Biz bize bakteri suşlarının plazmid ve gerekli protokolleri göndermek için Dr. Michael Cashel (Sağlık, Bethesda, MA, ABD Ulusal Sağlık Enstitüleri) teşekkür ederim. Biz SpecraMax plaka okuyucu kullanımı için Dr. John Glover (Biyokimya Anabilim Dalı, Toronto Üniversitesi) teşekkür ederim. İngiltere, Kanada Ulusal Bilimler ve Mühendislik Araştırma Konseyi (NSERC) Lisansüstü Bursu, Hastalıklara Bağlı Membran Proteinlerin Yapısal Biyoloji, Kanada Sağlık Araştırma Stratejik Eğitim Programı Enstitüleri ve Toronto Açık Bursu Üniversitesi alıcı. Bu çalışma WAH Kanada Sağlık Araştırma Enstitüsü (MOP-67.210) bir hibe ile desteklenmiştir.

1) Reaktifler ve Ekipmanları <ol><li> İlk olarak, aşağıdaki üç çözümleri hazırlamak: Çözüm 1 ml 8 mM L-lizin, 100 mM sodyum 2 yapıldığı A - (N-morfolino) ethanesulphonic asit (MES), pH 6.5, nükleotid nükleotid 0.2 mM, ya: guanozin difosfat (GSYİH), guanozin trifosfat (GTP), guanozin 5&#39;-difosfat, 3&#39;-difosfat (ppGpp), ya da guanozin 5&#39;-trifosfat, 3&#39;-difosfat (pppGpp), 0.1 mM piridoksal 5&#39;-fosfat (PLP) ve 1 mM β-mercaptoethanol / (β-ME). 100 mM sodyum (MES), pH 6.5, 0.1 mM PLP, 1 mM β-ME ve 50 nM LdcI oluşur Çözüm B 1 ml. Snider ve ark açıklandığı gibi LdcI saflaştırılmış 6 ve Kanjee ve ark. 14. Çözüm B aynıdır ama LdcI içermez Çözüm C 1 ml. </li><li> 100 ml, 96-iyi polistiren plaka çok kanallı pipet kullanarak her bir kuyunun içine 1 M sodyum karbonat (10,6 g/100 mL) ve 50 mcL kısım oluşan stop bir çözüm hazırlayın. Plaka 30 mcL su ekleyin ve sonra da kapsayacak. Su hacmi toplamına eklenir ve enzim reaksiyon sırasında çıkarılan örnek hacmi 50 mcL eşit olduğunu unutmayın. Bu durumda, 20 enzim reaksiyon örnek mcL silinecektir. </li><li> 294 mcL% 5 (w / v) TNBS stok, alüminyum folyo 4706 mcL su, şal ile seyreltilmesi ile 5 ml 10 mM TNBS çözüm hazırlayın ve buz üzerinde tutmak. </li><li> Eppendorf ThermoStat dengeye Plus 37 ° C ThermoStat Plus, 6 sütun 24 kuyu vardır. Şematik için Bkz: Şekil 2. (Başına bir sütun) test edilecek nükleotid kimliğini belirten Etiket 1.5 ml Eppendorf tüpleri: GTP (sütun A), GSYH (sütun B), ppGpp (C sütunu), pppGpp (D sütunu), herhangi bir nükleotid (E sütununda ), ve protein örnekleri (sütun F). </li><li> Raf her bir alternatif satır toplam dört satır ipuçları veren ihmal olduğu gibi 200 mcL ipuçları birkaç kutuları. Bu enzim tahlil sırasında ThermoStat Plus heatblock ile çok kanallı pipet kullanımı için gereklidir. </li><li> 42 Dijital Heatblock (VWR) dengelenmesi ° C. </li><li> Soğutmak için buz üzerinde 96-de 2.0 ml polipropilen levha yerleştirin. </li></ol> 2) LdcI Testi <ol><li> Çözüm kısım 50 mcL Eppendorf ThermoStat beş sütunların her biri 1.5 mL Eppendorf tüpleri için uygun nükleotid. </li><li> F sütunundaki üç tüp Çözüm B 330 mcL ekleyin ve sütun F. nihai tüp Çözüm C (protein kontrol) 330 mcL ekleyin </li><li> 37 çözümler dengeye ° C beş dakika boyunca. İpucu: 5 dakika sonra, sonraki kullanılmak üzere çok kanallı pipet ile müdahale bunları önlemek için, merkezi ısıtma-blok tüplerin kapakları kesilmiş. </li><li> F sütunundaki tüpleri, sütunların AE tüpleri her birine bir 5-50 mcL VWR çok kanallı pipet, transfer 50 mcL kullanma. En kısa sürede ilk tüp karışık olarak Sayacı başlat. </li><li> 2, 4 ve 6 dakika 20 mcL çok kanallı pipet kullanarak örnek çıkarın ve stop çözüm ekleyin. </li><li> Not: durak çözüm örnekleri, plastik ambalaj malzemesi ile kaplanmış ve daha sonraki işlem için -20 ° C&#39;de dondurulmuş olabilir. Plakalar TNBS ile reaksiyona önce oda sıcaklığında çözdürülmelidir. </li></ol> 3) TNBS Reaksiyon ve Renk Geliştirme <ol><li> 6 dakika sonra çok kanallı pipet ve 42 inkübe ° C kullanarak stop çözüm için 10 mM TNBS çözümü 50 mcL ekleyin. TNBS lizin