Wir bedanken uns bei Ron Davis, Adam Deutschbauer, und die ganze HIP HOP Labor an der University of Toronto für Gespräche und Beratung. CN wird durch Zuschüsse aus dem National Human Genome Research Institute (Grant Number HG000205), RO1 HG003317, CIHR MOP-84305, und der kanadischen Krebsgesellschaft (# 020380) unterstützt. JO wurde von der Stanford Genome Training Program (Grant Number T32 HG00044 vom National Human Genome Research Institute) und die National Institutes of Health (Grant Number P01 GH000205) unterstützt. GG wird durch die NHGRI RO1 HG003317 und der kanadischen Krebsgesellschaft, Grant # 020380, TD und der Donnelly Sequencing Center unterstützt wird zum Teil durch Zuschüsse aus dem kanadischen Stiftung für Innovation zu Drs unterstützt. Brenda Andrews und Jack Greenblatt. AMS wird von der Universität von Toronto öffnen Fellowship unterstützt.

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Keine Interessenskonflikte erklärt.

Hier erörtern wir ein Protokoll, mit bescheidenen Modifikation, leicht zu einer Vielzahl von bestehenden Sammlungen von Barcode-Mutante Sammlungen von verschiedenen Mikroorganismen getaggt mutierten Sammlungen erstellen angepasst werden kann. Wir betonen, dass wir zwar ein Protokoll über den markierten Transposon-Mutagenese haben berichtet, für den humanpathogenen Hefepilz C. albicans, ein sehr ähnliches Protokoll könnte zu einer Vielzahl von einzelligen Pilze angepasst werden. Geändert arbeitet dieses Protokoll auch in Bakterien 13, und derzeit Kollektionen für eine Reihe von zusätzlichen Pilz-und bakterielle Genome sind im Bau. Derzeit bietet dieser Test die einzige umfassende, genomweite unvoreingenommene Bildschirm für die Gen-kleine Molekül-Wechselwirkungen. Eine besonders nützliche Funktion des Tests ist, dass keine Vorkenntnisse des Gens oder kleines Molekül erforderlich ist. Trotz des Umfangs und der Macht dieser Tests hat ihre Übertragbarkeit auf andere Labors wurde ein wenig durch die Erstinvestition und Informatik-Werkzeuge für die Analyse der Ergebnisse erschwert. Mit der Verabschiedung der nächsten Generation Reihenfolge Auslesen mit robuster Werkzeuge für die Analyse kombiniert, erwarten wir ihre Annahme zu erhöhen.

