Comparison of Depth-Specific Prediction of Soil Properties: MIR vs. Vis-NIR Spectroscopy.

The prediction of soil properties at different depths is an important research topic for promoting the conservation of black soils and the development of precision agriculture. Mid-infrared spectroscopy (MIR, 2500-25000 nm) has shown great potential in predicting soil properties. This study aimed to explore the ability of MIR to predict soil organic matter (OM) and total nitrogen (TN) at five different depths with the calibration from the whole depth (0-100 cm) or the shallow layers (0-40 cm) and compare its performance with visible and near-infrared spectroscopy (vis-NIR, 350-2500 nm). A total of 90 soil samples containing 450 subsamples (0-10 cm, 10-20 cm, 20-40 cm, 40-70 cm, and 70-100 cm depths) and their corresponding MIR and vis-NIR spectra were collected from a field of black soil in Northeast China. Multivariate adaptive regression splines (MARS) were used to build prediction models. The results showed that prediction models based on MIR (OM: RMSEp = 1.07-3.82 g/kg, RPD = 1.10-5.80; TN: RMSEp = 0.11-0.15 g/kg, RPD = 1.70-4.39) outperformed those based on vis-NIR (OM: RMSEp = 1.75-8.95 g/kg, RPD = 0.50-3.61; TN: RMSEp = 0.12-0.27 g/kg; RPD = 1.00-3.11) because of the higher number of characteristic bands. Prediction models based on the whole depth calibration (OM: RMSEp = 1.09-2.97 g/kg, RPD = 2.13-5.80; TN: RMSEp = 0.08-0.19 g/kg, RPD = 1.86-4.39) outperformed those based on the shallow layers (OM: RMSEp = 1.07-8.95 g/kg, RPD = 0.50-3.93; TN: RMSEp = 0.11-0.27 g/kg, RPD = 1.00-2.24) because the soil sample data of the whole depth had a larger and more representative sample size and a wider distribution. However, prediction models based on the whole depth calibration might provide lower accuracy in some shallow layers. Accordingly, it is suggested that the methods pertaining to soil property prediction based on the spectral library should be considered in future studies for an optimal approach to predicting soil properties at specific depths. This study verified the superiority of MIR for soil property prediction at specific depths and confirmed the advantage of modeling with the whole depth calibration, pointing out a possible optimal approach and providing a reference for predicting soil properties at specific depths.

Controlling of spatial modes in multi-mode photonic crystal nanobeam cavity.

We numerically and experimentally present the characteristics of disturbed spatial modes (air mode and dielectric mode) in multi-mode photonic crystal nanobeam cavity (PCNC) in the mid-infrared wavelength range. The results show that the resonance wavelength of the spatial modes can be controlled by modifying the size, period and position of the central periodical mirrors in PCNC, achieving better utilization of the spectrum resource. Additionally, side coupling characteristics of PCNC supporting both air and dielectric modes are investigated for the first time. This work serves as a proof of design method that the spatial modes can be controlled flexibly in PCNC, paving the way to achieve integrated multi-function devices in a limited spectrum range.

Thermo-optically tunable slot waveguide-based dual mode-splitting resonators with enhanced sharp lineshapes.

Slot waveguide plays an essential role in achieving high-performance on-chip photonic sensors and nonlinear devices. Ideally, slot waveguide features a large evanescent field ratio and strong electric field intensity in the slot, leading to a high waveguide sensitivity. Unfortunately, the microring resonator (MRR) based on the slot waveguide suffers the less steep spectral slope due to the low quality factor induced by the huge optical propagation loss of the slot waveguide. In this work, a novel dual mode-splitting resonator based on the slot waveguide is proposed and demonstrated to steepen the slope of lineshapes. The device is implemented by two racetrack resonators based on a slot waveguide and a feedback waveguide to introduce coherent optical mode interference, which could induce mode-splitting resonance (MR) with sharp asymmetry line shape and large extinction ratio (ER). The proposed device is fabricated by the standard complementary metal-oxide-semiconductor (CMOS) technologies on silicon-on-insulator (SOI) platform, and the characterization results show dual MRs with an ER of 45.0 dB and a slope rate (SR) of 58.3 dB/nm, exhibiting a much steeper lineshape than that of the conventional MRR with slot waveguide. And the resonance can be tuned efficiently by applying various voltages of the TiN microheater. Investigations in dual MRs devices promote many potential applications in the field of optical switching, optical modulating, and on-chip optical sensing.

