Three-Dimensional Modeling of Maize Canopies Based on Computational Intelligence.

The 3-dimensional (3D) modeling of crop canopies is fundamental for studying functional-structural plant models. Existing studies often fail to capture the structural characteristics of crop canopies, such as organ overlapping and resource competition. To address this issue, we propose a 3D maize modeling method based on computational intelligence. An initial 3D maize canopy is created using the t-distribution method to reflect characteristics of the plant architecture. The subsequent model considers the 3D phytomers of maize as intelligent agents. The aim is to maximize the ratio of sunlit leaf area, and by iteratively modifying the azimuth angle of the 3D phytomers, a 3D maize canopy model that maximizes light resource interception can be constructed. Additionally, the method incorporates a reflective approach to optimize the canopy and utilizes a mesh deformation technique for detecting and responding to leaf collisions within the canopy. Six canopy models of 2 varieties plus 3 planting densities was constructed for validation. The average R2 of the difference in azimuth angle between adjacent leaves is 0.71, with a canopy coverage error range of 7% to 17%. Another 3D maize canopy model constructed using 12 distinct density gradients demonstrates the proportion of leaves perpendicular to the row direction increases along with the density. The proportion of these leaves steadily increased after 9 × 104 plants ha-1. This study presents a 3D modeling method for the maize canopy. It is a beneficial exploration of swarm intelligence on crops and generates a new way for exploring efficient resources utilization of crop canopies.

Plant microphenotype: from innovative imaging to computational analysis.

The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.

Research on the evolutionary history of the morphological structure of cotton seeds: a new perspective based on high-resolution micro-CT technology.

Cotton (Gossypium hirsutum L.) seed morphological structure has a significant impact on the germination, growth and quality formation. However, the wide variation of cotton seed morphology makes it difficult to achieve quantitative analysis using traditional phenotype acquisition methods. In recent years, the application of micro-CT technology has made it possible to analyze the three-dimensional morphological structure of seeds, and has shown technical advantages in accurate identification of seed phenotypes. In this study, we reconstructed the seed morphological structure based on micro-CT technology, deep neural network Unet-3D model, and threshold segmentation methods, extracted 11 basics phenotypes traits, and constructed three new phenotype traits of seed coat specific surface area, seed coat thickness ratio and seed density ratio, using 102 cotton germplasm resources with clear year characteristics. Our results show that there is a significant positive correlation (P< 0.001) between the cotton seed size and that of the seed kernel and seed coat volume, with correlation coefficients ranging from 0.51 to 0.92, while the cavity volume has a lower correlation with other phenotype indicators (r<0.37, P< 0.001). Comparison of changes in Chinese self-bred varieties showed that seed volume, seed surface area, seed coat volume, cavity volume and seed coat thickness increased by 11.39%, 10.10%, 18.67%, 115.76% and 7.95%, respectively, while seed kernel volume, seed kernel surface area and seed fullness decreased by 7.01%, 0.72% and 16.25%. Combining with the results of cluster analysis, during the hundred-year cultivation history of cotton in China, it showed that the specific surface area of seed structure decreased by 1.27%, the relative thickness of seed coat increased by 8.70%, and the compactness of seed structure increased by 50.17%. Furthermore, the new indicators developed based on micro-CT technology can fully consider the three-dimensional morphological structure and cross-sectional characteristics among the indicators and reflect technical advantages. In this study, we constructed a microscopic phenotype research system for cotton seeds, revealing the morphological changes of cotton seeds with the year in China and providing a theoretical basis for the quantitative analysis and evaluation of seed morphology.

Bacillus litorisediminis sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment.

