We would like to thank Dr. Garry Nolan from Stanford University for providing the Phoenix GP packaging cell line for the production of retroviral particles. We thank Dr. Roger Tsien at University of California San Diego for providing td Tomato. We would also like to thank the San Diego State University Flow Cytometry Core Facility for their service and help.

1. Preparation of Mammalian Cells, Viral Production and Transduction for Genetic Barcoding
<ol>
	<li>Plate 2.5 x 106 adherent cells in a 10 cm plate (or around 50-60% confluency) one day prior to transfection in Dulbecco&#8217;s modified eagle medium (DMEM) with 10% fetal calf serum (FCS). For retroviral production use packaging cell-line of choice such as Phoenix-GP (a kind gift from Gary Nolan, Stanford University). 
	NOTE: The packaging cell line stably expresses Gag and Pol proteins for retroviral p...

Here two well-established procedures have been combined; genetic engineering through retroviral technology and detection of fluorescent proteins utilizing flow cytometry. Fluorescent protein-based genetic barcoding for the production of unique cell lines provides a robust and simple way for multiplexed applications. Generating genetically engineered barcoded cells through retroviral technology, is initially a lengthy process, but allows one to obtain, once established, a reliable and stable source of cell material. The n...

Technologies such as fluorescence spectroscopy, fluorescence microscopy and flow cytometry, all rely on fluorescence, a property widely exploited in biochemical, biomedical, and chemical applications. Fluorescence, whether intrinsic or through labeling, has been exploited for the analysis of protein expression patterns and profiles, cell fate, protein interactions and biological functions1-9, and through fluorescence/F&#246;rster resonance energy transfer for the detection of biomolecule interactions and conformational changes10-13. Since the isolation of the Aequorea victoria green fluorescent protein (GFP)14, the discovery of additional naturally occurring fluorescent proteins from other cnidarians, particularly corals, has largely increased the number of existing fluorescent proteins with distinguishable excitation/emission spectra. These, together with the introduction of mutations in their genes15-19, have further expanded the possibilities, obtaining a true palette of fluorescent proteins available to scientists that exploit microscopy, flow cytometry and other fluorescence-based technologies for their research.
In parallel, although independently, the development of retroviral technology has drastically facilitated the stable expression of ectopic genetic information in mammalian cells20-23. It is thus not surprising that this technology has been used to transfer genes of fluorescent proteins into a broad number of cell types and tissues24-28 or for production of transgenic animals29-31. Following the nature of retroviruses, the genetic information of the ectopic fluorescent protein is introduced within the genome of the cell32 and the cell becomes fluorescent `for ever&#180;. This property has allowed tracking of cell fate, or of a single cell within a population of cells. The now fluorescent cell has thus acquired its own biosignature and can be defined as barcoded. Its unique biosignature identifies it from other cells, and importantly, distinguishes it from cells genetically manipulated to express different fluorescent proteins with distinguishable absorption/emission spectra. Biological applications such as the tracking of reprogramming factors toward pluripotency33, the analysis of subnuclear factors for the elucidation of nucleolar localization34, the construction of fluorescent reporter plasmids for transcriptional studies35 or the genetic labeling of neurons for the study of neuronal network architecture36, are just four examples of the many that have exploited different fluorescent protein genes for the same experimental setup.
Flow cytometry has been broadly utilized for the analysis of biological processes at the single cell level, such as gene expression, cell cycle, apoptosis, and signaling through phosphorylation37-43.The stable expression of fluorescent protein genes in mammalian cells has further enhanced the utility of flow cytometry for cell analysis38,44 and ligand-receptor interactions45. Enhanced capabilities have allowed flow cytometry to become a widely utilized methodology for high-throughput and high-content screening46. Despite the now expanded number of fluorometers and robotics technologies that can couple plate reader systems, imaging and flow cytometry, there seems to be a lack in experimental design that can exploit and fit these enhanced technological capabilities.
Fast, reliable, simple and robust cell-based methodologies are drastically needed for multiplexed applications that further enhance high-throughput capacity. This is especially true in the field of drug discovery where engineering cell-based assays in a multiplexed format can enhance the power of high-throughput screening39,47-50. Multiplexing, as it allows simultaneous analyses in one sample, further enhances high-throughput capabilities51-54. Fluorescent genetic barcoding not only allows for elegant multiplexing, but also, once engineered, circumvents the need of time consuming protocols, reduces costs accompanied with antibodies, beads and stains39,52,55, and can reduce the number of screens required for high-throughput applications. We have recently described how retroviral technology can enhance multiplexing through fluorescent genetic barcoding for biological applications, by expressing an assay previously developed to monitor HIV-1 protease activity56,57 with different clinically prevalent variants58. The methodology is explained in a more descriptive manner focusing on how to select and amplify genetically fluorescent barcoded cells and how to produce panels of clonal populations expressing distinct fluorescent proteins and/or different fluorescence intensities. Panels of cell populations distinguishable based on their fluorescent characteristics enhance multiplexed capabilities, which can be further exploited in combination with cell-based assays that tackle different biological questions. The protocol also describes how to engineer a panel of barcoded cells bearing one of the cell-based assays previously developed in the laboratory, as example59. This protocol is thus not intended to show the well-established retroviral/lentiviral technology for genetic transfer, the value of fluorescent proteins or the applications of flow cytometry60,48 but rather to show the enhancing power of combining the three for multiplexed applications.

