Bu çalışma NIH R01 GM47607, CA163296 ve CET NSF 1334493 tarafından desteklenmektedir. Biz yazının eleştirel okuma Turner laboratuar üyelerine teşekkür ediyorum. Bu raporda gösterilen tüm veriler Wormer ve ark., 2014 11 izni ile yeniden üretildi.

Durotaxis Chambers hazırlanması 1. <ol><li> Bir 6-yuvalı doku kültürü plakası hazırlanması için, 50 ml konik tüp ile denge dara. 50-ml tüp PDMS baz çözeltisi yaklaşık 10 gr tartılır (çözüm oldukça viskoz). </li><li> 90: 1 substrat (~ 1 kPa Uyum), gerekli çapraz bağlayıcı çözeltisinin doğru miktarını belirlemek için 90 ile tüp içinde PDMS baz çözeltisi ölçülen kilo bölün. Aynı tüp PDMS çapraz bağlayıcı çözeltisi hesaplanan miktar ekleyin. Örnek: 10 g / 90 = 0.11 g. PDMS baz çözeltisine PDMS çapraz bağlayıcı çözeltisi 0.11 g ekleyin. NOT: Baz ve çapraz bağlayıcı çözümleri hem PDMS kit sağlanmaktadır. </li><li> Şiddetle küçük bir spatula kullanılarak oda sıcaklığında 5 dakika boyunca PDMS baz / çapraz bağlayıcı karışımı karıştırın. Bu aşamada kanşım hava kabarcıkları çok sayıda içerir. </li><li> Bub çıkarmak için oda sıcaklığında 50 x g&#39;de 5 dakika boyunca, bir tezgah üstü santrifüj içinde PDMS substratı santrifüjbles. Varsa hala tekrar 5 dakika, santrifüj sonra kabarcıklar. </li><li> 90 pipetle 1 ml: Doku kültürü her oyuğuna 1 PDMS alt-tabaka 6 oyuklu plaka işlemden geçirildi. PDMS mevcut olan herhangi bir geri kalan hava kabarcıkları, bir 21 G iğnesi kullanılarak bunları haşhaş bu aşamada elimine edilebilir. PDMS oyuk 30 dakika boyunca yaymak için izin verir. </li><li> Kaynama 12 mm cam # 5 dakika için damıtılmış su içinde 1 lamelleri. Iki kez tekrarlanır ve damıtılmış su içinde lamelleri saklayın. </li><li> Yavaşça PDMS üzerine lamel damla PDMS çözeltisi içine lamel bir tarafını dokunarak doku kültür plakasının her bir oyuğuna, bir kurutulmuş, lamel yerleştirin. Lamel yerleşir gibi, PDMS lamel kenarları boyunca tecâvüz başlayacak, ama tamamen kapsayacak olmaz. Bu (B Şekil 1A bakınız) sertleştikten sonra PDMS ve cam arasında bir arayüz oluşturur. </li><li> PDMS tedavi (sertleşmesine) 16 saat için bir fırın içinde 70 ° C &#39;de plaka inkübe edin. Plat yerleştirinBir hücre kültürü kaputu ve UV e 10 dakika süreyle sterilize edin. NOT: Bu kullanım bir kaç gün içinde plakaları yapmak en iyisidir. Bununla birlikte, levha Herhangi bir tampon maddesi olmadan Parafilm ile sarılmış ve kalitede herhangi bir fark azalma olmadan, 2 hafta boyunca 4 ° C&#39;de muhafaza edilebilir. </li></ol> 2. Hücre Ekimi NOT: siRNA aracılı demonte etkisini inceleyerek varsa, üreticinin talimatlarına veya seçim hücre tipi için optimize edilmiş protokolü kullanılarak demonte gerçekleştirin. <ol><li> Kaplama, her 37 ° C &#39;de 1 saat süre ile, kalsiyum ve magnezyum olmaksızın / ml fibronektin PBS içinde 10 ug 1 ml bölmeyi durotaxis. Seçenek olarak ise, fibronektin, 4 ° C&#39;de 16 saat boyunca / ml fibronektin PBS içinde 10 ug PDMS inkübe ile analizden önce gün tatbik edilebilir. Tüm yüzey PBS çözüm fibronektin batmış olduğundan emin olun. </li><li> Isı ile denatüre edilmiş,% 1 BSA hazırlayın. 