The authors would like to thank Dr. Cliona M. McHale for critically reading and editing the manuscript. This work was funded by the National Institute of Environmental Health Sciences, National Institute of Health grant R01ES017452 to L Zhang.

1. Sample slide preparation
 <ul>
 <li>OctoChrome FISH is designed to examine chromosomal changes in metaphase spreads of human cells, including but not limited to cultured peripheral blood cells, stem/progenitor cells, and cell lines. Samples should be prepared following the standard procedure for harvesting metaphases3,11-13: by employing colcemid treatment to arrest cells in metaphase, hypotonic treatment to swell cells, and Carnoy's fixative to fix cells in suspension at approximately 0.5-1 x 106 cells per ml.</li>
 <li>Clean the 8-square slide (provided in the OctoChrome Kit, Catalogue #: PMP 803, Cytocell Ltd, Cambridge, UK, Figure 2) by dipping into pure ethanol for 2 min.</li>
 <li>Before making the sample slide, drop a small amount of cells onto a slide to check the cell density. If the cell density is too high (too many overlapping cells), dilute the suspension with fresh fixative. If the cell density is too low (too few cells on slide), spin down the cells and re-suspend in a smaller volume of fresh fixative. Pipette 5-10 &mu;l of cell suspension onto each of 8 areas of the template slide in a sequence of alternating squares 1/7 - 2/8 - 3/5 - 4/6. Once the first two squares has air-dried, spot the remaining squares in the same manner. This will prevent the cell spreads from interfering with each other.</li>
 <li>The dried slide can be stored at -20&deg;C in nitrogen atmosphere for greater than 5 years before hybridization.</li>
 </ul>
 2. Localization of metaphases using an automated system
 <ul>
 <li>Apply 20 &mu;l of 4',6-diamidino-2-phenylindole (0.2 &mu;g/ml) to the center of each half of the slide and then cover with a coverslip.</li>
 <li>Perform an automated scan of the sample slide to localize the metaphase cells using Metafer software (MetaSystems, Altlussheim, Germany). This facilitates location of all the metaphases and future re-evaluation of all cell images.</li>
 <li>View the scanning results manually and delete non-metaphase artifacts.</li>
 </ul>
 3. Hybridization
 <ol>
 <li>Preparation of the sample slide and OctoChrome device
 <ul>
 <li>Dip the sample slide in 2x SSC buffer at room temperature for 30 min to wash away DAPI.</li>
 <li>Dehydrate the sample slide through a series of ethanol washes (2 minutes each in 70%, 85% and 100% ethanol), allow to dry and place on a 37&deg;C hotplate for 5 minutes.</li>
 <li>Place the Chromoprobe Multiprobe Hybridization Chamber (provided in the OctoChrome Kit) in a 37&deg;C water bath and allow to equilibrate to 37&deg;C (+/- 1&deg;C).</li>
 <li>Mix the hybridization solution (provided in the OctoChrome Kit) by repeated pipetting and pre-warm a 25 &mu;l aliquot per OctoChrome device to 37&deg;C.</li>
 <li>Pre-warm each OctoChrome device (provided in the OctoChrome Kit, see Figure 2) to 37&deg;C by placing the device label side down on a hotplate. DO NOT touch the embossed surfaces of the OctoChrome device as they contain the probes.</li>
 </ul></li>
 <li>Positioning of the sample slide over the OctoChrome device (Figure 2)
 <ul>
 <li>Add 2 &mu;l of pre-warmed hybridization solution to each of the eight areas on the pre-warmed OctoChrome device while it remains at 37&deg;C.</li>
