The transcriptome of early chicken embryos reveals signaling pathways governing rapid asymmetric cellularization and lineage segregation.

The phylogenomics and comparative functional genomics of avian species were investigated in the Bird 10,000 Genomes (B10K) project because of the important evolutionary position of birds and their value as a research model. However, the systematic profiling of transcriptional changes prior to oviposition has not been investigated in avian species because of the practical difficulties in obtaining pre-oviposited eggs. In this study, a total of 137 pre-oviposited embryos were collected from hen ovaries and oviducts and subjected to RNA-sequencing analyses. Two waves of chicken zygotic genome activation (ZGA) were observed. Functionally distinct developmental programs involving Notch, MAPK, Wnt and TGFß signaling were separately detected during cleavage and area pellucida formation. Furthermore, the early stages of chicken development were compared with the human and mouse counterparts, highlighting chicken-specific signaling pathways and gradually analogous gene expression via ZGA. These findings provide a genome-wide understanding of avian embryogenesis and comparisons among amniotes.

A Capacitive Micromachined Ultrasonic Transducer-Based Resonant Sensor Array for Portable Volatile Organic Compound Detection with Wireless Systems.

The development of portable volatile organic compound (VOC) sensors is essential for home healthcare and workplace safety because VOCs are environmental pollutants that may critically affect human health. Here, we report a compact and portable sensor platform based on a capacitive micromachined ultrasonic transducer (CMUT) array offering multiplex detection of various VOCs (toluene, acetone, ethanol, and methanol) using a single read-out system. Three CMUT resonant devices were functionalized with three different layers: (1) phenyl-selective peptide, (2) colloids of single-walled nanotubes and peptide, and (3) poly(styrene-co-allyl alcohol). As each device exhibited different sensitivities to the four VOCs, we performed principal component analysis to achieve selective detection of all four gases. For the simultaneous detection of VOCs using CMUT sensors, the changes in the resonant frequencies of three devices were monitored in real time, but using only a single oscillator through an electrically controlled relay to achieve compactness. In addition, by devising a wireless system, measurement results were transmitted to a smartphone to monitor the concentration of VOCs. We used multiple sensors to obtain a larger number of fingerprints for pattern recognition to enhance selectivity but interfaced these sensors with a single read-out circuit to minimize the footprint of the overall system. The compact CMUT-based sensor array based on a multiplex detection scheme is a promising sensor platform for portable VOC monitoring.

Aptamer-Based Single-Step Assay by the Fluorescence Enhancement on Electroless Plated Nano Au Substrate.

A new single-step aptamer-based surface-enhanced fluorescent optical sensor is built, by combining an aptamer-target interaction for target recognition and a fluorophore interaction for signal enhancement. The developed aptasensor is simple, sensitive, specific and stable for the detection of thrombin. A new nanometallic Au structure in the range of 100 nm was constructed through effective electroless plating method on a Cu thin film. Cu⁺ ions act as sacrificial seeds for the reduction of Au2+/3+ ions to form Au nanolawns. In order to utilize the structure for a fluorescence-based sensor, aptamer conjugated with Cy3 was immobilized on the nanogold substrate through electrostatic attraction. The Au substrate was coated with chitosan (molecular weight 1000 Da). Thrombin binding aptamer (TBA) was applied as a model system demonstrating the aptamer-based fluorescence assay on nanogold substrates. Thrice-enhanced fluorescence emission was achieved with Cy3-conjugated TBA stably immobilized on the chitosan-coated Au substrate. The intensity change was proportional to the concentration of thrombin from 10 µM to 10 pM, whereas the intensity change was ignorable for other proteins such as human serum albumin (HSA). Aptamer-based assay benefited from simple immobilization of receptors and Au nanostructure contributed in building an effective surface enhancing/positively charged substrate was proved. Such an aptasensor holding high utilities for point-of-care devices by incorporating simplicity, sensitivity and selectivity in detection, low-cost for test, small sample volumes has been developed.

Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy.

Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.

Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection.

