Thanks to the Department of Neurosurgery of the Second Affiliated Hospital of Army Medical University for site support.&#160;Funding: This work was supported by the Natural Science Foundation of China (82104696).

The experiments in this study comply with the &#34;3Rs&#34; principle of animal ethics and have been approved by the Laboratory Animal Welfare and Ethnic Committee of the Army Medical University (AMUWEC20234543).
1. Preparation of rodent body fixation device
<ol>
	<li>Design a small animal holder based on the Chinese utility model patent9.</li>
	<li>Produce the device through 3D printing technology.</li>
	<li>Prepare a 2 m long rope and divide it into 6 ropes. Thread these 6 ropes through the holes in the fixator. Utilize the spring-loaded buckle to fasten the rope ends, facilitating loop size adjustment. 
	&#8203;NOTE: The fixator could be manufactured by any company equipped with 3D printing technology based on a design drawing. The design drawing of the device is shown in Figure 1. The fixator used in this study was produced by a 3D printer by a printing method called fused deposition modeling (FDM), also known as fused filament fabrication (FFF)10. This additive manufacturing method prints the parts of the design layer by layer by selectively depositing the material in the melted form in a predetermined path. The process uses thermoplastic polymers that come in filaments to create the final physical structure. The immobilization apparatus utilized in this study can secure three animals simultaneously, necessitating six ropes, with each animal requiring a pair of ropes: one for the neck and one for the trunk.</li>
</ol>
2. Preparation of rodents
<ol>
	<li>Purchase 3 Sprague-Dawley rats (10-40 g, 7-45 days old) and 3 C57 BL/C mice (5-40 g).</li>
	<li>Breed animals in a room with a 12 h day/night cycle, an ambient temperature of 21-23 &#176;C, and a humidity of 45%-60%. Disinfect and ventilate the feeding environment regularly, and allow the animals to eat and drink freely.</li>
</ol>
3. Fixing rodents to the fixator (prone position)
<ol>
	<li>Place the head of the rodent in the U-shaped hole in front of the fixator, with the rodent in a prone position. Pass the rodent&#39;s body through two rope loops.</li>
	<li>Fasten the ropes around the neck and abdomen of the rodent, ensuring that it cannot escape, but not so tightly as to cause respiratory distress and death.
	<ol>
		<li>The key step is to fix the neck in place. Leave a gap of 2-5 mm between the rodent&#39;s neck and the rope. Ensure that the rope is not too tight for the animals to strangle or too loose to escape.</li>
	</ol>
	</li>
	<li>Fix the other rodents in the same way in the device.</li>
	<li>Repeat the above fixation steps (3.1-3.2) for 3 days to minimize the potential stress response caused by the fixation procedure. Repeat the fixation procedure for 3 consecutive days, with each session lasting 5 min per day. 
	NOTE: To ensure that rodents were not over-stressed during the fixation procedure, we repeated the procedure for 3 consecutive days. Each session lasted 5 min per day, providing ample time for mice or rats to acclimate to the procedure and minimizing any potential discomfort.</li>
	<li>Strat EA from Day 4.</li>
	<li>To prevent the spread of disease, immerse a sterile cotton swab or ball in 75% alcohol and thoroughly wipe the holder to clean and disinfect it before and after each use. Use gloves and other protective equipment to avoid potential health risks when handling rodents.</li>
</ol>
4. Performing EA in mice or young rats (MS6)
<ol>
	<li>Choose 0.25 mm x 13 mm disposable sterile acupuncture needles.</li>
	<li>Find the acupoints by anatomical location and confirm the insertion depth at the acupoint. 
