The authors thank Chris Chartrand, HT(ASCP) for demonstrating the section cutting of the cell block with AV marker.

Introduction:
This is a video describing Shidham&rsquo;s method for cell block preparation from liquid based cytology (LBC) specimen using HistoGelTM (Thermo Scientific) (HG). As compared to other random approaches, the following are the two critical features of this protocol for preparing cell blocks from relatively hypocellular specimens with singly scattered loose cells (1-5).
<ol>
<li>This protocol involves steps to concentrate the cells along the plane parallel to the cutting surface of the cell block.</li>
<li>It also includes a beacon-like dark inclusion of AV-marker (Figure 1b), which serves two of the following purposes:<ol style="list-style-type:lower-alpha;">
<li>To visualize the level at which the cells are concentrated. The area of the cell block with the cells of interest now could be visualized by the histotechnologist when the dark colored beacon is exposed during cutting. This ability to monitor would prevent one from cutting through the level with most of the cells, or not cutting too superficial into the level with highest concentration of sample cells.</li>
<li>To serve as a locator reference point in serial cell block section on different slides. This reference point acts as a beacon to help locate particular cells or groups of cells for evaluation of a coordinate immunoreactivity pattern with the SCIP approach (6,7).</li>
</ol></li>
</ol>
PROTOCOL (Figure 2)
Preparation of the sample.
<ol>
<li>Transfer the residual LBC cervical cytology specimen to a flat bottom glass tube (15mm diameter x 45mm) (Figure 2.1 through 2.4).&nbsp; Place the glass tube into a larger plastic carrier tube (28 x 85mm) and centrifuge.&nbsp; Remove the glass bottom tube from the carrier tube and pour off the supernatant.</li>
<li>The glass tube is then capped (to prevent spillage of heating water in the next step) and placed back inside a larger flat bottom carrier plastic tube </li>
<li>The carrier plastic tube containing the glass tube is then capped, placed in a centrifuge (with swiveling cups and not fixed angle cups so that the cells fall perpendicularly to the flat bottom of the glass tube), and spun at 1805 G (3000 rpms, rotor radius- 17cm) for five minutes (Figure 2.5).</li>
<li>The tubes are then removed vertically from the centrifuge and the smaller glass tube is removed with forceps from the larger carrier plastic tube without disturbing the sedimented pellet with cells.</li>
<li>The glass tube with specimen is uncapped and the supernatant is poured off taking care not to disturb the flat layer of sediment cells at the bottom (Figure 2.6).</li>
</ol>
Inclusion of the reference coordinate AV-marker and addition of gel
<ol>
<li>A dark beacon AV-marker (about 2 mm X 2 mm size, flat surfaced, fragment of dark colored, sectionable material) (Figure 3) is added as a signpost to the glass tube (Figure 2.7).</li>
<li>Liquefy an aliquot of HG by melting it in microwave for 10 seconds at medium power.</li>
<li>Add 0.5 ml of molten HG to the tube, mix with the sediment quickly, and recap it (Figure 2.8) (Proceed to the next step quickly without allowing the HG to begin solidifying).</li>
<li>Add about 2.5 ml of warm (45&deg; C) water to the carrier plastic tube (Figure 2.9). </li>
<li>The smaller capped glass tube is placed inside the plastic tube with warm water. (This step is necessary to keep the HG from solidifying during the next steps) (Figure 2.9).</li>
<li>The carrier plastic tube is placed in the centrifuge (with swiveling cups and not fixed angle cups so that the cells fall perpendicularly to the flat bottom of the glass tube), and spun at 1805 G (3000 rpms, rotor radius- 17cm) for five minutes. The purpose of this centrifugation step is to push the AV-marker and to concentrate the cells into a layer closer to the cutting surface of the final paraffin embedded cell block (Figure 1d). </li>
<li>The tubes are then removed gently and vertically from the centrifuge taking care not to disturb the sedimented thin layer with sample cells at the bottom.</li>
<li>The larger plastic tube is uncapped and the smaller glass tube is removed vertically by a forceps without disturbing the sediment layer of specimen cells.</li>
<li>The small glass tube is refrigerated in vertical position for 15 minutes to cool and solidify the HG (Figure 2.11).</li>
</ol>
Removal of the cell block as a button of gel with specimen for final processing
<ol>
<li>The solidified HG disk, with the layer of concentrated/sediment specimen at the bottom is dislodged from the flat bottom glass tube by squirting 10% formalin through a 23 gauge needle with the syringe (Figure 2.12).</li>
<li>The needle is inserted along the side of the tube at the periphery of solidified HG disc with specimen (Figure 2.12).</li>
<li>The needle is rotated along the side of the tube while formalin is slowly pushed through the syringe. This results in the separation of the HG button along with dark colored beacon AV-marker and the concentrated specimen in it from the flat bottom of the glass tube (Figure 2.12).</li>
<li>The cell block (gel button with specimen cells) is then placed in a labeled cassette and submitted for tissue processing to prepare paraffin embedded cell blocks (Figure 2.13).</li>
</ol>
Embedding and cutting of the specimen
<ol>
<li>The disk is embedded in paraffin with the dark beacon marker side down as cutting surface (Figure 1). </li>
<li>The block is sectioned until the dark colored AV-marker as a beacon is exposed and clearly visible.</li>
<li>Three to four micron sections are cut from this level which should contain most of the singly scattered cells from the specimen.</li>
<li>The sections are collected on the glass slide for further staining, immunohistochemical staining, or other tests as indicated. The protocols for these tests including the type of slides to use for mounting the sections may vary. Generally for immunostaining, coated slides are used to prevent floating and loss of sections from the slides during the immunostaining steps.</li>
</ol>
Abbreviations used (in alphabetic order): CISH, chromogenic in-situ hybridization tests; FISH, Fluorescent in-situ hybridization tests; FFPE, formalin-fixed paraffin-embedded; FNA, fine needle aspiration; HG, HistoGel&trade; (Thermo Scientific); LBC, liquid based cytology; PCR polymerase chain reaction;
&nbsp;
<img src="/files/ftp_upload/1316/1382fig1.jpg" alt="figure 1" /> Figure 1. The structure of cell block prepared by Shidham&rsquo;s protocol.
<img src="/files/ftp_upload/1316/1382fig2.jpg" alt="figure 2" /> Figure 2. The summary of different steps for preparing cell block from LBC specimen by Shidham&rsquo;s protocol.
<img src="/files/ftp_upload/1316/1382fig3.jpg" alt="figure 3" /> Figure 3. Preparation of AV-marker from banana peels.
<img src="/files/ftp_upload/1316/1382fig4.jpg" alt="figure 4" /> Figure 4. Comparison of cell blocks and sections with and without AV-marker.
<img src="/files/ftp_upload/1316/1382fig5.jpg" alt="figure 5" /> Figure 5. Comparison of cellularity of sections of cell block with and without AV-marker.

<ol>
	<li>Shidham, V. B., Epple, J., Shidham, V. B., Atkinson, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+14,+Appendix+I:+Collection+and+processing+of+effusion+fluids+for+cytopathologic+evaluation.">Chapter 14, Appendix I: Collection and processing of effusion fluids for cytopathologic evaluation.</a> Cytopathologic Diagnosis of Serous Fluids. , .</li><li>Varsegi, G., D'Amore, K., Shidham, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=p16INK4a+Immunocytochemistry+as+an+Adjunct+to+Cervical+Cytology+-+Potential+Reflex+Testing+on+Specially+Prepared+Cellblocks+from+Residual+Liquid+Based+Cytology+(LBC)+Specimens.">p16INK4a Immunocytochemistry as an Adjunct to Cervical Cytology - Potential Reflex Testing on Specially Prepared Cellblocks from Residual Liquid Based Cytology (LBC) Specimens.</a> Modern Pathology 22: 98th Annual Meeting of United States and Canadian Academy of Pathology. , 97a-97a (2009).</li><li>Nigro, K., Tynski, Z., Wasman, J., Abdul-Karim, F., Wang, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+cell+block+preparation+methods+for+nongynecologic+ThinPrep+specimens.">Comparison of cell block preparation methods for nongynecologic ThinPrep specimens.</a> Diagn Cytopathol. 35, 640-643 (2007).</li><li>Saleh, H. A., Hammoud, J., Zakaria, R., Khan, A. Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+Thin-Prep+and+cell+block+preparation+for+the+evaluation+of+Thyroid+epithelial+lesions+on+fine+needle+aspiration+biopsy.">Comparison of Thin-Prep and cell block preparation for the evaluation of Thyroid epithelial lesions on fine needle aspiration biopsy.</a> CytoJournal. 5, 3-3 (2008).</li><li>Kyroudi, A., Paefthimiou, M., Symiakaki, H., Mentzelopoulou, P., Voulgaris, Z., Karakitsos, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increasing+diagnostic+accuracy+with+a+cell+block+preparation+from+thin-layer+endometrial+cytology:+a+feasibility+study.">Increasing diagnostic accuracy with a cell block preparation from thin-layer endometrial cytology: a feasibility study.</a> Acta Cytol. 50, 63-69 (2006).</li><li>Atkinson, B. F., Shidham, V. B., Atkinson, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+5:+Immunocytochemistry+of+effusion+fluids:+introduction+to+SCIP+approach+(Chapter+5.">Chapter 5: Immunocytochemistry of effusion fluids: introduction to SCIP approach (Chapter 5.</a> Cytopathologic Diagnosis of Serous Fluids. , (2007).</li><li>Shidham, V. B., Shidham, V. B., Atkinson, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+15,+Appendix+II:+Immunocytochemistry+of+effusions+processing+and+commonly+used+immunomarkers.">Chapter 15, Appendix II: Immunocytochemistry of effusions processing and commonly used immunomarkers.</a> Cytopathologic Diagnosis of Serous Fluids. , (2007).</li></ol>

Cell blocks are a valuable tool for evaluation of various cytology specimens (1). Most importantly, in addition to the architectural details of the specimen, cell blocks allow for evaluation of ancillary studies such as immunocytochemistry, fluorescent/chromogenic in-situ hybridization tests (FISH/CISH) and in-situ PCR. A variety of methods for preparation of cell block are described. However, most of these are suitable for non-gynecologic cytology specimens which contain relatively many cells and with tissue microfragments such as in FNA aspirates and some serous fluids such as effusions (1,3,4,5).
Because cell blocks primarily provide the opportunity for immunocytochemical evaluation, their processing should preferably be similar to that of the formalin-fixed paraffin-embedded (FFPE) tissues. Ultimately the results obtained after immunocytochemical evaluation of cell block sections are compared to those with the published literature performed predominantly on FFPE tissue sections. Any alterations in the protocol potentially compromise and nullify the validity of the results obtained on cell blocks processed through different fixatives and reagent sequences other than that used for routine FFPE. Some commercial techniques may have the drawback of processing through a protocol of exposure to other fixative-reagent exposure.
Various methods of cell block preparation are available for specimens with a significant quantity of sediment and tissue fragments. Principally, the concentrated sediments are supported by some gel or coagulation principle. The maneuverable button is then embedded in paraffin after processing like the surgical pathology specimens/biopsies.
The gels used include gelatin, agar, fibrinogen/plasma-thrombin, and other commercial gels such as HG. The methods of concentration vary from simple pelleting of the sediment by centrifugation to concentration of cells along various types of membranes. Examples include: Milipore, collodin (Celloidin) bags or scraping the cells from the cytology smears on glass slides (1). We also evaluated a variety of gels by trying different combinations of agar and gelatin. None of the combinations achieved the a firm enough consistency to obtain an easily maneuverable disc of solidified gel with embedded cells from the specimen in one piece. HG showed appropriate consistency and in our experience the immunostaining results on HG cell block sections have been excellent.
Liquid based cytology (LBC) specimens for cervicovaginal cytology are generally less cellular than non-gynecologic specimens as mentioned above. In addition, the gynecologic LBC specimens predominantly contain individual scattered exfoliated superficial cells from cervicovaginal mucosa. Due to this, appropriate cellularity within the cell block sections may not be achieved without a special approach. As these singly scattered cellular components in the the block cannot be seen by the histotechnologist during section cutting, the level at which the cells start appearing in the sections cannot be appreciated and may be missed, either by cutting past the level with most cells or not cutting deep enough into the level with highest concentration of sample cells (Figure 4). Shidham&rsquo;s protocol addresses both of these issues using HG as embedding medium and conventional lab equipments (2) (Figure 2).
This protocol involves following two major features (Figure 1):
<ol>
<li>Concentration and alignment of singly scattered cells in a narrow plane adjacent and parallel to the cutting surface of the cell block (Figure 5).</li>
<li>Inclusion of a beacon-like dark AV-marker as a signpost. This is critical for achieving following features:<ol style="list-style-type:lower-alpha;">
<li>Identifying and monitoring the level at which the cells are concentrated in the cell block. The exposure of the dark colored signpost highlights the level at which most of the singly scattered cells in the cell block are expected to be located (Figure 4). This prevents the overcutting (cutting past the level with most cells) or undercutting (not cutting deep enough into the level with highest concentration of sample cells) in to the cell block and allow selection of the sections from the level in the cell block corresponding with highest concentration of cells.</li>
<li>The dark colored signpost in the sections also serves as a reference point to survey and identify exactly the same cells in different serial sections of the cell block on different slides (Figure 4). This is critical while interpreting and evaluating the coordinate properties such immunoprofile of particular cells by the SCIP approach to follow the same cells in different sections (6,7).</li>
</ol></li>
</ol>
Although our protocol is standardized and reported for liquid based cervical cytology specimens, it can also be used to enhance diagnostic yield of many other non-gynecologic specimens such as effusion fluids, FNA, brushings, cyst contents etc. In addition the AV marker would facilitate improved application of SCIP approach during immunohistochemical evaluation of cell block sections of these specimens. The embedding medium may be replaced by other reagents with appropriate modifications at relevant steps. HG may be replaced by plasma (Fibrinogen) to be gelled by Thrombin at room temperature (1).

cell block preparation from cytology specimen with predominance of individually scattered cells

This video demonstrates Shidham's method for preparation of cell blocks from liquid based cervicovaginal cytology specimens containing individually scattered cells and small cell groups. This technique uses HistoGel (Thermo Scientific) with conventional laboratory equipment.
The use of cell block sections is a valuable ancillary tool for evaluation of non-gynecologic cytology. They enable the cytopathologist to study additional morphologic specimen detail including the architecture of the lesion. Most importantly, they allow for the evaluation of ancillary studies such as immunocytochemistry, in-situ hybridization tests (FISH/CISH) and in-situ polymerase chain reaction (PCR). Traditional cell block preparation techniques have mostly been applied to non-gynecologic cytology specimens, typically for body fluid effusions and fine needle aspiration biopsies.
Liquid based cervicovaginal specimens are relatively less cellular than their non-gynecologic counterparts with many individual scattered cells. Because of this, adequate cellularity within the cell block sections is difficult to achieve. In addition, the histotechnologist sectioning the block cannot visualize the level at which the cells are at the highest concentration. Therefore, it is difficult to monitor the appropriate level at which sections can be selected to be transferred to the glass slides for testing. As a result, the area of the cell block with the cells of interest may be missed, either by cutting past or not cutting deep enough. Current protocol for Shidham's method addresses these issues. Although this protocol is standardized and reported for gynecologic liquid based cytology specimens, it can also be applied to non-gynecologic specimens such as effusion fluids, FNA, brushings, cyst contents etc for improved quality of diagnostic material in cell block sections.

Watch this Scientific Journal Video about Cell Block Preparation from Cytology Specimen with Predominance of Individually Scattered Cells at JoVE.com

Cell Block Preparation from Cytology Specimen with Predominance of Individually Scattered Cells

Shidham's method for preparation of cell blocks with AV-marker from cytology specimens containing individually scattered cells and small cell groups.

This video demonstrates Shidham's method for preparation of cell blocks from liquid based cervicovaginal cytology specimens containing individually ...

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73.2K Views.  University of Wisconsin - Milwaukee. Shidham's method for preparation of cell blocks with AV-marker from cytology specimens containing individually scattered cells and small cell groups.

Video: Cell Block Preparation from Cytology Specimen with Predominance of Individually Scattered Cells

Human ES cells: Starting Culture from Frozen Cells

Here we demonstrate how our lab begins a HuES human embryonic stem cell line culture from a frozen stock.  First, a one to two day old ten cm plate of  approximately one (to two) million irradiated mouse embryonic fibroblast feeder cells is rinsed with HuES media to remove residual serum and cell debris, and then HuES media added and left to equilibrate in the cell culture incubator.  A frozen vial of cells from long term liquid nitrogen storage or a -80C freezer is sourced and quickly submerged in a 37C water bath for quick thawing.  Cells in freezing media are then removed from the vial and placed in a large volume of HuES media.  The large volume of HuES media facilitates removal of excess serum and DMSO, which can cause HuES human embryonic stem cells to differentiate.  Cells are gently spun out of suspension, and then re-suspended in a small volume of fresh HuES media that is then used to seed the MEF plate.  It is considered important to seed the MEF plate by gently adding the HuES cells in a drop wise fashion to evenly disperse them throughout the plate.  The newly established HuES culture plate is returned to the incubator for 48 hrs before media is replaced, then is fed every 24 hours thereafter.

Here we demonstrate how our lab begins a HuES human embryonic stem cell line culture from a frozen stock.

Here we demonstrate how our lab begins a HuES human embryonic stem cell line culture from a frozen stock.  First, a one to two day old ten cm plate of  ...

Derivation of Hematopoietic Stem Cells from Murine Embryonic Stem Cells

A stem cell is defined as a cell with the capacity to both self-renew and generate multiple differentiated progeny.  Embryonic stem cells (ESC) are derived from the blastocyst of the early embryo and are pluripotent in differentiative ability.  Their vast differentiative potential has made them the focus of much research centered on deducing how to coax them to generate clinically useful cell types.  The successful derivation of hematopoietic stem cells (HSC) from mouse ESC has recently been accomplished and can be visualized in this video protocol.  HSC, arguably the most clinically exploited cell population, are used to treat a myriad of hematopoietic malignancies and disorders.  However, many patients that might benefit from HSC therapy lack access to suitable donors.  ESC could provide an alternative source of HSC for these patients.  The following protocol establishes a baseline from which ESC-HSC can be studied and inform efforts to isolate HSC from human ESC.  In this protocol, ESC are differentiated as embryoid bodies (EBs) for 6 days in commercially available serum pre-screened for optimal hematopoietic differentiation.  EBs are then dissociated and infected with retroviral HoxB4.  Infected EB-derived cells are plated on OP9 stroma, a bone marrow stromal cell line derived from the calvaria of  M-CSF-/- mice, and co-cultured in the presence of hematopoiesis promoting cytokines for ten days.  During this co-culture, the infected cells expand greatly, resulting in the generation a heterogeneous pool of 100s of millions of cells.  These cells can then be used to rescue and reconstitute lethally irradiated mice.

This protocol details the derivation of transplantable hematopoietic stem cells from mouse embryonic stem cells (ESC) and their subsequent injection into lethally irradiated recipient mice. Briefly, ESC are differentiated as embryoid bodies, which are then infected with retroviral HoxB4 and co-cultured with OP9 stromal cells and hematopoietic cytokines.

A stem cell is defined as a cell with the capacity to both self-renew and generate multiple differentiated progeny.  Embryonic stem cells (ESC) are ...

Preparation of Neuronal Cultures from Midgastrula Stage Drosophila Embryos

This video illustrates the procedure for making primary neuronal cultures from midgastrula stage Drosophila embryos. The methods for collecting embryos and their dechorionation using bleach are demonstrated. Using a glass pipet attached to a mouth suction tube, we illustrate the removal of all cells from single embryos. The method for dispersing cells from each embyro into a small (5 l) drop of medium on an uncoated glass coverslip is demonstrated. A view through the microscope at 1 hour after plating illustrates the preferred cell density. Most of the cells that survive when grown in defined medium are neuroblasts that divide one or more times in culture before extending neuritic processes by 12-24 hours. A view through the microscope illustrates the level of neurite outgrowth and branching expected in a healthy culture at 2 days in vitro. The cultures are grown in a simple bicarbonate based defined medium, in a 5% CO2 incubator at 22-24&deg;C. Neuritic processes continue to elaborate over the first week in culture and when they make contact with neurites from neighboring cells they often form functional synaptic connections. Neurons in these cultures express voltage-gated sodium, calcium, and potassium channels and are electrically excitable. This culture system is useful for studying molecular genetic and environmental factors that regulate neuronal differentiation, excitability, and synapse formation/function.

This video demonstrates the preparation of primary neuronal cultures from midgastrula stage Drosophila embryos. Views of live cultures show cells 1 hour after plating and differentiated neurons after 2 days of growth in a bicarbonate-based defined medium. The neurons are electrically excitable and form synaptic connections.

This video illustrates the procedure for making primary neuronal cultures from midgastrula stage Drosophila embryos. The methods for collecting embryos ...

Preparation of Single-Cell Suspensions from Mouse Spleen with the gentleMACS Dissociator

Single-cell suspensions are a prerequisite for experiments in cell separation, cell analysis and cell culture.  To avoid tedious and often painful manual dissociations the gentleMACS Dissociator allows one to dissociate tissue very efficiently under controlled and reproducible conditions.  The gentleMACS Dissociator can optimally dissociate mouse spleen, combining timesaving and standardization with user-safety.

This video describes how to dissociate mouse spleens using the gentleMACS Dissociator, an automated bench-top device that can mechanically disrupt tissues using special tubes to produce viable cell suspensions. Following dissociation, spleens are filtered, centrifuged, and resuspended for further applications.

This video describes a simple, time-saving technique for automated tissue dissociation using the gentleMACS Dissociator to prepare single-cell suspensions of mouse splenocytes.

Single-cell suspensions are a prerequisite for experiments in cell separation, cell analysis and cell culture.  To avoid tedious and often painful manual ...

Preparation of Drosophila S2 cells for Light Microscopy

The ideal experimental system would be cheap and easy to maintain, amenable to a variety of techniques, and would be supported by an extensive literature and genome sequence database. Cultured Drosophila S2 cells, the product of disassociated 20-24 hour old embryos1, possess all these properties. Consequently, S2 cells are extremely well-suited for the analysis of cellular processes, including the discovery of the genes encoding the molecular components of the process or mechanism of interest. The features of S2 cells that are most responsible for their utility are the ease with which they are maintained, their exquisite sensitivity to double-stranded (ds)RNA-mediated interference (RNAi), and their tractability to fluorescence microscopy as either live or fixed cells.
S2 cells can be grown in a variety of media, including a number of inexpensive, commercially-available, fully-defined, serum-free media2. In addition, they grow optimally and quickly at 21-24&deg;C and can be cultured in a variety of containers. Unlike mammalian cells, S2 cells do not require a regulated atmosphere, but instead do well with normal air and can even be maintained in sealed flasks.
Complementing the ease of RNAi in S2 cells is the ability to readily analyze experimentally-induced phenotypes by phase or fluorescence microscopy of fixed or live cells. S2 cells grow in culture as a single monolayer but do not display contact inhibition. Instead, cells tend to grow in colonies in dense cultures. At low density, S2 cultures grown on glass or tissue culture-treated plastic are round and loosely-attached. However, the cytology of S2 cells can be greatly improved by inducing them to flatten extensively by briefly culturing them on a surface coated with the lectin, concanavalin A (ConA)3. S2 cells can also be stably transfected with fluorescently-tagged markers to label structures or organelles of interest in live or fixed cells. Therefore, the usual scenario for the microscopic analysis of cells is this: first, S2 cells (which can possess transgenes to express tagged markers) are treated by RNAi to eliminate a target protein(s). RNAi treatment time can be adjusted to allow for differences in protein turn-over kinetics and to minimize cell trauma/death if the target protein is important for viability. Next, the treated cells are transferred to a dish containing a coverslip pre-coated with conA to induce cells to spread and tightly adhere to the glass. Finally, cells are imaged with the researcher's choice of microscopy modes. S2 cells are particularly good for studies requiring extended visualization of live cells since these cells stay healthy at room temperature and normal atmosphere.

Preparation of Drosophila S2 cells for Light Microscopy

Drosophila Schneider (S2) cells are an increasingly popular system for the discovery and functional analysis of genes. Our goal is to describe some of the microscopic techniques that make S2 cells such an increasingly important experimental system.

The ideal experimental system would be cheap and easy to maintain, amenable to a variety of techniques, and would be supported by an extensive literature ...

Preparation of Quality Inositol Pyrophosphates

Myo-inositol is present in nature either unmodified or in more complex phosphorylated derivates. Of the latest, the two most abundant in eukaryotic cells are inositol pentakisphosphate (IP5) and inositol hexakisphosphate (phytic acid or IP6). IP5 and IP6 are the precursors of inositol pyrophosphate molecules that contain one or more pyrophosphate bonds1. Phosphorylation of IP6 generates diphoshoinositolpentakisphosphate (IP7 or PP-IP5) and bisdiphoshoinositoltetrakisphosphate (IP8 or (PP)2-IP4). Inositol pyrophosphates have been isolated from all eukaryotic organisms so far studied. In addition, the two distinct classes of enzymes responsible for inositol pyrophosphate synthesis are highly conserved throughout evolution2-4.
The IP6 kinases (IP6Ks) posses an enormous catalytic flexibility, converting IP5 and IP6 to PP-IP4 and IP7 respectively and subsequently, by using these products as substrates, promote the generation of more complex molecules5,6. Recently, a second class of pyrophosphate generating enzymes was identified in the form of the yeast protein VIP1 (also referred as PP-IP5K), which is able to convert IP6 to IP7 and IP87,8.
Inositol pyrophosphates regulate many disparate cellular processes such as insulin secretion9, telomere length10,11, chemotaxis12, vesicular trafficking13, phosphate homeostasis14 and HIV-1 gag release15. Two mechanisms of actions have been proposed for this class of molecules. They can affect cellular function by allosterically interacting with specific proteins like AKT16. Alternatively, the pyrophosphate group can donate a phosphate to pre-phosphorylated proteins17. The enormous potential of this research field is hampered by the absence of a commercial source of inositol pyrophosphates, which is preventing many scientists from studying these molecules and this new post-translational modification. The methods currently available to isolate inositol pyrophosphates require sophisticated chromatographic apparatus18,19. These procedures use acidic conditions that might lead to inositol pyrophosphate degradation20 and thus to poor recovery. Furthermore, the cumbersome post-column desalting procedures restrict their use to specialized laboratories.
In this study we describe an undemanding method for the generation, isolation and purification of the products of the IP6-kinase and PP-IP5-kinases reactions. This method was possible by the ability of polyacrylamide gel electrophoresis (PAGE) to resolve highly phosphorylated inositol polyphosphates20. Following IP6K1 and PP-IP5K enzymatic reactions using IP6 as the substrate, PAGE was used to separate the generated inositol pyrophosphates that were subsequently eluted in water.

Inositol pyrophosphates play an important role in human pathologies such cancer, diabetes and obesity; however, the exact mechanism of action is a matter of dispute. The lack of commercially available inositol pyrophosphates renders detailed studies problematic. Here we describe a simple protocol to produce and isolate milligrams of inositol pyrophosphates.

Myo-inositol is present in nature either unmodified or in more complex phosphorylated derivates. Of the latest, the two most abundant in eukaryotic cells ...

Chromosome Preparation From Cultured Cells

Chromosome (cytogenetic) analysis is widely used for the detection of chromosome instability. When followed by G-banding and molecular techniques such as fluorescence in situ hybridization (FISH), this assay has the powerful ability to analyze individual cells for aberrations that involve gains or losses of portions of the genome&#160;and rearrangements involving one or more chromosomes. In humans, chromosome abnormalities occur in approximately 1 per 160 live births1,2, 60-80% of all miscarriages3,4, 10% of stillbirths2,5, 13% of individuals with congenital heart disease6, 3-6% of infertility cases2, and in many patients with developmental delay&#160;and birth defects7. Cytogenetic analysis of malignancy is routinely used by researchers and clinicians, as observations of clonal chromosomal abnormalities have been shown to have both diagnostic and prognostic significance8,9.&#160; Chromosome isolation is invaluable for gene therapy and stem cell research of organisms including nonhuman primates and rodents10-13.
Chromosomes can be isolated from cells of live tissues, including blood lymphocytes, skin fibroblasts, amniocytes, placenta, bone marrow, and tumor specimens. Chromosomes are analyzed at the metaphase stage of mitosis, when they are most condensed and therefore more clearly visible. The first step of the chromosome isolation technique involves the disruption of the spindle fibers by incubation with Colcemid, to prevent the cells from proceeding to the subsequent anaphase stage. The cells are then treated with a hypotonic solution and preserved in their swollen state with Carnoy&#39;s fixative. The cells are then dropped on to slides and can then be utilized for a variety of procedures. G-banding involves trypsin treatment followed by staining with Giemsa to create characteristic light and dark bands. The same procedure to isolate chromosomes can be used for the preparation of cells for procedures such as fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and spectral karyotyping (SKY)14,15.

Chromosomes can be isolated from live cells such as lymphocytes or skin fibroblasts, and from organisms including humans or mice. These chromosome preparations can be further utilized for routine G-banding and molecular cytogenetic procedures such as fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and spectral karyotyping (SKY).

Chromosome (cytogenetic) analysis is widely used for the detection of chromosome instability. When followed by G-banding and molecular techniques such as ...

Preparation of Primary Myogenic Precursor Cell/Myoblast Cultures from Basal Vertebrate Lineages

Due to the inherent difficulty and time involved with studying the myogenic program in vivo, primary culture systems derived from the resident adult stem cells of skeletal muscle, the myogenic precursor cells (MPCs), have proven indispensible to our understanding of mammalian skeletal muscle development and growth. Particularly among the basal taxa of Vertebrata, however, data are limited describing the molecular mechanisms controlling the self-renewal, proliferation, and differentiation of MPCs. Of particular interest are potential mechanisms that underlie the ability of basal vertebrates to undergo considerable postlarval skeletal myofiber hyperplasia (i.e.&#160;teleost fish) and full regeneration following appendage loss (i.e.&#160;urodele amphibians). Additionally, the use of cultured myoblasts could aid in the understanding of regeneration and the recapitulation of the myogenic program and the differences between them. To this end, we describe in detail a robust and efficient protocol (and variations therein) for isolating and maintaining MPCs and their progeny, myoblasts and immature myotubes, in cell culture as a platform for understanding the evolution of the myogenic program, beginning with the more basal vertebrates. Capitalizing on the model organism status of the zebrafish (Danio rerio), we report on the application of this protocol to small fishes of the cyprinid clade Danioninae. In tandem, this protocol can be utilized to realize a broader comparative approach by isolating MPCs from the Mexican axolotl (Ambystomamexicanum) and even laboratory rodents. This protocol is now widely used in studying myogenesis in several fish species, including rainbow trout, salmon, and sea bream1-4.

In vitro culture systems have proven indispensible to our understanding of vertebrate myogenesis. However, much remains to be learned about nonmammalian skeletal muscle development and growth, particularly in basal taxa. An efficient and robust protocol for isolating the adult stem cells of this tissue, the myogenic precursor cells (MPCs), and maintaining their self-renewal, proliferation, and differentiation in a primary culture setting allows for the identification of conserved and divergent regulatory mechanisms throughout the vertebrate lineages.

Due to the inherent difficulty and time involved with studying the myogenic program in vivo, primary culture systems derived from the resident adult stem ...

Efficient Generation Human Induced Pluripotent Stem Cells from Human Somatic Cells with Sendai-virus

A few years ago, the establishment of human induced pluripotent stem cells (iPSCs) ushered in a new era in biomedicine. Potential uses of human iPSCs include modeling pathogenesis of human genetic diseases, autologous cell therapy after gene correction, and personalized drug screening by providing a source of patient-specific and symptom relevant cells. However, there are several hurdles to overcome, such as eliminating the remaining reprogramming factor transgene expression after human iPSCs production. More importantly, residual transgene expression in undifferentiated human iPSCs could hamper proper differentiations and misguide the interpretation of disease-relevant in vitro phenotypes. With this reason, integration-free and/or transgene-free human iPSCs have been developed using several methods, such as adenovirus, the piggyBac system, minicircle vector, episomal vectors, direct protein delivery and synthesized mRNA. However, efficiency of reprogramming using integration-free methods is quite low in most cases.
Here, we present a method to isolate human iPSCs by using Sendai-virus (RNA virus) based reprogramming system. This reprogramming method shows consistent results and high efficiency in cost-effective manner.

Here, we present our established method to reprogram human somatic cells into transgene-free human iPSCs with Sendai virus, which shows consistent outcome and enhanced efficiency.

A few years ago, the establishment of human induced pluripotent stem cells (iPSCs) ushered in a new era in biomedicine. Potential uses of human iPSCs ...

Cryo-electron Microscopy Specimen Preparation By Means Of a Focused Ion Beam

Here we present a protocol used to prepare cryo-TEM samples of Aspergillus niger spores, but which can easily be adapted for any number of microorganisms or solutions. We make use of a custom built cryo-transfer station and a modified cryo-SEM preparation chamber2. The spores are taken from a culture, plunge-frozen in a liquid nitrogen slush and observed in the cryo-SEM to select a region of interest. A thin lamella is then extracted using the FIB, attached to a TEM grid and subsequently thinned to electron transparency. The grid is transferred to a cryo-TEM holder and into a TEM for high resolution studies. Thanks to the introduction of a cooled nanomanipulator tip and a cryo-transfer station, this protocol is a straightforward adaptation to cryogenic temperature of the routinely used FIB preparation of TEM samples. As such it has the advantages of requiring a small amount of modifications to existing instruments, setups and procedures; it is easy to implement; it has a broad range of applications, in principle the same as for cryo-TEM sample preparation. One limitation is that it requires skillful handling of the specimens at critical steps to avoid or minimize contaminations.

Cryo Electron Microscopes, either Scanning (SEM) or Transmission (TEM), are widely used for characterization of biological samples or other materials with a high water content1. A SEM/Focused Ion Beam (FIB) is used to identify features of interest in samples and extract a thin, electron-transparent lamella for transfer to a cryo-TEM.

Here we present a protocol used to prepare cryo-TEM samples of Aspergillus niger spores, but which can easily be adapted for any number of microorganisms ...

Cell Block Preparation from Cytology Specimen with Predominance of Individually Scattered Cells

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Preparation of Primary Myogenic Precursor Cell/Myoblast Cultures from Basal Vertebrate Lineages

Efficient Generation Human Induced Pluripotent Stem Cells from Human Somatic Cells with Sendai-virus

Cryo-electron Microscopy Specimen Preparation By Means Of a Focused Ion Beam