עבודה זו נתמכה באופן מלא על ידי תוכנית מחקר בין החומות של, NIH המכון הלאומי להזדקנות. אנו מודים לד&quot;ר רודני רוטשטיין (קולומביה) על זני שמרים ד&quot;ר בראד ג&#39;ונסון (אוניברסיטת פנסילבניה הספר לרפואה, בפילדלפיה, פנסילבניה) לביטוי SGS1 הפלסמיד.

<ol>
	<li>Aggarwal, M., Brosh, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=WRN+helicase+defective+in+the+premature+aging+disorder+Werner+Syndrome+genetically+interacts+with+Topoisomerase+3+and+restores+the+top3+slow+growth+phenotype+of+sgs1+top3.">WRN helicase defective in the premature aging disorder Werner Syndrome genetically interacts with Topoisomerase 3 and restores the top3 slow growth phenotype of sgs1 top3.</a> Aging. 1, 219-233 (2009).</li><li>Gangloff, S., McDonald, J. P., Bendixen, C., Arthur, L., Rothstein, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+yeast+type+I+topoisomerase+Top3+interacts+with+Sgs1,+a+DNA+helicase+homolog:+a+potential+eukaryotic+reverse+gyrase.">The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase.</a> Mol Cell Biol. 14, 8391-8398 (1994).</li><li>Shor, E., Gangloff, S., Wagner, M., Weinstein, J., Price, G., Rothstein, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+homologous+recombination+genes+rescue+top3+slow+growth+in+Saccharomyces+cerevisiae.">Mutations in homologous recombination genes rescue top3 slow growth in Saccharomyces cerevisiae.</a> Genetics. 162, 647-662 (2002).</li><li>Sharma, S., Sommers, J. A., Brosh, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+function+of+the+conserved+non-catalytic+domain+of+Werner+syndrome+helicase+in+DNA+replication.">In vivo function of the conserved non-catalytic domain of Werner syndrome helicase in DNA replication.</a> Hum Mol Genet. 13, 2247-2261 (2004).</li><li>Gietz, R. D., Schiestl, R. H., Willems, A. R., Woods, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+on+the+transformation+of+intact+yeast+cells+by+the+LiAc/SS-DNA/PEG+procedure.">Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure.</a> Yeast. 11, 355-360 (1995).</li><li>von Kobbe, C., Thoma, N. H., Czyzewski, B. K., Pavletich, N. P., Bohr, V. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Werner+syndrome+protein+contains+three+structure+specific+DNA+binding+domains.">Werner syndrome protein contains three structure specific DNA binding domains.</a> J Biol Chem. 278, 52997-53006 (2003).</li></ol>

אחד היתרונות של שימוש בשמרים כמודל למערכת הוא הזמינות של מוטציות בשכפול הדנ&quot;א מוגדרים מסלולי תיקון אשר נשמרת בין שמרים ובני אדם. מבחר נוסף של transformants מחסה גנים ספציפיים קל ואמין כמו זנים במעבדה הם מוטנטים auxotrophic ו וקטורים עם סמנים auxotrophic זמינים. שימוש אלה וקטורים הביטוי של מוצרים גן יכול להיות מוסדר על ידי הצבתם בשליטת היזם ועין מתנהלת (למשל, מקדם גל ועין מתנהלת וכו &#39;). לאור יתרונות אלה, פיתחנו מודל מבוסס מערכת שמרים ללמוד את הדרישות הפונקציונליות של הגן WRN אדם פגום תסמונת ורנר במסלול כי נשמרת פוטנציאלי בין אדם שמרים. שימוש בגישות שתוארו, סיפקנו את ההוכחה הראשונה לכך WRN יכול לתפקד במסלול גנטית המשפיעה top3 הקשורות פנוטיפים. התצפיות שלנו הפקודה חקירה נוספת של האפשרות WRN תפקודית אינטראקציה עם Top3α בתאים אנושיים במהלך שכפול הדנ&quot;א רקומבינציה או הסלולר. מתקבל על הדעת, במצב BLM-לקוי, WRN עשוי חלקית תחליף BLM באמצעות השותפות שלה עם חלבון topoisomerase.

