This work benefited from the networking activities coordinated within the EU-funded COST ACTION FA1106 "An integrated systems approach to determine the developmental mechanisms controlling fleshy fruit quality in tomato and grapevine". This work was supported by the 'Completamento del Centro di Genomica Funzionale Vegetale' project funded by the CARIVERONA Bank Foundation and by the 'Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto)' project funded by the Italian Ministry of Agricultural and Forestry Policies. SDS was financed by the Italian Ministry of University and Research FIRB RBFR13GHC5 project "The Epigenomic Plasticity of Grapevine in Genotype per Environment Interactions".

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The authors have nothing to disclose.

Bu makalede, üzüm dut terroir kavramını yorumlamak için kullanılan metabolomik, transkriptomik ve istatistiksel analiz protokollerini açıklar. HPLC-ESI-MS ile metabolomik analiz aynı anda metabolitleri çok sayıda algılamak için yeterince duyarlı olmakla birlikte, göreceli kantitatif matris etkisi ve iyon bastırma / geliştirme etkilenir. Ancak, benzer bir yaklaşım zaten Corvina çilek olgunlaşmasını ve hasat sonrası soldurma tanımlamak için kullanılır olmuştur, ve matriks etkileri düzeltme so...

Bitkilerin genomları, transcriptomes, proteomlarda ve metabolomes dayalı büyük ölçekli veri analizi gibi asma bitkileri ve çevreleri arasındaki etkileşimleri yansıtan şarap terroir özellikleri gibi karmaşık sistemlerin, davranış içine görülmemiş fikir verir. aynı asma klonlar farklı bağlarında yetiştirilen bile bir şarap terroir farklı olabilir çünkü klonal genomları aynıdır, çünkü genomik analiz edilmesi bir fayda sağlamaz. Bunun yerine gen ifadesinin ve şarap kalitesi özelliklerini belirlemek çilek, metabolik özellikler arasındaki ilişkilere bakmak gerekir. mikrodiziler üzerinde immobilize problara hibridizasyon gibi olduğu genel özelliklerini kullanmak kantitatif analiz kolaylaştıran her transkript, benzer kimyasal özelliklere gelen transcriptome yararları seviyesinde gen ekspresyonunun analizi. proteomik A aksine, genel analitik yöntemlernd metabolomik nedeniyle bireysel protein ve metabolitleri büyük fiziksel ve kimyasal çeşitliliğin daha zordur. metabolomik durumunda bireysel metabolitleri boyutu, polarite, bolluk ve volatilitenin çok farklı olduğundan bu çeşitlilik daha aşırı, bu yüzden tek bir ekstraksiyon işlemi ya da analitik yöntem bütünsel bir yaklaşım sunuyor. uçucu olmayan metabolitler için uygun bir analitik platformlar arasında, yüksek performanslı sıvı kromatografisi dayananlar kütle spektrometrisi bağlanmış (HPLC-MS) çok daha hassas ultraviyole veya diyot dizi dedektörü ile HPLC (HPLC-UV, HPLC-DAD olarak alternatiflere göre ) ya da HPLC-MS ile nükleer manyetik rezonans (NMR) spektroskopi ancak kantitatif analiz, matris etki ve iyon bastırma / iyileştirme 1-3 fenomenler etkilenebilir. (HPLC-E elektrosprey iyonizasyon kaynağı kullanılarak HPLC-MS ile Corvina üzüm meyveleri analiz sırasında bu tür etkilerin incelenmesiSI-MS), düşük tutma süreleri ile şekerler ve diğer moleküller güçlü bir şekilde belki de bu bölgede molekül çok sayıda yansıtan yetersiz olarak gösterdi, ve diğer moleküllerin bolluğu matrisi etkisiyle fazla veya etkilenmez, küçümsenmeyecek ki ancak matris etkisi için veri normalleşme genel sonuçları 4,5&#39;ten üzerinde sınırlı bir etkisi var gibiydi. Burada tarif edilen yöntem, olgunlaşma sırasında üzüm meyveleri içinde yüksek seviyelerde birikmesine orta kutup Metabolitlerin analiz edilmesi için optimize edilir ve bu önemli ölçüde terroir etkilenmektedir. Birlikte renk, tat ve şarap sağlıkla ilgili özelliklerinin belirlenmesi antosiyaninler, flavoneller, Flavan-3-ol, prosiyanidinlerin, diğer