이 작품은 "1000plan" 프로그램, Tongji 대학, 그리고 NSFC 부여 # 21607115에서 시작 자금 및 21777116 (린)에 의해 지원 되었다.

1. 디자인 및 템플릿 개 Zebrafish 태아의 제조
<ol><li>
8에서 12, 96-잘 레이아웃을 표준 96 잘 접시를 맞는 arraying 서식 파일을 디자인 합니다. 크기는 위 태아 함정 챔버에 대 한 그림 1A 에 나열 된 사용 (보조 파일 참조).
	<ol>
<li>함정에 대 한 잘 그림 1B 및 1 D 에 표시 된 크기를 사용 합니다.</li>
		<li>그림 1C 의 크기를 사용 하 여 바닥 진공 챔버에 대 한.</li>
		<li>그림 1B 에서 치수를 사용 하 여에 어에 대 한 / 콘센트.</li>
	</ol>
</li>
	<li>(0.1 m m 정밀도)로 3D 프린터를 사용 하 여 인쇄 서식 파일; 인쇄에 사용할 권장된 수 지에 대 한 테이블의 자료 를 참조 하십시오. 참고: 0.1 m m 정밀 3D 프린터 arraying 서식 파일의 제작에 대 한 권장 ( 재료의 표참조). 서식 파일의 표면에 대 한 제안 된 색상은 어두운 회색 또는 검은색.</li>
</ol>2. Zebrafish 태아 산란
<ol><li>두 켤레 상자 1 일 산란 전에 짝짓기 당 남성과 여성의 물고기를 놓습니다. 별도 남성 그리고 투명 한 플라스틱 분배기에 의해 여성.</li>
	<li>벗을 디바이 더 아침에 남성과 여성의 생선을 혼합.</li>
	<li>남성과 여성의 물고기를 제거 하 고 zebrafish 태아 파인 메쉬 스 트레이너를 사용 하 여 수집 합니다. 세척 배아를 250 mL 계란 물 ( 재료의 표참조).</li>
	<li>접시 (직경 90 mm) Holtfreter의 솔루션에 수집 된 배아를 전송 ( 재료의 표참조) 죽음과 unfertilized 배아는 stereomicroscope를 사용 하 여 제거.</li>
	<li>28.5 ° C 인큐베이터에 배아를 놓습니다. 게시물 수정 (hpf)에서 4 h, 배아 관찰 하 고 모든 죽은 건강에 해로운 배아를 제거. 배아는 다음 단계에 대 한 준비가 지금입니다.</li>
</ol>3입니다. 개 서식 파일의 준비
<ol><li>템플릿 2-3 시간 500 mL 이온을 제거 된 물으로 세척 하 고 5 분 동안 건조 오븐 (45 ℃)에 넣어.</li>
	<li>테이프 씰링 필름 (그림 21 단계)의 조각으로 하단 챔버.</li>
	<li>서식 파일의 아래쪽에 공기 출구를 통해 진공 펌프를 연결 합니다. 참고: 권장된 최대 진공 진공 펌프에 대 한 0.1 Mpa 이다. 사용 하는 진공의 강도 알고 있어야 합니다. 부정적인 압력 너무 강한 경우에, 압력을 낮은 씰링 필름에 있는 십자가 모양의 구멍을 잘라.</li>
</ol>4. 96 잘 접시에 Zebrafish 태아 개
<ol><li>그림 2, 2 단계에서에서와 같이 약 150 배아는 서식 파일에 장소 플라스틱 전송 피 펫을 사용 하 여.</li>
	<li>3.3 단계에서 씰링 필름에 의해 봉인 챔버에 부정적인 압력 생성 하 공기 출구에 진공 펌프를 연결 합니다.</li>
	<li>각 잘 한 배아 속은 (그림 2, 3 단계) 때까지 가로 전체 템플릿 흔들. 참고: 경우에 Holtfreter의 솔루션은 배아 각 우물에 갇혀 있다 전에 마르면, 함정 챔버에 추가 Holtfreter의 솔루션을 추가 하 고이 단계를 반복.</li>
	<li>여분의 Holtfreter 솔루션 및 웰 스 (그림 2, 4 단계)에 침투 하지 배아 폐기.</li>
	<li>해제을 진공 펌프를 분리 합니다.</li>
	<li>(그림 2, 5 단계) 서식 파일에 대 한 표준 96 잘 접시를 거꾸로 배치 하 고 (그림 2, 6 단계) 동시에 회전.</li>
	<li>서식 파일의 아래쪽을 누르거나 공기 연결 콘센트 압축된 가스 뿌리에 96 잘 접시 (그림 2, 6 단계)에 서식 파일에서 모든 갇힌된 배아를 전송 할 수 있는.</li>
	<li>4.1 4.8 추가 멀티 잘 접시 준비 단계를 반복 합니다.</li>
	<li>씰링 필름을 제거 하 고 차후 사용을 위해 500 mL 이온된 물으로 아래로 위에서 3 번 템플릿 세척. 참고: 서식 파일 청소 같은 에탄올, 어떤 유기 용 매를 사용 하지 마십시오.</li>
</ol>

