Complete Prevention of Bubbles in a PDMS-Based Digital PCR Chip with a Multifunction Cavity.

In a chamber-based digital PCR (dPCR) chip fabricated with polydimethylsiloxane (PDMS), bubble generation in the chambers at high temperatures is a critical issue. Here, we found that the main reason for bubble formation in PDMS chips is the too-high saturated vapor pressure of water at an elevated temperature. The bubbles should be completely prevented by reducing the initial pressure of the system to under 13.6 kPa to eliminate the effects of increased-pressure water vapor. Then, a cavity was designed and fabricated above the PCR reaction layer, and Parylene C was used as a shell covering the chip. The cavity was used for the negative generator in sample loading, PDMS degassing, PCR solution degassing in the digitization process and water storage in the thermal reaction process. The analysis was confirmed and finally achieved a desirable bubble-free, fast-digitization, valve-free and no-tubing connection dPCR.

SPA, a Stigma-style-transmitting tract Physical microenvironment Assay for investigating mechano-signaling in pollen tubes.

Accurate sensing and responding to physical microenvironment are crucial for cell function and survival, but the underlying molecular mechanisms remain elusive. Pollen tube (PT) provides a perfect single-cell model for studying mechanobiology since it's naturally subjected to complex mechanical instructions from the pistil during invasive growth. Recent reports have revealed discrepant PT behaviors between in vivo and flat, two-dimensional in vitro cultures. Here, we established the Stigma-style-transmitting tract (TT) Physical microenvironment Assay (SPA) to recapitulate pressure changes in the pistil. This biomimetic assay has enabled us to swiftly identify highly redundant genes, GEF8/9/11/12/13, as new regulators for maintaining PTs integrity during style-to-TT emergence. In contrast to normal growth on solid medium, SPA successfully phenocopied gef8/9/11/12/13 PT in vivo growth-arrest deficiency. Our results suggest the existence of distinct signaling pathways regulating in vivo and in vitro PT integrity maintenance, underscoring the necessity of faithfully mimicking the physical microenvironment for studying plant cell biology.

Resonant-Cantilever-Detected Kinetic/Thermodynamic Parameters for Aptamer-Ligand Binding on a Liquid-Solid Interface.

Nucleic acid aptamers have been widely used as recognition elements on various biosensing interfaces, but quantitative kinetic/thermodynamic analysis for revealing the aptamer-ligand binding mechanism, which occurs on a liquid-solid interface, has not been realized due to a lack of usable biophysical tools. Herein we apply a resonant microcantilever sensor to continuously record the frequency shift according to the binding-induced mass change on the liquid-solid interface. The frequency-shift curve is used for tracing the reaction process and is fitted with classic equations to calculate a set of kinetic/thermodynamic parameters, such as rate constants (ka = 902.95 M-1 s-1, kd = 0.000141 s-1), equilibrium constants (KD = 1.55 µM), the Gibbs free energy (ΔG° = -32.57 kJ/mol), and the activation energy (Ea = 38.03 kJ/mol) for the immobilized aptamer and free ATP. This quantitative analysis method is label-free, calibration-free, and highly sensitive. The kinetic/thermodynamic parameter detection method provides new resolution to the in-depth understanding of the ligand-aptamer interaction on the liquid-solid interface for biosensing or lab-on-a-chip applications.

Effective cell trapping using PDMS microspheres in an acoustofluidic chip.