flavonoidler, resveratrol, stilbenler, hidroksisinamik asitler ve hidroksibenzoik asitler içerir. HPLC-MS ile niceleme güvenilir olduğu gibi şeker ve alifatik organik asitler gibi diğer metabolitleri nedeniyle effec matrise göz ardı edilirT ve iyon-bastırma fenomeni 5. Bu yöntemle seçilen polarite aralığında, yaklaşım mümkün 6 gibi birçok farklı metabolitleri tespit amaçlamaktadır ki hedefsiz olduğunu. Asma transkript binlerce eşzamanlı izlenmesine olanak tanır transkriptomik yöntemleri tam asma genom dizisinin 7,8 kullanılabilirliği ile kolaylaştırılır. yüksek verimli cDNA dizileme dayalı erken transkriptomik yöntemler kolektif RNA-Seq teknoloji olarak tanımlanan prosedürlerin bir koleksiyon haline gelecek nesil dizileme gelişiyle gelişmiştir. Bu yaklaşım hızla transkriptomik çalışmalar için tercih edilen bir yöntem haline gelmektedir. Ancak, transkript binlerce melezleme ile paralel olarak sayısal izin mikrodizide dayalı literatürün büyük bir gövde, dedikodu için birikmiş. RNA Seq bir ana teknoloji olmadan önce Nitekim, birçok özel ticari mikroarray platformları olmuştugeliştirilen izin asma transcriptome ayrıntılı olarak incelenecek olan. Platformların çok çeşitli arasında, sadece iki genom transcriptome analizi 9 izin verdi. En gelişmiş dizi böylece her bir deney maliyetlerini azaltarak, tek bir cihazda 12 adede kadar bağımsız örneklerin hibridizasyon izin verdi. 12 alt diziler her 29.549 asma transkript temsil eden 135,000 60-mer probları oluşmaktadır. Bu cihaz, çalışmaları 10-24 çok sayıda kullanılmaktadır. Bu iki platform şimdi kalkıyor ama yeni bir özel mikroarray son zamanlarda dizayn edilmiştir ve ek yeni keşfedilen asma genleri 25 temsil prob daha büyük bir sayı içeren gibi daha yeni bir gelişmeyi temsil etmektedir. transkriptomiks ve metabolomikler analizi ile üretilen büyük satış veri setleri farklı bir formda arasındaki ilişkiyi belirlemek için çok değişkenli teknikler de dahil olmak üzere veri analizi için uygun istatistiksel yöntemleri gerektirirVerilerin s. En yaygın olarak kullanılan çok değişkenli teknikler projeksiyona dayalı olanlardır ve bunlar gibi temel bileşenler analizi (PCA), ya da, denetimsiz olabilir gibi gizli yapıların diskriminant analizi (O2PLS-DA) 26 çift yönlü dik izdüşümü olarak, denetimli. Bu makalede sunulan protokol örneklerinin gruplar arasındaki farklılıkları belirlemek için keşif veri analizi ve O2PLS-DA için PCA kullanır.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Mill Grinder</td>
			<td>IKA</td>
			<td>IKA A11 basic</td>
			<td></td>
		</tr>
		<tr>
			<td>HPLC Autosampler</td>
			<td>Beckman Coulter</td>
			<td>&#160;-</td>
			<td>System Gold 508 Autosampler</td>
		</tr>
		<tr>
			<td>HPLC System</td>
			<td>Beckman Coulter</td>
			<td>&#160;-</td>
			<td>System Gold 127 Solvent Module HPLC</td>
		</tr>
		<tr>
			<td>C18 Guard Column</td>
			<td>Grace</td>
			<td>&#160;-</td>
			<td>Alltima HP C18 (7.5x2.1mm; 5&#956;m) Guard Column</td>
		</tr>
		<tr>
			<td>C18 Column</td>
			<td>Grace</td>
			<td>&#160;-</td>
			<td>Alltima HP C18 (150x2.1mm; 3&#956;m) Column</td>
		</tr>
		<tr>
			<td>Mass Spectometer</td>
			<td>Bruker Daltonics</td>
			<td>&#160;-</td>
			<td>Bruker Esquire 6000; The mass spectometer was equipped with an ESI source and the analyzer was an ion trap.</td>
		</tr>
		<tr>
			<td rowspan="4">Extraction solvents and HPLC buffers</td>
			<td>Sigma</td>
			<td>34966</td>
			<td>Methanol LC-MS grade</td>
		</tr>
		<tr>
			<td>Sigma</td>
			<td>94318</td>
			<td>Formic acid LC-MS grade</td>
		</tr>
		<tr>
			<td>Sigma</td>
			<td>34967</td>
			<td>Acetonitrile LC-MS grade</td>
		</tr>
		<tr>
			<td>Sigma</td>
			<td>39253</td>
			<td>Water&#160; LC-MS grade</td>
		</tr>
		<tr>
			<td>Minisart RC 4 Syringe filters (0.2 &#956;m)</td>
			<td>Sartorius</td>
			<td>17764</td>
			<td></td>
		</tr>
		<tr>
			<td>Softwares for data collection (a) and processing (b)</td>
			<td>Bruker Daltonics</td>
			<td>-</td>
			<td>Bruker Daltonics Esquire 5.2 Control (a); Esquire 3.2 Data Analysis and MzMine 2.2 softwares (b)</td>
		</tr>
		<tr>
			<td>Spectrum Plant Total RNA kit</td>
			<td>Sigma-Aldrich</td>
			<td>STRN250-1KT</td>
			<td>For total RNA extractino from grape pericarps</td>
		</tr>
		<tr>
			<td>Nanodrop 1000</td>
			<td>Thermo Scientific</td>
			<td>1000</td>
			<td></td>
		</tr>
		<tr>
			<td>BioAnalyzer 2100</td>
			<td>Agilent Technologies</td>
			<td>G2939A</td>
			<td></td>
		</tr>
		<tr>
			<td>RNA 6000 Nano Reagents</td>
			<td>Agilent Technologies</td>
			<td>5067-1511</td>
			<td></td>
		</tr>
		<tr>
			<td>RNA Chips</td>
			<td>Agilent Technologies</td>
			<td>5067-1511</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent Gene Expression Wash Buffer 1</td>
			<td>Agilent Technologies</td>
			<td>5188-5325</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent Gene Expression Wash Buffer 2</td>
			<td>Agilent Technologies</td>
			<td>5188-5326</td>
			<td></td>
		</tr>
		<tr>
			<td>LowInput QuickAmp Labeling kit One-Color</td>
			<td>Agilent Technologies</td>
			<td>5190-2305</td>
			<td></td>
		</tr>
		<tr>
			<td>Kit RNA Spike In - One-Color</td>
			<td>Agilent Technologies</td>
			<td>5188-5282</td>
			<td></td>
		</tr>
		<tr>
			<td>Gene Expression Hybridization Kit</td>
			<td>Agilent Technologies</td>
			<td>5188-5242</td>
			<td></td>
		</tr>
		<tr>
			<td>RNeasy Mini Kit (50)</td>
			<td>Qiagen</td>
			<td>74104</td>
			<td>For cRNA Purification</td>
		</tr>
		<tr>
			<td>Agilent SurePrint HD 4X44K 60-mer Microarray</td>
			<td>Agilent Technologies</td>
			<td>G2514F-048771&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>eArray</td>
			<td>Agilent Technologies</td>
			<td>-</td>
			<td><a href="https://earray.chem.agilent.com/earray/">https://earray.chem.agilent.com/earray/</a></td>
		</tr>
		<tr>
			<td>Gasket slides</td>
			<td>Agilent Technologies</td>
			<td>G2534-60012</td>
			<td>Enable Agilent SurePrint Microarray 4-array Hybridization</td>
		</tr>
		<tr>
			<td>Thermostatic bath</td>
			<td>Julabo</td>
			<td>-</td>
			<td></td>
		</tr>
		<tr>
			<td>Hybridization Chamber</td>
			<td>Agilent Technologies</td>
			<td>G2534-60001</td>
			<td></td>
		</tr>
		<tr>
			<td>Microarray Hybridization Oven</td>
			<td>Agilent Technologies</td>
			<td>G2545A</td>
			<td></td>
		</tr>
		<tr>
			<td>Hybridization Oven Rotator Rack</td>
			<td>Agilent Technologies</td>
			<td>G2530-60029</td>
			<td></td>
		</tr>
		<tr>
			<td>Rotator Rack Conversion Rod</td>
			<td>Agilent Technologies</td>
			<td>G2530-60030</td>
			<td></td>
		</tr>
		<tr>
			<td>Staining kit</td>
			<td>Bio-Optica</td>
			<td>10-2000</td>
			<td>Slide-staining dish and Slide rack</td>
		</tr>
		<tr>
			<td>Magnetic stirrer device</td>
			<td>AREX Heating Magnetic Stirrer</td>
			<td>F20540163&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermostatic Oven</td>
			<td>Thermo Scientific</td>
			<td>Heraeus - 6030</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent Microarray Scanner</td>
			<td>Agilent Technologies</td>
			<td>G2565CA</td>
			<td></td>
		</tr>
		<tr>
			<td>Scanner Carousel, 48-position</td>
			<td>Agilent Technologies</td>
			<td>G2505-60502</td>
			<td></td>
		</tr>
		<tr>
			<td>Slide Holders</td>
			<td>Agilent Technologies</td>
			<td>G2505-60525</td>
			<td></td>
		</tr>
		<tr>
			<td>Feature extraction software v11.5</td>
			<td>Agilent Technologies</td>
			<td>-</td>
			<td>inside the Agilent Microarray Scanner G2565CA</td>
		</tr>
		<tr>
			<td>SIMCA + V13 Software</td>
			<td>Umetrics</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

the terroir concept interpreted through grape berry metabolomics and transcriptomics

Terroir özellikle habitatlar ve yönetim uygulamalarına göre bu tür asma (Vitis vinifera) gibi ürünlerin özelliklerini etkileyen çevresel faktörlerin kombinasyonu ifade eder. Bu makale belli terroir imzalar çok değişkenli istatistiksel analiz kullanılarak asma çeşidi corvina&#39;nın berry metabolome ve transcriptome tespit edilebilir gösterir. yöntemi ilk uygun bir örnekleme planı gerektirir. Bu olgu sunumunda, Corvina çeşidinde belirli bir klon genetik farklılıkları en aza indirmek için seçildi ve numuneler üç farklı yetiştirme mevsimi boyunca üç farklı makro bölgeleri temsil eden yedi üzüm bağları toplanmıştır. Bir hedefsiz LC-MS metabolomik yaklaşımı MZmine yazılım ve parçalanma ağaç analizine dayalı bir metaboliti kimlik strateji kullanarak verimli veri işleme eşliğinde yüksek duyarlılığı nedeniyle tavsiye edilmektedir. Kapsamlı transcriptome analizi mikrodizileri kullanılarak elde edilebiliriçeren probları farklı terroirs bağlamında tüm farklı ifade genlerin aynı anda analizini sağlayan, ~ tüm tahmin asma genlerinin% 99 kapsayan. Son olarak, projeksiyon yöntemlerine dayalı çok değişkenli veri analizi metabolomik ve transkriptomiks verileri entegre ve bilgilendirici korelasyon tespit ayrıntılı olarak analiz edilecek izin, güçlü bağ bozumu-spesifik etkisini aşmak için kullanılabilir.

