This study was financially supported by the Korean Ministry of Science, ICT and Future Planning (Intelligent Synthetic Biology Center program 2012M3A6A8054887). P. Kim was supported by a fellowship from the Catholic University of Korea (2015).

1. Vorbereitung der Ausrüstung <ol><li> Besorgen Sie sich ein Chemostat Glas (150-250 ml) oder einem Erlenmeyerkolben (250 ml) mit einer Einlassöffnung und eine Austrittsöffnung enthält. Verbinden Sie die Anschlüsse mit Silikonschlauch so dass für Flussraten von 10 bis 100 ml / h. Optional kann ein Entlüftungsventil, eine Luftaustrittsöffnung, und temperiertes Wasser Einlass- und Auslasskanäle verwenden. </li><li> Besorgen Sie sich eine Vorrichtung, die geeignet für die chemostat Glas, die für das Rühren und Temperaturkontrolle bietet (oder einen Dreh Schüttelinkubator verwenden). </li><li> Erhalten zwei peristaltische Pumpen, um frisches Medium zu liefern und die Kultur zu sammeln. </li><li> Besorgen Sie sich ein Reservoir Glas (10-20 L) eine mittlere Austrittsöffnung und eine Lufteinlassöffnung enthält. </li><li> Erhalten Silikonschlauch geeignet für die Verdünnungsrate (dh ID 0,8 mm, Durchflussbereich von 0,06 bis 36 ml / min; L / S 13 Schläuche). </li></ol> 2. Medium Vorbereitung und Sterilisation <ol><li> Initial Medium <ol><li> Man löst 0,3 g Glucose, 0,08 g NH 4Cl, 0,05 g NaCl, 0,75 g Na 2 HPO 4 · 2H 2 O und 0,3 g KH 2 PO 4 in 90 ml destilliertem Wasser (DW) in einem Chemostat jar. </li><li> Seal die chemostat Glas zusammen mit dem Schlauch mit Schellen. Sie nicht die Lüftungsöffnung abzudichten. </li><li> Sterilisieren Sie die chemostat Glas in einem Autoklaven bei 121 ° C für 15 min. Nach der Sterilisation, speichern Sie die chemostat Glas bei Raumtemperatur. </li><li> Man löst 0,02 g MgSO 4 · 7H 2 O, 0,01 g CaCl 2 und 0,1 mg Thiamin in 10 ml DW (Lösung A). </li><li> Filterlösung A eine Spritze und eine vorge sterilisierten Spritzenfilter unter Verwendung von (a 0,45 um Porenfilter). </li><li> Fügen Sie die Lösung A Filtrate zum Chemostat Glas. </li></ol></li><li> Stress-Medium <ol><li> Man löst 30 g Glucose, 8 g NH 4 Cl, 5 g NaCl, 75 g Na 2 HPO 4 · 2H 2 O, 30 g KH 2 PO 4 und 300 g Dinatriumsuccinat Hexahydrat (Na 2 · Succinat · 6H &lt;sub&gt; 2 O; der Stressor in diesem Experiment verwendet) in 9,9 L DW in einem Reservoir jar. </li><li> Verschließen Sie den Behälter Glas zusammen mit dem Schlauch mit Schellen. Sie nicht die Lüftungsöffnung abzudichten. </li><li> Sterilisieren des Behälters jar in einem Autoklaven bei 121 ° C für 15 min. Nach der Sterilisation, speichern Sie das Gefäß bei Raumtemperatur. </li><li> Man löst 2 g MgSO 4 · 7H 2 O, 1 g CaCl 2 und 10 mg Thiamin in 100 ml DW (Lösung A). </li><li> Filter Lösung A mit einer Spritze und einem vorher sterilisierten Spritzenfilter (0,45 &amp; mgr; m ein Porenfilter). </li><li> Fügen Sie die Lösung A Filtrate zum Reservoir Glas. </li><li> Aseptisch schließen Sie das sterilisierte Silikonschlauch mit dem Reservoir Glas und die peristaltische Pumpen befestigen. </li></ol></li><li> High-Stress-Mittel <ol><li> Bereiten Sie das Medium , wie in Abschnitt 2.2, aber mit einer größeren Konzentration von Stressor (dh 3-5 g / l höher in der Succinat - Anpassung). Hinweis: Dieses