Biz Seth Darst RNAP ve MFD proteinler ve ifade vektörleri sağlamak için özellikle teşekkür ediyoruz. Ayrıca, teknik destek Greb ve Dan Zhang sağlamak için Sergei Borukhov teşekkür ediyoruz. Bu çalışma, Sağlık (MOD) National Institutes hibe ve Marie-josee ve Rockefeller Üniversitesi (RTP) Henry Kravis Bursu tarafından desteklenmiştir.

Bu yöntem bildirilen araştırmada kullanılan <a href="http://www.sciencemag.org/cgi/content-nw/full/327/5965/590/F3">Pomerantz ve O&#39;Donnell, Science 327, 590-592 (2010)</a> . 1. Durdurulmuş RNAP uzama kompleksi Meclisi şu şekilde yapıldı: E. 500 nM nihai konsantrasyonu coli RNAP HE 100 A (20 mM Tris-Cl (pH 7.5), 8 mM MgCl 2, 0.5 mM EDTA, 5 tampon ul T7A1 organizatörü içeren bir biotinlenmiş 3.6 kb DNA örneğinin 5 nM nihai konsantrasyonu ile karışık 70 σ 10 dk 37 mM DTT,% 10 gliserol) ° C. APU ve her biri 40 mcM, GTP, ATP ve CTP 100 mcM 37 ek bir 10 dakika ° C eklendi 2. Streptavidin boncuk üzerine durduruldu RNAP uzama kompleksi immobilizasyonu şu şekilde yapıldı: 200 ul streptavidin kaplı manyetik boncuk (Invitrogen) Yukarıdaki reaksiyon oda sıcaklığında 10 dakika ilave edildi. 3. Immobilize durduruldu RNAP uzama kompleksi Arıtma şu şekilde yapıldı: Boncuk tampon 0.9 ml A içeren 0.75 M NaCl, 200 mg / ml heparin ve 20 mg / ml Sonraki ssDNA (süpernatant manyetik ayırma her yıkama adımdan sonra kaldırıldı.), (Yukarıda) ile 5 kez yıkandı boncuk, 2 kez 0.9 ml tampon A. ile yıkandı 4. Baş-on RNAP şu şekilde yapılmıştır downstream göreceli bir replikasyon çatal Oluşumu ° C, boncuk (yukarıda) New England Biolabs tampon 4 ve Sap (New England Biolabs) 10 adet 100 ul yeniden süspanse 37 10 dakika eklendi. Boncuk 0.9 ml tampon A ile 3 kez yıkanır ve ardından Hızlı T4 ligasyon reaksiyon tamponu (New England Biolabs) 50 ul yeniden süspanse edildi. Hızlı T4 ligaz (New England Biolabs) 2 ul oda sıcaklığında 10 dakika için ön tav-çatallı DNA 6 nM final konsantrasyonu (RP10, RP22, RP25) ile birlikte eklendi. Boncuk 0.9 ml tampon A. ile 3 kez yıkandı 5. Çoğaltma çatal önde gelen iplikçik sentez replisome ve inisiyasyon Kurul şu şekilde yapıldı: Tampon boncuk 150 ul 448 pmol DnaB (hexamer gibi) ile inkübe edildi (20 mM Tris-Cl (pH 7.5), 8 mM MgCl 2, 0.5 mM EDTA, 5 mM DTT,% 10 gliserol) az 30 s 23 ° C Pol III 4.9 pmol * (Pol III HE eksi β), 15 pmol β, 2 mM ATP ve her biri 60 mcM dGTP ve dATP hacmi 200 ul eklenir ve 37 az bir 5 dakika daha ° C inkübe edildi Çoğaltma ile birlikte 10 mg SSB ve her biri 24 mcM dATP ve dTTP ekleyerek üzerine başlatılan [α-32 P] dTTP ve [α-32 P] dCTP (spesifik aktivite, 3.000-5.000 cpm / pmol) son hacmi 250 mcL. Reaksiyonları 12 ul 500 mM EDTA ekleyerek üzerine 10 dakika sonra sona erdirildi. 