	NOTE: MS6 is located on the lateral side of the head. This region in the head passes through the connection between Shencong (Ex-hn1) and Xuanli (GB6), also known as the anterior parietal (Du21). MS6 corresponds to the expression of the precentral gyrus of the cerebral cortex on the scalp. Ex-hn1 is located 0.5 cm behind the midpoint of the anterior-posterior midline of the head. GB6 is located at the midpoint of the front of the ear and the end angle of the eye. The superior supratrochlear nerve, supraorbital nerve, occipital nerve, and auriculotemporal nerve are distributed in it. MS6 is mainly used to treat stroke and encephalopathy, such as motor disorders.</li>
	<li>Slowly twist and insert sterile needles bilateral into MS6 at a depth of 3/5 from the anterior Shenchong (Exhn1) to the Xuanli (GB6) along the subcutaneous in 3 rodents, respectively.</li>
	<li>Connect one side of the connection cable to the EA instrument.</li>
	<li>Connect another side of the connection cable containing the positive and negative EA clips to the acupuncture needle shanks on the left and right MS6.</li>
	<li>Turn on the EA instrument.
	<ol>
		<li>Rotate the button (Function/ Choose Switch) to set the frequency and function mode.</li>
		<li>Set the Frequency to 10 Hz and choose a Continuous Wave mode.</li>
		<li>Rotate the corresponding button (Adjust Intensity) to set the intensity. Each adjust intensity button controls the current strength of the rodents of the wire connected below it. Adjust the current intensity to the acceptable range of rodents, usually 1-2 mA, lasting 5 min. 
		&#8203;NOTE: It is important to monitor the breathing and behavior of the rodents during the procedure to ensure that they are not experiencing any distress or discomfort. If the rat appears to be struggling or in pain, the procedure should be stopped immediately.</li>
	</ol>
	</li>
</ol>
5. Fixing rodents to the fixator (supine position)
<ol>
	<li>Place the heads of the rodent in the U-shaped hole in front of the fixator, with the rodent in a prone position. Pass the rodent&#39;s body through two rope loops.</li>
	<li>Fasten the rope around the neck and abdomen of the rodent, ensuring that it cannot escape, but not so tight as to cause respiratory distress and death. 
	NOTE: The points to be noted during fixation are the same as in step 3.2.</li>
	<li>Fix the other rodents in the same way.</li>
	<li>As in step 3.4, repeat the above fixation steps for 3 days to reduce the stress response of rodents.</li>
	<li>Strat EA from Day 4. 
	&#8203;NOTE: Disinfection is performed as mentioned in step 3.6.</li>
</ol>
6. Performing EA (ST25)
<ol>
	<li>Choose 0.25 mm x 13 mm disposable sterile acupuncture needles.</li>
	<li>Find the acupoints by anatomical location and confirm the insertion depth at the acupoint. 
	NOTE: ST25 is located at the level of the umbilicus. Positioning this point in rodents requires first measuring the length of the rodent&#39;s paw. ST25 is located at 2/3 the length of the paw next to the navel. For example, if the measured paw of the rodent is 0.6 cm, then ST25 is located 0.4 cm to the right and left of the umbilicus.</li>
	<li>Slowly twist and penetrate sterile needles into ST25 bilateral at a depth of 4-8 mm on 3 rodents, respectively.</li>
	<li>Connect one side of the connection cable to the EA instrument.</li>
	<li>Connect another side of the connection cable containing the positive and negative EA clips to the acupuncture needle shanks on the left and right ST25.</li>
	<li>Turn on the EA instrument.
	<ol>
		<li>Rotate the button (Function/ Choose Switch) to set the frequency and function mode.</li>
		<li>Set the Frequency to 10 Hz and choose Continuous Wave Mode.</li>
		<li>Rotate the corresponding button (Adjust Intensity) to set the intensity. Each adjust intensity button controls the current strength of the rat of the wire connected below it. Adjust the current intensity to the acceptable range of rodents, usually 1-2 mA, lasting 5 min. 
		NOTE: The observations were the same as in step 4.6.</li>
	</ol>
	</li>
</ol>