Protokoll zur Anpassung an eine Stress than kann über das Medium geliefert werden. Im Falle von physikalischen Stressoren, wie Temperatur, Rühren oder Beleuchtung, die Kultivierung sollte entsprechend ausgelegt werden. </li></ol></li></ol> 3. Erste Anbau <ol><li> Impfen eine einzige Kolonie von Wildtyp E. coli in einem 15 ml Teströhrchen mit 4 ml des anfänglichen Mediums. </li><li> Inkubieren des Teströhrchens in einem Schüttelinkubator 12 Stunden bei 37 ° C und 220 Umdrehungen pro Minute. </li><li> Aseptisch 1 ml der Vorkultur in Chemostat Glas. </li><li> Inkubieren Sie die chemostat Glas und bietet für die Belüftung (Luft 50 ml / min) und Rühren (200 Umdrehungen pro Minute), bei 37 ° C für 6 Stunden. </li></ol> 4. Stress-Anpassung <ol><li> Aseptisch schließen Sie das Ende des Silikonschläuche von den Pumpen zum Chemostat Glas. </li><li> Starten Sie den Ausgang Pumpe (10 ml / h oder höher) und sammeln Kultur. Hinweis: Die Kultur in der exponentiellen Phase sein sollte, in der Regel 4-8 Stunden nach der anfänglichen Kultivierung. </li><li> CHeck der optischen Dichte (600 nm) der Kultur aus dem Auslassschlauch. </li><li> Starten Sie den Zulaufpumpe (10 ml / h, auf eine Rate von Verdünnung von 0,1 h -1 entspricht). </li><li> Überprüfen Sie die optische Dichte der Kultur bei 600 nm von dem Auslass alle 24 h Schläuche. </li><li> Betreiben Sie den chemostat für 96 Stunden (9,6-fache Umsatz) oder mehr. Wenn die optische Dichte stabil ist, tauschen Sie das Reservoir, das den hochbelasteten Medium enthält. Wenn die optische Dichte von weniger als 0,2 ist, stoppen Sie die Fütterung Zulaufpumpe für 6 Stunden. Starten Sie den Zulaufpumpe und prüfen, ob die optische Dichte über 0,2 ist. </li><li> Nach und nach die Konzentration des Stressor erhöhen, indem sie zu einem Reservoir Ändern einer höheren Stressor Konzentration enthält. </li><li> Nehmen Sie Proben der angepassten Kultur , wenn es einen Meilenstein erreicht (zB ein Stamm angepasst bis 100 g / L Succinat Stress) und Speicher für weitere Genomanalyse. </li><li> Für die Probenlagerung, mischen Sie die Kulturprobe (0,5 ml) mit einer sterilisierten 80% Glycerin solutiauf (0,5 ml) und lagern Sie es bei -80 ° C. Hinweis: Wenn der Mikroorganismus die Fähigkeit erwirbt die Stressoren während der ALE-Verfahren abzubauen, die Stressor Konzentration in der Fermentations Glas wie in der frischen Reservoir ist nicht das Gleiche. </li></ol> 5. Einzelkolonie Isolierung des Stress angepasst Dehnungs <ol><li> Bereiten Agarplattenmedium (1,6% Agar), enthaltend die gleichen Stressor und bei der gleichen Konzentration des Mediums. </li><li> Platte die Austritts Kultur (0,1 ml) aus dem Chemostat und inkubieren bei 37 ° C für 16 Stunden. </li><li> Pick einzelne Kolonien von der Platte einen sterilen Zahnstocher und inokulieren sie in 15 ml Teströhrchen das gleiche Stressor enthält, und bei der gleichen mittleren Konzentration wie im Chemostat, und Inkubation für 6 Stunden. </li><li> 1 ml der Kulturbrühe in einen 250 ml Erlenmeyerkolben mit 50 ml Medium enthält. Ernte 0,5 ml der Kulturbrühe alle 1 h und Messung der OD bei 600 nm. Vergleichen Sie die Wachstumsrate des angepassten strain derjenigen des Wildtyp-Stamm der Stressor gegeben. </li></ol>