genetic studies of human dna repair proteins using yeast as a model system 

הבנת תפקידם של החלבונים תיקון דנ&quot;א אנושי במסלולים גנטי הוא אתגר עצום לחוקרים רבים. מחקרים גנטיים במערכות יונקים היה מוגבל בשל היעדר כלים זמינים כולל מוטציה קווים מוגדרים התא הגנטי, מערכות רגולטוריות הביטוי, וסמנים לבחירה המתאימה. כדי לעקוף את הקשיים הללו, מערכות מודל גנטי אאוקריוטים נמוך הפכו בחירה אטרקטיבית לחקר תפקודית נשמרת לתקן דנ&quot;א וחלבונים המסלולים. פיתחנו מודל שמרים המערכת כדי ללמוד את פונקציות גנטי מוגדר היטב של תסמונת ורנר helicase-nuclease (<em&gt; WRN</em&gt;) במטבוליזם של חומצות גרעין. פנוטיפים נייד הקשורים מוגדר backgrounds מוטציה גנטית יכולה להיחקר כדי להבהיר את הפונקציות תאית ומולקולרית של<em&gt; WRN</em&gt; באמצעות פעילות קטליטית שלה אינטראקציות חלבון. האדם<em&gt; WRN</em&gt; גנים וריאנטים הקשורים, משובטים לתוך פלסמידים DNA לביטוי בשמרים, ניתן למקם תחת שליטתו של אלמנט פלסמיד הרגולציה. לבנות הביטוי לאחר מכן ניתן להפוך את השמרים רקע מתאים מוטציה, ותפקוד גנטי assayed על ידי מגוון של מתודולוגיות. בגישה זו, קבענו כי<em&gt; WRN</em&gt; כמו RecQ שלה חברי משפחה הקשורים BLM ו Sgs1, פועל מסלול Top3 תלויי כי הוא עשוי להיות חשוב עבור יציבות גנומית. זה מתואר בפרסום האחרון שלנו [1] ב<a href="http://www.impactaging.com"&gt; Www.impactaging.com</a&gt;. שיטות מפורט של מבחני ספציפית ללימודי השלמה גנטית בשמרים ניתנים במאמר זה.

Watch this Scientific Journal Video about Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System at JoVE.com

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

מחקרים גנטיים שמרים יכול להיות מועסק לחקור את הפונקציות מולקולרית תאית של הגנים האנושיים במטבוליזם DNA התאי. מתוארות שיטות לאפיון הגנטי של האדם<em&gt; WRN</em&gt; הגן הפגום של תסמונת הזדקנות מוקדמת ורנר הפרעה תפקודית המסלולים נשמרת באמצעות שמרים כמודל למערכת ממושמע המוצר.

מחקרים גנטיים של חלבונים תיקון דנ&quot;א אנושי באמצעות שמרים כמודל למערכת

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

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Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

17.8K Views.  National Institute on Aging, NIH. מחקרים גנטיים שמרים יכול להיות מועסק לחקור את הפונקציות מולקולרית תאית של הגנים האנושיים במטבוליזם DNA התאי. מתוארות שיטות לאפיון הגנטי של האדם WRN הגן הפגום של תסמונת הזדקנות מוקדמת ורנר הפרעה תפקודית המסלולים נשמרת באמצעות שמרים כמודל למערכת ממושמע המו...

Video: Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Microinjection of Medaka Embryos for use as a Model Genetic Organism

In this video, we demonstrate the technique of microinjection into one-cell stage medaka embryos. Medaka is a small egg-laying freshwater fish that allows both genetic and embryological analyses and is one of the vertebrate model organisms in which genome-wide phenotype-driven mutant screens were carried out 1, as in zebrafish and the mouse. Divergence of functional overlap of related genes between medaka and zebrafish allows identification of novel phenotypes that are unidentifiable in a single species 2, thus medaka and zebrafish are complementary for genetic dissection of vertebrate genome functions.
To take advantage of medaka fish whose embryos are transparent and develop externally, microinjection is an essential technique to inject cell-tracers for labeling cells, mRNAs or anti-sense oligonucleotides for over-expressing and knocking-down genes of interest, and DNAs for making transgenic lines.