Bu makalede açıklanan vaka çalışması nispeten 189 örnekleri arasında sayısal moleküler iyonlar artı kendi izotopları, adüktleri ve bazı parçaları da dahil olmak üzere 552 sinyalleri (m / z özellikleri), (7 bağları x 3 olgunlaşma aşamaları x 3 büyüyen mevsim x içeren bir son veri matrisi vermiştir 3 biyolojik çoğaltır). veri noktaları için toplam sayısı, bu nedenle 104,328 idi. Parçalanma ağacı analizi metabolitleri ayrıca adüktleri, izotopl...

Watch this Scientific Journal Video about The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics at JoVE.com

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Bu makale, yani terroir kavramının, içgörü kazanmak için üzüm berry transkript ve metabolitleri hedefsiz metabolomik, transkriptomik ve çok değişkenli istatistiksel analiz uygulamasını açıklar, dut kalite özellikleri çevrenin etkisi.

Üzüm Berry metabolomik ve transkriptomik aracılığıyla yorumlanır Terroir Kavramı

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to ...

the-terroir-concept-interpreted-through-grape-berry-metabolomics

Research

JoVE Journal

Genetics

10.3K Görüntüleme.  University of Verona.  Bu makale, yani terroir kavramının, içgörü kazanmak için üzüm berry transkript ve metabolitleri hedefsiz metabolomik, transkriptomik ve çok değişkenli istatistiksel analiz uygulamasını açıklar, dut kalite özellikleri çevrenin etkisi. 

Video: The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

In Vitro Transcription Assays and Their Application in Drug Discovery

In vitro transcription assays have been developed and widely used for many years to study the molecular mechanisms involved in transcription. This process requires multi-subunit DNA-dependent RNA polymerase (RNAP) and a series of transcription factors that act to modulate the activity of RNAP during gene expression. Sequencing gel electrophoresis of radiolabeled transcripts is used to provide detailed mechanistic information on how transcription proceeds and what parameters can affect it. In this paper we describe the protocol to study how the essential elongation factor NusA regulates transcriptional pausing, as well as a method to identify an antibacterial agent targeting transcription initiation through inhibition of RNAP holoenzyme formation. These methods can be used a as platform for the development of additional approaches to explore the mechanism of action of the transcription factors which still remain unclear, as well as new antibacterial agents targeting transcription which is an underutilized drug target in antibiotic research and development.

In Vitro Transcription Assays and Their Application in Drug Discovery

In this manuscript, we describe a protocol to functionally examine transcription and the inhibitory activity of antibacterial agents targeting bacterial transcription.

İn Vitro Transkripsiyon Tahliller ve İlaç Keşfi Onların Uygulama

In vitro transcription assays have been developed and widely used for many years to study the molecular mechanisms involved in transcription. This process ...

Genetik

Delivery of Nucleic Acids through Embryo Microinjection in the Worldwide Agricultural Pest Insect, Ceratitis capitata

The Mediterranean fruit fly (medfly) Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) is a pest species with extremely high agricultural relevance. This is due to its reproductive behavior: females damage the external surface of fruits and vegetables when they lay eggs and the hatched larvae feed on their pulp. Wild C. capitata populations are traditionally controlled through insecticide spraying and/or eco-friendly approaches, the most successful being the Sterile Insect Technique (SIT). The SIT relies on mass-rearing, radiation-based sterilization and field release of males that retain their capacity to mate but are not able to generate fertile progeny. The advent and the subsequent rapid development of biotechnological tools, together with the availability of the medfly genome sequence, has greatly boosted our understanding of the biology of this species. This favored the proliferation of new strategies for genome manipulation, which can be applied to population control.
In this context, embryo microinjection plays a dual role in expanding the toolbox for medfly control. The ability to interfere with the function of genes that regulate key biological processes, indeed, expands our understanding of the molecular machinery underlying medfly invasiveness. Furthermore, the ability to achieve germ-line transformation facilitates the production of multiple transgenic strains that can be tested for future field applications in novel SIT settings. Indeed, genetic manipulation can be used to confer desirable traits that can, for example, be used to monitor sterile male performance in the field, or that can result in early life-stage lethality. Here we describe a method to microinject nucleic acids into medfly embryos to achieve these two main goals.

