Çalışma DOM programı ve Avrupa Birliği Topluluk FP7 Çerçeve programından hibe 211.684 (BACSIN) ile Stratejik Çevre Araştırma için İsveç Vakfı (mistra) tarafından desteklenmiştir. Biz kavramsal anlatım ile yardımcı olmak için X-ışını analizi ve L. Tang filme yardım için J. Engstrand teşekkür ederim.

1. P. yetiştirme ve hasat putida <ol><li> P. bir koloni ile triptik soy broth 100 ml (TSB) aşılayarak Pseudomonas putida bir starter kültür hazırlayın putida hücreleri triptik soya suyu (TSA) ile desteklenmiş agar üzerinde kültürlenmiştir. 130 rpm ayarlanmış bir sallayarak gemide 30 ° C de kültür tutun. </li><li> 7 saat taze TSB ortamı için marş kültür eşdeğer ana kültürün son hacminin 1/10 ile bir kısım aktardıktan sonra. 16 saat 130 rpm&#39;de sallayarak gemide 30 ° C hücreleri tutun. </li><li> Büyüme 16 saat sonra hücreler, oda sıcaklığında 20 dakika boyunca 1500 x g&#39;de hücre kültürü iplik ile hasat edilir. Süpernatant süzün ve pellet besiyerine izotonik olan bir NaCl çözeltisi içinde olan hücre yeniden süspanse ederek hücreleri yıkayın. Bu durumda, 150 mM NaCI çözeltisi kullanıldı. , Hücreler daha sonra bir kez daha santrifüje tabi tutulur ve yüzer madde formülasyonu ortam içinde yeniden süspansiyona önce dekante ediliradım 3.2. </li></ol> 2. Diğer türlerin ekimi <ol><li> Diğer bakteri türleri için protokol uyarlamak için yetiştirme ve hasat işlemleri bu türlerin ihtiyaçlarına göre değiştirilmelidir. Hasat ve yıkama adım (lar) ve hücreleri işlerken ozmotik şok önlemek için, çözümlerin ozmolalite hasatta büyüme ortamı uyumlu olması gerekmektedir. </li></ol> 3. Hücre Formülasyon <ol><li> Ilgili matris bileşenleri tartılarak formülasyonu çözümleri hazırlayın ve onları suda çözülür. Izotonik koşulları elde etmek için, ya yardımcı maddenin miktarını ayarlamak veya istediğiniz ozmolalite ulaşmak için NaCl veya başka bir hücre uyumlu çözünen ekleyin. Gibi disakaridler gibi düşük molekül ağırlıklı maddeler için miktarlarda kolayca izotonik koşullarına ulaşmak için ayarlanabilir. Yüksek moleküler ağırlığa sahip olan polimer gibi maddeler için, tonisite çok uyumlu hücre ile ayarlanmalıdırLutes, örneğin NaCl veya disakkaritler. Bir maddenin bir yanı da dondurma-kurutma davranışları ve hücre canlılığı etkileyebilir, formülasyonun fiziksel özelliklerine, etkileyecektir unutmayın. </li><li> Yıkama solüsyonu (bu durumda, NaCl) boşaltacaktır ve ilgili formülasyon dahil edilmesi, hücrelerin yeniden askıya. </li><li> Hücrelerin homojen bir şekilde disperse edilir olduğundan emin olun. Daha yüksek viskoziteler formülasyonlar kullanılarak karıştırılmış ise düşük viskoziteli formülasyonlar, örn., Bir karıştırma çubuğu eklenmesi ve homojen karışım elde edilene kadar kabı çalkalayarak vortekslenmiş. </li><li> Dondurarak kurutma şişeleri içine formülasyonlar bölün. Şişeleri önce ve dondurma-kurutma sırasında çıkarılan su miktarını hesaplamak için dondurularak kurutulduktan sonra numune ile, boş bir seçim yapılması gerekmektedir. </li><li> Şişeleri dondurma-kurutma makinesi içinde imzalanacak istiyorsak şişeleri için lastik tapalar ekle, 4.3 adıma bakın. </li><li> Dondurarak kurutmadan önce, her bir oluşum içinde hücrelerin Numaralandırma, adım 6 bkz. </li> &lt;/ Ol&gt; 4. Dondurma-kurutma <ol><li> Dondurarak kurutma koşulları, formülasyonun fiziksel özelliklerine göre ayarlanması gerekir. En önemli parametre, bu durumda, cam geçiş ısısı Tg, formülasyon, bu su hala mevcut olduğunu belirtmek için donma-konsantre numune için Tg &#39;anlamına gelir. Dondurarak konsantre formülasyonun Tg &#39;kolayca diferansiyel tarama kalorimetresi (DSC) ile ölçülür, adım 7 bkz. </li><li> Dondurarak kurutma işleminin parametrelerini ayarlama dolayısı ile de numunenin sıcaklığı, numunenin Tg altında ve bu her zaman olduğu oda basıncı, yani sekonder, formülasyon içinde bir buz hızlı süblimasyon, yani birincil kurutma ve artık su sağlar kurutulması. Numune sıcaklığı kurutma işlemi sırasında &#39;Tg üzerindeki ise önemli hücresel yaşam azaltabilir numunenin Parçalanmaya büyük bir risk vardır. </li><li> F sonra kuru ürünlerini korumak içinreeze kurutma örnek atmosfer