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	<li>Rando, O. J., Verstrepen, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Timescales+of+genetic+and+epigenetic+inheritance.">Timescales of genetic and epigenetic inheritance.</a> Cell. 128, 655-668 (2007).</li><li>Kim, H. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Short-term+differential+adaptation+to+anaerobic+stress+via+genomic+mutations+by+Escherichia+coli+strains+K-12+and+B+lacking+alcohol+dehydrogenase.">Short-term differential adaptation to anaerobic stress via genomic mutations by Escherichia coli strains K-12 and B lacking alcohol dehydrogenase.</a> Front Microbiol. 5, 476 (2014).</li><li>Mendizabal, I., Keller, T. E., Zeng, J., Yi, S. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epigenetics+and+evolution.">Epigenetics and evolution.</a> Integr Comp Biol. 54, 31-42 (2014).</li><li>Lee, J. Y., Seo, J., Kim, E. S., Lee, H. S., Kim, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adaptive+evolution+of+Corynebacterium+glutamicum+resistant+to+oxidative+stress+and+its+global+gene+expression+profiling.">Adaptive evolution of Corynebacterium glutamicum resistant to oxidative stress and its global gene expression profiling.</a> Biotechnol Lett. 35, 709-717 (2013).</li><li>Lee, J. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Artificial+oxidative+stress-tolerant+Corynebacterium+glutamicum.">Artificial oxidative stress-tolerant Corynebacterium glutamicum.</a> AMB Express. 4, 15 (2014).</li><li>Narang, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+steady+states+of+microbial+growth+on+mixtures+of+substitutable+substrates+in+a+chemostat.">The steady states of microbial growth on mixtures of substitutable substrates in a chemostat.</a> J Theor Biol. 190, 241-261 (1998).</li><li>Kwon, Y. D., Kim, S., Lee, S. Y., Kim, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+continuous+adaptation+of+Escherichia+coli+to+high+succinate+stress+and+transcriptome+analysis+of+the+tolerant+strain.">Long-term continuous adaptation of Escherichia coli to high succinate stress and transcriptome analysis of the tolerant strain.</a> J Biosci Bioeng. 111, 26-30 (2011).</li><li>Barrick, J. E., Lenski, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome+dynamics+during+experimental+evolution.">Genome dynamics during experimental evolution.</a> Nat Rev Genet. 14, 827-839 (2013).</li><li>Li, H., 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+Sequence+Alignment/Map+format+and+SAMtools.">The Sequence Alignment/Map format and SAMtools.</a> Bioinformatics. 25, 2078-2079 (2009).</li><li>McKenna, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Genome+Analysis+Toolkit:+a+MapReduce+framework+for+analyzing+next-generation+DNA+sequencing+data.">The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.</a> Genome Res. 20, 1297-1303 (2010).</li><li>Deatherage, D. E., Barrick, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+mutations+in+laboratory-evolved+microbes+from+next-generation+sequencing+data+using+breseq.">Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.</a> Methods Mol Biol. 1151, 165-188 (2014).</li></ol>