0,5 g BSA tartılır ve 50 ml PBS içinde çözülür.Filtre 12 dakika boyunca 80 ° C &#39;de, 0.22 um&#39;lik bir filtreden ve ısı yoluyla çözüm sterilize edin. Not: Bu çözüme 4 ° C&#39;de kaplama ve mağaza hücre öncesinde güne hazırlayın. </li><li> Fibronektin solüsyonu aspire edildi ve PBS ile 3 kez yıkayın. Her bir oyuğa, PBS içinde ısı ile denatüre BSA 1 ml ilave edilir ve oda sıcaklığında 30 dakika inkübe edilir. </li><li> Durotaxis odaları ısı denatüre BSA ile bloke ederken Trypsinize ve seçim hücreleri saymak. </li><li> Levha seçim, belirli bir hücre tipi için gerekli ortam kullanılarak durotaxis bölmesinin her bir kuyunun içine 2 ml lik bir hacim içinde, 1 x 10 5 hücre. Hücreler uygun ve% 5 CO2 ile 37 ° C &#39;de nemlendirilmiş bir kuluçka makinesi içinde 4 saat süre ile alt-tabaka üzerinde yayılmasına izin verir. Not: U2OS hücreleri rutin 2 mM L-glutamin, 1 mM sodyum piruvat ve 10 lU / ml penisilin, 10 ug / ml streptomisin ile takviye edilmiş,% 10 FBS bulunan DMEM içerisinde muhafaza edilir. NOT: Bu örnekte kullanılan hücre sayısı için optimize edilmiştirU2OS hücreleri. Diğer hücre türleri için optimizasyon gerekebilir. Bu yoğunluk hücreleri, diğer hücrelerle önemli etkileşimler olmadan geçirmek için yeterli oda verir. </li></ol> 3. Canlı hücre Görüntüleme <ol><li> 10X amacı ile faz kontrast kullanarak, ters bir mikroskop canlı hücre görüntüleme gerçekleştirin. Mikroskop, uzun vadeli görüntüleme sırasında 37 ° C sıcaklığın kontrol edilmesi ve% 5 CO2 sağlayan kapalı bir çevre, nemli bir bölmede ile donatılmış olmalıdır. </li><li> Hücreler yaklaşık 3.5 saat boyunca yayıldı sonra, mikroskop odasında plaka monte edin. Örnek (ler) 30 dakika boyunca oda içinde dengelenmeye bırakın. </li><li> Varsa mikroskop ziyaret otomatik, çok noktalı ayarlayın. 90 arasındaki arayüze odaklanın: 1 PDMS ve cam lamel ve tüm durotaxis odasına başına 40 sayılık bir ortalama ile arayüzü etrafında görüntü noktaları seçin. Resim hücreleri kadar 16 saat boyunca her 10 dakikada bir. NOT: Yenidenilgi gion lamel kenarı ve PDMS ve kapak arasında fiili bir arayüz karşılık gelen iç hat karşılık gelen dış hat ile, iki çizgi olarak görünür. Şekil 1B bakınız. </li></ol> 4. Veri Analizi <ol><li> Tablo 1 deki gibi bir elektronik tablo oluşturur. </li><li> Üretilen her film cam yüzey ve tersi PDMS gelen geçiş olaylarının sayısını. Excel uygun sütununda geçiş olaylarının numarasını kaydedin. NOT: Bir geçiş olayı her iki yönde PDMS ile cam arasındaki sınır üzerinden geçen hücre çekirdeğinde olarak tanımlanır. </li><li> Birden geçişleri ölçmek için, hücre arayüzü geçti sayısını saymak. Bu sayı, hücre filmin sonunda yer edildiği yüzeye karşılık gelen excel sütunda kayıt altına alınmalıdır. T arayüzü haçlar her hücre için analiz tekrarlayınO film. Görüntüleme sırasında görüş alanının dışına göç hücreleri hariç. NOT: Bu hücrelerin fibronektin kaplı PDMS ve cam lamel yüzeylerine eşit olarak yapışır mümkün olduğunu, denemenin başında sayma hücre tarafından, doğrulamak için de önemlidir. </li><li> Cam yüzey (yani, durotaxis yapıldı) için PDMS göç hücrelerinin yüzdesini hesaplayın. Yumuşak sert ve geçiş olaylarının toplam sayısına göre sert ve bölmek tarihinde sona eren birden geçiş olaylara olayları kapısı sayısını ekleyin. </li><li> Geçitlerin toplam sayısına göre birden geçişleri sayısına bölünmesiyle birden geçişleri yüzdesini hesaplayın. </li></ol>

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The authors have no conflicts to disclose.