Two aerobic, Gram-staining-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-47801T and FJAT-47835, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. Growth was observed at 25-55 °C (optimum, 50 °C) and pH 7.0-9.0 (optimum, pH 7.0), with up to 4.0% (w/v) NaCl (optimum, without NaCl). Strains FJAT-47801T and FJAT-47835 showed the highest 16S rRNA gene sequence similarity to Bacillus oleivorans (98.5%). The 16S rRNA gene sequence similarity between FJAT-47801T and FJAT-47835 was 99.9% indicating they were the same species. Phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 120 conserved bacterial single-copy genes) trees showed that strains FJAT-47801T and FJAT-47835 should be affiliated to the genus Bacillus. The of menaquinone of strain FJAT-47801T was MK-7. The major fatty acids of strain FJAT-47801T were iso-C15:0, anteiso-C15:0, iso-C17:0, and C16:0. The major polar lipids strain FJAT-47801T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The genomic DNA G+C content of strain FJAT-47801T was 39.3%. The average nucleotide identity (84.3%) and the digital DNA-DNA hybridization value (28.1%) between strain FJAT-47801T and B. oleivorans CCTCC AB 2013353T were below the cut-off level for species delineation. Based on the above results, strain FJAT-47801T represents a novel species of the genus Bacillus, for which the name Bacillus litorisediminis sp. nov., is proposed. The type strain is FJAT-47801T (=GDMCC 1.2712T = JCM 34875T).

Prediction of vertical distribution of SPAD values within maize canopy based on unmanned aerial vehicles multispectral imagery.

Real-time monitoring of canopy chlorophyll content is significant in understanding crop growth status and guiding precision agricultural management. Remote sensing methods have demonstrated great potential in this regard. However, the spatiotemporal heterogeneity of chlorophyll content within crop canopies poses challenges to the accuracy and stability of remote sensing estimation models. Hence, this study aimed to develop a novel method for estimating canopy chlorophyll content (represented by SPAD values) in maize (Zea mays L.) canopies. Firstly, we investigated the spatiotemporal distribution patterns of maize canopy SPAD values under varying nitrogen application rates and different growth stages. The results revealed a non-uniform, "bell-shaped" curve distribution of maize canopy SPAD values in the vertical direction. Nitrogen application significantly influenced the distribution structure of SPAD values within the canopy. Secondly, we achieved satisfactory results by fitting the Lorentz peak distribution function to the SPAD values of different leaf positions in maize. The fitting performance, evaluated using R2 and RMSE, ranged from 0.69 to 0.98 and 0.45 to 3.59, respectively, for the year 2021, and from 0.69 to 0.77 and 2.38 to 6.51, respectively, for the year 2022.Finally, based on the correlation between canopy SPAD values and vegetation indices (VIs) at different growth stages, we identified the sensitive leaf positions for the selected CCCI (Canopy Chlorophyll Index) in each growth stage. The 6th (r = 0.662), 4th (r = 0.816), 12th (r = 0.722), and 12th (r = 0.874) leaf positions exhibited the highest correlations. Compared to the estimation model using canopy wide SPAD values, the model based on sensitive leaf positions showed improved accuracy, with increases of 34%, 3%, 20%, and 3% for each growth stage, respectively. In conclusion, the findings of this study contribute to the enhancement of chlorophyll content estimation models in crop canopies and provide valuable insights for the integration of crop growth models with remote sensing methods.

Association of Versican Gene Polymorphisms with Intracranial Aneurysm Susceptibility in the Eastern Chinese Population.

OBJECTIVE: The proteoglycan versican (VCAN) plays an important role in extracellular matrix (ECM) assembly, and diminished maintenance of the ECM has been increasingly regarded as an important factor in the development of intracranial aneurysms (IAs). Previous studies have revealed that single-nucleotide polymorphisms (SNPs) of the VCAN gene are associated with susceptibility to IAs in European or Japanese populations. However, the association between IA susceptibility and VCAN SNPs in the Eastern Chinese population remains unclear. This study aimed to investigate the associations of the SNPs rs251124, rs2287926, and rs173686 with IA susceptibility in the Eastern Chinese population. METHODS: A total of 162 patients with IA and 182 controls were enrolled in this study. The study was conducted between January 2017 and December 2020. SNP genotyping for rs251124, rs2287926, and rs173686 was performed using Kompetitive Allele Specific PCR (KASP) after DNA extraction. The SNP data were analysed with CFX Manager Software version 3.1 (Bio-Rad). RESULTS: rs251124 and rs173686 were significantly associated with susceptibility to IA. The frequency of rs251124-TT in IA was higher than in controls (OR =1.26, 95% CI: 1.07-1.49; P<0.01), and its risk mainly came from the T allele. Furthermore, logistic regression analysis showed that the T/T genotype and T allele of rs251124 were independent risk factors for IA (OR=1.726, 95% CI: 1.136-2.263; P=0.011). Moreover, the G/G genotype and G allele of rs173686 were associated with increased IA susceptibility (OR=2.52, 95% CI: 1.261-5.037; P=0.009). CONCLUSION: The SNPs rs251124 and rs173686 were strongly associated with genetic susceptibility to IA in the Eastern Chinese population; however, no such association was found in the SNP rs2287926 of VCAN. Our findings suggest that the VCAN gene is an IA susceptible gene that should be further studied as a screening marker for IAs.