<ol>
	<li>Howe, 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+zebrafish+reference+genome+sequence+and+its+relationship+to+the+human+genome.">The zebrafish reference genome sequence and its relationship to the human genome.</a> Nature. 496 (7446), 498-503 (2013).</li><li>Leslie, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zebrafish+larvae+could+help+to+personalize+cancer+treatments.">Zebrafish larvae could help to personalize cancer treatments.</a> Science. 357 (6353), 745-745 (2017).</li><li>Lin, 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=Understanding+the+Transformation,+Speciation,+and+Hazard+Potential+of+Copper+Particles+in+a+Model+Septic+Tank+System+Using+Zebrafish+to+Monitor+the+Effluent.">Understanding the Transformation, Speciation, and Hazard Potential of Copper Particles in a Model Septic Tank System Using Zebrafish to Monitor the Effluent.</a> ACS Nano. 9 (2), 2038-2048 (2015).</li><li>Lin, 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=Aspect+ratio+plays+a+role+in+the+hazard+potential+of+ceo2+nanoparticles+in+mouse+lung+and+zebrafish+gastrointestinal+tract.">Aspect ratio plays a role in the hazard potential of ceo2 nanoparticles in mouse lung and zebrafish gastrointestinal tract.</a> ACS Nano. 8 (5), 4450-4464 (2014).</li><li>Baraban, S. C., Dinday, M. T., Hortopan, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug+screening+in+Scn1a+zebrafish+mutant+identifies+clemizole+as+a+potential+Dravet+syndrome+treatment.">Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment.</a> Nature Communications. 4, (2013).</li><li>Lin, 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=High+content+screening+in+zebrafish+speeds+up+hazard+ranking+of+transition+metal+oxide+nanoparticles.">High content screening in zebrafish speeds up hazard ranking of transition metal oxide nanoparticles.</a> ACS Nano. 5 (9), 7284-7295 (2011).</li><li>Kuipers, J., Kalicharan, R. D., Wolters, A. H. G., van Ham, T. J., Giepmans, B. N. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+Scanning+Transmission+electron+microscopy+(nanotomy)+of+healthy+and+injured+zebrafish+brain.">Large-scale Scanning Transmission electron microscopy (nanotomy) of healthy and injured zebrafish brain.</a> Journal of Visualized Experiments. (111), (2016).</li><li>Liu, R., 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=Automated+Phenotype+Recognition+for+Zebrafish+Embryo+Based+In+vivo+High+Throughput+Toxicity+Screening+of+Engineered+Nano-Materials.">Automated Phenotype Recognition for Zebrafish Embryo Based In vivo High Throughput Toxicity Screening of Engineered Nano-Materials.</a> PLoS One. 7 (4), (2012).</li><li>Tu, X., 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=Automatic+Categorization+and+Scoring+of+Solid,+Part-Solid+and+Non-Solid+Pulmonary+Nodules.">Automatic Categorization and Scoring of Solid, Part-Solid and Non-Solid Pulmonary Nodules.</a> in CT Images with Convolutional Neural Network. Scientific Reports. 7, 8533 (2017).</li><li>Mandrell, D., 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=Automated+zebrafish+chorion+removal+and+single+embryo+placement:+optimizing+throughput+of+zebrafish+developmental+toxicity+screens.">Automated zebrafish chorion removal and single embryo placement: optimizing throughput of zebrafish developmental toxicity screens.</a> Journal of Laboratory Automation. 17 (1), 66-74 (2012).</li><li>Lin, S., Zhao, Y., Nel, A. E., Lin, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zebrafish:+An+in+vivo+model+for+nano+EHS+studies.">Zebrafish: An in vivo model for nano EHS studies.</a> Small. 9 (9-10), 1608-1618 (2013).</li></ol>

저자는 설명된 3D 인쇄 서식 파일에 대 한 특허를 가득 있다.