ve cadaverine ile reaksiyona girerek çözüm, koyu sarı / turuncu renk dönecek. </li><li> 6 dakika sonra, tepki yavaşlaması, buz üzerinde plaka soğutun. </li><li> Örnek bir VWR 20-200 mcL çok kanallı pipet ve yer buz üzerinde soğutulur 2 mL derin kuyu plaka kullanarak 100 mcL çıkarın. Fumehood buz kovası aktarın. </li><li> HandyStep (Marka) tekrar pipet ve 12.5 ml pipet (Plastibrand) kullanarak her toluen 500 mcL ekleyin. </li><li> Bir kimwipe kullanarak herhangi bir aşırı toluen siliniz ve ambalaj bant şeritler ile plaka kapsayacak. Iyi bir sızdırmazlık elde etmek için sıkıca bastırın emin olun. 96-plaka düz bir kapak ile örtün ve sonra 1 dakika ve 30 saniye boyunca kuvvetlice çalkalanır. </li><li> Çözümleri 5 dakika dinlendiriniz bırakın. EGM-cadaverine EGM-lizin su (bkz. Şekil 1) çözünür kalırken, üst toluen faz şimdi. </li><li> Toluen okumak için 96-iyi bir plaka haline 20-200 mcL çok kanallı pipet kullanarak 200 mcL çıkarın. Not: Her numune kaldırılıyor açıktır ve herhangi bir alt sulu faz bulunmamış kontrol etmek için emin olun. Not: çok kanallı pipet toluen tarafından zarar görmesini önlemek için kullanılan bariyer ipuçları. </li><li> SPECTRAmax 340 plaka okuyucu 340 nm&#39;de absorbans okuyun. </li><li> Kuvars plağı temizlemek için, toluen su ile yıkayın ve büyük bir kuvars plakadavlumbaz cam tepsi. 100 mL% 70 (v / v) nitrik asit 07:03 karışımı üzerine dökün:% 95 (v / v) etanol ve ikinci bir cam tepsi ile kuvars tabak kapağı. Uyarı: reaksiyon çok ekzotermik ve bazen patlayıcı aşınma uygun koruma ve davlumbaz kanat alt 6 &quot;düzeyi ayarlanmış olduğundan emin olunuz Soğuduktan sonra nitrik asit, su ile yıkayın ve ardından% 95 etanol. </li></ol> 4) Temsilcisi Sonuçlar 1) Cadaverine Standart Eğrisi (Şekil 3) Herhangi bir L-lizin veya LdcI olmadan açıklanan, ancak tahlil yapıldı ve cadaverine yerine çeşitli konsantrasyonlarda ampirik testinin doğrusal aralığı belirlemek için kullanılır. Testin ~ 22 nmoles cadaverine (Şekil 3) karşılık gelen 0.25 OD 340 doğrusal oldu. LdcI, 2) Etkinlik (Şekil 4) Yalnız LdcI faaliyet 153.5 (± 18.1) nmoles cadaverine min-1 pH değeri 6.5 mg LdcI-1 olarak tespit edilmiştir LdcI faaliyet 100 mcM GTP veya GDP varlığı etkilenmez ama güçlü pppGpp ve ppGpp (Şekil 4) varlığı (&gt; 10 kat) inhibe edilir. <img src="/files/ftp_upload/2094/2094fig1.jpg" alt="Şekil 1" /> Şekil 1. LdcI reaksiyon şematik diyagramı, CO 2 ve cadaverine oluşturmak için L-lizin dekarboksilasyon reaksiyon, N, N&#39;-bistrinitrophenylcadaverine (EGM-cadaverine) ve N, N oluşturmak için de yüksek pH TNBS ile sonraki tepki olarak gösterilir &#39;-bistrinitrophenyllysine (EGM-lisin). Phan et al.11 <img src="/files/ftp_upload/2094/2094fig2.jpg" alt="Şekil 2" /> Şekil 2. Eppendorf Termostat Kurulumu iyi 24-Eppendorf ThermoStat örnekleri düzen testinin adımları açıklamasına (kalın olarak gösterilir) ile birlikte gösterilmiştir. Oklar reaksiyon çözümleri protokole göre transfer gösterir. 96-plaka durak çözüm tepki çözüm kaldırılması da belirtilir. <img src="/files/ftp_upload/2094/2094fig3.jpg" alt="Şekil 3" /> Şekil 3. Cadaverine Standart Eğrisi. Cadaverine, nmoles karşı 340 nm&#39;de absorbans bir arsa verilmiştir. Hata çubukları, en az üç bağımsız ölçümleri standart sapmasını temsil eder. En uygun hat da gösterilir ve 0,996 bir R2 sahiptir. <img src="/files/ftp_upload/2094/2094fig4.jpg" alt="Şekil 4" /> Şekil 4. LdcI tahlil sonuçları LdcI aktivite oranı arsa 100 mcM GTP, GSYİH, pppGpp, ppGpp varlığı ve yokluğu nükleotid gösterilmiştir (nmoles cadaverine min-1 mg-1 LdcI üretilen). Sıkı yanıt nükleotidler (p) ppGpp LdcI aktivite önemli ölçüde inhibe yeteneğine sahiptir. Hata çubukları, en az altı bağımsız ölçümleri standart sapmasını temsil eder.