<table border="1"><tbody><tr><td> Antibiotika </td><td> Hersteller und Katalog-Nummern </td></tr><tr><td> Carbenicillin </td><td> Sigma, Teil # C1613 </td></tr><tr><td> Kanamycin </td><td> Sigma, Teil # K1876 </td></tr><tr><td> Spectinomycin </td><td> Sigma, Teil # S0692 </td></tr><tr><td> Chloramphenicol </td><td> Sigma, Teil # C0378 </td></tr><tr><td> DNA Clean-up und die Konzentration Kits </td><td></td></tr><tr><td> QIAprep Spin Miniprep Kit </td><td> Qiagen, Teil # 27106 </td></tr><tr><td> HiSpeed ​​Plasmid Maxi Kit </td><td> Qiagen, Teil # 12663 </td></tr><tr><td> QIAquick PCR Purification Kit </td><td> Qiagen, Teil # 28106 </td></tr><tr><td> QIAquick Gel Extraction Kit </td><td> Qiagen, Teil # 28704 </td></tr><tr><td> PCR und Elektrophorese-Reagenzien </td><td></td></tr><tr><td> Taq DNA Polymerase (Mg-free) Buffer </td><td> New England Biolabs, Teil # M0320L </td></tr><tr><td> Desoxynukleotid Lösung Mix </td><td> New England Biolabs, Teil # N0447L </td></tr><tr><td> 25 mM MgCl 2 </td><td> Sigma, Teil # 63036 </td></tr><tr><td> Agarose, Loading-Farbstoff und Nukleinsäure-Fleck geeignet für Gel-Elektrophorese </td><td> Verschiedene </td></tr><tr><td> 10x TAE-Puffer </td><td> Sigma, Teil # T8280 </td></tr><tr><td> 1 Kb Plus-DNA Ladder </td><td> Invitrogen, Teil # 10787026 </td></tr><tr><td> YPD Brühe </td><td></td></tr><tr><td> 10 g Hefe-Extrakt </td><td> Sigma, Teil # Y1625 </td></tr><tr><td> 20 g Bacto Pepton </td><td> BD Biosciences, Teil # 211677 </td></tr><tr><td> 20 g Dextrose </td><td> Sigma, Teil # D9434 </td></tr><tr><td> Labware </td><td></td></tr><tr><td> Mehrkanalpipetten (1000, 200, und 20 ul) </td><td> Verschiedene </td></tr><tr><td> Einweg Pipettieren Stauseen </td><td> Verschiedene </td></tr><tr><td> 15 und 50 mL Zentrifugenröhrchen </td><td> Verschiedene </td></tr><tr><td> 96 - und 384-Well Deep Well Platten </td><td> Axygen Scientific, Teil # P-2ML-SQ-CS &amp; P-384240SQCS </td></tr><tr><td> 96-well und 384-well PCR-Platten und Dichtung Film </td><td> Verschiedene </td></tr><tr><td> Plattenroller zur Abdichtung Multi-Well-Platten </td><td> Sigma, Teil # R1275 </td></tr><tr><td> 30 ° C und 37 ° C Schüttelinkubatoren für den Anbau von Bakterien und Hefen auf Platten und in Rohren </td><td> Verschiedene </td></tr><tr><td> In-vitro-Transposon-Mutagenese </td><td></td></tr><tr><td> EZ-Tn5 Transposase </td><td> Epicentre Biotechnologies, Teil # TNP92110 </td></tr><tr><td> High-Throughput-Transformation </td><td></td></tr><tr><td> Seqprep 96 HT Plasmid Prep Kit </td><td> Edge-Biosystems, Teil # 84359 </td></tr><tr><td> Polyethylenglykol, Molekulargewicht 3350 </td><td> Verschiedene </td></tr><tr><td> Lithiumacetat </td><td> Sigma, Teil # 517992 </td></tr><tr><td> 6-Well-Platten, steril </td><td> Corning, Teil # 3335 </td></tr><tr><td> 50 mg / mL Uridin </td><td> Sigma, Teil # U3750 </td></tr><tr><td> 100X Tris-EDTA-Pufferlösung </td><td> Sigma, Teil # T9285 </td></tr><tr><td> 1X TE/0.1M LiOAc </td><td> Verschiedene </td></tr><tr><td> Lachs testis DNA </td><td> Sigma, Teil # 1626 </td></tr><tr><td> Das Wachstum der Barcode-Sammlungen </td><td></td></tr><tr><td> 48-Well-Platten, wenn wachsenden Kulturen in Platten </td><td> Greiner, Teil # M9437 </td></tr><tr><td> Klebeplatte Dichtungen </td><td> ABgene, Teil # AB-0580 </td></tr><tr><td> 200 ml Kulturflaschen </td><td> Verschiedene </td></tr><tr><td> Spektrophotometer für die Absorption </td><td> Verschiedene </td></tr><tr><td> Temperaturgeregelte Schüttler für 250 ml Flaschen oder Schütteln Spektralphotometer </td><td> Verschiedene </td></tr><tr><td> Safe-Lock Mikrozentrifugenröhrchen, 2 mL </td><td> Eppendorf, Teil # 0030 120.094 </td></tr><tr><td> Hybridisierung Ausrüstung </td><td></td></tr><tr><td> Hybridisierungsofen 640 </td><td> Affymetrix, Teil # 800138 </td></tr><tr><td> GeneChip Fluidic-Station 450 </td><td> Affymetrix, Teil # 00-0079 </td></tr><tr><td> GeneArray Scanner 3000 </td><td> Affymetrix, Teil # 00-0212 </td></tr><tr><td> Kochenden Wasserbad mit schwimmenden Rack </td><td> Verschiedene </td></tr><tr><td> Hybridisierung Verbrauchsmaterialien </td><td></td></tr><tr><td> Genflex Tag 16K Array v2 </td><td> Affymetrix, Teil # 511331 </td></tr><tr><td> Denhardt-Lösung, 50X Konzentrat </td><td> Sigma, Teil # D2532 </td></tr><tr><td> Streptavidin, R-Phycoerythrin-Konjugat (SAPE) </td><td> Invitrogen, Teil # S866 </td></tr><tr><td> Safe-Lock Mikrozentrifugenröhrchen, 0,5 mL </td><td> Eppendorf, Teil # 0030 123.301 </td></tr><tr><td> Teeny Tough-Spots </td><td> Diversified Biotech, Teil # LTTM-1000 </td></tr><tr><td> 0,5 M EDTA </td><td> BioRad, Teil # 161-0729 </td></tr><tr><td> 10% Tween </td><td> Sigma, Teil # T2700 </td></tr><tr><td> MES free-Monohydrat </td><td> Sigma, Teil # M5287 </td></tr><tr><td> MES Natriumsalz </td><td> Sigma, Teil # M5057 </td></tr><tr><td> 5 M NaCl </td><td> Sigma, Teil # 71386 </td></tr><tr><td> 20X SSPE </td><td> Sigma, Teil # S2015 </td></tr><tr><td> Molekularbiologie Wasser </td><td> Sigma, Teil # W4502 </td></tr><tr><td> Hybridisierung Primer </td><td> Verschiedene Anbieter (Standard Entsalzung) </td></tr><tr><td> Uptag </td><td> 5 &#39;GATGTCCACGAGGTCTCT 3&#39; </td></tr><tr><td> Buptagkanmx4 </td><td> 5 &#39;Biotin-GTCGACCTGCAGCGTACG 3&#39; </td></tr><tr><td> Dntag </td><td> 5 &#39;CGGTGTCGGTCTCGTAG 3&#39; </td></tr><tr><td> Bdntagkanmx4 </td><td> 5 &#39;Biotin-GAAAACGAGCTCGAATTCATCG 3&#39; </td></tr><tr><td> B213 </td><td> 5 &#39;Biotin-CTGAACGGTAGCATCTTGAC 3&#39; </td></tr><tr><td> Uptagkanmx </td><td> 5 &#39;GTCGACCTGCAGCGTACG 3&#39; </td></tr><tr><td> Dntagkanmx </td><td> 5&#39;GAAAACGAGCTCGAATTCATCG 3 &#39; </td></tr><tr><td> Uptagcomp </td><td> 5&#39;AGAGACCTCGTGGACATC 3 &#39; </td></tr><tr><td> Dntagcomp </td><td> 5&#39;CTACGAGACCGACACCG 3 &#39; </td></tr><tr><td> Upkancomp </td><td> 5&#39;CGTACGCTGCAGGTCGAC 3 &#39; </td></tr><tr><td> Dnkancomp </td><td> 5&#39;CGATGAATTCGAGCTCGTTTTC 3 &#39; </td></tr><tr><td> Sequenzierungsprimern: Illumina Plattform </td><td> Verschiedene Anbieter </td></tr><tr><td> UpTag Sturm (100um) </td><td> 5 &#39;CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC T GAT GTC CAC GAG GTC TCT 3&#39; </td></tr><tr><td> UpTag Reverse (100um) </td><td> 5 &#39;AAT GAT ACG GCG ACC ACC GAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T NNNNN GTC GAC CTG CAG CGT ACG 3&#39; </td></tr><tr><td> DownTag Sturm (100um) </td><td> 5 &#39;CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC T GAA AAC GAG CTC GAA TTC ATC G 3 &quot; </td></tr><tr><td> DownTag Reverse (100um) </td><td> 5 &#39;AAT GAT ACG GCG ACC ACC GAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T NNNNN CGG TGT CGG TCT CGT AG 3 ` </td></tr><tr><td> Lesen Sie 1 UP-tag seq-Primer (100 um) </td><td> 5 &#39;GTC GAC CTG CAG CGT ACG 3&#39; </td></tr><tr><td> Lesen Sie 1 AB-tag seq-Primer (100 um) </td><td> 5 &#39;CGG TGT CGG TCT CGT AG 3&#39; </td></tr><tr><td> Lesen Sie 2 Index-Sequenzierung Primer (Standard Illumina R1 Primer) (100 um) </td><td> 5 &#39;AC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T 3&#39; </td></tr><tr><td> Zusätzliche Sequencing Reagenzien / Equipment </td><td></td></tr><tr><td> Qiagen MinElute 96 UF PCR Purification Kit </td><td> Qiagen, Teil # 29051 </td></tr><tr><td> Vakuumpumpe </td><td> Jeder Anbieter </td></tr><tr><td> Macherey-Nagel Vacuum Manifold </td><td> Macherey-Nagel, Teil # 740 681 </td></tr><tr><td> Invitrogen Quant-iT dsDNA BR Assay Kit </td><td> Invitrogen, Teil # Q32853 </td></tr><tr><td> Invitrogen Qubit Teströhrchen </td><td> Invitrogen, Teil # Q32856 </td></tr><tr><td> 40% Acrylamid plus 1% N, N&#39;-Methylen-bis-Acrylamid, 37,5:1 </td><td> Bio Rad, Teil # 161-0148 </td></tr><tr><td> Tris Base </td><td> Sigma, Teil # T1503-1KG </td></tr><tr><td> Borsäure </td><td> Sigma, Teil # B6768-500G </td></tr><tr><td> 0,5 M EDTA, pH 8,0 </td><td> Teknova, Teil # E0306 </td></tr><tr><td> Ammoniumpersulfat </td><td> Sigma, Teil # A3678-25G </td></tr><tr><td> TEMED </td><td> BioShop, Teil # TEM001.25 </td></tr><tr><td> Ethidiumbromidlösung </td><td> BioShop, Teil # ETB444.10 </td></tr><tr><td> 0,5 M Ammoniumacetat </td><td> Teknova, Teil # A2000 </td></tr><tr><td> 10 mM Magnesium-Acetat-Tetrahydrat </td><td> Sigma, Teil # M0631-100G </td></tr><tr><td> 1mM EDTA, pH 8,0 </td><td> Siehe 0,5 M EDTA, pH 8,0 </td></tr><tr><td> Ethanol </td><td> Verschiedene </td></tr><tr><td> Natriumacetat, pH 5,2 </td><td> Teknova, Teil # S0297 </td></tr><tr><td> Speed-Vakuum </td><td> Verschiedene </td></tr><tr><td> Single-Read Cluster-Generation Kit </td><td> Illumina, part # GD-300-1001 </td></tr><tr><td> 36c Sequencing Kit v4 </td><td>Illumina, part # FC-104-4002 </td></tr><tr><td></td><td></td></tr></tbody></table> 10x TBE Rezept <table border="1"><tbody><tr><td> Beträge </td><td> Reagenzien </td></tr><tr><td> 108 Gramm </td><td> Tris Base </td></tr><tr><td> 55 Gramm </td><td> Borsäure </td></tr><tr><td> 40mL </td><td> 0,5 M EDTA (pH 8,0) </td></tr><tr><td colspan="2"> Add dH 2 O auf 1L markieren </td></tr></tbody></table> 12% Polyacrylamidgel Rezept <table border="1"><tbody><tr><td> Volumes </td><td> Reagenzien </td></tr><tr><td> 5,8 ml </td><td> 40% Acrylamid plus 1% N, N&#39;-Methylen-bis-Acrylamid, 37,5:1 </td></tr><tr><td> 12 ml </td><td> dH 2 O </td></tr><tr><td> 2 ml </td><td> 10x TBE </td></tr><tr><td> 140 ul </td><td> 10% Ammoniumpersulfat </td></tr><tr><td> Gesamtvolumen: 20 ml </td><td></td></tr></tbody></table> Uptag Primer-Mix: Resuspendieren Uptag und Buptagkanmx4 jeweils in ddH 2 O bei 100 nM, dann in einem Verhältnis von 1:1 mischen für eine Endkonzentration von 50 uM jeder. Lagerung bei -20 ° C. Downtag Primer-Mix: Resuspendieren Dntag und Bdntagkanmx4 jeweils in ddH 2 O bei 100 nM, dann in einem Verhältnis von 1:1 mischen für eine Endkonzentration von 50 uM jeder. Lagerung bei -20 ° C. Mixed-Oligonukleotide: Resuspendieren jedem der folgenden acht Oligos (Standard entsalzt) in ddH 2 O bei 100 uM: Uptag, Dntag, Uptagkanmx, Dntagkanmx, Uptagcomp, Dntagcomp, Upkancomp, Dnkancomp. Mix ein gleiches Volumen der acht Oligonukleotide für eine Endkonzentration von 12,5 uM jeder. 12X MES Lager: Für 10 ml, lösen sich 0,7 g MES free-Monohydrat und 1,93 g MES Natriumsalz in 8 ml Molekularbiologie Wasser. Nach dem Mischen gut, pH-Wert prüfen und einstellen, wenn bis zu einem pH von 6,5 bis 6,7 erforderlich. Fügen Sie Wasser bis zu einem Gesamtvolumen von 10 ml. Filter sterilisiert und bei 4 ° C vor Licht (zB Wickeln Sie das Rohr in Folie) geschützt. Ersetzen Sie, wenn Lösung wird sichtbar gelb oder nach 6 Monaten. 2X Hybridisierungspuffer: Für 50 ml, Mix 8,3 ml 12X MES Lager (ab 2.9.14), 17,7 ml 5 M NaCl, 4,0 ml 0,5 M EDTA, 0,1 ml 10% Tween 20 (vol / vol) und 19,9 ml gefiltert ddH 2 O. Filter sterilisieren. Wash A: 300 ml 20X SSPE, 1 mL 10% Tween (vol / vol), 699 ml ddH 2 O. Filter sterilisieren. Wash B: Mix 150 ml 20X SSPE, 1 mL 10% Tween (vol / vol), 849 ml ddH 2 O. Filter sterilisieren. Barcode Sequenzierungsprimern In UP-tag Primersequenzen die 5 &#39;tail (fett) sind Illumina Adapter-Sequenzen in der F-und R-Primer enthalten. Die variable Sequenz (kursiv) stellt die 5-mer Indizierung Tag in Multiplexen / index Auslesen verwendet. Die 3 &#39;tail (unterstrichen) vertritt die gemeinsamen Primer flankieren die uptag Barcode und wird benötigt, um die Hefe Barcodes zu verstärken. In AB-tag Primersequenzen der 5 &#39;Schwanz ist identisch mit 5&#39; Schwanz des UP-tag-Primer (Illumina bestimmten Reihenfolge), aber die 3 &#39;tail (unterstrichen) ist mit dem Gemeinsamen Primer, die verwendet werden, um die Verstärkung ersetzt DOWN- tag Barcodes.

