Name: precise, high-throughput analysis of bacterial growth
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1. 准备生长培养基 注意: 最小介质 M63 的化学成分如下:62 mm K 2 HPO 4 , 39 mm, 2 PO 4 , 15 mm (NH 4 ) 2 因此 4 、1.8 和 #181; m FeSO 4 、15和 #181; m 硫胺素-HCl、0.2 mm MgSO 4 和 22 mm 葡萄糖。M63 是由混合三库存解决方案: 五 X 解决方案, 20% 葡萄糖和 MgSO 4 硫胺素溶液。将所有解决方案存储在4和 #176; C. </...

<ol>
	<li>Kovarova-Kovar, K., Egli, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+kinetics+of+suspended+microbial+cells:+from+single-substrate-controlled+growth+to+mixed-substrate+kinetics.">Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics.</a> Microbiol Mol Biol Rev. 62 (3), 646-666 (1998).</li><li>Soupene, E., 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=Physiological+studies+of+Escherichia+coli+strain+MG1655:+growth+defects+and+apparent+cross-regulation+of+gene+expression.">Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression.</a> J Bacteriol. 185 (18), 5611-5626 (2003).</li><li>Sezonov, G., Joseleau-Petit, D., D'Ari, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Escherichia+coli+physiology+in+Luria-Bertani+broth.">Escherichia coli physiology in Luria-Bertani broth.</a> J Bacteriol. 189 (23), 8746-8749 (2007).</li><li>Egli, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+growth+and+physiology:+a+call+for+better+craftsmanship.">Microbial growth and physiology: a call for better craftsmanship.</a> Front Microbiol. 6, 287 (2015).</li><li>Kurokawa, M., Seno, S., Matsuda, H., Ying, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correlation+between+genome+reduction+and+bacterial+growth.">Correlation between genome reduction and bacterial growth.</a> DNA Res. 23 (6), 517-525 (2016).</li><li>Matsumoto, Y., Murakami, Y., Tsuru, S., Ying, B. W., Yomo, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+rate-coordinated+transcriptome+reorganization+in+bacteria.">Growth rate-coordinated transcriptome reorganization in bacteria.</a> BMC Genomics. 14, 808 (2013).</li><li>Nahku, 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=Specific+growth+rate+dependent+transcriptome+profiling+of+Escherichia+coli+K12+MG1655+in+accelerostat+cultures.">Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures.</a> J Biotechnol. 145 (1), 60-65 (2010).</li><li>Dai, 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=Reduction+of+translating+ribosomes+enables+Escherichia+coli+to+maintain+elongation+rates+during+slow+growth.">Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth.</a> Nat Microbiol. 2, 16231 (2016).</li><li>Madrid, R. E., Felice, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+biomass+estimation.">Microbial biomass estimation.</a> Crit Rev Biotechnol. 25 (3), 97-112 (2005).</li><li>Harris, C. M., Kell, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+estimation+of+microbial+biomass.">The estimation of microbial biomass.</a> Biosensors. 1 (1), 17-84 (1985).</li><li>Yates, G. T., Smotzer, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+lag+phase+and+initial+decline+of+microbial+growth+curves.">On the lag phase and initial decline of microbial growth curves.</a> J Theor Biol. 244 (3), 511-517 (2007).</li><li>Kargi, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Re-interpretation+of+the+logistic+equation+for+batch+microbial+growth+in+relation+to+Monod+kinetics.">Re-interpretation of the logistic equation for batch microbial growth in relation to Monod kinetics.</a> Lett Appl Microbiol. 48 (4), 398-401 (2009).</li><li>Peleg, M., Corradini, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+growth+curves:+what+the+models+tell+us+and+what+they+cannot.">Microbial growth curves: what the models tell us and what they cannot.</a> Crit Rev Food Sci Nutr. 51 (10), 917-945 (2011).</li><li>Sprouffske, K., Wagner, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growthcurver:+an+R+package+for+obtaining+interpretable+metrics+from+microbial+growth+curves.">Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.</a> BMC Bioinformatics. 17, 172 (2016).</li><li>Hall, B. G., Acar, H., Nandipati, A., Barlow, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+rates+made+easy.">Growth rates made easy.</a> Mol Biol Evol. 31 (1), 232-238 (2014).</li><li>Hermsen, R., Okano, H., You, C., Werner, N., Hwa, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+growth-rate+composition+formula+for+the+growth+of+E.coli+on+co-utilized+carbon+substrates.">A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates.</a> Mol Syst Biol. 11 (4), 801 (2015).</li><li>Engen, S., Saether, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=r-+and+K-selection+in+fluctuating+populations+is+determined+by+the+evolutionary+trade-off+between+two+fitness+measures:+Growth+rate+and+lifetime+reproductive+success.">r- and K-selection in fluctuating populations is determined by the evolutionary trade-off between two fitness measures: Growth rate and lifetime reproductive success.</a> Evolution. 71 (1), 167-173 (2017).</li></ol>

协议中的关键步骤包括准备一股指数增长的细胞的普通股, 以及在微的不同位置的多个井中复制相同的样品。以前, 微生物学从一夜培养开始了文化。虽然这种方法可以减少细菌生长的滞后时间, 但很难获得可再生的生长曲线。如图 2所示, 使用普通甘油库存的独立测量导致几乎相同的生长曲线, 从而提供了重现性和精确的结果。如图 3所示, 不同位置的水...