Medaka and zebrafish are complementary for genetic dissection of vertebrate genome functions. This protocol highlights the key points for successful microinjection into medaka embryos, an important technique for embryological and genetic analysis using medaka and zebrafish in a laboratory.

Microinjection עוברים Medaka לשימוש כמודל אורגניזם גנטי

In this video, we demonstrate the technique of microinjection into one-cell stage medaka embryos. Medaka is a small egg-laying freshwater fish that allows ...

Visualization of DNA Replication in the Vertebrate Model System DT40 using the DNA Fiber Technique

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not only ensure faithful genome duplication in the face of endogenous and exogenous DNA damage but also prevent genomic instability, a recognized causative factor in tumor development.
Here, we describe a simple and cost-effective fluorescence microscopy-based method to visualize DNA replication in the avian B-cell line DT40. This cell line provides a powerful tool to investigate protein function in vivo by reverse genetics in vertebrate cells1. DNA fiber fluorography in DT40 cells lacking a specific gene allows one to elucidate the function of this gene product in DNA replication and genome stability. Traditional methods to analyze replication fork dynamics in vertebrate cells rely on measuring the overall rate of DNA synthesis in a population of pulse-labeled cells. This is a quantitative approach and does not allow for qualitative analysis of parameters that influence DNA synthesis. In contrast, the rate of movement of active forks can be followed directly when using the DNA fiber technique2-4. In this approach, nascent DNA is labeled in vivo by incorporation of halogenated nucleotides (Fig 1A). Subsequently, individual fibers are stretched onto a microscope slide, and the labeled DNA replication tracts are stained with specific antibodies and visualized by fluorescence microscopy (Fig 1B). Initiation of replication as well as fork directionality is determined by the consecutive use of two differently modified analogues. Furthermore, the dual-labeling approach allows for quantitative analysis of parameters that influence DNA synthesis during the S-phase, i.e. replication structures such as ongoing and stalled forks, replication origin density as well as fork terminations. Finally, the experimental procedure can be accomplished within a day, and requires only general laboratory equipment and a fluorescence microscope.

DT40, a model vertebrate genetic system, provides a powerful tool to analyze protein function. Here we describe a simple method that allows qualitative analysis of parameters that influence DNA synthesis during the S-phase in DT40 cells at the single molecule level.

ויזואליזציה של שכפול ה-DNA של DT40 דגם מערכת החולייתנים באמצעות טכניקה סיב ה-DNA

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not ...

Modified Yeast-Two-Hybrid System to Identify Proteins Interacting with the Growth Factor Progranulin

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role in a variety of physiologic and disease processes, including early embryogenesis, wound healing 1, inflammation 2, 3, and host defense 4. PGRN also functions as a neurotrophic factor 5, and mutations in the PGRN gene resulting in partial loss of the PGRN protein cause frontotemporal dementia 6, 7. Our recent studies have led to the isolation of PGRN as an important regulator of cartilage development and degradation 8-11. Although PGRN, discovered nearly two decades ago, plays crucial roles in multiple physiological and pathological conditions, efforts to exploit the actions of PGRN and understand the mechanisms involved have been significantly hampered by our inability to identify its binding receptor(s). To address this issue, we developed a modified yeast two-hybrid (MY2H) approach based on the most commonly used GAL4 based 2-hybrid system. Compared with the conventional yeast two-hybrid screen, MY2H dramatically shortens the screen process and reduces the number of false positive clones. In addition, this approach is reproducible and reliable, and we have successfully employed this system in isolating the binding proteins of various baits, including ion channel 12, extracellular matrix protein 10, 13, and growth factor14. In this paper, we describe this MY2H experimental procedure in detail using PGRN as an example that led to the identification of TNFR2 as the first known PGRN-associated receptor 14, 15.