3D 인쇄 템플릿 개 zebrafish 태아의 성공적인 구현에 대 한 세심 한 관심을 필요로 하는이 프로토콜에서 두 가지 중요 한 단계가 있습니다.
Arraying 서식 파일의 디자인에서 가장 중요 한 요소는 함정을 잘 이다. 확실 하 게 하는 단 하나의 배아 각 우물에 갇혀, 하나 지름과 함정 우물의 깊이 통해 구멍의 지름에 세심 한 관심을 기울여야 한다. 권장된 직경 내에서 (를 포함 하 여는 ...

인기 모델 생물으로 zebrafish 의학 및 독극물1,2,,34의 분야에서 널리 사용 됩니다. 생체 외에서 플랫폼에 비해, zebrafish 제공 훨씬 더 큰 생물 복잡 하나 또는 2 개의 세포 유형 제공 하지 못했습니다. 모델, zebrafish의 큰 통치, 빠르고 동시 배아 개발 및 높은 기관 전체 유기 체 외 반투명 대규모 독성 또는 약/화합물5를 심사에 사용 될이 모델 독특한 이점을 주었다. 매주 성인 zebrafish의 한 쌍에 의해 생성 하는 배아의 수백 다른 모든 동물 모델을 능가 하 고 높은 처리량 검열을 위해 적당 한 만든.
제 브라를 사용 하 여 일반적인 심사 절차 많은 성인 zebrafish 산란, 태아 선택, 그리고 그들이 물 침수를 통해 노출 대상이 되 적당 한 용기에 배아를 개 같은 수동 작업이 포함 됩니다. 태아의 개발은 모니터링 및 사망률, hatchability 등 비정상적인 관찰 끝점 자주 수동으로 평가 화학 물질의 독성 또는의 효과의 표시의 예비 식별으로 사용 약 또는 화합물입니다. 속도 심사 절차를, 자동화 된 이미징 및 컴퓨터 기반 이미지 분석 등 접근은 이전 탐험 되었습니다 있다. 예를 들어 현미경 이미징 기능 높은 콘텐츠로 384 분의 96 잘 접시6에서 다양 한 발달 단계에서 자동화 된 밝은 필드 또는 형광 이미징 zebrafish 태아에 수행 적응 되었습니다. 현미경과 함께 미세 장치는 뇌 뉴런7의 이미징에 대 한 현재 조작을 통해 zebrafish 애벌레를 사용 되었다. 이러한 접근 수 크게 전통적인 수동 작업에 비해 이미지 취득의 효율성을 향상 시킵니다. 또한, 생성 되는 이미지의 큰 숫자, 이미지 분석 도구 또한 개발 되었습니다 속도 데이터 처리를 같이 리 외 와 화 외. 8 , 9.
이미징 및 이미지 분석의 처리량 수준을 증가, 심사에 대 한 속도 제한 단계 96-또는 384-잘 접시에 배열 하는 일반적으로 의미 노출 zebrafish 태아를 준비 하는 과정은 취소 되었습니다. 이 병목 단계를 해결 하기 위해 비전 가이드 로봇 Mandrell 외. 에 의해 개발 되었다 10 와 미국 수동 처리 하지만 악기를 대체 하는 이전11 꽤 되었고 이러한 기술을 구현 하는 깊은 학습 곡선입니다. 따라서, 사용 하기 쉬운 접근 된다 더 zebrafish 심사 처리량 수준을 개선 하는 하나의 중요 한 요소 이며이 작품의 주요 목적은 제공 하기.
이 작품에서는, 우리는 설계 및 3D 인쇄 하 여 서식 파일을 배열 하는 배아를 조작. 이러한 arraying 서식 파일 표준 96 잘 접시와 맞는 우물으로 zebrafish 태아를 모 함 하도록 설계 되었습니다. 배아를 선택 하 고 개별 음 하나 하나에 그들을 배열, 대신 하나를 수행할 수 배아 함정 및 배열 모든 96 배아 multiwall 격판덮개로 한 번에. 이 서식 파일 및 다음 프로토콜을 사용 하 여, 하나 크게 어느 것이 기간 부스트 심사 용량 적어도 열 배, 수동 조작에 비해 multiwall 접시에 배아를 배열의 효율성을 증가할 수 있었다. 프로토콜 아래에 설명 된 템플릿, zebrafish 산란, 배아 수집, 배열 및 배열에 대 한 전반적인 디자인을 포함 한다. 그림 1 에서는 arraying 서식 파일의 전반적인 디자인. 그림 2 는 부품 3 및 4에 설명 된 서식 파일을 사용 하 여 단계별 프로토콜에 대 한 개요를 보여 줍니다.

