A multiplex Taqman PCR assay for MRSA detection from whole blood.

Methicillin-resistant Staphylococcus aureus (MRSA) causes a wide range of hospital and community-acquired infections worldwide. MRSA is associated with worse clinical outcomes that can lead to multiple organ failure, septic shock, and death, making timely diagnosis of MRSA infections very crucial. In the present work, we develop a method that enables the positive enrichment of bacteria from spiked whole blood using protein coated magnetic beads, followed by their lysis, and detection by a real-time multiplex PCR directly. The assay targeted bacterial 16S rRNA, S. aureus (spa) and methicillin resistance (mecA). In addition, an internal control (lambda phage) was added to determine the assay's true negative. To validate this assay, staphylococcal and non-staphylococcal bacterial strains were used. The three-markers used in this study were detected as expected by monomicrobial and poly-microbial models of the S. aureus and coagulase-negative staphylococci (CoNS). The thermal cycling completed within 30 mins, delivering 100% specificity. The detection LoD of the pre-processing step was ∼ 1 CFU/mL from 2-5mL of whole blood and that of PCR was ∼ 1pg of NA. However, the combined protocol led to a lower detection limit of 100-1000 MRSA CFUs/mL. The main issue with the method developed is in the pre-processing of blood which will be the subject of our future study.

Microphysiological Modeling of Gingival Tissues and Host-Material Interactions Using Gingiva-on-Chip.

Gingiva plays a crucial barrier role at the interface of teeth, tooth-supporting structures, microbiome, and external agents. To mimic this complex microenvironment, an in vitro microphysiological platform and biofabricated full-thickness gingival equivalents (gingiva-on-chip) within a vertically stacked microfluidic device is developed. This design allowed long-term and air-liquid interface culture, and host-material interactions under flow conditions. Compared to static cultures, dynamic cultures on-chip enabled the biofabrication of gingival equivalents with stable mucosal matrix, improved epithelial morphogenesis, and barrier features. Additionally, a diseased state with disrupted barrier function representative of gingival/oral mucosal ulcers is modeled. The apical flow feature is utilized to emulate the mechanical action of mouth rinse and integrate the assessment of host-material interactions and transmucosal permeation of oral-care formulations in both healthy and diseased states. Although the gingiva-on-chip cultures have thicker and more mature epithelium, the flow of oral-care formulations induced increased tissue disruption and cytotoxic features compared to static conditions. The realistic emulation of mouth rinsing action facilitated a more physiological assessment of mucosal irritation potential. Overall, this microphysiological system enables biofabrication of human gingiva equivalents in intact and ulcerated states, providing a miniaturized and integrated platform for downstream host-material and host-microbiome applications in gingival and oral mucosa research.

Current commercial dPCR platforms: technology and market review.

Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.

Experiment-Simulation Comparison in Liquid Filling Process Driven by Capillarity.

This paper studies modifications made to the Bosanquet equation in order to fit the experimental observations of the liquid filling process in circular tubes that occurs by capillary force. It is reported that there is a significant difference between experimental observations and the results predicted by the Bosanquet equation; hence, it is reasonable to investigate these differences intensively. Here, we modified the Bosanquet equation such that it could consider more factors that contribute to the filling process. First, we introduced the air flowing out of the tube as the liquid inflow. Next, we considered the increase in hydraulic resistance due to the surface roughness of the inner tube. Finally, we further considered the advancing contact angle, which varies during the filling process. When these three factors were included, the modified Bosanquet equation was well correlated with the experimental results, and the R square-which indicates the fitting quality between the simulation and the experiment-significantly increased to above 0.99.

Biomolecule-Interactive Flexible Light Emitting Capacitor Display.

Ultrathin, lightweight, flexible, and conformable interactive displays that transduce external stimuli into human-readable signals are essential for emerging applications, such as wearable electronics, human-machine interfaces, and soft robots. Herein, a biomolecule-interactive flexible light emitting capacitor (LEC) display (BIO-LEC) capable of dynamic and quantitative visualization of biomolecules through naked-eye detectable electroluminescence (EL) emission is reported. BIO-LEC comprises a coplanar LEC light source at the bottom, and a designed microfluidic chip as sampling compartment at the top. The quantitative measurement feature of BIO-LEC is achieved by introducing the top liquid electrode, which possesses a unique long dielectric realization time, in the microfluidic chip. BIO-LEC is novel for the following reasons, 1) simple stimuli response principle based on correlating EL intensity to dielectric properties of the top liquid electrode; 2) simple test conditions whereby no labeling is required in the analyte solution to optically detect biomolecules; 3) effective sampling method through the design of an integrated microfluidic chip for hosting the top liquid electrode, ensuring good reproducibility and preventing contamination; 4) sensitive detection limit for heparin concentrations at clinically relevant levels, and 5) high compliance with industrial manufacturing standards.