Bu yazıda hücrelerin taşınmasıyla durotaxis incelemek için basit bir tahlil açıklar. Bu deneyde önemli bir gücü PDMS kullanarak durotaxis odaları hazırlamak kolaylığıdır. Alt-tabakaların sertliği, kolayca deneyinde, çeşitli katılıklarının bir çalışma sağlamak için bir çapraz bağlayıcı PDMS baz çözeltisi oranı değiştirilerek kontrol edilebilir. Ancak, sistemin bir potansiyel sınırlama daha sofistike sistemlerin 4 tarafından sağlanan bir sertlik degrade yaşandığı k...

Hücre dışı matris (ECM), kolajen, fibronektin ve laminin gibi yapısal ve çapraz bağlama proteinlerinin karmaşık bir dizi oluşur. De ECM hücre dokular için önemli bir yapısal destek sağlar tespit edilmesine rağmen, hücreler aktif olarak, hücre hayatta kalması, farklılaşma ve hücre göçü de dahil olmak üzere çok çeşitli hücresel işlemleri düzenleyen kendi ECM ortamında fiziksel değişikliklere yanıt olduğunu belirtmek için artan kanıtlar vardır. Sert (~ 25 kPa) yüzeyler osteojenik farklılaşma 1 teşvik Örneğin, ECM sertlik farklılıklar yumuşak yüzeylerde (~ 1 kPa) nörojenik soy teşvik ile, farklı soy karşı mezenkimal kök hücrelerin sürebilirim. Benzer şekilde, stromal matrisi katılıkta bir artış çevre doku 2,3 halinde meme epitelyal hücre tümörogenez ve işgali teşvik ettiği gösterilmiştir. Bu mechanosign için özellikle ilginç bir yönüHücreler daha sert bir alt-tabaka 4,5 doğru tercihli olarak göç ettiği durotaxis olarak bilinen bir işlemde aling etki gösterir. Hücreler sürekli ECM bağlanarak integrin reseptörü yoluyla hücre dışı ortamın fiziksel özelliklerini hissederler. Bu da, fokal yapışmalarda ve fokal temas 6,7 olarak bilinen yapıştırma yapıların oluşumunu sürücü sitoplazmik alanlarında çok sayıda yapısal ve sinyal proteinlerinin birikimi teşvik eder. Integrinlerinin hiçbir doğasında enzimatik aktiviteye sahip olduğundan, sinyaller değişen çevre 8 hücrenin yanıtı koordine etmek, bu aksesuar proteinleri aracılığıyla ECM&#39;den aktarılmaktadır. Buna göre, mechanosignaling ve durotaxis düzenleyen kilit rol oynayan proteinlerin belirlenmesi ve karakterizasyonu araştırılması gereken önemli bir alandır. Çeşitli model sistemler durotaxis in vitro incelemek için geliştirilmiştir, ancak çoğu varkullanılan kollajen kaplı poliakrilamid yüzeyler 4. Bununla birlikte, poliakrilamid substratlar hazırlanması teknik olarak zor olabilir ve bu deneylerde kullanılan kollajen alt-tabaka 9 kimyasal olarak çapraz bağlanmış olması gerekir. Polidimetilsiloksan (PDMS) alt-tabakalar poliakrilamid alt tabakalar 10 için karşılaştırılabilir mekanik özellikler göstermektedir gösterilmiştir. Bununla birlikte, alt-tabakalar, sadece çapraz bağlayıcı madde PDMS bazın bir karıştırma oranı ile hazırlanabilir ve bu alt-tabakalar bu şekilde PDMS hücre davranışı üzerindeki sertlik etkilerini incelemek için daha kolay bir araç yapan kimyasal çapraz bağlama için gerek kalmadan ECM proteinleri ile kaplanabilir. Bu yazıda, yumuşak bir PDMS substrat sert cam lamel ile entegre edildiği bir basit durotaxis odasını nasıl hazırlanacağını açıklar. Deney aşağıda açıklandığı gibi, durotaxis incelemek için hızlı ve basit bir yöntem temin etmektedir. Bu çalışma için siRNA aracılı ile birlikte, insan osteosarkoma hücreleri kullanılır U2OScdGAP demonte durotaxis 11 bu fokal yapışma proteininin rolünü araştırmak için. Önemli olarak, bu protokol, kolaylıkla kişisel gereksinimlere uyarlanabilir. Diğer hücre tipleri U2OS hücreleri için ikame edilebilir ve herhangi bir protein düşürülmüş olup durotaxis sırasında hücre davranışı üzerindeki etkilerini belirlemek için aşırı ifade edilebilir. Ayrıca, bu protokol dinamiklerini ve davranışları kullanılarak sıkı bağlamak ya da yaklaşımlar FRET analizi, floresan etiketli proteinler dahil adapte edilebilir.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Polydimethylsiloxane (PDMS)</td>
			<td>Dow Corning</td>
			<td>3097358-1004</td>
			<td>Sylgard 184 Silicone Elastomer Kit</td>
		</tr>
		<tr>
			<td>#1 Cover glass 12mm</td>
			<td>Fisher Scientific</td>
			<td>12-545-82</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well plate</td>
			<td>Celltreat</td>
			<td>229106</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Cellgro</td>
			<td>15-017-CM</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>Cellgro</td>
			<td>25-005-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Pyruvate</td>
			<td>Fisher Scientific</td>
			<td>BP356-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>Cellgro</td>
			<td>30-002-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>Fibronectin</td>
			<td>BD Biosciences</td>
			<td>610077</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Invitrogen</td>
			<td>21600-044</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon tubes</td>
			<td>Celltreat</td>
			<td>229456</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Atlanta Biologicals</td>
			<td>S11150</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Sigma</td>
			<td>A7906</td>
			<td></td>
		</tr>
		<tr>
			<td>U2OS cells</td>
			<td>ATCC</td>
			<td>HTB-96</td>
			<td></td>
		</tr>
	</tbody>
</table>