Delivery of Nucleic Acids through Embryo Microinjection in the Worldwide Agricultural Pest Insect, Ceratitis capitata

The Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera: Tephritidae) is a worldwide pest of agriculture. A deeper understanding of its biology is key to control medfly populations and thus reduce economic impact. Embryo microinjection is a fundamental tool allowing both germ-line transformation and reverse genetics studies in this species.

Dünya Tarım Pest Böcek Embriyo Mikroenjeksiyon yoluyla Nükleik Asitler teslim edilmesi,<em&gt; Ceratitis capitata</em

The Mediterranean fruit fly (medfly) Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) is a pest species with extremely high agricultural relevance. ...

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g. executing bash commands, visualization and management of large data sets. All command line code and further explanations of each command or step can be found on the wiki (<a href="https://wiki.cyverse.org/wiki/x/dgGtAQ">https://wiki.cyverse.org/wiki/x/dgGtAQ</a>). The Discovery Environment and Atmosphere platforms are connected together through the CyVerse Data Store. As such, once the initial raw sequencing data has been uploaded there is no more need to transfer large data files over an Internet connection, minimizing the amount of time needed to conduct analyses. This protocol is designed to analyze only two experimental treatments or conditions. Differential gene expression analysis is conducted through pairwise comparisons, and will not be suitable to test multiple factors. This workflow is also designed to be manual rather than automated. Each step must be executed and investigated by the user, yielding a better understanding of data and analytical outputs, and therefore better results for the user. Once complete, this protocol will yield de novo assembled transcriptome(s) for underserved (non-model) organisms without the need to map to previously assembled reference genomes (which are usually not available in underserved organism). These de novo transcriptomes are further used in pairwise differential gene expression analysis to investigate genes differing between two experimental conditions. Differentially expressed genes are then functionally annotated to understand the genetic response organisms have to experimental conditions. In total, the data derived from this protocol is used to test hypotheses about biological responses of underserved organisms.

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

This protocol outlines a comparative de novo transcriptome assembly and annotation workflow for novice bioinformaticians. The workflow is available for free entirely through CyVerse and connected by the Data Store. Command line and graphical user interfaces are used, but all code needed is available to copy and paste.

CyVerse Kaynaklarını Kaldıracak<emDe Novo</em&gt; Yetersiz Üretilmiş (Model Olmayan) Organizmaların Karşılaştırmalı Transkriptomikleri

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative ...

Controllable Ion Channel Expression through Inducible Transient Transfection

Transfection, the delivery of foreign nucleic acids into a cell, is a powerful tool in protein research. Through this method, ion channels can be investigated through electrophysiological analysis, biochemical characterization, mutational studies, and their effects on cellular processes. Transient transfections offer a simple protocol in which the protein becomes available for analysis within a few hours to days. Although this method presents a relatively straightforward and time efficient protocol, one of the critical components is calibrating the expression of the gene of interest to physiological relevant levels or levels that are suitable for analysis. To this end, many different approaches that offer the ability to control the expression of the gene of interest have emerged. Several stable cell transfection protocols provide a way to permanently introduce a gene of interest into the cellular genome under the regulation of a tetracycline-controlled transcriptional activation. While this technique produces reliable expression levels, each gene of interest requires a few weeks of skilled work including calibration of a killing curve, selection of cell colonies, and overall more resources. Here we present a protocol that uses transient transfection of the Transient Receptor Potential cation channel subfamily V member 1 (TRPV1) gene in an inducible system as an efficient way to express a protein in a controlled manner which is essential in ion channel analysis. We demonstrate that using this technique, we are able to perform calcium imaging, whole cell, and single channel analysis with controlled channel levels required for each type of data collection with a single transfection. Overall, this provides a replicable technique that can be used to study ion channels structure and function.

Studying ion channels through a heterologously expressing system has become a core technique in biomedical research. In this manuscript, we present a time efficient method to achieve tightly controlled ion channel expression by performing transient transfection under the control of an inducible promoter.

