Involvement of a rice mutation in storage protein biogenesis in endosperm and its genomic location.

MAIN CONCLUSION: A mutation was first found to cause the great generation of glutelin precursors (proglutelins) in rice (Oryza sativa L.) endosperm, and thus referred to as GPGG1. The GPGG1 was involved in synthesis and compartmentation of storage proteins. The PPR-like gene in GPGG1-mapped region was determined as its candidate gene. In the wild type rice, glutelins and prolamins are synthesized on respective subdomains of rough endoplasmic reticulum (ER) and intracellularly compartmentalized into different storage protein bodies. In this study, a storage protein mutant was obtained and characterized by the great generation of proglutelins combining with the lacking of 13 kD prolamins. A dominant genic-mutation, referred to as GPGG1, was clarified to result in the proteinous alteration. Novel saccular composite-ER was shown to act in the synthesis of proglutelins and 14 kD prolamins in the mutant. Additionally, a series of organelles including newly occurring several compartments were shown to function in the transfer, trans-plasmalemmal transport, delivery, deposition and degradation of storage proteins in the mutant. The GPGG1 gene was mapped to a 67.256 kb region of chromosome 12, the pentatricopeptide repeat (PPR)-like gene in this region was detected to contain mutational sites.

A hybrid particle swarm optimization algorithm for solving engineering problem.

To overcome the disadvantages of premature convergence and easy trapping into local optimum solutions, this paper proposes an improved particle swarm optimization algorithm (named NDWPSO algorithm) based on multiple hybrid strategies. Firstly, the elite opposition-based learning method is utilized to initialize the particle position matrix. Secondly, the dynamic inertial weight parameters are given to improve the global search speed in the early iterative phase. Thirdly, a new local optimal jump-out strategy is proposed to overcome the "premature" problem. Finally, the algorithm applies the spiral shrinkage search strategy from the whale optimization algorithm (WOA) and the Differential Evolution (DE) mutation strategy in the later iteration to accelerate the convergence speed. The NDWPSO is further compared with other 8 well-known nature-inspired algorithms (3 PSO variants and 5 other intelligent algorithms) on 23 benchmark test functions and three practical engineering problems. Simulation results prove that the NDWPSO algorithm obtains better results for all 49 sets of data than the other 3 PSO variants. Compared with 5 other intelligent algorithms, the NDWPSO obtains 69.2%, 84.6%, and 84.6% of the best results for the benchmark function ( f 1 - f 13 ) with 3 kinds of dimensional spaces (Dim = 30,50,100) and 80% of the best optimal solutions for 10 fixed-multimodal benchmark functions. Also, the best design solutions are obtained by NDWPSO for all 3 classical practical engineering problems.

The multi-slit very small angle neutron scattering instrument at the China Spallation Neutron Source.

A multi-slit very small angle neutron scattering (MS-VSANS) instrument has been finally accepted at the China Spallation Neutron Source (CSNS). It is the first spallation neutron source based VSANS instrument. MS-VSANS has a good signal-to-noise ratio and can cover a wide scattering vector magnitude range from 0.00028 to 1.4 Å-1. In its primary flight path, a combined curved multichannel beam bender and sections of rotary exchange drums are installed to minimize the background downstream of the instrument. An exchangeable multi-slit beam focusing system is integrated into the primary flight path, enabling access to a minimum scattering vector magnitude of 0.00028 Å-1. MS-VSANS has three modes, namely conventional SANS, polarizing SANS and VSANS modes. In the SANS mode, three motorized high-efficiency 3He tube detectors inside the detector tank cover scattering angles from 0.12 to 35° simultaneously. In the polarizing SANS mode, a double-V cavity provides highly polarized neutrons and a high-efficiency 3He polarization analyser allows full polarization analysis. In the VSANS mode, an innovative high-resolution gas electron multiplier detector covers scattering angles from 0.016 to 0.447°. The absolute scattering intensities of a selection of standard samples are obtained using the direct-beam technique; the effectiveness of this method is verified by testing the standard samples and comparing the results with those from a benchmark instrument. The MS-VSANS instrument is designed to be flexible and versatile and all the design goals have been achieved.

