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The current urban development in China has generally entered the stage of urban renewal. Facing the urban mix of old and new, different forms of collage picture, the urban design exploration of continuing the urban context has important theoretical value and practical significance for the urban renewal of the old urban area. Based on the analysis of the explicit and implicit context, this paper raises six strategies for urban design in the old city, namely texture improvement, building integration, interface reconstruction, information implantation, functional compounding, and benefit balancing. As an empirical evidence, the urban design of the old city further discusses the importance of the continuity of the context for urban renewal in the old city.

Road traffic accidents occur frequently and have significant impacts on life, property, and society. However, existing researches on road traffic accident risk pay little attention on establishing an effective road network model that accurately describes the transmission characteristics of traffic accident risk. As a result, the accuracy of risk evaluation is limited. To address this issue, we propose a network geographically weighted regression method based on arrival time cost. We conduct experiments using data from roads, traffic violations, traffic accidents, and urban points of interest (POIs) in a city from 2018 to 2020. The experimental results demonstrate that the network geographically weighted regression method, based on arrival time cost, incorporates the propagation nature of traffic accident risk on the road. It significantly reduces evaluation errors and effectively evaluates road traffic accident risk and its influencing factors. The downtown area of the city exhibits high accident risk, primarily concentrated at intersections with heavy traffic flow and certain road points with inadequate transportation facilities. The impact of different types of road traffic violations and urban POIs on the risk of road traffic accidents varies significantly and exhibits strong spatial heterogeneity.(道路交通事故频发，给生命财产造成重大损失，给社会生活带来重大影响。现有针对道路交通事故风险的研究未建立有效的道路网络模型，难以准确描述交通事故风险在道路上的传播特点，评估准确度不高。基于此，提出了一种基于抵达时间成本的网络地理加权回归方法，并利用某县级市2018—2020年的道路、交通违法、交通事故、城市POI等数据开展实验，结果表明，基于抵达时间成本的网络地理加权回归方法融合了交通事故风险在道路上的传播性质，显著降低了评估误差，能够有效评估道路交通事故风险及其影响因素；市中心区域道路交通事故高风险区域主要集中在车流量较大的道路交会处与部分交通设施尚不完备的道路；各类交通违法数量、城市POI对道路交通事故风险的影响程度不同，且具有很强的空间异质性。)

Abstract Background MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulated miRNAs have been identified in vegetative tissues in several plants, they are not well studied in reproductive tissues such as inflorescences. Results We used Illumina deep sequencing technology to sequence four small RNA libraries that were constructed from the inflorescences of rice plants that were grown under control condition and drought, cold, or salt stress. We identified 227 miRNAs that belong to 127 families, including 70 miRNAs that are not present in the miRBase. We validated 62 miRNAs (including 10 novel miRNAs) using published small RNA expression data in DCL1, DCL3, and RDR2 RNAi lines and confirmed 210 targets from 86 miRNAs using published degradome data. By comparing the expression levels of miRNAs, we identified 18, 15, and 10 miRNAs that were regulated by drought, cold and salt stress conditions, respectively. In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs). Conclusion We discovered novel miRNAs and stress-regulated miRNAs that may play critical roles in stress response in rice inflorescences. Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination.

Abstract Background Cowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes. Results We generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other. Conclusions These results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.

Abstract Background Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome component that can provide the raw material for novel selected functions and also indicate the mechanisms and history of genome evolution in any ancestral lineage. Despite their abundance, universality and significance, studies of genomic repeat content have been largely limited to analyses of the repeats in fully sequenced genomes. Results In order to facilitate a broader range of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been developed. This program, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in any genome. Testing of this program in maize indicated that it found and assembled all of the major repeats in one or more pseudomolecules, including coverage of the major Long Terminal Repeat retrotransposon families. Both Sanger sequence and 454 datasets were appropriate. Conclusion These results now indicate that hundreds of higher eukaryotic genomes can be efficiently characterized for the nature, abundance and evolution of their major repetitive DNA components.

Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber.

Simple Summary: Balclutha incisa is a widespread leafhopper found in the fields of rice and other crops, whose feeding habits and potential for pathogen transmission pose a threat to crop production. However, there is limited information about the viruses that B. incisa may carry. In this study, we used deep sequencing technology to examine the virome of B. incisa and reported the complete genomes of four novel viruses using rapid amplification of cDNA ends (RACE). Among these, B. incisa ollusvirus 1 (linear) and B. incisa ollusvirus 2 (circular) both exhibit the typical G-N-L genome structure characteristic of the order Jingchuvirales. Additionally, we identified two other viruses, B. incisa iflavirus 1 and B. incisa totivirus 1. Phylogenetic and sequence identity analyses suggest that these viruses represent new members of their respective families. Our study provides valuable insights into the virome of B. incisa and identifies four new viruses that may be potentially harmful to crops. Balclutha incisa (Cicadellidae: Deltocephalinae), a leafhopper prevalent in tropical and temperate regions, is notably abundant in grasses and rice. The virome of B. incisa was investigated using deep transcriptome sequencing, leading to the first identification of four viruses belonging to the families Aliusviridae, Iflaviridae, and Totiviridae in B. incisa. These viruses have been provisionally named B. incisa ollusvirus 1 (BiOV1), B. incisa ollusvirus 2 (BiOV2), B. incisa iflavirus 1 (BiIV1), and B. incisa totivirus 1 (BiTV1). The complete genome sequences of these viruses were obtained through rapid amplification of cDNA ends (RACE). BiOV1 has a linear genome of 15,125 nucleotides (nt), while BiOV2 possesses a circular genome of 14,853 nt. The BiIV1 genome, excluding the poly(A) tail, is 10,903 nt in length and encodes a single open reading frame (ORF) for a polyprotein consisting of 3194 amino acids (aa). The BiTV1 genome is 4357 nt long and contains two overlapping ORFs, with the viral RNA-dependent RNA polymerase (RdRp) translated via a −1 ribosomal frameshift. Phylogenetic and sequence identity analyses suggest that all these viruses are novel members of their respective families. This study significantly expands our understanding of the virome associated with B. incisa by reporting and characterizing these novel viruses. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored the roles of TEs in the genomes of Citrus and Citrus-related genera by constructing a pan-genome TE library from 20 published genomes of Citrus and Citrus-related accessions. Our results revealed an increase in TE content and the number of TE types compared to the original annotations, as well as a decrease in the content of unclassified TEs. The average length of TEs per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) to 64.76% (Citrus gilletiana) of the genomes, with a mean value of 56.95%. A significant positive correlation was found between genome size and both the number of TE types and TE content. Consistent with the difference in mean whole-genome size (39.83 Mb) between Citrus and Citrus-related genera, Citrus genomes contained an average of 34.36 Mb more TE sequences than Citrus-related genomes. Analysis of the estimated insertion time and half-life of long terminal repeat retrotransposons (LTR-RTs) suggested that TE removal was not the primary factor contributing to the differences among genomes. These findings collectively indicate that TEs are the primary determinants of genome size and play a major role in shaping genome structures. Principal coordinate analysis (PCoA) of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers revealed that the fragmented TEs were predominantly derived from ancestral genomes, while intact TEs were crucial in the recent evolutionary diversification of Citrus. Moreover, the presence or absence of intact TEs near the AdhE superfamily was closely associated with the bitterness trait in the Citrus species. Overall, this study enhances TE annotation in Citrus and Citrus-related genomes and provides valuable data for future genetic breeding and agronomic trait research in Citrus. [ABSTRACT FROM AUTHOR]

The evolutionarily conserved target of rapamycin (TOR) kinase acts as a master regulator that coordinates cell proliferation and growth by integrating nutrient, energy, hormone and stress signals in all eukaryotes.sup.1,2. Research has focused mainly on TOR-regulated translation, but how TOR orchestrates the global transcriptional network remains unclear. Here we identify ethylene-insensitive protein 2 (EIN2), a central integrator.sup.3-5 that shuttles between the cytoplasm and the nucleus, as a direct substrate of TOR in Arabidopsis thaliana. Glucose-activated TOR kinase directly phosphorylates EIN2 to prevent its nuclear localization. Notably, the rapid global transcriptional reprogramming that is directed by glucose-TOR signalling is largely compromised in the ein2-5 mutant, and EIN2 negatively regulates the expression of a wide range of target genes of glucose-activated TOR that are involved in DNA replication, cell wall and lipid synthesis and various secondary metabolic pathways. Chemical, cellular and genetic analyses reveal that cell elongation and proliferation processes that are controlled by the glucose-TOR-EIN2 axis are decoupled from canonical ethylene-CTR1-EIN2 signalling, and mediated by different phosphorylation sites. Our findings reveal a molecular mechanism by which a central signalling hub is shared but differentially modulated by diverse signalling pathways using distinct phosphorylation codes that can be specified by upstream protein kinases. In Arabidopsis, phosphorylation of EIN2 by TOR kinase in the presence of glucose prevents the nuclear localization of EIN2, showing that the glucose-TOR-EIN2 axis regulates the transcriptome independently of ethylene signalling pathways., Author(s): Liwen Fu [sup.1] [sup.2] , Yanlin Liu [sup.2] , Guochen Qin [sup.1] , Ping Wu [sup.3] , Hailing Zi [sup.1] , Zhongtian Xu [sup.1] , Xiaodi Zhao [sup.2] , [...]

Leafhoppers are economically important pests and may serve as vectors for pathogenic viruses that cause substantial crop damage. In this study, using deep transcriptome sequencing, we identified three novel viruses within the order Mononegavirales, including two viruses belonging to the family Rhabdoviridae and one to the family Lispiviridae. The complete genome sequences were obtained via the rapid amplification of cDNA ends and tentatively named Recilia dorsalis rhabdovirus 1 (RdRV1, 14,251 nucleotides, nt), Nephotettix virescens rhabdovirus 1 (NvRV1, 13,726 nt), and Nephotettix virescens lispivirus 1 (NvLV1, 14,055 nt). The results of a phylogenetic analysis and sequence identity comparison suggest that RdRV1 and NvRV1 represent novel species within the family Rhabdoviridae, while NvLV1 is a new virus belonging to the family Lispiviridae. As negative-sense single-strand RNA viruses, RdRV1 and NvRV1 contain the conserved transcription termination signal and intergenic trinucleotides in the non-transcribed region. Intergenomic sequence and transcriptome profile analyses suggested that all these genes were co-transcriptionally expressed in these viral genomes, facilitated by specific intergenic trinucleotides and putative transcription initiation sequences. [ABSTRACT FROM AUTHOR]

Simple Summary: The homopteran insect, Pyrops candelaria (longan lanternfly), mainly harms longan trees, lychees, olives and other crops by absorbing the sap on the trunk. In this study, the reverse etiology method was used to find the pathogens carried by P. candelaria. Through RNA–seq, we found a new iflavirus in P. candelaria, which was first reported in P. candelaria, and we named it PyCaV (Pyrops candelaria associated virus). Identified by a pair of specific primers, it is worth noting that the presence of PyCaV can be identified in the head, chest and abdomen of P. candelaria, and that PyCaV infection rate of P. candelaria is affected by time and location. The above results provide new insights to reveal the role of P. candelaria as a potential vehicle for microbial pathogens and extend our understanding to iflavirus. Pyrops candelaria is one of the common pests of fruit trees, but the research on the pathogenic microorganisms it may carry is very limited. Therefore, it is essential to reveal the pathogenic microbes it carries and their potential hazards. This study found a new virus from the transcriptome of P. candelaria, which was first reported in P. candelaria and named PyCaV (Pyrops candelaria associated virus). RACE and bioinformatics assay revealed that the full length of PyCaV is 10,855 bp with the polyA tail, containing a single open-reading frame (ORF) encoding a polyprotein consisting of 3171 amino acid (aa). The virus has a typical iflavirus structure, including two rhv domains, an RNA helicase domain (HEL), a 3C cysteine protease domain (Pro), and an RNA–dependent RNA polymerase domain (RdRp). Further phylogenetic analysis revealed that this virus belongs to family Iflaviridae and sequence alignments analysis suggested PyCaV is a new member in an unassigned genus of family Iflaviridae. Further in-depth analysis of the virus infection showed that PyCaV is distributed throughout the whole P. candelaria, including its head, chest, and abdomen, but more PyCaV was identified in the chest. The distribution of PyCaV in different parts of P. candelaria was further explored, which showed that more PyCaV was detected in its piercing–sucking mouthparts and chest viscera. Statistical analysis showed that the PyCaV infection was affected by time and location. [ABSTRACT FROM AUTHOR]

Land surface temperature (LST) has a wide application in Earth Science-related fields, and spatial downscaling is an important method to retrieve high-resolution LST data. However, existing LST downscaling methods have difficulties in simultaneously constructing and expressing spatial non-stationarity, spatial autocorrelation, and complex non-linearity during the LST downscaling process, which limits the performance of the models. Moreover, there is a lack of research on high-resolution nighttime land surface temperature (NLST) reconstruction based on spatial downscaling, which does not meet the data needs for urban-scale nighttime urban heat island (UHI) studies. Therefore, this study combined Geographically Neural Network Weighted Regression (GNNWR) with Area-to-Point Kriging interpolation (ATPK) to propose a Geographically Neural Network Weighted Regression Kriging (GNNWRK) model for NLST downscaling. To verify the model's generality and robustness, this study selected four study areas with different landform and climate type for NLST spatial downscaling experiments. The GNNWRK was compared with four benchmark downscaling methods, including TsHARP, Random Forest, Geographically Weighted Regression, and GNNWR. The results show that compared to these four benchmark methods, the GNNWRK method has higher accuracy in NLST downscaling, with a maximum Pearson's Correlation Coefficient (Pcc) of 0.930 and a minimum Root Mean Square Error (RMSE) of 0.886 K. Moreover, the validation based on MODIS NLST data and ground-measured NLST data also indicates that the GNNWRK model can obtain more accurate, high-resolution NLST with richer and more detailed texture. This enhances the potential of NLST in studying the effects of urban nighttime heat islands at a finer scale. [ABSTRACT FROM AUTHOR]

Plant meristems are responsible for the generation of all plant tissues and organs. Here we show that the transcription factor (TF) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) plays an important role in both floral meristem (FM) determinacy and shoot apical meristem maintenance in Arabidopsis, in addition to its well-known multifaceted roles in plant growth and development during the vegetative stage. Through genetic analyses, we show that WUSCHEL (WUS) and CLAVATA3 (CLV3), two central players in the establishment and maintenance of meristems, are epistatic to FHY3 Using genome-wide ChIP-seq and RNA-seq data, we identify hundreds of FHY3 target genes in flowers and find that FHY3 mainly acts as a transcriptional repressor in flower development, in contrast to its transcriptional activator role in seedlings. Binding motif-enrichment analyses indicate that FHY3 may coregulate flower development with three flower-specific MADS-domain TFs and four basic helix-loop-helix TFs that are involved in photomorphogenesis. We further demonstrate that CLV3, SEPALLATA1 (SEP1), and SEP2 are FHY3 target genes. In shoot apical meristem, FHY3 directly represses CLV3, which consequently regulates WUS to maintain the stem cell pool. Intriguingly, CLV3 expression did not change significantly in fhy3 and phytochrome B mutants before and after light treatment, indicating that FHY3 and phytochrome B are involved in light-regulated meristem activity. In FM, FHY3 directly represses CLV3, but activates SEP2, to ultimately promote FM determinacy. Taken together, our results reveal insights into the mechanisms of meristem maintenance and determinacy, and illustrate how the roles of a single TF may vary in different organs and developmental stages.

The genus Phytophthora consists of many notorious pathogens of crops and forestry trees. At present, battling Phytophthora diseases is challenging due to a lack of understanding of their pathogenesis. We investigated the role of small RNAs in regulating soybean defense in response to infection by Phytophthora sojae, the second most destructive pathogen of soybean. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are universal regulators that repress target gene expression in eukaryotes. We identified known and novel small RNAs that differentially accumulated during P. sojae infection in soybean roots. Among them, miR393 and miR166 were induced by heat-inactivated P. sojae hyphae, indicating that they may be involved in soybean basal defense. Indeed, knocking down the level of mature miR393 led to enhanced susceptibility of soybean to P. sojae; furthermore, the expression of isoflavonoid biosynthetic genes was drastically reduced in miR393 knockdown roots. These data suggest that miR393 promotes soybean defense against P. sojae. In addition to miRNAs, P. sojae infection also resulted in increased accumulation of phased siRNAs (phasiRNAs) that are predominantly generated from canonical resistance genes encoding nucleotide binding-leucine rich repeat proteins and genes encoding pentatricopeptide repeat-containing proteins. This work identifies specific miRNAs and phasiRNAs that regulate defense-associated genes in soybean during Phytophthora infection.