kontrol edilmesi gerekir. Mümkünse vakum dondurarak kurutma döngüsünün sonunda serbest bırakılmadan önce, dondurularak-kurutma örnekleri mühür. Seçenek olarak ise, tercih edilen şişe, atmosfer ile doldurulabilir. Bu depolama atmosferdeki nem ve oksijen mevcut olduğu gibi ortam koşullarına örnekleri maruz kalmasını önlemek için önemli olan hücrelerin hayatta kalma etkileyecektir. </li><li> Şişeleri tartılır. </li></ol> 5. Rehidrasyon <ol><li> Iyonu giderilmiş ve steril su ile örnekleri rehidrate. Ilave edilecek su miktarı, dondurarak kurutma sırasında çıkarılan ve boş bir flakon, dondurarak kurutma öncesi ve sonrası örnek ile aynı flakonun ağırlığı hesaplanır miktarı olarak aynı olmalıdır. Vortex örnekleri şimdi ve sonra tekrar çözümler homojen görünür kadar. </li></ol> 6. Sayım <ol><li> Her bir örnekten 100 ul çizmek ve 10-kat seri dilüsyonları olun. Inte dilüsyonları itibarengeri kalan 100 ul TSA-plakalar üzerinde kaplıdır. Plakalar gerekli olan sıcaklık ve süre inkübe edilir. </li></ol> 7. Donma Davranış formülasyonu karakterizasyonu <ol><li> Küçük bir miktar, Take 5 - 10 mg, örnek ve kapaklı bir DSC-alüminyum tava içine alın. Bir referans olarak boş bir tava hazırlayın. </li><li> DSC sıcaklık tarama programı ayarlayın. Soğutma programı dondurarak kurutma programına dondurma basamağı taklit etmek için ayarlanır. Soğutma kinetik sulu formülasyonların Tg &#39;etkileyebilir olarak bu yapılır. Isıtma tarama de normal olarak incelenmiştir formülasyonların beklenen Tg &#39;, -100 ° C&#39;nin altında bir sıcaklıkta, çökertmek başlamadan önce </li><li> 40 ° C / dak kullanılır - uygun bir ısıtma hızında, 5 normal olarak bir ısıtma hızı seç. Kaydedilen ısı akışı sinyal watt olarak ifade edilir ve ısıtma hızı etkilenir. Daha yüksek ısıtma hızı Tg &#39;daha büyük bir sinyal verecektir. </li><li> Sıcaklık aralığı ayarlayın, böylece it Tg &#39;ve formülasyonun erime kapsar. </li></ol> 8. Sulu Formülasyonlarının Yüzey Gerilimi Ölçümleri <ol><li> Bu deneyde kullanılan deney düzeneği yüzey ölçmek için du Nouy yöntemine göre. </li><li> Dikkatlice platin halkası ve ölçüm kabı temizleyin. Geminin, aseton ile durulanır tüy bırakmayan bir doku ile sildi ve daha sonra renksiz bir alev ile iç yakılır. Halka renksiz bir alev kırmızı renkte yanar. </li><li> Çözüm ile gemi doldurun ve yüzey ölçmeden önce yerleşmek izin. Denge durumu sadece uzun bir süre sonra ulaşıldığında çözümler için, örneğin polimerler, burada kullanılan basit kurulum nitel veriler sağlayacaktır. </li><li> Yüksek viskoziteli,% 2 arasında örneğin, çözeltiler (w / w) olan formülasyonlar için HEC veya HPMC, yüzey gerilimi daha düşük konsantrasyonlarda çözümlerine ölçülmelidir çıkılarak ve daha sonra. Bu gerçeği yararlanarak yapılabilir ki% 0.5 altındaki konsantrasyonlarda (a / a) de yüzey gerilimi seviyeleri kapalı düşüş. </li></ol> 9. Kuru formülasyonlar arasından X-ray Analizi <ol><li> Matris / bakteri az miktarda alın ve bir numune tutucu üzerine yük. </li><li> X-ray difraktometresi içine numune tutucu monte edin. </li><li> Örnek herhangi bir kristal faz analiz etmek üzere Bruker ikinci EVA program paketi kullanılabilir. </li></ol> 10. Elektron Mikroskobu <ol><li> Şişeleri matris / bakteri küçük bir miktar dışarı atın ve bir SEM saplama üzerine sabitleyin. </li><li> Sıçramasına-lak (Bu çalışmada kullanılan Thermo VGScientific Polaron SC7640) ve Au / Pd veya Pt birkaç nm ile kat örnek SEM tutucu yükleyin. Bu deneylerde püskürtme parametreler: Bir ~ 5 için 1.900 V, 20 mA ve 20 sn, - 10 nm Au / Pd kaplama. Kaplama görüntü alımı sırasında elektrik şarj azaltır. Şarj devam ve görüntü neden ise, ince bir kaplama ile başlamak önerilir veeşya, numune tekrar kaplanmalıdır. </li><li> SEM odasında SEM tutucu yükleyin. Uygun görüntüleme parametreleri seçin. Şekil 2 (FEI Strata DB235) kullanılan alet için biz 5 kV hızlandırma gerilimi, spotsize 3, 5 mm ve ikincil elektron dedektörü bir çalışma mesafesi kullanılır. </li><li> İsteğe bağlı olarak, daha fazla ayrıntıları ortaya çıkarmak için, polimer içinde gömülü bakteri çapraz kesitleri için odaklanmış iyon yaygı kullanmak mümkündür. </li></ol>

