Shipborne single-photon fluorescence oceanic lidar: instrumentation and inversion.

Laser-induced fluorescence (LIF) technology has been widely applied in remote sensing of aquatic phytoplankton. However, due to the weak fluorescence signal induced by laser excitation and the significant attenuation of laser in water, profiling detection becomes challenging. Moreover, it remains difficult to simultaneously retrieve the attenuation coefficient (K l i d a r m f) and the fluorescence volume scattering function at 180° (ßf) through a single fluorescence lidar. To address these issues, a novel all-fiber fluorescence oceanic lidar is proposed, characterized by: 1) obtaining subsurface fluorescence profiles using single-photon detection technology, and 2) introducing the Klett inversion method for fluorescence lidar to simultaneously retrieve K l i d a r m f and ßf. According to theoretical analysis, the maximum relative error of ßf for the chlorophyll concentration ranging from 0.01 mg/m3 to 10 mg/m3 within a water depth of 10 m is less than 20%, while the maximum relative error of K l i d a r m f is less than 10%. Finally, the shipborne single-photon fluorescence lidar was deployed on the experimental vessel for continuous experiments of over 9 hours at fixed stations in the offshore area, validating its profiling detection capability. These results demonstrate the potential of lidar in profiling detection of aquatic phytoplankton, providing support for studying the dynamic changes and environmental responses of subsurface phytoplankton.

Simultaneous sensing profiles of beam attenuation coefficient and volume scattering function at 180° using a single-photon underwater elastic-Raman lidar.

Lidar has emerged as a promising technique for vertically profiling optical parameters in water. The application of single-photon technology has enabled the development of compact oceanic lidar systems, facilitating their deployment underwater. This is crucial for conducting ocean observations that are free from interference at the air-sea interface. However, simultaneous inversion of the volume scattering function at 180° at 532 nm (ßm) and the lidar attenuation coefficient at 532 nm (K l i d a r m) from the elastic backscattered signals remains challenging, especially in the case of near-field signals affected by the geometric overlap factor (GOF). To address this challenge, this work proposes adding a Raman channel, obtaining Raman backscattered profiles using single-photon detection. By normalizing the elastic backscattered signals with the Raman signals, the sensitivity of the normalized signal to variations in the lidar attenuation coefficient is significantly reduced. This allows for the application of a perturbation method to invert ßm and subsequently obtain the K l i d a r m. Moreover, the influence of GOF and fluctuations in laser power on the inversion can be reduced. To further improve the accuracy of the inversion algorithm for stratified water bodies, an iterative algorithm is proposed. Additionally, since the optical telescope of the lidar adopts a small aperture and narrow field of view design, K l i d a r m tends to the beam attenuation coefficient at 532 nm (cm). Using Monte Carlo simulation, a relationship between cm and K l i d a r m is established, allowing cm derivation from K l i d a r m. Finally, the feasibility of the algorithm is verified through inversion error analysis. The robustness of the lidar system and the effectiveness of the algorithm are validated through a preliminary experiment conducted in a water tank. These results demonstrate that the lidar can accurately profile optical parameters of water, contributing to the study of particulate organic carbon (POC) in the ocean.

Hafnium (Hf)-Chelating Porphyrin-Decorated Gold Nanosensitizers for Enhanced Radio-Radiodynamic Therapy of Colon Carcinoma.

X-ray-induced radiodynamic therapy (RDT) that can significantly reduce radiation dose with an improved anticancer effect has emerged as an attractive and promising therapeutic modality for tumors. However, it is highly significant to develop safe and efficient radiosensitizing agents for tumor radiation therapy. Herein, we present a smart nanotheranostic system FA-Au-CH that consists of gold nanoradiosensitizers, photosensitizer chlorin e6 (Ce6), and folic acid (FA) as a folate-receptor-targeting ligand for improved tumor specificity. FA-Au-CH nanoparticles have been demonstrated to be able to simultaneously serve as radiosensitizers and RDT agents for enhanced computed tomography (CT) imaging-guided radiotherapy (RT) of colon carcinoma, owing to the strong X-ray attenuation capability of high-Z elements Au and Hf, as well as the characteristics of Hf that can transfer radiation energy to Ce6 to generate ROS from Ce6 under X-ray irradiation. The integration of RT and RDT in this study demonstrates great efficacy and offers a promising therapeutic modality for the treatment of malignant tumors.