<table border="0" cellpadding="0" cellspacing="0" width="1138">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Name of Material/ Equipment</td>
			<td style="width:160px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:515px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">10mL syringes</td>
			<td style="width:160px;">BD&#160;&#160;</td>
			<td>309604</td>
			<td>used for filtering the virus</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.45&#181;m plytetrafluoroethylen filter</td>
			<td style="width:160px;">pall corporation</td>
			<td>4219</td>
			<td>used for filtering the virus</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">DMEM (Dulbecco&#39;s Modified Eagle Medium)</td>
			<td style="width:160px;">Corning</td>
			<td style="width:119px;">45000-304</td>
			<td>cell growth media for HEK 293T cells</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PEI (Polyethylenimine)</td>
			<td style="width:160px;">poly sciences</td>
			<td>23966-2</td>
			<td>&#160;2mg/mL concentration used</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Hanging bucket centrifuge (refrigerated)</td>
			<td style="width:160px;">Eppendorf&#160;</td>
			<td style="width:119px;">5805 000.017</td>
			<td>used for spin infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">PBS (phosphate buffered saline)</td>
			<td style="width:160px;">Corning</td>
			<td>21-040-CV</td>
			<td>used for washing of cells</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Polybrene (hexadimethreen bromide)</td>
			<td style="width:160px;">Sigma-Aldrich</td>
			<td>107689</td>
			<td>Used to increase viral infection efficiency.&#160; Used at a 5&#181;g/mL concentration.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">FACSAria</td>
			<td style="width:160px;">BD Biosciences</td>
			<td style="width:119px;"></td>
			<td>instrument used for sorting cell populations</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">FACSCanto</td>
			<td style="width:160px;">BD Biosciences</td>
			<td style="width:119px;"></td>
			<td>instrument used for cell analysis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Phoenix-GP</td>
			<td style="width:160px;">Gift from Gary Nolan</td>
			<td style="width:119px;"></td>
			<td>cell line used to produced retroviral particles</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Fetal calf serum</td>
			<td style="width:160px;">Mediatech</td>
			<td>MT35015CV&#160;</td>
			<td>used for cell growth and sorting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">&#160;SupT1 cells</td>
			<td style="width:160px;">ATCC</td>
			<td>CRL-1942</td>
			<td>Human T lymphoblasts</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">HEK 293T cells</td>
			<td style="width:160px;">ATCC</td>
			<td>CRL-11268</td>
			<td>Human Embryonic Kidney cells that also contain the SV40 large T-antigen</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">RPMI 1640</td>
			<td style="width:160px;">Corning</td>
			<td>10-040-CV</td>
			<td>cell growth media for SupT1 cells</td>
		</tr>
	</tbody>
</table>

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.