6. Arıtma ve radyo-işaretli DNA ürünlerin konsantrasyonu şu şekilde yapıldı: Reaksiyon boncuk DNA kaldırmak için sona erdirildi sonra boncuk (yukarıda) kaynatılır. 50 - 30 dk 10 ul hacmi proteinaz K ile boncuk tedavi ° C boncuklar bağlı kalan herhangi bir kalıntı DNA tarafından kaldırıldı Boncuk sonra kaynatılmış ve manyetik ayırma süpernatantı tarafından kaldırıldı. DNA içeren kombine süpernatant Qiagen PCR Temizleme kiti kullanarak saflaştırılmış. Saf radyo-işaretli DNA ürünleri daha sonra alkali agaroz jel analiz edildi. * Baş RNAP uzama kompleksi yukarıdaki gibi yapıldı durdurdu, ancak σ 70 yokluğunda Çoğaltma atlandı. Temsilcisi Sonuçlar: Çarpışma ile replisome bir baş-RNAP genellikle 2,5 kb ve uzunluğu 3,6 kb iki ürün ile sonuçlanır. 2,5 kb ürün durduruldu RNAP ve RNAP ile çarpışması üzerine durdurduklarını replisome sonuçları çatal DNA uzunluğu temsil eder. 3.6 kb ürün eksik RNAP organizatörü doluluk veya kısmi replisome baş RNAP salt yoluyla tam uzunlukta DNA ve sonuçları temsil eder. Iyi ya da doğru bir sonucu, yaklaşık% 50 tam uzunlukta DNA olduğunu göstermektedir. Ancak, bazı durumlarda RNAP organizatörü az doluluk oluşur ve daha yüksek bir yüzdesi tam uzunlukta DNA replisomes daha büyük bir nüfus beri gözlemlenen bir baş-RNAP karşılaşma yok. Sadece tam uzunlukta DNA (3.6 kb) durduruldu RNAP sonuçları yokluğunda Çoğaltma. <img src="/files/ftp_upload/1919/1919fig1.jpg" alt="Şekil 1" /> Şekil. 1 replisome baş RNAP engellemektedir. (A) Deneysel kurulum. A E. coli RNAP durduruldu uzama kompleks, daha önce açıklandığı gibi T7A1 organizatörü (9) içeren bir biotinlenmiş DNA üzerine monte edildi . Kısaca, durdurulmuş bir uzama kompleksi APU, GTP, ATP ve CTP bir 10 dakika daha ilave edilerek 10 dakika için biotinlenmiş DNA ile RNAP holoenzyme kuluçka organizatörü 20 bps downstream kuruldu. Streptavidin boncuk boncuk 0.75 m NaCl, 200 mg / ml heparin içeren ve 100 nM tek iplikli DNA kararsız RNAP-DNA kompleksleri ve aşırı UTP&#39;larının kaldırmak için 0.9 ml tampon beş kez yıkandı ek bir 10 dakika ilave edildi . DNA sonra Sapi ile sindirilmiş, yıkanmış ve bir ön tav-çatallı DNA bağlandı oldu. Boncuk replisome montaj öncesinde tekrar yıkandı. (B) DnaB sonra replisome toplandı eklendi ve çoğaltma ya varlığında başlatılan (şeritli 2) veya yokluğu (şeritli 1) organizatörü çatal 2,5 kb bulunan ve çatal yönelik doğrudan transkripsiyon yönelik. baş üzerinde RNAP.