The authors have nothing to disclose.

Mikroorganismen sind in der Lage aufgrund ihrer schnellen Wachstumsrate und der genetischen Vielfalt zu fast allen Umgebungen anzupassen. Adaptive Laborentwicklung ermöglicht Mikroorganismen unter Bedingungen entwickelt, zu entwickeln, die eine Möglichkeit der Auswahl der einzelnen Organismen beherbergt spontane Mutationen bereit, die unter den gegebenen Bedingungen von Vorteil sind. Die chemostat Technik ist robuster für den folgenden Gründen künstlich angetrieben Evolution als Übertr...

Mikroorganismen können auf unterschiedliche Umgebungen überleben und sich anzupassen. Unter starkem Stress, Anpassung kann 1-3 über Erwerb von positiven Phänotypen durch statistische genomische Mutationen und anschließende positive Selektion auftreten. Daher kann mikrobiellen Zellen anzupassen durch metabolische oder regulatorische Netzwerke für ein optimales Wachstum zu ändern, die &quot;adaptive Evolution&quot; bezeichnet wird. Vor kurzem sind wichtige mikrobielle Tendenzen, wie Ausbrüche von Superbugs und dem Auftreten von robusten mikrobielle Stämme, sind sehr eng miteinander verbunden Evolution unter Stressbedingungen zu adaptiv. Unter definierten Laborbedingungen, sind wir die Mechanismen der molekularen Evolution zu studieren können und sogar die Richtung der mikrobiellen Evolution für verschiedene Anwendungen zu steuern. Im Gegensatz zu mehrzelligen Organismen sind einzellige Organismen gut geeignet, um adaptive Labor Entwicklung (ALE) aus den folgenden Gründen: sie regenerieren schnell, sie pflegen große Populationen, und es ist leicht hom zu erstellen und zu pflegenogeneous Umgebungen. In Kombination mit den jüngsten Fortschritten in der DNA-Sequenzierungstechniken und Hochdurchsatz-Technologien, ermöglicht ALE für die direkte Beobachtung von genomischen Veränderungen, die zu einer systemischen regulatorischen Veränderungen führen. Mutations Dynamik und Vielfalt der Bevölkerung sind auch zu beobachten. Die Gentechnik - Strategien können aus der Analyse der ALE - Stämme 4,5 bestimmt werden. Chemostatkultur ist eine Methode verwendet Steady-State - Zellen zu erhalten und die Produktivität bei Fermentationsprozessen 6 erhöhen. Frisches Medium wird zugesetzt und Kulturbrühe wird während des Verfahrens geerntet (letzteres enthält Medium und Biomasse). Langzeit Chemostat - Kultur, ändert jedoch den steady-state Produktivität der Kultur und bewirkt die Anhäufung von spontanen Mutationen und Selektion während der Kultivierung (Abbildung 1a). Unter verschiedenen Selektionsdruck (Stressoren), wird die Akkumulation von Mutationen verbessert. Eine allmähliche Zunahme der Spannung in einem langfristigen<html> Chemostat sorgt für eine kontinuierliche Auswahl von Mutationen , die gegen den gegebenen Stressoren arbeiten, wie beispielsweise Temperatur, pH, osmotischer Druck, Nährstoffmangel, Oxidation, toxische Endprodukte usw. Colony Übertragung von einem festen Medium und serielle Übertragung aus einem flüssigen Medium (wiederholte Batch - Kultur) erlauben auch Forscher entwickelten Mikroorganismen (Abbildung 1b und 1c) zu erhalten. Obwohl Chemostatkultur komplizierte Methoden erfordert, ist der Pool der Vielfalt (Anzahl der Replikationen und Populationsgröße) höher als die durch Kolonie-Transfer und serielle Übertragungstechniken erhalten. Die stabile Stressbelastung auf einzelne Zellen und verringerte Veränderung der zellulären Zustand während Chemostatkultur (Steady State) sind weitere Vorteile von ALE im Vergleich zu Batch-Kultur-basierte Techniken. Stress-induzierten ALE von Escherichia coli zu hoher Succinat Bedingungen unterworfen wird in diesem Artikel eingeführt. iles / ftp_upload / 54446 / 54446fig1.jpg &quot;/&gt; Abbildung 1: Methoden der adaptiven Labor Evolution (A) Chemostat;. (B) eine serielle Übertragung; (C) Kolonie übertragen. Die Top - Zahlen das Konzept der Methoden für das ALE illustrieren, und die unteren Zahlen die Anzahl der Zellen darstellen , die während ALE wuchs. <a href="https://www.jove.com/files/ftp_upload/54446/54446fig1large.jpg" target="_blank">Bitte klicken Sie hier</a> , um <a href="https://www.jove.com/files/ftp_upload/54446/54446fig1large.jpg" target="_blank">eine größere Version dieser Figur zu sehen.</a>

<table border="0" cellpadding="0" cellspacing="0" width="573">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Mini-chemostat fermentor</td>
			<td style="width:71px;">Biotron Inc.</td>
			<td style="width:119px;">-</td>
			<td style="width:167px;">manufactured by special order</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">silicon tubing</td>
			<td style="width:71px;">Cole-Parmer</td>
			<td style="width:119px;">Masterflex L/S 13</td>
			<td>tubing size can be varied depending on the dilution rate and the size of fermentor jar.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">reservoir jar</td>
			<td style="width:71px;">Bellco</td>
			<td style="width:119px;">Media storage bottle&#160;</td>
			<td>20 L</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">chemicals</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">-</td>
			<td>reagent grade</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">glucose</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">G5767</td>
			<td>ACS reagent</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NH4Cl</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">A9434</td>
			<td>for molecular biology, suitable for cell culture, &#8805;99.5%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NaCl</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td align="right" style="width:119px;">746398</td>
			<td>ACS reagent, &#8805;99%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Na2HPO4&#183;2H2O</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td align="right" style="width:119px;">4272</td>
			<td>98.5-101%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">KH2PO4&#160;</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td align="right" style="width:119px;">795488</td>
			<td>ACS reagent, &#8805;99%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">MgSO4&#183;7H2O</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td align="right" style="width:119px;">230391</td>
			<td>ACS reagent, &#8805;98%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">CaCl2</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td align="right" style="width:119px;">793639</td>
			<td>ACS reagent, &#8805;96%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">thiamine&#183;HCl&#160;</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">T4625</td>
			<td>reagent grade, &#8805;99%</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Na2&#183;succinate&#183;6H2O</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">S2378</td>
			<td>ReagentPlus, &#8805;99%</td>
		</tr>
	</tbody>
</table>