Using a 3D Printed Holder for Bulk Electroacupuncture in Small Animals

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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+randomised-controlled+trial+in+Sweden+of+acupuncture+and+care+interventions+for+the+relief+of+inflammatory+symptoms+of+the+breast+during+lactation.">A randomised-controlled trial in Sweden of acupuncture and care interventions for the relief of inflammatory symptoms of the breast during lactation.</a> Midwifery. 23 (2), 184-195 (2007).</li><li>Boram, L., Chan-Young, K., Sun Haeng, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effectiveness+and+safety+of+auriculotherapy+for+breastfeeding:+a+systematic+review.">Effectiveness and safety of auriculotherapy for breastfeeding: a systematic review.</a> Journal of Traditional Chinese Medicine. 40 (5), 721-737 (2020).</li></ol>

The authors declared that no competing conflicts of interest exist.

Electroacupuncture (EA) is a form of acupuncture that involves the use of electrical stimulation on acupuncture needles11. This technique involves the use of micro-pulse currents of specific intensity and frequency to stimulate acupuncture points and achieve enhanced therapeutic effects3. However, the mechanism of EA for healing is limited and requires extensive basic research to prove1,2,<sup class="xref...

<a href="https://app.jove.com/t/6632">This corrects</a> the article <a href="https://dx.doi.org/10.3791/65648">10.3791/65648</a>

An erratum was issued for:&#160;<a href="https://www.jove.com/t/65648">Bulk Electroacupuncture Operation for Mice or Young Rats</a>. Figure 3 was updated.

Erratum: Bulk Electroacupuncture Operation for Mice or Young Rats

Electroacupuncture (EA) therapy is a unique method in which acupuncture needles are inserted into the scalp and connected to an electro-machine to stimulate specific points1. Unlike manual stimulation, EA allows better control of stimulation by stabilizing specific frequencies and waveforms to achieve optimal therapeutic effects2. According to a survey, 81.2% of medical institutions in China use EA or manual acupuncture to treat cerebral palsy, neuralgia, facial palsy, and other conditions. Despite its popularity, the specific mechanism of efficacy of EA is still unknown, which has hindered its promotion and application in the rehabilitation treatment of neurological diseases1,2,3. Further research is needed to fully understand the mechanism of EA&#39;s effectiveness and to promote its use in the rehabilitation treatment of neurological diseases.
As the influence of acupuncture expands worldwide, many studies have already investigated the mechanisms of EA performed on rodent models, such as rat or mouse models1,2,3. Several issues are often encountered in EA&#39;s rodent experiments. The first is how to immobilize rodents without anesthesia, as acupuncture performed on awake subjects is more reflective of clinical practice. In addition, some experiments require animals to be awake to observe treatment effects2,3. Another challenge is accurately locating the acupoints in mice or rats that correspond to those in humans. The precise localization of acupoints in experimental rodents is currently being studied by many scholars4,5. In this protocol, MS6 and ST25 were selected, which have been clearly defined in rodents by the transformation of human anatomical localization. MS6 is commonly used for the treatment of some brain diseases, such as Parkinson&#39;s disease6. ST25 is usually used to treat gastrointestinal problems, such as diarrhea7. These two acupoints were chosen primarily to demonstrate how rodents can be effectively immobilized in both supine and prone positions. Moreover, these acupoints have been extensively studied and offer significant insights for research purposes6,7.
The previous method of immobilizing a single rat for experiments is not only time-consuming but also difficult to handle by a single person8. Additionally, due to the non-cooperation of animals, the success rate is relatively low in practice. Therefore, there is a critical need to create an easily established animal model with stable characteristics to improve experiment efficiency. In this article, a 3D printed holder for small animals was introduced that could easily immobilize multiple rodents, leading to motor restriction. The aim of this paper is to administer EA treatments to a batch of young rats or mice, focusing on the strategies for bulk restriction of mice, identification, and stimulation of MS6 and ST25 acupoints.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3D printing batch mice fixator</td>
			<td>MESH INVENT</td>
			<td>Custom made</td>
			<td>The fixator produced by 3D printer. The printing method is called fused deposition modeling (FDM), also known as fused filament fabrication (FFF).&#160;&#160;</td>
		</tr>
		<tr>
			<td>Electroacupuncture instrument</td>
			<td>Hwato, Suzhou Medical Appliance Factory</td>
			<td>SDZ-III</td>
			<td>www.Hwato-med.com</td>
		</tr>
		<tr>
			<td>Disposable sterile acupuncture needle</td>
			<td>Suzhou Medical Appliance Factory</td>
			<td>N/A</td>
			<td>0.25 mm x 13 mm</td>
		</tr>
	</tbody>
</table>

bulk electroacupuncture operation for mice or young rats

Electroacupuncture (EA) is widely used to treat various health conditions. However, the underlying mechanism of EA treatment remains unclear, hindering its promotion. The mechanistic study requires mouse or rat models to address this issue. However, these animals are not obedient to the experimental process, which is time-consuming. To solve these problems, we designed a 3D-printed small animal body bulk fixator to improve the efficiency of EA's animal experiments. This video shows in detail how to use the fixator to perform bulk EA on mice or young rats. For the selection of acupoints, the anterior oblique line of vertex temporal (MS6 head) and Tianshu point (ST25 belly) were chosen to verify the effect of the fixation device with prone positioning and supine positioning. Using the 3D-printed small animal holder allows multiple rodents to be immobilized and treated simultaneously, reducing the time and resources required for the experiment. This technique could be applied to other animal models by 3D printing different sizes and could potentially be used for various fixing conditions. The device is beneficial for the promotion of experimental scientific research in EA.

The floor plan of the animal body fixator we designed is shown in Figure 1. In addition, a 3D graphic model of this fixator was submitted to provide a comprehensive view of the design (Supplementary File 1). This is a device that allows 3 rodents to be immobilized and perform EA simultaneously. Rats and mice were restricted to the fixator in the awake state, and both prone and supine positions could be firmly fixed without causing injury to the rodents (...

Watch this Scientific Journal Video about Bulk Electroacupuncture Operation for Mice or Young Rats at JoVE.com

Author Spotlight: Using a 3D-Printed Holder for Simultaneous Multiple Electroacupuncture Operation

Here, we present a protocol for efficient and rapid electroacupuncture (EA) in mice or young rats using a three-dimensional (3D) printed holder. This technique allows simultaneous operation on multiple animals, saving time and increasing experimental efficiency.

Bulk Electroacupuncture Operation for Mice or Young Rats

Electroacupuncture (EA) is widely used to treat various health conditions. However, the underlying mechanism of EA treatment remains unclear, hindering ...

bulk-electroacupuncture-operation-for-mice-or-young-rats

Microsoft Bing

Research

JoVE Journal

Biology

547 Views.  Army Medical University. Here, we present a protocol for efficient and rapid electroacupuncture (EA) in mice or young rats using a three-dimensional (3D) printed holder. This technique allows simultaneous operation on multiple animals, saving time and increasing experimental efficiency.

Video: Author Spotlight: Using a 3D-Printed Holder for Simultaneous Multiple Electroacupuncture Operation

The Microfluidic Probe: Operation and Use for Localized Surface Processing

Microfluidic devices allow assays to be performed using minute amounts of sample and have recently been used to control the microenvironment of cells. Microfluidics is commonly associated with closed microchannels which limit their use to samples that can be introduced, and cultured in the case of cells, within a confined volume. On the other hand, micropipetting system have been used to locally perfuse cells and surfaces, notably using push-pull setups where one pipette acts as source and the other one as sink, but the confinement of the flow is difficult in three dimensions. Furthermore, pipettes are fragile and difficult to position and hence are used in static configuration only. 
The microfluidic probe (MFP) circumvents the constraints imposed by the construction of closed microfluidic channels and instead of enclosing the sample into the microfluidic system, the microfluidic flow can be directly delivered onto the sample, and scanned across the sample, using the MFP. . The injection and aspiration openings are located within a few tens of micrometers of one another so that a microjet injected into the gap is confined by the hydrodynamic forces of the surrounding liquid and entirely aspirated back into the other opening. The microjet can be flushed across the substrate surface and provides a precise tool for localized deposition/delivery of reagents which can be used over large areas by scanning the probe across the surface. 
In this video we present the microfluidic probe1 (MFP). We explain in detail how to assemble the MFP, mount it atop an inverted microscope, and align it relative to the substrate surface, and finally show how to use it to process a substrate surface immersed in a buffer.

In this video we present the microfluidic probe1 (MFP). We explain in detail how to assemble the MFP, mount it atop an inverted microscope, and align it relative to the substrate surface, and finally show how to use it to process a substrate surface immersed in a buffer solution.

Microfluidic devices allow assays to be performed using minute amounts of sample and have recently been used to control the microenvironment of cells. ...

Fabrication and Operation of an Oxygen Insert for Adherent Cellular Cultures 

Oxygen is a key modulator of many cellular pathways, but current devices permitting in vitro oxygen modulation fail to meet the needs of biomedical research. The hypoxic chamber offers a simple system to control oxygenation in standard culture vessels, but lacks precise temporal and spatial control over the oxygen concentration at the cell surface, preventing its application in studying a variety of physiological phenomena. Other systems have improved upon the hypoxic chamber, but require specialized knowledge and equipment for their operation, making them intimidating for the average researcher. A microfabricated insert for multiwell plates has been developed to more effectively control the temporal and spatial oxygen concentration to better model physiological phenomena found in vivo. The platform consists of a polydimethylsiloxane insert that nests into a standard multiwell plate and serves as a passive microfluidic gas network with a gas-permeable membrane aimed to modulate oxygen delivery to adherent cells. The device is simple to use and is connected to gas cylinders that provide the pressure to introduce the desired oxygen concentration into the platform. Fabrication involves a combination of standard SU-8 photolithography, replica molding, and defined PDMS spinning on a silicon wafer. The components of the device are bonded after surface treatment using a hand-held plasma system. Validation is accomplished with a planar fluorescent oxygen sensor. Equilibration time is on the order of minutes and a wide variety of oxygen profiles can be attained based on the device design, such as the cyclic profile achieved in this study, and even oxygen gradients to mimic those found in vivo. The device can be sterilized for cell culture using common methods without loss of function. The device's applicability to studying the in vitro wound healing response will be demonstrated.

Fabrication and Operation of an Oxygen Insert for Adherent Cellular Cultures

Fabrication and validation of an add-on platform that offers enhanced control over the spatial and temporal oxygenation in a 6-well plate. The device is adaptable to a number of culture systems and can be used to investigate the effects of oxygen on wound healing.

Oxygen is a key modulator of many cellular pathways, but current devices permitting in vitro oxygen modulation fail to meet the needs of biomedical ...

Manual Restraint and Common Compound Administration Routes in Mice and Rats

Being able to safely and effectively restrain mice and rats is an important part of conducting research. Working confidently and humanely with mice and rats requires a basic competency in handling and restraint methods. This article will present the basic principles required to safely handle animals. One-handed, two-handed, and restraint with specially designed restraint objects will be illustrated. Often, another part of the research or testing use of animals is the effective administration of compounds to mice and rats. Although there are a large number of possible administration routes (limited only by the size and organs of the animal), most are not used regularly in research. This video will illustrate several of the more common routes, including intravenous, intramuscular, subcutaneous, and oral gavage. The goal of this article is to expose a viewer unfamiliar with these techniques to basic restraint and substance administration routes. This video does not replace required hands-on training at your facility, but is meant to augment and supplement that training.