 <li>Carefully invert the template slide over the OctoChrome device such that the number 1, which is now upside down, is located over the top right hand area of the OctoChrome device. To help locate square 1, its position on the device has been marked in Orange.</li>
 <li>Make sure that the template slide is carefully aligned with the matching areas on the OctoChrome device. Carefully lower the slide over the OctoChrome device so that the drops of hybridization solution make contact with the slide. Apply gentle, even pressure to ensure that the hybridization solution is spread to the edges of each of the raised areas on the OctoChrome device.</li>
 <li>Lift the slide/OctoChrome, carefully holding the frosted end of the glass slide, and invert so that the slide is underneath the OctoChrome device. Make sure the device does not smear across the template slide as this could cause cross-contamination of the probes.</li>
 <li>Place on a 37&deg;C (+/- 1&deg;C) hotplate for 10 minutes.</li>
 </ul></li>
 <li>Denaturation
 <ul>
 <li>Transfer the sample slide/OctoChrome device to the hotplate taking particular care to hold it level. Ensure the sample slide evenly contacts the hotplate.</li>
 <li>Denature on the hotplate at 75&deg;C (+/- 1&deg;C) for 5 minutes.</li>
 </ul></li>
 <li>Hybridization
 <ul>
 <li>Place sample slide/OctoChrome device in the Chromoprobe Multiprobe Hybridization Chamber.</li>
 <li>Replace the lid and float the chamber in the 37&deg;C (+/- 1&deg;C) water bath (non - stirring) overnight. Please note: DO NOT seal the lid on the hybridization chamber; DO NOT seal the lid on the water bath; DO NOT hybridize in an incubator. These steps are critical to controlling humidity.</li>
 </ul></li>
 <li>Post-hybridization washes
 <ul>
 <li>Preparation of wash solutions 
 Solution 1: Prepare a Coplin/Hellendahl jar containing 0.4x SSC. Equilibrate to 72&deg;C (+/- 1&deg;C) in a water bath and adjust the pH to 7.0. 
 Solution 2: Prepare a Coplin/Hellendahl jar containing 2x SSC and 0.05% Tween 20. Allow to stand at room temperature.</li>
 <li>Remove the OctoChrome device carefully from the slide and place the slide in Solution 1 for 2 minutes.</li>
 <li>Place the slide into Solution 2 for 30 seconds.</li>
 </ul>
</li>
 </ol>
 4. Mounting and visualization of results
 <ul>
 <li>Apply 20 &mu;l of DAPI to the center of each half of the slide and apply a coverslip.</li>
 <li>Incubate in the dark for 10 minutes at room temperature before viewing by fluorescence microscopy.</li>
 </ul>
5. Representative Results
Figure 3A shows a normal metaphase cell in Square 2. (1)-(3): Chromosomes 8, 21 and 12 were painted red, green, and blue, and are visualized through a Texas Red, FITC, and DEAC filter, respectively; (4): Visualization through a DAPI/FITC/Texas Red triple filter. Generally, the chromosomes painted with blue are not clear through the triple filter and need to be viewed under the specific DEAC filter.
Figure 3B shows representative abnormal cells with leukemia-specific chromosomal translocation and aneuploidy. (1): t(8;21), a common chromosomal translocation in acute myeloid leukemia; (2): Trisomy 21, three copies of chromosome 21, a common aneuploidy in leukemia.
<img alt="Figure 1" src="/files/ftp_upload/3619/3619fig1.jpg" />
Figure 1. Arrangement of chromosome combinations on the OctoChrome device and expected chromosomal painting results.
<img alt="Figure 2" src="/files/ftp_upload/3619/3619fig2.jpg" />
Figure 2. Positioning of sample slide over the OctoChrome device.






















Figure 3. Representative results obtained from OctoChrome FISH (Square 2).
<img alt="Figure 3A" src="/files/ftp_upload/3619/3619fig3A.jpg" />
Figure 3A. A normal cell with chromosomes 8, 12, 21 painted in Square 2.
<img alt="Figure 3B" src="/files/ftp_upload/3619/3619fig3B.jpg" />
Figure 3B. Representative abnormal cells with leukemia-specific chromosomal translocation and aneuploidy in Square 2.

<ol>
	<li>Levsky, J. M., Singer, R. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+in+situ+hybridization:+past,+present+and+future.">Fluorescence in situ hybridization: past, present and future.</a> J. Cell. Sci. 116, 2833-2838 (2003).</li><li>Zhang, L., Eastmond, D. A., Smith, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+nature+of+chromosomal+aberrations+detected+in+humans+exposed+to+benzene.">The nature of chromosomal aberrations detected in humans exposed to benzene.</a> Crit. Rev. Toxicol. 32, 1-42 (2002).</li><li>Zhang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aberrations+in+chromosomes+associated+with+lymphoma+and+therapy-related+leukemia+in+benzene-exposed+workers.">Aberrations in chromosomes associated with lymphoma and therapy-related leukemia in benzene-exposed workers.</a> Environ. Mol. Mutagen. 48, 467-474 (2007).</li><li>Zhang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Benzene+increases+aneuploidy+in+the+lymphocytes+of+exposed+workers:+a+comparison+of+data+obtained+by+fluorescence+in+situ+hybridization+in+interphase+and+metaphase.">Benzene increases aneuploidy in the lymphocytes of exposed workers: a comparison of data obtained by fluorescence in situ hybridization in interphase and metaphase.</a> Environ. Mol. Mutagen. 34, 260-268 (1999).</li><li>Zhang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+aneusomy+and+long+arm+deletion+of+chromosomes+5+and+7+in+the+lymphocytes+of+Chinese+workers+exposed+to+benzene.">Increased aneusomy and long arm deletion of chromosomes 5 and 7 in the lymphocytes of Chinese workers exposed to benzene.</a> Carcinogenesis. 19, 1955-1961 (1998).</li><li>Smith, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+translocations+and+aneusomy+in+chromosomes+8+and+21+among+workers+exposed+to+benzene.">Increased translocations and aneusomy in chromosomes 8 and 21 among workers exposed to benzene.</a> Cancer. Res. 58, 2176-2181 (1998).</li><li>Bayani, J., Squire, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+the+detection+of+chromosomal+aberrations+using+spectral+karyotyping.">Advances in the detection of chromosomal aberrations using spectral karyotyping.</a> Clin. Genet. 59, 65-73 (2001).</li><li>Zhang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromosome-wide+aneuploidy+study+(CWAS)+in+workers+exposed+to+an+established+leukemogen,+benzene.">Chromosome-wide aneuploidy study (CWAS) in workers exposed to an established leukemogen, benzene.</a> Carcinogenesis. 32, 605-612 (2011).</li><li>Rowley, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+chromosome+translocations+in+leukemogenesis.">The role of chromosome translocations in leukemogenesis.</a> Semin. Hematol. 36, 59-72 (1999).</li><li>Zhang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+OctoChrome+fluorescence+in+situ+hybridization+to+detect+specific+aneuploidy+among+all+24+chromosomes+in+benzene-exposed+workers.">Use of OctoChrome fluorescence in situ hybridization to detect specific aneuploidy among all 24 chromosomes in benzene-exposed workers.</a> Chem. Biol. Interact. , 153-154 (2005).</li><li>Barch, M. J., Lawce, H. J., Arsham, M. S., Barch, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> In The ACT cytogenetics laboratory. , 17-30 (1991).</li><li>Zhang, L., Yang, W., Hubbard, A. E., Smith, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nonrandom+aneuploidy+of+chromosomes+1,+5,+6,+7,+8,+9,+11,+12,+and+21+induced+by+the+benzene+metabolites+hydroquinone+and+benzenetriol.">Nonrandom aneuploidy of chromosomes 1, 5, 6, 7, 8, 9, 11, 12, and 21 induced by the benzene metabolites hydroquinone and benzenetriol.</a> Environ. Mol. Mutagen. 45, 388-396 (2005).</li><li>Smith, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydroquinone,+a+benzene+metabolite,+increases+the+level+of+aneusomy+of+chromosomes+7+and+8+in+human+CD34-positive+blood+progenitor+cells.">Hydroquinone, a benzene metabolite, increases the level of aneusomy of chromosomes 7 and 8 in human CD34-positive blood progenitor cells.</a> Carcinogenesis. 21, 1485-1490 (2000).</li><li>Smith, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+understanding+benzene+health+effects+and+susceptibility.">Advances in understanding benzene health effects and susceptibility.</a> Annu. Rev. Public. Health. 31, 133-148 (2010).</li></ol>

We have nothing to disclose.

This novel OctoChrome-FISH assay allows one to simultaneously examine all 24 human chromosomes in a single hybridization on one slide. The arrangement of chromosome combinations on the 8 squares has been designed to facilitate the identification of the non-random chromosome rearrangements in the most common leukemias and lymphomas. Thus, the assay can detect numerical (aneuploidy) as well as structural (translocations) chromosome alterations concurrently. 
The most critical step in this assay ...

<table border="1">
	<tbody>
 	<tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 <td>Comments (optional)</td>
 <tr>
 <tr>
 	 <td>OctoChrome Kit </td>
 <td>Cytocell Ltd, Cambridge, UK </td>
 <td>PMP 803</td>
 <td>&nbsp;</td>
 </tr>
 <tr>
 	 <td>phytohaemagglutinin (PHA)</td>
 <td>Invitrogen Corporation</td>
 <td>10576-015</td>
 <td>&nbsp;</td>
 </tr>
 <tr>
 	 <td>Colcemid </td>
 <td>Invitrogen Corporation </td>
 <td>15212-012</td>
 <td>&nbsp;</td>
 </tr>
 <tr>
 	 <td>Carnoy&#x2019;s fixative</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>Methanol : glacial acetic acid = 3: 1</td>
 </tr>
 <tr>
 	 <td>Fluorescence microscope </td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>Equipped with filters to view DAPI, Texas Red, FITC, and Coumarin spectra individually and a DAPI/FITC/Texas Red triple filter to view different colors simultaneously </td>
 </tr>
 <tr>
 	 <td>Metafer software </td>
 <td>MetaSystems, Altlussheim, Germany</td>
 <td>&nbsp;</td>
 <td>Facilitate to locate all metaphases and to re-evaluate the abnormalities </td>
 </tr>
 </tbody>
</table>

chromosomics: detection of numerical and structural alterations in all 24 human chromosomes simultaneously using a novel octochrome fish assay

Fluorescence in situ hybridization (FISH) is a technique that allows specific DNA sequences to be detected on metaphase or interphase chromosomes in cell nuclei1. The technique uses DNA probes with unique sequences that hybridize to whole chromosomes or specific chromosomal regions, and serves as a powerful adjunct to classic cytogenetics. For instance, many earlier studies reported the frequent detection of increased chromosome aberrations in leukemia patients related with benzene exposure, benzene-poisoning patients, and healthy workers exposed to benzene, using classic cytogenetic analysis2. Using FISH, leukemia-specific chromosomal alterations have been observed to be elevated in apparently healthy workers exposed to benzene3-6, indicating the critical roles of cytogentic changes in benzene-induced leukemogenesis. 
Generally, a single FISH assay examines only one or a few whole chromosomes or specific loci per slide, so multiple hybridizations need to be conducted on multiple slides to cover all of the human chromosomes. Spectral karyotyping (SKY) allows visualization of the whole genome simultaneously, but the requirement for special software and equipment limits its application7. Here, we describe a novel FISH assay, OctoChrome-FISH, which can be applied for Chromosomics, which we define here as the simultaneous analysis of all 24 human chromosomes on one slide in human studies, such as chromosome-wide aneuploidy study (CWAS)8. The basis of the method, marketed by Cytocell as the Chromoprobe Multiprobe System, is an OctoChrome device that is divided into 8 squares, each of which carries three different whole chromosome painting probes (Figure 1). Each of the three probes is directly labeled with a different colored fluorophore, green (FITC), red (Texas Red), and blue (Coumarin). The arrangement of chromosome combinations on the OctoChrome device has been designed to facilitate the identification of the non-random structural chromosome alterations (translocations) found in the most common leukemias and lymphomas, for instance t(9;22), t(15;17), t(8;21), t(14;18)9. Moreover, numerical changes (aneuploidy) in chromosomes can be detected concurrently. The corresponding template slide is also divided into 8 squares onto which metaphase spreads are bound (Figure 2), and is positioned over the OctoChrome device. The probes and target DNA are denatured at high-temperature and hybridized in a humid chamber, and then all 24 human chromosomes can be visualized simultaneously. 
OctoChrome FISH is a promising technique for the clinical diagnosis of leukemia and lymphoma and for detection of aneuploidies in all chromosomes. We have applied this new Chromosomic approach in a CWAS study of benzene-exposed Chinese workers8,10.