procedure for adaptive laboratory evolution of microorganisms using a chemostat

Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) refers to the experimental situation in which evolution is observed using living organisms under controlled conditions and stressors; organisms are thereby artificially forced to make evolutionary changes. Microorganisms are subject to a variety of stressors in the environment and are capable of regulating certain stress-inducible proteins to increase their chances of survival. Naturally occurring spontaneous mutations bring about changes in a microorganism's genome that affect its chances of survival. Long-term exposure to chemostat culture provokes an accumulation of spontaneous mutations and renders the most adaptable strain dominant. Compared to the colony transfer and serial transfer methods, chemostat culture entails the highest number of cell divisions and, therefore, the highest number of diverse populations. Although chemostat culture for ALE requires more complicated culture devices, it is less labor intensive once the operation begins. Comparative genomic and transcriptome analyses of the adapted strain provide evolutionary clues as to how the stressors contribute to mutations that overcome the stress. The goal of the current paper is to bring about accelerated evolution of microorganisms under controlled laboratory conditions.

Für High-Succinat Stress Anpassung, die Wildtyp - E coli - W3110 - Stamm war in einem Chemostat bei D kultiviert = 0,1 h -1 für 270 Tage (Abbildung 2). <img alt="Figur 2" src="/files/ftp_upload/54446/54446fig2.jpg" /> Abbildung 2: High-Succinat Stress Anpassung von E. coli W3110 unter Verwendung Chemostat - Kultur. Dünne Pfeile zeigen die Zeiten , bei denen die Konzentrati...

Watch this Scientific Journal Video about Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat at JoVE.com

Verfahren zur adaptiven Laborevolution von Mikroorganismen unter Verwendung eines Chemostaten | Genetik | Video

Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat

mit Chemostatkultur Hier präsentieren wir ein Protokoll adaptive gerichtete Evolution von Mikroorganismen unter Bedingungen zu erhalten. Auch genomische Analyse des entwickelten Stamm wird diskutiert.

Verfahren für Adaptive Labor Entwicklung von Mikroorganismen Mit einem Chemostat

Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) ...

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14.1K Aufrufe.  Korea Research Institute of Bioscience and Biotechnology (KRIBB).  mit Chemostatkultur Hier präsentieren wir ein Protokoll adaptive gerichtete Evolution von Mikroorganismen unter Bedingungen zu erhalten. Auch genomische Analyse des entwickelten Stamm wird diskutiert. 

Serie: Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat

Design and Use of a Low Cost, Automated Morbidostat for Adaptive Evolution of Bacteria Under Antibiotic Drug Selection

We describe a low cost, configurable morbidostat for characterizing the evolutionary pathway of antibiotic resistance. The morbidostat is a bacterial culture device that continuously monitors bacterial growth and dynamically adjusts the drug concentration to constantly challenge the bacteria as they evolve to acquire drug resistance. The device features a working volume of ~10 ml and is fully automated and equipped with optical density measurement and micro-pumps for medium and drug delivery. To validate the platform, we measured the stepwise acquisition of trimethoprim resistance in Escherichia coli MG 1655, and integrated the device with a multiplexed microfluidic platform to investigate cell morphology and antibiotic susceptibility. The approach can be up-scaled to laboratory studies of antibiotic drug resistance, and is extendible to adaptive evolution for strain improvements in metabolic engineering and other bacterial culture experiments.

We describe a low cost, configurable morbidostat that enables the characterization of antibiotic drug resistance by dynamically adjusting the drug concentration. The device can be integrated with a multiplexed microfluidic platform. The approach can be scaled up for laboratory antibiotic drug resistance studies.

Design und die Verwendung eines Low Cost, Automatisierte Morbidostat für Adaptive Evolution der Bakterien unter Antibiotikums Selection

We describe a low cost, configurable morbidostat for characterizing the evolutionary pathway of antibiotic resistance. The morbidostat is a bacterial ...