We present a facile particle-based cell manipulation method using acoustic radiation forces. In this work, we selected several representative particles including poly(lactic-co-glycolic acid) (PLGA) microspheres, silica-coated magnetic microbeads, polydimethylsiloxane (PDMS) microspheres and investigated the responses of these particle systems to ultrasonic standing waves (USWs) in a microfluidic chip. We show that depending on the nature (positive or negative acoustic contrast factors) of the particles, these particle systems display different alignment behaviors along the microfluidic channel under USWs. Specifically, PLGA microspheres and silica-coated magnetic microbeads are able to be aligned in the middle of the microfluidic channel, while PDMS microspheres are translocated to the side walls of the channel, which is beneficial for cell trapping and manipulation. Further results demonstrate that the functional PDMS microspheres with a negative acoustic contrast factor can be used to trap cells to the pressure antinodes in the acoustofluidic chip. Cell viability tests reveal that the ultrasonic manipulation does not exert any harmful effect to the cells. This acoustic-based particle and cell manipulation technique may hold a great promise for the development of rapid, noninvasive, continuous assays for detecting of cells and separation of biological samples.

Hyaluronic acid-functionalized electrospun PLGA nanofibers embedded in a microfluidic chip for cancer cell capture and culture.

Circulating tumor cells (CTCs) are important markers of metastatic cancer. The isolation and detection of CTCs from peripheral blood provides valuable information for cancer diagnosis and precision medicine. However, cost-efficient targeted separation of CTCs of different origins with clinically significant specificity and efficiency remains a major challenge. In this study, a facile approach was developed to fabricate a thin sheet of hyaluronic acid (HA)-functionalized PLGA nanofibrous membrane and integrate it into a microfluidic chamber. The HA was covalently conjugated onto polyethyleneimine (PEI)-modified electrospun poly(lactic-co-glycolic acid) (PLGA) nanofibers. Different techniques were employed to characterize the resulted nanofibers. The results show that the CD44+ carcinoma of various origins (HeLa, KB, A549, and MCF-7 cells) could be selectively captured by the PLGA-PEI-HA nanofibers in the microfluidic platform. Importantly, the PLGA-PEI-HA nanofibrous membrane was more efficient to capture HeLa cancer cells under flowing conditions than in static dishes, and at a really low density (20 cells per mL). Furthermore, with constant media perfusion, the captured HeLa cells could grow on the nanofibrous membrane in the microchip for days without compromised cell viability. This is the first trial of using HA-functionalized electrospun nanofibers in a lab-chip device for cancer cell capture and culture. Compared to conventional CTC capture methods, the integration of inexpensive functional electrospun nanofibers and microfluidic technologies may expand the frontiers of using advanced nanomaterials in portable diagnostic applications.

µ-'Diving suit' for liquid-phase high-Q resonant detection.

A resonant cantilever sensor is, for the first time, dressed in a water-proof 'diving suit' for real-time bio/chemical detection in liquid. The µ-'diving suit' technology can effectively avoid not only unsustainable resonance due to heavy liquid-damping, but also inevitable nonspecific adsorption on the cantilever body. Such a novel technology ensures long-time high-Q resonance of the cantilever in solution environment for real-time trace-concentration bio/chemical detection and analysis. After the formation of the integrated resonant micro-cantilever, a patterned photoresist and hydrophobic parylene thin-film are sequentially formed on top of the cantilever as sacrificial layer and water-proof coat, respectively. After sacrificial-layer release, an air gap is formed between the parylene coat and the cantilever to protect the resonant cantilever from heavy liquid damping effect. Only a small sensing-pool area, located at the cantilever free-end and locally coated with specific sensing-material, is exposed to the liquid analyte for gravimetric detection. The specifically adsorbed analyte mass can be real-time detected by recording the frequency-shift signal. In order to secure vibration movement of the cantilever and, simultaneously, reject liquid leakage from the sensing-pool region, a hydrophobic parylene made narrow slit structure is designed surrounding the sensing-pool. The anti-leakage effect of the narrow slit and damping limited resonance Q-factor are modelled and optimally designed. Integrated with electro-thermal resonance excitation and piezoresistive frequency readout, the cantilever is embedded in a micro-fluidic chip to form a lab-chip micro-system for liquid-phase bio/chemical detection. Experimental results show the Q-factor of 23 in water and longer than 20 hours liquid-phase continuous working time. Loaded with two kinds of sensing-materials at the sensing-pools, two types of sensing chips successfully show real-time liquid-phase detection to ppb-level organophosphorous pesticide of acephate and E.coli DH5α in PBS, respectively. The proposed method fundamentally solves the long-standing problem of being unable to operate a resonant micro-sensor in liquid well.