Watch this Scientific Journal Video about Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay at JoVE.com

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

A novel fluorescence in situ hybridization (FISH) method that simultaneously examines both numerical and structural chromosome alterations, particularly the specific chromosomal translocations associated with leukemia and lymphoma, of all 24 human chromosomes on a single device in one hybridization, is described.

Fluorescence in situ hybridization (FISH) is a technique that allows specific DNA sequences to be detected on metaphase or interphase chromosomes in cell ...

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18.7K Views.  University of California, Berkeley. A novel fluorescence in situ hybridization (FISH) method that simultaneously examines both numerical and structural chromosome alterations, particularly the specific chromosomal translocations associated with leukemia and lymphoma, of all 24 human chromosomes on a single device in one hybridization, is described.

Video: Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Fluorescence in situ hybridization (FISH) Protocol in Human Sperm

Aneuploidies are the most frequent chromosomal abnormalities in humans. Most of these abnormalities result from meiotic errors during the gametogenic process in the parents. In human males, these errors can lead to the production of spermatozoa with numerical chromosome abnormalities which represent an increased risk of transmitting these anomalies to the offspring.
For this reason, the technique of fluorescence in situ hybridization (FISH) on sperm nuclei has become a protocol widely incorporated in the context of clinical diagnosis. This practice provides an estimate of the frequencies of numerical chromosome abnormalities in the gametes of the patients that seek for genetic reproductive advice.
To date, the chromosomes most frequently included in sperm FISH analysis are chromosomes X, Y, 13, 18 and 21.
This video-article describes, step by step, how to process and fix a human semen sample, how to decondense and denature the sperm chromatin, how to proceed to obtain sperm FISH preparations, and how to visualize the results at the microscope. Special remarks of the most relevant steps are given to achieve the best results.

Fluorescence in situ hybridization FISH Protocol in Human Sperm

This video-article describes, step by step, how to process a semen sample to achieve good-quality fluorescence in situ hybridization on human spermatozoa. Preparations obtained can be used for aneuploidy screening in the context of clinical diagnosis.

Aneuploidies are the most frequent chromosomal abnormalities in humans. Most of these abnormalities result from meiotic errors during the gametogenic ...

Detection of Signaling Effector-Complexes Downstream of BMP4 Using in situ PLA, a Proximity Ligation Assay

BMPs are responsible for a wide range of developmental and biological effects. BMP receptors activate (phosphorylate) the Smad1/5/8 effectors, which then, form a complex with Smad4 and translocate to the nucleus where they function as transcription factors to initiate BMP specific downstream effects 1. Traditional immuno-fluorescence techniques with antibodies against phospho-Smad peptides exhibit low sensitivity, high background and offer gross quantification as they rely on intensity of the antibody signal particularly if this is photosensitive fluorescent. In addition, phospho-Smads may not all be in complex with Smad4 and engaged in active transcription.
In situ PLA is a technology capable of detecting protein interactions with high specificity and sensitivity 2-4. This new technology couples antibody recognition with the amplification of DNA surrogate of the protein. It generates a localized, discrete signal in a form of spots revealing the exact position of the recognition event. The number of signals can be counted and compared providing a measurement. We applied in situ PLA, using the Duolink kit, with a combination of antibodies that allows the detection of the BMP signaling effectors phospho-Smad1/5/8 and Smad4 only when these are in proximity i.e. in a complex, which occurs only with signaling activation. This allowed for the first time, the visualization and measurement of endogenous BMP signaling with high specificity and sensitivity in a time course experiment under BMP4 stimulation.