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CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy

As a promising genome editing platform, the CRISPR/Cas9 system has great potential for efficient genetic manipulation, especially for targeted integration of transgenes. However, due to the low efficiency of homologous recombination (HR) and various indel mutations of non-homologous end joining (NHEJ)-based strategies in non-dividing cells, in vivo genome editing remains a great challenge. Here, we describe a homology-mediated end joining (HMEJ)-based CRISPR/Cas9 system for efficient in vivo precise targeted integration. In this system, the targeted genome and the donor vector containing homology arms (~800 bp) flanked by single guide RNA (sgRNA) target sequences are cleaved by CRISPR/Cas9. This HMEJ-based strategy achieves efficient transgene integration in mouse zygotes, as well as in hepatocytes in vivo. Moreover, a HMEJ-based strategy offers an efficient approach for correction of fumarylacetoacetate hydrolase (Fah) mutation in the hepatocytes and rescues Fah-deficiency induced liver failure mice. Taken together, focusing on targeted integration, this HMEJ-based strategy provides a promising tool for a variety of applications, including generation of genetically modified animal models and targeted gene therapies.

CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy

The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system provides a promising tool for genetic engineering, and opens up the possibility of targeted integration of transgenes. We describe a homology-mediated end joining (HMEJ)-based strategy for efficient DNA targeted integration in vivo and targeted gene therapies using CRISPR/Cas9.

CRISPR/Cas9-vermittelten gezielte Integration In Vivo mit einer Homologie-vermittelte Ende verbinden-basierte Strategie

As a promising genome editing platform, the CRISPR/Cas9 system has great potential for efficient genetic manipulation, especially for targeted integration ...

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Multicopy plasmids are extremely abundant in prokaryotes but their role in bacterial evolution remains poorly understood. We recently showed that the increase in gene copy number per cell provided by multicopy plasmids could accelerate the evolution of plasmid-encoded genes. In this work, we present an experimental system to test the ability of multicopy plasmids to promote gene evolution. Using simple molecular biology methods, we constructed a model system where an antibiotic resistance gene can be inserted into Escherichia coli MG1655, either in the chromosome or on a multicopy plasmid. We use an experimental evolution approach to propagate the different strains under increasing concentrations of antibiotics and we measure survival of bacterial populations over time. The choice of the antibiotic molecule and the resistance gene is so that the gene can only confer resistance through the acquisition of mutations. This &#34;evolutionary rescue&#34; approach provides a simple method to test the potential of multicopy plasmids to promote the acquisition of antibiotic resistance. In the next step of the experimental system, the molecular bases of antibiotic resistance are characterized. To identify mutations responsible for the acquisition of antibiotic resistance we use deep DNA sequencing of samples obtained from whole populations and clones. Finally, to confirm the role of the mutations in the gene under study, we reconstruct them in the parental background and test the resistance phenotype of the resulting strains.

Here we present an experimental method to test the role of multicopy plasmids in the evolution of antibiotic resistance.

Testen die Rolle des Multicopy Plasmide in der Entwicklung von Antibiotika-Resistenzen

Multicopy plasmids are extremely abundant in prokaryotes but their role in bacterial evolution remains poorly understood. We recently showed that the ...

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Accurate transcription is required for the faithful expression of genetic information. Surprisingly though, little is known about the mechanisms that control the fidelity of transcription. To fill this gap in scientific knowledge, we recently optimized the circle-sequencing assay to detect transcription errors throughout the transcriptome of Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. This protocol will provide researchers with a powerful new tool to map the landscape of transcription errors in eukaryotic cells so that the mechanisms that control the fidelity of transcription can be elucidated in unprecedented detail.

This protocol provides researchers with a new tool to monitor the fidelity of transcription in multiple model organisms.

Genomweite Überwachung der Übertragungsfehler in Eukaryonten

Accurate transcription is required for the faithful expression of genetic information. Surprisingly though, little is known about the mechanisms that ...

High-Resolution Comparison of Bacterial Conjugation Frequencies

Bacterial conjugation is an important step in the horizontal transfer of antibiotic resistance genes via a conjugative DNA element. In-depth comparisons of conjugation frequency under different conditions are required to understand how the conjugative element spreads in nature. However, conventional methods for comparing conjugation frequency are not appropriate for in-depth comparisons because of the high background caused by the occurrence of additional conjugation events on the selective plate. We successfully reduced the background by introducing a most probable number (MPN) method and a higher concentration of antibiotics to prevent further conjugation in selective liquid medium. In addition, we developed a protocol for estimating the probability of how often donor cells initiate conjugation by sorting single donor cells into recipient pools by fluorescence-activated cell sorting (FACS). Using two plasmids, pBP136 and pCAR1, the differences in conjugation frequency in Pseudomonas putida cells could be detected in liquid medium at different stirring rates. The frequencies of conjugation initiation were higher for pBP136 than for pCAR1. Using these results, we can better understand the conjugation features in these two plasmids.