Chloroplast genome of Gaura parviflora Douglas and its comparative analysis.

Gaura parviflora Douglas (Onagraceae) is an annual or perennial herbaceous plant from the prairie of North America. It has become a harmful exotic invading plant in China due to its strong adaptability, fast growth, massive propagation and reproduction. The complete chloroplast (cp) genome of G. parviflora was reported in this study. The size of the complete cp genome of G. parviflora is 161,318 bp in length, including a pair of inverted repeat (IR) regions of 27,402 bp, a large single-copy (LSC) region of 89,132 bp, and a small single-copy (SSC) region of 17,382 bp. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparison of cp genomes of four species from Onagraceae indicated that Onagraceae cp genomes had high nucleotide diversity. In addition, a few highly variable regions of these cp genomes were also detected. The phylogenetic tree showed that G. parviflora is closely related to Oenothera. Thus, the chloroplast genome of G. parviflora can provide valuable genetic information for species identification and phylogenetic analysis.

Microfluidic chip for stacking, separation and extraction of multiple DNA fragments.

A disposable integrated microfluidic device was developed for rapid sample stacking, separation and extraction of multiple DNA fragments from a relatively large amount of sample. Isotachophoresis hyphenated gel electrophoresis (ITP-GE) was used to pre-concentrate and separate DNA fragments, followed by extraction of pure DNA fragments with electroelution on-chip. DNA fragments of 200bp, 500bp and 1kbp were successfully separated and collected in the extraction chamber within 25min. The extraction efficiency obtained from the chip was 49.9%, 52.1% and 53.7% for 200bp, 500bp and 1kbp DNA fragments, respectively. The extracted DNA fragments exhibited compatibility with downstream enzymatic reactions, for example PCR. The chip was also used to extract DNA fragments with specific size range from sheared genomic DNA and demonstrated similar performance to that using traditional gel cutting method. The whole assay can finish in 32min, 6 times faster than traditional method.

A lab-on-a-chip system integrating tissue sample preparation and multiplex RT-qPCR for gene expression analysis in point-of-care hepatotoxicity assessment.

A truly practical lab-on-a-chip (LOC) system for point-of-care testing (POCT) hepatotoxicity assessment necessitates the embodiment of full-automation, ease-of-use and "sample-in-answer-out" diagnostic capabilities. To date, the reported microfluidic devices for POCT hepatotoxicity assessment remain rudimentary as they largely embody only semi-quantitative or single sample/gene detection capabilities. In this paper, we describe, for the first time, an integrated LOC system that is somewhat close to a practical POCT hepatotoxicity assessment device - it embodies both tissue sample preparation and multiplex real-time RT-PCR. It features semi-automation, is relatively easy to use, and has "sample-in-answer-out" capabilities for multiplex gene expression analysis. Our tissue sample preparation module incorporating both a microhomogenizer and surface-treated paramagnetic microbeads yielded high purity mRNA extracts, considerably better than manual means of extraction. A primer preloading surface treatment procedure and the single-loading inlet on our multiplex real-time RT-PCR module simplify off-chip handling procedures for ease-of-use. To demonstrate the efficacy of our LOC system for POCT hepatotoxicity assessment, we perform a preclinical animal study with the administration of cyclophosphamide, followed by gene expression analysis of two critical protein biomarkers for liver function tests, aspartate transaminase (AST) and alanine transaminase (ALT). Our experimental results depict normalized fold changes of 1.62 and 1.31 for AST and ALT, respectively, illustrating up-regulations in their expression levels and hence validating their selection as critical genes of interest. In short, we illustrate the feasibility of multiplex gene expression analysis in an integrated LOC system as a viable POCT means for hepatotoxicity assessment.

Multidimensional microchip-capillary electrophoresis device for determination of functional proteins in infant milk formula.

Functional proteins have been found in infant milk formula as supplements, added by an increasing number of manufacturers. Their supplementations are expected to be controlled and monitored. Here, we describe a microchip-integrated CE method for the determination of these low levels of functional proteins in a protein-rich sample matrix. On-chip isoelectric focusing (IEF) is used to separate high-abundance proteins from low-abundance proteins instead of using some complicated time-consuming protein purification process. After that, transient isotachophoresis hyphenated capillary zone electrophoresis (t-ITP-CZE) can preconcentrate, separate, and analyze transferred functional proteins in the embedded capillary under UV detection.

Assessment of adulteration of soybean proteins in dairy products by 2D microchip-CE device.