Microring resonator based on polarization multiplexing for simultaneous sensing of refractive index and temperature on silicon platform.

Silicon photonic integrated sensors based on microring resonators are a promising candidate to achieve high-performance on-chip sensing. In this work, a novel dual-parameters sensor based on polarization multiplexing on silicon-on-insulator (SOI) platform is proposed and demonstrated experimentally, simultaneously achieving refractive index (RI) and temperature sensing with high sensitivity and large detection range (DR). The experimental results show that the RI sensitivity and temperature sensitivity of the TM-operated sensor are 489.3 nm/RIU and 20.0 pm/°C, respectively, and that of the TE-operated sensor are 102.6 nm/RIU and 43.3 pm/°C, respectively. Moreover, the DR of the fabricated sensor is 0.0296 RIU, which is 4.2 times that of the conventional TM-operated sensor based on the microring resonator. The dual-parameters sensor based on polarization multiplexing can successfully realize the simultaneous measurement of the RI and the temperature, showing potential applications of silicon photonic on-chip sensors in reality.

Multi-omics analysis reveals the mechanism of seed coat color formation in Brassica rapa L.

KEYMESSAGE: Multi-omics analysis of the transcriptome, metabolome and genome identified major and minor loci and candidate genes for seed coat color and explored the mechanism of flavonoid metabolites biosynthesis in Brassica rapa. Yellow seed trait is considered an agronomically desirable trait with great potential for improving seed quality of Brassica crops. Mechanisms of the yellow seed trait are complex and not well understood. In this study, we performed an integrated metabolome, transcriptome and genome-wide association study (GWAS) on different B. rapa varieties to explore the mechanisms underlying the seed coat color formation. A total of 2,499 differentially expressed genes and 116 differential metabolites between yellow and black seeds with strong association with the flavonoid biosynthesis pathway was identified. In addition, 330 hub genes involved in the seed coat color formation, and the most significantly differential flavonoids biosynthesis were detected based on weighted gene co-expression network analysis. Metabolite GWAS analysis using the contents of 42 flavonoids in developing seeds of 159 B. rapa lines resulted in the identification of 1,626 quantitative trait nucleotides (QTNs) and 37 chromosomal intervals, including one major locus on chromosome A09. A combination of QTNs detection, transcriptome and functional analyses led to the identification of 241 candidate genes that were associated with different flavonoid metabolites. The flavonoid biosynthesis pathway in B. rapa was assembled based on the identified flavonoid metabolites and candidate genes. Furthermore, BrMYB111 members (BraA09g004490.3C and BraA06g034790.3C) involved in the biosynthesis of taxifolin were functionally analyzed in vitro. Our findings lay a foundation and provide a reference for systematically investigating the mechanism of seed coat color in B. rapa and in the other plants.

Genome-wide identification of U-box genes and protein ubiquitination under PEG-induced drought stress in potato.

Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U-box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water-deficit stress in Arabidopsis and rice. U-box gene family and large-scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U-box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG-induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up-regulated. The ubiquitination modification in potato protein was enhanced under PEG-induced drought stress, and U-box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG-induced drought stress and the ubiquitination modification involved in potato U-box genes in response to PEG-induced drought stress.

TET1 mutations as a predictive biomarker for immune checkpoint inhibitors in colon adenocarcinoma.

BACKGROUND: The ten-eleven translocation 1 (TET1), which is essential for active DNA demethylation, plays a multifaceted role in the pathogenesis of colorectal cancer. The study has demonstrated the association of TET1 mutations with a high response to immune checkpoint inhibitors (ICIs) in diverse cancers. However, the relationship between TET1 mutations and the response to ICIs in colon cancer is still lacking. METHODS: The prognosis, predictive markers, immune characteristics, mutation number of DNA damage repair (DDR) pathways, pathway enrichment, and drug sensitivity conditions were all compared between TET1-mutated and wild-type patients with colon adenocarcinoma (COAD). RESULTS: The overall survival of patients with TET1 mutations in the ICI-treated cohort was significantly longer than those without (p = 0.0059). Compared with the wild-type patients, TET1-mutated patients had higher tumor mutational burden and neoantigen load, enhanced abundance of tumor-infiltrating immune cells, increased expression of immune-related genes, and mutation number of DDR pathways. Additionally, the patients with TET1 mutations were found to be more sensitive to lapatinib and 5-fluorouracil. CONCLUSION: These findings suggest that TET1 mutations may serve as a potential biomarker for the response to ICIs in COAD patients.