a simplified system for evaluating cell mechanosensing and durotaxis in vitro

Ekstraselüler matriks kompozisyonu ve mekanik özellikleri, doku tipleri arasında oldukça değişkendir. Bu bağ dokusu stroma ölçüde çeşitlilik etkileri, hücre davranış hücre çoğalması, farklılaşması, yapışma sinyalizasyon ve yön göç de dahil olmak üzere, normal ve patolojik süreçleri düzenler. Bu bağlamda, bazı hücre tiplerinin doğal yeteneğini durotaxis olarak ifade edilir, bir katı ya da daha az uyumlu bir matriks substrat tabakasına doğru göç. Bu olgu, embriyonik gelişim, yara iyileşmesi ve kanser hücresi yayılımını tamamen sırasında önemli bir rol oynar. Burada, polidimetilsiloksan (PDMS) alt tabakalar kullanarak, in vitro olarak durotaxis çalışma için basit bir deney tarif eder. Odaları durotaxis tarif hazırlanması nispeten yumuşak PDMS jel ve katı bir cam lamel arasında bir sertlik arabirimi oluşturur. Verilen örnekte, cdc42 bir rol göstermek için bu durotaxis odaları kullandık / Rac1 GTPaz aktive protecdGAP bölgesi, mechanosensing ve insan U2OS osteosarkoma hücrelerinde durotaxis düzenlenmesinde. Bu deney, mechanosignaling ve durotaxis bunların rollerini araştırmak için başka hücre tipleri ve / veya önemli diğer proteinlerin demonte kolaylıkla uyarlanabilir.

Durotaxis bölmesinin şematik Şekil 1A &#39;de gösterilmiştir. Yumuşak PDMS alt-tabaka (90: çözüm çapraz bağlayıcı PDMS baz 1 karışımı) 6 iyi bir çanak içinde yayılır ve bir cam lamel böylece bir ara yüzey oluşturarak, daha sonra kısmen lamel üst yüzeyini kaplayan PDMS, üst üste yerleştirilir Farklı uyum iki alt tabaka arasında yer almaktadır. Yumuşak PDMS alt-tabakanın sertliği cam sertliği yaklaşık GPa&#39;dır 01-02 Ocak iken, beyin dokusu tipik bir uy...

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A Simplified System for Evaluating Cell Mechanosensing and Durotaxis In Vitro

Many mammalian cells preferentially migrate towards a more rigid matrix or substrate through durotaxis. The goal of this protocol is to provide a simple in vitro system that can be used to study and manipulate cell durotaxis behaviors by incorporating polydimethylsiloxane (PDMS) substrates of defined rigidity, interfacing with glass coverslips.

Değerlendirilmesi Hücre Mechanosensing ve Durotaxis için Basitleştirilmiş Sistemi<em&gt; İn Vitro</em

The composition and mechanical properties of the extracellular matrix are highly variable between tissue types. This connective tissue stroma diversity ...