Amphiphilic α-Peptoid-deoxynojirimycin Conjugate-based Multivalent Glycosidase Inhibitor for Hypoglycemic Effect and Fluorescence Imaging.

Multivalent glycosidase inhibitors based on 1-deoxynojirimycin derivatives against α-glucosidases have been rapidly developed. Nonetheless, the mechanism based on self-assembled multivalent glucosidase inhibitors in living systems needs to be further studied. It remains to be determined whether the self-assembly possesses sufficient stability to endure transit through the small intestine and subsequently bind to the glycosidases located therein. In this paper, two amphiphilic compounds, 1-deoxynojirimycin and α-peptoid conjugates (LP-4DNJ-3C and LP-4DNJ-6C), were designed. Their self-assembling behaviors, multivalent α-glucosidase inhibition effect, and fluorescence imaging on living organs were studied. LP-4DNJ-6C exhibited better multivalent α-glucosidase inhibition activities in vitro. Moreover, the self-assembly of LP-4DNJ-6C could effectively form a complex with Nile red. The complex showed fluorescence quenching effect upon binding with α-glucosidases and exhibited potent fluorescence imaging in the small intestine. This result suggests that a multivalent hypoglycemic effect achieved through self-assembly in the intestine is a viable approach, enabling the rational design of multivalent hypoglycemic drugs.

Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications.

Efficient preparation of DNA oligonucleotides containing unnatural nucleobases (UBs) that can pair with their cognates to form unnatural base pairs (UBPs) is an essential prerequisite for the application of UBPs in vitro and in vivo. Traditional preparation of oligonucleotides containing unnatural nucleobases largely relies on solid-phase synthesis, which needs to use unstable nucleoside phosphoramidites and a DNA synthesizer, and is environmentally unfriendly and limited in product length. To overcome these limitations of solid-phase synthesis, we developed enzymatic methods for daily laboratory preparation of DNA oligonucleotides containing unnatural nucleobase dNaM, dTPT3, or one of the functionalized dTPT3 derivatives, which can be used for orthogonal DNA labeling or the preparation of DNAs containing UBP dNaM-dTPT3, one of the most successful UBPs to date, based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT). Here, we first provide a detailed procedure for the TdT-based preparation of DNA oligonucleotides containing 3'-nucleotides of dNaM, dTPT3, or one of dTPT3 derivatives. We then present the procedures for enzyme-linked oligonucleotide assay (ELONA) and imaging of bacterial cells using DNA oligonucleotides containing 3'-nucleotides of dTPT3 derivatives with different functional groups. The procedure for enzymatic synthesis of DNAs containing an internal UBP dNaM-dTPT3 is also described. Hopefully, these methods will greatly facilitate the application of UBPs and the construction of semi-synthetic organisms with an expanded genetic alphabet.

Spectral-Spatial Feature Fusion for Hyperspectral Anomaly Detection.

Hyperspectral anomaly detection is used to recognize unusual patterns or anomalies in hyperspectral data. Currently, many spectral-spatial detection methods have been proposed with a cascaded manner; however, they often neglect the complementary characteristics between the spectral and spatial dimensions, which easily leads to yield high false alarm rate. To alleviate this issue, a spectral-spatial information fusion (SSIF) method is designed for hyperspectral anomaly detection. First, an isolation forest is exploited to obtain spectral anomaly map, in which the object-level feature is constructed with an entropy rate segmentation algorithm. Then, a local spatial saliency detection scheme is proposed to produce the spatial anomaly result. Finally, the spectral and spatial anomaly scores are integrated together followed by a domain transform recursive filtering to generate the final detection result. Experiments on five hyperspectral datasets covering ocean and airport scenes prove that the proposed SSIF produces superior detection results over other state-of-the-art detection techniques.

A strategy to reduce the byproduct glucose by simultaneously producing levan and single cell oil using an engineered Yarrowia lipolytica strain displaying levansucrase on the surface.

Currently, levan is attracting attention due to its promising applications in the food and biomedical fields. Levansucrase synthesizes levan by polymerizing the fructosyl unit in sucrose. However, a large amount of the byproduct glucose is produced during this process. In this paper, an engineered oleaginous yeast (Yarrowia lipolytica) strain was constructed using a surface display plasmid containing the LevS gene of Gluconobacter sp. MP2116. The levansucrase activity of the engineered yeast strain reached 327.8 U/g of cell dry weight. The maximal levan concentration (58.9 g/l) was achieved within 156 h in the 5-liter fermentation. Over 81.2 % of the sucrose was enzymolyzed by the levansucrase, and the byproduct glucose was converted to 21.8 g/l biomass with an intracellular oil content of 25.5 % (w/w). The obtained oil was comprised of 91.3 % long-chain fatty acids (C16-C18). This study provides new insight for levan production and comprehensive utilization of the byproduct in levan biosynthesis.

Effect of dissolved oxygen concentration on performance and mechanism of simultaneous nitrification and denitrification in integrated fixed-film activated sludge sequencing batch reactors.

Integrated fixed-film activated sludge (IFAS) is a superior system for achieving simultaneous nitrification and denitrification (SND), however, the impact of dissolved oxygen (DO) has not been fully elucidated. Therefore, this study investigated the effect of DO concentration on performance and mechanism of SND in IFAS system. Results showed that IFAS outperformed control systems and achieved optimal SND performance at a DO concentration of 0.5 mg/L, with an SND efficiency of 88.51% and total nitrogen removal efficiency of 82.78%. Typical cycles analysis demonstrated limited-DO promoted SND performance. Further analysis implied biofilms exhibited high biomass and denitrification activity with decreasing DO. Microbial community analysis revealed low DO concentrations were responsible for abundant functional groups and genes associated with SND and promoted unconventional nitrogen removal pathways. Moreover, co-occurrence network analysis elucidated microbial interactions, responses to DO, and keystone genera. This study helps understanding the roles of DO for enhanced SND in IFAS.

Transcriptome and Metabolome Integration Reveals the Impact of Fungal Elicitors on Triterpene Accumulation in Sanghuangporus sanghuang.

Sanghuangporus sanghuang is a large wood-decaying mushroom highly valued in traditional Chinese medicine due to its medicinal properties, including hypoglycemic, antioxidant, antitumor, and antibacterial properties effects. Its key bioactive compounds include flavonoids and triterpenoids. Specific fungal genes can be selectively induced by fungal elicitors. To investigate the effect of fungal polysaccharides derived from Perenniporia tenuis mycelia on the metabolites of S. sanghuang, we conducted metabolic and transcriptional profiling with and without elicitor treatment (ET and WET, respectively). Correlation analysis showed significant differences in triterpenoid biosynthesis between the ET and WET groups. In addition, the structural genes associated with triterpenoids and their metabolites in both groups were verified using quantitative real-time polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Through metabolite screening, three triterpenoids were identified: betulinol, betulinic acid, and 2-hydroxyoleanolic acid. Excitation treatment increased the level of betulinic acid by 2.62-fold and 2-hydroxyoleanolic acid by 114.67-fold compared to WET. The qRT-PCR results of the four genes expressed in secondary metabolic pathways, defense gene activation, and signal transduction showed significant variation between the ET and WET groups. Overall, our study suggests that the fungal elicitor induced the aggregation of pentacyclic triterpenoid secondary metabolites in S. sanghuang.

Flexible solar cells based on foldable silicon wafers with blunted edges.

Flexible solar cells have a lot of market potential for application in photovoltaics integrated into buildings and wearable electronics because they are lightweight, shockproof and self-powered. Silicon solar cells have been successfully used in large power plants. However, despite the efforts made for more than 50 years, there has been no notable progress in the development of flexible silicon solar cells because of their rigidity1-4. Here we provide a strategy for fabricating large-scale, foldable silicon wafers and manufacturing flexible solar cells. A textured crystalline silicon wafer always starts to crack at the sharp channels between surface pyramids in the marginal region of the wafer. This fact enabled us to improve the flexibility of silicon wafers by blunting the pyramidal structure in the marginal regions. This edge-blunting technique enables commercial production of large-scale (>240 cm2), high-efficiency (>24%) silicon solar cells that can be rolled similarly to a sheet of paper. The cells retain 100% of their power conversion efficiency after 1,000 side-to-side bending cycles. After being assembled into large (>10,000 cm2) flexible modules, these cells retain 99.62% of their power after thermal cycling between -70 °C and 85 °C for 120 h. Furthermore, they retain 96.03% of their power after 20 min of exposure to air flow when attached to a soft gasbag, which models wind blowing during a violent storm.

Enhanced anaerobic degradation of azo dyes by biofilms supported by novel functionalized carriers.

Azo dyes are significant organic pollutants known for their adverse effects on humans and aquatic life. In this study, anthraquinone-2-sulfonate (AQS) immobilized on biochar (BC) was employed as a novel carrier in up-flow anaerobic fixed-bed reactors to induce specific biofilm formation and promote the biotransformation efficiency of azo dyes. Novel carrier-packed reactor 1 (R1) and BC-packed reactor 2 (R2) were used to treat red reactive 2 (RR2) under continuous operation for 175 days. The decolorization rates of R1 and R2 were 96-83% and 91-73%, respectively. The physicochemical characteristics and extracellular polymeric substances (EPS) of the biofilm revealed a more stable structure in R1. Furthermore, the microbial community in R1 interacted more closely with each other and contained more keystone genera. Overall, this study provides a feasible method for improving the biotransformation of azo dyes, thus providing support for practical applications in wastewater treatment projects.

Fluorescence sensing and glycosidase inhibition effect of multivalent glycosidase inhibitors based on Naphthalimide-deoxynojirimycin conjugates.

Synthetic glycoconjugates as chemical probes have been widely developed for the detection of glycosidase enzymes. However, the binding interactions between iminosugar derivatives and glycosidases were limited, especially for the binding interactions between multivalent glycosidase inhibitors and α-glycosidases. In this paper, three naphthalimide-DNJ conjugates were synthesized. Furthermore, the binding interactions and glycosidase inhibition effects of them were investigated. It was found that the strong binding interactions of multivalent glycosidase inhibitors with enzymes were related to the efficient inhibitory activity against glycosidase. Moreover, the lengths of the chain between DNJ moieties and the triazole ring for the naphthalimide-DNJ conjugates influenced the self-assembly properties, binding interactions and glycosidase inhibition activities with multisource glycosidases. Compound 13 with six carbons between the DNJ moiety and triazole ring showed the stronger binding interactions and better glycosidase inhibition activities against α-mannosidase (jack bean) and α-glucosidase (aspergillus niger). In addition, compound 13 showed an effective PBG inhibition effect in mice with 51.18 % decrease in blood glucose at 30 min. This result opens a way for detection of multivalent glycosidase inhibition effect by a fluorescent sensing method.

The ornithine-urea cycle involves fumaric acid biosynthesis in Aureobasidium pullulans var. aubasidani, a green and eco-friendly process for fumaric acid production.

The current petroleum chemical methods for fumaric acid production can cause heavy pollution and global warming. In this study, the engineered strains of A. pullulans var. aubasidani were found to be suitable for green fumaric acid producer. Removal and complementation of the relevant genes showed only the ornithine-urea cycle (OUC) was involved in high level fumarate biosynthesis which was controlled by the Ca2+ signaling pathway. Removal of both the GOX gene encoding glucose oxidase and the PKS1 gene encoding the polyketide synthase for 3,5-dihydroxydecanoic acid biosynthesis and overexpression of the PYC gene encoding pyruvate carboxylase made the strain e-PYC produce 88.1 ± 4.3 g/L of fumarate at flask level and 93.9 ± 0.8 g/L of fumarate during the fed-batch fermentation. As a yeast-like fungal strain, it was very easy to cultivate A. pullulans var. aubasidani DH177 and their mutants in the bioreactor and to edit its genomic DNAs to enhance fumarate production. It was found that 2 mol of CO2 could be fixed during a maximal theoretical yield of 2 mol of fumarate per mole of glucose consumed in the OUC. Therefore, the OUC-mediated fumarate biosynthesis pathway in A. pullulans var. aubasidani was a green and eco-friendly process for the global sustainable development and carbon neutrality.

Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology.

Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.

Enzymatic Synthesis of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase.

Development of unnatural base pairs (UBPs) has significantly expanded the genetic alphabet both in vitro and in vivo and led to numerous potential applications in the biotechnology and biopharmaceutical industry. Efficient synthesis of oligonucleotides containing unnatural nucleobases is undoubtedly an essential prerequisite for making full use of the UBPs, and de novo synthesis of oligonucleotides with terminal deoxynucleotidyl transferases (TdTs) has emerged as a method of great potential to overcome limitations of traditional solid-phase synthesis. Herein, we report the efficient template-independent incorporation of nucleotides of unnatural nucleobases dTPT3 and dNaM, which have been designed to make one of the most successful UBPs to date, dTPT3-dNaM, into DNA oligonucleotides with a TdT enzyme under optimized conditions. We also demonstrate the efficient TdT incorporation of dTPT3 derivatives with different functional linkers into oligonucleotides for orthogonal labeling of nucleic acids and applications thereof. The development of a method for the daily laboratory preparation of DNAs with UBPs at arbitrary sites with the assistance of TdT is also described.

Identification of Heavy Metals and Organic Micropollutants in Drinking Water Sources in Typical Villages and Towns in Northeast China.

This study identified and detected the existence of major pollutants in northeast China. As an alpine region and an agricultural base, this region has representative significance in pollution research. We selected 56 samples from drinking water sources of typical villages and towns, focusing on the analysis of heavy metals and organic micropollutants in northeast China. The analysis results showed that Fe and Mn were the main metal elements exceeding the standard. The exceeding rates were 17.9% and 19.6%. Experiments showed that there were 19 kinds of pesticides, 6 kinds of OPEs, 2 kinds of PAEs, 22 kinds of PPCPs. The detection rate of these 49 kinds of organic micro-pollutants were 1.79~82.14%. The characteristics of organic pollution were extensive and varied. Many underground water samples had high level of micropollutants. The water quality parameters of drinking water sources in villages and towns showed close relation to local geological conditions and agricultural activities. Actions must be taken to control these parameters from the source of pollution.

Multiscale Analysis of Bi-Layer Lattice-Filled Sandwich Structure Based on NIAH Method.

Bi-layer lattice-filled sandwich structures have good application prospects for multi-physics problems; however, high-precision numerical analysis methods are lacking. Recently, the newly proposed asymptotic homogenization method called the novel numerical implementation of asymptotic homogenization (NIAH) was further developed based on the Mindlin plate theory, which is a potential method for overcoming the above limitation. This study investigates the feasibility of this method for Bi-layer lattice-filled sandwich structures. The obtained results are compared to those from homogenization methods developed based on the Kirchhoff theory, and accordingly, the influence of the shear effect on the accuracy of the structural responses of the considered structures is studied. Subsequently, the impacts of the size effect, macrostructure type, and lattice type are also considered. The analysis results showed that, for most cases, the NIAH method can yield high-precision results for Bi-layer lattice-filled sandwich structures. When the number of lattice cells is insufficient or different layers of the lattice have excessive differences in their stiffness, the accuracy of the results obtained using the NIAH method is degraded.

Metabolome and Transcriptome Profiling Reveal Carbon Metabolic Flux Changes in Yarrowia lipolytica Cells to Rapamycin.

Yarrowia lipolytica is an oleaginous yeast for the production of oleochemicals and biofuels. Nitrogen deficiency is beneficial to lipids biosynthesis in Y. lipolytica. Target of rapamycin (TOR) regulates the utilization of nutrients, which is inhibited in nitrogen starvation or by rapamycin treatment. However, under nitrogen-rich conditions, the lipids biosynthesis in Y. lipolytica after inhibition of TOR by rapamycin is elusive. Combining metabolomics and transcriptomics analysis, we found that rapamycin altered multiple metabolic processes of Y. lipolytica grown in nitrogen-rich medium, especially the metabolisms of amino acids and lipids. A total of 176 differentially accumulated metabolites were identified after rapamycin treatment. Rapamycin increased the levels of tryptophan, isoleucine, proline, serine, glutamine, histidine, lysine, arginine and glutamic acid, and decreased the levels of threonine, tyrosine and aspartic acid. Two fatty acids in lipid droplets, stearic acid (down-regulated) and stearidonic acid (up-regulated), were identified. The expression of 2224 genes changed significantly after rapamycin treatment. Further analysis revealed that rapamycin reduced carbon flux through lipids biosynthesis, accompanied by increased carbon flux through fatty acids degradation and amino acid (especially glutamic acid, glutamine, proline and arginine) biosynthesis. The dataset provided here is valuable for understanding the molecular mechanisms of amino acid and lipids metabolisms in oleaginous yeast.

Ethyl acetate produced by Hanseniaspora uvarum is a potential biocontrol agent against tomato fruit rot caused by Phytophthora nicotianae.

In this study, an oomycete strain FQ01 of Phytophthora nicotianae, which could cause destructive postharvest disease, was isolated. At present, chemical fungicides are the main reagents used for controlling Phytophthora diseases. It is necessary to find new control techniques that are environmentally friendly. The biocontrol activity of Hanseniaspora uvarum MP1861 against P. nicotianae FQ01 was therefore investigated. Our results revealed that the volatile organic compounds (VOCs) released by the yeast strain MP1861 could inhibit the development of P. nicotianae FQ01. The major component of the VOCs produced by the yeast strain MP1861 was identified to be ethyl acetate (70.8%). Biocontrol experiments showed that Phytophthora disease in tomato fruit could be reduced by 95.8% after the yeast VOCs treatment. Furthermore, ethyl acetate inhibited the mycelial growth of the oomycete strain FQ01, and damaged the pathogen cell membrane. This paper describes the pioneering utilization of the yeast strain MP1861 for biocontrol of postharvest fruit rot in tomato caused by P. nicotianae.

Multivalent glucosidase inhibitors based on perylene bisimide and iminosugar conjugates.

Although multivalent glucosidase inhibitors based on iminosugars have shown enhanced inhibition activity, an effective way to improve their hypoglycemic effect in vivo, is still in infancy and needs further development. In this paper, PBI-5DNJ and PBI-6DNJ, with three or four DNJ moieties respectively conjugated at the bay position were synthesized. PBI-6DNJ evidenced stronger π-π stacking interactions and, when self-assembled, a smaller size than that of PBI-5DNJ. It was found that PBI-6DNJ exhibited superior α-glucosidases (from mice) inhibition activity (Ki = 0.14 ± 0.007 µM) in vitro than that (Ki = 0.31 ± 0.01) of PBI-5DNJ and in vivo hypoglycemic effects in mice models. PBI-6DNJ possessed good hypoglycemic effects with the percentages of PBG levels of 40.40 ± 3.33% and 39.23 ± 4.84% at a dose of 2.0 mg/kg after 15 min and 30 min of administration, respectively. In terms of measuring percentage decrease of PBG level per DNJ unit, PBI-6DNJ displayed a 2.1-fold enhancement than miglitol, demonstrating a consistency between in vitro and in vivo experiments. This paves the way to the connection between in vivo hypoglycemic potency and in vitro glucosidase inhibition assay, leading to reliable and simplified assessment of hypoglycemic potency determination, and opening a basic understanding of the design of multivalent glucosidase inhibitors.