The authors would like to thank Drs. Roger Cone and Chao Zhang for their contributions to validating the application of this assay as previously published. This work was supported by NIH 1F32DK082167-01 (BJR).

Nota: Questo protocollo segue le linee guida della University of Arizona Ufficio per una gestione responsabile della Ricerca ed è stato approvato dalla cura degli animali e del Comitato Usa Istituzionale 1. Allevamento Zebrafish e Embryo manutenzione <ol><li> Preparare E3 embrione media 8. Fare 60x soluzione madre, sciogliere 34,8 g di NaCl, 1,6 g KCl, 5.8g CaCl 2 ● 2H 2 O, e 9,78 g MgCl 2 ● 6H 2 O a 1,95 L ddiH 2 O. Regolare il pH a 7,2 con NaOH e HCl Regolare il volume a 2 L utilizzando ddiH 2 O. </li><li> Per preparare 1x E3 medio embrione, diluire 16,5 ml 60x magazzino in 1 L ddiH20. Aggiungere 100 ml 1% di blu di metilene. </li><li> Allevamento <ol><li> Casa Maschio e femmina nidiata magazzino (7 - 18 mesi di età) separatamente per massimizzare la fecondità. </li><li> Spegnere le luci 1-2 ore prima del giorno precedente uova sono desiderati. Impostare l&#39;accoppiamento (1 maschio e 1 - 2 femmine) in cgabbie Rossing come precedentemente descritto 9. Gabbie Crossing consentono per le uova di sfuggire predazione che passano attraverso la base forata dell&#39;inserto vasca in cui i pesci adulti sono detenuti. </li><li> Optional:. Per la riproduzione temporizzata, (come sarebbe necessario per gli studi che coinvolgono morfolino iniezione), separare il maschio e pesce femmina da un chiaro divisorio in plastica, Rimuovi questa mattina di provocare temporizzato deposizione delle uova e la fecondazione. Per morpholino studi, eseguire calcoli di potenza per valutare il numero di pesci embrionale necessaria per il trattamento. Senza una stima della dimensione dell&#39;effetto o variazione, una prova preliminare può essere eseguito con un n = 8. </li></ol></li><li> Versare le uova da gabbia traversata in una capsula di Petri (100 - 150 embrioni / 10 centimetri di Petri). Lasciare le uova di depositarsi sul fondo del piatto e versare l&#39;acqua. Rimuovere eventuale acqua residua con una punta fine trasferimento monouso pipetta. Aggiungere indietro medio E3 embrione fatto in fase 1.1. </li><li> Fai afzoppo pipetta monouso lucido per il futuro di uova e il trasferimento del pesce. Utilizzando le forbici, tagliare una pipetta di trasferimento monouso diplomato al diploma 0,25 ml. Per rimuovere i bordi irregolari, polacco fiamma la punta taglio sopra un becco Bunsen. </li><li> Mantenere pesce embrionale a 4 giorni dopo la fecondazione (DPF) di 10 cm capsule di Petri in zebrafish media E3 embrione a 28,5 ○ C. Due volte al giorno, utilizzare fiamme lucido laureato monouso pipetta di trasferimento per rimuovere eventuali uova non fecondate o embrioni morti (aspetto bianco opaco). Una volta al giorno, sostituire E3 medio embrione. Eliminare E3 medio embrione, rimuovere il liquido restante con una punta fine trasferimento monouso pipetta e aggiungere di nuovo pre-riscaldato (28,5 ○ C) E3 medio embrione. </li></ol> 2. Preparare Assay Solution <ol><li> Preparare la soluzione test secondo la Tabella 1. Soluzione saggio Filtro sterile utilizzando un filtro da 0,22 micron. Prima del dosaggio iniziazione, scaldare la soluzione test sterile in una 28,5 ○ Cbagnomaria. </li></ol><table fo:keep-together.within-page="1"><tbody><tr><td> Ingrediente </td><td> % Del totale </td><td> Volume (ml / 10 ml) </td></tr><tr><td> 60x E3 Embrione Media </td><td> 1.667 </td><td> 166,7 </td></tr><tr><td> Doppia deionizzata (DDI) H 2 0 </td><td> 96,233 </td><td> 9.623,3 </td></tr><tr><td> Alamar blu </td><td> 1 </td><td> 100 </td></tr><tr><td> NaOH 400 mm </td><td> 1 </td><td> 100 </td></tr><tr><td> DMSO </td><td> 0.1 </td><td> 10 </td></tr></tbody></table> Tabella 1. Assay Media 3. Eseguire Assay <ol><li> Sciacquare embrioni di zebrafish 3 volte con sterile filtrata medio embrione E3. Unire tutti gli embrioni vitali zebrafish dalla frizione in un bicchiere. Filtro sterile da 75 ml E3 medio embrione. Utilizzando una punta fine trasferimento monouso pipetta, rispostare tanto del mezzo embrione E3 dagli embrioni zebrafish possibile. Aggiungere 20 