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	<li>Gale, E. F., Epps, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+the+pH+of+the+medium+during+growth+on+the+enzymic+activities+of+bacteria+(Escherichia+coli+and+Micrococcus+lysodeikticus)+and+the+biological+significance+of+the+changes+produced.">The effect of the pH of the medium during growth on the enzymic activities of bacteria (Escherichia coli and Micrococcus lysodeikticus) and the biological significance of the changes produced.</a> Biochem J. 36, 600-618 (1942).</li><li>Foster, J. W. <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+acid+resistance:+tales+of+an+amateur+acidophile.">Escherichia coli acid resistance: tales of an amateur acidophile.</a> Nat Rev Microbiol. 2, 898-907 (2004).</li><li>Castanie-Cornet, M. P., Penfound, T. A., Smith, D., Elliott, J. 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Lisin dekarboksilaz tayininde, TNBS EGM-lizin ve EGM-cadaverine adducts (Şekil 1) oluşturmak için L-lizin ve cadaverine birincil aminler ile reaksiyona girer. Karboksilik asit grubu eksik EGM-cadaverine, toluen 11 bölünme yeteneğine sahip iken, EGM-lizin karboksilik asit grubun varlığı nedeniyle, bu adduct suda çözünür kalır. Bu tip testin bir karboksilik asit grubu kaybı reaksiyon sırasında ortaya çıkan amino asitler diğer türleri hakkında daha geniş kullanılabilir. Bu indüklenebilir...

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<td>2,4,6-trinitrobenzensulfonic acid </td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>P2297</td>
<td>&nbsp;</td>
<tr>
<td>0.1 mM pyridoxal 5'-phosphate (PLP)</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>P9255</td>
<td>&nbsp;</td>
<tr>
<td>Cadaverine</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>D22606</td>
<td>&nbsp;</td>
<tr>
<td>96 well polystyrene plates</td>
<td>&nbsp;</td>
<td>Sarstedt</td>
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<td>&nbsp;</td>
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<td>96-well quartz plate</td>
<td>&nbsp;</td>
<td>Hellma</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
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<td>VWR Digital Heatblock</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
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<td>ThermoStat Plus</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
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<td>2.0 mL 96-well polypropylene plates</td>
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<td>Axygen</td>
<td>P-DW-20-C</td>
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<td>Handy Step Repeat Pipettor</td>
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<td>Brand</td>
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<td>12.5 mL Repeat Pipettor Tips</td>
<td>&nbsp;</td>
<td>Brand (Plastibrand)</td>
<td>702378</td>
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<td>SpectraMax 340PC Plate Reader</td>
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<td>SpectraMax</td>
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an assay for measuring the activity of escherichia coli inducible lysine decarboxyase