Sensing profiles of the volume scattering function at 180° using a single-photon oceanic fluorescence lidar.

A novel oceanic fluorescence lidar technique has been proposed and demonstrated for remotely sensing the volume scattering function at 180° (ßf), which can be used to further retrieve the profiles of the absorption coefficient of phytoplankton (aph) at 532 nm and chlorophyll concentration (Chl). This scheme has these features. 1) The single-photon detection technology is employed to enhance the detection sensitivity to the single-photon level, enabling the oceanic lidar to obtain fluorescence backscatter profiles. 2) In terms of algorithms, the Raman backscattered signals of the water are utilized to normalize the backscattered signals of chlorophyll fluorescence, effectively minimizing the depth-dependent variation of the differential lidar attenuation coefficient (Δ K l i d a r f r). To reduce the contamination of fluorescence signals in the Raman backscatter signals, a Raman filter with a bandwidth of 6 nm was chosen. Subsequently, a perturbation method is utilized to invert the ßf of the fluorescence lidar. Finally, aph and Chl profiles can be inverted based on empirical models. 3) The value of Δ K l i d a r f r used in inversion is obtained through a semi-analytic Monte Carlo simulation. According to theoretical analysis, the maximum relative error of ßf for Chl ranging from 0.01 mg/m3 to 10 mg/m3 is less than 13 %. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, resulting in continuous subsurface profiles of ßf, aph, and Chl. These measurements confirm the robustness and reliability of the oceanic single-photon fluorescence lidar system and the inversion algorithm.

Remote sensing oil in water with an all-fiber underwater single-photon Raman lidar.

The detection of oil in water is of great importance for maintaining subsurface infrastructures such as oil pipelines. As a potential technology for oceanic application, an oceanic lidar has proved its advantages for remote sensing of optical properties and subsea materials. However, current oceanic lidar systems are highly power-consuming and bulky, making them difficult to deploy underwater to monitor oil in water. To address this issue, we have developed a compact single-photon Raman lidar by using a single-photon detector with high quantum efficiency and low dark noise. Due to the single-photon sensitivity, the detection of the relatively weak Raman backscattered signal from underwater oil was realized with a laser with a pulse energy of 1 µJ and a telescope with a diameter of 22.4 mm. An experimental demonstration was conducted to obtain the distance-resolved Raman backscatter of underwater oil of different thicknesses up to a distance of 12 m. The results indicate the single-photon Raman lidar's potential for inspecting underwater oil pipelines.

Sensing the profile of particulate beam attenuation coefficient through a single-photon oceanic Raman lidar.

A lidar technique has been proposed and demonstrated for remotely sensing particulate beam attenuation coefficient (cp) profiles using the Raman backscattered signal from water. In Raman lidar, the backscatter coefficient at 180° can be considered constant, allowing for the determination of the lidar attenuation coefficient (Klidar) from the Raman backscattered signal. This scheme has these features. 1) The bandwidth of the filter that used to extract the Raman component from the backscattered signal of the lidar was optimized to ensure sufficient lidar signal strength while minimizing the influence of chlorophyll fluorescence on inversion. 2) A receiving telescope with narrow field of view (FOV) and small aperture was utilized to suppress multi-scattering components in the backscattered signal. 3) A relationship between the beam attenuation coefficient (c) and Klidar was established after simulations via a semi-analytic Monto Carlo. 4) The value of cp was obtained by subtracting the attenuation coefficient of pure seawater (cw) from c. According to the theoretical analysis, the maximum relative error of cp is less than 15% for chlorophyll concentrations up to 10 mg/m3. Due to the water Raman backscattered signal being several orders of magnitude lower than the elastic backscattered signal, a single-photon detector is required to significantly improve the detection sensitivity to the single-photon level. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, and continuous subsurface profiles of cp were obtained. These measurements confirm the robustness and reliability of the oceanic single-photon Raman lidar system and the inversion method.