Multiplexing fluorescent genetically barcoded cells for the purpose of biological applications can only be achieved once individual clonal populations have been generated. Multiplexing is most effective when barcoded populations have clear distinct fluorescent characteristics with minimal spectral overlap. The example shown in Figure 1 with clonal populations of mammalian SupT1 cells illustrates that barcoded cells with mCherry and cyano fluorescent protein (CFP) can be easily analyzed simultaneously wit...

Watch this Scientific Journal Video about Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications at JoVE.com

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

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.

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

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JoVE Journal

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9.2K ビュー.  San Diego State University. 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. 

ビデオ: Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

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.

phospho flow cytometry with fluorescent cell barcoding for single cell signaling analysis and biomarker discovery

Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery

Here, a protocol for medium- to high-throughput analysis of protein phosphorylation events at the cellular level is presented. Phospho flow cytometry is a powerful approach to characterize signaling aberrations, identify and validate biomarkers, and assess...

multiplexed barcoding image analysis for immunoprofiling and spatial mapping characterization in the single-cell analysis of paraffin tissue samples

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Multiplexed barcoding image analysis has recently improved the characterization of the tumor microenvironment, permitting comprehensive studies of cell composition, functional state, and cell-cell interactions. Herein, we describe a staining and imaging protocol using the barcoding of oligonucleotide-conjugated antibodies and cycle imaging, which allows for the use of a high-dimensional image&#160;analysis...

highly-multiplexed tissue imaging with raman dyes

Highly-Multiplexed Tissue Imaging with Raman Dyes

Electronic pre-resonance stimulated Raman scattering (epr-SRS) imaging of rainbow-like Raman dyes is a new platform for highly multiplexed epitope-based protein imaging. Here, we present a practical guide including antibody preparation, tissue sample staining, SRS microscope assembly, and epr-SRS tissue...

multiplexed fluorescent immunohistochemical staining, imaging, and analysis in histological samples of lymphoma

Multiplexed Fluorescent Immunohistochemical Staining, Imaging, and Analysis in Histological Samples of Lymphoma

Here we describe a protocol for multiplex fluorescent immunohistochemical staining and imaging for the simultaneous localization of multiple cancer-associated antigens in lymphoma. This protocol can be extended to the colocalization analysis of biomarkers within all tissue...

multiplexed fluorescent immunohistochemical staining of four endometrial immune cell types in recurrent miscarriage

Multiplexed Fluorescent Immunohistochemical Staining of Four Endometrial Immune Cell Types in Recurrent Miscarriage

Despite the advancements in multiplex immunohistochemistry and multispectral imaging, characterizing the density and clustering of major immune cells simultaneously in the endometrium remains a challenge. This paper describes a detailed multiplex staining protocol and imaging for the simultaneous localization of four immune cell types in the...

multiplexed fluorescent microarray for human salivary protein analysis using polymer microspheres and fiber-optic bundles

Multiplexed Fluorescent Microarray for Human Salivary Protein Analysis Using Polymer Microspheres and Fiber-optic Bundles

We describe a procedure for profiling salivary proteins using multiplexed microsphere-based antibody arrays. Monoclonal antibodies were covalently linked to fluorescent dye-encoded 4.5 &#x03BC;m polymer microspheres using carbodiimide chemistry. The modified microspheres were deposited in fiber-optic microwells to measure protein levels in saliva using fluorescence sandwich...

measurement of four uterine nk cell subtypes using multiplexed fluorescent immunohistochemical staining in women with repeated implantation failure

Author Spotlight: Multiplex Immunohistochemistry for Understanding Immune Regulation by Uterine NK Cells in Pregnancy

This study presents a pioneering method for quantifying uterine natural killer cell subsets during the window of implantation using advanced multiplexed fluorescent immunohistochemical staining...