Stress response mechanisms and description of three novel species Shewanella avicenniae sp. nov., Shewanella sedimentimangrovi sp. nov. and Shewanella yunxiaonensis sp. nov., isolated from mangrove ecosystem.

Three Gram-staining negative, facultatively anaerobic, rod-shaped and motile strains, FJAT-51800T, FJAT-52962T and FJAT-54481T were isolated from the sediment samples of Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequencing results indicated they could be novel members of the genus Shewanella. The optimum temperature for growth was 30 °C. The respiratory quinones of the strains were ubiquinone Q-7 or Q-8, and menaquinone MK-7. Polar lipids of the strains FJAT-52962T and FJAT-51800T were phosphatidyl glycerol, phosphatidyl ethanolamine, and unidentified aminophospholipids while strain FJAT-54481 consist of phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipids, two unidentified aminolipids and four unidentified lipids. The major fatty acid of the three strains was iso-C15:0. The genomic DNA G + C contents of strains FJAT-51800T, FJAT-52962T and FJAT-54481T were 48.2, 55.3 and 48.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strains FJAT-51800T, FJAT-52962T and FJAT-54481T and other closely related Shewanella members were below the cut-off level (95-96%) for species identification. Genome analysis showed that these strains encode genes for osmo-regulation. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains FJAT-51800T, FJAT-52962T and FJAT-54481T represent three novel species of the genus Shewanella, for which the names Shewanella avicenniae sp. nov., Shewanella sedimentimangrovi sp. nov., and Shewanella yunxiaonensis sp. nov., are proposed. The type strains are FJAT-51800T (= GDMCC 1.2204T = KCTC 82448T), FJAT-52962T (= MCCC 1K05496T = KCTC 82445T) and FJAT-54481T (= GDMCC 1.2348T = KCTC 82646T).

Transcriptome dynamic landscape underlying the improvement of maize lodging resistance under coronatine treatment.

BACKGROUND: Lodging is one of the important factors causing maize yield. Plant height is an important factor in determining plant architecture in maize (Zea mays L.), which is closely related to lodging resistance under high planting density. Coronatine (COR), which is a phytotoxin and produced by the pathogen Pseudomonas syringae, is a functional and structural analogue of jasmonic acid (JA). RESULTS: In this study, we found COR, as a new plant growth regulator, could effectively reduce plant height and ear height of both hybrids (ZD958 and XY335) and inbred (B73) maize by inhibiting internode growth during elongation, thus improve maize lodging resistance. To study gene expression changes in internode after COR treatment, we collected spatio-temporal transcriptome of inbred B73 internode under normal condition and COR treatment, including the three different regions of internode (fixed, meristem and elongation regions) at three different developmental stages. The gene expression levels of the three regions at normal condition were described and then compared with that upon COR treatment. In total, 8605 COR-responsive genes (COR-RGs) were found, consist of 802 genes specifically expressed in internode. For these COR-RGs, 614, 870, 2123 of which showed expression changes in only fixed, meristem and elongation region, respectively. Both the number and function were significantly changed for COR-RGs identified in different regions, indicating genes with different functions were regulated at the three regions. Besides, we found more than 80% genes of gibberellin and jasmonic acid were changed under COR treatment. CONCLUSIONS: These data provide a gene expression profiling in different regions of internode development and molecular mechanism of COR affecting internode elongation. A putative schematic of the internode response to COR treatment is proposed which shows the basic process of COR affecting internode elongation. This research provides a useful resource for studying maize internode development and improves our understanding of the COR regulation mechanism based on plant height.

Atomic-Scale Fabrication of In-Plane Heterojunctions of Few-Layer MoS2 via In Situ Scanning Transmission Electron Microscopy.

Layered MoS2 is a prospective candidate for use in energy harvesting, valleytronics, and nanoelectronics. Its properties strongly related to its stacking configuration and the number of layers. Due to its atomically thin nature, understanding the atomic-level and structural modifications of 2D transition metal dichalcogenides is still underdeveloped, particularly the spatial control and selective precision. Therefore, the development of nanofabrication techniques is essential. Here, an atomic-scale approach used to sculpt 2D few-layer MoS2 into lateral heterojunctions via in situ scanning/transmission electron microscopy (STEM/TEM) is developed. The dynamic evolution is tracked using ultrafast and high-resolution filming equipment. The assembly behaviors inherent to few-layer 2D-materials are observed during the process and included the following: scrolling, folding, etching, and restructuring. Atomic resolution STEM is employed to identify the layer variation and stacking sequence for this new 2D-architecture. Subsequent energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy analyses are performed to corroborate the elemental distribution. This sculpting technique that is established allows for the formation of sub-10 nm features, produces diverse nanostructures, and preserves the crystallinity of the material. The lateral heterointerfaces created in this study also pave the way for the design of quantum-relevant geometries, flexible optoelectronics, and energy storage devices.

Electron Beam Irradiation-Induced Deoxidation and Atomic Flattening on the Copper Surface.

Electron beam (e-beam) has been developed for nanomaterial observation and moreover to induce structural evolutions in atomic scale. In this work, we demonstrate the deoxidation of cuprous oxide (Cu2O) and the formation of an atomically flat surface on a Cu nanowire by e-beam irradiation. To develop e-beam irradiation applications, the relation between e-beam radiation and the atomic surface is significant. Through the density functional theory simulation of atomic sputtering, an obvious disparity in the sputtering threshold has been found under different structural conditions, which leads to different structural evolutions. Both surface deoxidation and atomic surface flattening reactions have been identified as self-limiting and irreversible processes via in situ transmission electron microscope observation. Under e-beam irradiation, the dynamic mechanism of atomic surface flattening is driven by the convergence of total surface energy and confirmed by climbing-image nudged elastic band (ci-NEB) calculations. With precise control, e-beam irradiation reveals enormous potentials in atomic surface engineering.

A novel ABA functional analogue B2 enhances drought tolerance in wheat.

Drought stress negatively affects wheat growth and yield. Application of drought agent is an effective way to improve crop drought tolerance, therefore increasing crop yield. Based on the structure of abscisic acid (ABA), Pyrabactin and coronatine (COR), we designed the target compound B2. To investigate the function of B2 in alleviating drought stress on wheat, the drought-resistant variety ND212 and drought-sensitive variety LX99 were used under hydroponic conditions. The results showed that B2 had a similar function with ABA, especially 0.01 µmol·L-1 B2. Under drought stress conditions, 0.01 µmol·L-1 B2 increased the water content of wheat, enhanced the osmotic adjustment ability of leaves, and reduced the toxicity of reactive oxygen species on cells. What's more, 0.01 µmol·L-1 B2 improved the expression level of ABA-responsive genes TaSnRK2.4 and TaMYB3R1. It also improved the expression level of drought-responsive genes TaSRHP and TaERF3. Taken together, B2 enhanced drought tolerance in wheat by activating ABA signaling pathway.

Observing phase transformation in CVD-grown MoS2via atomic resolution TEM.

We utilized in situ transmission electron microscopy to observe phase transformation in CVD-grown MoS2. Significantly, the reaction was performed under electron irradiation through appropriate control of the electron dose and exposure time. Moreover, we proposed a new route between the 2H and 1T phases that involved the higher energy states TS1/TS2.

In Situ Investigation of Defect-Free Copper Nanowire Growth.

The fabrication and placement of high purity nanometals, such as one-dimensional copper (Cu) nanowires, for interconnection in integrated devices have been among the most important technological developments in recent years. Structural stability and oxidation prevention have been the key issues, and the defect control in Cu nanowire growth has been found to be important. Here, we report the synthesis of defect-free single-crystalline Cu nanowires by controlling the surface-assisted heterogeneous nucleation of Cu atomic layering on the graphite-like loop of an amorphous carbon (a-C) lacey film surface. Without a metal-catalyst or induced defects, the high quality Cu nanowires formed with high aspect ratio and high growth rate of 578 nm/s. The dynamic study of the growth of heterogeneous nanowires was conducted in situ with a high-resolution transmission electron microscope. The study illuminates the new mechanism by heterogeneous nucleation control and laying the groundwork for better understanding of heterosurface-assisted nucleation of defect-free Cu nanowire on a-C lacey film.

In Situ TEM Investigation of the Electrochemical Behavior in CNTs/MnO2-Based Energy Storage Devices.

Transition metal oxides have attracted much interest owing to their ability to provide high power density in lithium batteries; therefore, it is important to understand the electrochemical behavior and mechanism of lithiation-delithiation processes. In this study, we successfully and directly observed the structural evolution of CNTs/MnO2 during the lithiation process using transmission electron microscopy (TEM). CNTs/MnO2 were selected due to their high surface area and capacitance effect, and the lithiation mechanism of the CNT wall expansion was systematically analyzed. Interestingly, the wall spacings of CNTs/MnO2 and CNTs were obviously expanded by 10.92% and 2.59%, respectively. The MnO2 layer caused structural defects on the CNTs surface that could allow penetration of Li+ and Mn4+ through the tube wall and hence improve the ionic transportation speed. This study provided direct evidence for understanding the role of CNTs/MnO2 in the lithiation process used in lithium ion batteries and also offers potential benefits for applications and development of supercapacitors.

Interactions between mangroves and exotic Spartina in an anthropogenically disturbed estuary in southern China.

Cordgrass (Spartina alterniflora) was introduced to China in 1979 from the United States for reducing coastal erosion. It grows vigorously in China and has spread over much of the Chinese coast, from Leizhou Peninsula to Liaoning, a range of more than 19 degrees of latitude. On the southern coast of China, S. alterniflora has invaded mangrove-dominated habitats during the last two decades, but little is known about interactions between native mangroves and invasive S. alterniflora. We studied the distribution and competitive interactions between native mangroves and S. alterniflora in the Zhangjiang Estuary at four tidal sites along a salinity gradient: oligohaline upstream, mesohaline, polyhaline, and euhaline downstream. S. alterniflora occurred at all four sites, and several mangrove species occurred at all but the downstream euhaline site. S. alterniflora has invaded the estuary widely and has spread to the lower tidal margins of mangroves. It has not invaded mangrove areas with a closed canopy but has established in the mangrove zone where the canopy was opened by human disturbance. Ramets of S. alterniflora transplanted into the understory of mangrove stands with closed canopies died within 10 weeks, but 37.5% survived and grew well on open mud flats. S. alterniflora had virtually no competitive effect on mangrove seedlings planted at the upstream oligohaline site. However, S. alterniflora competitively reduced biomass of mangrove seedlings to 33% over a period of 14 weeks at the mesohaline and polyhaline sites where human disturbance has opened the mangrove canopy. In contrast, S. alterniflora marginally facilitated growth and survival of experimental seedlings at the downstream euhaline site. In China, mangroves occur along the coastline south of Whenzhou, but they have been severely disturbed and removed widely, mainly by mariculture activities. Natural vegetation patterns and our experimental results suggest that, without intervention, S. alterniflora could gradually replace these mangroves in mid-salinity regions of Chinese estuaries.