Working safely and humanely with research rodents requires a core competency in handling and restraint methods. This article will present the basic principles required to safely handle and effectively administer compounds to mice and rats.

Being able to safely and effectively restrain mice and rats is an important part of conducting research.  Working confidently and humanely with mice and ...

Diagnostic Necropsy and Selected Tissue and Sample Collection in Rats and Mice

There are multiple sample types that may be collected from a euthanized animal in order to help diagnose or discover infectious agents in an animal colony. Proper collection of tissues for further histological processing can impact the quality of testing results. This article describes the conduct of a basic gross examination including identification of heart, liver, lungs, kidneys, and spleen, as well as how to collect those organs. Additionally four of the more difficult tissue/sample collection techniques are demonstrated. Lung collection and perfusion can be particularly challenging as the tissue needs to be properly inflated with a fixative in order for inside of the tissue to fix properly and to enable thorough histologic evaluation. This article demonstrates the step by step technique to remove the lung and inflate it with fixative in order to achieve optimal fixation of the tissue within 24 hours. Brain collection can be similarly challenging as the tissue is soft and easily damaged. This article demonstrates the step by step technique to expose and remove the brain from the skull with minimal damage to the tissue. The mesenteric lymph node is a good sample type in which to detect many common infectious agents as enteric viruses persist longer in the lymph node than they are shed in feces. This article demonstrates the step by step procedure for locating and aseptically removing the mesenteric lymph node. Finally, identification of infectious agents of the respiratory tract may be performed by bacterial culture or PCR testing of nasal and/or bronchial fluid aspirates taken at necropsy. This procedure describes obtaining and preparing the respiratory aspirate sample for bacterial culture and PCR testing.

This article describes the procedures for conducting a basic postmortem examination of a mouse or rat, and the collection of basic organs, as well as more challenging sample types from for histological, microbiological, and PCR evaluation.

There are multiple sample types that may be collected from a euthanized animal in order to help diagnose or discover infectious agents in an animal ...

Ovariectomy and 17&beta;-estradiol Replacement in Rats and Mice: A Visual Demonstration

Estrogens are a family of female sexual hormones with an exceptionally wide spectrum of effects. When rats and mice are used in estrogen research they are commonly ovariectomized in order to ablate the rapidly cycling hormone production, replacing the 17&beta;-estradiol exogenously. There is, however, lack of consensus regarding how the hormone should be administered to obtain physiological serum concentrations. This is crucial since the 17&beta;-estradiol level/administration method profoundly influences the experimental results1-3. We have in a series of studies characterized the different modes of 17&beta;-estradiol administration, finding that subcutaneous silastic capsules and per-oral nut-cream Nutella are superior to commercially available slow-release pellets (produced by the company Innovative Research of America) and daily injections in terms of producing physiological serum concentrations of 17&beta;-estradiol4-6. Amongst the advantages of the nut-cream method, that previously has been used for buprenorphine administration7, is that when used for estrogen administration it resembles peroral hormone replacement therapy and is non-invasive. The subcutaneous silastic capsules are convenient and produce the most stable serum concentrations. This video article contains step-by-step demonstrations of ovariectomy and 17&beta;-estradiol hormone replacement by silastic capsules and peroral Nutella in rats and mice, followed by a discussion of important aspects of the administration procedures.

Ovariectomy and 17&#946;-estradiol Replacement in Rats and Mice: A Visual Demonstration

Ovariectomy and subsequent replacement of 17&beta;-estradiol by means of silastic capsules and peroral Nutella are demonstrated in rats and mice.

Estrogens are a family of female sexual hormones with an exceptionally wide spectrum of effects. When rats and mice are used in estrogen research they are ...