Measurement of Four Uterine NK Cell Subtypes Using Multiplexed Fluorescent Immunohistochemical Staining in Women with Repeated Implantation Failure

localization of sumo-modified proteins using fluorescent sumo-trapping proteins

Localization of SUMO-modified Proteins Using Fluorescent Sumo-trapping Proteins

SUMO is an essential and highly conserved, small ubiquitin-like modifier protein. In this protocol we are describing the use of a stress-tolerant recombinant SUMO-trapping protein (kmUTAG) to visualize native, untagged SUMO conjugates and their localization in a variety of cell...

analyzing the interaction of fluorescent-labeled proteins with artificial phospholipid microvesicles using quantitative flow cytometry

Analyzing the Interaction of Fluorescent-Labeled Proteins with Artificial Phospholipid Microvesicles using Quantitative Flow Cytometry

Here, we describe a set of methods for characterizing the interaction of proteins with membranes of cells or...

patterning bioactive proteins or peptides on hydrogel using photochemistry for biological applications

Patterning Bioactive Proteins or Peptides on Hydrogel Using Photochemistry for Biological Applications

In this method, we use photopolymerization and click chemistry techniques to create protein or peptide patterns on the surface of polyethylene glycol (PEG) hydrogels, providing immobilized bioactive signals for the study of cellular responses in...

microfluidic platform with multiplexed electronic detection for spatial tracking of particles

Microfluidic Platform with Multiplexed Electronic Detection for Spatial Tracking of Particles

We demonstrate a microfluidic platform with an integrated surface electrode network that combines resistive pulse sensing (RPS) with code division multiple access (CDMA), to multiplex detection and sizing of particles in multiple microfluidic...

fluorescent silver staining of proteins in polyacrylamide gels

Fluorescent Silver Staining of Proteins in Polyacrylamide Gels

Here, we describe a detailed protocol outlining a new fluorescent staining technique for total protein detection in polyacrylamide gels. The protocol utilizes a silver ion-specific fluorescence turn-on probe, which detects Ag+-protein complexes, and eliminates certain limitations of traditional chromogenic silver...

combining intravital fluorescent microscopy (ivfm) with genetic models to study engraftment dynamics of hematopoietic cells to bone marrow niches

Combining Intravital Fluorescent Microscopy IVFM with Genetic Models to Study Engraftment Dynamics of Hematopoietic Cells to Bone Marrow Niches

Intravital fluorescence microscopy (IVFM) of the calvarium is applied in combination with genetic animal models to study the homing and engraftment of hematopoietic cells into bone marrow (BM) niches.

Combining Intravital Fluorescent Microscopy (IVFM) with Genetic Models to Study Engraftment Dynamics of Hematopoietic Cells to Bone Marrow Niches

intravital microscopy for imaging subcellular structures in live mice expressing fluorescent proteins

Intravital Microscopy for Imaging Subcellular Structures in Live Mice Expressing Fluorescent Proteins

Intravital microscopy is a powerful tool that enables imaging various biological processes in live animals. In this article, we present a detailed method for imaging the dynamics of subcellular structures, such as the secretory granules, in the salivary glands of live...

super-resolution imaging of bacterial secreted proteins using genetic code expansion

Super-Resolution Imaging of Bacterial Secreted Proteins Using Genetic Code Expansion

This article provides a straightforward and clear protocol to label Salmonella secreted effectors using genetic code expansion (GCE) site-specifically and image the subcellular localization of secreted proteins in HeLa cells using direct stochastic optical reconstruction microscopy (dSTORM)...

fluorescent labeling of antibodies for imaging low abundance proteins in drosophila

Fluorescent Labeling of Antibodies for Imaging Low Abundance Proteins in  Drosophila   

Fluorescent Labeling of Antibodies for Imaging Low Abundance Proteins in Drosophila

single-cell multiplexed fluorescence imaging to visualize viral nucleic acids and proteins and monitor hiv, htlv, hbv, hcv, zika virus, and influenza infection

Single-Cell Multiplexed Fluorescence Imaging to Visualize Viral Nucleic Acids and Proteins and Monitor HIV, HTLV, HBV, HCV, Zika Virus, and Influenza Infection