We have modified the conventional yeast two-hybrid screening, an effective genetic tool in identifying protein interaction. This modification markedly shortens the process, reduces the workload, and most importantly, reduces the number of false positives. In addition, this approach is reproducible and reliable.

השתנה שמרים-Two-Hybrid System כדי לזהות חלבונים אינטראקציה עם גורם הגדילה Progranulin

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role ...

Generation of Human Cardiomyocytes: A Differentiation Protocol from Feeder-free Human Induced Pluripotent Stem Cells

In order to investigate the events driving heart development and to determine the molecular mechanisms leading to myocardial diseases in humans, it is essential first to generate functional human cardiomyocytes (CMs). The use of these cells in drug discovery and toxicology studies would also be highly beneficial, allowing new pharmacological molecules for the treatment of cardiac disorders to be validated pre-clinically on cells of human origin. Of the possible sources of CMs, induced pluripotent stem (iPS) cells are among the most promising, as they can be derived directly from readily accessible patient tissue and possess an intrinsic capacity to give rise to all cell types of the body 1. Several methods have been proposed for differentiating iPS cells into CMs, ranging from the classical embryoid bodies (EBs) aggregation approach to chemically defined protocols 2,3. In this article we propose an EBs-based protocol and show how this method can be employed to efficiently generate functional CM-like cells from feeder-free iPS cells.

Pluripotent stem cells, either embryonic or induced pluripotent stem (iPS) cells, constitute a valuable source of human differentiated cells, including cardiomyocytes. Here, we will focus on cardiac induction of iPS cells, showing how to use them to obtain functional human cardiomyocytes through an embryoid bodies-based protocol.

דור של cardiomyocytes אדם: פרוטוקול בידול מתאי גזע מושרה pluripotent אדם ללא מזין

In order to investigate the events driving heart development and to determine the molecular mechanisms leading to myocardial diseases in humans, it is ...

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism

The folding and assembly of proteins is essential for protein function, the long-term health of the cell, and longevity of the organism. Historically, the function and regulation of protein folding was studied in vitro, in isolated tissue culture cells and in unicellular organisms. Recent studies have uncovered links between protein homeostasis (proteostasis), metabolism, development, aging, and temperature-sensing. These findings have led to the development of new tools for monitoring protein folding in the model metazoan organism Caenorhabditis elegans. In our laboratory, we combine behavioral assays, imaging and biochemical approaches using temperature-sensitive or naturally occurring metastable proteins as sensors of the folding environment to monitor protein misfolding. Behavioral assays that are associated with the misfolding of a specific protein provide a simple and powerful readout for protein folding, allowing for the fast screening of genes and conditions that modulate folding. Likewise, such misfolding can be associated with protein mislocalization in the cell. Monitoring protein localization can, therefore, highlight changes in cellular folding capacity occurring in different tissues, at various stages of development and in the face of changing conditions. Finally, using biochemical tools ex vivo, we can directly monitor protein stability and conformation. Thus, by combining behavioral assays, imaging and biochemical techniques, we are able to monitor protein misfolding at the resolution of the organism, the cell, and the protein, respectively.

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism

To study the relationship between protein homeostasis, stress and aging, we monitored changes in protein folding by following protein dysfunction, protein localization in the cell and protein stability at the organismal, cellular and protein levels, using the genetically tractable metazoan Caenorhabditis elegans as a model system.

The folding and assembly of proteins is essential for protein function, the long-term health of the cell, and longevity of the organism. Historically, the ...

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3&#8217;-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.

Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

הדמיה בזמן אמת של יחיד תכנון הנדסי RNA תמלילים בתאים חיים באמצעות משואות bimolecular רציומטרי

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded &#180;indefinitely&#180;. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.