Combined transcriptomic and metabolomic analyses of high temperature stress response of quinoa seedlings.

BACKGROUND: Quinoa (Chenopodium quinoa Willd.) originates in high altitude areas, such as the Andes, and has some inherent characteristics of cold, drought, and salinity tolerance, but is sensitive to high temperature. RESULTS: To gain insight into the response mechanism of quinoa to high temperature stress, we conducted an extensive targeted metabolomic study of two cultivars, Dianli-3101 and Dianli-3051, along with a combined transcriptome analysis. A total of 794 metabolites and 54,200 genes were detected, in which the genes related to photosynthesis were found down-regulated at high temperatures, and two metabolites, lipids and flavonoids, showed the largest changes in differential accumulation. Further analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and transcription factors revealed that quinoa inhibits photosynthesis at high temperatures, and the possible strategies being used for high temperature stress management are regulation of heat stress transcription factors (HSFs) to obtain heat tolerance, and regulation of purine metabolism to enhance stress signals for rapid response to high temperature stress. The tolerant genotype could have an enhanced response through lower purine levels. The induction of the stress response could be mediated by HSF transcription factors. The results of this study may provide theoretical references for understanding the response mechanism of quinoa to high temperature stress, and for screening potential high temperature tolerant target genes and high temperature tolerant strains. CONCLUSIONS: These findings reveal the regulation of the transcription factor family HSF and the purinergic pathway in response to high temperature stress to improve quinoa varieties with high temperature tolerance.

CryoEM single particle reconstruction with a complex-valued particle stack.

Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these conditions result in a broader PSF that requires larger padding and slower calculations to integrate information for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined to optimize data processing. Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an image that has complex values. This is a complex value image considered in real space, opposed to standard SPR data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept provides multiple advantages because the particle box size can be small and calculations crucial for high resolution reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus refinement can be performed on the small box data.

Monomer and dimer structures of cytochrome bo3 ubiquinol oxidase from Escherichia coli.

The Escherichia coli cytochrome bo3 ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts-the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74).

Grain color formation and analysis of correlated genes by metabolome and transcriptome in different wheat lines at maturity.

Colored wheat has been recognized broadly for its nutritional value because of its natural content of the colorant anthocyanin. To investigate the reasons for the formation of the wheat grain color at maturity, metabolomic and transcriptomic analyses were performed on three different grain colors of wheat. Through metabolome analysis, 628 metabolites were identified. Of the 102 flavonoids, there are 9 kinds of anthocyanins related to color formation, mainly cyanidin and peonidin, and their metabolite content was the lowest in white-grain wheat. Among the genes associated with color formation, the structural gene TraesCS2D02G392900 in F3H with the bHLH transcription factor could elucidate the origin of wheat coloration. Multi-omics analysis showed that color formation is mainly influenced by the regulation of genes affecting anthocyanin and related synthesis. The results of this study may provide a theoretical basis for grain color formation at maturity and the nutritional and product development potential of colored wheat lines.

Alkaline Phosphatase-Controllable and Red Light-Activated RNA Modification Approach for Precise Tumor Suppression.

RNA interference (RNAi) has proved to be a promising modality for disease treatment. However, the promise of conventional RNA therapeutics for clinical application is severely impeded by low delivery efficiency and susceptibility of RNAs to serum RNases. Therefore, developing advanced RNAi technology is an increasing demand for achieving precise medicine. Herein, for the first time, we propose an alkaline phosphatase (ALP)-controllable and red light-activated RNA modification (ALARM) approach for anti-tumor therapeutic application. An ALP-responsive NIR fluorogenic probe f-RCP consisting of a tumor-targeting cyclic RGD peptide, an ALP-activated photosensitizer CyOP, and an 1O2-susceptible furan module for RNA modification was rationally designed and synthesized. Studies have demonstrated that f-RCP can specifically target to liver carcinoma HepG2 cells and spontaneously emit activated NIR/photoacoustic signals upon cleavage by the ALP enzyme, allowing for sensitive detection of ALP-positive tumors. More notably, we surprisingly found that the capability of f-RCP producing singlet oxygen (1O2) under red light irradiation could be simultaneously unlocked, which can ignite the covalent cyclization reaction between furan and nucleobases of intracellular RNA molecules, leading to significant mitochondrial damage and severe apoptosis of tumor cells, in consequence realizing efficient tumor suppression. Most importantly, the potential therapeutic mechanism was first explored on the transcriptomic level. This delicate ALARM strategy may open up new insights into cancer gene therapy.

Metabolome and transcriptome profiles in quinoa seedlings in response to potassium supply.

BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is a herb within the Quinoa subfamily of Amaranthaceae, with remarkable environmental adaptability. Its edible young leaves and grains are rich in protein, amino acids, microorganisms, and minerals. Although assessing the effects of fertilization on quinoa yield and quality has become an intensive area of research focus, the associated underlying mechanisms remain unclear. As one of the three macro nutrients in plants, potassium has an important impact on plant growth and development. In this study, extensive metabolome and transcriptome analyses were conducted in quinoa seedlings 30 days after fertilizer application to characterize the growth response mechanism to potassium.  RESULTS: The differential metabolites and genes present in the seedlings of white and red quinoa cultivars were significantly enriched in the photosynthetic pathway. Moreover, the PsbQ enzyme on photosystem II and delta enzyme on ATP synthase were significantly down regulated in quinoa seedlings under potassium deficiency. Additionally, the differential metabolites and genes of red quinoa seedlings were significantly enriched in the arginine biosynthetic pathway. CONCLUSIONS: These findings provide a more thorough understanding of the molecular changes in quinoa seedlings that occur under deficient, relative to normal, potassium levels. Furthermore, this study provides a theoretical basis regarding the importance of potassium fertilizers, as well as their efficient utilization by growing quinoa seedlings.

The His-tag as a decoy modulating preferred orientation in cryoEM.

The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein's surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.

Integrating transcriptomics and metabolomics to analyze quinoa (Chenopodium quinoa Willd.) responses to drought stress and rewatering.

The crop production of quinoa (Chenopodium quinoa Willd.), the only plant meeting basic human nutritional requirements, is affected by drought stress. To better understand the drought tolerance mechanism of quinoa, we screened the drought-tolerant quinoa genotype "Dianli 129" and studied the seedling leaves of the drought-tolerant quinoa genotype after drought and rewatering treatments using transcriptomics and targeted metabolomics. Drought-treatment, drought control, rewatering-treated, and rewatered control were named as DR, DC, RW, and RC, respectively. Among four comparison groups, DC vs. DR, RC vs. RW, RW vs. DR, and RC vs. DC, we identified 10,292, 2,307, 12,368, and 3 differentially expressed genes (DEGs), and 215, 192, 132, and 19 differentially expressed metabolites (DEMs), respectively. A total of 38,670 genes and 142 pathways were annotated. The results of transcriptome and metabolome association analysis showed that gene-LOC110713661 and gene-LOC110738152 may be the key genes for drought tolerance in quinoa. Some metabolites accumulated in quinoa leaves in response to drought stress, and the plants recovered after rewatering. DEGs and DEMs participate in starch and sucrose metabolism and flavonoid biosynthesis, which are vital for improving drought tolerance in quinoa. Drought tolerance of quinoa was correlated with gene expression differences, metabolite accumulation and good recovery after rewatering. These findings improve our understanding of drought and rewatering responses in quinoa and have implications for the breeding of new drought-tolerance varieties while providing a theoretical basis for drought-tolerance varieties identification.

Integrative Analysis of the Metabolome and Transcriptome Provides Insights into the Mechanisms of Flavonoid Biosynthesis in Quinoa Seeds at Different Developmental Stages.

Quinoa (Chenopodium quinoa Willd.) is a crop with high nutritional and health benefits. Quinoa seeds are rich in flavonoid compounds; however, the mechanisms behind quinoa flavonoid biosynthesis remain unclear. We independently selected the high-generation quinoa strain 'Dianli-3260', and used its seeds at the filling, milk ripening, wax ripening, and mature stages for extensive targeted metabolome analysis combined with joint transcriptome analysis. The results showed that the molecular mechanism of flavonoid biosynthesis in quinoa seeds was mainly concentrated in two pathways: "flavonoid biosynthesis pathway" and "flavone and flavonol biosynthesis pathway". Totally, 154 flavonoid-related metabolites, mainly flavones and flavonols, were detected in the four development stages. Moreover, 39,738 genes were annotated with KEGG functions, and most structural genes of flavonoid biosynthesis were differentially expressed during grain development. We analyzed the differential flavonoid metabolites and transcriptome changes between the four development stages of quinoa seeds and found that 11 differential flavonoid metabolites and 22 differential genes were the key factors for the difference in flavonoid biosynthesis. This study provides important information on the mechanisms underlying quinoa flavonoid biosynthesis, the screening of potential quinoa flavonoid biosynthesis regulation target genes, and the development of quinoa products.

Transcriptomic and Metabolomic Analysis of the Response of Quinoa Seedlings to Low Temperatures.

Quinoa, a cool-weather high-altitude crop, is susceptible to low-temperature stress throughout its reproductive phase. Herein, we performed broadly targeted metabolic profiling of quinoa seedlings to explore the metabolites' dynamics in response to low-temperature stress and transcriptome analysis to determine the underlying genetic mechanisms. Two variants, namely, Dian Quinoa 2324 and Dian Quinoa 281, were exposed to temperatures of -2, 5, and 22 °C. A total of 794 metabolites were detected; 52,845 genes, including 6628 novel genes, were annotated using UPLC-MS/MS analysis and the Illumina HiSeq system. Combined with morphological indicators to resolve the mechanism underlying quinoa seedling response to low-temperature stress, the molecular mechanisms of quinoa changed considerably based on temperature exposure. Soluble sugars heavily accumulated in plants with cold damage and changes in regulatory networks under freeze damage, such as the upregulation of α-linolenic acid metabolism and a reduction in energy substrates, may explain the spatial patterns of biosynthesis and accumulation of these metabolites. Genes that are actively expressed during cold responses, as revealed by co-expression analyses, may be involved in the regulation thereof. These results provide insights into the metabolic factors in quinoa under low-temperature stress and provide a reference for the screening of quinoa varieties resistant to low temperature.

Mechanisms of Resistance to Spot Blotch in Yunnan Iron Shell Wheat Based on Metabolome and Transcriptomics.

Spot blotch (SB) is a fungal disease that threatens wheat yield and quality. Presently, the molecular mechanism against SB is unclear. In this study, the resistant variety Zhenkang iron shell wheat (Yunmai 0030) and susceptible variety Lincang iron shell wheat (Yunmai 0608) were selected by identifying SB of Yunnan iron shell wheat. The metabolome and transcriptome of leaves of two varieties at different positions were detected using the systemic acquired resistance theory to investigate the molecular and physiological changes in Yunnan iron shell wheat under SB stress. We found that the genes and metabolites related to benzoxazinoid biosynthesis and arginine and proline metabolism were highly enriched after infection with leaf blight. The enriched differential metabolites mainly included phenolic acids, alkaloids, and flavonoids. We further observed that DIBOA- and DIMBOA-glucoside positively affected iron shell wheat resistance to leaf blight and proline and its derivatives were important for plant self-defense. Furthermore, we confirmed that the related metabolites in benzoxazinoid biosynthesis and arginine and proline metabolism positively affected Triticum aestivum ssp. resistance to SB. This study provides new insights into the dynamic physiological changes of wheat in response to SB, helps us better understand the mechanism of resistance to SB, and contributes to the breeding and utilization of resistant varieties.

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Quinoa Seedlings to Different Phosphorus Stresses.

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli-1299 and Dianli-71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa.

α-Functionalization of ketones promoted by sunlight and heterogeneous catalysis in the aqueous phase.

Herein, a protocol that combines heterogeneous catalysis and solar photocatalysis for the regioselective α-substitution of asymmetric ketones with quinoxalinones has been reported. The result indicates that the reaction is more likely to occur on the α-carbon. This strategy provides a green and efficient way for the α-functionalization of ketones. A singlet oxygen involved mechanism is suggested for the transformation.