Presented here is a protocol for a fluorescence imaging approach, multiplex immunofluorescent cell-based detection of DNA, RNA, and protein (MICDDRP), a method capable of simultaneous fluorescence single-cell visualization of viral protein and nucleic acids of different type and strandedness. This approach can be applied to a diverse range of...

fluorescent labeling of cos-7 expressing snap-tag fusion proteins for live cell imaging

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone...

a barcoding assay for phenotypic and functional characterization of immune cells

This video highlights a single-cell proteomic method that employs heavy-metal-conjugated antibodies for distinct cell barcoding. Subsequently, immunostaining and mass cytometry are applied to evaluate immune phenotypic and functional alterations in human whole blood-derived immune...

A Barcoding Assay for Phenotypic and Functional Characterization of Immune Cells

Labeling Stem Cells with Fluorescent Dyes for non-invasive Detection with Optical Imaging

Optical imaging (OI) is an easy, fast and inexpensive tool for in vivo monitoring of new stem cell based therapies. The technique is based on ex vivo labeling of stem cells with a fluorescent dye, subsequent intravenous injection of the labeled cells and visualization of their accumulation in specific target organs or pathologies. The presented technique demonstrates how we label human mesenchymal stem cells (hMSC) by simple incubation with the lipophilic fluorescent dye DiD (C67H103CIN2O3S) and how we label human embryonic stem cells (hESC) with the FDA approved fluorescent dye Indocyanine Green (ICG). The uptake mechanism is via adherence and diffusion of the lypophilic dye across the phospholipid cell membrane bilayer. The labeling efficiency is usually improved if the cells are incubated with the dye in serum-free media as opposed to incubation in serum-containing media. Furthermore, the addition of the transfection agent Protamine Sulfate significantly improves contrast agent uptake.

This video shows techniques for labeling of human embryonic stem cells and mesenchymal stem cells with fluorescent dyes. This technique can be used for an in vivo tracking of transplanted stem cells with optical imaging and for histopathological correlations with fluorescence microscopy.

Optical imaging (OI) is an easy, fast and inexpensive tool for in vivo monitoring of new stem cell based therapies. The technique is based on ex vivo ...

Method for Culture of Early Chick Embryos ex vivo (New Culture)

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  the formation and patterning of brain, neural tube, somite and heart primordia. Applications of chick embryo culture include electroporation of DNA or RNA constructs in order to analyze gene function, grafts of growth factor coated beads such as FGFs and BMPs , as well as whole mount in situ hybridization and immunohistochemistry. This video demonstrates the different steps in chick embryo culture; First, the embryo is explanted in saline. Then, the embryo is centered on a glass ring. The membranes surrounding the embryo are lifted along the walls of the ring. The ring is then placed in a culture dish containing a pool of albumine. The culture dish is sealed and placed in a humid chamber, where the embryo is cultured for up to 24 hrs. Finally, the embryo is removed from the ring, fixed and processed for further applications. A troubleshooting guide is also presented.

Method for Culture of Early Chick Embryos ex vivo New Culture

This video demonstrates New culture, a method by which chick embryos are cultured outside the egg for up to 24 hr. This method enables one to study early development (primitive streak to 14 som.), a period corresponding to E7-9 in mouse. Applications of this technique include electroporation, in situ hybridization and immunohistochemistry.

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Double Whole Mount in situ Hybridization of Early Chick Embryos

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  gene expression in brain, neural tube, somite and heart primordia formation. This video demonstrates the different steps in 2-color whole mount in situ hybridization; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, the embryo is processed for prehybridization. The embryo is then hybridized with two different probes, one coupled to DIG, and one coupled to FITC.  Following overnight hybridization, the embryo is incubated with DIG coupled antibody. Color reaction for DIG substrate is performed, and the region of interest appears blue. The embryo is then incubated with FITC coupled antibody. The embryo is processed for color reaction with FITC, and the region of interest appears red. Finally, the embryo is fixed and processed for phtograph and sectioning. A troubleshooting guide is also presented.