<ol>
	<li>Wessman, P., Mahlin, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+matrix+properties+on+the+survival+of+freeze-dried+bacteria.">Impact of matrix properties on the survival of freeze-dried bacteria.</a> J. Sci. Food Agric. 91 (14), 2518-2528 (2011).</li><li>Ablett, S., Izzard, M. 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=Differential+Scanning+Calorimetric+Study+of+Frozen+Sucrose+and+Glycerol+Solutions.">Differential Scanning Calorimetric Study of Frozen Sucrose and Glycerol Solutions.</a> Journal of the Chemical Society-Faraday Transactions. 88 (6), 789-794 (1992).</li><li>Knopp, S. A., Chongprasert, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+relationship+between+type+TMDSC+curve+of+frozen+sucrose+solutions+and+collapse+during+freeze-drying.">The relationship between type TMDSC curve of frozen sucrose solutions and collapse during freeze-drying.</a> Journal of Thermal Analysis and Calorimetry. 54 (2), 659-672 (1998).</li><li>Crowe, J. H., Leslie, S. B., 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=Is+Vitrification+Sufficient+to+Preserve+Liposomes+during+Freeze-Drying.">Is Vitrification Sufficient to Preserve Liposomes during Freeze-Drying.</a> Cryobiology. 31 (4), 355-366 (1994).</li><li>Jain, P., Sen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+glass-forming+biopreservatives+on+head+group+rotational+dynamics+in+freeze-dried+phospholipid+bilayers:+A+P-31+NMR+study.">Effect of glass-forming biopreservatives on head group rotational dynamics in freeze-dried phospholipid bilayers: A P-31 NMR study.</a> Journal of Chemical Physics. 131 (2), (2009).</li><li>Stock, J. B., Rauch, B., 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=Periplasmic+Space+in+Salmonella-Typhimurium+and+Escherichia-Coli.">Periplasmic Space in Salmonella-Typhimurium and Escherichia-Coli.</a> Journal of Biological Chemistry. 252 (21), 7850-7861 (1977).</li><li>Crowe, J. H., Hoekstra, F. 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=Anhydrobiosis.">Anhydrobiosis.</a> Annual Review of Physiology. 54, 579-599 (1992).</li><li>Leslie, S. B., Israeli, 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=Trehalose+and+Sucrose+Protect+Both+Membranes+and+Proteins+in+Intact+Bacteria+during+Drying.">Trehalose and Sucrose Protect Both Membranes and Proteins in Intact Bacteria during Drying.</a> Applied and Environmental Microbiology. 61 (10), 3592-3597 (1995).</li><li>Nesarikar, V. V., Nassar, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+cations+and+anions+on+glass+transition+temperatures+in+excipient+solutions.">Effect of cations and anions on glass transition temperatures in excipient solutions.</a> Pharmaceutical Development and Technology. 12 (3), 259-264 (2007).</li><li>You, Y., Ludescher, R. D. <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+sodium+chloride+on+molecular+mobility+in+amorphous+sucrose+detected+by+phosphorescence+from+the+triplet+probe+erythrosin+B.">The effect of sodium chloride on molecular mobility in amorphous sucrose detected by phosphorescence from the triplet probe erythrosin B.</a> Carbohydr. Res. 343 (2), 350-363 (2008).</li><li>Crowe, J. H., Hoekstra, F. A., Nguyen, K. H. N., Crowe, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Is+vitrification+involved+in+depression+of+the+phase+transition+temperature+in+dry+phospholipids.">Is vitrification involved in depression of the phase transition temperature in dry phospholipids.</a> Biochim. Biophys. Acta Biomembr. 1280, 187-196 (1996).</li></ol>

Çıkar çatışması ilan etti.

Bu çalışma için itici dondurarak kurutma sırasında hücre hayatta kalmak için önemli olabilecek bazı formülasyon özellikleri araştırmaktır. Içsel kurutma tolerans farklı türler arasında farklılıklar göstermekle beraber, Şekil 1A, farklı formülasyonları destek hücre sağkalım benzer ne kadar iyi eğilim gösterildiği. Bu sakaroz ve Ficoll bir karşılaştırma ile başlamak bilgilendirici. Bu hücre hayatta kalma desteklemek için bir formülasyon için önemli bir faktördür...

