The functional divergence of homologous GPAT9 genes contributes to the erucic acid content of Brassica napus seeds.

BACKGROUND: The early allopolyploid Brassica napus was a hybrid of two Brassica species, that had undergone a whole genome duplication event followed by genome restructuring, including deletions and small scale duplications. A large number of homologous genes appeared functional divergence during species domestication. Due to the high conservation of de novo glycerolipid biosynthesis, multiple homologues of glycerol-3-phosphate acyltransferases (GPATs) have been found in B. napus. Moreover, the functional variances among these homologous GPAT-encoding genes are unclear. RESULTS: In this study, four B. napus homologous genes encoding glycerol-3-phosphate acyltransferase 9 (BnaGPAT9) were characterized. Although a bioinformatics analysis indicated high protein sequence similarity, the homologues demonstrated tissue-specific expression patterns and functional divergence. Yeast genetic complementation assays revealed that BnaGPAT9-A1/C1 homologues but not BnaGPAT9-A10/C9 homologues encoded functional GPAT enzymes. Furthermore, a single nucleotide polymorphism of BnaGPAT9-C1 that occurred during the domestication process was associated with enzyme activity and contributed to the fatty acid composition. The seed-specific expression of BnGPAT9-C11124A increased the erucic acid content in the transformant seeds. CONCLUSIONS: This study revealed that BnaGPAT9 gene homologues evolved into functionally divergent forms with important roles in erucic acid biosynthesis.

DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore.

Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.

DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals.

Nanopores have developed into powerful single-molecule sensors capable of identifying and characterizing small polymers, such as DNA, by electrophoretically driving them through a nanoscale pore and monitoring temporary blockades in the ionic pore current. However, the relationship between nanopore signals and the physical properties of DNA remains only partly understood. Herein, we introduce a programmable DNA carrier platform to capture carefully designed DNA nanostructures. Controlled translocation experiments through our glass nanopores allowed us to disentangle this relationship. We vary DNA topology by changing the length, strand duplications, sequence, unpaired nucleotides, and rigidity of the analyte DNA and find that the ionic current drop is mainly determined by the volume and flexibility of the DNA nanostructure in the nanopore. Finally, we use our understanding of the role of DNA topology to discriminate circular single-stranded DNA molecules from linear ones with the same number of nucleotides using the nanopore signal.

Synthesis of NiCo-BNSA/RGO/MDCF with three-dimensional porous network structure as an excellent microwave absorber.

Melamine-derived carbon foam (MDCF) and nickel-cobalt bimetallic nanosheet arrays (NiCo-BNSA) possess unique porous structures and excellent microwave absorption (MA) properties, making them potentially useful in MA applications. In this investigation, we fabricated NiCo-BNSA/reduced graphene oxide/MDCF (NiCo-BNSA/RGO/MDCF) composites utilizing a two-stage synthesis protocol. This process incorporated melamine foam (MF) pretreatment, carbonization, and a subsequent in-situ growth stage, resulting in the creation of a three-dimensional porous network structure. By adjusting the RGO volume, we were able to manipulate the structure and composition of the NiCo-BNSA/RGO/MDCF composites, leading to an enhancement in their MA performance. It was also observed that the NiCo-BNSA was evenly distributed on the surface of both the RGO and MDCF. The composites exhibited an optimal reflection loss (RLmin) of -67.8 dB at a thickness of 2.50 mm, and by varying their thickness, the effective absorption bandwidth (EAB, RL ≤ -10 dB) extended to 9.80 GHz, encompassing the entire C and X bands. This study presents a novel approach for fabricating lightweight and efficient carbon-based MA composites.

Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches.

Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.

Simultaneous identification of viruses and viral variants with programmable DNA nanobait.

Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.

Lego-Like Catalytic Hairpin Assembly Enables Controllable DNA-Oligomer Formation and Spatiotemporal Amplification in Single Molecular Signaling.

While the solid-state nanopore shows increasing potential during sensitive and label-free single molecular analysis, target concentration and signal amplification method is in urgent need. In this article, a solution via designing a model nucleic acid circuit reaction that can produce "Y" shape-structure three-way DNA oligomers with controllable size and polymerization degree is proposed. Such a so-called lego-like three-way catalytic hairpin assembly (LK-3W-CHA) can provide both concentration amplification (via CHA circuit) and programmable size control (via lego-like building mode) to enhance spatiotemporal resolution in single molecular sensing of solid-state nanopore. Oligomers containing 1-4 DNA three-way junctions (Y monomers, Y1-Y4) are designed in proof-of-concept experiments and applications. When the oligomers are applied to direct translocation measurements, Y2-Y4 can significantly increase the signal resolution and stability than that of Y1. Meanwhile, Y1 to Y4 can be used as the tags on the long DNA carrier to provide very legible secondary signals for specific identification, multiple assays, and information storage. Compared with other possible tags, Y1-Y4 provides higher signal density and amplitude, and quasi-linear "inner reference" for each other, which may provide more systematic, reliable, and controllable experimental results.

Parallel DNA circuits by autocatalytic strand displacement and nanopore readout.

DNA nanotechnology provides a unique opportunity for molecular computation, with strand displacement reactions enabling controllable reorganization of nanostructures. Additional DNA strand exchange strategies with high selectivity for input will enable novel complex systems including biosensing applications. Herein, we propose an autocatalytic strand displacement (ACSD) circuit: initiated by DNA breathing and accelerated by a seesaw catalytic reaction, ACSD ensures that only the correct base sequence starts the catalytic cycle. Analogous to an electronic circuit with a variable resistor, two ACSD reactions with different rates are connected in parallel to mimic a parallel circuit containing branches with different resistances. Finally, we introduce a multiplexed nanopore sensing platform to report the output results of a parallel path selection system at the single-molecule level. By combining the ACSD strategy with fast and sensitive single-molecule nanopore readout, a new generation of DNA-based computing tools is established.

DNA-Based Optical Quantification of Ion Transport across Giant Vesicles.

Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.

Binding of the transcription factor MYC2-like to the ABRE of the OsCYP2 promoter enhances salt tolerance in Oryza sativa.

Cyclophilins, a type of peptidyl-prolyl cis-trans isomerase, function as important molecular chaperones in a series of biological processes. However, the expression pattern and signal transduction pathway of cyclophilins are still unclear. Here, we showed that the promoter of OsCYP2 could function as a tissue-specific promoter by GUS staining. Moreover, we found that the promoter sequence contained not only core elements but also inducible elements. Then, the ABA-responsive element was used for cDNA library screening, and the transcription factor MYC2-like was identified by a yeast one-hybrid assay and confirmed through an electrophoretic mobility shift assay. Furthermore, the relative expression showed that MYC2-like was induced by abscisic acid. In addition, MYC2-like overexpression enhanced salt tolerance in transformants and partially restored the cyp2-RNAi line. In summary, we explored a novel transcriptional signal mediated by MYC2-like, a potential regulator of salt stress-related physiological processes in rice.

Dual-ZIF-derived "reassembling strategy" to hollow MnCoS nanospheres for aqueous asymmetric supercapacitors.

Construction of delicate nanostructures with a facile, mild-condition and economical method is a key issue for building high-performance electrode materials. We demonstrate a facile and novel "reassembling strategy" to hollow MnCoS nanospheres derived from dual-ZIF for supercapacitors. The spherical shell's surface structure, thickness and Mn distribution were controlled by regulating the solvothermal reaction time. The chemical composition, phases, specific surface areas and microstructure were studied and the electrochemical performances were systematically estimated. As the unique low-crystalline and optimized hollow nanosphere structure contributes to increasing active sites, MnCoS nanospheres exhibit excellent electrochemical performance. The test results show that the specific capacitance increases with increasing solvothermal time, and the MCS with a 5 h reaction time exhibits optimal electrochemical properties with a high specific capacity of 957 C g-1 (1 A g-1). Furthermore, an MCS-5//AC asymmetric supercapacitor device delivers a specific energy as high as 36.9 W h kg-1 at a specific power of 750 W kg-1.

Identification of GmGPATs and their effect on glycerolipid biosynthesis through seed-specific expression in soybean.

BACKGROUND: Genetic improvement of soybean oil content depends on in-depth study of the glycerolipid biosynthesis pathway. The first acylation reaction catalysed by glycerol-3-phosphate acyltransferase (GPAT) is the rate-limiting step of triacylglycerol biosynthesis. However, the genes encoding GPATs in soybean remain unknown. METHODS: We used a novel yeast genetic complementation system and seed-specific heterologous expression to identify GmGPAT activity and molecular function in glycerolipid biosynthesis. RESULTS: Sixteen GmGPAT genes were cloned by reverse transcription-PCR for screening in yeast genetic complementation. The results showed that GmGPAT9-2 could restore the conditional lethal double knockout mutant strain ZAFU1, and GmGPAT1-1 exhibited low acyltransferase activity in serial dilution assays. In addition, the spatiotemporal expression pattern of GmGPAT9-2 exhibited tissue specificity in leaves, flowers and seeds at different developmental stages. Furthermore, both the proportion of arachidic acid and erucic acid were significantly elevated in Arabidopsis thaliana transgenic lines containing the seed-specific GmGPAT9-2 compared wild type, but the oil content was not affected. CONCLUSION: Together, our results provide reference data for future engineering of triacylglycerol biosynthesis and fatty acid composition improvement through GPATs in soybean.

Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids.

Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.

Lifetime of glass nanopores in a PDMS chip for single-molecule sensing.

Nanopore sensing is an emerging technology that has many biosensing applications ranging from DNA sequencing using biological pores to biomolecular analysis using solid-state pores. Solid-state nanopores that are more stable are an attractive choice for biosensing applications. Still, biomolecule interactions with the nanopore surface reduce nanopore stability and increase usage costs. In this study, we investigated the biosensing capability for 102 quartz glass nanopores with a diameter of 11-18 nm that were fabricated using laser-assisted capillary pulling. Nanopores were assembled into multiple microfluidic chips that were repeatedly used for up to 19 weeks. We find that using vacuum storage combined with minimal washing steps improved the number of use cycles for nanopores. The single-molecule biosensing capability over repeated use cycles was demonstrated by quantitative analysis of a DNA carrier designed for detection of short single-stranded DNA oligonucleotides.

In-situ synthesis of graphite carbon nitride nanotubes/Cobalt@Carbon with castor-fruit-like structure as high-efficiency electromagnetic wave absorbers.

The increasingly electromagnetic wave (EMW) pollution has rendered the study and development of new, high-efficiency EMW absorbers a sought-after topic. In this study, graphite carbon nitride nanotubes/cobalt@carbon (GCNNs/Co@C) composites were fabricated using an in-situ synthesis method, which included facile grinding and carbonization pyrolysis. The synthesized GCNNs/Co@C composites exhibited a unique castor-fruit-like structure, that is, GCNNs formed an entwined three-dimensional (3D) network structure on the surface of cobalt@carbon (Co@C), which improved the EMW absorption properties of composites. The obtained GCNNs/Co@C composites exhibited excellent EMW absorption performance. For the fabricated GCNNs/Co@C composites, the minimum reflection loss (RLmin) value reached -63.90 dB at a thickness of 1.96 mm, and the effective absorption bandwidth (EAB, RL ≤  -10 dB) achieved 4.44 GHz at an ultra-thin thickness of 1.51 mm. The EAB covered the entire X and Ku bands (6.96-18.00 GHz) through thickness adjustment from 1.51 to 2.50 mm. Underlying EMW absorption mechanisms were briefly discussed. This study presents a novel design method to prepare light-weight and highly-efficient EMW absorbing absorbers.

In-situ hydrothermal synthesis of NiCo alloy particles@hydrophilic carbon cloth to construct corncob-like heterostructure for high-performance electromagnetic wave absorbers.

NiCo alloy particles (NiCo-APs)@hydrophilic carbon cloth (HCC) composites were successfully prepared by uniformly decorating magnetic NiCo-APs on the surface of three-dimensional HCC by employing an in-situ hydrothermal method. The NiCo-APs@HCC composites exhibited a unique corncob-like network structure that helped improve the electromagnetic wave (EMW) absorption performance of composites. The EMW absorption properties of the composites could be controlled by altering the Ni/Co molar ratio. The optimal minimum reflection loss (RLmin) of -41.80 dB was achieved with the NiCo-APs@HCC composite thickness of 2.29 mm. The effective absorption bandwidth (EAB) reached the maximum of 5.8 GHz, spanning nearly the entire Ku band. In addition, the improved EMW absorption performance was further promoted by favorable impedance matching, strong conduction loss, magnetic loss, dipole polarization, interface polarization, multiple reflections, and scattering. A novel strategy for designing magnetic metal/carbon matrix composites with excellent EMW absorption performance is reported in this study.

Gas Dispersion Characteristics in a Novel Jet-Stirring Coupling Flotation Device.

A jet-stirring coupling flotation device (JSCFD) was proposed to analyze the distribution characteristics of gas holdup and bubble Sauter mean diameter (D 32) in a gas-liquid system under various parameters. Results of studies suggested that the gas holdup increased with methyl isobutyl carbinol concentration, feeding pressure, and gas flow rate. The maximal gas holdup in the absence of the stirring impeller was ∼23.29% for the bubble size of 0.59 mm, which was considerably lower than the maximum gas holdup of 66.27% for the bubble size of 0.31 mm in the presence of the stirring impeller; the gas holdup was raised by ∼43% due to the bubbles torn by the stirring impeller to generate extensive smaller size bubbles and increase the content of small bubbles, and increasing the stirring impeller speed was conducive to reduce the bubble size and increase the gas holdup in JSCFD. Compared to traditional flotation machines, the size of bubbles generated by JSCFD was smaller, and the gas holdup distribution conforms to the following order: JSCFD > mechanical flotation machine > column flotation, which demonstrated that the JSCFD had a noticeable effect on increasing the gas holdup and reducing the bubble size.

Constructing interpenetrating structured NiCo2O4/HCNT composites with heterogeneous interfaces as low-thickness microwave absorber.

Low matching thickness, broad effective absorption bandwidth (EAB, RL < -10 dB) and excellent reflection loss (RL) are desirable properties for the advanced microwave absorption materials (MAMs). We synthesized novel interpenetrating structured rod-like nickel cobaltite (NiCo2O4)/helical carbon nanotubes (HCNT) composites using the facile hydrothermal technique and heat-treatment process. Owing to the optimum structural design and electromagnetic parameter regulation, the NiCo2O4/HCNT composites displayed outstanding microwave absorption (MA) across regions of low thickness. When the thickness was only 1.35 mm, the optimized RL and EAB reached -55.9 dB and 4.8 GHz (13.2-18.0 GHz), respectively. Furthermore, the EAB was 10 GHz as the corresponding thickness was regulated with 1.35-2.10 mm, covering both X and the Ku bands. Multiple reflection and scattering, natural resonance, eddy current loss, strong conduction loss, interface polarization, cross-poalarization, and dipolar polarization can be considered to improve MA. Our study proposes a simple approach of synthesizing low-thickness MAMs based on NiCo2O4 and HCNT.

FeII 4L4 tetrahedron binds and aggregates DNA G-quadruplexes.

Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biological processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA-cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5' end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, circular dichroism and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease.

Preparation of Mesoporous Biochar from Cornstalk for the Chromium (VI) Elimination by Using One-Step Hydrothermal Carbonation.

Hydrothermal carbon (HTC) was prepared by the one-step hydrothermal method for Cr (VI) removal from wastewater, which was considered a "green chemistry" method. The specific surface area (SBET) of HTC was 85 m2/g with the pore size in range of 2.0-24.0 nm. FT-IR spectra analysis showed that the HTC had abundant chemical surface functional groups. The influence of adsorption parameters such as pH, HTC dosage, Cr (VI) concentration, and contact time on the removal efficiency of Cr (VI) had been investigated. When the initial concentration was 50 mg/L, pH = 6, amount of adsorbent was 0.2 g/50 ml, and adsorption time was 90 min; the Cr (VI) absorbed rate of HTC reached 98%. Batch adsorption experiments indicated that Cr (VI) adsorption data of HTC fitted the Freundlich isothermal and pseudo-second-order kinetic models. Overall, our findings provide a promising material in treatment of Cr (VI)-rich wastewater and give a clear picture of its application, which is worthy of further study.