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Biology

A Simplified System for Evaluating Cell Mechanosensing and Durotaxis In Vitro

8.1K Görüntüleme.  SUNY Upstate Medical University. Many mammalian cells preferentially migrate towards a more rigid matrix or substrate through durotaxis. The goal of this protocol is to provide a simple in vitro system that can be used to study and manipulate cell durotaxis behaviors by incorporating polydimethylsiloxane (PDMS) substrates of defined rigidity, interfacing with glass coverslips.

Video: A Simplified System for Evaluating Cell Mechanosensing and Durotaxis In Vitro

Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences

The completion of the human genome sequence, along with that of many other species, has highlighted the challenge of ascribing specific function to non coding sequences. One prominent function carried out by the non coding fraction of the genome is to regulate gene transcription; however, there are no effective methods to broadly predict cis-regulatory elements from primary DNA sequence. We have developed an efficient protocol to functionally evaluate potential cis-regulatory elements through zebrafish transgenesis. Our approach offers significant advantages over cell-culture based techniques for developmentally important genes, since it provides information on spatial and temporal gene regulation. Conversely, it is faster and less expensive than similar experiments in transgenic mice, and we routinely apply it to sequences isolated from the human genome. Here we demonstrate our approach to selecting elements for testing based on sequence conservation and our protocol for cloning sequences and microinjecting them into zebrafish embryos.

We demonstrate our approach to finding potential enhancer elements from developmentally regulated genes and evaluating their function through mosaic zebrafish transgenesis.

Mozaik Zebra balığı Transgenesis Enhancer Diziler değerlendirilmesi için

The completion of the human genome sequence, along with that of many other species, has highlighted the challenge of ascribing specific function to non ...

Biyoloji

Efficient Derivation of Human Cardiac Precursors and Cardiomyocytes from Pluripotent Human Embryonic Stem Cells with Small Molecule Induction

To date, the lack of a suitable human cardiac cell source has been the major setback in regenerating the human myocardium, either by cell-based transplantation or by cardiac tissue engineering1-3. Cardiomyocytes become terminally-differentiated soon after birth and lose their ability to proliferate. There is no evidence that stem/progenitor cells derived from other sources, such as the bone marrow or the cord blood, are able to give rise to the contractile heart muscle cells following transplantation into the heart1-3. The need to regenerate or repair the damaged heart muscle has not been met by adult stem cell therapy, either endogenous or via cell delivery1-3. The genetically stable human embryonic stem cells (hESCs) have unlimited expansion ability and unrestricted plasticity, proffering a pluripotent reservoir for in vitro derivation of large supplies of human somatic cells that are restricted to the lineage in need of repair and regeneration4,5. Due to the prevalence of cardiovascular disease worldwide and acute shortage of donor organs, there is intense interest in developing hESC-based therapies as an alternative approach. However, how to channel the wide differentiation potential of pluripotent hESCs efficiently and predictably to a desired phenotype has been a major challenge for both developmental study and clinical translation. Conventional approaches rely on multi-lineage inclination of pluripotent cells through spontaneous germ layer differentiation, resulting in inefficient and uncontrollable lineage-commitment that is often followed by phenotypic heterogeneity and instability, hence, a high risk of tumorigenicity6-8 (see a schematic in Fig. 1A). In addition, undefined foreign/animal biological supplements and/or feeders that have typically been used for the isolation, expansion, and differentiation of hESCs may make direct use of such cell-specialized grafts in patients problematic9-11. To overcome these obstacles, we have resolved the elements of a defined culture system necessary and sufficient for sustaining the epiblast pluripotence of hESCs, serving as a platform for de novo derivation of clinically-suitable hESCs and effectively directing such hESCs uniformly towards clinically-relevant lineages by small molecules12 (see a schematic in Fig. 1B). After screening a variety of small molecules and growth factors, we found that such defined conditions rendered nicotinamide (NAM) sufficient to induce the specification of cardiomesoderm direct from pluripotent hESCs that further progressed to cardioblasts that generated human beating cardiomyocytes with high efficiency (Fig. 2). We defined conditions for induction of cardioblasts direct from pluripotent hESCs without an intervening multi-lineage embryoid body stage, enabling well-controlled efficient derivation of a large supply of human cardiac cells across the spectrum of developmental stages for cell-based therapeutics.

We have established a protocol for induction of cardioblasts direct from pluripotent human embryonic stem cells maintained under defined conditions with small molecules, which enables derivation of a large supply of human cardiac progenitors and functional cardiomyocytes for cardiovascular repair.