<table border="0" cellpadding="0" cellspacing="0" width="1557">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Zebrafish Facility</td>
			<td style="width:425px;">Shanghai Haisheng Biotech Co., Ltd.</td>
			<td style="width:229px;">Z-A-S5</td>
			<td style="width:429px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Mating box</td>
			<td style="width:425px;">Shanghai Haisheng Biotech Co., Ltd.</td>
			<td style="width:229px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Wash Bottle, 500 ml</td>
			<td style="width:425px;">Sangon Biotech</td>
			<td style="width:229px;">F505001-0001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium chloride</td>
			<td style="width:425px;">Vetec</td>
			<td style="width:229px;">V900058-500G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Potassium Chloride</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">10016318</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calcium chloride</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">20011160</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium bicarbonate&#160;</td>
			<td style="width:425px;">Vetec</td>
			<td style="width:229px;">v900182-500G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methylene Blue Hydrate</td>
			<td style="width:425px;">TCI</td>
			<td style="width:229px;">M0501</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hydrochloric acid</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">10011008</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Sea Salts</td>
			<td>Instant Ocean</td>
			<td style="width:229px;">SS15-10</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pipetter</td>
			<td style="width:425px;">Fisherbrand</td>
			<td style="width:229px;">13-675M</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Controlled Drop Pasteur Pipet</td>
			<td style="width:425px;">Fisherbrand</td>
			<td style="width:229px;">13-678-30</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Microscope</td>
			<td style="width:425px;">OLYMPUS</td>
			<td style="width:229px;">SZ61</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Biochemical incubator</td>
			<td>Shanghai Yiheng Scientific Instrument Co., Ltd.</td>
			<td>LRH-250</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">3D printer</td>
			<td>UnionTech</td>
			<td>Lite600</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Photosensitive resin</td>
			<td>UnionTech</td>
			<td>UTR9000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vacuum pump</td>
			<td>Shanghai Yukang Scientific Instrument Co., Ltd.</td>
			<td>SHB-IIIA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Adhesive PCR Plate Seals</td>
			<td style="width:425px;">Solarbio</td>
			<td style="width:229px;">YA0245</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">96 well plate</td>
			<td style="width:425px;">Costar</td>
			<td style="width:229px;">3599</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Multi 8-channel pipette 30 - 300 &#956;l</td>
			<td style="width:425px;">Eppendorf</td>
			<td style="width:229px;">3122000.051</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Compressed Gas Duster</td>
			<td style="width:425px;">Shanghai Zhantu Chemical Co., Ltd.</td>
			<td style="width:229px;">ST1005</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">DI Water</td>
			<td style="width:425px;">Thermo</td>
			<td style="width:229px;">GenPure Pro UV/UF</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Drying oven</td>
			<td style="width:425px;">Shanghai Yiheng Scientific Instrument Co., Ltd.</td>
			<td style="width:229px;">BPG-9106A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">System water</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Water out of the facility&#8217;s water system</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:475px;">Egg water</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Dilute 60mg &#8220;Instant Ocean&#8221; sea salts and 0.25 mg/L methylene blue in 1 L DI water</td>
		</tr>
		<tr height="116">
			<td height="116" style="height:116px;width:475px;">Holtfreter&#8217;s solution</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Dissolve 7.0 g Sodium chloride (NaCl), 0.4 g Sodium bicarbonate (NaHCO3), 0.1 g Potassium Chloride (KCl), 0.235 g Calcium chloride (CaCl2.2H2O) in 1.9 L DI water. Adjust pH to 7 using HCl and adjust volume to 2 L using Di water</td>
		</tr>
	</tbody>
</table>

a 3-dimensional (3d)-printed template for high throughput zebrafish embryo arraying

제 브라는 세계적으로 인정된 민물 유기 체 자주 사용 개발 생물학, 환경 독성, 그리고 인간의 질병에 관련된 연구 분야 이다. 큰 통치, 배아 반투명, 빠르고 동시 개발, 등, 등의 독특한 기능 zebrafish 태아는 종종 대규모 화학 물질의 독성 평가 및 사용 약물/화합물 심사. 일반적인 심사 절차 포함 성인 zebrafish 산란, 배아 선택, 다 잘 판에 배아를 개. 거기에서 태아 노출 및 화학 물질, 독성을 복종 된다 또는 마약/화합물의 효과 phenotypic 관측에 따라 상대적으로 신속 하 게 평가할 수 있습니다. 이러한 프로세스 중 개 배아 처리량 수준을 제한 하는 가장 시간이 많이 걸리는 하 고 노동 집약적인 단계 중 하나입니다. 이 프로토콜에서 선물이 3D 인쇄 arraying 서식 파일의 사용과 결합 하 게 진공 속도이 힘 드는 단계를 조작 하는 혁신적인 접근 방식. 본 프로토콜 arraying 템플릿, 상세한 실험 설정 및 대표 결과 다음 단계별 절차의 전반적인 디자인을 설명 합니다. 구현 될 때,이 방법은 테스트 과목으로 zebrafish 태아를 사용 하 여 연구 응용 프로그램의 다양 한에서 도움이 증명 해야 합니다.