İndüklenebilir geçici transfeksiyon yoluyla kontrol edilebilir iyon kanal İfade

Transfection, the delivery of foreign nucleic acids into a cell, is a powerful tool in protein research. Through this method, ion channels can be ...

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. However, for first-time users and bioinformatics' amateurs, self-learning and familiarization with these platforms can be time-consuming and daunting. We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples.

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Galaxy and DAVID have emerged as popular tools that allow investigators without bioinformatics training to analyze and interpret RNA-Seq data. We describe a protocol for C. elegans researchers to perform RNA-Seq experiments, access and process the dataset using Galaxy and obtain meaningful biological information from the gene lists using DAVID.

arasında Transkriptomik Analizi<em&gt; C</em&gt;.<em&gt; elegans</emGalaxy Projesi Smokin Suite sayesinde&gt; RNA Sıralama Veri

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged ...

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

This article demonstrates a detailed protocol for DNA isolation and high-throughput sequencing library construction from herbarium material including rescue of exceptionally poor-quality DNA.

Sağlam DNA izolasyon ve yüksek işlem hacmi sıralama kitaplığı inşaat sulak numuneler için

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with ...

Isolating, Sequencing and Analyzing Extracellular MicroRNAs from Human Mesenchymal Stem Cells

Extracellular and circulating RNAs (exRNA) are produced by many cell types of the body and exist in numerous bodily fluids such as saliva, plasma, serum, milk and urine. One subset of these RNAs are the posttranscriptional regulators &#8211; microRNAs (miRNAs). To delineate the miRNAs produced by specific cell types, in vitro culture systems can be used to harvest and profile exRNAs derived from one subset of cells. The secreted factors of mesenchymal stem cells are implicated in alleviating numerous diseases and is used as the in vitro model system here. This paper describes the process of collection, purification of small RNA and library generation to sequence extracellular miRNAs. ExRNAs from culture media differ from cellular RNA by being low RNA input samples, which calls for optimized procedures. This protocol provides a comprehensive guide to small exRNA sequencing from culture media, showing quality control checkpoints at each step during exRNA purification and sequencing.

This protocol demonstrates how to purify extracellular microRNAs from cell culture media for small RNA library construction and next generation sequencing. Various quality control checkpoints are described to allow readers to understand what to expect when working with low input samples like exRNAs.

İzole, sıralama ve insan Mezenkimal Kök hücreleri ekstrasellüler mikroRNA'lar analiz

Extracellular and circulating RNAs (exRNA) are produced by many cell types of the body and exist in numerous bodily fluids such as saliva, plasma, serum, ...

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

In the process of drug development of RNA-targeting small molecules, elucidating the structural changes upon their interactions with target RNA sequences is desired. We herein provide a detailed in vitro and in-cell selective 2&#39;-hydroxyl acylation analyzed by primer extension (SHAPE) protocol to study the RNA structural change in the presence of an experimental drug for spinal muscular atrophy (SMA), survival of motor neuron (SMN)-C2, and in exon 7 of the pre-mRNA of the SMN2 gene. In in vitro SHAPE, an RNA sequence of 140 nucleotides containing SMN2 exon 7 is transcribed by T7 RNA polymerase, folded in the presence of SMN-C2, and subsequently modified by a mild 2&#39;-OH acylation reagent, 2-methylnicotinic acid imidazolide (NAI). This 2&#39;-OH-NAI adduct is further probed by a 32P-labeled primer extension and resolved by polyacrylamide gel electrophoresis (PAGE). Conversely, 2&#39;-OH acylation in in-cell SHAPE takes place in situ with SMN-C2 bound cellular RNA in living cells. The pre-mRNA sequence of exon 7 in the SMN2 gene, along with SHAPE-induced mutations in the primer extension, was then amplified by PCR and subject to next-generation sequencing. Comparing the two methodologies, in vitro SHAPE is a more cost-effective method and does not require computational power to visualize results. However, the in vitro SHAPE-derived RNA model sometimes deviates from the secondary structure in a cellular context, likely due to the loss of all interactions with RNA-binding proteins. In-cell SHAPE does not need a radioactive material workplace and yields a more accurate RNA secondary structure in the cellular context. Furthermore, in-cell SHAPE is usually applicable for a larger range of RNA sequences (~1,000 nucleotides) by utilizing next-generation sequencing, compared to in vitro SHAPE (~200 nucleotides) that usually relies on PAGE analysis. In case of exon 7 in SMN2 pre-mRNA, the in vitro and in-cell SHAPE derived RNA models are similar to each other.