A wireless bio-sensing microfluidic chip based on resonating 'µ-divers'.

A magneto-elastic resonant 'micro-diver' system (MER-µDS) is proposed and developed for rapid liquid-phase detection of pathogens in a wireless way. The magneto-elastic micro-resonator (i.e., the µ-diver) is placed in the micro-chamber of the MER-µDS that is connected to the inlet/outlet for flow of the liquid analyte and a closed-loop micro-channel. After specific attachment of the analyte onto the µ-diver, the µ-diver is conveyed by the flow into the detection segment of the channel, around which a metal micro-coil is wound for both excitation resonance of the µ-diver and reading of its resonance frequency signal. After the pre-functionalized µ-diver captures the analyte and, then, is driven into the detection channel segment, the added mass induced resonant frequency shift can be wirelessly sensed by the coil. The micro-system features rapid and repeatable liquid-phase bio-sensing and the wireless signal readout scheme is favorable to real-time pathogen detection in liquid food, e.g., milk or juice, for food safety applications. An equivalent circuit model is established for design of the magneto-elastic µ-diver. After a bar-shaped µ-diver with length-extensional bulk-resonance mode is optimally designed and micro-fabricated, the MER-µDS is formed by micro-machining/assembling techniques. By placing a biotin-immobilized µ-diver into the wireless micro-sensing system, avidin-attached magnetic beads are detected to calibrate the mass sensitivity as 0.061 Hz pg(-1), which well confirms the modeling result. By using the antibody-immobilized µ-diver, PBS solution with an E. coli concentration of 10(2)-10(8) CFU mL(-1) is detected, resulting in a corresponding wireless f0-shift sensing signal of about 300-2300 Hz and a limit of detection of 10(2) CFU mL(-1). Food safety application potential of the MER-µDS technique is proven by detection of E. coli added to orange and apple juices (E. coli concentration: 10(4)-10(8) CFU mL(-1)).

Advanced nanoporous materials for micro-gravimetric sensing to trace-level bio/chemical molecules.

Functionalized nanoporous materials have been developed recently as bio/chemical sensing materials. Due to the huge specific surface of the nano-materials for molecular adsorption, high hopes have been placed on gravimetric detection with micro/nano resonant cantilevers for ultra-sensitive sensing of low-concentration bio/chemical substances. In order to enhance selectivity of the gravimetric resonant sensors to the target molecules, it is crucial to modify specific groups onto the pore-surface of the nano-materials. By loading the nanoporous sensing material onto the desired region of the mass-type transducers like resonant cantilevers, the micro-gravimetric bio/chemical sensors can be formed. Recently, such micro-gravimetric bio/chemical sensors have been successfully applied for rapid or on-the-spot detection of various bio/chemical molecules at the trace-concentration level. The applicable nanoporous sensing materials include mesoporous silica, zeolite, nanoporous graphene oxide (GO) and so on. This review article focuses on the recent achievements in design, preparation, functionalization and characterization of advanced nanoporous sensing materials for micro-gravimetric bio/chemical sensing.

Real-time enzyme-digesting identification of double-strand DNA in a resonance-cantilever embedded micro-chamber.