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

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

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

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

Profiling Individual Human Embryonic Stem Cells by Quantitative RT-PCR

Heterogeneity of stem cell population hampers detailed understanding of stem cell biology, such as their differentiation propensity toward different lineages. A single cell transcriptome assay can be a new approach for dissecting individual variation. We have developed the single cell qRT-PCR method, and confirmed that this method works well in several gene expression profiles. In single cell level, each human embryonic stem cell, sorted by OCT4::EGFP positive cells, has high expression in OCT4, but a different level of NANOG expression. Our single cell gene expression assay should be useful to interrogate population heterogeneities.

Single cell gene expression assay is needed for understanding stem cell heterogeneities.

Heterogeneity of stem cell population hampers detailed understanding of stem cell biology, such as their differentiation propensity toward different ...

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays.
We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method&#160;applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout.
Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology.

We describe an endpoint digital assay for quantifying nucleic acids with a simplified (analog) readout. We measure bulk fluorescence of droplet-based digital assays using a standard qPCR machine rather than specialized instrumentation and confirm our results by microscopy.

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are ...

Employing Digital Droplet PCR to Detect BRAF V600E Mutations in Formalin-fixed Paraffin-embedded Reference Standard Cell Lines

ddPCR is a highly sensitive PCR method that utilizes a water-oil emulsion system. Using a droplet generator, an extracted nucleic acid sample is partitioned into ~20,000 nano-sized, water-in-oil droplets, and PCR amplification occurs in individual droplets. The ddPCR approach is in identifying sequence mutations, copy number alterations, and select structural rearrangements involving targeted genes. Here, we demonstrate the use of ddPCR as a powerful technique for precisely quantitating rare BRAF V600E mutations in FFPE reference standard cell lines, which is helpful in identifying individuals with cancer. In conclusion, ddPCR technique offers the potential to precisely profile the specific rare mutations in different genes in various types of FFPE samples.

The goal of this video is to demonstrate how to perform&#160;automated DNA extraction from formalin-fixed paraffin-embedded (FFPE) reference standard cell lines and digital droplet PCR&#160;(ddPCR) analysis to detect rare mutations in a clinical setting. Detecting mutations in FFPE samples demonstrates the clinical utility of ddPCR in FFPE samples.

ddPCR is a highly sensitive PCR method that utilizes a water-oil emulsion system. Using a droplet generator, an extracted nucleic acid sample is ...

The Lactate Dehydrogenase Sequestration Assay &#8212; A Simple and Reliable Method to Determine Bulk Autophagic Sequestration Activity in Mammalian Cells

Bulk autophagy is characterized by the sequestration of large portions of cytoplasm into double/multi-membrane structures termed autophagosomes. Here a simple protocol to monitor this process is described. Moreover, typical results and experimental validation of the method under autophagy-inducing conditions in various types of cultured mammalian cells are provided. During bulk autophagy, autophagosomes sequester cytosol, and thereby also soluble cytosolic proteins, alongside other autophagic cargo. LDH is a stable and highly abundant, soluble cytosolic enzyme that is non-selectively sequestered into autophagosomes. The amount of LDH sequestration therefore reflects the amount of bulk autophagic sequestration. To efficiently and accurately determine LDH sequestration in cells, we employ an electrodisruption-based fractionation protocol that effectively separates sedimentable from cytosolic LDH, followed by measurement of enzymatic activity in sedimentable fractions versus whole-cell samples. Autophagic sequestration is determined by subtracting the proportion of sedimentable LDH in untreated cells from that in treated cells. The advantage of the LDH sequestration assay is that it gives a quantitative measure of the autophagic sequestration of endogenous cargo, as opposed to other methods that either involve ectopic expression of sequestration probes or semi-quantitative protease protection analyses of autophagy markers or receptors.

Here a simple and well-validated protocol for measuring bulk autophagic sequestration activity in mammalian cells is described. The method is based on quantifying the proportion of lactate dehydrogenase (LDH) in sedimentable cell fractions compared to total cellular LDH levels.

Bulk autophagy is characterized by the sequestration of large portions of cytoplasm into double/multi-membrane structures termed autophagosomes. Here a ...