ml di nuovo sterile filtrata medio embrione E3. Rimuovere e sostituire E3 medio embrione 3 volte. </li><li> Tavola 1 pesce in ciascuno dei 93 pozzetti di una nera 96 ​​pozzetti lati chiara piatto fondo. Trasferire il pesce embrionale alla piastra catturando individualmente un embrione all&#39;interno di una fiamma lucido laureato plastica pipetta usa e getta (punto 1.5) e l&#39;espulsione delicatamente nel pozzo. Trasferire E3 embrione medio tratto dal bicchiere contenente pesce risciacquati nei 3 pozzetti del bianco. Questo assicura che i pozzi vuoti sono stati esposti per la stessa acqua dei pozzi che contengono pesci. Entrambi i pozzetti che contengono pesce e pozzetti vuoti devono essere almeno a metà (200 microlitri) al termine di questa fase. </li><li> Sostituire E3 medio embrione con la soluzione di test in tutti i 96 pozzi, tra cui pozzetti del bianco. Questa operazione deve essere eseguita 1 colonna alla volta per ciascuna delle 12 colonne in una piastra da 96 pozzetti. Utilizzando una punta fine e getta transfer pipetta, rimuovere E3 medio embrione da ciascun pozzetto in una colonna della piastra (8 pozzetti). Fare attenzione a non toccare l&#39;embrione zebrafish. Aggiungere 300 ml di soluzione di dosaggio per ciascun pozzetto da cui l&#39;acqua è stata rimossa. Ripetere la rimozione di E3 medio embrione e sostituzione con la soluzione test per tutte le colonne 12 della piastra. </li><li> Opzionale: Per testare il cambiamento di tasso metabolico in risposta ad un composto, fare una soluzione che è 100 volte (100x) la concentrazione trattamento desiderato. Di nota, assicurarsi che la soluzione 100x non supera il 10% DMSO a limitare la concentrazione finale di DMSO a non più di 0,1%. Aggiungere 3 ml di soluzione 100x a ciascuno dei pozzetti di trattamento. NOTA: eseguire calcoli di potenza per valutare il numero di pozzi di trattamento. Tuttavia, senza una stima della entità della risposta o variazione, una prova preliminare può essere eseguito in 8 compound trattata e 8 veicoli trattati pozzetti di controllo contenenti pesci. <ol><li> Aggiungere 3 ml di controllo del veicolo al controllo (senza drug trattamento) pozzi che contengono pesci. Per assicurare che la risposta fluorescente composto è un risultato di azioni ai pesci, applicare trattamenti farmacologici e veicoli a 3 pozzetti di bianco in una piastra da 96 pozzetti. </li></ol></li><li> Leggi pesce piatto pieno su lettore fluorescente piatto con lunghezza d&#39;onda di eccitazione a 530 nm e lunghezza d&#39;onda di emissione a 590 nm. </li><li> Posizionare la piastra in incubatore umidificato impostata a 28,5 ○ C (mantenere piastra al buio per tutta test per evitare photobleaching di soluzione test). Il saggio può essere eseguito per periodi di tempo che vanno da 1 ora a 24 ore. La durata del saggio dipende dallo scopo dello studio. Per testare la risposta ad una breve composto non stabile recitazione breve durata può essere più adatto. Tuttavia, per le prove di composti stabili o test di effetti genetici, massimizzando durata saggio è preferibile sfruttare i vantaggi connessi con il segnale cumulativo. </li><li> In un punto tempo predeterminato (vedere la fase 3.6 per aiutare a determinare i tempi)leggere la fluorescenza di piatto di pesce pieno di nuovo con le stesse impostazioni di passo 3.5. </li></ol> 4. Valutare la variazione relativa a fluorescenza associata al trattamento con <ol><li> Calcolare variazione di fluorescenza di ciascun pozzetto sottraendo la fluorescenza al tempo 0 dal fluorescenza al termine dello studio. Wells senza pesce (spazi) devono avere valori prossimi a 0, ben al di sotto dei valori da pozzi che contengono pesci. Cambia in Fluorescenza = Fluorescenza a conclusione - Fluorescenza al tempo 0 </li><li> Per accertare la variazione relativa di fluorescenza, calcolare la variazione media della fluorescenza per pozzetti di controllo poi dividono la variazione di fluorescenza di ciascun bene dal variazione media di fluorescenza dei pozzetti di controllo. Da segnalare, i controlli potrebbero essere sia comandi del veicolo o controlli genetici. <img alt="Equazione 1" src="/files/ftp_upload/53297/53297eq1.jpg" /></li></ol>