1 ve inanılmaz derecede düşük pH düşebilir memeli mide geçişi de dahil olmak üzere aşırı asit vurguluyor hayatta kalmak için - Escherichia coli, pH değerleri (9 pH 5) geniş bir yelpazede üzerinde büyüyen yetenekli bir enterik bakteridir pH 1 - 2 2. Asidik pH hayatta kalma, E. gibi geniş bir yelpazede etkinleştirmek için coli, bir proton-bağımlı bir şekilde decarboxylate kendi substrat amino asitler dolayısıyla iç pH yükselterek dört farklı indüklenebilir amino asit dekarboksilaz sahiptir . Dekarboksilaz glutamik asit dekarboksilaz GADA ve GadB 3, arginin dekarboksilaz adia 4, lisin dekarboksilaz LdcI 5, 6 ve ornitin dekarboksilaz SpeF 7 içerir. Tüm bu enzimlerin piridoksal-5&#39;-fosfat, co-faktör 8 olarak kullanmaktadır ve dış ortama taze substrat karşılığında 2 dekarboksilasyon ürünleri kaldırın iç membran substrat ürün antiporters birlikte işlev görür. LdcI durumunda, lizin-cadaverine antiporter CadB denir. Son zamanlarda, 2.0 Å LdcI X-ray kristal yapısı belirlenir ve LdcI sıkı yanıt regülatör guanozin 5&#39;-difosfat, 3&#39;-difosfat (ppGpp) 14 bağlı bir roman küçük molekül keşfetti. Katlanarak büyüyen hücrelerin besin yoksunluğu ya da diğer stresler 9 bir dizi deneyim sıkı bir tepki oluşur. Sonuç olarak, hücreler, üstel büyüme, sabit faz büyüme 10 vardiya sonuçlanan bir sinyal kaskad yol açar ppGpp üretirler . Biz ppGpp LdcI 14 spesifik bir inhibitörü olduğunu göstermiştir. Burada Phan ve arkadaşları tarafından geliştirilen testin modifiye lisin dekarboksilaz deneyi açıklar. 11, LdcI faaliyeti ve bu faaliyetin pppGpp / ppGpp etkisini belirlemek için kullanmış olduğunuz. LdcI dekarboksilasyon tepki L-lizin α-karboksi grubu kaldırır ve karbon dioksit ve poliamin cadaverine (1,5-diaminopentane) 5 üretir. L-lizin ve cadaverine sırasıyla, N, N&#39;-bistrinitrophenylcadaverine (EGM-cadaverine) ve N, N&#39;-bistrinitrophenyllysine (EGM-lisin) oluşturmak için yüksek pH 2,4,6-trinitrobenzensulfonic asit (TNBS) ile reaksiyona girer. 11. EGM-cadaverine, ikincisi ise (Bakınız Şekil 1) eski, toluen gibi organik çözücülerde çözünür olarak EGM-lizin ayrılabilir. Testin doğrusal aralığı, ampirik olarak saflaştırılmış cadaverine kullanarak tespit edildi.

Watch this Scientific Journal Video about An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase at JoVE.com

An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

Indüklenebilir lizin dekarboksilaz aktivitesi toluen diferansiyel çözünürlüğü adducts oluşturmak için substrat L-lizin ve ürün cadaverine 2,4,6-trinitrobenzensulfonic asit ile reaksiyona girerek izlenir.

Etkinlik Ölçüm Bir Testi Escherichia coli Lizin Decarboxyase Đndüklenebilir

Escherichia coli is an enteric bacterium that is capable of growing over a wide range of pH values (pH 5 - 9)1 and, incredibly, is able to survive extreme ...

an-assay-for-measuring-activity-escherichia-coli-inducible-lysine

Research

JoVE Journal

Biology

An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

14.1K Görüntüleme.  University of Toronto. Indüklenebilir lizin dekarboksilaz aktivitesi toluen diferansiyel çözünürlüğü adducts oluşturmak için substrat L-lizin ve ürün cadaverine 2,4,6-trinitrobenzensulfonic asit ile reaksiyona girerek izlenir.