To determine the adulteration of soybean proteins in dairy product, a microchip-CE device was developed to isolate selected fraction of soybean and milk proteins in pI range from 5.5 ∼ 7.0 by 1D IEF, followed by ITP/CZE in the embedded capillary for preconcentration, separation and UV detection at 280 nm. Compared to IEF-CZE without ITP preconcentration, the enhancement factor (EF) in detection of soybean proteins was 20 times. Adulteration of 0.1% soybean protein in total dairy proteins can be detected in less than 10 min.

Multi-dimension microchip-capillary electrophoresis device for determination of functional proteins in infant milk formula.

To improve resolution of important minor proteins and eliminate time-consuming precipitation of major protein with associated analyte co-precipitation risk, a multi-dimension strategy is adopted in the 2D microchip-CE device to isolate major proteins on-chip, enrich minor proteins in capillary before their separation in CE for UV quantitation. A standard fluorescent protein mixture containing FITC-BSA, myoglobin and cytochrome as specific pI markers has prepared to demonstrate capability of the device to fractionate minor proteins by IEF. The results using a standard protein mixture with profile resembling infant milk formula show a complete isolation of high abundance proteins by a 2-min 1D IEF run. The subsequent t-ITP/CZE run by on-chip high voltage switching delivers a high stacking ratio, realizing 60 folds enrichment of isolated protein fractions. All five important functional proteins (LF, IgG, α-LA, ß-LgA and ß-LgB) known to fortify infant milk formula are isolated and determined using two consecutive t-ITP-CZE runs within a 18-min total assay time, a significant saving compared to several hours conventional pretreatment. For a 100g infant milk formula sample, working ranges of 20-8000mg, repeatability 3.8-5.3% and detection limits 2.3-10mg have been achieved to meet government regulations. Method reliability is established by 100% recoveries and agreeable results within expected ranges and labeled values. The capability of the device for field operation, rapid assay with quick results, label-free universal detection, simple operation by aqueous dissolution before injection, and the demanding matching in 2D separation based on isolated fractions at specified pI ranges, closely matched migration time and baseline-resolved peak shape makes the device a general tool to detect unknown proteins and determine known minor proteins in protein-rich samples with interfering constituents.

2-D t-ITP/CZE determination of clinical urinary proteins using a microfluidic-chip capillary electrophoresis device.

To replace the time-consuming sample pretreatment procedure, a microfluidic chip-CE device incorporating on-chip sample desalting/preconcentration with transient isotachophoresis (ITP)/capillary zone electrophoresis (CZE) was fabricated to perform sequential on-chip sample pretreatment and CE determination of four urinary proteins in clinical samples. On-chip sample desalting, clean-up and analyte preconcentration enable removing interfering sample matrix prior to transferring analytes to separation capillary for transient ITP/CZE determination. Four important urinary proteins transferrin, ß2-microglobulin, human serum albumin (HSA) and immunoglobulin G (IgG), investigated were shown to achieve quantitation limits sufficiently high to meet medical requirements, sensitivity enhancement up to 40-fold and detection limits down to 0.3, 0.05, 0.6, 0.5 mg/L, respectively. Compared to the stacking effect, the use of a large sample size was found to be the major factor for sensitivity enhancement. The method reliability is established by close to 100% recoveries and statistical agreement of results from the method developed with currently used clinical radio-immunoassay method for all four proteins investigated. Moreover, an assay time of less than 10 min is needed in the method developed as compared to 7 h for the radio-immunoassay method.

Capillary electrophoresis with LIF detection for assessment of mitochondrial number based on the cardiolipin content.

Cardiolipin is a mitochondria-specific phospholipid known to be intimately involved with numerous mitochondrial functions. Accordingly, quantitative determination of cardiolipin provides a valuable aspect for assessing mitochondrial content and function. The current study was undertaken to develop a simple and reliable method for direct analysis of cardiolipin with particular application for the assessment of mitochondrial number of HepG2 cells. The method presented is based on the online 10-N-nonyl acridine orange (NAO) interaction with cardiolipin using CE with LIF detection. An aqueous-organic solvent system composed of 10% H(2) O-40% methanol-50% ACN (all v/v) containing 20 µM NAO provides both short analysis time within 2 min and a definite fluorescence enhancement at 525 nm for NAO-cardiolipin complex as compared with NAO alone. Under the optimum condition, a calibration curve between the peak area and the concentration of cardiolipin was established in the range of 0.1-200 µM with a correlation coefficient of 0.9955. The detection limit is 9 nM. The proposed method was successfully applied to the analysis of cardiolipin in mitochondria from HepG2 cells. A new biochemical method estimating the mitochondrial number per cell was developed and used together with the proposed method for cardiolipin per cell measurement and cardiolipin per mitochondrion reported before.