This video demonstrates 2-color whole mount in situ hybridization, a method by which the spatial and temporal expression pattern of 2 different genes can be visualized in young chick embryos. This method was originally introduced by David Wilkinson, Domingos Henrique, Phil Ingham and David Ish -Horowicz.

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

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

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

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

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

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells.

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again.

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest ...

Closed System Cell Culture Protocol Using HYPERStack Vessels with Gas Permeable Material Technology

Large volume adherent cell culture is currently standardized on stacked plate cell growth products when microcarrier beads are not an optimal choice. HYPERStack vessels allow closed system scale up from the current stacked plate products and delivers >2.5X more cells in the same volumetric footprint. The HYPERStack vessels function via gas permeable material which allows gas exchange to occur, therefore eliminating the need for internal headspace within a vessel. The elimination of headspace allows the compartment where cell growth occurs to be minimized to reduce space, allowing more layers of cell growth surface area within the same volumetric footprint.
For many applications such as cell therapy or vaccine production, a closed system is required for cell growth and harvesting. The HYPERStack vessel allows cell and reagent addition and removal via tubing from media bags or other methods.
This protocol will explain the technology behind the gas permeable material used in the HYPERStack vessels, gas diffusion results to meet the metabolic needs of cells, closed system cell growth protocols, and various harvesting methods.

An Introduction into the technology, protocol and handling of the Corning HYPERStack Vessels and accessories used for high yield adherent cell culture. The protocol will show how to use the closed system vessels for increasing cell harvesting over current stacked plate products.

Large volume adherent cell culture is currently standardized on stacked plate cell growth products when microcarrier beads are not an optimal choice.   ...

Absolute Quantum Yield Measurement of Powder Samples

Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and research of illumination, AV equipment, organic EL material, films, filters and fluorescent probes for bio-industry.
Quantum yield is calculated as the ratio of the number of photons absorbed, to the number of photons emitted by a material. The higher the quantum yield, the better the efficiency of the fluorescent material.
For the measurements featured in this video, we will use the Hitachi F-7000 fluorescence spectrophotometer equipped with the Quantum Yield measuring accessory and Report Generator program. All the information provided applies to this system. 
Measurement of quantum yield in powder samples is performed following these steps:
<ol>
 <li>Generation of instrument correction factors for the excitation and emission monochromators. This is an important requirement for the correct measurement of quantum yield. It has been performed in advance for the full measurement range of the instrument and will not be shown in this video due to time limitations.</li>
 <li>Measurement of integrating sphere correction factors. The purpose of this step is to take into consideration reflectivity characteristics of the integrating sphere used for the measurements.</li>
 <li>Reference and Sample measurement using direct excitation and indirect excitation.</li>
 <li>Quantum Yield calculation using Direct and Indirect excitation. Direct excitation is when the sample is facing directly the excitation beam, which would be the normal measurement setup. However, because we use an integrating sphere, a portion of the emitted photons resulting from the sample fluorescence are reflected by the integrating sphere and will re-excite the sample, so we need to take into consideration indirect excitation. This is accomplished by measuring the sample placed in the port facing the emission monochromator, calculating indirect quantum yield and correcting the direct quantum yield calculation.</li>
 <li>Corrected quantum yield calculation.</li>
 <li>Chromaticity coordinates calculation using Report Generator program.</li>
</ol>
The Hitachi F-7000 Quantum Yield Measurement System offer advantages for this
application, as follows:
<ul>
 <li>High sensitivity (S/N ratio 800 or better RMS). Signal is the Raman band of water measured under the following conditions: Ex wavelength 350 nm, band pass Ex and Em 5 nm, response 2 sec), noise is measured at the maximum of the Raman peak. High sensitivity allows measurement of samples even with low quantum yield. Using this system we have measured quantum yields as low as 0.1 for a sample of salicylic acid and as high as 0.8 for a sample of magnesium tungstate.</li>
 <li>Highly accurate measurement with a dynamic range of 6 orders of magnitude allows for measurements of both sharp scattering peaks with high intensity, as well as broad fluorescence peaks of low intensity under the same conditions. </li>
 <li>High measuring throughput and reduced light exposure to the sample, due to a high scanning speed of up to 60,000 nm/minute and automatic shutter function. </li>
 <li>Measurement of quantum yield over a wide wavelength range from 240 to 800 nm.</li>
 <li>Accurate quantum yield measurements are the result of collecting instrument spectral response and integrating sphere correction factors before measuring the sample.</li>
 <li>Large selection of calculated parameters provided by dedicated and easy to use software.
</li>
</ul> 
During this video we will measure sodium salicylate in powder form which is known to have a quantum yield value of 0.4 to 0.5.