Efficient pathogen enrichment and nucleic acid isolation are critical for accurate and sensitive diagnosis of infectious diseases, especially those with low pathogen levels. Our study introduces a biporous silica nanofilms-embedded sample preparation chip for pathogen and nucleic acid enrichment/isolation. This chip features unique biporous nanostructures comprising large and small pore layers. Computational simulations confirm that these nanostructures enhance the surface area and promote the formation of nanovortex, resulting in improved capture efficiency. Notably, the chip demonstrates a 100-fold lower limit of detection compared to conventional methods used for nucleic acid detection. Clinical validations using patient samples corroborate the superior sensitivity of the chip when combined with the luminescence resonance energy transfer assay. The enhanced sample preparation efficiency of the chip, along with the facile and straightforward synthesis of the biporous nanostructures, offers a promising solution for polymer chain reaction-free detection of nucleic acids.

Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance.

Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.

Electrocatalytic effects of carbon dissolution in Pd nanoparticles.

Highly dispersed Pd nanoparticles were prepared by borohydride reduction of Pd(acac)(2) in 1,2-propanediol at an elevated temperature. They were uniformly dispersed on carbon black without significant aggregation. X-ray diffraction showed that carbons from the Pd precursor dissolved in Pd, increasing its lattice parameter. A modified reduction process was tested to remove the carbon impurities. Carbon removal greatly enhanced catalytic activity toward the oxygen reduction reaction. It also generated an inconsistency between the electronic modifications obtained from X-ray photoelectron spectroscopy and the electrochemical method. CO displacement measurements showed that the formation of Pd-C bonds decreased the work function of the surface Pd atoms.

A new combination MALDI matrix for small molecule analysis: application to imaging mass spectrometry for drugs and metabolites.

Since the development of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, this procedure has been specifically used for analyzing proteins or high molecular weight compounds because of the interference of matrix signals in the regions of the low mass range. Recently, scientists have been using a wide range of chemical compounds as matrices that ionize small molecules in a mass spectrometer and overcome the limitations of MALDI mass spectrometry. In this study, we developed a new combination matrix of 3-hydroxycoumarin (3-HC) and 6-aza-2-thiothymine (ATT), which is capable of ionizing small molecules, including drugs and single amino acids. In addition to ionization of small molecules, the combination matrix by itself gives less signals in the low mass region and can be used for performing imaging mass spectrometry (IMS) experiments on tissues, which confirms the vacuum stability of the matrix inside a MALDI chamber. The drug donepezil was mapped in the intact tissue slices of mice simultaneously with a spatial resolution of 150 µm during IMS. IMS analysis clearly showed that intact donepezil was concentrated in the cortical region of the brain at 60 min after oral administration. Our observations and results indicate that the new combination matrix can be used for analyzing small molecules in complex samples using MALDI mass spectrometry.

Zirconia Toughened Alumina-Based Separator Membrane for Advanced Alkaline Water Electrolyzer.

Hydrogen is nowadays considered a favorable and attractive energy carrier fuel to replace other fuels that cause global warming problems. Water electrolysis has attracted the attention of researchers to produce green hydrogen mainly for the accumulation of renewable energy. Hydrogen can be safely used as a bridge to successfully connect the energy demand and supply divisions. An alkaline water electrolysis system owing to its low cost can efficiently use renewable energy sources on large scale. Normally organic/inorganic composite porous separator membranes have been employed as a membrane for alkaline water electrolyzers. However, the separator membranes exhibit high ionic resistance and low gas resistance values, resulting in lower efficiency and raised safety issues as well. Here, in this study, we report that zirconia toughened alumina (ZTA)-based separator membrane exhibits less ohmic resistance 0.15 Ω·cm2 and low hydrogen gas permeability 10.7 × 10-12 mol cm-1 s-1 bar-1 in 30 wt.% KOH solution, which outperforms the commercial, state-of-the-art Zirfon® PERL separator. The cell containing ZTA and advanced catalysts exhibit an excellent performance of 2.1 V at 2000 mA/cm2 at 30 wt.% KOH and 80 °C, which is comparable with PEM electrolysis. These improved results show that AWEs equipped with ZTA separators could be superior in performance to PEM electrolysis.