微生物研究经常从细菌细胞的培养和细菌生长曲线的评估开始, 这代表细菌生理学的一个基本现象1,2,3。基本文化原则在已出版的研究文献和教科书中得到广泛应用, 因为细菌培养是一种基本的方法。在替补席上, 传统上一直关注于优化生长培养基和培养条件, 但控制生长速度, 这可能会提供更大的理解微生物生理学, 没有广泛研究了4。对于指数生长的细菌来说, 细胞状态的一个关键参数是生长速率, 据报告, 它与基因组、转录和蛋白质群相协调5,6,7,8.因此, 对细菌生长的定量评价是了解微生物生理学的关键。
为了评价细菌的生长, 用于估计生物量的实验方法已经建立了9,10 , 并基于检测生化、物理或生物参数, 如光学浊度。此外, 用于捕获生长变化动态特性的分析方法通常基于建立的非线性模型11,12,13, 例如, 逻辑方程。生长动力学通常通过测量光学浊度或进行菌落形成单元 (CFU) 测定来获得细胞生长的定时取样。这些培养和检测方法的局限性在于, 数据点不是人口动态的真实反映, 因为测量间隔通常是小时, 因为培养条件 (例如, 温度的变化和曝气) 在取样时受到干扰。必须利用技术和理解方面的最新发展来更新文化和分析技术。微读者的最新进展使 real-time 观察细菌生长, 并大大降低劳动力成本。利用这些先进的设备, 最新的细菌生长研究报告了高通量测量的分析方法14,15。
本议定书的目的是以高通量的方式评估精确的增长动态, 这对于最终解决增长率如何确定以及影响增长率的问题的定量研究将是有价值的。该议定书处理的所有因素, 应考虑到可重复和精确的定量细菌生长。本文主要对实验方法和分析进行了详细的介绍。这种方法允许以高通量的方式精确和重现地分析细菌的生长。微生物学可以利用这个协议从他们的实验证据中获得额外的定量结果。该协议也可用于系统生物学的研究, 试图得出概念性结论或实现对增长的理论概述。

<table>
	<tbody>
		<tr>
			<td>K2HPO4</td>
			<td>Wako</td>
			<td>164-04295</td>
			<td></td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Wako</td>
			<td>166-04255</td>
			<td></td>
		</tr>
		<tr>
			<td>(NH4)2SO4</td>
			<td>Wako</td>
			<td>019-03435</td>
			<td></td>
		</tr>
		<tr>
			<td>MgSO4-7H2O</td>
			<td>Wako</td>
			<td>138-00415</td>
			<td></td>
		</tr>
		<tr>
			<td>Thiamine-HCl</td>
			<td>Wako</td>
			<td>201-00852</td>
			<td></td>
		</tr>
		<tr>
			<td>glucose</td>
			<td>Wako</td>
			<td>049-31165</td>
			<td></td>
		</tr>
		<tr>
			<td>HCl</td>
			<td>Wako</td>
			<td>080-01066</td>
			<td></td>
		</tr>
		<tr>
			<td>Iron (II) sulfate heptahydrate (FeSO4-7H2O)</td>
			<td>Wako</td>
			<td>094-01082</td>
			<td></td>
		</tr>
		<tr>
			<td>KOH</td>
			<td>Wako</td>
			<td>168-21815</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Wako</td>
			<td>075-00611</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge tube (50 mL, sterilized)</td>
			<td>WATSON</td>
			<td>1342-050S</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 200 &#181;L</td>
			<td>WATSON</td>
			<td>110-705Y</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 1000 &#181;L</td>
			<td>WATSON</td>
			<td>110-8040</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtube (1.5 mL)</td>
			<td>WATSON</td>
			<td>131-715C</td>
			<td></td>
		</tr>
		<tr>
			<td>8 multichannel-pipette</td>
			<td>WATSON</td>
			<td>NT-8200</td>
			<td></td>
		</tr>
		<tr>
			<td>PASORINA STIRRER</td>
			<td>AS ONE</td>
			<td>2-4990-02</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass cylinder (200 mL)</td>
			<td>AS ONE</td>
			<td>1-8562-07</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision pH mater</td>
			<td>AS ONE</td>
			<td>AS800 / 1-054-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipetman P-200</td>
			<td>GILSON</td>
			<td>1-6855-05</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipetman P-1000</td>
			<td>GILSON</td>
			<td>1-6855-06</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable Serolocical Pipettes (10 mL)</td>
			<td>SANPLATEC</td>
			<td>SAN27014</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable Serolocical Pipettes (25 mL)</td>
			<td>SANPLATEC</td>
			<td>SAN27015</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtube stand</td>
			<td>BM Bio</td>
			<td>801-02Y</td>
			<td></td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>BM Bio</td>
			<td>BM-V1</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Costar 96-well microplate with lid (Flat bottom, Clear)</td>
			<td>Sigma-Aldrich</td>
			<td>Corning, 3370</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Costar reagent reservoir (50 mL)</td>
			<td>Sigma-Aldrich</td>
			<td>Corning, 4870</td>
			<td></td>
		</tr>
		<tr>
			<td>Stericup GV PVDF (250 mL, 0.22 &#181;M)</td>
			<td>Merck Millipore</td>
			<td>SCGVU02RE</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipet-Aid XP</td>
			<td>DRUMMOND</td>
			<td>4-000-101</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioshaker (BR-23UM MR)</td>
			<td>TAITEC</td>
			<td>0053778-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposal cell (1.5 mL)</td>
			<td>Kartell</td>
			<td>1938 / 2-478-02</td>
			<td></td>
		</tr>
		<tr>
			<td>DU 730 Life Science UV/Vis Spectrophotometer</td>
			<td>Beckman Coulter</td>
			<td>A23616</td>
			<td></td>
		</tr>
		<tr>
			<td>EPOCH2</td>
			<td>BioTek</td>
			<td>2014-EP2-002 / EPOCH2T</td>
			<td></td>
		</tr>
		<tr>
			<td>Beaker (500 mL)</td>
			<td>IWAKI</td>
			<td>82-0008</td>
			<td></td>
		</tr>
		<tr>
			<td>BIO clean bench</td>
			<td>Panasonic</td>
			<td>MCV-B131F</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass tubes</td>
			<td>NICHIDEN RIKA GLASS</td>
			<td>P-10M~P-30 /101019</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicone rubber stoppers</td>
			<td>ShinEtsu Polymer</td>
			<td>T-19</td>
			<td></td>
		</tr>
		<tr>
			<td>Bacterial strains</td>
			<td>Strain bank organization; National Bio Resource Project (NBRP) in Japan</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