Detailed protocols for both in vitro and in-cell selective 2&#39;-hydroxyl acylation analyzed by primer extension (SHAPE) experiments to determine the secondary structure of pre-mRNA sequences of interest in the presence of an RNA-targeting small molecule are presented in this article.

İn vitro ve hücre içi şeklinde küçük molekül araştırmak için kullanarak Pre-mRNA yapısal değişiklikler indüklenen

In the process of drug development of RNA-targeting small molecules, elucidating the structural changes upon their interactions with target RNA sequences ...

Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation

Inducible, tissue-specific expression is an important and powerful tool to study the spatio-temporal dynamics of genetic perturbation. Combining the flexible and efficient GreenGate cloning system with the proven and benchmarked LhGR system (here termed GR-LhG4) for the inducible expression, we have generated a set of transgenic Arabidopsis lines that can drive the expression of an effector cassette in a range of specific cell types in the three main plant meristems. To this end, we chose the previously developed GR-LhG4 system based on a chimeric transcription factor and a cognate pOp-type promoter ensuring tight control over a wide range of expression levels. In addition, to visualize the expression domain where the synthetic transcription factor is active, an ER-localized mTurquoise2 fluorescent reporter under control of the pOp4 or pOp6 promoter is encoded in driver lines. Here, we describe the steps necessary to generate a driver or effector line and demonstrate how cell type specific expression can be induced and followed in the shoot apical meristem, the root apical meristem and the cambium of Arabidopsis. By using several or all driver lines, the context specific effect of expressing one or multiple factors (effectors) under control of the synthetic pOp promoter can be assessed rapidly, for example in F1 plants of a cross between one effector and multiple driver lines. This approach is exemplified by the ectopic expression of VND7, a NAC transcription factor capable of inducing ectopic secondary cell wall deposition in a cell autonomous manner.

Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation

Here, we describe the generation and application of a set of transgenic Arabidopsis thaliana lines enabling inducible, tissue-specific expression in the three main meristems, the shoot apical meristem, the root apical meristem, and the cambium.

İndüklenebilir, hücre türüne özgü ifade Arabidopsis thaliana aracılığıyla LhGR-aracılı Trans-harekete geçirmek

Inducible, tissue-specific expression is an important and powerful tool to study the spatio-temporal dynamics of genetic perturbation. Combining the ...

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

The study of small RNAs (sRNAs) by next-generation sequencing (NGS) is challenged by bias issues during library preparation. Several types of sRNA such as plant microRNAs (miRNAs) carry a 2&#39;-O-methyl (2&#39;-OMe) modification at their 3&#39;&#160;terminal nucleotide. This modification adds another difficulty as it inhibits 3&#39;&#160;adapter ligation. We previously demonstrated that modified versions of the &#39;TruSeq (TS)&#39;&#160;protocol have less bias and an improved detection of 2&#39;-OMe RNAs. Here we describe in detail protocol &#39;TS5&#39;, which showed the best overall performance. TS5 can be followed either using homemade reagents or reagents from the TS kit, with equal performance.

We present a detailed small RNA library reparation protocol with less bias than standard methods and an increased sensitivity for 2&#39;-O-methyl RNAs. This protocol can be followed using homemade reagents to save cost or using kits for convenience.

Küçük RNA-seq iyileştirilmesi: Daha Az Önyargı ve 2'-O-Metil RNA'ların Daha İyi Tespiti

The study of small RNAs (sRNAs) by next-generation sequencing (NGS) is challenged by bias issues during library preparation. Several types of sRNA such as ...

Üzüm Berry metabolomik ve transkriptomik aracılığıyla yorumlanır Terroir Kavramı

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