Direct Reverse Transcription Real-Time PCR of Viral RNA from Saliva Samples Using Hydrogel Microparticles.

In recent decades "saliva" has emerged as an important non-invasive biofluid for diagnostic purposes in both human and animal health sectors. However, with the rapid evolution of molecular detection technologies, the limitation has been the lack of an efficient method for the facile amplification of target RNA from such a complex matrix. Herein, we demonstrate the novel application of hydrogel microparticles of primer-immobilized networks (PIN) for direct quantitative reverse transcription PCR (dirRT-qPCR) of viral RNA from saliva samples without prior RNA purification. Each of these highly porous PIN particles operates as an independent reactor. They filter in micro-volumes of the analyte solution. Viral RNA is captured and converted to complementary DNA (cDNA) through the RT step using covalently incorporated RT primers. The PIN with cDNA of the viral target will be ready for subsequent highly specific qPCR. Preceded by heat-treatment for viral lysis, we were able to conduct PIN dirRT-qPCR with 95% efficiency of the matrix (M) gene for influenza A virus (IAV) and 5' untranslated region (5' UTR) for chicken coronavirus spiked into saliva samples. The addition of reverse transcriptase enzyme (RTase) and 10% dilution of the matrix improved the assay sensitivity considerably. PIN particles' compatibility with microfluidic PCR chip technology has significantly reduced total sample processing time to 50 min, instead of an average of 120 min that are normally used by other assays. We anticipate this technology will be useful for other viral RNA targets by changing the incorporated RT primer sequences and can be adapted for onsite diagnostics. Supplementary Information: The online version contains supplementary material available at 10.1007/s13206-022-00065-0.

Novel human skin surface antimicrobial peptide quantification method using a skin patch test chamber: A pilot study.

INTRODUCTION: Antimicrobial peptides (AMPs) on the skin surface are related to the innate immunity of the skin in preventing external infection. Skin rinsing and tape stripping (TS) are acceptable methods for analyzing AMPs on the skin surface but have limitations, such as causing skin damage. In this study, we proposed a noninvasive method to measure AMPs on the skin surface with minimal skin damage. METHODS: Using the patch test assay, we aimed to analyze the skin surface human ß-defensin (hBDs) levels without damaging the skin barrier. The concentrations of hBDs on the skin surface were evaluated through the skin patch testing of 13 healthy subjects, and hBD-1 concentrations were compared with those obtained using the TS method in this proof-of-concept study. In addition, changes in skin physiology and concentration of hBDs under 1% sodium lauryl sulfate stimulation were monitored in 14 healthy subjects (8 young and 6 elderly subjects) for 150 h. RESULTS: The correlation between the two methods had a Pearson's coefficient of 0.640, and skin patch analysis led to a relatively less impaired barrier with no significant increase in transepidermal water loss after analysis. Age-specific comparisons suggested that higher skin surface hBD-2 concentrations were present in the young group as compared with the elderly group. Skin surface expression of hBD-2 after skin barrier disruption was also higher in the young group. CONCLUSION: Our findings show that skin patch analysis is a convenient method to analyze hBDs on the skin surface. hBDs are factors of innate immunity that can be used as an index to predict a decreased chemical immune response of skin due to aging.

Ultrafast Real-Time PCR in Photothermal Microparticles.