<table border="1">
	<tbody>
		<tr>
			<td>Name of the reagent</td>
			<td>Company</td>
			<td>Catalogue number</td>
			<td>Comments (optional)</td>
		</tr>
		<tr>
			<td>Ficoll PM 400</td>
			<td>GE-healthcare</td>
			<td>17-0300-10</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>HEC (Natrosol-M Pharm Grade)</td>
			<td>Ashland</td>
			<td>&nbsp;</td>
			<td>Gift from Ashland</td>
		</tr>
		<tr>
			<td>HPMC (Methocel F4M)</td>
			<td>Dow</td>
			<td>&nbsp;</td>
			<td>Gift from the Department of Pharmacy, Uppsala University</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma-Aldrich</td>
			<td>S2395</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>71376</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Tryptic Soy broth</td>
			<td>Merck</td>
			<td>105459</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Tryptic Soy Agar</td>
			<td>Merck</td>
			<td>105458</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Lyostar II</td>
			<td>FTS Kinetics</td>
			<td>N.A.</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Pyris Diamond DSC</td>
			<td>Perkin-Elmer</td>
			<td>N.A.</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Bruker AXS SMART CCD 1k Diffractometer</td>
			<td>Bruker</td>
			<td>N.A</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Dual-beam FEI Strata DB235 FIB/SEM</td>
			<td>FEI</td>
			<td>N.A</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Kr&uuml;ss Educational Tensiometer</td>
			<td>Kr&uuml;ss</td>
			<td>N.A.</td>
			<td>&nbsp;</td>
		</tr>
	</tbody>
</table>

formulations for freeze-drying of bacteria and their influence on cell survival

Hücresel su geri dönüşümlü depolama kolaylaştırmak için mikroorganizmaların inaktive kaldırılabilir. Kaldırma Böyle bir yöntem, hafif bir dehidrasyon yöntemi olarak kabul edilir dondurarak kurutma vardır. Kurutma esnasında hücrenin hayatta kalması kolaylaştırmak için, hücreler, genellikle daha önce formüle edilmektedir. Formülasyon hücreleri katıştırır ve dondurma ve kurutma sırasında hücrelerin üzerine uygulanan çeşitli zararlı stresleri koruyan bir matris oluşturur. Burada ve dondurularak kurutulduktan sonra hücrelerin hayatta kalma oranını değerlendirmek için genel bir yöntem sunmak ve dört farklı formülasyonları ile elde edilen sonuçların karşılaştırılması ile de gösterilmiştir: disakarid sukroz, polimer Ficoll PM400 elde sakaroz ve ilgili polisakkaritler, hidroksietil selüloz (HEC iki bakteri suşları, P.) ve hidroksipropil metil selüloz (HPMC), putida KT2440 ve A. chlorophenolicus A6. Bu çalışmada biz dondurarak kurutma için formülasyonları hazırlamak için nasıl ve mekanik araştırmak için nasıl göstermekdiferansiyel taramalı kalorimetre (DSC), yüzey gerilimi ölçümleri, X-ışını analizi ve elektron mikroskobu kullanarak ve sağkalım oranları için bu verileri ilgili formülasyonu karakterize tarafından rehidrasyon sonra hücre canlılığı izm. Polimerler, değişen derecelerde ilgili polisakarit benzeyen sukroz, monomer cinsi bir yapı elde etmek için seçilmiştir. Bu yöntemi kurulum kullanarak biz formülasyonun bazı fiziksel özellikleri 1 kontrol eğer polimerler disakkaritler kadar etkili hücre sağkalım destekleyebilir gösterdi.

Tablo 1, formülasyon bileşimi verileri, dondurulmuş formülasyonları, kuru numune yapısını ve formülasyonun çözümler yüzey gerilimi ısıtma esnasında DSC tarafından kaydedilen ve termal olay gösterir. Sakaroz T g &#39;-40 ° C de 2, 3 ile tespit edilmiştir ve% 20 ağ / ağ aşağıdaki sukroz konsantrasyonu tespit etmek için zor olabilir. -35 ° C termal olay muhtemelen buz 2 çözünme başlangıcı ile ilgilidir. Kristal yapısı HEC ve HPMC ...

Watch this Scientific Journal Video about Formulations for Freeze-drying of Bacteria and Their Influence on Cell Survival at JoVE.com

Formulations for Freeze-drying of Bacteria and Their Influence on Cell Survival

Dondurma-kurutma genellikle canlı bakteri hücrelerinin kuru ürün elde etmek kolay ve kullanışlı bir yoludur. Sürecin bir sorun hücre hayatta kalabilmek. Burada ayrıntılı dondurarak kurutma esnasında hücre hayatta kullanılan formülasyonunun özelliklerini nasıl etkilediğini araştırmak için bir işlem.