competitive genomic screens of barcoded yeast libraries

Durch Fortschritte in der Sequenzierung der nächsten Generation Technologien haben wir Zugang zu neuen Genom-Sequenzen fast täglich. Das Tempo dieser Fortschritte ist die Beschleunigung, vielversprechende größere Tiefe und Breite. In Anbetracht dieser außergewöhnlichen Fortschritte, wird die Notwendigkeit für eine schnelle, parallele Methoden zur Gen-Funktion zu definieren immer mehr an Bedeutung. Sammlungen von genomweiten Deletionsmutanten in Hefe und E. coli wurden als Arbeitstiere für die funktionelle Charakterisierung der Genfunktion serviert, aber dieser Ansatz ist nicht skalierbar, erfordern aktuelle Gen-Deletion Ansätze jeder der Tausenden von Genen, die ein Genom zu löschen und überprüft werden sollen, umfassen. Erst nachdem diese Arbeit abgeschlossen ist können wir verfolgen, High-Throughput-Phänotypisierung. In den vergangenen zehn Jahren hat unser Labor ein Portfolio von wettbewerbsfähigen, miniaturisierte, High-Throughput-genomweite Tests, die in parallel ausgeführt werden können, verfeinert. Diese Parallelisierung ist wegen der Aufnahme von DNA &#39;Tags&#39; oder &#39;Barcodes, &quot;in jeder Mutante möglich, mit dem Barcode dient als Proxy für die Mutation, und man kann den Barcode Fülle Maßnahme zur mutierten Fitness zu bewerten. In dieser Studie wollen wir die Lücke zwischen DNA-Sequenz und Barcode-Mutante Sammlungen zu füllen. Um dies zu erreichen führen wir eine kombinierte Störung Transposon-Barcoding Ansatz, der sich öffnet parallel Barcode-Assays neu sequenziert, aber schlecht charakterisiert Mikroben. Zur Veranschaulichung dieses Ansatzes präsentieren wir eine neue Candida albicans Barcode Störungen Sammlung und beschreiben, wie beide Microarray-basierte und Sequenzierung der nächsten Generation-Plattformen verwendet werden kann auf 10.000 zu sammeln - 1.000.000 Gen-Gen-und Drogen-Gen-Interaktionen in einem einzigen Experiment.

Watch this Scientific Journal Video about Competitive Genomic Screens of Barcoded Yeast Libraries at JoVE.com

Competitive Genomic Screens of Barcoded Yeast Libraries

Wir verfügen über umfassende, unvoreingenommene genomweiten Screens entwickelt, um Gen-Medikament und Gen-Umwelt-Interaktionen zu verstehen. Methoden für das Screening dieser mutierten Sammlungen präsentiert werden.

Competitive Genomic Screens von Barcoded Hefe Bibliotheken

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily.  The tempo of these advances is ...

competitive-genomic-screens-of-barcoded-yeast-libraries

Research

JoVE Journal

Biology

18.1K Aufrufe.  University of Toronto. Wir verfügen über umfassende, unvoreingenommene genomweiten Screens entwickelt, um Gen-Medikament und Gen-Umwelt-Interaktionen zu verstehen. Methoden für das Screening dieser mutierten Sammlungen präsentiert werden.

Serie: Competitive Genomic Screens of Barcoded Yeast Libraries

Large-Scale Screens of Metagenomic Libraries

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation. Generating a streamlined procedure for creating and screening metagenomic libraries is therefore useful for efficient high-throughput investigations into the genetic and metabolic properties of uncultured microbial assemblages. Here, key protocols are presented on video, which we propose is the most useful format for accurately describing a long process that alternately depends on robotic instrumentation and (human) manual interventions. First, we employed robotics to spot library clones onto high-density macroarray membranes, each of which can contain duplicate colonies from twenty-four 384-well library plates. Automation is essential for this procedure not only for accuracy and speed, but also due to the miniaturization of scale required to fit the large number of library clones into highly dense spatial arrangements. Once generated, we next demonstrated how the macroarray membranes can be screened for genes of interest using modified versions of standard protocols for probe labeling, membrane hybridization, and signal detection. We complemented the visual demonstration of these procedures with detailed written descriptions of the steps involved and the materials required, all of which are available online alongside the video.

Large-Scale-Bildschirme von Metagenombanken

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation.  Generating a ...