그림 3 은 전형적인 3D 인쇄 arraying 템플릿을 보여준다. 이 감광 성 수 지 원료로 사용 하 여 템플릿과 3D 프린터;에 의해 만들어진 블랙 페인트의 레이어 배아의 색상에 더 나은 대조를 제공 하기 위해 적용 되었습니다. 96 웰 스 (8으로 12)의 위치는 표준 96 잘 접시와 맞게 설계 되었다. 마찬가지로, 384 (16 24) 잘 서식 파일 또한 디자인 될 수 하 고 동일한 ?...

Watch this Scientific Journal Video about A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying at JoVE.com

A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying

여기, 우리 디자인 하 고 서식 파일, 높은 처리량 zebrafish 태아 96 잘 접시에 배열에 대 한 같은 서식 파일의 사용에 자세한 절차 뒤 개 zebrafish 태아 조작 프로토콜을 제시.

3 차원 (3D)-배열 하는 높은 처리량 Zebrafish 태아에 대 한 서식 파일을 인쇄

The zebrafish is a globally recognized fresh water organism frequently used in developmental biology, environmental toxicology, and human disease related ...

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A 3-dimensional (3D)-printed Template for High Throughput Zebrafish Embryo Arraying

6.7K 조회수.  Tongji University. 여기, 우리 디자인 하 고 서식 파일, 높은 처리량 zebrafish 태아 96 잘 접시에 배열에 대 한 같은 서식 파일의 사용에 자세한 절차 뒤 개 zebrafish 태아 조작 프로토콜을 제시.

비디오: A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying

Determination of Microbial Extracellular Enzyme Activity in Waters, Soils, and Sediments using High Throughput Microplate Assays

Much of the nutrient cycling and carbon processing in natural environments occurs through the activity of extracellular enzymes released by microorganisms. Thus, measurement of the activity of these extracellular enzymes can give insights into the rates of ecosystem level processes, such as organic matter decomposition or nitrogen and phosphorus mineralization. Assays of extracellular enzyme activity in environmental samples typically involve exposing the samples to artificial colorimetric or fluorometric substrates and tracking the rate of substrate hydrolysis. Here we describe microplate based methods for these procedures that allow the analysis of large numbers of samples within a short time frame. Samples are allowed to react with artificial substrates within 96-well microplates or deep well microplate blocks, and enzyme activity is subsequently determined by absorption or fluorescence of the resulting end product using a typical microplate reader or fluorometer. Such high throughput procedures not only facilitate comparisons between spatially separate sites or ecosystems, but also substantially reduce the cost of such assays by reducing overall reagent volumes needed per sample.

Microplate based procedures are described for the colorimetric or fluorometric analysis of extracellular enzyme activity. These procedures allow for the rapid assay of such activity in large numbers of environmental samples within a manageable time frame.

높은 처리량 마이크로 분석 실험을 사용하여 워터스, 토양 및 퇴적물에있는 미생물 세포 외 효소 활성의 결정

Much of the nutrient cycling and carbon  processing in natural environments occurs through the activity of extracellular  enzymes released by ...

연구

환경과학

High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities

Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be assimilated for energy and nutrients. Measuring soil microbial enzyme activity is crucial in understanding soil ecosystem functional dynamics. The general concept of the fluorescence enzyme assay is that synthetic C-, N-, or P-rich substrates bound with a fluorescent dye are added to soil samples. When intact, the labeled substrates do not fluoresce. Enzyme activity is measured as the increase in fluorescence as the fluorescent dyes are cleaved from their substrates, which allows them to fluoresce. Enzyme measurements can be expressed in units of molarity or activity. To perform this assay, soil slurries are prepared by combining soil with a pH buffer. The pH buffer (typically a 50 mM sodium acetate or 50 mM Tris buffer), is chosen for the buffer&#39;s particular acid dissociation constant (pKa) to best match the soil sample pH. The soil slurries are inoculated with a nonlimiting amount of fluorescently labeled (i.e. C-, N-, or P-rich) substrate. Using soil slurries in the assay serves to minimize limitations on enzyme and substrate diffusion. Therefore, this assay controls for differences in substrate limitation, diffusion rates, and soil pH conditions; thus detecting potential enzyme activity rates as a function of the difference in enzyme concentrations (per sample).
Fluorescence enzyme assays are typically more sensitive than spectrophotometric (i.e. colorimetric) assays,&#160;but can suffer from interference caused by impurities and the instability of many fluorescent compounds when exposed to light; so caution is required when handling fluorescent substrates. Likewise, this method only assesses potential enzyme activities under laboratory conditions when substrates are not limiting. Caution should be used when interpreting the data representing cross-site comparisons with differing temperatures or soil types, as in situ soil type and temperature can influence enzyme kinetics.