Hücre Survival üzerinde Bakteriler ve Etki Dondurma-kurutma için formülasyonlar

Cellular water can be removed to reversibly inactivate microorganisms to facilitate storage. One such method of removal is freeze-drying, which is ...

formulations-for-freeze-drying-bacteria-their-influence-on-cell

Research

JoVE Journal

Biology

23.2K Görüntüleme.  Swedish University of Agricultural Sciences. Dondurma-kurutma genellikle canlı bakteri hücrelerinin kuru ürün elde etmek kolay ve kullanışlı bir yoludur. Sürecin bir sorun hücre hayatta kalabilmek. Burada ayrıntılı dondurarak kurutma esnasında hücre hayatta kullanılan formülasyonunun özelliklerini nasıl etkilediğini araştırmak için bir işlem.

Video: Formulations for Freeze-drying of Bacteria and Their Influence on Cell Survival

Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria

Studies concerning the role of the immune system in mediating molecular signaling between beneficial bacteria and their hosts have, in recent years, made significant contributions to our understanding of the co-evolution of eukaryotes with their microbiota. The symbiotic association between the Hawaiian bobtail squid, Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri has been utilized as a model system for understanding the effects of beneficial bacteria on animal development. Recent studies have shown that macrophage-like hemocytes, the sole cellular component of the squid host's innate immune system, likely play an important role in mediating the establishment and maintenance of this association. This protocol will demonstrate how to obtain hemocytes from E. scolopes and then use these cells in bacterial binding assays. Adult squid are first anesthetized before hemolymph is collected by syringe from the main cephalic blood vessel. The host hemocytes, contained in the extracted hemolymph, are adhered to chambered glass coverslips and then exposed to green fluorescent protein-labeled symbiotic Vibrio fischeri and non-symbiotic Vibrio harveyi. The hemocytes are counterstained with a fluorescent dye (Cell Tracker Orange, Invitrogen) and then visualized using fluorescent microscopy.

Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria

This video will demonstrate how to obtain hemocytes (blood cells) from the Hawaiian bobtail squid, Euprymna scolopes for use in cell biological and bacterial adhesion assays. Hemocytes will be stained with a fluorescent dye and exposed to GFP-labeled bacteria.

Hawaii Bobteylleri Squid Hemocytes Alınması Euprymna scolopes Ve Simbiyotik ve Non-Simbiyotik Bakteriler bağlılık Gözlem

Studies concerning the role of the immune system in mediating molecular signaling between beneficial bacteria and their hosts have, in recent years, made ...

Biyoloji

Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 base pairs of DNA associated with two each of histones H2A, H2B, H3, and H41. The N-terminal tails of histones are rich in lysine and arginine and are modified post-transcriptionally by acetylation, methylation, and other post-translational modifications (PTMs). The PTM configuration of nucleosomes can affect the transcriptional activity of associated DNA, thus providing a mode of gene regulation that is epigenetic in nature 2,3. We developed a method called nucleosome ELISA (NU-ELISA) to quantitatively determine global PTM signatures of nucleosomes extracted from cells. NU-ELISA is more sensitive and quantitative than western blotting, and is useful to interrogate the epiproteomic state of specific cell types. This video journal article shows detailed procedures to perform NU-ELISA analysis.

Nucleosome ELISA (NU-ELISA) is a sensitive and quantitative method to detect global patterns of post-translational modifications in preparations of native, intact nucleosomes. These modifications include methylations, acetylations, and phosphorylations at specific histone amino acid residues, and hence NU-ELISA provides a global proteomic assay of the overall chromatin modification states of specific cell types.

ELISA yöntemi ile yerli bozulmamış nükleozom Post-translasyonel modifikasyonlar Algılama

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 ...

Analyzing the Function of Small GTPases by Microinjection of Plasmids into Polarized Epithelial Cells