Video: An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

Measuring the Bending Stiffness of Bacterial Cells Using an Optical Trap

We developed a protocol to measure the bending rigidity of filamentous rod-shaped bacteria. Forces are applied with an optical trap, a microscopic three-dimensional spring made of light that is formed when a high-intensity laser beam is focused to a very small spot by a microscope's objective lens. To bend a cell, we first bind live bacteria to a chemically-treated coverslip. As these cells grow, the middle of the cells remains bound to the coverslip but the growing ends are free of this restraint. By inducing filamentous growth with the drug cephalexin, we are able to identify cells in which one end of the cell was stuck to the surface while the other end remained unattached and susceptible to bending forces. A bending force is then applied with an optical trap by binding a polylysine-coated bead to the tip of a growing cell. Both the force and the displacement of the bead are recorded and the bending stiffness of the cell is the slope of this relationship.

We present a protocol for bending filamentous bacterial cells attached to a cover-slip surface with an optical trap to measure the cellular bending stiffness.

Optik Tuzak kullanarak Bakteriyel Hücre Bükme Rijitlik Ölçüm

We developed a protocol to measure the bending rigidity of filamentous rod-shaped bacteria. Forces are applied with an optical trap, a microscopic ...

Biyoloji

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted into fuel alcohols1. The potential for enzymatic hydrolysis of cellulosic biomass to provide renewable energy has intensified efforts to engineer cellulases for economical fuel production2. Of particular interest are fungal cellulases3-8, which are already being used industrially for foods and textiles processing.
Identifying active variants among a library of mutant cellulases is critical to the engineering process; active mutants can be further tested for improved properties and/or subjected to additional mutagenesis. Efficient engineering of fungal cellulases has been hampered by a lack of genetic tools for native organisms and by difficulties in expressing the enzymes in heterologous hosts. Recently, Morikawa and coworkers developed a method for expressing in E. coli the catalytic domains of endoglucanases from H. jecorina3,9, an important industrial fungus with the capacity to secrete cellulases in large quantities. Functional E. coli expression has also been reported for cellulases from other fungi, including Macrophomina phaseolina10 and Phanerochaete chrysosporium11-12. 
We present a method for high throughput screening of fungal endoglucanase activity in E. coli. (Fig 1) This method uses the common microbial dye Congo Red (CR) to visualize enzymatic degradation of carboxymethyl cellulose (CMC) by cells growing on solid medium. The activity assay requires inexpensive reagents, minimal manipulation, and gives unambiguous results as zones of degradation (&#x201C;halos&#x201D;) at the colony site. Although a quantitative measure of enzymatic activity cannot be determined by this method, we have found that halo size correlates with total enzymatic activity in the cell. Further characterization of individual positive clones will determine , relative protein fitness. 
Traditional bacterial whole cell CMC/CR activity assays13 involve pouring agar containing CMC onto colonies, which is subject to cross-contamination, or incubating cultures in CMC agar wells, which is less amenable to large-scale experimentation. Here we report an improved protocol that modifies existing wash methods14 for cellulase activity: cells grown on CMC agar plates are removed prior to CR staining. Our protocol significantly reduces cross-contamination and is highly scalable, allowing the rapid screening of thousands of clones. In addition to H. jecorina enzymes, we have expressed and screened endoglucanase variants from the Thermoascus aurantiacus and Penicillium decumbens (shown in Figure 2), suggesting that this protocol is applicable to enzymes from a range of organisms.

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

We describe a low cost, high throughput method to screen for fungal endoglucanase activity in E. coli. The method relies on a simple visual readout of substrate degradation, does not require enzyme purification, and is highly scalable. This allows for the rapid screening of large libraries of enzyme variants.

Mantar Endoglucanase Faaliyet Yüksek Verimli Tarama Escherichia coli</em

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted ...