precise, high-throughput analysis of bacterial growth

细菌生长是现代微生物生理学发展的一个中心概念, 也是在系统层面上对细胞动力学的研究。最近的研究报告了细菌生长和全基因组事件之间的相关性, 如基因组减少和转录重组。正确分析细菌生长对理解生长依赖的基因功能和细胞成分的协调至关重要。因此, 需要以高通量的方式对细菌生长进行精确的定量评价。新兴的技术发展提供了新的实验工具, 允许更新用于研究细菌生长的方法。这里介绍的协议雇用了一个微的读者与一个高度优化的实验程序, 对细菌生长的可再生和精确的评估。此协议用于评估以前描述的几种大肠杆菌菌株的生长情况。该议定书的主要步骤如下: 在小瓶中制备大量的细胞储存, 用于重复试验, 具有重现性的结果, 使用 96-井板进行高通量增长评价, 并手工计算两个主要表示增长动态的参数 (即、最大增长率和人口密度)。与传统的菌落形成单元 (CFU) 测定法相比, 它对琼脂板上的玻璃管中培养的细胞进行了计数, 目前的方法更加有效, 提供了更详细的生长变化的时间记录, 但具有更严格低人口密度的检测限制。总之, 所描述的方法有利于精确和可重复的高通量分析细菌生长, 可用于绘制概念性结论或作出理论观察。

所描述的方法提供了一种手段, 以连续的, 高通量的方式捕捉动态细菌生长, 利用96井格式的阅读器, 在不同的时间间隔采取多种光学密度测量 (从分钟到小时到天)。在一个单一的实验中, 可以精确地获得表达各种基因组的大肠杆菌菌株的生长曲线 (图 1A)。与所描述的方法相比, 传统方法 (CFU 分析) 通常需要更长的采样时间间隔 (图 ...

Watch this Scientific Journal Video about Precise, High-throughput Analysis of Bacterial Growth at JoVE.com

Precise, High-throughput Analysis of Bacterial Growth

细菌生长的精确、高通量分析

细菌生长的定量评价是理解微生物生理学作为系统级现象的关键。本文介绍了一种实验操作和分析方法的协议, 允许对细菌生长进行精确、高通量的分析, 这是系统生物学研究的一个重要课题。

Bacterial growth is a central concept in the development of modern microbial physiology, as well as in the investigation of cellular dynamics at the ...

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pHluorin的申请在芽殖酵母细胞内吞的定量，动力学和高通量分析

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal ...

Isolation, Characterization, And High Throughput Extracellular Flux Analysis of Mouse Primary Renal Tubular Epithelial Cells

小鼠原发性肾管上皮细胞的分离、鉴定及高通量的细胞外流量分析

Mitochondrial dysfunction in the renal tubular epithelial cells (TECs) can lead to renal fibrosis, a major cause of&#160;chronic kidney disease (CKD). ...