Epithelial cells polarize their plasma membrane into biochemically and functionally distinct apical and basolateral domains where the apical domain faces the 'free' surfaces and the basolateral membrane is in contact with the substrate and neighboring cells. Both membrane domains are separated by tight junctions, which form a diffusion barrier. Apical-basolateral polarization can be recapitulated successfully in culture when epithelial cells such as Madin-Darby Canine Kidney (MDCK) cells are seeded at high density on polycarbonate filters and cultured for several days 1 2. Establishment and maintenance of cell polarity is regulated by an array of small GTPases of the Ras superfamily such as RalA, Cdc42, Rab8, Rab10 and Rab13 3 4 5 6 7. Like all GTPases these proteins cycle between an inactive GDP-bound state and an active GTP-bound state. Specific mutations in the nucleotide binding regions interfere with this cycling 8. For example, Rab13T22N is permanently locked in the GDP-form and thus dubbed 'dominant negative', whereas Rab13Q67L can no longer hydrolyze GTP and is thus locked in a 'dominant active' state 7. To analyze their function in cells both dominant negative and dominant active alleles of GTPases are typically expressed at high levels to interfere with the function of the endogenous proteins 9. An elegant way to achieve high levels of overexpression in a short amount of time is to introduce the plasmids encoding the relevant proteins directly into the nuclei of polarized cells grown on filter supports using microinjection technique. This is often combined with the co-injection of reporter plasmids that encode plasma membrane receptors that are specifically sorted to the apical or basolateral domain. A cargo frequently used to analyze cargo sorting to the basolateral domain is a temperature sensitive allele of the vesicular stomatitis virus glycoprotein (VSVGts045) 10. This protein cannot fold properly at 39&deg;C and will thus be retained in the endoplasmic reticulum (ER) while the regulatory protein of interest is assembled in the cytosol. A shift to 31&deg;C will then allow VSVGts045 to fold properly, leave the ER and travel to the plasma membrane 11. This chase is typically performed in the presence of cycloheximide to prevent further protein synthesis leading to cleaner results. Here we describe in detail the procedure of microinjecting plasmids into polarized cells and subsequent incubations including temperature shifts that allow a comprehensive analysis of regulatory proteins involved in basolateral sorting.

This article details the procedures involved in overexpression and analysis of small GTPases in polarized epithelial cells using microinjection technique.

Polarize Epitel Hücreleri içine Plazmidler, Mikroenjeksiyon Küçük GTPases Fonksiyon Analizi

Epithelial cells polarize their plasma membrane into biochemically and functionally distinct apical and basolateral domains where the apical domain faces ...

Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation between cells within a tissue. Isolation of pure cardiomyocyte populations through a collagenase perfusion of mouse hearts facilitates the generation of single cell microarrays for whole transcriptome gene expression, or qPCR of specific targets using nanofluidic arrays. We describe here a procedure to examine single cell gene expression profiles of cardiomyocytes isolated from the heart. This paradigm allows for the evaluation of metrics of interest which are not reliant on the mean (for example variance between cells within a tissue) which is not possible when using conventional whole tissue workflows for the evaluation of gene expression (Figure 1). We have achieved robust amplification of the single cell transcriptome yielding micrograms of double stranded cDNA that facilitates the use of microarrays on individual cells. In the procedure we describe the use of NimbleGen arrays which were selected for their ease of use and ability to customize their design. Alternatively, a reverse transcriptase - specific target amplification (RT-STA) reaction, allows for qPCR of hundreds of targets by nanofluidic PCR. Using either of these approaches, it is possible to examine the variability of expression between cells, as well as examining expression profiles of rare cell types from within a tissue. Overall, the single cell gene expression approach allows for the generation of data that can potentially identify idiosyncratic expression profiles that are typically averaged out when examining expression of millions of cells from typical homogenates generated from whole tissues.

Single cell expression profiling allows the detailed gene expression analysis of individual cells. We describe methods for the isolation of cardiomyocytes, and preparing the resulting lysates for either whole transcriptome microarray or qPCR of specific targets.

Yetişkin Fare kardiyomiyositlerde Tek Hücre transkripsiyonel Profilleme

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation ...

Isolation and Culture of Individual Myofibers and their Satellite Cells from Adult Skeletal Muscle

Muscle regeneration in the adult is performed by resident stem cells called satellite cells. Satellite cells are defined by their position between the basal lamina and the sarcolemma of each myofiber. Current knowledge of their behavior heavily relies on the use of the single myofiber isolation protocol. In 1985, Bischoff described a protocol to isolate single live fibers from the Flexor Digitorum Brevis (FDB) of adult rats with the goal to create an in vitro system in which the physical association between the myofiber and its stem cells is preserved 1. In 1995, Rosenblattmodified the Bischoff protocol such that myofibers are singly picked and handled separately after collagenase digestion instead of being isolated by gravity sedimentation 2, 3. The Rosenblatt or Bischoff protocol has since been adapted to different muscles, age or conditions 3-6. The single myofiber isolation technique is an indispensable tool due its unique advantages. First, in the single myofiber protocol, satellite cells are maintained beneath the basal lamina. This is a unique feature of the protocol as other techniques such as Fluorescence Activated Cell Sorting require chemical and mechanical tissue dissociation 7. Although the myofiber culture system cannot substitute for in vivo studies, it does offer an excellent platform to address relevant biological properties of muscle stem cells. Single myofibers can be cultured in standard plating conditions or in floating conditions. Satellite cells on floating myofibers are subjected to virtually no other influence than the myofiber environment. Substrate stiffness and coating have been shown to influence satellite cells' ability to regenerate muscles 8, 9 so being able to control each of these factors independently allows discrimination between niche-dependent and -independent responses. Different concentrations of serum have also been shown to have an effect on the transition from quiescence to activation. To preserve the quiescence state of its associated satellite cells, fibers should be kept in low serum medium 1-3. This is particularly useful when studying genes involved in the quiescence state. In serum rich medium, satellite cells quickly activate, proliferate, migrate and differentiate, thus mimicking the in vivo regenerative process 1-3. The system can be used to perform a variety of assays such as the testing of chemical inhibitors; ectopic expression of genes by virus delivery; oligonucleotide based gene knock-down or live imaging. This video article describes the protocol currently used in our laboratory to isolate single myofibers from the Extensor Digitorum Longus (EDL) muscle of adult mice (6-8 weeks old).

