The authors thank professor Paul Cos and LMPH, University of Antwerp, Belgium for his support during the filming process in his laboratory. This work was funded by Academy of Finland projects (projects 272266 and 282981) and Svenska Tekniska Vetenskapsakademien i Finland. The technical contributions of MSc Janni Kujala are acknowledged.

1. Growing the Bacteria
<ol>
	<li>Pre-culture the bacteria overnight in a tryptic soy broth (TSB) at 37 &#176;C with 220 rpm shaking (16-18 hr).</li>
	<li>Dilute the pre-culture 100-1,000 times (depending on the growth rate of the bacteria; here, 1,000 times is used for S. aureus) in fresh TSB and let it grow at 37 &#176;C and 200 rpm to reach exponential growth (optical density at 595 nm (OD595) between 0.2 and 0.6). 
	NOTE: This step requires strain-specific optimization.</li>
</ol>
2. Biofilm Formation: Pre- and Post-exposure
<ol>
	<li>Dilute the exponentially grown culture 100 times (this equals approximately 106 colony-forming units per milliliter (CFU/ml)).</li>
	<li>Pre-exposure protocol
	<ol>
		<li>For untreated control samples, add 200 &#181;l of the diluted bacterial culture per well of a sterile 96-microwell plate.</li>
		<li>Add 4 &#181;l of a test compound or a control antibiotic (50x stock solution) and 196 &#181;l of the diluted bacterial culture per well.</li>
		<li>Incubate it at 37 &#176;C on a plate shaker at 200 rpm for 18 hr. 
		Note: Here we use a shaker with a 2 mm orbit.</li>
	</ol>
	</li>
	<li>Post-exposure protocol
	<ol>
		<li>For all samples, add 200 &#181;l of the diluted bacterial culture per well of a sterile 96-microwell plate.</li>
		<li>Incubate it at 37 &#176;C on a plate shaker at 200 rpm for 18 hr. 
		Note: Here we use a shaker with a 2 mm orbit.</li>
		<li>Remove the entire planktonic solution carefully, without touching the biofilm, using a multichannel pipette.</li>
		<li>Add 4 &#181;l of a test compound or a control antibiotic (50x stock solution) and 196 &#181;l of TSB per well.</li>
		<li>Incubate it at 37 &#176;C on a plate shaker at 200 rpm for an additional 24 hr. 
		Note: Here we use a shaker with a 2 mm orbit.</li>
	</ol>
	</li>
</ol>
3. Resazurin Staining Protocol for the Viability Assessment of Biofilms
<ol>
	<li>Prepare a stock solution of 0.1 mg/ml resazurin (0.4 mM) in sterile PBS. Keep this stock sterile, protected from light exposure, and at 4 &#176;C.</li>
	<li>Dilute the resazurin stock 1:50 in sterile phosphate-buffered saline (PBS) to achieve a final concentration of 20 &#181;M.</li>
	<li>Transfer the entire planktonic solution (leaving the biofilms in the wells) carefully, without touching the biofilms or creating air bubbles, to a separate, clean 96-well plate using a multichannel pipette.</li>
	<li>Wash the biofilms once with sterile PBS by adding 200 &#181;l per well, and remove it carefully using a multichannel pipette.</li>
	<li>Add 200 &#181;l of the diluted resazurin per well of the biofilm plate using a multichannel pipette.</li>
	<li>Incubate it in darkness, at room temperature (RT), and 200 rpm, shaking for approximately 20 min until the untreated biofilm controls are evenly pink.</li>
	<li>Measure the fluorescence at &#955;exc = 560 nm and &#955;em = 590 nm with a plate reader (top reading).</li>
</ol>
4. Crystal Violet Staining Protocol for Biomass Quantification of Biofilms Using the Same Plate as in Step 3
<ol>
	<li>Remove the resazurin stain carefully from the wells using a multichannel pipette.</li>
	<li>Fix the biofilms with 200 &#181;l of methanol for 15 min.</li>
	<li>Let the plate air dry for 10 min.</li>
	<li>Add 190 &#181;l of 0.02 % (vol/vol, diluted in deionized water) crystal violet solution, carefully using a multichannel pipette. Avoid touching the sides of the wells with the stain while pipetting and prevent the formation of air bubbles by not pressing the pipette to complete blow-out.</li>
	<li>Incubate it for 5 min at RT.</li>
	<li>Remove the stain carefully, using a multichannel pipette.</li>
	<li>Wash it twice with deionized water (200 &#181;l each time).</li>
	<li>Let the wells dry for 5 min at RT and dissolve the remaining stain in 96% ethanol or 33% acetic acid.</li>
	<li>Incubate it for 1 hr at RT and read the absorbance at 595 nm.</li>
</ol>
5. Evaluating the Bactericidal Effect on Planktonic Bacteria Using the Same Sample Plate as for the Biofilms
<ol>
	<li>Measure the turbidity at 595 nm of the plate with the planktonic solution from 3.3.</li>
	<li>Stain the planktonic bacteria with resazurin by adding 10 &#181;l of the resazurin stock per well. Mix well by pipetting.</li>
	<li>Incubate it in darkness at RT for approximately 5 min, until the untreated controls are evenly pink.</li>
	<li>Measure the fluorescence at &#955;exc = 560 nm and &#955;em = 590 nm.</li>
</ol>
6. Wheat Germ Agglutinin Staining for Matrix Quantification and Fluorescence Microscopy Imaging of Biofilms
<ol>
	<li>Matrix quantification
	<ol>
		<li>Prepare a 5 &#181;g/ml solution of the WGA probe in sterile PBS.</li>
		<li>Use a parallel sample plate for this staining. Remove the planktonic solution from the wells and wash once with sterile PBS (200 &#181;l per well), carefully using a multichannel pipette without touching the biofilms.</li>
		<li>Add 200 &#181;l of WGA solution per well to be stained.</li>
		<li>Incubate it in darkness at 4 &#176;C for 2 hr.</li>
		<li>Remove the unbound stain by washing the wells with 200 &#181;l of PBS three times.</li>
		<li>Let the plate dry for 15 min at RT.</li>
		<li>Dissolve the bound stain in 33% acetic acid, using 200 &#181;l per well.</li>
		<li>Seal the wells with strip caps and sonicate them using a water bath sonicator for 30 sec at RT and 40 kHz.</li>
		<li>Incubate the plate for 1 hr at RT.</li>
		<li>Repeat the sonication step. The wells can remain sealed between the sonication steps.</li>
		<li>Measure the fluorescence at &#955;ex = 495 nm and &#955;em = 520 nm with a plate reader (top reading).</li>
	</ol>
	</li>
	<li>Visualizing the matrix with fluorescence microscopy
	<ol>
		<li>Use the same protocol as above until step 6.1.6.</li>
		<li>After the drying step, visualize the samples with a fluorescence microscope, using a FITC filter (or another suitable green excitation filter).</li>
	</ol>
	</li>
</ol>
7. Staining Viable and Dead Cells within the Biofilms for Imaging with Fluorescence Microscopy and Quantification of the Signal for the Green-to-red-ratio (G/R)
<ol>
	<li>Imaging with fluorescence microscopy
	<ol>
		<li>Prepare a solution of each probe (one staining viable cells and the other one staining dead cells), according to the manufacturer&#39;s guidelines.</li>
		<li>Remove the planktonic solution from the wells and wash once with sterile PBS (200 &#181;l per well) using a multichannel pipette.</li>
		<li>Add 6 &#181;l of the staining solution per well.</li>
		<li>Incubate the plate in darkness for 15 min.</li>
		<li>Before the microscopy, remove the excess liquid manually using a multichannel pipette.</li>
		<li>Capture the images using a fluorescence microscope, using for instance a FITC filter (for green fluorescence, viable cells) or a TRITC filter (red fluorescence, dead cells).</li>
	</ol>
	</li>
	<li>Quantification of the signal as a green-to-red-fluorescence ratio (G/R)
	<ol>
		<li>Follow the same protocol as in steps 7.1.1 and 7.1.2.</li>
		<li>Add 200 &#181;l of the staining solution per well and incubate them for 15 min in darkness.</li>
		<li>Measure the fluorescence with a plate reader at excitation/emission wavelengths 485/535 nm and 485/635 for green and red fluorescence, respectively (top reading).</li>
	</ol>
	</li>
</ol>

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The authors have no conflicts of interest to disclose.

There is no single method that can simultaneously measure the effect of a compound on the viability, biomass, and biofilm matrix. Therefore, there is a need for combining assays in order to detect an effect on the three endpoints, preferably at a primary screening stage.
Resazurin is a very simple staining protocol consisting only of the addition of the redox probe. However, establishing the optimal incubation time of the biofilms with the resazurin is crucial to the success of this assay. In ...

Bacteria can switch between two very different lifestyles, planktonic and sessile, of which a biofilm is the most common example. In biofilms, bacteria form structured communities embedded in a self-produced matrix1. This self-produced matrix is a barrier between the bacteria and their external environment, and it protects the microbial cells, keeping them in close proximity. The composition of the biofilm matrix varies between and even within species, but it mostly consists of a tight network of lipopolysaccharides, extracellular DNA, and proteins. The matrix serves as a physical barrier inhibiting the entrance of harmful agents, but it also protects the biofilm from dehydration and prevents nutrients from escaping the cell2.
Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are purportedly responsible for over 80% of antibiotic-tolerant infections3. They display an inherently high tolerance against external threats: humidity, osmotic pressure, mechanical stress4, heat, UV radiation5, disinfectants, antimicrobial agents, and the host immune system1. For example, the required antimicrobial agent concentration required to kill a biofilm has been shown to be up to 1,000 times higher in comparison to that required to kill planktonic bacteria. The explanation for this higher tolerance seems to be multifactorial. The matrix provides a physical barrier that decreases the penetration of antibiotics into the biofilm. Also, cells within the biofilms are phenotypically diverse; they transition between different metabolic states due to an existing gradient of oxygen, nutrients, and metabolites between the inner and outer parts of the biofilm6. Hence, in some biofilm regions, such as the core, bacteria are deprived of oxygen and nutrients and live in a metabolically less active or a completely dormant state7. The completely dormant cells are referred to as persister cells, and they are not susceptible to conventional antimicrobial treatments8. Thus, it is likely that biofilm resilience arises from a combination of the presently suggested and other, yet unknown, mechanisms. Staphylococcus spp. are still among the most problematic gram-positive bacteria, causing severe, often biofilm-related, infections4. It is suggested that up to 99% of all bacteria are associated within biofilms, making it the predominant bacterial lifestyle3. However, all of the currently existing antibiotics have been developed against single-cell (planktonic) bacteria. So far, a very limited repertoire of molecules exists that can selectively act on mature biofilms. This situation has driven a progressive paradigm shift in drug discovery, in which searching for anti-biofilms has been urged to occupy a more prominent place.
From a methodological perspective, additional challenges exist, as only a limited number of biofilm methods have been developed by standard-setting organizations, especially those applicable to the high-throughput screening of chemical libraries. All standardized assays (with only one exception) are based upon biofilm reactors, and these methods require large working volumes and large amounts of compounds to be tested, which are usually unavailable during the early investigational stage9-12. The only existing standardized screening-applicable assay is the so-called Calgary Biofilm Device, from which the commercially available minimum biofilm eliminating concentration (MBEC) system was developed13-15. However, the limitation of this assay is that the biofilms are grown on pegs, and not all bacterial species or even strains within the same species are able to form biofilms on this device. Moreover, methods that can be particularly applied to the exploration of natural compounds are needed. Natural products have been the major source for innovation in antimicrobial drug discovery over the past century16. They can provide novel anti-biofilm compounds with unique mechanisms of action that can also be effective against persister cells. Thus, the exploration of natural and naturally inspired libraries has high chances of producing promising and unique anti-biofilm leads.
Here, we present the experimental details of a platform of assays that was developed for the chemical screening of anti-biofilm compounds using three assays to measure the effects on the viability, total biomass, and matrix of Staphylococcus aureus biofilms. The first assay measures biofilm viability, and it is based on resazurin staining. Resazurin is a redox stain that is blue and non-fluorescent in its oxidized state and turns into pink, highly fluorescent resorufin when reduced by the metabolic activity of the bacteria. It is a very simple and fast method suitable for primary screenings17-20. The second assay, based on crystal violet staining, measures total biofilm mass. Crystal violet is a widely used stain for studying bacteria and bacteria in biofilms19,21-23. The assay is based on inexpensive reagents and has a simple absorbance endpoint reading. Finally, the third assay targets the extracellular polymeric substance (EPS)-matrix of the biofilm via wheat germ agglutinin (WGA), which binds specifically to poly-N-acetyl-glucosamine residues (PNAG) present in the matrix of staphylococcal biofilms24. The WGA is conjugated with a fluorophore that can be detected using fluorescence intensity readers25. We present here the rationale and details of the platform we developed, including examples of applications.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Resazurin</td>
			<td>Sigma Aldrich</td>
			<td>R7017</td>
			<td></td>
		</tr>
		<tr>
			<td>Crystal violet</td>
			<td>Sigma Aldrich</td>
			<td>HT90132&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Wheat Germ Agglutinin, Alexa Fluor 488 Conjugate</td>
			<td>Thermo Fisher Scientific</td>
			<td>W11261</td>
			<td></td>
		</tr>
		<tr>
			<td>LIVE/DEAD BacLight&#160;</td>
			<td>Molecular Probes</td>
			<td>L7012</td>
			<td>SYTO 9 for staining viable cells green and propidium iodide for staining dead cells red</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptone soy agar</td>
			<td>Lab M, Neogen</td>
			<td>LAB011</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptine soy broth</td>
			<td>Lab M, Neogen</td>
			<td>LAB004</td>
			<td></td>
		</tr>
		<tr>
			<td>F96 Well Plate Polystyrene Sterile Clear Flat bottom</td>
			<td>Thermo Fisher Scientific</td>
			<td>161093</td>
			<td></td>
		</tr>
		<tr>
			<td>BRAND caps, strips of 8</td>
			<td>Sigma Aldrich</td>
			<td>BR781413-300EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Branson CPX series ultrasonic bath</td>
			<td>Sigma Aldrich</td>
			<td>Z769428-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Multipipette</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Multidrop dispenser</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Biomek 3000</td>
			<td>Beckman Coulter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Varioskan Flash Multiplate reader</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Staphylococcus aureus</td>
			<td>ATCC&#160;</td>
			<td>25923</td>
			<td></td>
		</tr>
	</tbody>
</table>

a platform of anti-biofilm assays suited to the exploration of natural compound libraries

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of antibiotic-tolerant infections. Biofilms have displayed an exceptionally high tolerance for chemotherapy, which is thought to be multifactorial. For instance, the matrix provides a physical barrier that decreases the penetration of antibiotics into the biofilm. Also, cells within the biofilms are phenotypically diverse. Likely, biofilm resilience arises from a combination of these and other, yet unknown, mechanisms. All of the currently existing antibiotics have been developed against single-cells (planktonic) bacteria. Therefore, so far, a very limited repertoire of molecules exists that can selectively act on mature biofilms. This situation has driven a progressive paradigm shift in drug discovery, in which searching for anti-biofilms has been urged to occupy a more prominent place. An additional challenge is that there are a very limited number of standardized methods for biofilm research, especially those that can be used for large-throughput screening of chemical libraries. Here, an experimental anti-biofilm platform for chemical screening is presented. It uses three assays to measure biofilm viability (with resazurin staining), total biomass (with crystal violet staining), and biofilm matrix (using a wheat germ agglutinin, WGA-fluorescence-based staining of the poly-N-acetyl-glucosamine, PNAG, fraction). All the assays were developed using Staphylococcus aureus as the model bacteria. Examples of how the platform can be used for primary screening as well as for functional characterization of identified anti-biofilm hits are presented. This experimental sequence further allows for the classification of the hits based upon the measured end-points. It also provides information on their mode of action, especially on long-term versus short-term chemotherapeutic effects. Thus, it is very advantageous for the quick identification of high-quality hit compounds that can serve as starting points for various biomedical applications.

In the proposed platform, the effects on the viability, biomass, and biofilm matrix are quantified. In the working sequence (Figure 1), one sample plate is stained with resazurin and subsequently with crystal violet to simultaneously evaluate the effects on bacterial biofilm viability and on total biofilm biomass. Both assays can be performed consecutively in the same plate because it was demonstrated earlier that a first staining with resazurin had no statistically signi...

Watch this Scientific Journal Video about A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries at JoVE.com

A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries

Biofilm infections show high tolerance towards chemotherapy. No single assay captures the complexity of biofilms. Instead, complementary assays are needed. We present a screening platform (developed for S. aureus) that combines assays for viability, biomass, and biofilm matrix. It allows anti-biofilm drug discovery, including the assessment of long-term chemotherapeutic effects.

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of ...

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Research

JoVE Journal

Immunology and Infection

17.5K Views.  University of Helsinki. Biofilm infections show high tolerance towards chemotherapy. No single assay captures the complexity of biofilms. Instead, complementary assays are needed. We present a screening platform (developed for S. aureus) that combines assays for viability, biomass, and biofilm matrix. It allows anti-biofilm drug discovery, including the assessment of long-term chemotherapeutic effects. 

Video: A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries

Scalable High Throughput Selection From  Phage-displayed Synthetic Antibody Libraries

The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. However, it is apparent that traditional monoclonal technologies are not alone up to this task. This has led to the development of alternate methods to satisfy the demand for high quality and renewable affinity reagents to all accessible elements of the proteome. Toward this end, high throughput methods for conducting selections from phage-displayed synthetic antibody libraries have been devised for applications involving diverse antigens and optimized for rapid throughput and success. Herein, a protocol is described in detail that illustrates with video demonstration the parallel selection of Fab-phage clones from high diversity libraries against hundreds of targets using either a manual 96 channel liquid handler or automated robotics system. Using this protocol, a single user can generate hundreds of antigens, select antibodies to them in parallel and validate antibody binding within 6-8 weeks. Highlighted are: i) a viable antigen format, ii) pre-selection antigen characterization, iii) critical steps that influence the selection of specific and high affinity clones, and iv) ways of monitoring selection effectiveness and early stage antibody clone characterization. With this approach, we have obtained synthetic antibody fragments (Fabs) to many target classes including single-pass membrane receptors, secreted protein hormones, and multi-domain intracellular proteins. These fragments are readily converted to full-length antibodies and have been validated to exhibit high affinity and specificity. Further, they have been demonstrated to be functional in a variety of standard immunoassays including Western blotting, ELISA, cellular immunofluorescence, immunoprecipitation and related assays. This methodology will accelerate antibody discovery and ultimately bring us closer to realizing the goal of generating renewable, high quality antibodies to the proteome.

A method is described with visual accompaniment for conducting scalable, high throughput selections from phage-displayed combinatorial synthetic antibody libraries against hundreds of antigens simultaneously. Using this parallel approach, we have isolated antibody fragments that exhibit high affinity and specificity for diverse antigens that are functional in standard immunoassays.

The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. ...

Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials

Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods to screen for target enzymes prior to investing greater research effort and resources. The goal of this protocol is to demonstrate two complementary assays for conducting these initial evaluations. The microslide diffusion assay provides an initial or simple detection screen to enable the qualitative and rapid assessment of proteolytic activity against an array of both viable and heat-killed bacterial target substrates. As a counterpart, the increased sensitivity and reproducibility of the dye-release assay provides a quantitative platform for evaluating and comparing environmental influences affecting the hydrolytic activity of protein antimicrobials. The ability to label specific heat-killed cell culture substrates with Remazol brilliant blue R dye expands this capability to tailor the dye-release assay to characterize enzymatic activity of interest.

Here, we present protocols to rapidly screen and characterize enzymes for antimicrobial activity. The microslide diffusion assay and the dye-release assay utilize target bacterial substrates for qualitative and quantitative enzymatic activity evaluation.

Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods ...

Flow Cytometric Analysis of Natural Killer Cell Lytic Activity in Human Whole Blood

NK cell cytotoxicity is a widely used measure to determine the effect of outside intervention on NK cell function. However, the accuracy and reproducibility of this assay can be considered unstable, either because of user&#39;s errors or because of the sensitivity of NK cells to experimental manipulation. To eliminate these issues, a workflow that reduces them to a minimum was established and is presented here. To illustrate, we obtained blood samples, at various time points, from runners (n = 4) that were submitted to an intense bout of exercise. First, NK cells are simultaneously identified and isolated through CD56 tagging and magnetic-based sorting, directly from whole blood and from as little as one milliliter. The sorted NK cells are removed of any reagent or capping antibodies. They can be counted in order to establish an accurate NK cell count per milliliter of blood. Secondly, the sorted NK cells (effectors cells or E) can be mixed with 3,3&#39;-Diotadecyloxacarbocyanine Perchlorate (DiO) tagged K562 cells (target cells or T) at an assay-optimal 1:5 T:E ratio, and analyzed using an imaging flow-cytometer that allows for the visualization of each event and the elimination of any false positive or false negatives (such as doublets or effector cells). This workflow can be completed in about 4 h, and allows for very stable results even when working with human samples. When available, research teams can test several experimental interventions in human subjects, and compare measurements across several time points without compromising the data&#39;s integrity.

This work describes an advanced workflow for the accurate and fast determination of NK (Natural Killer) cell count and NK cell cytotoxicity in human blood samples.

NK cell cytotoxicity is a widely used measure to determine the effect of outside intervention on NK cell function. However, the accuracy and ...

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below outlines a method for high efficiency transfer between bacterial strains of a plasmid harboring a transposon containing a kanamycin resistance marker. The plasmid-borne transposase is encoded by a variant tnp gene that inserts the transposon into the genome of the recipient strain with very low insertional bias. This method thus allows the creation of large mutant libraries in which transposons have been inserted into unique genomic positions in a recipient strain of either Escherichia coli or Shigella flexneri bacteria. By using bacterial conjugation, as opposed to other methods such as electroporation or chemical transformation, large libraries with hundreds of thousands of unique clones can be created. This yields high-density insertion libraries, with insertions occurring as frequently as every 4-6 base pairs in non-essential genes. This method is superior to other methods as it allows for an inexpensive, easy to use, and high efficiency method for the creation of a dense transposon insertion library. The transposon library can be used in downstream applications such as transposon sequencing (Tn-Seq), to infer genetic interaction networks, or more simply, in mutational (forward genetic) screens.

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Presented here is a simple method for creating a high-density transposon insertion library in Escherichia coli or Shigella flexneri using bacterial conjugation. This protocol allows the creation of a collection of hundreds of thousands of unique mutants in bacteria by the random genomic insertion of a transposon.

Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below ...

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple condensation reactions. DHDDS (dehydrodolichyl diphosphate synthase) is a eukaryotic long-chain cis-PT (forming cis double bonds from the condensation reaction) that catalyzes chain elongation of farnesyl diphosphate (FPP, an allylic diphosphate) via multiple condensations with isopentenyl diphosphate (IPP). DHDDS is of biomedical importance, as a non-conservative mutation (K42E) in the enzyme results in retinitis pigmentosa, ultimately leading to blindness. Therefore, the present protocol was developed in order to acquire large quantities of purified DHDDS, suitable for mechanistic studies. Here, the usage of protein fusion, optimized culture conditions and codon-optimization were used to allow the overexpression and purification of functionally active human DHDDS in E. coli. The described protocol is simple, cost-effective and time sparing. The homology of cis-PT among different species suggests that this protocol may be applied for other eukaryotic cis-PT as well, such as those involved in natural rubber synthesis.

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

A simple protocol for overexpression and purification of codon-optimized, human cis-prenyltransferase, under non-denaturing conditions, from Escherichia coli, is described, along with an enzymatic activity assay. This protocol can be generalized for production of other cis- prenyltransferase proteins in quantity and quality suitable for mechanistic studies.

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple ...

Building Up a High-throughput Screening Platform to Assess the Heterogeneity of HER2 Gene Amplification in Breast Cancers

Targeted therapies against the human epidermal growth factor receptor 2 (HER2) have radically changed the outcome of patients with HER2-positive breast cancers. However, a minority of cases displays a heterogeneous distribution of HER2-positive cells, which generates major clinical challenges. To date, no reliable and standardized protocols for the characterization and quantification of HER2 heterogeneous gene amplification in large cohorts have been proposed. Here, we present a high-throughput methodology to simultaneously assess the HER2 status across different topographic areas of multiple breast cancers. In particular, we illustrate the laboratory procedure to construct enhanced tissue microarrays (TMAs) incorporating a targeted mapping of the tumors. All TMA parameters have been specifically optimized for the silver in situ hybridization (SISH) of formalin-fixed paraffin-embedded (FFPE) breast tissues. Immunohistochemical analysis of the prognostic and predictive biomarkers (i.e., ER, PR, Ki67, and HER2) should be performed using automated procedures. A customized SISH protocol has been implemented to allow a high-quality molecular analysis across multiple tissues that underwent different fixation, processing, and storage procedures. In this study, we provide a proof-of-principle that specific DNA sequences could be localized simultaneously in distinct topographic areas of multiple and heterogeneously processed breast cancers using an efficient and cost-effective method.

Heterogeneous distribution of HER2-positive cells can be observed in a subset of breast cancers and generates clinical dilemmas. Here, we introduce a reliable and cost-effective protocol to define, quantify, and compare HER2 intra-tumor genetic heterogeneity in a large series of heterogeneously processed breast cancers.

Targeted therapies against the human epidermal growth factor receptor 2 (HER2) have radically changed the outcome of patients with HER2-positive breast ...

A Novel Feeder-free System for Mass Production of Murine Natural Killer Cells In Vitro

Natural killer (NK) cells belong to the innate immune system and are a first-line anti-cancer immune defense; however, they are suppressed in the tumor microenvironment and the underlying mechanism is still largely unknown. The lack of a consistent and reliable source of NK cells limits the research progress of NK cell immunity. Here, we report an in vitro system that can provide high quality and quantity of bone marrow-derived murine NK cells under a feeder-free condition. More importantly, we also demonstrate that siRNA-mediated gene silencing successfully inhibits the E4bp4-dependent NK cell maturation by using this system. Thus, this novel in vitro NK cell differentiating system is a biomaterial solution for immunity research.

A Novel Feeder-free System for Mass Production of Murine Natural Killer Cells In Vitro

Here, we present a protocol to mass-produce gene-silencing murine NK cells by using a feeder-free differentiation system for mechanistic study in vitro and in vivo.

Natural killer (NK) cells belong to the innate immune system and are a first-line anti-cancer immune defense; however, they are suppressed in the tumor ...

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components. Differential centrifugation provides further separation of virions from plant contaminants. Then proteinase K treatment removes the capsids. Then the viral DNA is concentrated and used for next-generation sequencing (NGS). The NGS data are used to assemble contigs which are submitted to NCBI-BLASTn to identify a subset of virus sequences in the generated dataset. In a parallel pipeline, RNA is isolated from infected leaves using a standard column-based RNA extraction method. Then ribosome depletion is carried out to enrich for a subset of mRNA and virus transcripts. Assembled sequences derived from RNA sequencing (RNA-seq) were submitted to NCBI-BLASTn to identify a subset of virus sequences in this dataset. In our study, we identified two related full-length badnavirus genomes in the two datasets. This method is preferred to another common approach which extracts the aggregate population of small RNA sequences to reconstitute plant virus genomic sequences. This latter metagenomic pipeline recovers virus related sequences that are retro-transcribing elements inserted into the plant genome. This is coupled to biochemical or molecular assays to further discern the actively infectious agents. The approach documented in this study, recovers sequences representative of replicating viruses that likely indicate active virus infection.

Here we present a new approach to identify plant viruses with double-strand DNA genomes. We use standard methods to extract DNA and RNA from infected leaves and carry out next-generation sequencing. Bioinformatic tools assemble sequences into contigs, identify contigs representing virus genomes and assign genomes to taxonomic groups.

This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low ...

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella spp./Shigella spp. The gold standard method for the detection of Salmonella spp./Shigella spp. is direct culture but this is labor-intensive and time-consuming. Here, we describe a high-throughput platform for Salmonella spp./Shigella spp. screening, using real-time polymerase chain reaction (PCR) combined with guided culture. There are two major stages: real-time PCR and the guided culture. For the first stage (real-time PCR), we explain each step of the method: sample collection, pre-enrichment, DNA extraction and real-time PCR. If the real-time PCR result is positive, then the second stage (guided culture) is performed: selective culture, biochemical identification and serological characterization. We also illustrate representative results generated from it. The protocol described here would be a valuable platform for the rapid, specific, sensitive and high-throughput screening of Salmonella spp./Shigella spp.

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Salmonella spp./Shigella spp. are common pathogens attributed to diarrhea. Here, we describe a high-throughput platform for the screening of Salmonella spp./Shigella spp. using real-time PCR combined with guided culture.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella ...

Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform

Caenorhabditis elegans is a well-established animal model in biomedical research, widely employed in functional genomics and ageing studies. To assess the health and fitness of the animals under study, one typically relies on motility readouts, such as the measurement of the number of body bends or the speed of movement. These measurements usually involve manual counting, making it challenging to obtain good statistical significance, as time and labor constraints often limit the number of animals in each experiment to 25 or less. Since high statistical power is necessary to obtain reproducible results and limit false positive and negative results when weak phenotypic effects are investigated, efforts have recently been made to develop automated protocols focused on increasing the sensitivity of motility detection and multi-parametric behavioral profiling. In order to extend the limit of detection to the level needed to capture the small phenotypic changes that are often crucial in genetic studies and drug discovery, we describe here a technological development that enables the study of up to 5,000 individual animals simultaneously, increasing the statistical power of the measurements by about 1,000-fold compared to manual assays and about 100-fold compared to other available automated methods.

Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform

We describe protocols for using the wide field-of-view nematode tracking platform (WF-NTP), which enables high-throughput phenotypic characterization of large populations of Caenorhabditis elegans. These protocols can be used to characterize subtle behavioral changes in mutant strains or in response to pharmacological treatment in a highly scalable fashion.

Caenorhabditis elegans is a well-established animal model in biomedical research, widely employed in functional genomics and ageing studies. To assess the ...