Detection of Signaling Effector-Complexes Downstream of BMP4 Using in situ PLA, a Proximity Ligation Assay

Here we show how to use Proximity Ligation Assay (PLA), with a combination of antibodies to visualize Bone Morphogenetic Protein (BMP) signaling in fixed cells. This technique allowed us to follow the nuclear accumulation of endogenous BMP activated effector-complexes and quantify their levels over time under BMP4 stimulation.

BMPs are responsible for a wide range of developmental and biological effects. BMP receptors activate (phosphorylate) the Smad1/5/8 effectors, which then, ...

High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace 
the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties 
of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the 
phenolic polymer lignin, that is also difficult to digest 1. In order to improve the digestibility of plant materials we need to discover the main bottlenecks 
for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification 2. These tasks require 
a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has 
been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes 
for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.
This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant 
materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded 
amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for 
analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this 
station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90&deg;C. The pretreatment solution 
is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme
mixture for a variable length of time at 50&deg;C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH 
colorimetric method.

A simple, rapid method for determining the saccharification potential of large numbers of plant biomass samples is described. The automated platform for this analysis involves the preparation of the plant biomass for analysis in 96 well plates and the subsequent performance of pretreatment, hydrolysis and quantification of the sugars released.

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing ...

Detection of Viral RNA by Fluorescence in situ Hybridization (FISH)

Viruses that infect cells elicit specific changes to normal cell functions which serve to divert energy and resources for viral replication. Many aspects of host cell function are commandeered by viruses, usually by the expression of viral gene products that recruit host cell proteins and machineries. Moreover, viruses engineer specific membrane organelles or tag on to mobile vesicles and motor proteins to target regions of the cell (during de novo infection, viruses co-opt molecular motor proteins to target the nucleus; later, during virus assembly, they will hijack cellular machineries that will help in the assembly of viruses). Less is understood on how viruses, in particular those with RNA genomes, coordinate the intracellular trafficking of both protein and RNA components and how they achieve assembly of infectious particles at specific loci in the cell. The study of RNA localization began in earlier work. Developing lower eukaryotic embryos and neuronal cells provided important biological information, and also underscored the importance of RNA localization in the programming of gene expression cascades. The study in other organisms and cell systems has yielded similar important information. Viruses are obligate parasites and must utilise their host cells to replicate. Thus, it is critical to understand how RNA viruses direct their RNA genomes from the nucleus, through the nuclear pore, through the cytoplasm and on to one of its final destinations, into progeny virus particles 1.
FISH serves as a useful tool to identify changes in steady-state localization of viral RNA. When combined with immunofluorescence (IF) analysis 22, FISH/IF co-analyses will provide information on the co-localization of proteins with the viral RNA3. This analysis therefore provides a good starting point to test for RNA-protein interactions by other biochemical or biophysical tests 4,5, since co-localization by itself is not enough evidence to be certain of an interaction. In studying viral RNA localization using a method like this, abundant information has been gained on both viral and cellular RNA trafficking events 6. For instance, HIV-1 produces RNA in the nucleus of infected cells but the RNA is only translated in the cytoplasm. When one key viral protein is missing (Rev) 7, FISH of the viral RNA has revealed that the block to viral replication is due to the retention of the HIV-1 genomic RNA in the nucleus 8. 
Here, we present the method for visual analysis of viral genomic RNA in situ. The method makes use of a labelled RNA probe. This probe is designed to be complementary to the viral genomic RNA. During the in vitro synthesis of the antisense RNA probe, the ribonucleotide that is modified with digoxigenin (DIG) is included in an in vitro transcription reaction. Once the probe has hybridized to the target mRNA in cells, subsequent antibody labelling steps (Figure 1) will reveal the localization of the mRNA as well as proteins of interest when performing FISH/IF.

Detection of Viral RNA by Fluorescence in situ Hybridization FISH

A fluorescence in situ hybridization (FISH) method was developed to visually detect viral genomic RNA using fluorescence microscopy. A probe is made with specificity to the viral RNA that can then be identified using a combination of hybridization and immunofluorescence techniques. This technique offers the advantage of identifying the localization of the viral RNA or DNA at steady-state, providing information on the control of intracellular virus trafficking events.

