This study was made possible by funding from the Dutch Cancer Society (KWF; EMCR 2012-5473) and the World Cancer Research Funds International (WCRF; project no. 2014-1181)

All procedures were done according to local animal welfare laws and guidelines.
1. Preparation of Instruments, Culture Media, and Dishes
<ol>
	<li>Autoclave 1 set of intestinal scissors, normal scissors, and forceps in a sterile container.</li>
	<li>Place a 96-well (flat bottom) dish in an incubator at 37 &#176;C.</li>
	<li>Prepare 10 mL of complete culture medium with the reagents listed in table of materials.</li>
	<li>Incubate the complete medium at 37 &#176;C in a water bath.</li>
	<li>Thaw reconstituted basement membrane by placing it in an ice bucket. The reconstituted basement membrane will become liquid at 4 &#176;C .</li>
	<li>Fill 4 Petri dishes with cold phosphate-buffered saline or abbreviated PBS (4 &#176;C).</li>
</ol>
2. Isolation of Small Intestinal Crypts
<ol>
	<li>Sacrifice by CO2 inhalation a Lgr5-eGFP-IRES-CreERt2 mouse on a C57BL6/J background. Dissect the peritoneum longitudinally with a pair of scissors.</li>
	<li>Hold the stomach with the forceps and cut it transversally in half.</li>
	<li>Using the intestinal scissors from now on, pull out the intestine and place it in a Petri dish containing PBS. 
	NOTE: Intestinal scissors have a sharp and a blunt tip. The blunt tip of these scissors is meant to not damage the crypt-villus architecture while opening the intestine.</li>
	<li>Start by placing the blunt tip into the stomach and gently push it through the pylorus. Proceed by cutting with the scissors and pulling with the forceps.</li>
	<li>Once the whole small intestine is opened longitudinally, wash it in cold PBS by holding it with the forceps and gently rinse it in the PBS solution with U-shaped movements.</li>
	<li>Once all the stool remnants are cleared, proceed to flatten the intestine on a cutting board, luminal side up. The luminal side is easily recognizable by the absence of blood vessels and by its pale appearance when compared with the outer part.</li>
	<li>With a glass slide, gently remove the villi by scraping the flattened intestine. Perform this step twice along the whole length of the tissue.</li>
	<li>Cut the small intestine with a sterile surgical blade into 2 - 5 mm pieces.</li>
	<li>Place the small intestinal fragments in a 50 mL tube containing 10 mL of ice cold PBS.</li>
	<li>Clean the tissue fragments, removing any remaining impurities by pipetting them up and down in the PBS. Discard supernatant and repeat this step until the PBS is completely clear.</li>
	<li>Add 15 mL cold PBS, to bring the total final volume of PBS to 25 mL. Add 2 mM ethylenediaminetetraacetic acid (EDTA) and incubate for 45 min on a roller at 4 &#176;C.</li>
	<li>Discard the PBS/EDTA.</li>
	<li>Add 10 mL of PBS and detach the crypts by harshly pipetting the tissue fragments up and down (at least three times). Collect the supernatant.</li>
	<li>Repeat step 2.13 four times. Add culture medium to reach a final volume of 50 mL.</li>
	<li>Pellet the cells by centrifugation (300 x g for 5 min).</li>
	<li>Resuspend the pellet in 10 mL of culture medium and pellet the crypts by centrifugation (80 x g for 3 min).</li>
</ol>
3. Single Cell Preparation
<ol>
	<li>Discard the supernatant of the pelleted crypts and resuspend them in 1 mL trypsin like-enzymes together with 50 &#181;L DNAse (50 &#181;g/mL).</li>
	<li>Incubate the cells in a water bath at 32 &#176;C for 2 min.</li>
	<li>Add 10 mL of culture medium. Dissociate the crypts into single cells by harshly pipetting up and down at least 5 times.</li>
	<li>Filter the solution through a 40 &#181;m strainer (to eliminate clumps and other impurities) and pellet the single cells at 300 x g for 5 min.</li>
</ol>
4. Flow Cytometry and Plating
<ol>
	<li>Prepare 50 mL of 1x&#160;Hank&#39;s buffered salt solution or HBSS/2% fetal cow serum (FCS) solution and resuspend the pellet in 1 mL for every 106 cells</li>
	<li>Add to the cell suspension BV421 Lin- (CD31, CD45, TER119) at a concentration of 1:100, and CD24-APC and CD117-PE both at a concentration of 1:250 antibodies for 30 min.</li>
	<li>Sort Lgr5+ stem cells and Paneth cells into separate low bind tubes. For details on sorting protocols for Lgr5+ and Paneth cells, please see Roth et al.7 and Schewe et al.6
	<ol>
		<li>Centrifuge the sorted cells at 300 x g for 5 min. Resuspend the cells in 100 &#181;L medium with the components described as in 1.3 (see the Table of Materials).</li>
	</ol>
	</li>
	<li>Treat (e.g., by chemical or genetic modification) the Paneth cells (n = 2000) or the Lgr5+ stem cells (n = 2000).
	<ol>
		<li>To treat cells, use 5 &#181;L of liposome-mediated transfection reagent in a total volume of 100 &#181;L culture medium and small interfering RNA (siRNA) at a concentration of 100 nM. Incubate for 30 min at 37 &#176;C for siRNA or for the time necessary for the chosen modification.</li>
	</ol>
	</li>
	<li>Wash the cells twice in 500 &#181;L culture medium.</li>
	<li>Centrifuge at 300 x g for 5 min and resuspend the cells in 10 &#181;L culture medium.</li>
	<li>Pool the two cellular components (Paneth or Lgr5+ cells) in a 20 &#181;l total volume and centrifuge at 300 x g for 5 min at RT.</li>
	<li>Co-incubate the Paneth and Lgr5+ cells for 10 min at RT.</li>
	<li>Remove 10 &#181;L of the supernatant and leave a meniscus of liquid to be sure to not aspirate the cell pellet.</li>
	<li>Add 30 &#181;L of reconstituted basement membrane to the cells for a total volume of 40 &#181;L, resuspend the cells and plate in a pre-warmed 96 well plate. After 10 min, add 200 &#181;L of complete medium (see the Table of Materials). Change medium every 48 h.</li>
	<li>Count organoid multiplicity at day 5.</li>
</ol>

<ol>
	<li>Barker, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+stem+cells+in+small+intestine+and+colon+by+marker+gene+Lgr5.">Identification of stem cells in small intestine and colon by marker gene Lgr5.</a> Nature. 449, 1003-1007 (2007).</li><li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paneth+cells+constitute+the+niche+for+Lgr5+stem+cells+in+intestinal+crypts.">Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts.</a> Nature. 469, 415-418 (2011).</li><li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+Lgr5+stem+cells+build+crypt-villus+structures+in+vitro+without+a+mesenchymal+niche.">Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.</a> Nature. 459, 262-265 (2009).</li><li>Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+Development+and+Disease+with+Organoids.">Modeling Development and Disease with Organoids.</a> Cell. 165, 1586-1597 (2016).</li><li>Cantrell, M. A., Kuo, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organoid+modeling+for+cancer+precision+medicine.">Organoid modeling for cancer precision medicine.</a> Genome Med. 7, 32 (2015).</li><li>Schewe, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Secreted+Phospholipases+A2+Are+Intestinal+Stem+Cell+Niche+Factors+with+Distinct+Roles+in+Homeostasis,+Inflammation,+and+Cancer.">Secreted Phospholipases A2 Are Intestinal Stem Cell Niche Factors with Distinct Roles in Homeostasis, Inflammation, and Cancer.</a> Cell Stem Cell. 19, 38-51 (2016).</li><li>Roth, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paneth+cells+in+intestinal+homeostasis+and+tissue+injury.">Paneth cells in intestinal homeostasis and tissue injury.</a> PLoS One. 7, e38965 (2012).</li><li>Rodriguez-Colman, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interplay+between+metabolic+identities+in+the+intestinal+crypt+supports+stem+cell+function.">Interplay between metabolic identities in the intestinal crypt supports stem cell function.</a> Nature. 543, 424-427 (2017).</li><li>Dow, L. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apc+Restoration+Promotes+Cellular+Differentiation+and+Reestablishes+Crypt+Homeostasis+in+Colorectal+Cancer.">Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer.</a> Cell. 161, 1539-1552 (2015).</li><li>Yilmaz, O. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mTORC1+in+the+Paneth+cell+niche+couples+intestinal+stem-cell+function+to+calorie+intake.">mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake.</a> Nature. 486, 490-495 (2012).</li><li>Igarashi, M., Guarente, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mTORC1+and+SIRT1+Cooperate+to+Foster+Expansion+of+Gut+Adult+Stem+Cells+during+Calorie+Restriction.">mTORC1 and SIRT1 Cooperate to Foster Expansion of Gut Adult Stem Cells during Calorie Restriction.</a> Cell. , 436-450 (2016).</li></ol>

The authors have no competing financial interest or other conflicts of interest

The ORA allows the refined functional analysis of the two essential components of the intestinal stem cell niche, namely Lgr5+ and Paneth cells. This approach has been previously employed by us and others with slight modifications6,10,11. Here, we present the ORA procedure as a reproducible and standardized laboratory protocol. Also, we report on the effects of Apc downregulation in Lgr5<sup...

The intestinal epithelium is the most rapidly self-renewing tissue in the mammalian body and, as such, has been the object of a plethora of studies aimed at the identification and functional characterization of the adult stem cells residing at the bottom of the crypt of Lieberk&#252;hn, earmarked by expression of the Lgr5 gene and dependent on canonical Wnt signals1. Notably, Lgr5+ stem cells are flanked and supported by specialized niche cells, i.e. Paneth cells, which also depend on Wnt signaling for their maturation2. Together, these two cell types underlie self-renewal of the intestinal epithelial lining and preserve the daily homeostatic equilibrium: Lgr5+ stem cells rapidly divide and give rise to progenitor and more specialized intestinal epithelial cells; Paneth cells provide essential niche factors (e.g., Dll1, Wnt3, EGF) to Lgr5+ stem cells2. The capacity of intestinal crypts when plated ex vivo to form organized and self-renewing structures called organoids, or &#34;mini-guts&#34;, has been exploited as an experimental tool to provide insight into processes such as self-renewal and differentiation in normal and pathological conditions including cancer4. Organoid cultures have been established from several tissues, including the intestine, pancreas, liver, and kidney, from both mouse and human samples4. The extraction method and the growth factors employed to develop these organoid cultures are tissue-specific and designed to drive multi-lineage differentiation and mimic as closely as possible the original stem cell niche in vivo. Organoids may have potential applications including the treatment of genetic diseases, the assessment of therapeutic efficacy in cancer, the analysis of drug toxicity, or the study of organogenesis in vitro5.
Overall, the main limitation of organoid cultures when established from tissue samples is a lack of cell-specificity. For example, intestinal organoids established from whole intestinal crypts do not allow the analysis of individual cellular components encompassed within the tissue source (e.g., whole crypts contain Lgr5+, Paneth, and progenitor cells).
Here, we describe a novel method, referred to as ORA, that combines the advantages of intestinal organoid cultures with the functional analysis of its most fundamental components, namely stem (Lgr5+) and niche (Paneth) cells. This is achieved through the unique ability of Paneth and Lgr5+ cells to physically associate with each other when co-incubated and give rise to organoids2,6,10. We took advantage of this feature and pre-treated the two cell types individually before allowing them to reconstitute organoids. When doing so, each cell component can be exposed to any given drug, growth factor, biochemical inhibitor, genetic modification, or chemical treatment prior to reconstitution and organoid formation. Therefore, using the ORA assay will allow the determination of whether a specific drug treatment or genetic modification has a specific effect on the stem cells or their niche counterpart.

<table>
	<tbody>
		<tr>
			<td>Advanced DMEM F12 *</td>
			<td>Thermo Fisher Scientific</td>
			<td>12634-010</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax *</td>
			<td>Thermo Fisher Scientific</td>
			<td>35050061</td>
			<td>Final concentration: 10 mM</td>
		</tr>
		<tr>
			<td>Penicillin/streptomycin *</td>
			<td>Thermo Fisher Scientific</td>
			<td>15140122</td>
			<td>Final concentration: 1%</td>
		</tr>
		<tr>
			<td>Hepes *</td>
			<td>Thermo Fisher Scientific</td>
			<td>15630080</td>
			<td>Final concentration: 10 mM</td>
		</tr>
		<tr>
			<td>Recombinant murine EGF *</td>
			<td>Thermo Fisher Scientific</td>
			<td>PMG8041</td>
			<td>Final concentration: 50 ng/ml</td>
		</tr>
		<tr>
			<td>Recombinant murine Noggin *</td>
			<td>Peprotech</td>
			<td>250-38</td>
			<td>Final concentration: 100 ng/ml</td>
		</tr>
		<tr>
			<td>y27632 *</td>
			<td>Sigma</td>
			<td>Y0503</td>
			<td>Final concentration: 10 &#181;M</td>
		</tr>
		<tr>
			<td>Jagged-1 *</td>
			<td>Anaspec Bio</td>
			<td>AS-61298</td>
			<td>Final concentration: 1 &#181;M</td>
		</tr>
		<tr>
			<td>Recombinant murine R-spondin *</td>
			<td>R&#38;D systems</td>
			<td>3474-RS-050</td>
			<td>Final concentration: 1 mg/ml</td>
		</tr>
		<tr>
			<td>Flexitube Gene solution siRNA APC</td>
			<td>Qiagen</td>
			<td>GS11789</td>
			<td>Final concentration: 100 nM</td>
		</tr>
		<tr>
			<td>Lipofectamine 2000</td>
			<td>Thermo Fisher Scientific</td>
			<td>11668019</td>
			<td></td>
		</tr>
		<tr>
			<td>CD24 APC</td>
			<td>Biolegend</td>
			<td>101814</td>
			<td></td>
		</tr>
		<tr>
			<td>c-kit PE</td>
			<td>Biolegend</td>
			<td>105808</td>
			<td></td>
		</tr>
		<tr>
			<td>BV 421 CD31</td>
			<td>Biolegend</td>
			<td>102424</td>
			<td></td>
		</tr>
		<tr>
			<td>BV 421 CD45</td>
			<td>Biolegend</td>
			<td>103134</td>
			<td></td>
		</tr>
		<tr>
			<td>BV421 TER119</td>
			<td>Biolegend</td>
			<td>116234</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Thermo Fisher Scientific</td>
			<td>14180046</td>
			<td></td>
		</tr>
		<tr>
			<td>B6.129P2-Lgr5tm1(cre/ERT2)Cle/J</td>
			<td>Jackson Laboratories</td>
			<td>008875</td>
			<td></td>
		</tr>
		<tr>
			<td>Low binding tubes</td>
			<td>Eppendorf</td>
			<td>Z666548-250EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel</td>
			<td>Corning</td>
			<td>356230</td>
			<td></td>
		</tr>
		<tr>
			<td>* The combination of these reagents constitutes the complete culture medium</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

the organoid reconstitution assay (ora) for the functional analysis of intestinal stem and niche cells

The intestinal epithelium is characterized by an extremely rapid turnover rate. In mammals, the entire epithelial lining is renewed within 4 - 5 days. Adult intestinal stem cells reside at the bottom of the crypts of Lieberk&#252;hn, are earmarked by expression of the Lgr5 gene, and preserve homeostasis through their characteristic high proliferative rate1. Throughout the small intestine, Lgr5+ stem cells are intermingled with specialized secretory cells called Paneth cells. Paneth cells secrete antibacterial compounds (i.e., lysozyme and cryptdins/defensins) and exert a controlling role on the intestinal flora. More recently, a novel function has been discovered for Paneth cells, namely their capacity to provide niche support to Lgr5+ stem cells through several key ligands as Wnt3, EGF, and Dll12.
When isolated ex vivo and cultured in the presence of specific growth factors and extracellular matrix components, whole intestinal crypts give rise to long-lived and self-renewing 3D structures called organoids that highly resemble the crypt-villus epithelial architecture of the adult small intestine3. Organoid cultures, when established from whole crypts, allow the study of self-renewal and differentiation of the intestinal stem cell niche, though without addressing the contribution of its individual components, namely the Lgr5+ and Paneth cells.
Here, we describe a novel approach to the organoid assay that takes advantage of the ability of Paneth and Lgr5+ cells to associate and form organoids when co-cultured. This approach, here referred to as &#34;organoid reconstitution assay&#34; (ORA), allows the genetic and biochemical modification of Paneth or Lgr5+ stem cells, followed by reconstitution into organoids. As such, it allows the functional analysis of the two main components of the intestinal stem cell niche.

The organoid reconstitution assay allows the separate functional analysis of the essential niche and stem cell components of the intestinal epithelium, here demonstrated by small interfering RNA (siRNA) of the Apc gene.
To achieve this aim, we first utilized fluorescent activated cell sorting (FACS) to separate 8000 Lgr5+ cells and 6000 Paneth cells from inbred C57BL6/J mice. In ...

Watch this Scientific Journal Video about The Organoid Reconstitution Assay ORA for the Functional Analysis of Intestinal Stem and Niche Cells at JoVE.com

The Organoid Reconstitution Assay ORA for the Functional Analysis of Intestinal Stem and Niche Cells

Intestinal organoid cultures are established from whole crypts and do not allow the analysis of self-renewal and differentiation in a cell-specific fashion. This protocol describes reconstitution of sorted stem (Lgr5+) and niche (Paneth) cells, which give rise to organoids while enabling their prior biochemical and genetic modification and functional analysis.

The Organoid Reconstitution Assay (ORA) for the Functional Analysis of Intestinal Stem and Niche Cells

The intestinal epithelium is characterized by an extremely rapid turnover rate. In mammals, the entire epithelial lining is renewed within 4 - 5 days. ...

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10.4K Views.  Erasmus University Medical Center. Intestinal organoid cultures are established from whole crypts and do not allow the analysis of self-renewal and differentiation in a cell-specific fashion. This protocol describes reconstitution of sorted stem (Lgr5+) and niche (Paneth) cells, which give rise to organoids while enabling their prior biochemical and genetic modification and functional analysis.

Video: The Organoid Reconstitution Assay ORA for the Functional Analysis of Intestinal Stem and Niche Cells

Use of Human Perivascular Stem Cells for Bone Regeneration

Human perivascular stem cells (PSCs) can be isolated in sufficient numbers from multiple tissues for purposes of skeletal tissue engineering1-3. PSCs are a FACS-sorted population of 'pericytes' (CD146+CD34-CD45-) and 'adventitial cells' (CD146-CD34+CD45-), each of which we have previously reported to have properties of mesenchymal stem cells. PSCs, like MSCs, are able to undergo osteogenic differentiation, as well as secrete pro-osteogenic cytokines1,2. In the present protocol, we demonstrate the osteogenicity of PSCs in several animal models including a muscle pouch implantation in SCID (severe combined immunodeficient) mice, a SCID mouse calvarial defect and a femoral segmental defect (FSD) in athymic rats. The thigh muscle pouch model is used to assess ectopic bone formation. Calvarial defects are centered on the parietal bone and are standardly 4 mm in diameter (critically sized)8. FSDs are bicortical and are stabilized with a polyethylene bar and K-wires4. The FSD described is also a critical size defect, which does not significantly heal on its own4. In contrast, if stem cells or growth factors are added to the defect site, significant bone regeneration can be appreciated. The overall goal of PSC xenografting is to demonstrate the osteogenic capability of this cell type in both ectopic and orthotopic bone regeneration models.

Human perivascular stem cells (PSCs) are a novel stem cell class for skeletal tissue regeneration similar to mesenchymal stem cells (MSCs). PSCs can be isolated by FACS (fluorescence activated cell sorting) from adipose tissue procured during standard liposuction procedures, then combined with an osteoinductive scaffold to achieve bone formation in vivo.

Human perivascular stem cells (PSCs) can be isolated in sufficient numbers from multiple tissues for purposes of skeletal tissue engineering1-3. PSCs are ...

Alginate Microcapsule as a 3D Platform for Propagation and Differentiation of Human Embryonic Stem Cells (hESC) to Different Lineages

Human embryonic stem cells (hESC) are emerging as an attractive alternative source for cell replacement therapy since they can be expanded in culture indefinitely and differentiated to any cell types in the body. Various types of biomaterials have also been used in stem cell cultures to provide a microenvironment mimicking the stem cell niche1-3. The latter is important for promoting cell-to-cell interaction, cell proliferation, and differentiation into specific lineages as well as tissue organization by providing a three-dimensional (3D) environment4 such as encapsulation. The principle of cell encapsulation involves entrapment of living cells within the confines of semi-permeable membranes in 3D cultures2. These membranes allow for the exchange of nutrients, oxygen and stimuli across the membranes, whereas antibodies and immune cells from the host that are larger than the capsule pore size are excluded5. Here, we present an approach to culture and differentiate hESC DA neurons in a 3D microenvironment using alginate microcapsules. We have modified the culture conditions2 to enhance the viability of encapsulated hESC. We have previously shown that the addition of p160-Rho-associated coiled-coil kinase (ROCK) inhibitor, Y-27632 and human fetal fibroblast-conditioned serum replacement medium (hFF-CM) to the 3D platform significantly enhanced the viability of encapsulated hESC in which the cells expressed definitive endoderm marker genes1. We have now used this 3D platform for the propagation of hESC and efficient differentiation to DA neurons. Protein and gene expression analyses after the final stage of DA neuronal differentiation showed an increased expression of tyrosine hydroxylase (TH), a marker for DA neurons, &gt;100 folds after 2 weeks. We hypothesized that our 3D platform using alginate microcapsules may be useful to study the proliferation and directed differentiation of hESC to various lineages. This 3D system also allows the separation of feeder cells from hESC during the process of differentiation and also has potential for immune-isolation during transplantation in the future.

Alginate Microcapsule as a 3D Platform for Propagation and Differentiation of Human Embryonic Stem Cells hESC to Different Lineages

We have optimized a microencapsulation technique as an effective 3D platform for propagation and differentiation of embryonic stem cells to endoderm and dopaminergic (DA) neurons. It also provides an opportunity for immune-isolation of cells from the host during transplantation. This platform can be adapted for other cell types.

Human embryonic stem cells (hESC) are emerging as an attractive alternative source for cell replacement therapy since they can be expanded in culture ...

A Microfluidic Chip for the Versatile Chemical Analysis of Single Cells

We present a microfluidic device that enables the quantitative determination of intracellular biomolecules in multiple single cells in parallel. For this purpose, the cells are passively trapped in the middle of a microchamber. Upon activation of the control layer, the cell is isolated from the surrounding volume in a small chamber. The surrounding volume can then be exchanged without affecting the isolated cell. However, upon short opening and closing of the chamber, the solution in the chamber can be replaced within a few hundred milliseconds. Due to the reversibility of the chambers, the cells can be exposed to different solutions sequentially in a highly controllable fashion, e.g. for incubation, washing, and finally, cell lysis. The tightly sealed microchambers enable the retention of the lysate, minimize and control the dilution after cell lysis. Since lysis and analysis occur at the same location, high sensitivity is retained because no further dilution or loss of the analytes occurs during transport. The microchamber design therefore enables the reliable and reproducible analysis of very small copy numbers of intracellular molecules (attomoles, zeptomoles) released from individual cells. Furthermore, many microchambers can be arranged in an array format, allowing the analysis of many cells at once, given that suitable optical instruments are used for monitoring. We have already used the platform for proof-of-concept studies to analyze intracellular proteins, enzymes, cofactors and second messengers in either relative or absolute quantifiable manner.

In this article we present a microfluidic chip for single cell analysis. It allows the quantification of intracellular proteins, enzymes, cofactors, and second messengers by means of fluorescent assays or immunoassays.&#160;

We present a microfluidic device that enables the quantitative determination of intracellular biomolecules in multiple single cells in parallel. For this ...

Lignin Down-regulation of Zea mays via dsRNAi and Klason Lignin Analysis

To facilitate the use of lignocellulosic biomass as an alternative bioenergy resource, during biological conversion processes, a pretreatment step is needed to open up the structure of the plant cell wall, increasing the accessibility of the cell wall carbohydrates. Lignin, a polyphenolic material present in many cell wall types, is known to be a significant hindrance to enzyme access. Reduction in lignin content to a level that does not interfere with the structural integrity and defense system of the plant might be a valuable step to reduce the costs of bioethanol production. In this study, we have genetically down-regulated one of the lignin biosynthesis-related genes, cinnamoyl-CoA reductase (ZmCCR1) via a double stranded RNA interference technique. The ZmCCR1_RNAi construct was integrated into the maize genome using the particle bombardment method. Transgenic maize plants grew normally as compared to the wild-type control plants without interfering with biomass growth or defense mechanisms, with the exception of displaying of brown-coloration in transgenic plants leaf mid-ribs, husks, and stems. The microscopic analyses, in conjunction with the histological assay, revealed that the leaf sclerenchyma fibers were thinned but the structure and size of other major vascular system components was not altered. The lignin content in the transgenic maize was reduced by 7-8.7%, the crystalline cellulose content was increased in response to lignin reduction, and hemicelluloses remained unchanged. The analyses may indicate that carbon flow might have been shifted from lignin biosynthesis to cellulose biosynthesis. This article delineates the procedures used to down-regulate the lignin content in maize via RNAi technology, and the cell wall compositional analyses used to verify the effect of the modifications on the cell wall structure.

Lignin Down-regulation of Zea mays via dsRNAi and Klason Lignin Analysis

A double stranded RNA interference (dsRNAi) technique is employed to down-regulate the maize cinnamoyl coenzyme A reductase (ZmCCR1) gene to lower plant lignin content. Lignin down-regulation from the cell wall is visualized by microscopic analyses and quantified by the Klason method. Compositional changes in hemicellulose and crystalline cellulose are analyzed.

To facilitate the use of lignocellulosic biomass as an alternative bioenergy resource, during biological conversion processes, a pretreatment step is ...

A Quantitative Fluorescence Microscopy-based Single Liposome Assay for Detecting the Compositional Inhomogeneity Between Individual Liposomes

Most research employing liposomes as membrane model systems or drug delivery carriers relies on bulk read-out techniques and thus intrinsically assumes all liposomes of the ensemble to be identical. However, new experimental platforms able to observe liposomes at the single-particle level have made it possible to perform highly sophisticated and quantitative studies on protein-membrane interactions or drug carrier properties on individual liposomes, thus avoiding errors from ensemble averaging. Here we present a protocol for preparing, detecting, and analyzing single liposomes using a fluorescence-based microscopy assay, facilitating such single-particle measurements. The setup allows for imaging individual liposomes in a massive parallel manner and is employed to reveal intra-sample size and compositional inhomogeneities. Additionally, the protocol describes the advantages of studying liposomes at the single liposome level, the limitations of the assay, and the important features to be considered when modifying it to study other research questions.

This protocol describes the fabrication of liposomes and how these can be immobilized on a surface and imaged individually in a massive parallel manner using fluorescence microscopy. This allows for the quantification of the size and compositional inhomogeneity between single liposomes of the population.

Most research employing liposomes as membrane model systems or drug delivery carriers relies on bulk read-out techniques and thus intrinsically assumes ...

Bioparticle Microarrays for Chemotactic and Molecular Analysis of Human Neutrophil Swarming in vitro

Neutrophil swarming is a cooperative process by which neutrophils seal off a site of infection and promote tissue reorganization. Swarming has classically been studied in vivo in animal models showing characteristic patterns of cell migration. However, in vivo models have several limitations, including intercellular mediators that are difficult to access and analyze, as well as the inability to directly analyze human neutrophils. Because of these limitations, there is a need for an in vitro platform that studies swarming with human neutrophils and provides easy access to the molecular signals generated during swarming. Here, a multistep microstamping process is used to generate a bioparticle microarray that stimulates swarming by mimicking an in vivo infection. The bioparticle microarray induces neutrophils to swarm in a controlled and stable manner. On the microarray, neutrophils increase in speed and form stable swarms around bioparticle clusters. Additionally, supernatant generated by the neutrophils was analyzed and 16 proteins were discovered to have been differentially expressed over the course of swarming. This in vitro swarming platform facilitates direct analysis of neutrophil migration and protein release in a reproducible, spatially controlled manner.

This protocol generates bioparticle microarrays that provide spatially controlled neutrophil swarming. It provides easy access to the mediators that neutrophils release during migration and allows for quantitative imaging analysis.

Neutrophil swarming is a cooperative process by which neutrophils seal off a site of infection and promote tissue reorganization. Swarming has classically ...

Isolation, Expansion, and Differentiation of Mesenchymal Stem Cells from the Infrapatellar Fat Pad of the Goat Stifle Joint

The IFP, present in the knee joint, serves as a promising source of MSCs. The IFP is an easily accessible tissue as it is routinely resected and discarded during arthroscopic procedures and knee replacement surgeries. Additionally, its removal is associated with minimal donor site morbidity. Recent studies have demonstrated that IFP-MSCs do not lose their proliferation capacity during in vitro expansion and have age-independent osteogenic differentiation potential. IFP-MSCs possess superior chondrogenic differentiation potential compared to bone marrow-derived MSCs (BMSCs) and adipose-derived stem cells (ADSCs). Although these cells are easily obtainable from aged and diseased patients, their effectiveness is limited. Hence, using IFP-MSCs from healthy donors is important to determine their efficacy in biomedical applications. As access to a healthy human donor is challenging, animal models could be a better alternative to enable fundamental understanding. Large animals such as dogs, horses, sheep, and goats play a crucial role in translational research. Amongst these, the goat could be a preferred model since the stifle joint of the goat has the closest anatomy to the human knee joint. Moreover, goat-IFP can fulfill the higher MSC numbers needed for tissue regeneration applications. Furthermore, low cost, availability, and compliance with the 3R principles for animal research make them an attractive model. This study demonstrates a simple protocol for isolating IFP-MSCs from the stifle joint of goats and in vitro culture conditions for their expansion and differentiation. The aseptically isolated IFP from the goat was washed, minced, and digested enzymatically. After filtration and centrifugation, the collected cells were cultured. These cells were adherent, had MSCs-like morphology, and demonstrated remarkable clonogenic ability. Further, they differentiated into adipogenic, chondrogenic, and osteogenic lineages, demonstrating their multipotency. In conclusion, the study demonstrates the isolation and expansion of MSCs, which show potential in tissue engineering and regenerative medicine applications.

Infrapatellar fat pad mesenchymal&#160;stem cells (IFP-MSCs) can be isolated easily from the infrapatellar fat pad of the knee joint. They proliferate well in vitro, form CFU-F colonies, and differentiate into adipogenic, chondrogenic, and osteogenic lineages. Herein, the methodology for the isolation, expansion, and differentiation of IFP-MSCs from goat stifle joint is provided.

The IFP, present in the knee joint, serves as a promising source of MSCs. The IFP is an easily accessible tissue as it is routinely resected and discarded ...

Preparation and Characterization of Graphene-Based 3D Biohybrid Hydrogel Bioink for Peripheral Neuroengineering

Peripheral neuropathies can occur as a result of axonal damage, and occasionally due to demyelinating diseases. Peripheral nerve damage is a global problem that occurs in 1.5%-5% of emergency patients and may lead to significant job losses. Today, tissue engineering-based approaches, consisting of scaffolds, appropriate cell lines, and biosignals, have become more applicable with the development of three-dimensional (3D) bioprinting technologies. The combination of various hydrogel biomaterials with stem cells, exosomes, or bio-signaling molecules is frequently studied to overcome the existing problems in peripheral nerve regeneration. Accordingly, the production of injectable systems, such as hydrogels, or implantable conduit structures formed by various bioprinting methods has gained importance in peripheral neuro-engineering. Under normal conditions, stem cells are the regenerative cells of the body, and their number and functions do not decrease with time to protect their populations; these are not specialized cells but can differentiate upon appropriate stimulation in response to injury. The stem cell system is under the influence of its microenvironment, called the stem cell niche. In peripheral nerve injuries, especially in neurotmesis, this microenvironment cannot be fully rescued even after surgically binding severed nerve endings together. The composite biomaterials and combined cellular therapies approach increases the functionality and applicability of materials in terms of various properties such as biodegradability, biocompatibility, and processability. Accordingly, this study aims to demonstrate the preparation and use of graphene-based biohybrid hydrogel patterning and to examine the differentiation efficiency of stem cells into nerve cells, which can be an effective solution in nerve regeneration.

In this manuscript, we demonstrate the preparation of a biohybrid hydrogel bioink containing graphene for use in peripheral tissue engineering. Using this 3D biohybrid material, the neural differentiation protocol of stem cells is performed. This can be an important step in bringing similar biomaterials to the clinic.

Peripheral neuropathies can occur as a result of axonal damage, and occasionally due to demyelinating diseases. Peripheral nerve damage is a global ...

Formulating and Characterizing an Exosome-based Dopamine Carrier System

Exosomes between 40 and 200 nm in size constitute the smallest subgroup of extracellular vesicles. These bioactive vesicles secreted by cells play an active role in intercellular cargo and communication. Exosomes are mostly found in body fluids such as plasma, cerebrospinal fluid, urine, saliva, amniotic fluid, colostrum, breast milk, joint fluid, semen, and pleural acid. Considering the size of exosomes, it is thought that they may play an important role in central nervous system diseases because they can pass through the blood-brain barrier (BBB). Hence, this study aimed to develop an exosome-based nanocarrier system by encapsulating dopamine into exosomes isolated from Wharton's jelly mesenchymal stem cells (WJ-MSCs). Exosomes that passed the characterization process were incubated with dopamine. The dopamine-loaded exosomes were recharacterized at the end of incubation. Dopamine-loaded exosomes were investigated in drug release and cytotoxicity assays. The results showed that dopamine could be successfully encapsulated within the exosomes and that the dopamine-loaded exosomes did not affect fibroblast viability.

Here, we aimed to obtain a formulation by dopamine loading of the isolated exosomes of stem cells from Wharton's jelly mesenchymal stem cells. Exosome isolation and characterization, drug loading into the resulting exosomes, and the cytotoxic activity of the developed formulation are described in this protocol.

Exosomes between 40 and 200 nm in size constitute the smallest subgroup of extracellular vesicles. These bioactive vesicles secreted by cells play an ...

Combining Human Organoids and Organ-on-a-Chip Technology to Model Intestinal Region-Specific Functionality

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, and metabolism of nutrients and xenobiotics while facilitating a symbiotic relationship with microbiota and restricting the invasion of microorganisms. Functional interaction between various cell types and their physical and biochemical environment is vital to establish and maintain intestinal tissue homeostasis. Modeling these complex interactions and integrated intestinal physiology in vitro is a formidable goal with the potential to transform the way new therapeutic targets and drug candidates are discovered and developed.
Organoids and Organ-on-a-Chip technologies have recently been combined to generate human-relevant intestine chips suitable for studying the functional aspects of intestinal physiology and pathophysiology in vitro. Organoids derived from the biopsies of the small (duodenum) and large intestine are seeded into the top compartment of an organ chip and then successfully expand&#160;as monolayers while preserving the distinct cellular, molecular, and functional features of each intestinal region. Human intestine tissue-specific microvascular endothelial cells are incorporated in the bottom compartment of the organ chip to recreate the epithelial-endothelial interface. This novel platform facilitates luminal exposure to nutrients, drugs, and microorganisms, enabling studies of intestinal transport, permeability, and host-microbe interactions.
Here, a detailed protocol is provided for the establishment of intestine chips representing the human duodenum (duodenum chip) and colon (colon chip), and their subsequent culture under continuous flow and peristalsis-like deformations. We demonstrate methods for assessing drug metabolism and CYP3A4 induction in duodenum chip using prototypical inducers and substrates. Lastly, we provide a step-by-step procedure&#160;for the in vitro modeling of interferon gamma (IFN&#947;)-mediated barrier disruption (leaky gut syndrome) in a colon chip, including methods for evaluating the alteration of paracellular permeability, changes in cytokine secretion, and transcriptomic profiling of the cells within the chip.

Biopsy-derived intestinal organoids and organ-on-a-chips technologies are combined into a microphysiological platform to recapitulate region-specific intestinal functionality.

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, ...

The Organoid Reconstitution Assay (ORA) for the Functional Analysis of Intestinal Stem and Niche Cells

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A Quantitative Fluorescence Microscopy-based Single Liposome Assay for Detecting the Compositional Inhomogeneity Between Individual Liposomes

Bioparticle Microarrays for Chemotactic and Molecular Analysis of Human Neutrophil Swarming in vitro

Isolation, Expansion, and Differentiation of Mesenchymal Stem Cells from the Infrapatellar Fat Pad of the Goat Stifle Joint

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Combining Human Organoids and Organ-on-a-Chip Technology to Model Intestinal Region-Specific Functionality