As the turnaround time of diagnosis becomes important, there is an increasing demand for rapid, point-of-care testing (POCT) based on polymerase chain reaction (PCR), the most reliable diagnostic tool. Although optical components in real-time PCR (qPCR) have quickly become compact and economical, conventional PCR instruments still require bulky thermal systems, making it difficult to meet emerging needs. Photonic PCR, which utilizes photothermal nanomaterials as heating elements, is a promising platform for POCT as it reduces power consumption and process time. Here, we develop a photonic qPCR platform using hydrogel microparticles. Microparticles consisting of hydrogel matrixes containing photothermal nanomaterials and primers are dubbed photothermal primer-immobilized networks (pPINs). Reduced graphene oxide is selected as the most suitable photothermal nanomaterial to generate heat in pPIN due to its superior light-to-heat conversion efficiency. The photothermal reaction volume of 100 nL (predefined by the pPIN dimensions) provides fast heating and cooling rates of 22.0 ± 3.0 and 23.5 ± 2.6 °C s-1, respectively, enabling ultrafast qPCR within 5 min only with optical components. The microparticle-based photonic qPCR facilitates multiplex assays by loading multiple encoded pPIN microparticles in a single reaction. As a proof of concept, four-plex pPIN qPCR for bacterial discrimination are successfully demonstrated.

Preparation of mesoporous carbon-carbon nanotube composites using the template method.

Reported herein is a simple template method for preparing mesoporous carbons (MPCs) from a mesophase pitch, using homemade nano-sized MgOs and MgO-carbon nanotube (CNT) composites as templates. Nano-sized MgO particles containing iron-molybdenum were synthesized through the heat treatment of the precursor ash, and the MgO-CNT composites were prepared via catalytic chemical vapor deposition of CH4 over the MgO-based particles. MPCs with a high surface area of 443-578 m2/g were obtained through the heat treatment of well-mixed mesophase pitch-MgO (or MgO-CNT), followed by mild-acid treatment to remove the MgO and other catalyst components. All the materials (the precursors, nano-particles, and MPCs) were analyzed via powder X-ray diffraction, N2 adsorption-desorption isotherms, scanning electron microscopy, and high resolution transmission electron microscopy. The formation of the pore structure in the MPCs is discussed, and the potential application of the MPC-CNT composite is demonstrated through cyclic voltammetry.

Characteristics of porous carbon nano-fibers synthesized by selective catalytic gasification.

Carbon nanofibers (CNFs) with uniquely oriented channels were prepared via selective catalytic gasification in air at 450 and 500 degrees C, using Pt or Ru nano particles as catalysts. Catalytic gasification was chosen because it can selectively generate channels in the vicinity of the catalyst particles at relatively low temperatures, where thermal oxidation does not intensively occur. The structures and surface properties of the CNFs were examined via X-ray diffraction, analysis of the nitrogen adsorption-desorption isotherms, and high-resolution transmission electron microscopy. The effects of the catalyst species and loading amount on the formation of pores (channels) were investigated. The gasification mechanism, especially the channeling direction, throught the selection of the gasification catalysts, is discussed based on the results. This process can be effectively utilized for preparation of porous carbons, which have a well-aligned graphitic structure, and also channel-type pores can be designed by selection of gasification catalysts and conditions. The present porous CNF can be applied for catalyst support in fuel cells, without further treatment (e.g., acid treatment for the removal of metallic components).

Study on the water flooding in the cathode of direct methanol fuel cells.

Water flooding phenomena in the cathode of direct methanol fuel cells were analyzed by using electrochemical impedance spectroscopy. Two kinds of commercial gas diffusion layers with different PTFE contents of 5 wt% (GDL A5) and 20 wt% (GDL B20) were used to investigate the water flooding under various operating conditions. Water flooding was divided into two types: catalyst flooding and backing flooding. The cathode impedance spectra of each gas diffusion layer was obtained and compared under the same conditions. The diameter of the capacitive semicircle became larger with increasing current density for both, and this increase was greater for GDL B20 than GDL A5. Catalyst flooding is dominant and backing flooding is negligible when the air flow rate is high and current density is low. An equivalent model was suggested and fitted to the experimental data. Parameters for catalyst flooding and backing flooding were individually obtained. The capacitance of the catalyst layer decreases as the air flow rate decreases when the catalyst flooding is dominant.

Electrochemical catalytic activity for oxygen reduction reaction of nitrogen-doped carbon nanofibers.