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The authors have no competing financial interests to disclose.

La contaminazione con batteri o funghi limiterà notevolmente l&#39;applicazione di questo test. Il blu di metilene in mezzo embrione E3 limita la possibilità di contaminazione fungina. Nel corso embrione rialzando è fondamentale che la cura è presa per eliminare l&#39;embrione è morto due volte al giorno. Inoltre, è essenziale risciacquare abbondantemente gli embrioni con E3 sterile medio embrione del giorno di dosaggio iniziazione. Questi 2 passaggi limitano il potenziale di contaminazione batterica degli embrion...

Il mouse è attualmente il modello predominante per la ricerca di obesità. L&#39;intervallo breve generazione e strumenti genetiche disponibili nel topo sono stati fino ad oggi senza pari. Tuttavia, il pesce zebra ha anche un intervallo di generazione breve (3 - 4 mesi) e supera anche il mouse in facilità di manipolazione genetica 1,2. Il pesce zebra mantiene quasi il 90% dei geni dei mammiferi, mentre di gran lunga superiore il mouse in numero di figli e il potenziale per l&#39;uso in schermi genetici e droga 3. Per sfruttare il potenziale del modello di zebrafish per gli studi in obesità, le analisi devono essere sviluppati per indagare i fattori che influenzano il corpo regolazione del peso, comprese le spese di energia. Come metaboliti vengono elaborati tramite β-ossidazione e l&#39;ossigeno ciclo degli acidi tricarbossilici viene consumato e NADH 2 viene prodotto. Così, NADH 2 è un indicatore diretto del flusso di metaboliti attraverso vie metaboliche (metabolita ossidazione). In poikilotherms, H + perdite attraverso la membrana mitocondriale interna, che disaccoppia NADH 2 ossidazione dalla sintesi di ATP, è 4 - 5 volte inferiore negli esseri omeotermi 4. Di conseguenza, in NADH zebrafish 2 è molto strettamente legata alla produzione di ATP attraverso la fosforilazione ossidativa. Qui, descriviamo un metodo che misura NADH 2 produzione nel zebrafish larvale come proxy per dispendio energetico 5. Il consumo di ossigeno è il gold standard per la misurazione della spesa energetica. Tuttavia, per sfruttare al meglio l&#39;elevato potenziale rendimento del zebrafish, saggi di dispendio energetico devono essere suscettibili di high-throughput. Sistemi di consumo di ossigeno che dipendono da una camera chiusa sistema di circolazione sono limitati nella velocità per il numero di camere disponibili 6. Open air consumo di O 2 / CO 2 test di produzione è stato applicato anche nel zebrafish 5,7. Questi all&#39;aperto 96 pozzetti piastra di basesistemi d sono suscettibili di throughput elevato. Sfortunatamente, lo scambio di gas con l&#39;ambiente limita sensibilità di questi test. Abbiamo recentemente pubblicato l&#39;applicazione di un metodo che monitora NADH 2 utilizzando l&#39;indicatore redox alamarBlue 5. Questo saggio supera i limiti di produttività e sensibilità comune per analisi di consumo di ossigeno in zebrafish. Il pesce zebra sta diventando un modello sempre più importante per gli studi di tutto omeostasi energia del corpo. In parte, perché zebrafish sono suscettibili di utilizzare schermi genetici avanti e schermi di droga. Inoltre, mirata manipolazione genetica, tra cui knockdown e knock-in, può essere applicato rapidamente. Abbiamo precedentemente dimostrato che questo test può essere combinato con l&#39;applicazione di droga bagno e atterramento genetica o knockout per identificare i composti e geni che alterano il tasso metabolico 5. Inoltre, questo test è stato progettato per sfruttare i vantaggi di throughput elevati inerenti il ​​pesce zebra. </p&gt;

<table border="0" cellpadding="0" cellspacing="0" width="966">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:379px;">AlamarBlue</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">10-230-103</td>
			<td style="width:307px;">Manufactured by Thermo Scientific</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:379px;">Fine Tip DisposableTransfer Pipette</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td>13-711-26</td>
			<td>Manufactured by Thermo Scientific</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:379px;">Fisherbrand Graduated Disposable Transfer Pipette</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td>13-771-9AM</td>
			<td>Manufactured by Thermo Scientific</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:379px;">Black sided clear bottom 96-well plates</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">50-320-785</td>
			<td>Manufactured by E&#38;K Scientific Products Inc.</td>
		</tr>
	</tbody>
</table>

high throughput danio rerio energy expenditure assay

Zebrafish sono un importante organismo modello con vantaggi inerenti che hanno il potenziale per fare zebrafish un modello ampiamente utilizzato per lo studio della omeostasi energetica e obesità. Le piccole dimensioni di zebrafish permette di saggi sugli embrioni da condurre in un formato piatto 96- o 384 pozzetti, tecnologie Morpholino e CRISPR basate promuovere la facilità di manipolazione genetica, e il trattamento farmacologico per applicazione bagno è praticabile. Inoltre, zebrafish sono ideali per schermi genetici a termine che consentono di scoperta del gene romanzo. Data la relativa novità di zebrafish come modello per l&#39;obesità, è necessario sviluppare strumenti che sfruttino appieno questi benefici. Qui, si descrive un metodo per misurare il dispendio energetico in migliaia di zebrafish embrioni contemporaneamente. Abbiamo sviluppato una piattaforma completamente microplacca animale in cui usiamo piastre a 96 pozzetti per isolare singoli pesci e noi valutare cumulativo NADH 2 produzione utilizzando il disponibile in commercio coltura cellulare vitalità reagente alamarBlue. Nel poichilotermi il rapporto tra NADH 2 produzione e la spesa energetica è strettamente legata. Questo test dispendio energetico crea il potenziale per lo screening rapido manipolazioni farmacologiche o genetiche che alterano direttamente la spesa energetica o alterano la risposta ad un farmaco applicato (ad esempio sensibilizzatori dell&#39;insulina).

Soluzione Assay non aumenta la fluorescenza in assenza di pesci embrionali (Figura 1). Tuttavia, l&#39;analisi è molto sensibile a piccole variazioni del tasso metabolico nel pozzo. Un singolo pesce entro un ben crea un segnale significativamente diverso da pozzetti bianchi entro 1 ora (p &lt;0,0001). La Figura 2 fornisce una rappresentazione visiva dei segnali generati dai pesci embrionale dopo 24 ore di incubazione. Ai fini di questa immagine sono stati utilizzati ch...

Watch this Scientific Journal Video about High Throughput Danio Rerio Energy Expenditure Assay at JoVE.com

High Throughput Danio Rerio Energy Expenditure Assay

Zebrafish are an important model organism for the study of energy homeostasis. By utilizing a NADH2 sensitive redox indicator, alamar Blue, we have developed an assay that measures the metabolic rate of zebrafish larvae in a 96 well plate format and can be applied to drug or gene discovery.

High Throughput<em&gt; Danio Rerio</em&gt; Energia spese Assay

Zebrafish are an important model organism with inherent advantages that have the potential to make zebrafish a widely applied model for the study of ...

high-throughput-danio-rerio-energy-expenditure-assay

Research

JoVE Journal

Biology

High Throughput Danio Rerio Energy Expenditure Assay

12.6K Views.  Vanderbilt University Medical Center. Zebrafish are an important model organism for the study of energy homeostasis. By utilizing a NADH2 sensitive redox indicator, alamar Blue, we have developed an assay that measures the metabolic rate of zebrafish larvae in a 96 well plate format and can be applied to drug or gene discovery. 

Video: High Throughput Danio Rerio Energy Expenditure Assay

Gross and Fine Dissection of Inner Ear Sensory Epithelia in Adult Zebrafish (Danio rerio)

Neurosensory epithelia in the inner ear are the crucial structures for hearing and balance functions. Therefore, it is important to understand the cellular and molecular features of the epithelia, which are mainly composed of two types of cells: hair cells (HCs) and supporting cells (SCs). Here we choose to study the inner ear sensory epithelia in adult zebrafish not only because the epithelial structures are highly conserved in all vertebrates studied, but also because the adult zebrafish is able to regenerate HCs, an ability that mammals lose shortly after birth. We use the inner ear of adult zebrafish as a model system to study the mechanisms of inner ear HC regeneration in adult vertebrates that could be helpful for clinical therapy of hearing/balance deficits in human as a result of HC loss.
Here we demonstrate how to do gross and fine dissections of inner ear sensory epithelia in adult zebrafish. The gross dissection removes the tissues surrounding the inner ear and is helpful for preparing tissue sections, which allows us to examine the detailed structure of the sensory epithelia. The fine dissection cleans up the non-sensory-epithelial tissues of each individual epithelium and enables us to examine the heterogeneity of the whole epithelium easily in whole-mount epithelial samples.

Gross and Fine Dissection of Inner Ear Sensory Epithelia in Adult Zebrafish Danio rerio

The inner ear sensory epithelium of adult zebrafish is a good model system for understanding the mechanisms of hair cell regeneration in adult vertebrates. This protocol demonstrates the fine dissection of the epithelia, through which we can get tissue samples for studying the regenerative events at cellular and subcellular levels.

Dissezione lordo e Arti di epiteli sensoriali dell&#39;orecchio interno in adulti Zebrafish ( Danio rerio)

Neurosensory epithelia in the inner ear are the crucial structures for hearing and balance functions. Therefore, it is important to understand the ...

Ricerca

Biologia

High-throughput Yeast Plasmid Overexpression Screen

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, including those with direct relevance to human disease. Because of its short generation time and well-characterized genome, a major experimental advantage of the yeast model system is the ability to perform genetic screens to identify genes and pathways that are involved in a given process. Over the last thirty years such genetic screens have been used to elucidate the cell cycle, secretory pathway, and many more highly conserved aspects of eukaryotic cell biology 1-5. In the last few years, several genomewide libraries of yeast strains and plasmids have been generated 6-10. These collections now allow for the systematic interrogation of gene function using gain- and loss-of-function approaches 11-16. Here we provide a detailed protocol for the use of a high-throughput yeast transformation protocol with a liquid handling robot to perform a plasmid overexpression screen, using an arrayed library of 5,500 yeast plasmids. We have been using these screens to identify genetic modifiers of toxicity associated with the accumulation of aggregation-prone human neurodegenerative disease proteins. The methods presented here are readily adaptable to the study of other cellular phenotypes of interest.

Here we describe a plasmid overexpression screen in Saccharomyces cerevisiae, using an arrayed plasmid library and a high-throughput yeast transformation protocol with a liquid handling robot.

High-throughput iperespressione schermo lievito plasmidi

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, ...

Heart Dissection in Larval, Juvenile and Adult Zebrafish, Danio rerio

Zebrafish have become a beneficial and practical model organism for the study of embryonic heart development (see recent reviews1-6), however, work examining post-embryonic through adult cardiac development has been limited7-10. Examining the changing morphology of the maturing and aging heart are restricted by the lack of techniques available for staging and isolating juvenile and adult hearts. In order to analyze heart development over the fish's lifespan, we dissect zebrafish hearts at numerous stages and photograph them for further analysis11. The morphological features of the heart can easily be quantified and individual hearts can be further analyzed by a host of standard methods. Zebrafish grow at variable rates and maturation correlates better with fish size than age, thus, post-fixation, we photograph and measure fish length as a gauge of fish maturation. This protocol explains two distinct, size dependent dissection techniques for zebrafish, ranging from larvae 3.5mm standard length (SL) with hearts of 100&mu;m ventricle length (VL), to adults, with SL of 30mm and VL 1mm or larger. Larval and adult fish have quite distinct body and organ morphology. Larvae are not only significantly smaller, they have less pigment and each organ is visually very difficult to identify. For this reason, we use distinct dissection techniques.
We used pre-dissection fixation procedures, as we discovered that hearts dissected directly after euthanization have a more variable morphology, with very loose and balloon like atria compared with hearts removed following fixation. The fish fixed prior to dissection, retain in vivo morphology and chamber position (data not shown). In addition, for demonstration purposes, we take advantage of the heart (myocardial) specific GFP transgenic Tg(myl7:GFP)twu34 (12), which allows us to visualize the entire heart and is particularly useful at early stages in development when the cardiac morphology is less distinct from surrounding tissues. Dissection of the heart makes further analysis of the cell and molecular biology underlying heart development and maturation using in situ hybridization, immunohistochemistry, RNA extraction or other analytical methods easier in post-embryonic zebrafish. This protocol will provide a valuable technique for the study of cardiac development maturation and aging.

Heart Dissection in Larval, Juvenile and Adult Zebrafish, Danio rerio

A clear, standardized method for dissection and isolation of the zebrafish heart at multiple developmental stages are described. Annotation and quantification techniques are also discussed.

Dissezione di cuore in larvale, Zebrafish giovanile e degli adulti, Danio rerio</em

Zebrafish have become a beneficial and practical model organism for the study of embryonic heart development (see recent reviews1-6), however, work ...

High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace 
the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties 
of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the 
phenolic polymer lignin, that is also difficult to digest 1. In order to improve the digestibility of plant materials we need to discover the main bottlenecks 
for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification 2. These tasks require 
a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has 
been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes 
for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.
This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant 
materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded 
amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for 
analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this 
station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90&deg;C. The pretreatment solution 
is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme
mixture for a variable length of time at 50&deg;C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH 
colorimetric method.

A simple, rapid method for determining the saccharification potential of large numbers of plant biomass samples is described. The automated platform for this analysis involves the preparation of the plant biomass for analysis in 96 well plates and the subsequent performance of pretreatment, hydrolysis and quantification of the sugars released.

High-throughput per l&#39;analisi Saccarificazione materiali lignocellulosici

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing ...

Regular Care and Maintenance of a Zebrafish (Danio rerio) Laboratory: An Introduction

This protocol describes regular care and maintenance of a zebrafish laboratory. Zebrafish are now gaining popularity in genetics, pharmacological and behavioural research. As a vertebrate, zebrafish share considerable genetic sequence similarity with humans and are being used as an animal model for various human disease conditions. The advantages of zebrafish in comparison to other common vertebrate models include high fecundity, low maintenance cost, transparent embryos, and rapid development. Due to the spur of interest in zebrafish research, the need to establish and maintain a productive zebrafish housing facility is also increasing. Although literature is available for the maintenance of a zebrafish laboratory, a concise video protocol is lacking. This video illustrates the protocol for regular housing, feeding, breeding and raising of zebrafish larvae. This process will help researchers to understand the natural behaviour and optimal conditions of zebrafish husbandry and hence troubleshoot experimental issues that originate from the fish husbandry conditions. This protocol will be of immense help to researchers planning to establish a zebrafish laboratory, and also to graduate students who are intending to use zebrafish as an animal model.

Regular Care and Maintenance of a Zebrafish Danio rerio Laboratory: An Introduction

This protocol outlines regular maintenance and care to maintain optimal conditions for zebrafish husbandry. The video illustrates the protocol for system maintenance, regular housing, feeding, breeding, and raising of zebrafish larvae.

Cura e manutenzione periodiche di Zebrafish (<em&gt; Danio rerio</em&gt;) Laboratorio: Introduzione

This protocol describes regular care and maintenance of a zebrafish laboratory. Zebrafish are now gaining popularity in genetics, pharmacological and ...

High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay

We present a rapid and inexpensive high-throughput screening protocol to identify transcriptional regulators of alpha-synuclein, a gene associated with Parkinson&#39;s disease. 293T cells are transiently transfected with plasmids from an arrayed ORF expression library, together with luciferase reporter plasmids, in a one-gene-per-well microplate format. Firefly luciferase activity is assayed after 48 hr to determine the effects of each library gene upon alpha-synuclein transcription, normalized to expression from an internal control construct (a hCMV promoter directing Renilla luciferase). This protocol is facilitated by a bench-top robot enclosed in a biosafety cabinet, which performs aseptic liquid handling in 96-well format. Our automated transfection protocol is readily adaptable to high-throughput lentiviral library production or other functional screening protocols requiring triple-transfections of large numbers of unique library plasmids in conjunction with a common set of helper plasmids. We also present an inexpensive and validated alternative to commercially-available, dual luciferase reagents which employs PTC124, EDTA, and pyrophosphate to suppress firefly luciferase activity prior to measurement of Renilla luciferase. Using these methods, we screened 7,670 human genes and identified 68 regulators of alpha-synuclein. This protocol is easily modifiable to target other genes of interest.

We present a rapid and inexpensive screening method for identifying transcriptional regulators using high-throughput robotic transfections and a homemade dual-glow luciferase assay. This protocol rapidly generates direct side-by-side functional data for thousands of genes and is easily modifiable to target any gene of interest.

High-throughput screening funzionale utilizzando una casalinga Dual-glow Luciferase Assay

We present a rapid and inexpensive high-throughput screening protocol to identify transcriptional regulators of alpha-synuclein, a gene associated with ...

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Here, we present methods for the development of assays to query potentially clinically significant nonsynonymous changes using in vivo complementation in zebrafish. Zebrafish (Danio rerio) are a useful animal system due to their experimental tractability; embryos are transparent to enable facile viewing, undergo rapid development ex vivo, and can be genetically manipulated.1 These aspects have allowed for significant advances in the analysis of embryogenesis, molecular processes, and morphogenetic signaling. Taken together, the advantages of this vertebrate model make zebrafish highly amenable to modeling the developmental defects in pediatric disease, and in some cases, adult-onset disorders. Because the zebrafish genome is highly conserved with that of humans (~70% orthologous), it is possible to recapitulate human disease states in zebrafish. This is accomplished either through the injection of mutant human mRNA to induce dominant negative or gain of function alleles, or utilization of morpholino (MO) antisense oligonucleotides to suppress genes to mimic loss of function variants. Through complementation of MO-induced phenotypes with capped human mRNA, our approach enables the interpretation of the deleterious effect of mutations on human protein sequence based on the ability of mutant mRNA to rescue a measurable, physiologically relevant phenotype. Modeling of the human disease alleles occurs through microinjection of zebrafish embryos with MO and/or human mRNA at the 1-4 cell stage, and phenotyping up to seven days post fertilization (dpf). This general strategy can be extended to a wide range of disease phenotypes, as demonstrated in the following protocol. We present our established models for morphogenetic signaling, craniofacial, cardiac, vascular integrity, renal function, and skeletal muscle disorder phenotypes, as well as others.

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Here, we present a systematic approach for developing physiologically relevant, sensitive and specific in vivo assays for interpreting variation in human pathology. Transient genetic manipulation via microinjection of WT and mutant human mRNA and morpholino (MO) antisense oligonucleotides harness the tractability of the developing zebrafish embryo to rapidly assay pathogenic mutations, especially, but not exclusively, in the context of human developmental disorders.

In Vivo Modellazione del genoma umano Morbid utilizzando Danio rerio

Here,  we present methods for the development of assays to query potentially clinically  significant nonsynonymous changes using in  vivo complementation ...

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or design1,2. Here, a peptide-MHC II binding assay is scaled to 384-well format. The scaled down protocol reduces reagent costs by 75% and is higher throughput than previously described 96-well protocols1,3-5. Specifically, the experimental design permits robust and reproducible analysis of up to 15 peptides against one MHC II allele per 384-well ELISA plate. Using a single liquid handling robot, this method allows one researcher to analyze approximately ninety test peptides in triplicate over a range of eight concentrations and four MHC II allele types in less than 48 hr. Others working in the fields of protein deimmunization or vaccine design and development may find the protocol to be useful in facilitating their own work. In particular, the step-by-step instructions and the visual format of JoVE should allow other users to quickly and easily establish this methodology in their own labs.

Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or design. &#160;Here, a peptide-MHC II binding assay scaled to 384-well plates is described. This cost effective format should prove useful in the fields of protein deimmunization and vaccine design and development.

Un saggio di legame High Throughput MHC II per l&#39;analisi quantitativa dei peptidi epitopi

Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or ...

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays focus on transcriptional regulation, being essentially aimed at the identification of promoter-targeting molecules. As a result, post-transcriptional mechanisms are largely uncovered by gene expression targeted drug development. Here we describe a cell-based assay aimed at investigating the role of the 3&#39; untranslated region (3&#8217; UTR) in the modulation of the fate of its mRNA, and at identifying compounds able to modify it. The assay is based on the use of a luciferase reporter construct containing the 3&#8217; UTR of a gene of interest stably integrated into a disease-relevant cell line. The protocol is divided into two parts, with the initial focus on the primary screening aimed at the identification of molecules affecting luciferase activity after 24 hr of treatment. The second part of the protocol describes the counter-screening necessary to discriminate compounds modulating luciferase activity specifically through the 3&#8217; UTR. In addition to the detailed protocol and representative results, we provide important considerations about the assay development and the validation of the hit(s) on the endogenous target. The described cell-based reporter gene assay will allow scientists to identify molecules modulating protein levels via post-transcriptional mechanisms dependent on a 3&#8217; UTR.

Here we describe a cell-based reporter gene assay as a valuable tool to screen chemical libraries for compounds modulating post-transcriptional control mechanisms exerted through 3&#8217; UTR.

Screening ad alto rendimento per i modulatori chimici di Genes post-trascrizionale regolamentati

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays ...

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Luminescent Identification of Functional Elements in 3&#8217;UTRs (3&#8217;LIFE) allows the rapid identification of targets of specific miRNAs within an array of hundreds of queried 3&#8217;UTRs. Target identification is based on the dual-luciferase assay, which detects binding at the mRNA level by measuring translational output, giving a functional readout of miRNA targeting. 3&#8217;LIFE uses non-proprietary buffers and reagents, and publically available reporter libraries, making genome-wide screens feasible and cost-effective. 3&#8217;LIFE can be performed either in a standard lab setting or scaled up using liquid handling robots and other high-throughput instrumentation. We illustrate the approach using a dataset of human 3&#8217;UTRs cloned in 96-well plates, and two test miRNAs, let-7c and miR-10b. We demonstrate how to perform DNA preparation, transfection, cell culture and luciferase assays in 96-well format, and provide tools for data analysis. In conclusion 3&#39;LIFE is highly reproducible, rapid, systematic, and identifies high confidence targets.

Luminescent identification of functional elements in 3&#8217; untranslated regions (3&#8217;UTRs) (3&#8217;LIFE) is a technique to identify functional regulation in 3&#8217;UTRs by miRNAs or other regulatory factors. This protocol utilizes high-throughput methodology such as 96-well transfection and luciferase assays to screen hundreds of putative interactions for functional repression.

Rivelazione di bersagli miRNA in high-throughput usando il saggio 3&#39;LIFE

Luminescent Identification of Functional Elements in 3&#8217;UTRs (3&#8217;LIFE) allows the rapid identification of targets of specific miRNAs within an ...