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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+DNA+repair:+two+decades+of+progress+and+surprises.">Transcription-coupled DNA repair: two decades of progress and surprises.</a> Science. 266, 1957-1957 (1994).</li><li>Selby, C. P., Sancar, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+repair+and+human+disease.">Transcription-coupled repair and human disease.</a> J Biol Chem. 270, 4882-4882 (1995).</li><li>Liu, B., Alberts, B. 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Çamaşır durduruldu uzama kompleksi yüksek tuz ile boncuklar bağlı herhangi bir dengesiz veya non-spesifik bağlı RNAP molekülleri kaldırmak için kritik öneme sahiptir. RNAP astar şablon türü DNA yapıları için son derece yüksek bir afinitesi vardır. Bu nedenle, astar şablon çoğaltma gerçekleştirmek için, non-spesifik RNAP-DNA kompleksleri kaldırmak için gereklidir. Qiagen PCR saflaştırma kiti kullanılarak, radyo-işaretli DNA ürünler Yoğunlaştırmalı jel görülebilir, yeterince yüksek bir radyoaktif sinyal elde etmek için de kritik öneme sahiptir.

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<td>Dynabeads M-270</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
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<td>SapI</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>R0569S</td>
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<td>T4 Quick Ligase</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>M2200S</td>
<td>&nbsp;</td>
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<td>PCR Purification Kit</td>
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<td>Qiagen</td>
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direct restart of a replication fork stalled by a head-on rna polymerase

In vivo çalışmalarda çoğaltma çatal ile baş-transkripsiyon kompleksleri nedeniyle karşılaşmalar tutuklandı olduğunu düşündürmektedir. Ancak, replisome ve RNA polimeraz (RNAP) kaderi şu kafa kafaya çarpışmada bilinmiyor. Burada bulduğumuz E. replisome tezgahları ile çarpışması üzerine coli baş-transkripsiyon kompleksi, ama yerine çöken, çoğaltma çatal son derece kararlı kalır ve sonunda DNA RNAP yerinden sonra uzama devam eder. Biz transkripsiyon-onarım bağlantı faktörü, MFD, çatal RNAP yerinden kolaylaştırarak çarpışma sonucu doğrudan yeniden teşvik olduğunu da bulabilirsiniz. Bu bulgular içsel istikrar ve çoğaltma cihazı RNAP blok geçmiş çoğaltma teşvik transkripsiyon birleştiğinde onarım yolu için yeni bir rol göstermektedir.

Watch this Scientific Journal Video about Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase at JoVE.com

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Bir çarpışma replisome kaderi ile baş-RNA polimeraz (RNAP) bilinmiyor. Biz DNA RNAP yerinden sonra uzama replisome baş RNAP ile çarpışması üzerine tezgahları, ancak devam eder ki bulabilirsiniz. MFD çarpışmadan sonra RNAP yerinden kolaylaştırarak çoğaltma işlemini yeniden başlatın teşvik etmektedir.

Head-On RNA Polimeraz Stalled Çoğaltma Fork Doğrudan yeniden başlatın

In vivo studies suggest that replication forks are arrested due to encounters with head-on transcription complexes. Yet, the fate of the replisome and RNA ...

direct-restart-replication-fork-stalled-head-on-rna

Research

JoVE Journal

Biology

13.5K Görüntüleme.  Rockefeller University. Bir çarpışma replisome kaderi ile baş-RNA polimeraz (RNAP) bilinmiyor. Biz DNA RNAP yerinden sonra uzama replisome baş RNAP ile çarpışması üzerine tezgahları, ancak devam eder ki bulabilirsiniz. MFD çarpışmadan sonra RNAP yerinden kolaylaştırarak çoğaltma işlemini yeniden başlatın teşvik etmektedir.

Video: Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Production of Replication-Defective Retrovirus by Transient Transfection of 293T cells

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, Bcr-PDGFR&#945;, etc.). We are able to model and study a human-like disease in our mouse model, by transplanting bone marrow cells previously infected with a retrovirus expressing the oncogene of interest. Replication-defective retrovirus encoding a human oncogene and a marker (GFP, RFP, antibiotic resistance gene, etc.) is produced by a transient transfection protocol using 293T cells, a human renal epithelial cell line transformed by the adenovirus E1A gene product. 293 cells have the unusual property of being highly transfectable by calcium phosphate (CaPO4), with up to 50-80% transfection efficiency readily attainable. Here, we co-transfect 293 cells with a retroviral vector expressing the oncogene of interest and a plasmid that expresses the gag-pol-env packaging functions, such as the single-genome packaging constructs kat or pCL, in this case the EcoPak plasmid. The initial transfection is further improved by use of chloroquine. Stocks of ecotropic virus, collected as culture supernatant 48 hrs. post-transfection, can be stored at -80&deg;C and used for infection of cell-lines in view of transformation and in vitro studies, or primary cells such as mouse bone marrow cells, that can then be used for transplant in our mouse model.

This technique demonstrates an efficient way to prepare replication-defective retroviral stocks encoding a human oncogene, and subsequently used for induction of myeloproliferative disease in the mouse model.

293T hücreleri geçici Transfeksiyon Çoğaltma-Arızalı Retrovirus Üretimi

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, ...

Biyoloji

Derivation of Human Embryonic Stem Cells by Immunosurgery

The ability of human embryonic stem cells to self-renew and differentiate into all cell types of 
the body suggests that they hold great promise for both medical applications and as a research 
tool for addressing fundamental questions in development and disease. Here, we provide a 
concise, step-by-step protocol for the derivation of human embryonic stem cells from embryos 
by immunosurgical isolation of the inner cell mass. 


The ability of human embryonic stem cells to self-renew and differentiate into all cell types of 
the body suggests that they hold great promise for both medical applications and as a research 
tool for addressing fundamental questions in development and disease. Here, we provide a 
concise, step-by-step protocol for the derivation of human embryonic stem cells from embryos 
by immunosurgical isolation of the inner cell mass.

Immunosurgery İnsan Embriyonik Kök Hücreleri türetilmesi

The ability of human embryonic stem cells to self-renew and differentiate into all cell types of 
the body suggests that they hold great promise for both ...

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.


This protocol demonstrates a simple single-molecule fluorescence microscopy technique for visualizing DNA replication by individual replisomes in real time.

Floresan Mikroskop ile görselleştirme Tek molekül DNA replikasyonu

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA ...

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. Linearized &lambda; DNA is modified to have a biotin on the end of one strand, and a digoxigenin moiety on the other end of the same strand. The biotinylated end is attached to a functionalized glass coverslip and the digoxigeninated end to a small bead. The assembly of these DNA-bead tethers on the surface of a flow cell allows a laminar flow to be applied to exert a drag force on the bead. As a result, the DNA is stretched close to and parallel to the surface of the coverslip at a force that is determined by the flow rate (Figure 1). The length of the DNA is measured by monitoring the position of the bead. Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. Measuring the position of the bead allows precise determination of the rates and processivities of DNA unwinding and polymerization (Figure 2).

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system.

Enzimlerin Klonlanması DNA Doğrudan Gözlem Tek bir molekülü DNA Testi Esneme

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. ...

Visualizing RNA Localization in Xenopus Oocytes

RNA localization is a conserved mechanism of establishing cell polarity. Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to spatially restrict gene expression of Vg1 protein. Tight control of Vg1 distribution in this manner is required for proper germ layer specification in the developing embryo. RNA sequence elements in the 3' UTR of the mRNA, the Vg1 localization element (VLE) are required and sufficient to direct transport. To study the recognition and transport of Vg1 mRNA in vivo, we have developed an imaging technique that allows extensive analysis of trans-factor directed transport mechanisms via a simple visual readout. 
To visualize RNA localization, we synthesize fluorescently labeled VLE RNA and microinject this transcript into individual oocytes. After oocyte culture to allow transport of the injected RNA, oocytes are fixed and dehydrated prior to imaging by confocal microscopy. Visualization of mRNA localization patterns provides a readout for monitoring the complete pathway of RNA transport and for identifying roles in directing RNA transport for cis-acting elements within the transcript and trans-acting factors that bind to the VLE (Lewis et al., 2008, Messitt et al., 2008). We have extended this technique through co-localization with additional RNAs and proteins (Gagnon and Mowry, 2009, Messitt et al., 2008), and in combination with disruption of motor proteins and the cytoskeleton (Messitt et al., 2008) to probe mechanisms underlying mRNA localization.

Visualizing RNA Localization in Xenopus Oocytes

Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy.

Görselleştirme RNA Yerelleştirme Xenopus Oosit

RNA localization is a conserved mechanism of establishing cell polarity.  Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to ...

Direct Delivery of MIF Morpholinos Into the Zebrafish Otocyst by Injection and Electroporation Affects Inner Ear Development

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the eye, brain, and somites of zebrafish. The advantage of electroporation over other methods of genetic manipulation is that specific tissues can be targeted, both spatially and temporally, for the introduction of macromolecules by the application of electrical current. Here we describe the use of electroporation for transfecting mif and mif-like morpholinos into the tissues of the developing inner ear of the zebrafish. In past studies, mif morpholino injected into embryos at the 1- to 8-cell stage resulted in widespread morphological changes in the nervous system and eye, as well as the ear. By targeting the tissues of the inner ear at later stages in development, we can determine the primary effects of MIF in the developing inner ear, as opposed to secondary effects that may result from the influence of other tissues. By using phalloidin and acetylated tubulin staining to study the morphology of neurons, neuronal processes, and hair cells associated with the posterior macula, we were able to assess the efficacy of electroporation as a method for targeted transfection in the zebrafish inner ear. The otic vesicles of 24hpf embryos were injected with morpholinos and electroporated and were then compared to embryos that had received no treatment or had been only injected or electroporated. Embryos that were injected and electroporated showed a decrease in hair cell numbers, decreased innervation by the statoacoustic ganglion (SAG) and fewer SAG neurons compared with control groups. Our results showed that direct delivery of morpholinos into otocysts at later stages avoids the non-specific nervous system and neural crest effects of morpholinos delivered at the 1-8 cell stage. It also allows examination of effects that are directed to the inner ear and not secondary effects on the ear from primary effects on the brain, neural crest or periotic mesenchyme.