A novel direct identification of double-strand DNA is proposed by using real-time enzyme-digestion in a resonant-cantilever embedded microfluidic chip. The new gene-level detection method is expected to replace the conventional DNA-hybridization based gene-detection that suffers from not only nonspecific adsorption induced false-positives but also complicated single-strand DNA preparation and hybridization. Since a detected DNA chain features a unique cutting site for a certain restriction-enzyme, the accurately cut-off mass (representing the length of the digested segment) can be online recorded by the frequency-shift signal of the resonant micro-cantilever sensor. This enzyme-digestion technique is confirmed by experimental identification of the stx2 gene of E. coli O157:H7. The direct-PCR sample is directly analyzed by using our lab-made cantilever-embedded microfluidic-chip. The 3776 bp DNA is immobilized via biotin-streptavidin binding and the added mass is recorded by a frequency-decrease of 15.9 kHz within 10 min. Then, with EcoRV-enzyme digestion at the site of 2635 bp, the cut-off mass is real-time detected by a frequency-increase of 10.2 kHz within 6 min. The detected frequency-shift ratio of 15.9/10.2 = 64.2% is consistent with the length ratio between the cut-off fragment and the whole DNA chain (2635/3776 = 69.8%). Hence, the simple and accurate double-strand detection method is verified experimentally.

Mechanism of the cycloaddition of carbon dioxide and epoxides catalyzed by cobalt-substituted 12-tungstenphosphate.

Co(II)-substituted α-Keggin-type 12-tungstenphosphate [(n-C(4)H(9))(4)N](4)H[PW(11)Co(H(2)O)O(39)]-(PW(11)Co) is synthesized and used as a single-component, solvent-free catalyst in the cycloaddition reaction of CO(2) and epoxides to form cyclic carbonates. The mechanism of the cycloaddition reaction is investigated using DFT calculations, which provides the first computational study of the catalytic cycle of polyoxometalate-catalyzed CO(2) coupling reactions. The reaction occurs through a single-electron transfer from the doublet Co(II) catalyst to the epoxide and forms a doublet Co(III)-carbon radical intermediate. Subsequent CO(2) addition forms the cyclic carbonate product. The existence of radical intermediates is supported by free-radical termination experiments. Finally, it is exhilarating to observe that the calculated overall reaction barrier (30.5 kcal mol(-1)) is in good agreement with the real reaction rate (83 h(-1)) determined in the present experiments (at 15 °C).

A chelating-bond breaking and re-linking technique for rapid re-immobilization of immune micro-sensors.

With high sensitivity and specificity to antigen, immune micro-sensors can be used in rapid detection of pathogenic microbial. This study proposes and develops a method for rapidly regeneration of antibody on a resonant micro-cantilever sensor. A nitrilotriacetic acid (NTA) derivative is synthesized with cystine and bromoacetic acid, then added with 2-mercaptoethanol to prepare a mixed self-assembled monolayer (SAM) on Au (111) surface of the cantilever. Ni²âº ions are thereafter chelated on the mixed SAM to form a breakable and re-linkable chelating-bond layer. Repeatable cycles of antibody immobilization and erasing are experimentally validated with a detectable marker of synthesized biotinylated poly peptides harboring six histidine residues (named as His-Bio). Two distinguished pathogenic microbial, Escherichia. coli O157:H7 and Bacillus Anthracis, are detected with the rapidly regenerated sensor. The E. coli O157:H7 sensor exhibits a three-time repeated detection to the 10³ CFU/ml concentration microbial. Then, an E. coli O157:H7 sensor is eluted with Tris-HCl (20 mM Tris, 150 mM NaCl, 0.1% Tween 20, pH = 3.0) and rapidly reconstructed into a B. Anthracis sensor by changing the re-immobilized antibody. The cantilever sensor no longer responses to E. coli O157:H7 even in a high concentration of 107 CFU/ml. In contrast, the sensor is experimentally confirmed being resoluble to low concentration B. Anthracis at 10³ spores/ml level. The proposed fast regeneration method is promising in repeatedly or multi-target detection applications of micro/nano immune-sensors, e.g. the resonant micro-cantilevers.

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.

