Genome-wide association analysis and transgenic characterization for amylose content regulating gene in tuber of Dioscorea zingiberensis.

BACKGROUND: Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients' diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation. RESULTS: To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele. CONCLUSIONS: Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes.

Freshness Identification of Oysters Based on Colorimetric Sensor Array Combined with Image Processing and Visible Near-Infrared Spectroscopy.

Volatile organic compounds (VOCs) could be used as an indicator of the freshness of oysters. However, traditional characterization methods for VOCs have some disadvantages, such as having a high instrument cost, cumbersome pretreatment, and being time consuming. In this work, a fast and non-destructive method based on colorimetric sensor array (CSA) and visible near-infrared spectroscopy (VNIRS) was established to identify the freshness of oysters. Firstly, four color-sensitive dyes, which were sensitive to VOCs of oysters, were selected, and they were printed on a silica gel plate to obtain a CSA. Secondly, a charge coupled device (CCD) camera was used to obtain the "before" and "after" image of CSA. Thirdly, VNIS system obtained the reflected spectrum data of the CSA, which can not only obtain the color change information before and after the reaction of the CSA with the VOCs of oysters, but also reflect the changes in the internal structure of color-sensitive materials after the reaction of oysters' VOCs. The pattern recognition results of VNIS data showed that the fresh oysters and stale oysters could be separated directly from the principal component analysis (PCA) score plot, and linear discriminant analysis (LDA) model based on variables selection methods could obtain a good performance for the freshness detection of oysters, and the recognition rate of the calibration set was 100%, while the recognition rate of the prediction set was 97.22%. The result demonstrated that the CSA, combined with VNIRS, showed great potential for VOCS measurement, and this research result provided a fast and nondestructive identification method for the freshness identification of oysters.

Quantum Dot Nanobeads as Multicolor Labels for Simultaneous Multiplex Immunochromatographic Detection of Four Nitrofuran Metabolites in Aquatic Products.

A multicolor immunochromatographic assay platform based on quantum dot nanobeads (QBs) for the rapid and simultaneous detection of nitrofuran metabolites in different aquatic products is documented. These metabolites include 3-amino-2-oxazolidinone (AOZ), 1-aminohydantoin (AHD), semicarbazide (SEM), and 3-amino-5-morpholino-methyl-1,3-oxazolidinone (AMOZ). QBs with emission colors of red, yellow, green, and orange were employed and functionalized with the corresponding antibodies to each analyte to develop a multicolor channel. The visual detection limits (cutoff values) of our method for AOZ, AHD, SEM, and AMOZ reached up to 50 ng/mL, which were 2, 20, 20, and 20 times lower than those of traditional colloidal gold test strips, respectively. The test strip is capable of detection within 10 min in real samples while still achieving good stability and specificity. These results demonstrate that the developed multicolor immunochromatographic assay platform is a promising technique for multiplex, highly sensitive, and on-site detection of nitrofuran metabolites.

Silicon-photonics multi-wavelength common-gain tunable laser providing both source and pump for an amplified transceiver.

We propose and demonstrate a silicon-photonics-based laser that outputs multiple independently tunable wavelengths using a single InP gain element. We use it to generate a C-band tunable source for a coherent transceiver and simultaneously a 1480-nm source to pump an Er-doped fiber amplifier on the transmitter output.

Silicon-photonic laser emitting tunable dual wavelengths with highly correlated phase noise.

A silicon-photonic tunable laser emitting two tunable wavelengths simultaneously is demonstrated. The laser consists of a single semiconductor optical amplifier that provides shared gain and a silicon-photonic chip that provides wavelength selections. A total optical power of 29.3 mW is shown, with 300 mA of gain current at 40°C. Continuous tuning of frequency spacing from 69.5 GHz to 114.1 GHz is demonstrated. The two simultaneous laser channels show highly correlated phase noise, with a phase noise correlation coefficient of 90.7%.

Hydrolytically Stable and Trifunctional Zirconium-Based Organic Frameworks toward Cr2O72- Detection, Capture, and Photoreduction.