With an aim to understand the behaviors of various bacterial conjugative DNA elements under different conditions, we describe a protocol for detecting differences in conjugation frequency, with high resolution, to estimate how efficiently the donor bacterium initiates conjugation.

Hochauflösende Vergleich der bakteriellen Konjugation Frequenzen

Bacterial conjugation is an important step in the horizontal transfer of antibiotic resistance genes via a conjugative DNA element. In-depth comparisons ...

Producing Gene Deletions in Escherichia coli by P1 Transduction with Excisable Antibiotic Resistance Cassettes

A first approach to study the function of an unknown gene in bacteria is to create a knock-out of this gene. Here, we describe a robust and fast protocol for transferring gene deletion mutations from one Escherichia coli strain to another by using generalized transduction with the bacteriophage P1. This method requires that the mutation be selectable (e.g., based on gene disruptions using antibiotic cassette insertions). Such antibiotic cassettes can be mobilized from a donor strain and introduced into a recipient strain of interest to quickly and easily generate a gene deletion mutant. The antibiotic cassette can be designed to include flippase recognition sites that allow the excision of the cassette by a site-specific recombinase to produce a clean knock-out with only a ~100-base-pair-long scar sequence in the genome. We demonstrate the protocol by knocking out the tamA gene encoding an assembly factor involved in autotransporter biogenesis and test the effect of this knock-out on the biogenesis and function of two trimeric autotransporter adhesins. Though gene deletion by P1 transduction has its limitations, the ease and speed of its implementation make it an attractive alternative to other methods of gene deletion.

Producing Gene Deletions in Escherichia coli by P1 Transduction with Excisable Antibiotic Resistance Cassettes

Here we present a protocol for the use of pre-existing antibiotic resistance-cassette deletion constructs as a basis for making deletion mutants in other E. coli strains. Such deletion mutations can be mobilized and inserted into the corresponding locus of a recipient strain using P1 bacteriophage transduction.

Herstellung von Gen-Deletionen in Escherichia coli durch P1 Transduktion mit verbrauchsteuerpflichtigen Antibiotikaresistenz Kassetten

A first approach to study the function of an unknown gene in bacteria is to create a knock-out of this gene. Here, we describe a robust and fast protocol ...

qKAT: Quantitative Semi-automated Typing of Killer-cell Immunoglobulin-like Receptor Genes

Killer cell immunoglobulin-like receptors (KIRs) are a set of inhibitory and activating immune receptors, on natural killer (NK) and T cells, encoded by a polymorphic cluster of genes on chromosome 19. Their best-characterized ligands are the human leukocyte antigen (HLA) molecules that are encoded within the major histocompatibility complex (MHC) locus on chromosome 6. There is substantial evidence that they play a significant role in immunity, reproduction, and transplantation, making it crucial to have techniques that can accurately genotype them. However, high-sequence homology, as well as allelic and copy number variation, make it difficult to design methods that can accurately and efficiently genotype all KIR genes. Traditional methods are usually limited in the resolution of data obtained, throughput, cost-effectiveness, and the time taken for setting up and running the experiments. We describe a method called quantitative KIR semi-automated typing (qKAT), which is a high-throughput multiplex real-time polymerase chain reaction method that can determine the gene copy numbers for all genes in the KIR locus. qKAT is a simple high-throughput method that can provide high-resolution KIR copy number data, which can be further used to infer the variations in the structurally polymorphic haplotypes that encompass them. This copy number and haplotype data can be beneficial for studies on large-scale disease associations, population genetics, as well as investigations on expression and functional interactions between KIR and HLA.

Quantitative killer cell immunoglobulin-like receptor (KIR) semi-automated typing (qKAT) is a simple, high-throughput, and cost-effective method to copy number type KIR genes for their application in population and disease association studies.

qKAT: Quantitative Flugbuchungssystem Typisierung von Killer-Zelle Immunoglobulin-Like-Rezeptor-Gene

Killer cell immunoglobulin-like receptors (KIRs) are a set of inhibitory and activating immune receptors, on natural killer (NK) and T cells, encoded by a ...