A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting its own DNA by site-specific phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred both host-specific restriction and DNA S-modification on E. coli. Mutational analysis of the gene cluster proved unambiguously that the S-modification prevented host-specific restriction specified by the same gene cluster. Restriction activity required three genes in addition to at least four contiguous genes necessary for DNA S-modification. This functional overlap ensures that restriction of heterologous DNA occurs only when the host DNA is protected by phosphorothioation. Meanwhile, this novel type of host-specific restriction and modification system was identified in many diverse bacteria. As in the case of methylation-specific restriction systems, targeted inactivation of this gene cluster should facilitate genetic manipulation of these bacteria, as we demonstrate in Salmonella.

DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.

BACKGROUND: A novel DNA phosphorothioate modification (DNA sulfur modification), in which one of the non-bridging oxygen atoms in the phosphodiester bond linking DNA nucleotides is exchanged by sulphur, was found to be genetically determined by dnd or dnd-counterpart loci in a wide spectrum of bacteria from diverse habitats. A detailed mutational analysis of the individual genes within the dnd locus in Streptomyces lividans responsible for DNA phosphorothioation was performed and is described here. It should be of great help for the mechanistic study of this intriguing system. RESULTS: A 6,665-bp DNA region carrying just five ORFs (dndA-E) was defined as the sole determinant for modification of the DNA backbone in S. lividans to form phosphorothioate. This provides a diagnostically reliable and easily assayable Dnd (DNA degradation) phenotype. While dndA is clearly transcribed independently, dndB-E constitute an operon, as revealed by RT-PCR analysis. An efficient mutation-integration-complementation system was developed to allow for detailed functional analysis of these dnd genes. The Dnd- phenotype caused by specific in-frame deletion of the dndA, C, D, and E genes or the enhanced Dnd phenotype resulting from in-frame deletion of dndB could be restored by expression vectors carrying the corresponding dnd genes. Interestingly, overdosage of DndC or DndD, but not other Dnd proteins, in vivo was found to be detrimental to cell viability. CONCLUSION: DNA phosphorothioation is a multi-enzymatic and highly coordinated process controlled by five dnd genes. Overexpression of some proteins in vivo prevented growth of host strain, suggesting that expression of the gene cluster is strictly regulated in the native host.

Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1.

DNA phosphorothioation is widespread in many bacterial species. By homology analysis of the dnd gene cluster in Pseudomonas fluorescens Pf0-1, a spfBCDE gene cluster involved in DNA phosphorothioation was localized. Disruption of the spfD gene, a dndD homolog, caused the loss of the Dnd phenotype and demonstrated the involvement of spfD in DNA phosphorothioation in P. fluorescens Pf0-1. The ATPase activity of SpfD suggests that SpfD could hydrolyze ATP to provide the energy required in the DNA phosphorothioate modification process.

Phosphorothioation of DNA in bacteria by dnd genes.

Modifications of the canonical structures of DNA and RNA play critical roles in cell physiology, DNA replication, transcription and translation in all organisms. We now report that bacterial dnd gene clusters incorporate sulfur into the DNA backbone as a sequence-selective, stereospecific phosphorothioate modification. To our knowledge, unlike any other DNA or RNA modification systems, DNA phosphorothioation by dnd gene clusters is the first physiological modification described on the DNA backbone.

A novel DNA modification by sulphur.

Streptomyces lividans has a novel DNA modification, which sensitises its DNA to degradation during electrophoresis (the Dnd phenotype). The entire gene cluster (dnd) involved in this modification was localized on an 8 kb DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and in several heterologous hosts. Disruption of the dnd locus abolishes the Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype respectively. Extensive analysis of the dnd gene cluster revealed five open reading frames, whose hypothetic functions suggested an incorporation of sulphur or a sulphur-containing substance into S. lividans genome, yet in an unknown manner. The Dnd phenotype was also discovered to exist in DNA of widespread bacterial species of variable origin and diverse habitat. Similarly organized gene clusters were found in several bacterial genomes representing different genera and in eDNA of marine organisms, suggesting such modification as a widespread phenomenon. A coincidence between the Dnd phenotype and DNA modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo(35)S-labelling experiments.