Küçük Molekül İndüksiyon Pluripotent İnsan Embriyonik Kök Hücreleri İnsan Kardiyak Öncüleri ve kardiyomiyositlerde Verimli türetilmesi

To date, the lack of a suitable human cardiac cell source has been the major setback in regenerating the human myocardium, either by cell-based ...

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated tools and resources for studies in this system are facilitating continued discovery of genes with more subtle phenotypes or roles. 
Here we present a generalized protocol we adapted for identifying C. elegans genes with postembryonic phenotypes of interest using RNAi2. This procedure is easily modified to assay the phenotype of choice, whether by light or fluorescence optics on a dissecting or compound microscope. This screening protocol capitalizes on the physical assets of the organism and molecular tools the C. elegans research community has produced. As an example, we demonstrate the use of an integrated transgene that expresses a fluorescent product in an RNAi screen to identify genes required for the normal localization of this product in late stage larvae and adults. First, we used a commercially available genomic RNAi library with full-length cDNA inserts. This library facilitates the rapid identification of multiple candidates by RNAi reduction of the candidate gene product. Second, we generated an integrated transgene that expresses our fluorecently tagged protein of interest in an RNAi-sensitive background. Third, by exposing hatched animals to RNAi, this screen permits identification of gene products that have a vital embryonic role that would otherwise mask a post-embryonic role in regulating the protein of interest. Lastly, this screen uses a compound microscope equipped for single cell resolution.

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

We describe a sensitized method to identify postembryonic regulators of protein expression and localization in C. elegans using an RNAi-based genomic screen and an integrated transgene that expresses a functional, fluorescently tagged protein.

Içinde Postembryonic Fenotiplerin Belirleme RNAi Tarama C. elegans</em

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated ...

Do-It-Yourself Device for Recovery of Cryopreserved Samples Accidentally Dropped into Cryogenic Storage Tanks

Liquid nitrogen is colorless, odorless, extremely cold (-196 &deg;C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term storage of biological materials such as blood, cells and tissues 1,2. The cryogenic nature of liquid nitrogen, while ideal for sample preservation, can cause rapid freezing of live tissues on contact - known as 'cryogenic burn'2, which may lead to severe frostbite in persons closely involved in storage and retrieval of samples from Dewars. Additionally, as liquid nitrogen evaporates it reduces the oxygen concentration in the air and might cause asphyxia, especially in confined spaces2.
In laboratories, biological samples are often stored in cryovials or cryoboxes stacked in stainless steel racks within the Dewar tanks1. These storage racks are provided with a long shaft to prevent boxes from slipping out from the racks and into the bottom of Dewars during routine handling. All too often, however, boxes or vials with precious samples slip out and sink to the bottom of liquid nitrogen filled tank. In such cases, samples could be tediously retrieved after transferring the liquid nitrogen into a spare container or discarding it. The boxes and vials can then be relatively safely recovered from emptied Dewar. However, the cryogenic nature of liquid nitrogen and its expansion rate makes sunken sample retrieval hazardous. It is commonly recommended by Safety Offices that sample retrieval be never carried out by a single person. Another alternative is to use commercially available cool grabbers or tongs to pull out the vials3. However, limited visibility within the dark liquid filled Dewars poses a major limitation in their use.
In this article, we describe the construction of a Cryotolerant DIY retrieval device, which makes sample retrieval from Dewar containing cryogenic fluids both safe and easy.

Here we present a low cost, durable cryotolerant device for sample retrieval from Dewar tanks filled with liquid nitrogen. The ease of construction and modular design of the device makes the process of sample retrieval from cryogenic tanks safe and easy.

KRİYOPREZERVE Numune Kurtarma için Do-It-Yourself Aygıt yanlışlıkla Kriyojenik Depolama Tankları içine Dropped

Liquid nitrogen is colorless, odorless, extremely cold (-196 &deg;C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term ...