Forschung

Biologie

Isolation of Genomic DNA from Mouse Tails

Isolierung genomischer DNA aus Maus-Tails

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Array comparative genomic hybridization (array CGH) is a method for detecting gains and losses of DNA segments or gene dosage in the genome 1. Recent advances in this technology have enabled high resolution comparison of whole genomes for the identification of genetic alterations in cancer and other genetic diseases 2. The Sub-Megabase Resolution Tiling-set array (or SMRT) array is comprised of a set of approximately thirty thousand overlapping bacterial artificial chromosome (BAC) clones that span the human genome in ~100 kilobase pair (kb) segments 2. These BAC targets are individually synthesized and spotted in duplicate on a single glass slide 2-4. Array CGH is based on the principle of competitive hybridization. Sample and reference DNA are differentially labeled with Cyanine-3 and Cyanine-5 fluorescent dyes, and co-hybridized to the array. After an incubation period the unbound samples are washed from the slide and the array is imaged. A freely available custom software package called SeeGH (www.flintbox.ca) is used to process the large volume of data collected - a single experiment generates 53,892 data points. SeeGH visualizes the log2 signal intensity ratio between the 2 samples at each BAC target which is vertically aligned with chromosomal position 5,6. The SMRT array can detect alterations as small as 50 kb in size 7. The SMRT array can detect a variety of DNA rearrangement events including DNA gains, losses, amplifications and homozygous deletions. A unique advantage of the SMRT array is that one can use DNA isolated from formalin fixed paraffin embedded samples. When combined with the low input requirements of unamplified DNA (25-100ng) this allows profiling of precious samples such as those produced by microdissection 7,8. This is attributed to the large size of each BAC hybridization target that allows the binding of sufficient labeled samples to produce signals for detection. Another advantage of this platform is the tolerance of tissue heterogeneity, decreasing the need for tedious tissue microdissection 8. This video protocol is a step-by-step tutorial from labeling the input DNA through to signal acquisition for the whole genome tiling path SMRT array.

This video is a technical demonstration of the hybridization protocol for whole genome tiling path array CGH, which scans the entire human genome using only 25-100 ng of DNA that can be isolated from a variety of sources, including archival formalin fixed material.

Technische Demonstration von Whole Genome Array Comparative Genomic Hybridization

Array comparative genomic hybridization (array CGH) is a method for detecting gains and losses of DNA segments or gene dosage in the genome 1.  Recent ...

Large Insert Environmental Genomic Library Production

The vast majority of microbes in nature currently remain inaccessible to traditional cultivation methods. Over the past decade, culture-independent environmental genomic (i.e. metagenomic) approaches have emerged, enabling researchers to bridge this cultivation gap by capturing the genetic content of indigenous microbial communities directly from the environment. To this end, genomic DNA libraries are constructed using standard albeit artful laboratory cloning techniques. Here we describe the construction of a large insert environmental genomic fosmid library with DNA derived from the vertical depth continuum of a seasonally hypoxic fjord. This protocol is directly linked to a series of connected protocols including coastal marine water sampling [1], large volume filtration of microbial biomass [2] and a DNA extraction and purification protocol [3]. At the outset, high quality genomic DNA is end-repaired with the creation of 5 -phosphorylated blunt ends. End-repaired DNA is subjected to pulsed-field gel electrophoresis (PFGE) for size selection and gel extraction is performed to recover DNA fragments between 30 and 60 thousand base pairs (Kb) in length. Size selected DNA is purified away from the PFGE gel matrix and ligated to the phosphatase-treated blunt-end fosmid CopyControl vector pCC1 (EPICENTRE <a href="http://www.epibio.com/item.asp?ID=385">http://www.epibio.com/item.asp?ID=385</a>). Linear concatemers of pCC1 and insert DNA are subsequently headfull packaged into phage particles by lambda terminase, with subsequent infection of phage-resistant E. coli cells. Successfully transduced clones are recovered on LB agar plates under antibiotic selection and archived in 384-well plate format using an automated colony picking robot (Qpix2, GENETIX). The current protocol draws from various sources including the CopyControl Fosmid Library Production Kit from EPICENTRE and the published works of multiple research groups [4-7]. Each step is presented with best practice in mind. Whenever possible we highlight subtleties in execution to improve overall quality and efficiency of library production. The whole process of fosmid library production and automated colony picking takes at least 7-10 days as there are many incubation steps included. However, there are several stopping points possible which are mentioned within the protocol.

Construction of a fosmid library with environmental genomic DNA isolated from the vertical depth continuum of a seasonally hypoxic fjord is described. The resulting clone library is picked into 384-well plates and archived for downstream sequencing and functional screening by the application of an automated colony picking system.

Large Insert Environmental Genomic Bibliothek Produktion

The vast majority of microbes in nature currently remain inaccessible to traditional cultivation methods. Over the past decade, culture-independent ...

Purification of Mitochondria from Yeast Cells

Mitochondria are the main site of ATP production during aerobic metabolism in eukaryotic non-photosynthetic cells1. These complex organelles also play essential roles in apoptotic cell death2, cell survival3, mammalian development4, neuronal development and function4, intracellular signalling5, and longevity regulation6. Our understanding of these complex biological processes controlled by mitochondria relies on robust methods for assessing their morphology, their protein and lipid composition, the integrity of their DNA, and their numerous vital functions. The budding yeast Saccharomyces cerevisiae, a genetically and biochemically manipulable unicellular eukaryote with annotated genome and well-defined proteome, is a valuable model for studying the molecular and cellular mechanisms underlying essential biological functions of mitochondria. For these types of studies, it is crucial to have highly pure mitochondria. Here we present a detailed description of a rapid and effective method for purification of yeast mitochondria. This method enables the isolation of highly pure mitochondria that are essentially free of contamination by other organelles and retain their structural and functional integrity after their purification. Mitochondria purified by this method are suitable for cell-free reconstitution of essential mitochondrial processes and can be used for the analysis of mitochondrial structure and functions, mitochondrial proteome and lipidome, and mitochondrial DNA.