Viruses  that infect cells elicit specific changes to normal cell functions which serve  to divert energy and resources for viral replication. Many ...

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Efforts to detect and investigate key oncogenic mutations have proven valuable to facilitate the appropriate treatment for cancer patients. The establishment of high-throughput, massively parallel "next-generation" sequencing has aided the discovery of many such mutations. To enhance the clinical and translational utility of this technology, platforms must be high-throughput, cost-effective, and compatible with formalin-fixed paraffin embedded (FFPE) tissue samples that may yield small amounts of degraded or damaged DNA. Here, we describe the preparation of barcoded and multiplexed DNA libraries followed by hybridization-based capture of targeted exons for the detection of cancer-associated mutations in fresh frozen and FFPE tumors by massively parallel sequencing. This method enables the identification of sequence mutations, copy number alterations, and select structural rearrangements involving all targeted genes. Targeted exon sequencing offers the benefits of high throughput, low cost, and deep sequence coverage, thus conferring high sensitivity for detecting low frequency mutations.

We describe the preparation of barcoded DNA libraries and subsequent hybridization-based exon capture for detection of key cancer-associated mutations in clinical tumor specimens by massively parallel "next generation" sequencing. Targeted exon sequencing offers the benefits of high throughput, low cost, and deep sequence coverage, thus yielding high sensitivity for detecting low frequency mutations.

Efforts  to detect and investigate key oncogenic mutations have proven valuable to  facilitate the appropriate treatment for cancer patients. The ...

Efficient Production and Purification of Recombinant Murine Kindlin-3 from Insect Cells for Biophysical Studies

Kindlins are essential coactivators, with talin, of the cell surface receptors&#160;integrins and also participate in integrin outside-in signalling, and the control of gene transcription in the cell nucleus. The kindlins are ~75 kDa multidomain proteins and bind to an NPxY motif and upstream T/S cluster of the integrin &#946;-subunit cytoplasmic tail. The hematopoietically-important kindlin isoform, kindlin-3, is critical for platelet aggregation during thrombus formation, leukocyte rolling in response to infection and inflammation and osteoclast podocyte formation in bone resorption. Kindlin-3&#39;s role in these processes has resulted in extensive cellular and physiological studies. However, there is a need for an efficient method of acquiring high quality milligram quantities of the protein for further studies. We have developed a protocol, here described, for the efficient expression and purification of recombinant murine kindlin-3 by use of a baculovirus-driven expression system in Sf9 cells yielding sufficient amounts of high purity full-length protein to allow its biophysical characterization. The same approach could be taken in the study of the other mammalian kindlin isoforms.

Kindlins are fundamental to cell adhesion through integrins but studies of them have been hampered by the difficulty encountered in expressing them recombinantly in bacterial hosts. We describe here methods for their efficient production in baculovirus-infected insect cells.

Kindlins are essential coactivators, with talin, of the cell surface receptors&#160;integrins and also participate in integrin outside-in signalling, and ...

Assessing Species-specific Contributions To Craniofacial Development Using Quail-duck Chimeras

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to the histological and morphological development of vertebrate embryos. In particular, the use of chimeric embryos has established the importance of neural crest in directing the species-specific morphology of the craniofacial complex. The method described herein utilizes two avian species, duck and quail, with remarkably different craniofacial morphology. This method greatly facilitates the investigation of molecular and cellular regulation of species-specific pattern in the craniofacial complex.&#160;Experiments in quail and duck chimeric embryos have already revealed neural crest-mediated tissue interactions and cell-autonomous behaviors that regulate species-specific pattern in the craniofacial skeleton, musculature, and integument. The great diversity of neural crest derivatives suggests significant potential for future applications of the quail-duck chimeric system to understanding vertebrate development, disease, and evolution.

This article describes a method to generate chimeric embryos that are&#160;designed to test the species-specific contributions of neural crest and/or other tissues to craniofacial development.

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to ...

Recombinant Protein Expression for Structural Biology in HEK 293F Suspension Cells: A Novel and Accessible Approach

The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two decades, prokaryotic expression systems such as E. coli have dominated the scientific literature over costly and less efficient eukaryotic cell lines. Despite the clear advantage in terms of yields and costs of expressing recombinant proteins in bacteria, the absence of specific co-factors, chaperones and post-translational modifications may cause loss of function, mis-folding and can disrupt protein-protein interactions of certain eukaryotic multi-subunit complexes, surface receptors and secreted proteins. The use of mammalian cell expression systems can address these drawbacks since they provide a eukaryotic expression environment. However, low protein yields and high costs of such methods have until recently limited their use for structural biology. Here we describe a simple and accessible method for expressing and purifying milligram quantities of protein by performing transient transfections of suspension grown HEK (Human Embryonic Kidney) 293F cells.

The expression of recombinant proteins by mammalian systems is becoming an attractive method for producing protein complexes for structural biology. Here we present a simple yet highly efficient expression system using suspension grown mammalian cells to purify protein complexes for structural studies.

The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two ...

Detection of Intracellular Gene Expression in Live Cells of Murine, Human and Porcine Origin Using Fluorescence-labeled Nanoparticles

The reprogramming of somatic cells to induced pluripotent stem cells (iPS) has successfully been performed in different mammalian species including mouse, rat, human, pig and others. The verification of iPS clones mainly relies on the detection of the endogenous expression of different pluripotency genes. These genes mostly represent transcription factors which are located in the cell nucleus. Traditionally, the proof of their endogenous expression is supplied by immunohistochemical staining after fixation of the cells. This approach requires replicate cultures of each clone at this early stage to preserve validated clones for further experiments. The present protocol describes an approach with gene-specific nanoparticles which allows the evaluation of intracellular gene expression directly in live cells by fluorescence. The nanoparticles consist of a central gold particle coupled to a capture strand carrying a sequence complementary to the target mRNA as well as a quenched reporter strand. These nanoparticles are actively endocytosed and the target mRNA displaces the reporter strand which then start to fluoresce. Therefore, specific target gene expression can be detected directly under the microscope. In addition, the emitted fluorescence allows the identification, isolation and enrichment of cells expressing a specific gene by flow cytometry. This method can be applied directly to live cells in culture without any manipulation of the target cells.

This manuscript describes a novel technique which allows the detection of intracellular gene expression after endocytosis of fluorescence-labeled nanoparticles directly in live cells. The method does not require manipulation of the cells and is not restricted with respect to the target gene or species.

The reprogramming of somatic cells to induced pluripotent stem cells (iPS) has successfully been performed in different mammalian species including mouse, ...

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

The presence of ribonucleotides in nuclear DNA has been shown to be a source of genomic instability. The extent of ribonucleotide incorporation can be assessed by alkaline hydrolysis and gel electrophoresis as RNA is highly susceptible to hydrolysis in alkaline conditions. This, in combination with Southern blot analysis can be used to determine the location and strand into which the ribonucleotides have been incorporated. However, this procedure is only semi-quantitative and may not be sensitive enough to detect small changes in ribonucleotide content, although strand-specific Southern blot probing improves the sensitivity. As a measure of one of the most striking biological consequences of ribonucleotides in DNA, spontaneous mutagenesis can be analyzed using a forward mutation assay. Using appropriate reporter genes, rare mutations that results in the loss of function can be selected and overall and specific mutation rates can be measured by combining data from fluctuation experiments with DNA sequencing of the reporter gene. The fluctuation assay is applicable to examine a wide variety of mutagenic processes in specific genetic background or growth conditions.

Ribonucleotides are among the most abundant non-canonical nucleotides incorporated into the genome during eukaryotic nuclear DNA replication. If not properly removed, ribonucleotides can cause DNA damage and mutagenesis. Here, we present two experimental approaches that are used to assess the abundance of ribonucleotide incorporation into DNA and its mutagenic effects.

The presence of ribonucleotides in nuclear DNA has been shown to be a source of genomic instability. The extent of ribonucleotide incorporation can be ...