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

The development of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) into therapeutic modalities requires the avoidance of its potentially deleterious off-target effects. Several methods have been devised to reduce such effects. Here, we present an Escherichia coli-based directed evolution method called Sniper-screen to obtain a Cas9 variant with optimized specificity and retained on-target activity, called Sniper-Cas9. Using Sniper-screen, positive and negative selection can be performed simultaneously. The screen can also be repeated with other single-guide RNA (sgRNA) sequences to enrich for the true positive hits. By using the CMV-PltetO1 dual promoter to express Cas9 variants, the performance of the pooled library can be quickly checked in mammalian cells. Methods to increase the specificity of Sniper-Cas9 are also described. First, the use of truncated sgRNAs has previously been shown to increase Cas9 specificity. Unlike other engineered Cas9s, Sniper-Cas9 retains a wild-type (WT) level of on-target activity when combined with truncated sgRNAs. Second, the delivery of Sniper-Cas9 in a ribonucleoprotein (RNP) format instead of a plasmid format is possible without affecting its on-target activity.

Here, we present a protocol to optimize CRISPR-Cas9 to achieve a higher specificity without the loss of on-target activity. We use a directed evolution approach called Sniper-screen to find a mutant Cas9 with the desired characteristics. Sniper-Cas9 is compatible with truncated single-guide RNAs and delivery in a ribonucleoprotein format, well-known strategies for achieving higher specificities.

Verwendung von Sniper-Cas9, Off-Target Auswirkungen von CRISPR-Cas9 ohne den Verlust der Zielaktivität durch gerichtete Evolution

The development of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) into therapeutic modalities requires the ...

A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands

To understand the function of an organ, it is often useful to understand the role of its constituent cell populations. Unfortunately, the rarity of individual cell populations often makes it difficult to obtain enough material for molecular studies. For example, the accessory gland of the Drosophila male reproductive system contains two distinct secretory cell types. The main cells make up 96% of the secretory cells of the gland, while the secondary cells (SC) make up the remaining 4% of cells (about 80 cells per male). Although both cell types produce important components of the seminal fluid, only a few genes are known to be specific to the SCs. The rarity of SCs has, thus far, hindered transcriptomic analysis study of this important cell type. Here, a method is presented that allows for the purification of SCs for RNA extraction and sequencing. The protocol consists in first dissecting glands from flies expressing a SC-specific GFP reporter and then subjecting these glands to protease digestion and mechanical dissociation to obtain individual cells. Following these steps, individual, living, GFP-marked cells are sorted using a fluorescent activated cell sorter (FACS) for RNA purification. This procedure yields SC-specific RNAs from ~40 males per condition for downstream RT-qPCR and/or RNA sequencing in the course of one day. The rapidity and simplicity of the procedure allows for the transcriptomes of many different flies, from different genotypes or environmental conditions, to be determined in a short period of time.

A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands

Here, we present a protocol to dissociate and sort a specific cell population from the Drosophila male accessory glands (secondary cells) for RNA sequencing and RT-qPCR. Cell isolation is accomplished through FACS purification of GFP-expressing secondary cells after a multistep-dissociation process requiring dissection, proteases digestion and mechanical dispersion.

Ein FACS-basiertes Protokoll zur Isolierung von RNA aus den Sekundärzellen der Drosophila Male Accessory Dlands

To understand the function of an organ, it is often useful to understand the role of its constituent cell populations. Unfortunately, the rarity of ...

A New Toolkit for Evaluating Gene Functions using Conditional Cas9 Stabilization

The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 (CRISPR/Cas9) technology has become a prevalent laboratory tool to introduce accurate and targeted modifications in the genome. Its enormous popularity and rapid spread are attributed to its easy use and accuracy compared to its predecessors. Yet, the constitutive activation of the system has limited applications. In this paper, we describe a new method that allows temporal control of CRISPR/Cas9 activity based on conditional stabilization of the Cas9 protein. Fusing an engineered mutant of the rapamycin-binding protein FKBP12 to Cas9 (DD-Cas9) enables the rapid degradation of Cas9 that in turn can be stabilized by the presence of an FKBP12 synthetic ligand (Shield-1). Unlike other inducible methods, this system can be adapted easily to generate bi-cistronic systems to co-express DD-Cas9 with another gene of interest, without conditional regulation of the second gene. This method enables the generation of traceable systems as well as the parallel, independent manipulation of alleles targeted by Cas9 nuclease. The platform of this method can be used for the systematic identification and characterization of essential genes and the interrogation of the functional interactions of genes in in vitro and in vivo settings.

Here, we describe a genome-editing tool based on the temporal and conditional stabilization of clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 (Cas9) under the small molecule, Shield-1. The method can be used for cultured cells and animal models.

Ein neues Toolkit zur Bewertung von Genfunktionen mit bedingter Cas9-Stabilisierung

The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 (CRISPR/Cas9) technology has become a prevalent laboratory ...