We describe a rapid and effective method for purification of mitochondria from the yeast Saccharomyces cerevisiae. This method enables the high-yield isolation of pure mitochondria that are essentially free of contamination by other organelles and retain their structural and functional integrity after their purification.

Reinigung von Mitochondrien aus Hefezellen

Mitochondria are the main site of ATP production during aerobic metabolism in eukaryotic non-photosynthetic cells1. These complex organelles also play ...

Development of automated imaging and analysis for zebrafish chemical screens. 

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK pathway in zebrafish embryos. The zebrafish embryo is an ideal system for in vivo high-content chemical screens. The 1-day old embryo is approximately 1mm in diameter and can be easily arrayed into 96-well plates, a standard format for high throughput screening. During the first day of development, embryos are transparent with most of the major organs present, thus enabling visualization of tissue formation during embryogenesis. The complete automation of zebrafish chemical screens is still a challenge, however, particularly in the development of automated image acquisition and analysis. We previously generated a transgenic reporter line that expresses green fluorescent protein (GFP) under the control of FGF activity and demonstrated their utility in chemical screens 1. To establish methodology for high throughput whole organism screens, we developed a system for automated imaging and analysis of zebrafish embryos at 24-48 hours post fertilization (hpf) in 96-well plates 2. In this video we highlight the procedures for arraying transgenic embryos into multiwell plates at 24hpf and the addition of a small molecule (BCI) that hyperactivates FGF signaling 3. The plates are incubated for 6 hours followed by the addition of tricaine to anesthetize larvae prior to automated imaging on a Molecular Devices ImageXpress Ultra laser scanning confocal HCS reader. Images are processed by Definiens Developer software using a Cognition Network Technology algorithm that we developed to detect and quantify expression of GFP in the heads of transgenic embryos. In this example we highlight the ability of the algorithm to measure dose-dependent effects of BCI on GFP reporter gene expression in treated embryos.

Development of automated imaging and analysis for zebrafish chemical screens.

We report the development of a system for automated imaging and analysis of zebrafish transgenic embryos in multiwell plates. This demonstrates the ability to measure dose dependent effects of a small molecule, BCI, on Fibroblast Growth Factor reporter gene expression and provide technology for establishing high-throughput zebrafish chemical screens.

Entwicklung von automatisierten Imaging und Analyse für Zebrafisch chemische Bildschirme.

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK ...

Yeast Colony Embedding Method

Patterning of different cell types in embryos is a key mechanism in metazoan development. Communities of microorganisms, such as colonies and biofilms also display patterns of cell types. For example, in the yeast S. cerevisiae, sporulated cells and pseudohyphal cells are not uniformly distributed in colonies. The functional importance of patterning and the molecular mechanisms that underlie these patterns are still poorly understood.
One challenge with respect to investigating patterns of cell types in fungal colonies is that unlike metazoan tissue, cells in colonies are relatively weakly attached to one another. In particular, fungal colonies do not contain the same extensive level of extracellular matrix found in most tissues . Here we report on a method for embedding and sectioning yeast colonies that reveals the interior patterns of cell types in these colonies. The method can be used to prepare thick sections (0.5 &mu;) useful for light microscopy and thin sections (0.1 &mu;) suitable for transmission electron microscopy. Asci and pseudohyphal cells can easily be distinguished from ovoid yeast cells by light microscopy , while the interior structure of these cells can be visualized by EM.
The method is based on surrounding colonies with agar, infiltrating them with Spurr's medium, and then sectioning. Colonies with a diameter in the range of 1-2 mm are suitable for this protocol. In addition to visualizing the interior of colonies, the method allows visualization of the region of the colony that invades the underlying agar.

A method for embedding yeast colonies allowing sectioning for light and electron microscopy. This protocol allows determination of the distribution of sporulated cells and pseudohyphal cells within colonies providing a new tool toward understanding the organization of cell types within a fungal community.

Hefekolonie Embedding-Methode

Patterning of  different cell types in embryos is a key mechanism in metazoan development. Communities of microorganisms, such as colonies and biofilms ...

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova &amp; Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009).
Here we demonstrate a freely available Internet resource -- the Genomic MRI program package -- designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al. 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences. The main goal of this resource is to facilitate examination of vast regions of non-coding DNA that are still scarcely investigated and await thorough exploration and recognition.

