</td>
			<td>Use the lm function of the stats package and the equiv.boot function of the equivalence package in the R computing environment.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">1.5ml tube rack</td>
			<td style="width:367px;">Evergreen</td>
			<td style="width:189px;">240-6388-030</td>
			<td>Pour liquid nitrogen into a few empty wells to freeze and grind tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">1.5mL collection tubes with pestle</td>
			<td style="width:367px;">Grainger</td>
			<td style="width:189px;">6HAX6</td>
			<td>RNase free</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Centrifuge</td>
			<td style="width:367px;">Thermo Scientific</td>
			<td style="width:189px;">11178160</td>
			<td>Spin down frozen tissue to keep at bottom of 1.5 mL tube.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Primer-BLAST Primer Designing tool</td>
			<td style="width:367px;">NCBI</td>
			<td style="width:189px;">n/a</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

アエからの活動電位のトレース記録。ネッタイシマカ味覚感覚器（ 図1）化学物質の範囲の直接刺激の有効性を示す。この技術は、合理的な時間範囲（一般に500ms未満）にわたって所定の振幅と持続時間のスパイクをカウントすることによって、任意の刺激の化学への応答を定量することができる。トレース記録は、実験条件の所定のセットの下で容易に再現可能で...

Watch this Scientific Journal Video about Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti at JoVE.com

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

電気生理学的検査によって決定されるようネッタイシマカの主要な味覚付属における遺伝子発現を評価するために2つの方法を使用して、我々は、推定される苦味反発化合物に神経細胞応答の根底にある遺伝子のセットを同定した。

生理的録音と黄熱病の蚊の味覚付属器RNAの配列決定<em&gt;ネッタイシマカ</em

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

physiological-recordings-rna-sequencing-gustatory-appendages-yellow

Research

JoVE Journal

Biology

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

8.0K ビュー.  United States Department of Agriculture. 電気生理学的検査によって決定されるようネッタイシマカの主要な味覚付属における遺伝子発現を評価するために2つの方法を使用して、我々は、推定される苦味反発化合物に神経細胞応答の根底にある遺伝子のセットを同定した。 

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

Building a Better Mosquito: Identifying the Genes Enabling Malaria and Dengue Fever Resistance in A. gambiae and A. aegypti Mosquitoes

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus infections.   Explanation is given for how key refractory genes, those genes conferring resistance to vector pathogens, are identified in the mosquito and how this knowledge can be used to generate transgenic mosquitoes that are unable to carry the malaria parasite or dengue virus.

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus infections. Explanation is given for how key refractory genes, those genes conferring resistance to vector pathogens, are identified in the mosquito and how this knowledge can be used to generate transgenic mosquitoes that are unable to carry the malaria parasite or dengue virus.

より良い蚊の構築：A. gambiaeとA.ネッタイシマカ蚊のマラリアとデング熱の抵抗を使用可能にする遺伝子を特定

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus ...

生物学

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.

RNAiによる遺伝子ノックダウンと<emインビボで&gt;</em大人の女性の&gt;利尿アッセイ<em&gt;ネッタイシマカ</em&gt;蚊

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

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.

モスキートガットメタゲノムRNA-seqのためのリボソームRNAの枯渇

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

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.

Characterizing microbial community has been a longstanding goal in environmental microbiology. Next-generation sequencing methods now allow for the characterization of microbial communities at an unprecedented depth with minimal cost and labor. We detail here our approach to sequence bacterial 16S ribosomal RNA genes using a benchtop sequencer.

16SリボソームRNA遺伝子アンプリコンの次世代シーケンシング

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the ...

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Photoperiodic diapause is an important adaptation that allows individuals to escape harsh seasonal environments via a series of physiological changes, most notably developmental arrest and reduced metabolism. Global gene expression profiling via RNA-Seq can provide important insights into the transcriptional mechanisms of photoperiodic diapause. The Asian tiger mosquito, Aedes albopictus, is an outstanding organism for studying the transcriptional bases of diapause due to its ease of rearing, easily induced diapause, and the genomic resources available. This manuscript presents a general experimental workflow for identifying diapause-induced transcriptional differences in A. albopictus. Rearing techniques, conditions necessary to induce diapause and non-diapause development, methods to estimate percent diapause in a population, and RNA extraction and integrity assessment for mosquitoes are documented. A workflow to process RNA-Seq data from Illumina sequencers culminates in a list of differentially expressed genes. The representative results demonstrate that this protocol can be used to effectively identify genes differentially regulated at the transcriptional level in A. albopictus due to photoperiodic differences. With modest adjustments, this workflow can be readily adapted to study the transcriptional bases of diapause or other important life history traits in other mosquitoes.

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

RNA-Seq analyses are becoming increasingly important for identifying the molecular underpinnings of adaptive traits in non-model organisms. Here, a protocol to identify differentially expressed genes between diapause and non-diapause Aedes albopictus mosquitoes is described, from mosquito rearing, to RNA sequencing and bioinformatics analyses of RNA-Seq data.

アジアのタイガーモスキートにおける日長休眠のRNA-seqの分析のための実験とバイオインフォマティクス·プロトコル、<em&gt;ヒトスジシマカ</em

Photoperiodic diapause is an important adaptation that allows individuals to escape harsh seasonal environments via a series of physiological changes, ...

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study.
RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34- cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34- cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment.
In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo.

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

RNAシーケンシング解析によりEML造血前駆細胞における自己再生および分化を調節する重要な要因の同定

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as ...

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.

We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.

遺伝子発現およびゲノム変化を特徴づけるために、RNAシーケンシングアッセイをターゲットに

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding ...

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.

ネッタイシマカジカのベクトルで脂肪ボディ臓器培養システム

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.

ネッタイシマカ蚊ボルバキアに感染維持

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

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.

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.

24ウェル組織培養プレート(EAgaLプレート)を用いた Aedes aegypti のフェクアンディティと不妊治療アッセイの改善

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