Low-loss silicon nitride strip-slot mode converter based on MMI.

Slot waveguide has attracted a lot of attention due to its ability to confine light in the low refractive index region, while strip waveguide acts as the basic component of guiding light due to its relatively low optical loss. In the multifunctional photonic integrated chips, it is critical to achieve the low loss transition between the strip waveguide and the slot waveguide. In this work, a silicon nitride strip-slot mode converter with high efficiency, large bandwidth, and large fabrication tolerance are proposed and demonstrated through the numerical investigation and experiments. The coupling efficiency of the mode converter is up to - 0.1 dB (97.7%), which enables the extremely low transition loss between the strip waveguide and the slot waveguide. Moreover, the fabrication process of silicon nitride photonic devices with high performance is introduced, which is fully compatible with the CMOS technology. Photonic devices based on silicon nitride with the characteristics of the low optical loss and the temperature insensitivity represent a new paradigm in realizing silicon-based photonic multifunctional chips.

Wide-range, ultra-compact, and high-sensitivity ring resonator biochemical sensor with CMOS-compatible hybrid plasmonic waveguide.

A ring resonator-based biochemistry sensor with a wide range, ultra-compact footprint, and high sensitivity is proposed, which utilizes a suspended slot hybrid plasmonic (SSHP) waveguide. The waveguide consists of a suspended Si nanowire separated from a Cu metal surface by a nanoscale air gap. The hybridization of fundamental mode of a Si channel waveguide with the surface plasmon polariton (SPP) mode of Cu-Si interface achieves a strong light confinement, high waveguide sensitivity (Sw), and low optical loss, showing a great potential in integrated optical sensor. The sensitivity, the detection limit and the detection range of the SSHP waveguide-based biochemistry sensor with a miniaturized radius of 1 µm are numerically demonstrated as 458.1 nm/RIU, 3.7 × 10-5 RIU and 0.225 RIU, respectively. These superior performances as well as the fully CMOS compatibility enable the integrated optical sensing applications.

Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea.

The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism.

Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress.

BACKGROUND: Diacylglycerol kinases (DGKs) are signaling enzymes that play pivotal roles in response to abiotic and biotic stresses by phosphorylating diacylglycerol (DAG) to form phosphatidic acid (PA). However, no comprehensive analysis of the DGK gene family had previously been reported in B. napus and its diploid progenitors (B. rapa and B. oleracea). RESULTS: In present study, we identified 21, 10, and 11 DGK genes from B. napus, B. rapa, and B. oleracea, respectively, which all contained conserved catalytic domain and were further divided into three clusters. Molecular evolutionary analysis showed that speciation and whole-genome triplication (WGT) was critical for the divergence of duplicated DGK genes. RNA-seq transcriptome data revealed that, with the exception of BnaDGK4 and BnaDGK6, BnaDGK genes have divergent expression patterns in most tissues. Furthermore, some DGK genes were upregulated or downregulated in response to hormone treatment and metal ion (arsenic and cadmium) stress. Quantitative real-time PCR analysis revealed that different BnaDGK genes contribute to seed oil content. CONCLUSIONS: Together, our results indicate that DGK genes have diverse roles in plant growth and development, hormone response, and metal ion stress, and in determining seed oil content, and lay a foundation for further elucidating the roles of DGKs in Brassica species.

Modeling and design of a coupled PhC slab sensor for simultaneous detection of refractive index and temperature with strong anti-interference ability.

In this paper, we propose a coupled-double-photonic-crystal-slab (CDPCS) sensor for simultaneously detecting refractive index (RI) and temperature (T) with high accuracy and strong anti-interference ability, using transverse magnetic-like (TM-like) mode and transverse electric-like (TE-like) mode. Based on the temporal coupled-mode theory, the theoretical model of the structure is established and the transmission formula is derived. The agreement between the theoretical and the simulated transmission spectra is proved. In order to achieve both high quality (Q)-factor and high modulation depth, the structure is optimized by adjusting the geometric parameters. The Q-factors of both TM-like mode and TE-like mode reach a magnitude order of 105. For the dual-parameter sensing, high RI sensitivities of 960 nm/RIU and 210 nm/RIU, and T sensitivities of -66.5 pm/K and 50.75 pm/K, are obtained for TM-like mode and TE-like mode, respectively. The relative deviations of RI and T sensing are as low as 0.6% and 1.0%, respectively, indicating high detection accuracy. Even considering the influence of external interference, the sensor can effectively resist external interference. The proposed CDPCS sensor has remarkable performance improvements in sensitivity, Q-factor, detection accuracy, and anti-interference ability. This study shows great potential in on-chip sensing and multi-parameter detection.

Demonstration of mid-infrared slow light one-dimensional photonic crystal ring resonator with high-order photonic bandgap.

Integrated mid-infrared sensing offers opportunities for the compact, selective, label-free and non-invasive detection of the absorption fingerprints of many chemical compounds, which is of great scientific and technological importance. To achieve high sensitivity, the key is to boost the interaction between light and analytes. So far, approaches like leveraging the slow light effect, increasing optical path length and enhancing the electric field confinement (f) in the analyte are envisaged. Here, we experimentally investigate a slow light one-dimensional photonic crystal ring resonator operating at high-order photonic bandgap (PBG) in mid-infrared range, which features both strong field confinement in analyte and slow light effect. And the optical path length can also be improved by the resoantor compared with waveguide structure. The characteristics of the first- and second-order bandgap edges are studied by changing the number of patterned periodical holes while keeping other parameters unchanged to confine the bands in the measurement range of our setup between 3.64 and 4.0 µm. Temperature sensitivity of different modes is also experimentally studied, which helps to understand the field confinement. Compared to the fundamental PBG edge modes, the second PBG edge modes show a higher field confinement in the analyte and a comparable group index, leading to larger light-matter interaction. Our work could be used for the design of ultra-sensitive integrated mid-infrared sensors, which have widespread applications including environment monitoring, biosensing and chemical analysis.

Integration of MEMS IR detectors with MIR waveguides for sensing applications.

Waveguides have been utilized for label-free and miniaturized mid-infrared gas sensors that operate on the evanescent field absorption principle. For integrated systems, photodetectors based on the photocarrier generation principle are previously integrated with waveguides. However, due to the thermal excitation of carriers at room temperature, they suffer from large dark currents and noise in the long-wavelength region. In this paper, we introduce the integration of a MEMS-based broadband infrared thermopile sensor with mid-infrared waveguides via flip-chip bonding technology and demonstrate a proof-of-concept gas (N2O) sensor working at 3.9 µm. A photonic device with input and output grating couplers designed at 3.72 µm was fabricated on a silicon-on-insulator (SOI) platform and integrated with a bare thermopile chip on its output side via flip-chip bonding in order to realize an integrated photonic platform for a myriad range of sensing applications. A responsivity of 69 mV/W was measured at 3.72 µm for an 11 mm waveguide. A second device designed at 3.9 µm has a 1800 ppm resolution for N2O sensing.

Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance.

Phosphorus transporter (PHT) genes encode H2PO4-/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1-PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.

Simultaneous sensing of refractive index and temperature based on a three-cavity-coupling photonic crystal sensor.

Healthcare and biosensing have attracted wide attention worldwide, with the development of chip integration technology in recent decades. In terms of compact sensor design with high performance and high accuracy, photonic crystal structures based on Fano resonance offer superior solutions. Here, we design a photonic crystal structure for sensing applications by proposing modeling for a three-cavity-coupling system and derive the transmission expression based on temporal coupled-mode theory (TCMT). The correlations between the structural parameters and the transmission are discussed. Ultimately, the geometry, composed of an air mode cavity, a dielectric mode cavity and a cavity of wide linewidth, is proved to be feasible for simultaneous sensing of refractive index (RI) and temperature (T). For the air mode cavity, the RI and T sensitivities are 523 nm/RIU and 2.5 pm/K, respectively. For the dielectric mode cavity, the RI and T sensitivities are 145 nm/RIU and 60.0 pm/K, respectively. The total footprint of the geometry is only 14 × 2.6 (length × width) µm2. Moreover, the deviation ratios of the proposed sensor are approximately 0.6% and 0.4% for RI and T, respectively. Compared with the researches lately published, the sensor exhibits compact footprint and high accuracy. Therefore, we believe the proposed sensor will contribute to the future compact lab-on-chip detection system design.

Coexistence of air and dielectric modes in single nanocavity.

A deterministic design method and experimental demonstration of single photonic crystal nanocavity supporting both air and dielectric modes in the mid-infrared wavelength region are reported here. The coexistence of both modes is realized by a proper design of photonic dispersion to confine air and dielectric bands simultaneously. By adding central mirrors to make the resonance modes be confined at the bandgap edges, high experimental Q-factors of 2.32 × 104 and 1.59 × 104 are achieved at the resonance wavelength of about 3.875µm and 3.728µm for fundamental dielectric and air modes, respectively. Moreover, multiple sets of air and dielectric modes can be realized by introducing central aperiodic mirrors with multiple bandgaps. The realization of coexistence of air and dielectric modes in single nanocavity will offer opportunities for multifunctional devices, paving the way to integrated multi-parameter sensors, filters, nonlinear devices, and compact light sources.

Hepatitis C virus nonstructural protein 5A perturbs lipid metabolism by modulating AMPK/SREBP-1c signaling.

BACKGROUND: Steatosis is an important clinical manifestation associated with chronic hepatitis C virus (HCV) infection. AMP-activated protein kinase (AMPK), a major mediator of lipid metabolism, regulates HCV-associated hepatic steatosis, but the underlying mechanisms remain obscure. Here we investigated the mechanism of HCV nonstructural protein 5A (NS5A)-induced lipid accumulation by the AMPK/SREBP-1c pathway. METHODS: We generated model mice by injecting recombinant lentiviral particles expressing the NS5A protein (genotype 3a) via the tail vein. The serum levels of alanine aminotransferase (ALT), free fatty acids (FFAs) and triglycerides (TG) were examined. H&E and Oil Red O staining were used to examine lipid droplets. Immunohistochemistry staining, quantitative real-time PCR and Western blotting were used to determine the expression of lipogenic genes. RESULTS: Our results showed that the serum levels of ALT, FFAs and TG, as well as the accumulation of hepatic lipid droplets, were increased significantly in mice infected with NS5A-expressing lentiviral particles. NS5A inhibited AMPK phosphorylation and increased the expression levels of sterol regulatory element binding protein-1c (SREBP-1c), acetyl-coenzyme A carboxylase 1 (ACC1) and fatty acid synthase (FASN) in vivo and in vitro. Further investigation revealed that pharmacological activation or ectopic expression of AMPK neutralized the upregulation of SREBP-1c, ACC1 and FASN, and ameliorated hepatic lipid accumulation induced by NS5A. Ectopic expression of SREBP-1c enhanced NS5A-induced hepatic lipid accumulation, which was dramatically reversed by pharmacological activation of AMPK. CONCLUSIONS: Collectively, we demonstrate that NS5A induces hepatic lipid accumulation via the AMPK/SREBP-1c pathway.

High-sensitivity broad free-spectral-range two-dimensional three-slot photonic crystal sensor integrated with a 1D photonic crystal bandgap filter.

We present a novel high-sensitivity broad free-spectral-range (FSR) two-dimensional three-slot photonic crystal sensor integrated with a 1D photonic crystal tapered nanobeam bandgap filter (1DPC-TNBF) based on thin-film silicon. Designed to lie in the wavelength at around 1550 nm, the resonance of the two-dimensional photonic crystal three-slot cavity (2DPC-TSC) shows strong light-matter interaction in the slot region, which enhances the bulk refractive index sensitivity of the sensor significantly. The simulated sensitivity is over 900 nm/refractive index unit (RIU). By connecting an additional 1DPC-TNBF to a 2DPC-TSC in series, the high-order modes are suppressed, which means only a fundamental mode exists with a broad FSR over 200 nm. Thus, the proposed structure is promising in designing lab-on-a-chip applications, especially in compact parallel-integrated sensor arrays.

Deterministic aperiodic photonic crystal nanobeam supporting adjustable multiple mode-matched resonances.

We investigate nanocavities in deterministic aperiodic photonic crystal (PhC) nanobeams. We reveal that even a single nanocavity can support multiple mode-matched resonances, which show an almost perfect field overlap in the cavity region. The unique property is enabled by the existence of adjustable multiple bandgaps in deterministic aperiodic PhC nanobeams. Our investigation may inspire related studies on low threshold lasers, integrated nonlinear devices, optical filters, and on-chip sensors.