Since the discovery of the green fluorescent protein gene, fluorescent proteins have impacted molecular cell biology. This protocol describes how expression of distinct fluorescent proteins through genetic engineering is used for barcoding individual cells. The procedure enables tracking distinct populations in a cell mixture, which is ideal for multiplexed applications.

Barcoding הגנטי עם חלבונים ניאון עבור יישומי Multiplexed

Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery ...

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging (ESI)

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in cell biology. Many phenomena cannot be explained by in vitro analysis in simplified systems and need additional structural information in situ, particularly in the range between 1 nm and 0.1 &#181;m, in order to be fully understood. Here, electron spectroscopic imaging, a transmission electron microscopy technique that allows simultaneous mapping of the distribution of proteins and nucleic acids, and an expression tag, miniSOG, are combined to study the structure and organization of DNA double-strand break repair foci.

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Electron spectroscopic imaging can image and distinguish nucleic acid from protein at nanometer resolution. It can be combined with the miniSOG system, which is able to specifically label tagged proteins in transmission electron microscopy samples. We illustrate the use of these technologies using double-strand break repair foci as an example.

הדמיה של חלבונים תיקון ה- DNA miniSOG תייג בשילוב עם אלקטרונים Spectroscopic הדמיה (ESI)

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in ...

DNA Electroporation, Isolation and Imaging of Myofibers

Mature muscle has a unique structure that is amenable to live cell imaging. Herein, we describe the experimental protocol for expressing fluorescently labeled proteins in the flexor digitorum brevis (FDB) muscle. Conditions have been optimized to provide a large number of high quality myofibers expressing the electroporated plasmid while minimizing muscle damage. The method employs fluorescent tags on various proteins. Combining this expression method with high resolution confocal microscopy permits live cell imaging, including imaging after laser-induced damage. Fluorescent dyes combined with imaging of fluorescently-tagged proteins provides information regarding the basic structure of muscle and its response to stimuli.

This protocol utilizes electroporation to introduce and express fluorescently labeled proteins in mouse muscle fibers. Following recovery after electroporation, fibers are isolated. Individual fibers are then imaged using high resolution confocal microscopy to visualize muscle structure.

DNA Electroporation, בידוד והדמיה של Myofibers

Mature muscle has a unique structure that is amenable to live cell imaging. Herein, we describe the experimental protocol for expressing fluorescently ...

Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System

The recent development of a high-throughput single-cell assay technique enables the screening of novel enzymes based on functional activities from a large-scale metagenomic library1. We previously proposed a genetic enzyme screening system (GESS) that uses dimethylphenol regulator activated by phenol or p-nitrophenol. Since a vast amount of natural enzymatic reactions produce these phenolic compounds from phenol deriving substrates, this single genetic screening system can be theoretically applied to screen over 200 different enzymes in the BRENDA database. Despite the general applicability of GESS, applying the screening process requires a specific procedure to reach the maximum flow cytometry signals. Here, we detail the developed screening process, which includes metagenome preprocessing with GESS and the operation of a flow cytometry sorter. Three different phenolic substrates (p-nitrophenyl acetate, p-nitrophenyl-&#946;-D-cellobioside, and phenyl phosphate) with GESS were used to screen and to identify three different enzymes (lipase, cellulase, and alkaline phosphatase), respectively. The selected metagenomic enzyme activities were confirmed only with the flow cytometry but DNA sequencing and diverse in vitro analysis can be used for further gene identification.

This work presents a method of high-throughput screening using a universal genetic enzyme screening system that can be theoretically applied to over 200 enzymes. Here, the single screening system identifies three different enzymes (lipase, cellulase, and alkaline phosphatase) by simply changing the substrate used (p-nitrophenyl acetate, p-nitrophenyl-&#946;-D-cellobioside, and phenyl phosphate).

הקרנה רב-אנזים באמצעות מערכת הקרנת אנזים הגנטי תפוקה גבוהה

The recent development of a high-throughput single-cell assay technique enables the screening of novel enzymes based on functional activities from a ...