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the messagefor review see 1. However, it's now widely accepted that synonymous codon usage is the primary cause of non-uniform translational elongation rates1. Synonymous codons are not used with identical frequency. A bias exists in the use of synonymous codons with some codons used more frequently than others2. Codon bias is organism as well as tissue specific2,3. Moreover, frequency of codon usage is directly proportional to the concentrations of cognate tRNAs4. Thus, a frequently used codon will have higher multitude of corresponding tRNAs, which further implies that a frequent codon will be translated faster than an infrequent one. Thus, regions on mRNA enriched in rare codons (potential pause sites) will as a rule slow down ribosome movement on the message and cause accumulation of nascent peptides of the respective sizes5-8. These pause sites can have functional impact on the protein expression, mRNA stability and protein foldingfor review see 9. Indeed, it was shown that alleviation of such pause sites can alter ribosome movement on mRNA and subsequently may affect the efficiency of co-translational (in vivo) protein folding1,7,10,11. To understand the process of protein folding in vivo, in the cell, that is ultimately coupled to the process of protein synthesis it is essential to gain comprehensive insights into the impact of codon usage/tRNA content on the movement of ribosomes along mRNA during translational elongation.
Here we describe a simple technique that can be used to locate major translation pause sites for a given mRNA translated in various cell-free systems6-8. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA. The rationale is that at low-frequency codons, the increase in the residence time of the ribosomes results in increased amounts of nascent peptides of the corresponding sizes. In vitro transcribed mRNA is used for in vitro translational reactions in the presence of radioactively labeled amino acids to allow the detection of the nascent chains. In order to isolate ribosome bound nascent polypeptide complexes the translation reaction is layered on top of 30% glycerol solution followed by centrifugation. Nascent polypeptides in polysomal pellet are further treated with ribonuclease A and resolved by SDS PAGE. This technique can be potentially used for any protein and allows analysis of ribosome movement along mRNA and the detection of the major pause sites. Additionally, this protocol can be adapted to study factors and conditions that can alter ribosome movement and thus potentially can also alter the function/conformation of the protein.

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.

Ribozom Bağlı Doğan Polipeptitler İzolasyonu<em&gt; In vitro</em&gt; MRNA boyunca Translasyonel Duraklat Siteleri Belirleme

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

In vitro Cell Migration and Invasion Assays

Migration is a key property of live cells and critical for normal development, immune response, and disease processes such as cancer metastasis and inflammation. Methods to examine cell migration are very useful and important for a wide range of biomedical research such as cancer biology, immunology, vascular biology, cell biology and developmental biology. Here we use tumor cell migration and invasion as an example and describe two related assays to illustrate the commonly used, easily accessible methods to measure these processes. The first method is the cell culture wound closure assay in which a scratch is generated on a confluent cell monolayer. The speed of wound closure and cell migration can be quantified by taking snapshot pictures with a regular inverted microscope at several time intervals. More detailed cell migratory behavior can be documented using the time-lapse microscopy system. The second method described in this paper is the transwell cell migration and invasion assay that measures the capacity of cell motility and invasiveness toward a chemo-attractant gradient. It is our goal to describe these methods in a highly accessible manner so that the procedures can be successfully performed in research laboratories even just with basic cell biology setup.

In vitro Cell Migration and Invasion Assays

Commonly used, highly accessible methods for examining cell migration and invasion in vitro are described. The first method is the cell wound closure assay that measures cell motility. The second method is the transwell migration and invasion assay that assesses the chemotactic and invasive capacity of cells.

Vitro Hücre Göç ve Invasion Tahliller

Migration is a key property of live cells and critical for normal development, immune response, and disease processes such as cancer metastasis and ...

Assaying Proteasomal Degradation in a Cell-free System in Plants

The ubiquitin-proteasome pathway for protein degradation has emerged as one of the most important mechanisms for regulation of a wide spectrum of cellular functions in virtually all eukaryotic organisms. Specifically, in plants, the ubiquitin/26S proteasome system (UPS) regulates protein degradation and contributes significantly to development of a wide range of processes, including immune response, development and programmed cell death. Moreover, increasing evidence suggests that numerous plant pathogens, such as Agrobacterium, exploit the host UPS for efficient infection, emphasizing the importance of UPS in plant-pathogen interactions.
The substrate specificity of UPS is achieved by the E3 ubiquitin ligase that acts in concert with the E1 and E2 ligases to recognize and mark specific protein molecules destined for degradation by attaching to them chains of ubiquitin molecules. One class of the E3 ligases is the SCF (Skp1/Cullin/F-box protein) complex, which specifically recognizes the UPS substrates and targets them for ubiquitination via its F-box protein component. To investigate a potential role of UPS in a biological process of interest, it is important to devise a simple and reliable assay for UPS-mediated protein degradation. Here, we describe one such assay using a plant cell-free system. This assay can be adapted for studies of the roles of regulated protein degradation in diverse cellular processes, with a special focus on the F-box protein-substrate interactions.

Targeted protein degradation represents a major regulatory mechanism for cell function. It occurs via a conserved ubiquitin-proteasome pathway, which attaches polyubiquitin chains to the target protein that then serve as molecular &#8220;tags&#8221; for the 26S proteasome. Here, we describe a simple and reliable cell-free assay for proteasomal degradation of proteins.

Bitkilerde bir Cell-serbest Sistemde proteozomal indirgenme Assaying

The ubiquitin-proteasome pathway for protein degradation has emerged as one of the most important mechanisms for regulation of a wide spectrum of cellular ...

One-channel Cell-attached Patch-clamp Recording

Ion channel proteins are universal devices for fast communication across biological membranes. The temporal signature of the ionic flux they generate depends on properties intrinsic to each channel protein as well as the mechanism by which it is generated and controlled and represents an important area of current research. Information about the operational dynamics of ion channel proteins can be obtained by observing long stretches of current produced by a single molecule. Described here is a protocol for obtaining one-channel cell-attached patch-clamp current recordings for a ligand gated ion channel, the NMDA receptor, expressed heterologously in HEK293 cells or natively in cortical neurons. Also provided are instructions on how to adapt the method to other ion channels of interest by presenting the example of the mechano-sensitive channel PIEZO1. This method can provide data regarding the channel&#8217;s conductance properties and the temporal sequence of open-closed conformations that make up the channel&#8217;s activation mechanism, thus helping to understand their functions in health and disease.

Described here is a procedure for obtaining long stretches of current recording from one ion channel with the cell-attached patch-clamp technique. This method allows for observing, in real time, the pattern of open-close channel conformations that underlie the biological signal. These data inform about channel properties in undisturbed biological membranes.

Tek kanallı bir hücre-bağlı Patch-clamp kayıt

Ion channel proteins are universal devices for fast communication across biological membranes. The temporal signature of the ionic flux they generate ...

Quantitation of Endothelial Cell Adhesiveness In Vitro

One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen of the blood vessel to the surrounding tissue. This occurs when endothelial cells, which line blood vessels, become adhesive to circulating immune cells such as monocytes. In vitro measurement of this adhesiveness has until now been done by quantifying the total number of monocytes that adhere to an endothelial layer either as a direct count or by indirect measurement of the fluorescence of adherent monocytes. While such measurements do indicate the average adhesiveness of the endothelial cell population, they are confounded by a number of factors, such as cell number, and do not reveal the proportion of endothelial cells that are actually adhesive. Here we describe and demonstrate a method which allows the enumeration of adhesive cells within a tested population of endothelial monolayer. Endothelial cells are grown on glass coverslips and following desired treatment are challenged with monocytes (that may be fluorescently labeled). After incubation, a rinsing procedure, involving multiple rounds of immersion and draining, the cells are fixed. Adhesive endothelial cells, which are surrounded by monocytes are readily identified and enumerated, giving an adhesion index that reveals the actual proportion of endothelial cells within the population that are adhesive.

Quantitation of Endothelial Cell Adhesiveness In Vitro

We report an in vitro method that allows the quantitation of the actual number of adhesive cells within an endothelial cell monolayer.

Endotel Hücre yapışma miktarının belirlenmesi<em&gt; In Vitro</em

One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen of the blood vessel to the surrounding tissue. This ...

A Protocol for Laboratory Housing of Turquoise Killifish (Nothobranchius furzeri)

The development of husbandry practices in non-model laboratory fish used for experimental purposes has greatly benefited from the establishment of reference fish model systems, such as zebrafish and medaka. In recent years, an emerging fish &#8211; the turquoise killifish (Nothobranchius furzeri) &#8211; has been adopted by a growing number of research groups in the fields of biology of aging and ecology. With a captive life span of 4 - 8 months, this species is the shortest-lived vertebrate raised in captivity and allows the scientific community to test &#8211; in a short time &#8211; experimental interventions that can lead to alterations of the aging rate and life expectancy. Given the unique biology of this species, characterized by embryonic diapause, explosive sexual maturation, marked morphological and behavioral sexual dimorphism - and their relatively short adult life span -&#160;ad hoc husbandry practices are in urgent demand. This protocol reports a set of key husbandry measures that allow optimal turquoise killifish laboratory care, enabling the scientific community to adopt this species as a powerful laboratory animal model.

A Protocol for Laboratory Housing of Turquoise Killifish Nothobranchius furzeri

Laboratory housing of turquoise killifish can be scaled up&#160;to house and efficiently raise thousands of individual fish in a centralized water filtration system, employing the same infrastructure used for standard zebrafish facilities. Here we detail a list of standardized procedures that allow efficient killifish maintenance.