Chromium Cr(VI) is frequently used in many fields and has been intensively researched for detection and/or removal from contaminated water. However, the existing approaches are still of low efficiency, high cost, and cumbersome in operation. It is thus highly imperative to hunt for alternative avenues to get out of the predicament. In this work, two bcu topological and highly stable zirconium-metal-organic frameworks (Zr-MOFs) of 1 and 2 have been deliberately prepared, displaying channel-type interior spaces replete with free bipyridine/biquinoline matrices and Zr-O defect sites. Because of their unique intrinsic features of high porosity and photosensitivity, 1 and 2 were deployed as versatile platforms to sense, adsorb, and catalytically reduce Cr(VI) ions. Indeed, the Zr-MOF of 1 performs excellently in fluorescence sensing and adsorption trapping of Cr(VI), with an ultralow detection limit of 0.0176 ppm and a fairly high saturated adsorption capacity of 145.77 mg/g, while 2 is more powerful than 1 in photochemical removal of Cr(VI), exhibiting a remarkable reduction efficiency of 98.05% just within 70 min and still up to 92.21% even after five consecutive photocatalytic cycles. Furthermore, possible photoluminescence, quenching, and reduction mechanisms were also tentatively proposed. This study may open up a new avenue for addressing some unresolved environmental issues, that is, the decontamination of highly toxic Cr(VI) from water.

Low-chirp push-pull dual-ring modulator with 144 Gb/s PAM-4 data transmission.

We experimentally demonstrate a low-chirp high-speed push-pull dual-ring modulator. The device is formed by two parallel cascaded add-drop ring modulators which has a Fabry-Perot resonance spectrally similar as electromagnetically induced transparency (EIT) effect. Differential drive signals are applied to the two rings to shift the individual resonances towards opposite directions, creating intensity modulation with suppressed frequency chirp. We present static and dynamic characterization of the device, including chirp parameter. We also demonstrate 144 Gb/s PAM-4 data transmission with 1-km standard single-mode fiber (SSMF) with BER below hard-decision forward error correction (HD-FEC) threshold with 7% overhead.

In vitro and in vivo evaluation of chitosan scaffolds combined with simvastatin-loaded nanoparticles for guided bone regeneration.

The objective of this study was to fabricate and characterize chitosan combined with different amounts of simvastatin-loaded nanoparticles and to investigate their potential for guided bone regeneration in vitro and in vivo. Different SIM-CSN formulations were combined into a chitosan scaffold (SIM-CSNs-S), and the morphology, simvastatin release profile, and effect on cell proliferation and differentiation were investigated. For in vivo experiments, ectopic osteogenesis and the critical-size cranial defect model in SD rats were chosen to evaluate bone regeneration potential. All three SIM-CSNs-S formulations had a porous structure and exhibited sustained simvastatin release. CSNs-S showed excellent degradation and biocompatibility characteristics. The 4 mg SIM-CSNs-S formulation stimulated higher BMSC ALP activity levels, demonstrated significantly earlier collagen enhancement, and led to faster bone regeneration than the other formulations. SIM-CSNs-S should have a significant effect on bone regeneration.

Rapidly reconfigurable high-fidelity optical arbitrary waveform generation in heterogeneous photonic integrated circuits.

This paper demonstrates rapidly reconfigurable, high-fidelity optical arbitrary waveform generation (OAWG) in a heterogeneous photonic integrated circuit (PIC). The heterogeneous PIC combines advantages of high-speed indium phosphide (InP) modulators and low-loss, high-contrast silicon nitride (Si3N4) arrayed waveguide gratings (AWGs) so that high-fidelity optical waveform syntheses with rapid waveform updates are possible. The generated optical waveforms spanned a 160 GHz spectral bandwidth starting from an optical frequency comb consisting of eight comb lines separated by 20 GHz channel spacing. The Error Vector Magnitude (EVM) values of the generated waveforms were approximately 16.4%. The OAWG module can rapidly and arbitrarily reconfigure waveforms upon every pulse arriving at 2 ns repetition time. The result of this work indicates the feasibility of truly dynamic optical arbitrary waveform generation where the reconfiguration rate or the modulator bandwidth must exceed the channel spacing of the AWG and the optical frequency comb.

Environmentally Benign, Rapid, and Selective Extraction of Gold from Ores and Waste Electronic Materials.

The extraction of gold from ores and electronic waste is an important topic worldwide, as this precious metal has immense value in a variety of fields. However, serious environmental pollution and high energy consumption due to the use of toxic oxidation reagents and harsh reaction conditions is a well-known problem in the gold industry. Herein, we report a new chemical method based on the combined use of N-bromosuccinimide (NBS) and pyridine (Py), which has a greatly decreased environmental impact and reagent cost, as well as mild reaction requirements. This method can directly leach Au0 from gold ore and electronic waste to form AuIII in water. The process is achieved in a yield of approximately 90 % at room temperature and a nearly neutral pH. The minimum dose of NBS/Py is as low as 10 mm, which exhibits low toxicity towards mammalian cells and animals as well as aquatic creatures. The high leaching selectivity of Au over other metals during gold leaching is demonstrated, showing that this method has great potential for practical industrial application towards the sustainable refining of gold from ores and electronic waste.

Low-loss compact multilayer silicon nitride platform for 3D photonic integrated circuits.

We design, fabricate, and demonstrate a silicon nitride (Si(3)N(4)) multilayer platform optimized for low-loss and compact multilayer photonic integrated circuits. The designed platform, with 200 nm thick waveguide core and 700 nm interlayer gap, is compatible for active thermal tuning and applicable to realizing compact photonic devices such as arrayed waveguide gratings (AWGs). We achieve ultra-low loss vertical couplers with 0.01 dB coupling loss, multilayer crossing loss of 0.167 dB at 90° crossing angle, 50 µm bending radius, 100 × 2 µm(2) footprint, lateral misalignment tolerance up to 400 nm, and less than -52 dB interlayer crosstalk at 1550 nm wavelength. Based on the designed platform, we demonstrate a 27 × 32 × 2 multilayer star coupler.

Athermal silicon ring resonators clad with titanium dioxide for 1.3µm wavelength operation.

We investigate the athermal characteristics of silicon waveguides clad with TiO(2) designed for 1.3 µm wavelength operation. Using CMOS-compatible fabrication processes, we realize and experimentally demonstrate silicon photonic ring resonators with resonant wavelengths that vary by less than 6 pm/°C at 1.3 µm. The measured ring resonance wavelengths across the 20-50°C temperature range show nearly complete cancellation of the first-order thermo-optical effects and exhibit second-order thermo-optical effects expected from the combination of TiO(2) and Si.

All-fiber mode-group-selective photonic lantern using graded-index multimode fibers.

We demonstrate the first all-fiber mode-group-selective photonic lantern using multimode graded-index fibers. Mode selectivity for mode groups LP(01), LP(11) and LP(21)+LP(02) is 20-dB, 10-dB and 7-dB respectively. The insertion loss when butt coupled to multimode graded-index fiber is below 0.6-dB. The use of the multimode graded-index fibers in the taper can significantly reduce the adiabaticity requirement.

Free-space coherent optical communication with orbital angular, momentum multiplexing/demultiplexing using a hybrid 3D photonic integrated circuit.

We demonstrate free-space space-division-multiplexing (SDM) with 15 orbital angular momentum (OAM) states using a three-dimensional (3D) photonic integrated circuit (PIC). The hybrid device consists of a silica planar lightwave circuit (PLC) coupled to a 3D waveguide circuit to multiplex/demultiplex OAM states. The low excess loss hybrid device is used in individual and two simultaneous OAM states multiplexing and demultiplexing link experiments with a 20 Gb/s, 1.67 b/s/Hz quadrature phase shift keyed (QPSK) signal, which shows error-free performance for 379,960 tested bits for all OAM states.

CMOS-compatible, athermal silicon ring modulators clad with titanium dioxide.

We present the design, fabrication and characterization of athermal nano-photonic silicon ring modulators. The athermalization method employs compensation of the silicon core thermo-optic contribution with that from the amorphous titanium dioxide (a-TiO(2)) overcladding with a negative thermo-optic coefficient. We developed a new CMOS-compatible fabrication process involving low temperature RF magnetron sputtering of high-density and low-loss a-TiO(2) that can withstand subsequent elevated-temperature CMOS processes. Silicon ring resonators with 275 nm wide rib waveguide clad with a-TiO(2) showed near complete athermalization and moderate optical losses. Small-signal testing of the micro-resonator modulators showed high extinction ratio and gigahertz bandwidth.

Oxydextran-based photodynamic antibacterial nanoplatform with broad-Spectrum antibacterial activity.

The compounding of polysaccharide macromolecules and antibacterial agents always has been the preferred strategy to prepare antibacterial products, attracting increasing interest. Herein, a novel acid-responsive oxidized dextran-based nanoplatform (OTP NP) has been fabricated for photodynamic antibacterial therapy by combing photosensitizer monoaminoporphyrin (TPP-NH2) with oxidized dextran (ODex) via the Schiff Base reaction. OTP NP of about 100 nm is composed of an inner hydrophobic core of 30 nm and peripheral polysaccharide macromolecules. The OTP NP killed 99.9 % of E. coli and S. aureus within 1.5 light cycles at a concentration of 200 µg/mL. Concurrently, OTP NP exhibited excellent cytocompatibility at a concentration of 1 mg/mL (about 5 folds bactericidal concentration). Particularly, except for the recognized antibacterial mechanism of photodynamic therapy, a novel mechanism of bacterial membrane damage was discovered: the bacterial cell membrane was peeled off and formed spherical particles that aggregated around the bacteria to accelerate bacterial apoptosis under the combined action of ROS and nanomaterials. Moreover, the slightly soluble drug levofloxacin (Lev) as a model drug was loaded into OTP NP to test its carrier function, providing a practicable strategy to design multifunctional polysaccharide-based photodynamic antibacterial materials.

Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation.

Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. In this study, we found that the previously identified PWWP-EPCR-ARID-TRB (PEAT) complex components interact with both the ubiquitin-specific protease UBP5 and the redundant histone acetyltransferases HAM1 and HAM2 (HAM1/2) to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. HAM1/2 are shared subunits of the PEAT complex and the conserved NuA4 histone acetyltransferase complex, and are responsible for histone H4K5 acetylation. Within the PEAT complex, the PWWP components (PWWP1, PWWP2, and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. Collectively, our study not only identifies dual roles of the PEAT complex in H2A deubiquitination and H4K5 acetylation but also illustrates how these processes collaborate at the whole-genome level to regulate the transcription and development in plants.

Rapid and complete hitless defragmentation method using a coherent RX LO with fast wavelength tracking in elastic optical networks.

This paper demonstrates a rapid and full hitless defragmentation method in elastic optical networks exploiting a new technique for fast wavelength tracking in coherent receivers. This technique can be applied to a single-carrier connection or each of the subcarriers forming a super-channel. A proof-of-concept demonstration shows hitless defragmentation of a 10 Gb/s QPSK single-carrier connection from 1547.75 nm to 1550.1 nm in less than 1 µs. This was obtained using a small (0.625 kB) link-layer transmitter buffer without the need for any additional transponder. We also demonstrated that the proposed defragmentation technique is capable of hopping over an existing connection, i.e. 10 Gb/s OOK at 1548.5 nm, without causing any degradation of its real-time Bit Error Rate (BER) value. The proposed scheme gives advantages in terms of overall network blocking probability reduction up to a factor of 40.

Full-field technique for measuring the spectral evolution of reconfigurable photonic filters.

This Letter demonstrates a measurement technique based on frequency-to-time mapping and coherent detection, which enables the complete (i.e., amplitude and phase) characterization of dynamically reconfigurable photonic filters. We apply this technique to a unit cell from a silicon CMOS-compatible photonic lattice filter that has a rapidly changing transfer function with an 8.33 ns update time, 120 MHz spectral resolution, and 12 GHz bandwidth. These dynamic measurements allow characterization of transients, thermal effects, filter fidelity, and other time-dependent phenomena during switching.

A dicyanoisophorone-based fluorescent probe for hypochlorite with a fast response and its applications in bioimaging.

One kind of phenolic substituted dicyanoisophorone derivative (Is-OL) has been designed and successfully synthesized for the detection of hypochlorite in water samples, test strips and living HeLa cells. The probe Is-OL showed high sensitivity and selectivity to hypochlorite over other competitive ROS and metal ions. Moreover, Is-OL can react instantaneously with hypochlorite (<5 s) while exhibiting a significant color change from yellow to colorless, which makes "naked-eye" detection possible with a low detection limit (0.095 µM). The results based on water tests and living HeLa cell experiments showed that Is-OL could be applied as a potential candidate for the detection of hypochlorite.