In this video we will demonstrate measuring and calculating absolute quantum yield and chromaticity coordinates directly in powder samples using the Hitachi F-7000 Quantum Yield Measuring System.

Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and ...

Here we describe a procedure to image subcellular structures in live rodents that is based on the use of confocal intravital microscopy. As a model organ, we use the salivary glands of live mice since they provide several advantages. First, they can be easily exposed to enable access to the optics, and stabilized to facilitate the reduction of the motion artifacts due to heartbeat and respiration. This significantly facilitates imaging and tracking small subcellular structures. Second, most of the cell populations of the salivary glands are accessible from the surface of the organ. This permits the use of confocal microscopy that has a higher spatial resolution than other techniques that have been used for in vivo imaging, such as two-photon microscopy. Finally, salivary glands can be easily manipulated pharmacologically and genetically, thus providing a robust system to investigate biological processes at a molecular level.
In this study we focus on a protocol designed to follow the kinetics of the exocytosis of secretory granules in acinar cells and the dynamics of the apical plasma membrane where the secretory granules fuse upon stimulation of the beta-adrenergic receptors. Specifically, we used a transgenic mouse that co-expresses cytosolic GFP and a membrane-targeted peptide fused with the fluorescent protein tandem-Tomato. However, the procedures that we used to stabilize and image the salivary glands can be extended to other mouse models and coupled to other approaches to label in vivo cellular components, enabling the visualization of various subcellular structures, such as endosomes, lysosomes, mitochondria, and the actin cytoskeleton.

Intravital microscopy is a powerful tool that enables imaging various biological processes in live animals. In this article, we present a detailed method for imaging the dynamics of subcellular structures, such as the secretory granules, in the salivary glands of live mice.

Here we describe a procedure to image subcellular structures in live rodents that is based on the use of confocal intravital microscopy. As a model organ, ...

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.

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

Simultaneous Measurement of Mitochondrial Calcium and Mitochondrial Membrane Potential in Live Cells by Fluorescent Microscopy

Apart from their essential role in generating ATP, mitochondria also act as local calcium (Ca2+) buffers to tightly regulate intracellular Ca2+ concentration. To do this, mitochondria utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester Ca2+. The influx of Ca2+ into the mitochondria stimulates three rate-limiting dehydrogenases of the citric acid cycle, increasing electron transfer through the oxidative phosphorylation (OXPHOS) complexes. This stimulation maintains &#916;&#936;m, which is temporarily dissipated as the positive calcium ions cross the mitochondrial inner membrane into the mitochondrial matrix.
We describe here a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using confocal microscopy. By permeabilizing the cells, mitochondrial Ca2+ can be measured using the fluorescent Ca2+ indicator Fluo-4, AM, with measurement of &#916;&#936;m using the fluorescent dye tetramethylrhodamine, methyl ester, perchlorate (TMRM). The benefit of this system is that there is very little spectral overlap between the fluorescent dyes, allowing accurate measurement of mitochondrial Ca2+ and &#916;&#936;m simultaneously. Using the sequential addition of Ca2+ aliquots, mitochondrial Ca2+ uptake can be monitored, and the concentration at which Ca2+ induces mitochondrial membrane permeability transition and the loss of &#916;&#936;m determined.

Mitochondria can utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester calcium (Ca2+), allowing them to shape cytosolic Ca2+ signaling within the cell. We describe a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using fluorescent dyes and confocal microscopy.