To measure potential rates of soil extracellular enzyme activities, synthetic substrates that are bound to a fluorescent dye are added to soil samples. Enzyme activity is measured as the fluorescent dye is released from the substrate by an enzyme-catalyzed reaction, where higher fluorescence indicates more substrate degradation.

잠재적 인 토양 세포 외 효소 활동의 높은 처리량 형광 측정 측정

Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be ...

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of natural proteins have a molecular mass between 40 - 200 kDa1,2, a robust and high-throughput method with a nanometer resolution capability is needed. Negative staining (NS) electron microscopy (EM) is an easy, rapid, and qualitative approach which has frequently been used in research laboratories to examine protein structure and protein-protein interactions. Unfortunately, conventional NS protocols often generate structural artifacts on proteins, especially with lipoproteins that usually form presenting rouleaux artifacts. By using images of lipoproteins from cryo-electron microscopy (cryo-EM) as a standard, the key parameters in NS specimen preparation conditions were recently screened and reported as the optimized NS protocol (OpNS), a modified conventional NS protocol 3 . Artifacts like rouleaux can be greatly limited by OpNS, additionally providing high contrast along with reasonably high&#8208;resolution (near 1 nm) images of small and asymmetric proteins. These high-resolution and high contrast images are even favorable for an individual protein (a single object, no average) 3D reconstruction, such as a 160 kDa antibody, through the method of electron tomography4,5. Moreover, OpNS can be a high&#8208;throughput tool to examine hundreds of samples of small proteins. For example, the previously published mechanism of 53 kDa cholesteryl ester transfer protein (CETP) involved the screening and imaging of hundreds of samples 6. Considering cryo-EM rarely successfully images proteins less than 200 kDa has yet to publish any study involving screening over one hundred sample conditions, it is fair to call OpNS a high-throughput method for studying small proteins. Hopefully the OpNS protocol presented here can be a useful tool to push the boundaries of EM and accelerate EM studies into small protein structure, dynamics and mechanisms.

More than half of proteins are small proteins (molecular mass &#60;200 kDa) that are challenging for both electron microscope imaging and three-dimensional reconstructions. Optimized negative staining is a robust and high-throughput protocol to obtain high contrast and relatively high resolution (~1 nm) images of small asymmetric proteins or complexes under different physiological conditions.

최적화 된 음의 염색 : 전자 현미경으로 작은 비대칭 단백질 구조 검사를위한 높은 처리량 프로토콜

Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of ...

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce (Lactuca sativa) Germplasm Collections

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely drought-tolerance traits. Fresh water availability for agricultural use is a growing concern across the United States as well as many regions of the world. Short-term drought events along with regulatory intervention in the regulation of water availability coupled with the looming threat of long-term climate shifts that may lead to reduced precipitation in many important agricultural regions has increased the need to hasten the development of crops adapted for improved water use efficiency in order to maintain or expand production in the coming years. This protocol is not meant as a step-by-step guide to identifying at either the physiological or molecular level drought-tolerance traits in lettuce, but rather is a method developed and refined through the screening of thousands of different lettuce varieties. The nature of this screen is based in part on the streamlined measurements focusing on only three water-stress indicators: leaf relative water content, wilt, and differential plant growth following drought-stress. The purpose of rapidly screening a large germplasm collection is to narrow the candidate pool to a point in which more intensive physiological, molecular, and genetic methods can be applied to identify specific drought-tolerant traits in either the lab or field. Candidates can also be directly incorporated into breeding programs as a source of drought-tolerance traits.

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce Lactuca sativa Germplasm Collections

This protocol was developed to screen a large germplasm collection of the leafy vegetable lettuce (Lactuca sativa L.) for drought-tolerance, in order to identify a small candidate pool of lettuce for use in physiological, molecular, and genetic studies to identify underlying drought-tolerance traits along with breeding programs.

추 잠재적 가뭄 내성 세미 높은 처리량 검열 (<em&gt; 왕 고들빼기 속 sativa로구나</em&gt;) 유전자 원의 컬렉션

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely ...