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity

Recently, epigenetic regulators have been discovered as key players in many different diseases 1-3. As a result, these enzymes are prime targets for small molecule studies and drug development 4. Many epigenetic regulators have only recently been discovered and are still in the process of being classified. Among these enzymes are lysine demethylases which remove methyl groups from lysines on histones and other proteins. Due to the novel nature of this class of enzymes, few assays have been developed to study their activity. This has been a road block to both the classification and high throughput study of histone demethylases. Currently, very few demethylase assays exist. Those that do exist tend to be qualitative in nature and cannot simultaneously discern between the different lysine methylation states (un-, mono-, di- and tri-). Mass spectrometry is commonly used to determine demethylase activity but current mass spectrometric assays do not address whether differentially methylated peptides ionize differently. Differential ionization of methylated peptides makes comparing methylation states difficult and certainly not quantitative (Figure 1A). Thus available assays are not optimized for the comprehensive analysis of demethylase activity.
Here we describe a method called MassSQUIRM (mass spectrometric quantitation using isotopic reductive methylation) that is based on reductive methylation of amine groups with deuterated formaldehyde to force all lysines to be di-methylated, thus making them essentially the same chemical species and therefore ionize the same (Figure 1B). The only chemical difference following the reductive methylation is hydrogen and deuterium, which does not affect MALDI ionization efficiencies. The MassSQUIRM assay is specific for demethylase reaction products with un-, mono- or di-methylated lysines. The assay is also applicable to lysine methyltransferases giving the same reaction products. Here, we use a combination of reductive methylation chemistry and MALDI mass spectrometry to measure the activity of LSD1, a lysine demethylase capable of removing di- and mono-methyl groups, on a synthetic peptide substrate 5. This assay is simple and easily amenable to any lab with access to a MALDI mass spectrometer in lab or through a proteomics facility. The assay has ~8-fold dynamic range and is readily scalable to plate format 5.

We present a method for using MALDI mass spectrometry and reductive methylation chemistry to quantify changes in lysine methylation.

Lizin demetilaz Faaliyet Kantitatif Ölçümler MassSQUIRM Uygulaması

Recently, epigenetic regulators have been discovered as key players in many different diseases 1-3. As a result, these enzymes are prime targets for small ...

Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has become the method of choice for introducing DNA into prokaryotes that are not naturally competent. Electroporation is a rapid, efficient, and streamlined transformation method that, in addition to purified DNA and competent bacteria, requires commercially available gene pulse controller and cuvettes. In contrast to the pulsing step, preparation of electrocompetent cells is time consuming and labor intensive involving repeated rounds of centrifugation and washes in decreasing volumes of sterile, cold water, or non-ionic buffers of large volumes of cultures grown to mid-logarithmic phase of growth. Time and effort can be saved by purchasing electrocompetent cells from commercial sources, but the selection is limited to commonly employed E. coli laboratory strains. We are hereby disseminating a rapid and efficient method for preparing electrocompetent E. coli, which has been in use by bacteriology laboratories for some time, can be adapted to V. cholerae and other prokaryotes. While we cannot ascertain whom to credit for developing the original technique, we are hereby making it available to the scientific community.

Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae

Electroporation is a commonly employed method for introducing DNA into bacteria in a process known as transformation. Traditional protocols for the preparation of electrocompetent cells are time consuming and labor intensive. This article describes an alternate, rapid, and efficient method for the preparation of electrocompetent cells presently employed by some laboratories.

Elektrokompetan Hazırlanması için hızlı Protokolü<em&gt; Escherichia coli</em&gt; Ve<em&gt; Vibrio cholerae</em

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has ...

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.7 The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.6,8 Accompanying mathematical models are available.9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.

Bir uygulama için Protokoller<em&gt; Escherichia coli</emSentetik Biyoloji&gt; Tabanlı TX-TL Hücre-Özgür İfade Sistemi

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for ...

Detection of Live Escherichia coli O157:H7 Cells by PMA-qPCR

A unique open reading frame (ORF) Z3276 was identified as a specific genetic marker for E. coli O157:H7. A qPCR assay was developed for detection of E. coli O157:H7 by targeting ORF Z3276. With this assay, we can detect as low as a few copies of the genome of DNA of E. coli O157:H7. The sensitivity and specificity of the assay were confirmed by intensive validation tests with a large number of E. coli O157:H7 strains (n = 369) and non-O157 strains (n = 112). Furthermore, we have combined propidium monoazide (PMA) procedure with the newly developed qPCR protocol for selective detection of live cells from dead cells. Amplification of DNA from PMA-treated dead cells was almost completely inhibited in contrast to virtually unaffected amplification of DNA from PMA-treated live cells. Additionally, the protocol has been modified and adapted to a 96-well plate format for an easy and consistent handling of a large number of samples. This method is expected to have an impact on accurate microbiological and epidemiological monitoring of food safety and environmental source.

Detection of Live Escherichia coli O157:H7 Cells by PMA-qPCR

A qPCR assay was developed for detection of Escherichia coli O157:H7 targeting a unique genetic marker, Z3276. The qPCR was combined with propidium monoazide (PMA) treatment for live cell detection. This protocol has been modified and adapted to a 96-well plate format for easy and consistent handling of numerous samples

Live Algılama<em&gt; Escherichia coli</em&gt; O157: PMA-qPCR H7 Hücreler

A unique open reading frame (ORF) Z3276 was identified as a specific genetic marker for E. coli O157:H7. A qPCR assay was developed for detection of E. ...

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

A streamlined approach to screening for the expression of recombinant membrane proteins in Escherichia coli based on fusion to green fluorescent protein is presented.

Membran proteinlerinin Yeşil floresan proteini temelli Ekspresyon elemesinde<em&gt; Escherichia coli</em

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and ...

The Multifaceted Benefits of Protein Co-expression in Escherichia coli

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in vitro. In particular, we show that the poor solubility of Escherichia coli DNA polymerase III &#949; subunit (featuring 3&#8217;-5&#8217; exonuclease activity) is highly improved when the same protein is co-expressed with the &#945; and &#952; subunits (featuring DNA polymerase activity and stabilizing &#949;, respectively). We also show that protein co-expression in E. coli can be used to efficiently test the competence of subunits from different bacterial species to associate in a functional protein complex. We indeed show that the &#945; subunit of Deinococcus radiodurans DNA polymerase III can be co-expressed in vivo with the &#949; subunit of E. coli. In addition, we report on the use of protein co-expression to modulate mutation frequency in E. coli. By expressing the wild-type &#949; subunit under the control of the araBAD promoter (arabinose-inducible), and co-expressing the mutagenic D12A variant of the same protein, under the control of the lac promoter (inducible by isopropyl-thio-&#946;-D-galactopyranoside, IPTG), we were able to alter the E. coli mutation frequency using appropriate concentrations of the inducers arabinose and IPTG. Finally, we discuss recent advances and future challenges of protein co-expression in E. coli.

The Multifaceted Benefits of Protein Co-expression in Escherichia coli

Protein co-expression is a powerful alternative to the reconstitution in vitro of protein complexes, and is of help in performing biochemical and genetic tests in vivo. Here we report on the use of protein co-expression in Escherichia coli to obtain protein complexes, and to tune the mutation frequency of cells.

Protein birlikte-ifade edilme yönlü Faydalar<em&gt; Escherichia coli</em

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in ...

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

An easy-to-use, cell-free expression protocol for the residue-specific incorporation of noncanonical amino acid analogs into proteins, including downstream analysis, is presented for medical, pharmaceutic, structural and functional studies.

Bir Kullanarak Modeli Proteinler içine Kuralsız Amino Asit kalıntı özgü Ortaklığın<em&gt; Escherichia coli</em&gt; Hücre içermeyen Transkripsiyon-çeviri Sistemi

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes ...

Measuring Lactase Enzymatic Activity in the Teaching Lab

Understanding how enzymes work, and relating this to real life examples, is critical to a wide range of undergraduate degrees in the biological and biomedical sciences. This easy to follow protocol was developed for first year undergraduate pharmacy students and provides an entry-level introduction to enzyme reactions and analytical procedures for enzyme analysis. The enzyme of choice is lactase, as this represents an example of a commercially available enzyme relevant to human disease/pharmaceutical practice. Lactase is extracted from dietary supplement tablets, and assessed using a colorimetric assay based upon hydrolysis of an artificial substrate for lactase (ortho-nitrophenol-beta-D-galactopyranoside, ONPG). Release of ortho-nitrophenol following the hydrolytic cleavage of ONPG by lactase is measured by a change in absorbance at 420 nm, and the effect of the temperature on the enzymatic reaction is evaluated by carrying out the reaction on ice, at room temperature and at 37 &#176;C. More advanced analysis can be implemented using this protocol by assessing the enzyme activity under different conditions and using different reagents.

The enzymatic activity of lactase is essential for the catabolic processing of the disaccharide lactose. Here, the activity of lactase found in dietary supplements is assayed using a colorimetric assay. This provides students with an experimental platform for understanding the activity of lactase and enzyme kinetics.

Laktaz enzim etkinliğin ölçülmesi öğretim laboratuarında

Understanding how enzymes work, and relating this to real life examples, is critical to a wide range of undergraduate degrees in the biological and ...