Isolation and culture of myofibers is the gold standard in vitro system to study the transition of satellite cells through quiescence, activation and differentiation. Importantly, the single myofiber culture system preserves the myofiber/stem cell association, which is an essential component of the muscle stem cell niche.

Yetişkin İskelet Kası gelen bireysel Myofibers ve Uydu Hücre İzolasyonu ve Kültür

Muscle  regeneration in the adult is performed by resident stem cells called satellite  cells. Satellite cells are defined by  their position between the ...

Strategies for Tracking Anastasis, A Cell Survival Phenomenon that Reverses Apoptosis

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important checkpoints of apoptosis, including mitochondrial fragmentation, release of mitochondrial cytochrome c into the cytosol, activation of caspases, chromatin condensation, DNA damage, nuclear fragmentation, plasma membrane blebbing, cell shrinkage, cell surface exposure of phosphatidylserine, and formation of apoptotic bodies. Anastasis can occur when apoptotic stimuli are removed prior to death, thereby allowing dying cells to reverse apoptosis and potentially other death mechanisms. Therefore, anastasis appears to involve physiological healing processes that could also sustain damaged cells inappropriately. The functions and mechanisms of anastasis are still unclear, hampered in part by the limited tools for detecting past events after the recovery of apparently healthy cells. Strategies to detect anastasis will enable studies of the physiological mechanisms, the hazards of undead cells in disease pathology, and potential therapeutics to modulate anastasis. Here, we describe effective strategies using live cell microscopy and a mammalian caspase biosensor&#160;for identifying and tracking anastasis in mammalian cells.

The term anastasis refers to the phenomenon in which dying cells reverse a cell suicide process at a late stage, repair themselves, and ultimately survive. Here we demonstrate protocols for detecting and tracking cells that undergo anastasis.

Takip inişi, Apoptosisi tersine Cep Survival Fenomeni için Stratejiler

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important ...

A Standardized Method for the Analysis of Liver Sinusoidal Endothelial Cells and Their Fenestrations by Scanning Electron Microscopy

Liver sinusoidal endothelial cells are the gateway to the liver, their transcellular fenestrations allow the unimpeded transfer of small and dissolved substances from the blood into the liver parenchyma for metabolism and processing. Fenestrations are dynamic structures - both their size and/or number can be altered in response to various physiological states, drugs, and disease, making them an important target for modulation. An understanding of how LSEC morphology is influenced by various disease, toxic, and physiological states and how these changes impact on liver function requires accurate measurement of the size and number of fenestrations. In this paper, we describe scanning electron microscopy fixation and processing techniques used in our laboratory to ensure reproducible specimen preparation and accurate interpretation. The methods include perfusion fixation, secondary fixation and dehydration, preparation for the scanning electron microscope and analysis. Finally, we provide a step by step method for standardized image analysis which will benefit all researchers in the field.

The fenestrated liver sinusoidal endothelial cell is a biologically important filter system that is highly influenced by various diseases, toxins, and physiological states. These changes significantly impact on liver function. We describe methods for the standardisation of the measurement of the size and number of fenestrations in these cells.

Taramalı Elektron Mikroskobu Karaciğer Sinüs Endotel Hücreleri Analizi ve Bunların fenestrasyonlar için Standart Yöntemi

Liver sinusoidal endothelial cells are the gateway to the liver, their transcellular fenestrations allow the unimpeded transfer of small and dissolved ...

Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions

Rotifers are microscopic cosmopolitan zooplankton used as models in ecotoxicological and aging studies due to their several advantages such as short lifespan, ease of culture, and parthenogenesis that enables clonal culture. However, caution is required when measuring their survival time as it is affected by maternal age and maternal feeding conditions. Here we provide a protocol for powerful and reproducible measurement of the survival time in Brachionus rotifers following a careful synchronization of culture conditions over several generations. Empirically, poor synchronization results in early mortality and a gradual decrease in survival rate, thus resulting in weak statistical power. Indeed, under such conditions, calorie restriction (CR) failed to significantly extend the lifespan of B. plicatilis although CR-induced longevity has been demonstrated with well-synchronized rotifer samples in past and present studies. This protocol is probably useful for other invertebrate models, including the fruitfly Drosophila melanogaster and the nematode Caenorhabditis elegans, because maternal age effects have also been reported in these species.

Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions

Rotifers are microscopic zooplankton used as models in ecotoxicological and aging studies. Here we provide a protocol for powerful and reproducible measurement of survival time in Brachionus rotifers. Synchronization of culture conditions over several generations is of particular importance because maternal condition affects life history of offspring.

Hayatta kalma Süre deneyinde<em&gt; Brachionus</em&gt; Rotiferler: Maternal Koşullarının Senkronizasyon

Rotifers are microscopic cosmopolitan zooplankton used as models in ecotoxicological and aging studies due to their several advantages such as short ...

Investigating the Detrimental Effects of Low Pressure Plasma Sterilization on the Survival of Bacillus subtilis Spores Using Live Cell Microscopy

Plasma sterilization is a promising alternative to conventional sterilization methods for industrial, clinical, and spaceflight purposes. Low pressure plasma (LPP) discharges contain a broad spectrum of active species, which lead to rapid microbial inactivation. To study the efficiency and mechanisms of sterilization by LPP, we use spores of the test organism Bacillus subtilis because of their extraordinary resistance against conventional sterilization procedures. We describe the production of B. subtilis spore monolayers, the sterilization process by low pressure plasma in a double inductively coupled plasma reactor, the characterization of spore morphology using scanning electron microscopy (SEM), and the analysis of germination and outgrowth of spores by live cell microscopy. A major target of plasma species is genomic material (DNA) and repair of plasma-induced DNA lesions upon spore revival is crucial for survival of the organism. Here, we study the germination capacity of spores and the role of DNA repair during spore germination and outgrowth after treatment with LPP by tracking fluorescently-labelled DNA repair proteins (RecA) with time-resolved confocal fluorescence microscopy. Treated and untreated spore monolayers are activated for germination and visualized with an inverted confocal live cell microscope over time to follow the reaction of individual spores. Our observations reveal that the fraction of germinating and outgrowing spores is dependent on the duration of LPP-treatment reaching a minimum after 120 s. RecA-YFP (yellow fluorescence protein) fluorescence was detected only in few spores and developed in all outgrowing cells with a slight elevation in LPP-treated spores. Moreover, some of the vegetative bacteria derived from LPP-treated spores showed an increase in cytoplasm and tended to lyse. The described methods for analysis of individual spores could be exemplary for the study of other aspects of spore germination and outgrowth.

Investigating the Detrimental Effects of Low Pressure Plasma Sterilization on the Survival of Bacillus subtilis Spores Using Live Cell Microscopy

This protocol illustrates the important consecutive steps required to assess the relevance of monitoring vitality parameter and DNA repair processes in reviving Bacillus subtilis spores after treatment with low pressure plasma by tracking fluorescence-labelled DNA repair proteins via time-resolved confocal microscopy and scanning electron microscopy.

Zararlı etkileri, düşük basınç plazma sterilizasyon Bacillus subtilis sporlar kullanarak canlı cep mikroskobu sağkalıma soruşturma

Plasma sterilization is a promising alternative to conventional sterilization methods for industrial, clinical, and spaceflight purposes. Low pressure ...

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Post-translational modification (PTM) of protein lysine residues by N&#400;-acylation induces structural changes that can dynamically regulate protein functions, for example, by changing enzymatic activity or by mediating interactions. Precise quantification of site-specific protein acylation occupancy, or stoichiometry, is essential for understanding the functional consequences of both global low-level stoichiometry and individual high-level acylation stoichiometry of specific lysine residues. Other groups have reported measurement of lysine acetylation stoichiometry by comparing the ratio of peptide precursor isotopes from endogenous, natural abundance acylation and exogenous, heavy isotope-labeled acylation introduced after quantitative chemical acetylation of proteins using stable isotope-labeled acetic anhydride. This protocol describes an optimized approach featuring several improvements, including: (1) increased chemical acylation efficiency, (2) the ability to measure protein succinylation in addition to acetylation, and (3) improved quantitative accuracy due to reduced interferences using fragment ion quantification from data-independent acquisitions (DIA) instead of precursor ion signal from data-dependent acquisition (DDA). The use of extracted peak areas from fragment ions for quantification also uniquely enables differentiation of site-level acylation stoichiometry from proteolytic peptides containing more than one lysine residue, which is not possible using precursor ion signals for quantification. Data visualization in Skyline, an open source quantitative proteomics environment, allows for convenient data inspection and review. Together, this workflow offers unbiased, precise, and accurate quantification of site-specific lysine acetylation and succinylation occupancy of an entire proteome, which may reveal and prioritize biologically relevant acylation sites.

Here, we present unbiased quantification of site-specific protein acetylation and/or succinylation occupancy (stoichiometry) of an entire proteome through a ratiometric analysis of endogenous modifications to modifications introduced after quantitative chemical acylation using stable isotope-labeled anhydrides. In combination with sensitive data-independent acquisition mass spectrometry, accurate site occupancy measurements are obtained.

Siteye özel Protein lizin asetilasyon ve Succinylation veri bağımsız edinme kütle spektrometresi kullanılarak Stoichiometry miktar

Post-translational modification (PTM) of protein lysine residues by N&#400;-acylation induces structural changes that can dynamically regulate protein ...