High-throughput Screening of Recalcitrance Variations in Lignocellulosic Biomass: Total Lignin, Lignin Monomers, and Enzymatic Sugar Release

The conversion of lignocellulosic biomass to fuels, chemicals, and other commodities has been explored as one possible pathway toward reductions in the use of non-renewable energy sources. In order to identify which plants, out of a diverse pool, have the desired chemical traits for downstream applications, attributes, such as cellulose and lignin content, or monomeric sugar release following an enzymatic saccharification, must be compared. The experimental and data analysis protocols of the standard methods of analysis can be time-consuming, thereby limiting the number of samples that can be measured. High-throughput (HTP) methods alleviate the shortcomings of the standard methods, and permit the rapid screening of available samples to isolate those possessing the desired traits. This study illustrates the HTP sugar release and pyrolysis-molecular beam mass spectrometry pipelines employed at the National Renewable Energy Lab. These pipelines have enabled the efficient assessment of thousands of plants while decreasing experimental time and costs through reductions in labor and consumables.

Plant cell wall structure and chemistry traits are evaluated to identify ideal feedstocks for biofuels and bio-materials. Standard methods have limitations when applied to large data sets. These high-throughput pretreatment, enzyme saccharification, and pyrolysis-molecular beam mass spectrometry methods compare large numbers of biomass samples with decreased experimental time and cost.

총 리그닌, 리그닌 단량체, 및 효소 설탕 자료 : 리그 노 셀룰로오스 바이오 매스의 반항의 변화의 높은 처리량 검열

The conversion of lignocellulosic biomass to fuels, chemicals, and other commodities has been explored as one possible pathway toward reductions in the ...

RGB and Spectral Root Imaging for Plant Phenotyping and Physiological Research: Experimental Setup and Imaging Protocols

Better understanding of plant root dynamics is essential to improve resource use efficiency of agricultural systems and increase the resistance of crop cultivars against environmental stresses. An experimental protocol is presented for RGB and hyperspectral imaging of root systems. The approach uses rhizoboxes where plants grow in natural soil over a longer time to observe fully developed root systems. Experimental settings are exemplified for assessing rhizobox plants under water stress and studying the role of roots. An RGB imaging setup is described for cheap and quick quantification of root development over time. Hyperspectral imaging improves root segmentation from the soil background compared to RGB color based thresholding. The particular strength of hyperspectral imaging is the acquisition of chemometric information on the root-soil system for functional understanding. This is demonstrated with high resolution water content mapping. Spectral imaging however is more complex in image acquisition, processing and analysis compared to the RGB approach. A combination of both methods can optimize a comprehensive assessment of the root system. Application examples integrating root and aboveground traits are given for the context of plant phenotyping and plant physiological research. Further improvement of root imaging can be obtained by optimizing RGB image quality with better illumination using different light sources and by extension of image analysis methods to infer on root zone properties from spectral data.

An experimental protocol is presented for assessment of soil grown plant root systems with RGB and hyperspectral imaging. Combination of RGB image time series with chemometric information from hyperspectral scans optimizes insights into plant root dynamics.

RGB 및 식물 형질 및 생리 적 연구에 대 한 스펙트럼 루트 이미징: 실험적인 체제 및 프로토콜을 이미징

Better understanding of plant root dynamics is essential to improve resource use efficiency of agricultural systems and increase the resistance of crop ...

Basic Research in Plasma Medicine - A Throughput Approach from Liquids to Cells

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive species known to redox regulate biological processes in health and disease. Pre-clinical and clinical evidence points to beneficial effects of plasma treatment in the healing of chronic ulcer of the skin. Other emerging topics, such as plasma cancer treatment, are receiving increasing attention. Plasma medical research requires interdisciplinary expertise in physics, chemistry, and biomedicine. One goal of plasma research is to characterize plasma-treated cells in a variety of specific applications. This includes, for example, cell count and viability, cellular oxidation, mitochondrial activity, cytotoxicity and mode of cell death, cell cycle analysis, cell surface marker expression, and cytokine release. This study describes the essential equipment and workflows required for such research in plasma biomedicine. It describes the proper operation of an atmospheric pressure argon plasma jet, specifically monitoring its basic emission spectra and feed gas settings to modulate reactive species output. Using a high-precision xyz-table and computer software, the jet is hovered in millisecond-precision over the cavities of 96-well plates in micrometer-precision for maximal reproducibility. Downstream assays for liquid analysis of redox-active molecules are shown, and target cells are plasma-treated. Specifically, melanoma cells are analyzed in an efficient sequence of different consecutive assays but using the same cells: measurement of metabolic activity, total cell area, and surface marker expression of calreticulin, a molecule important for the immunogenic cell death of cancer cells. These assays retrieve content-rich biological information about plasma effects from a single plate. Altogether, this study describes the essential steps and protocols for plasma medical research.

A high-throughput cold physical plasma treatment protocol of liquids and cells is shown. It involves setting up different feed gas compositions for plasma ignition, measuring the plasma&#39;s emission spectra, and the subsequent analysis of liquids and cellular activity after plasma treatment.

플라즈마 의학-세포 액체에서 처리량 접근 기초 연구

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive ...

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize (Zea mays L.)

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole grain composition and processing characteristics vary among maize hybrids and can impact the quality of the final processed product. Therefore, in order to produce healthier processed food products from maize, it is necessary to know how to optimize processing parameters for particular sets of germplasm to account for these differences in grain composition and processing characteristics. This includes a better understanding of how current processing techniques impact the nutritional quality of the final processed food product. Here, we describe a microscale protocol that both simulates the processing pipeline to produce cornflakes from large flaking grits and allows for the processing of multiple grain samples simultaneously. The flaking grits, the intermediate processed products, or final processed product, as well as the corn grain itself, can be analyzed for nutritional content as part of a high-throughput analytical pipeline. This procedure was developed specifically for incorporation into a maize breeding research program, and it can be modified for other grain crops. We provide an example of the analysis of insoluble-bound ferulic acid and p-coumaric acid content in maize. Samples were taken at five different processing stages. We demonstrate that sampling can take place at multiple stages during microscale processing, that the processing technique can be utilized in the context of a specialized maize breeding program, and that, in our example, most of the nutritional content was lost during food product processing.

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize Zea mays L.

Here, we present a microscale protocol for processing grain samples and for incorporating this microscale approach into a high-throughput analytical pipeline. This is a higher throughput adaptation of currently available protocols.

높은 처리량, 처리 파라미터 분석 및 옥수수 (지 시 메이 스 L.) 영양 자질에 대 한 미 프로토콜

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole ...

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO2] and methane [CH4]) production resulting from the decomposition of NOM, a molecular-level characterization coupled with microbial proteome analyses is necessary. Further, climate and environmental changes are expected to perturb natural ecosystems, potentially upsetting complex interactions that influence both the supply of organic matter substrates and the microorganisms performing the transformations. A detailed molecular characterization of the organic matter, microbial proteomics, and the pathways and transformations by which organic matter is decomposed will be necessary to predict the direction and magnitude of the effects of environmental changes. This article describes a methodological throughput for comprehensive metabolite characterization in a single sample by direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography mass spectrometry (LC-MS), and proteomics analysis. This approach results in a fully-paired dataset which improves statistical confidence for inferring pathways of organic matter decomposition, the resulting CO2 and CH4 production rates, and their responses to environmental perturbation. Herein we present results of applying this method to NOM samples collected from peatlands; however, the protocol is applicable to any NOM sample (e.g., peat, forested soils, marine sediments, etc.).

This protocol describes a single throughput for complementary analytical and omics techniques culminating in a fully-paired characterization of natural organic matter and microbial proteomics in different ecosystems. This approach permits robust comparisons for identifying metabolic pathways and transformations important for describing greenhouse gas production and predicting responses to environmental change.

복잡 한 자연 유기 물질 혼합물을 특성화에 대 한 단일 처리량 보완 고해상도 분석 기법

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to ...

Evaluation of the Productivity of Social Wasp Colonies (Vespinae) and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables researchers to estimate more accurately the number of adults produced, counting the number of meconia (the stools left in the cells by wasp larvae when pupating into adults, per 100 cells) in each comb. This method can be applied before or after colony collapse (i.e., in active or inactive nests). The paper also describes how to locate wild Vespula wasp colonies by &#34;flagging&#34; wasp baits and chasing the wasp collecting them, using a method traditionally performed by local people in central Japan (as illustrated in the associated video). The Vespula chasing method described has several advantages: it is easy to reinitiate the chase from a point where the forager flying back to the nest was lost, and it is easy to pinpoint the nest location as marked wasps often lose their flag at the nest entrance. These methods for estimating colony productivity and collecting nests can be valuable for researchers studying social wasps.

Evaluation of the Productivity of Social Wasp Colonies Vespinae and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

This methodological paper evaluates the productivity of a social wasp colony by examining the number of meconia per 100 cells of comb, to estimate the total number of adults the wasps produced. The associated video describes how to search for Vespula wasp nests, a method developed by amateur wasp chasers.

사회 말스박 식민지의 생산성 평가 (베스피나) 및 전통적인 일본 베스풀라 말스프 사냥 기술 소개

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables ...