We thank other members of the Lyon INSA-ENS iGEM team (Viviane Chansavang, Mathilde Dumond, Alexandre Duprey, M&eacute;lanie Geffroy, Cl&eacute;mence Gonthier, Margaux Jaulin, Aur&eacute;lie Haag, Goki Ly, Thomas Poinsot, B&eacute;ryl Royer-Bertrand, Julie Soula, Michael Vonzy, Pierre Yves Zundel, Soufiane Bouhmadi, Olivier Brette, Ga&euml;l Chambonnier, Laura Izard, Aurianne Kroiss, Philippe Lejeune, Agn&egrave;s Rodrigue, Arnaud Rondelet, Sylvie Reverchon and Val&eacute;rie Desjardin), our sponsors for their financial support (bioM&eacute;rieux, Assystem, EDF, Fondation INSA, ENS-Lyon and the Department of Biosciences INSA-Lyon), F. Wisniewski-Dy&eacute; for critical reading of this manuscript and Dr C.C. Sze for strain gift. B. Drogue receives a Ph.D. fellowship from R&eacute;gion Rh&ocirc;ne-Alpes.

1. Biobrick Design and Synthesis of the Curli Operon
<ol>
	<li>Determine the genetic organization and localize the endogenous transcriptional and translational signals of the curli genes. These informations are gathered in specialized databases such as RegulonDBa or EcoGeneb and completed by a careful reading of pertinent publications. Data management and in silico preanalysis were performed with Clone Manager softwarec.</li>
	<li>Select the pertinent coding sequences. A set of five absolutely required genes for curli synthesis (csgB and csgA encoding fiber monomers) and export (csgE csgF and csgG, encoding the curlin secretion complex) were selected to construct the synthetic operon. Extract the chosen sequences from the data base in FASTA format. 
	As the csgGFE cluster is antisense in E. coli genome, convert this sequence into its reverse complement counterpart by using the Clone Manager tools Operations&gt; Process molecule&gt;Invert molecule. Paste the csgEFG sequence behind csgBA by using the function "Ligate" (Clone&gt; Ligate).</li>
	<li>Add the appropriate promoter. By placing the five selected curli genes under control of the promoter Prcn, curli are predicted to be over-produced in presence of cobalt and nickel. The rcn locus encodes an efflux pump responsible for Ni and Co detoxification (rcnA) and its cognate metallo-regulator (rcnR). RcnR controls the expression of rcnA and its own gene in response to Ni and Co 19. The rcn sequence comprising rcnR CDS, the whole rcn intergenic region plus the 41 first nucleotides of rcnA was placedin front of the csgBAEFG chimerical sequence (Figure 1, the sequence of the whole construct is provided as supplementary data).</li>
	<li>Optimize the transcriptional signals. A perfect ribosome binding site (or perfect RBS= AAGGAGGTATATA) was added in front of the first ATG of the csgBA DNA sequence. A second perfect RBS was added in front of the csgEFG sequence. Endogenous RBS for the csgB and csgF and csgG genes were conserved.</li>
	<li>To fit iGEM standards, the device must be flanked by a standard BioBrick prefix and suffix, containing restriction sites for EcoRI, PstI (prefix) and SpeI and XbaI (suffix). Paste the corresponding sequences at each end of the deviced.</li>
	<li>Eliminate any EcoRI, PstI, SpeI and XbaI recognition site in the device. To facilitate further assembly process, the BioBrick part itself may not contain any of these restriction sites. In silico restriction analysis of the device revealed one PstI site in the csgA sequence, one PstI site in the rcnR sequence and one EcoRI site in the csgE gene. These sites are respectively located in position 80 (Mut1), 1340 (Mut2) and 1830 (Mut3) of the device sequence (supplementary data) and were modified as follow by silent mutations. 
	Mut1 PstI site CTGCAG changed in CGTCTG 
	Mut2 PstI site CTGCAG changed in CAGCAG 
	Mut3 EcoRI site GAATTC changed in GAATT</li>
	<li>Run through the translation simulation using the Clone Manager software (Operation&gt;Process molecules&gt;Translate molecules). Use the sequence alignment program BLAST to verify the perfect homology between the wild type curli protein and the proteins encoded by the synthetic operon.</li>
	<li>Order the synthetic operon. Commercial gene synthesis services are available from numerous companies worldwide, our partner was Genecust (Luxembourg). 4 &mu;g of the artificial operon (3165 bp) were received few weeks later and inserted into pUC57 (pIG2).</li>
</ol>
2. Visualize and Quantify Adherent Bacteria on Polystyrene
<ol>
	<li>Fill each well of a 24-well polystyrene plate with 2 ml of M63 minimal medium (glucose 0.2%) and inoculate each well with 106 cells of an overnight culture. Grow bacteria at 30 &deg;C for 18 to 48 hr without shaking. Each column (4 wells) represents a modality. Add the proper amount of cobalt (25 to 100 mM) and antibiotic (ampicillin 100 &mu;g.L-1) when needed. The 3 first rows of the 24-well plate are used to quantify the adherent bacteria by averaging the 3 repetitions, the last row left is used to visualize the biofilm.</li>
	<li>For the 3 first rows of the 24-well plate: for each well, recover the supernatant containing the planktonic cells.</li>
	<li>Carefully rinse each well with 1 ml of M63 and pool the 1 ml wash with the initial supernatant obtained in 2.2). This pool is referred to as swimming cells (=S).</li>
	<li>Recover the biofilm in 1 ml of M63 by scraping and pipetting up and down (=B). Vortex 15 sec. Estimate the number of surface-attached and swimming bacteria from the optical density at 600 nm (OD600) to give the adherence percentage corresponding to each modality.</li>
	<li>The percentage of adherence is calculated by using the formula: Bx100/(3xS+B).</li>
	<li>Only for the last row of the 24-well plate: discard planktonic cells.</li>
	<li>Rinse with 1 ml of M63 the biofilm which had developed on the bottom of the plate.</li>
	<li>Dry the open plate for 1 hr at 80 &deg;C.</li>
	<li>Add 100 &mu;l of 20% crystal violet for 2 min in each well followed by extensive washes with water to visualize the surface-attached bacteria. 
	Three independent assays (plates) have to be performed to ensure reproducibility.</li>
</ol>
3. Visualize Adherent Bacteria on Glass by Microscopy
<ol>
	<li>Get a fluorescent chassis. The E. coli SCC1e strain which constitutively expresses green fluorescent protein (GFP) with no observable difference from the parent strain MG1655 20 is a suitable host for the plasmid bearing the synthetic curli operon.</li>
	<li>Transform SCC1 with the pIG2 plasmid (=synthetic curli operon inserted at the EcoRI/PstI site of the pUC57 plasmid) to obtain the S23 strain. Transform SCC1 with a control plasmid (pUC18) to obtain the control strain S24 21.</li>
	<li>Grow overnight precultures of the S23 and of the control (S24) strains at 30 &deg;C in M63 medium supplemented with glucose (0.2 %) and ampicillin (100 &mu;g.L-1).</li>
	<li>Inoculate 15 ml of the same medium in Petri dishes with 100 &mu;l of the precultures. Add the appropriate concentration of cobalt (i.e. 25 &mu;M) and don't forget the negative control without cobalt. Introduce 3 rectangular glass coverslip in each Petri dish. Incubate overnight at 30 &deg;C without shaking.</li>
	<li>Remove the coverslip from the Petri dish and carefully drain it. Carefully clean the lower face with a small cotton stuff impregnated with 70 &deg; ethanol by wiping off every bacterial residue. For confocal observation, clean both upper ends on a few millimeters to allow further fixation of the coverslip.</li>
	<li>Adherent bacteria can be visualized directly but quickly under fluorescence microscope, but carefully avoid drying of the sample.</li>
	<li>For confocal observation, deposit the coverslip on a glass slide with the upper face covered by the biofilm placed face up. The biofilm is then covered with a larger coverslip, which is fixed to the glass slide with varnish. Invert the setup so that the biofilm will now be on the lower face.</li>
	<li>Place the setup under the confocal laser microscope. A right Axioplan2 LSM510 (Zeiss) confocal laser microscope was used at the Platim platformf.</li>
	<li>Setting. Excite GFP at 488 nm, and collect the bacterial fluorescence in the range 500 to 600 nm. Use 40x oil immersion objective for acquiring images in laser scanning confocal mode. Scan the overall three-dimensional structures of the biofilms from the solid surface to the interface with the growth medium, using a step of 1 &mu;m.</li>
	<li>Perform three-dimensional projections with IMARIS software (Bitplane, Z&uuml;rich, Switzerland). Determine biofilm thickness by the analysis of the average z value along statistical longitudinal sections. Quantification of biofilm biovolumes can be extracted from confocal z-stacks as described elsewhere 22.</li>
</ol>
aRegulonDB provides mechanistic information about operon organization and their decomposition into transcription units, promoters and their sigma type, genes and their ribosome binding sites, terminators, binding sites of specific transcriptional regulators,as well as their organization into regulatory phrases. <a href="http://regulondb.cs.purdue.edu/index.jsp" target="_blank">http://regulondb.cs.purdue.edu/index.jsp</a>
bThe EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. <a href="http://ecogene.org/" target="_blank">http://ecogene.org/</a>
c<a href="http://www.scied.com/dl_cmp9d.htm" target="_blank">http://www.scied.com/dl_cmp9d.htm</a>
d<a href="http://partsregistry.org/wiki/index.php?title=Help:BioBrick_Prefix_and_Suffix" target="_blank">http://partsregistry.org/wiki/index.php?title=Help:BioBrick_Prefix_and_Suffix</a>
eGift of Chun Chau Sze, Nan Yang Technical University, Singapore.
fPlatim microscopic platform UMS3444 BioSciences Gerland - Lyon Sud.

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No conflicts of interest declared.

Critical steps
The most critical step in this synthetic biology approach is the gene design. Synthetic gene design has to be meticulous to ensure an efficient system production. Two genes encoding the fiber monomers and three genes encoding proteins involved in their secretion system have been assembled with a strong and metal-inducible promoter to create a new functional unit for a novel application: the bio-decontamination of nuclear effluent. As planned and predicted, this device leads to...

Bacterial adherence to abiotic support plays a major role in bioremediation, biocatalysis or microbial fuel cells. Bioremediation processes use the capacities of microorganisms to degrade organic substances, or to modify the metal distribution (immobilization, volatilization) or speciation. These beneficial activities are observed in aquatic and terrestrial ecosystems, but also in the artificial systems developed to treat polluted water of industrial and domestic wastes. The intensity and the quality of the microbial activity depend on physico-chemical factors, but also on the lifestyle of microorganisms (free-floating or embedded into biofilm). The biofilm formation is associated with a metabolism promoting resistance to biocides by diverse mechanisms. This phenomenon will therefore be encouraged in most bioremediation processes. Moreover, engineering Escherichia coli cells to control the biofilm formation has been successfully applied to immobilize whole-cell sensors on biochips2-3.
Adaptation of microorganisms to high concentration of metals occurs via diverse mechanisms such as adsorption to extracellular matrix components, activation of efflux pump or specific carriers able to concentrate the metal into the cell. Boosting these bacterial activities via genetic engineering allows efficient and cheap treatment of metal pollution at the laboratory scale, especially in the case of highly toxic metals in weak quantity as described by Raghu et al. 2008 4. Bacterial remediation represents in this case a competitive and cost saving method compared to classical chemical processes using ion exchange resins. The authors described an E. coli chassis genetically engineered for cobalt uptake and retention first by knocking out the efflux pump encoding gene rcnA, and then by transformation with a multi copy plasmid allowing overproduction of a transporter with preferential uptake for cobalt. Such a strain appears as an efficient alternative to ion exchange resins to treat radioactive effluent, but a key unresolved issue is the recovery of contaminated bacteria at the end of the process 4. The objective of our work was therefore to engineer a custom-designed strain able to stick to abiotic supports such as glass or plastic.
Amongst the whole set of adhesins and adherent fimbriae identified in Gram- bacteria, we chose to design a system allowing curli production. Curli are thin (2-5 nm diameter) and highly aggregative amyloid fibers that protrude from the E. coli and Salmonella surface as a non-crystalline and insoluble matrix 5-7. Curli are also involved in the colonization of abiotic surfaces and the development of biofilms 8. Curli were recently shown to bind mercury ions 9. Amyloids are indeed known to possess high affinity for metals ions such as Cu2+, Zn2+ and Fe3+ 10. This property might further improve the decontamination of metal polluted effluents. The csg cluster is responsible for the production of curli fibers and is constituted of two divergently transcribed operons (Figure 1). The csgB, csgA and csgC genes constitute the sense operon, encoding the two curli subunits, CsgA and CsgB. CsgC seems to be involved in redox activity within the curli biogenesis system and to affect CsgG pore behavior 11. However, the absence of csgC in the majority of curli-producing bacteria indicates that the corresponding protein provides only a secundary level of control over the curli biogenesis. To simplify the system, we have been chosen to work with the minimum number of genes.
The csgDEFG operonencodes proteins essential in the regulation and transportation of CsgA and CsgB to the cell surface. CsgD is a transcriptional activator of the csgBAC operon and plays a key role in the control of biofilm formation by controlling the production of curli fimbriae and other biofilm components such as cellulose 12 and by inhibiting the flagellum production 13. CsgE, CsgF and CsgG constitute a curli-specific secretory apparatus in the outer-membrane through which the major curli subunit protein CsgA is secreted as a soluble protein. The polymerization of CsgA is dependent in vivo on the membrane-bound nucleator protein CsgB (reviewed in 14). Complex regulatory pathways involving several two-component systems have been shown to control curli gene expression 15-16. These complex regulations allow bacteria to form thick biofilms via the curli production in response to environmental cues, but are difficult to control for industrial applications. To facilitate the recovery of the metal-stuffed bacteria during an industrial process, bacterial fixation to a solid support indeed needs to be controlled by well defined parameter(s). The adherent properties of curli are linked to their amyloid nature 17 and could be used to improve bioremediation processes, but a simpler and easily controlled device has to be created.
Amongst these 7 genes 18, a set of 5 absolutely required genes for curli synthesis (csgB and csgA encoding fiber monomers) and export (csgE csgF and csgG, encoding the curli secretion complex) were selected to construct the synthetic operon. To escape the "natural" regulation of curli, a synthetic operon comprising these 5 csg genes under the control of a strong and cobalt-overinducible promoter (Figure 2) was designed and synthesized. The step-by-step analysis of the curli-encoding region and the design procedure for a functional synthetic operon are described. Two methods to visualize and quantify bacterial adherence to polystyrene and glass are explained.

<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>pIG2</td>
 <td></td>
 <td></td>
 <td>pUC57(pMB1 ori, 2710 bp) with a 3165 bp EcoRI/PstI fragment containing the synthetic Prcn-csgBAEFG operon ; Ampr </td>
 </tr>
 <tr>
 <td>pUC18</td>
 <td></td>
 <td></td>
 <td>Multicopy plasmid (pMB1 ori, 2686 bp), Ampr </td>
 </tr>
 <tr>
 <td>S23</td>
 <td></td>
 <td></td>
 <td>SSC1 (= GFP-tagged MG1655, gift of C.C. Sze)/pIG2</td>
 </tr>
 <tr>
 <td>S24</td>
 <td></td>
 <td></td>
 <td>SSC1/pUC18</td>
 </tr>
 <tr>
 <td>CoCl2</td>
 <td>Sigma</td>
 <td></td>
 <td>0,1M stock solution kept at Room Temperature</td>
 </tr>
 <tr>
 <td>M63</td>
 <td></td>
 <td></td>
 <td>29 </td>
 </tr>
 <tr>
 <td>24-well plate </td>
 <td>Nunc</td>
 <td>55429</td>
 <td>Polystyrene 24-well plates</td>
 </tr>
 </tbody>
</table>

engineering adherent bacteria by creating a single synthetic curli operon

The method described here consists in redesigning E. coli adherence properties by assembling the minimum number of curli genes under the control of a strong and metal-overinducible promoter, and in visualizing and quantifying the resulting gain of bacterial adherence. This method applies appropriate engineering principles of abstraction and standardization of synthetic biology, and results in the BBa_K540000 Biobrick (Best new Biobrick device, engineered, iGEM 2011).
The first step consists in the design of the synthetic operon devoted to curli overproduction in response to metal, and therefore in increasing the adherence abilities of the wild type strain. The original curli operon was modified in silico in order to optimize transcriptional and translational signals and escape the "natural" regulation of curli. This approach allowed to test with success our current understanding of curli production. Moreover, simplifying the curli regulation by switching the endogenous complex promoter (more than 10 transcriptional regulators identified) to a simple metal-regulated promoter makes adherence much easier to control.
The second step includes qualitative and quantitative assessment of adherence abilities by implementation of simple methods. These methods are applicable to a large range of adherent bacteria regardless of biological structures involved in biofilm formation. Adherence test in 24-well polystyrene plates provides a quick preliminary visualization of the bacterial biofilm after crystal violet staining. This qualitative test can be sharpened by the quantification of the percentage of adherence. Such a method is very simple but more accurate than only crystal violet staining as described previously 1 with both a good repeatability and reproducibility. Visualization of GFP-tagged bacteria on glass slides by fluorescence or laser confocal microscopy allows to strengthen the results obtained with the 24-well plate test by direct observation of the phenomenon.

In silico annotation of the wild type csg sequence of E. coli K12 associated with the optimization of transcriptional and translational signals has allowed to design the single synthetic curli operon Prcn-csg shown in Figure 3 (full sequence in supplementary data). Protocol 2 and protocol 3 were used to visualize and quantify adherence associated with curli production. Using crystal violet staining on 24-well polystyrene plates (protocole 2) biofilm formation at the bo...

Watch this Scientific Journal Video about Engineering Adherent Bacteria by Creating a Single Synthetic Curli Operon at JoVE.com

Engineering Adherent Bacteria by Creating a Single Synthetic Curli Operon

The design of a synthetic operon encoding both the secretory apparatus and the structural monomers of curli fibers is described. Overproduction of these amyloids and adherent polymers allows a measurable gain of adherence of the E. coli chassis1. Easy ways to visualize and quantify adherence are explained.

The  method described here consists in redesigning E. coli adherence properties by assembling the minimum number of  curli genes under the control of a ...

engineering-adherent-bacteria-creating-single-synthetic-curli

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Bioengineering

14.4K Views.  Université de Lyon. The design of a synthetic operon encoding both the secretory apparatus and the structural monomers of curli fibers is described. Overproduction of these amyloids and adherent polymers allows a measurable gain of adherence of the E. coli chassis1. Easy ways to visualize and quantify adherence are explained.

Video: Engineering Adherent Bacteria by Creating a Single Synthetic Curli Operon

Procedure for Lung Engineering

Lung tissue, including lung cancer and chronic lung diseases such as chronic obstructive pulmonary disease, cumulatively account for some 280,000 deaths annually; chronic obstructive pulmonary disease is currently the fourth leading cause of death in the United States1. Contributing to this mortality is the fact that lungs do not generally repair or regenerate beyond the microscopic, cellular level. Therefore, lung tissue that is damaged by degeneration or infection, or lung tissue that is surgically resected is not functionally replaced in vivo. To explore whether lung tissue can be generated in vitro, we treated lungs from adult rats using a procedure that removes cellular components to produce an acellular lung extracellular matrix scaffold. This scaffold retains the hierarchical branching structures of airways and vasculature, as well as a largely intact basement membrane, which comprises collagen IV, laminin, and fibronectin. The scaffold is mounted in a bioreactor designed to mimic critical aspects of lung physiology, such as negative pressure ventilation and pulsatile vascular perfusion. By culturing pulmonary epithelium and vascular endothelium within the bioreactor-mounted scaffold, we are able to generate lung tissue that is phenotypically comparable to native lung tissue and that is able to participate in gas exchange for short time intervals (45-120 minutes). These results are encouraging, and suggest that repopulation of lung matrix is a viable strategy for lung regeneration. This possibility presents an opportunity not only to work toward increasing the supply of lung tissue for transplantation, but also to study respiratory cell and molecular biology in vitro for longer time periods and in a more accurate microenvironment than has previously been possible.

We have developed a decellularized lung extracellular matrix and novel biomimetic bioreactor that can be used to generate functional lung tissue. By seeding cells into the matrix and culturing in the bioreactor, we generate tissue that demonstrates effective gas exchange when transplanted in vivo for short periods of time.

Lung tissue, including lung cancer and chronic lung diseases such as chronic obstructive pulmonary disease, cumulatively account for some 280,000 deaths ...

Creating Two-Dimensional Patterned Substrates for Protein and Cell Confinement

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1 While microcontact printing can be employed to directly print a large number of molecules, including proteins,2 DNA,3 and silanes,4 the formation of self-assembled monolayers (SAMs) from long chain alkane thiols on gold provides a simple way to confine proteins and cells to specific patterns containing adhesive and resistant regions. This confinement can be used to control cell morphology and is useful for examining a variety of questions in protein and cell biology. Here, we describe a general method for the creation of well-defined protein patterns for cellular studies.5 This process involves three steps: the production of a patterned master using photolithography, the creation of a PDMS stamp, and microcontact printing of a gold-coated substrate. Once patterned, these cell culture substrates are capable of confining proteins and/or cells (primary cells or cell lines) to the pattern.
The use of self-assembled monolayer chemistry allows for precise control over the patterned protein/cell adhesive regions and non-adhesive regions; this cannot be achieved using direct protein stamping. Hexadecanethiol, the long chain alkane thiol used in the microcontact printing step, produces a hydrophobic surface that readily adsorbs protein from solution. The glycol-terminated thiol, used for backfilling the non-printed regions of the substrate, creates a monolayer that is resistant to protein adsorption and therefore cell growth.6 These thiol monomers produce highly structured monolayers that precisely define regions of the substrate that can support protein adsorption and cell growth. As a result, these substrates are useful for a wide variety of applications from the study of intercellular behavior7 to the creation of microelectronics.8
While other types of monolayer chemistry have been used for cell culture studies, including work from our group using trichlorosilanes to create patterns directly on glass substrates,9 patterned monolayers formed from alkane thiols on gold are straight-forward to prepare. Moreover, the monomers used for monolayer preparation are commercially available, stable, and do not require storage or handling under inert atmosphere. Patterned substrates prepared from alkane thiols can also be recycled and reused several times, maintaining cell confinement.10

Self-assembled monolayers (SAMs) formed from long chain alkane thiols on gold provide well-defined substrates for the formation of protein patterns and cell confinement. Microcontact printing of hexadecanethiol using a polydimethylsiloxane (PDMS) stamp followed by backfilling with a glycol-terminated alkane thiol monomer produces a pattern where protein and cells adsorb only to the stamped hexadecanethiol region.

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1  While microcontact printing ...

Synthetic, Multi-Layer, Self-Oscillating Vocal Fold Model Fabrication

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties 1. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone 2 and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders.
Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes).
Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry 3,4, clinical instrument development 5, laryngeal aerodynamics 6-9, vocal fold contact pressure 10, and subglottal acoustics 11 (a more comprehensive list can be found in Kniesburges et al. 12)
Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds 1 that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages 3,6,8 such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration).
In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers 1. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.

The methodology for fabricating synthetic vocal fold models is described. The models are life-sized and mimic the multi-layer structure of the human vocal folds. Results show the models to self-oscillate at pressures comparable to lung pressure and demonstrate flow-induced vibratory responses that are similar to those of human vocal folds.

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing ...

Analyzing Cellular Internalization of Nanoparticles and Bacteria by Multi-spectral Imaging Flow Cytometry

Nanoparticulate systems have emerged as valuable tools in vaccine delivery through their ability to efficiently deliver cargo, including proteins, to antigen presenting cells1-5. Internalization of nanoparticles (NP) by antigen presenting cells is a critical step in generating an effective immune response to the encapsulated antigen. To determine how changes in nanoparticle formulation impact function, we sought to develop a high throughput, quantitative experimental protocol that was compatible with detecting internalized nanoparticles as well as bacteria. To date, two independent techniques, microscopy and flow cytometry, have been the methods used to study the phagocytosis of nanoparticles. The high throughput nature of flow cytometry generates robust statistical data. However, due to low resolution, it fails to accurately quantify internalized versus cell bound nanoparticles. Microscopy generates images with high spatial resolution; however, it is time consuming and involves small sample sizes6-8. Multi-spectral imaging flow cytometry (MIFC) is a new technology that incorporates aspects of both microscopy and flow cytometry that performs multi-color spectral fluorescence and bright field imaging simultaneously through a laminar core. This capability provides an accurate analysis of fluorescent signal intensities and spatial relationships between different structures and cellular features at high speed.
	Herein, we describe a method utilizing MIFC to characterize the cell populations that have internalized polyanhydride nanoparticles or Salmonella enterica serovar Typhimurium. We also describe the preparation of nanoparticle suspensions, cell labeling, acquisition on an ImageStreamX system and analysis of the data using the IDEAS application. We also demonstrate the application of a technique that can be used to differentiate the internalization pathways for nanoparticles and bacteria by using cytochalasin-D as an inhibitor of actin-mediated phagocytosis.

In this article, we describe a method utilizing multi-spectral imaging flow cytometry to quantify the internalization of polyanhydride nanoparticles or bacteria by RAW 264.7 cells.

Nanoparticulate  systems have emerged as valuable tools in vaccine delivery through their  ability to efficiently deliver cargo, including proteins, to ...

Density Gradient Multilayered Polymerization (DGMP): A Novel Technique for Creating Multi-compartment, Customizable Scaffolds for Tissue Engineering

Complex tissue culture matrices, in which types and concentrations of biological stimuli (e.g. growth factors, inhibitors, or small molecules) or matrix structure (e.g. composition, concentration, or stiffness of the matrix) vary over space, would enable a wide range of investigations concerning how these variables affect cell differentiation, migration, and other phenomena. The major challenge in creating layered matrices is maintaining the structural integrity of layer interfaces without diffusion of individual components from each layer1. Current methodologies to achieve this include photopatterning2-3, lithography4, sequential functionalization5, freeze drying6, microfluidics7, or centrifugation8, many of which require sophisticated instrumentation and technical skills. Others rely on sequential attachment of individual layers, which may lead to delamination of layers9. 
DGMP overcomes these issues by using an inert density modifier such as iodixanol to create layers of varying densities10. Since the density modifier can be mixed with any prepolymer or bioactive molecule, DGMP allows each scaffold layer to be customized. Simply varying the concentration of the density modifier prevents mixing of adjacent layers while they remain aqueous. Subsequent single step polymerization gives rise to a structurally continuous multilayered scaffold, in which each layer has distinct chemical and mechanical properties. The density modifier can be easily removed with sufficient rinsing without perturbation of the individual layers or their components. This technique is therefore well suited for creating hydrogels of various sizes, shapes, and materials.
A protocol for fabricating a 2D-polyethylene glycol (PEG) gel, in which alternating layers incorporate RGDS-350, is outlined below. We use PEG because it is biocompatible and inert. RGDS, a cell adhesion peptide11, is used to demonstrate spatial restriction of a biological cue, and the conjugation of a fluorophore (Alexa Fluor 350) enables us to visually distinguish various layers. This procedure can be adapted for other materials (e.g. collagen, hyaluronan, etc.) and can be extended to fabricate 3D gels with some modifications10.

Density Gradient Multilayered Polymerization DGMP: A Novel Technique for Creating Multi-compartment, Customizable Scaffolds for Tissue Engineering

Here we describe a unique strategy for creating biocompatible, layered matrices with continuous interfaces between distinct layers for tissue engineering. Such a scaffold could provide an ideal customizable environment to modulate cell behavior by various biological, chemical or mechanical cues

Complex tissue culture matrices, in which types and concentrations of biological stimuli (e.g. growth factors, inhibitors, or small molecules) or matrix ...

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors

A label-free optical biosensor based on a nanostructured porous Si is designed for rapid capture and detection of Escherichia coli K12 bacteria, as a model microorganism. The biosensor relies on direct binding of the target bacteria cells onto its surface, while no pretreatment (e.g.&#160;by cell lysis) of the studied sample is required. A mesoporous Si thin film is used as the optical transducer element of the biosensor. Under white light illumination, the porous layer displays well-resolved Fabry-P&#233;rot fringe patterns in its reflectivity spectrum. Applying a fast Fourier transform (FFT) to reflectivity data results in a single peak. Changes in the intensity of the FFT peak are monitored. Thus, target bacteria capture onto the biosensor surface, through antibody-antigen interactions, induces measurable changes in the intensity of the FFT peaks, allowing for a &#39;real time&#39; observation of bacteria attachment.
The mesoporous Si film, fabricated by an electrochemical anodization process, is conjugated with monoclonal antibodies, specific to the target bacteria. The immobilization, immunoactivity and specificity of the antibodies are confirmed by fluorescent labeling experiments. Once the biosensor is exposed to the target bacteria, the cells are directly captured onto the antibody-modified porous Si surface. These specific capturing events result in intensity changes in the thin-film optical interference spectrum of the biosensor. We demonstrate that these biosensors can detect relatively low bacteria concentrations (detection limit of 104 cells/ml) in less than an hour.

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors

A label-free optical biosensor for rapid bacteria detection is introduced. The biosensor is based on a nanostructured porous Si, which is designed to directly capture the target bacteria cells onto its surface. We use monoclonal antibodies, immobilized onto the porous transducer, as the capture probes. Our studies demonstrate the applicability of these biosensors for the detection of low bacterial concentrations within minutes with no prior sample processing (such as cell lysis).

A label-free optical biosensor based on a nanostructured porous Si is designed for rapid capture and detection of Escherichia coli K12 bacteria, as a ...

Nanomanipulation of Single RNA Molecules by Optical Tweezers

A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be increasingly important. As RNA function often depends on its ability to adopt alternative structures, it is difficult to predict RNA three-dimensional structures directly from sequence. Single-molecule approaches show potentials to solve the problem of RNA structural polymorphism by monitoring molecular structures one molecule at a time. This work presents a method to precisely manipulate the folding and structure of single RNA molecules using optical tweezers. First, methods to synthesize molecules suitable for single-molecule mechanical work are described. Next, various calibration procedures to ensure the proper operations of the optical tweezers are discussed. Next, various experiments are explained. To demonstrate the utility of the technique, results of mechanically unfolding RNA hairpins and a single RNA kissing complex are used as evidence. In these examples, the nanomanipulation technique was used to study folding of each structural domain, including secondary and tertiary, independently. Lastly, the limitations and future applications of the method are discussed.

Optical tweezers have been used to study RNA folding by stretching individual molecules from their 5&#8217; and 3&#8217; ends. Here common procedures are described to synthesize RNA molecules for tweezing, calibration of the instrument, and methods to manipulate single molecules.

A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be ...

Tissue Engineering by Intrinsic Vascularization in an In Vivo Tissue Engineering Chamber

In reconstructive surgery, there is a clinical need for an alternative to the current methods of autologous reconstruction which are complex, costly and trade one defect for another. Tissue engineering holds the promise to address this increasing demand. However, most tissue engineering strategies fail to generate stable and functional tissue substitutes because of poor vascularization. This paper focuses on an in vivo tissue engineering chamber model of intrinsic vascularization where a perfused artery and a vein either as an arteriovenous loop or a flow-through pedicle configuration is directed inside a protected hollow chamber. In this chamber-based system angiogenic sprouting occurs from the arteriovenous vessels and this system attracts ischemic and inflammatory driven endogenous cell migration which gradually fills the chamber space with fibro-vascular tissue. Exogenous cell/matrix implantation at the time of chamber construction enhances cell survival and determines specificity of the engineered tissues which develop. Our studies have shown that this chamber model can successfully generate different tissues such as fat, cardiac muscle, liver and others. However, modifications and refinements are required to ensure target tissue formation is consistent and reproducible. This article describes a standardized protocol for the fabrication of two different vascularized tissue engineering chamber models in vivo.

Tissue Engineering by Intrinsic Vascularization in an In Vivo Tissue Engineering Chamber

This is a guideline for constructing in vivo vascularized tissue using a microsurgical arteriovenous loop or a flow-through pedicle configuration inside a tissue engineering chamber. The vascularized tissues generated can be employed for organ regeneration and replacement of tissue defects, as well as for drug testing and disease modeling.

In reconstructive surgery, there is a clinical need for an alternative to the current methods of autologous reconstruction which are complex, costly and ...

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the optical window where biological samples are most transparent. Here, we outline techniques to adsorb amphiphilic polymers and polynucleic acids onto the surface of SWNTs to engineer their corona phases and create novel molecular sensors for small molecules and proteins. These functionalized SWNT sensors are both biocompatible and stable. Polymers are adsorbed onto the nanotube surface either by direct sonication of SWNTs and polymer or by suspending SWNTs using a surfactant followed by dialysis with polymer. The fluorescence emission, stability, and response of these sensors to target analytes are confirmed using absorbance and near-infrared fluorescence spectroscopy. Furthermore, we demonstrate surface immobilization of the sensors onto glass slides to enable single-molecule fluorescence microscopy to characterize polymer adsorption and analyte binding kinetics.

We present a protocol for engineering the corona phase of near infrared fluorescent single walled carbon nanotubes (SWNTs) using amphiphilic polymers and DNA to develop sensors for molecular targets without known recognition elements.

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the ...

Using Synthetic Biology to Engineer Living Cells That Interface with Programmable Materials

We have developed an abiotic-biotic interface that allows engineered cells to control the material properties of a functionalized surface. This system is made by creating two modules: a synthetically engineered strain of E. coli cells and a functionalized material interface. Within this paper, we detail a protocol for genetically engineering selected behaviors within a strain of E. coli using molecular cloning strategies. Once developed, this strain produces elevated levels of biotin when exposed to a chemical inducer. Additionally, we detail protocols for creating two different functionalized surfaces, each of which is able to respond to cell-synthesized biotin. Taken together, we present a methodology for creating a linked, abiotic-biotic system that allows engineered cells to control material composition and assembly on nonliving substrates.

This paper presents a series of protocols for developing engineered cells and functionalized surfaces that enable synthetically engineered E. coli to control and manipulate programmable material surfaces.

We have developed an abiotic-biotic interface that allows engineered cells to control the material properties of a functionalized surface. This system is ...