A method to deliver morpholinos directly into the zebrafish otocyst at 24hpf has been developed. Using microinjection of morpholinos into the lumen of otic vesicle and electroporation to effect penetration, we were able to bypass the effect of morpholinos on the brain and obtain effects specific to the inner ear.

Enjeksiyon ve Elektroporasyon Zebra balığı Otocyst içine MIF Morpholinos Stoktan teslim İç Kulak Geliştirme etkiler

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the ...

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

HeLa Hücre Transfeksiyon Ardından Gaussia Lusiferaz mRNA in vitro transkripsiyon ve Kapatma yılında

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Marine elasmobranchs are valued animal models for biomedical and genomic studies as they are the most primitive vertebrates to have adaptive immunity and have unique mechanisms for osmoregulation 1-3. As the most primitive living jawed-vertebrates with paired appendages, elasmobranchs are an evolutionarily important model, especially for studies in evolution and development. Marine elasmobranchs have also been used to study aquatic toxicology and stress physiology in relationship to climate change 4. Thus, development and adaptation of methodologies is needed to facilitate and expand the use of these primitive vertebrates to multiple biological disciplines. Here I present the successful adaptation of RNA whole mount in situ hybridization and histological techniques to study gene expression and cell histology in elasmobranchs.
Monitoring gene expression is a hallmark tool of developmental biologists, and is widely used to investigate developmental processes 5. RNA whole mount in situ hybridization allows for the visualization and localization of specific gene transcripts in tissues of the developing embryo. The expression pattern of a gene's message can provide insight into what developmental processes and cell fate decisions a gene may control. By comparing the expression pattern of a gene at different developmental stages, insight can be gained into how the role of a gene changes during development.
While whole mount in situ's provides a means to localize gene expression to tissue, histological techniques allow for the identification of differentiated cell types and tissues. Histological stains have varied functions. General stains are used to highlight cell morphology, for example hematoxylin and eosin for general staining of nuclei and cytoplasm, respectively. Other stains can highlight specific cell types. For example, the alcian blue stain reported in this paper is a widely used cationic stain to identify mucosaccharides. Staining of the digestive tract with alcian blue can identify the distribution of goblet cells that produce mucosaccharides. Variations in mucosaccharide constituents on short peptides distinguish goblet cells by function within the digestive tract 6. By using RNA whole mount in situ's and histochemical methods concurrently, cell fate decisions can be linked to gene-specific expression.
Although RNA in situ's and histochemistry are widely used by researchers, their adaptation and use in marine elasmobranchs have met limited and varied success. Here I present protocols developed for elasmobranchs and used on a regular basis in my laboratory. Although further modification of the RNA in situ's hybridization method may be needed to adapt to different species, the protocols described here provide a strong starting point for researchers wanting to adapt the use of marine elasmobranchs to their scientific inquiries.

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

By combining methods for RNA whole mount in situ hybridization and histology, gene expression can be linked with cell fate decisions in the developing embryo. These methods have been adapted to marine elasmobranchs and facilitate the use of these animals as model organisms for biomedical, toxicology and comparative studies.

RNA<em&gt; Yerinde</emTüm Dağı Embriyolar ve Hücre histolojisi&gt; Hibridizasyon Deniz Elasmobranchs İçin Uyarlanmış

Marine  elasmobranchs are valued animal models for biomedical and genomic studies as  they are the most primitive vertebrates to have adaptive immunity ...

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.

We report a procedure to isolate RNA with high integrity from the ribonuclease rich mouse pancreas.

Fare pankreasından alınan RNA İzolasyonu: A Ribonuclease zengin Doku

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge.  As a primary function of the pancreas is to aid ...

Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Provided is a protocol for developing a real-time recombinase polymerase amplification assay to quantify initial concentration of DNA samples using either a thermal cycler or a microscope and stage heater. Also described is the development of an internal positive control. Scripts are provided for processing raw real-time fluorescence data.

İç Pozitif Kontrol ile Kantitatif Recombinase Polimeraz Amplifikasyon Testi Geliştirme

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...