The electrocatalytic activity of nitrogen-doped carbon nanofibers (N-CNFs), which are synthesized directly from vaporized acetonitrile over nickel-iron based catalysts, for oxygen reduction reaction (ORR), was investigated. The nitrogen content and specific surface area of N-CNFs can be controlled through the synthesis temperature (300-680 degrees C). The graphitization degree of N-CNFs also are significantly affected by the temperature, whereas the chemical compositions of nitrogen species are similar irrespective of the synthesis conditions. From measurement of the electrochemical double layer capacitance, the surface of N-CNFs is found to have stronger interaction with ions than undoped-carbon surfaces. Although N-CNFs show higher over-potential than Pt catalysts do, N-CNFs were observed to have a noticeable ORR activity, as opposed to the carbon samples without nitrogen doping. The activity dependency of N-CNFs on the content of the nitrogen with which they were doped is discussed, based on the experiment results. The single cell of the direct methanol fuel cell (DMFC) was tested to investigate the performance of a membrane-electrode assembly that includes N-CNFs as the cathode catalyst layer.

Highly sensitive and multiplexed one-step RT-qPCR for profiling genes involved in the circadian rhythm using microparticles.

Given the growing interest in molecular diagnosis, highly extensive and selective detection of genetic targets from a very limited amount of samples is in high demand. We demonstrated the highly sensitive and multiplexed one-step RT-qPCR platform for RNA analysis using microparticles as individual reactors. Those particles are equipped with a controlled release system of thermo-responsive materials, and are able to capture RNA targets inside. The particle-based assay can successfully quantify multiple target RNAs from only 200 pg of total RNA. The assay can also quantify target RNAs from a single cell with the aid of a pre-concentration process. We carried out 8-plex one-step RT-qPCR using tens of microparticles, which allowed extensive mRNA profiling. The circadian cycles were shown by the multiplex one-step RT-qPCR in human cell and human hair follicles. Reliable 24-plex one-step RT-qPCR was developed using a single operation in a PCR chip without any loss of performance (i.e., selectivity and sensitivity), even from a single hair. Many other disease-related transcripts can be monitored using this versatile platform. It can also be used non-invasively for samples obtained in clinics.

An NIR dual-emitting/absorbing inorganic compact pair: A self-calibrating LRET system for homogeneous virus detection.

Many conventional optical biosensing systems use a single responsive signal in the visible light region. This limits their practical applications, as the signal can be readily perturbed by various external environmental factors. Herein, a near-infrared (NIR)-based self-calibrating luminescence resonance energy transfer (LRET) system was developed for background-free detection of analytes in homogeneous sandwich-immunoassays. The inorganic LRET pair was comprised of NIR dual-emitting lanthanide-doped nanoparticles (LnNPs) as donors and NIR-absorbing LnNPs as acceptors, which showed a narrow absorption peak (800 nm) and long-term stability, enabling stable LRET with a built-in self-calibrating signal. Screened single-chain variable fragments (scFvs) were used as target avian influenza virus (AIV)-binding antibodies to increase the LRET efficiency in sandwich-immunoassays. The compact sensor platform successfully detected AIV nucleoproteins with a 0.38 pM limit of detection in buffer solution and 64 clinical samples. Hence, inorganic LnNP pairs may be effective for self-calibrating LRET systems in the background-free NIR region.

The Structural Effect of Electrode Mesh on Hydrogen Evolution Reaction Performance for Alkaline Water Electrolysis.

Alkaline water electrolysis (AWE) is a mature water electrolysis technology that can produce green hydrogen most economically. This is mainly attributed to the use of Ni-based materials that are easy to process and inexpensive. The nickel-based meshes with various structures such as woven mesh and expanded mesh are widely used as electrode in the AWE due to its common availability and easy fabrication. However, the morphological effect of meshes on hydrogen evolution reaction (HER) performance has not been studied. Here a new parameter to determine the structural effect of mesh on HER performance was first proposed. The key factors of the parameter were found to be the strand width, pore width and the strand surface area. The woven mesh with the ratio of pore width to strand width that converges to 1 showed the lowest the overpotential. The expanded mesh with the higher the structural surface area exhibited the lowest the overpotential. This study will help to choose an optimal structure for the mesh with the HER electrode.

Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection.

As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.