We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.

Genomic MRI - eine öffentliche Ressource für ein Studium Sequence Patterns in genomischer DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in ...

Genomic Transformation of the Picoeukaryote Ostreococcus tauri

Common problems hindering rapid progress in Plant Sciences include cellular, tissue and whole organism complexity, and notably the high level of genomic redundancy affecting simple genetics in higher plants. The novel model organism Ostreococcus tauri is the smallest free-living eukaryote known to date, and possesses a greatly reduced genome size and cellular complexity1,2, manifested by the presence of just one of most organelles (mitochondrion, chloroplast, golgi stack) per cell, and a genome containing only ~8000 genes. Furthermore, the combination of unicellularity and easy culture provides a platform amenable to chemical biology approaches. Recently, Ostreococcus has been successfully employed to study basic mechanisms underlying circadian timekeeping3-6. Results from this model organism have impacted not only plant science, but also mammalian biology7. This example highlights how rapid experimentation in a simple eukaryote from the green lineage can accelerate research in more complex organisms by generating testable hypotheses using methods technically feasible only in this background of reduced complexity. Knowledge of a genome and the possibility to modify genes are essential tools in any model species. Genomic1, Transcriptomic8, and Proteomic9 information for this species is freely available, whereas the previously reported methods6,10 to genetically transform Ostreococcus are known to few laboratories worldwide.
In this article, the experimental methods to genetically transform this novel model organism with an overexpression construct by means of electroporation are outlined in detail, as well as the method of inclusion of transformed cells in low percentage agarose to allow selection of transformed lines originating from a single transformed cell. Following the successful application of Ostreococcus to circadian research, growing interest in Ostreococcus can be expected from diverse research areas within and outside plant sciences, including biotechnological areas. Researchers from a broad range of biological and medical sciences that work on conserved biochemical pathways may consider pursuing research in Ostreococcus, free from the genomic and organismal complexity of larger model species.

Genomic Transformation of the Picoeukaryote Ostreococcus tauri

This article describes genetic transformation of the unicellular marine alga Ostreococcus tauri by electroporation. This eukaryotic organism is an effective model platform for higher plants, possesing greatly reduced genomic and cellular complexity and being readily amenable to both cell culture and chemical biology.

Genomic Transformation des Picoeukaryote<em&gt; Ostreococcus tauri</em

Common problems hindering rapid progress in Plant Sciences include cellular, tissue and whole organism complexity, and notably the high level of genomic ...

Selective Capture of 5-hydroxymethylcytosine from Genomic DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer1. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), was discovered in mammalian cells, in particular in embryonic stem (ES) cells and neuronal cells2-4. 5-hmC is generated by oxidation of 5-mC catalyzed by TET family iron (II)/&alpha;-ketoglutarate-dependent dioxygenases2, 3. 5-hmC is proposed to be involved in the maintenance of embryonic stem (mES) cell, normal hematopoiesis and malignancies, and zygote development2, 5-10. To better understand the function of 5-hmC, a reliable and straightforward sequencing system is essential. Traditional bisulfite sequencing cannot distinguish 5-hmC from 5-mC11. To unravel the biology of 5-hmC, we have developed a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically12.
Here we describe a straightforward two-step procedure for selective chemical labeling of 5-hmC. In the first labeling step, 5-hmC in genomic DNA is labeled with a 6-azide-glucose catalyzed by &beta;-GT, a glucosyltransferase from T4 bacteriophage, in a way that transfers the 6-azide-glucose to 5-hmC from the modified cofactor, UDP-6-N3-Glc (6-N3UDPG). In the second step, biotinylation, a disulfide biotin linker is attached to the azide group by click chemistry. Both steps are highly specific and efficient, leading to complete labeling regardless of the abundance of 5-hmC in genomic regions and giving extremely low background. Following biotinylation of 5-hmC, the 5-hmC-containing DNA fragments are then selectively captured using streptavidin beads in a density-independent manner. The resulting 5-hmC-enriched DNA fragments could be used for downstream analyses, including next-generation sequencing.
Our selective labeling and capture protocol confers high sensitivity, applicable to any source of genomic DNA with variable/diverse 5-hmC abundances. Although the main purpose of this protocol is its downstream application (i.e., next-generation sequencing to map out the 5-hmC distribution in genome), it is compatible with single-molecule, real-time SMRT (DNA) sequencing, which is capable of delivering single-base resolution sequencing of 5-hmC.

Described is a two-step labeling process using &beta;-glucosyltransferase (&beta;-GT) to transfer an azide-glucose to 5-hmC, followed by click chemistry to transfer a biotin linker for easy and density-independent enrichment. This efficient and specific labeling method enables enrichment of 5-hmC with extremely low background and high-throughput epigenomic mapping via next-generation sequencing.

Selektive Aufnahme von 5-Hydroxymethylcytosin aus genomischer DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene ...