mlsa-iai-msu-lab/ru_sci_bench_zho_cite_reranking huggingface dataset:
Does the Regional Ecological Security Pattern Benefit Eco-Environmental Protection? A Case Study of Yangtze River Delta

The construction of regional ecological security patterns (RESPs) has practical significance in guiding cross-regional synergistic ecological conservation; however, quantitative comparative studies within and beyond RESPs are lacking. Here, RESPs were constructed using the minimum cumulative resistance model for the Yangtze River Delta region as the case area, and land use and eco-environmental quality indices within and beyond RESPs were quantitatively analyzed. Ecological land dominated the land use categories within RESPs, with forestland and water bodies accounting for 40.93% and 32.46% of the total area, respectively. Land use within and beyond the RESP region differed in high-intensity land use regions, and the eco-environmental quality index (EQI) variations were notable. Among the analyzed cities, land use intensity within the RESP region was lower than that beyond the RESP region, and the EQI within the RESP region was generally higher than that beyond the RESP region. Land use intensities were typically less than 2% in southeastern Zhejiang and southern Anhui. The EQI data were supported by the examination of the remote sensing ecological index. The established RESP restricts the expansion of construction land and encourages ecological protection, according to the comparative analysis of land use transitions.
Spatial Risk Assessment and Source Identification of Heavy Metals in Riverine Sediments of Lake Chaohu Basin,China

In recent decades,the rivers in Lake Chaohu Basin have been subjected to intensive anthropogenic disturbance.However,previous studies have mainly focused on Lake Chaohu,and the inflowing and outflowing rivers have not been well examined.To characterize the pollution status of heavy metals in the entire Lake Chaohu Basin,8 heavy metals (Cu,Zn,Pb,Cr,Cd,As,Hg,and Ni) in riverine surface sediments were measured at 131 sampling sites in 7 subbasins.Spatial patterns and pollution characteristics were evaluated based on the potential ecological risk,geoaccumulation,and pollution load indexes.The results showed that Cr and Hg were the 2 main heavy metal pollutants in the surface sediments,with mean contents exceeding background values by a factor of 4.12 and 2.64,respectively.The Nanfei River (NF),which flows through Hefei city (a metropolis of the capital of Anhui Province),is characterized by large amounts of domestic and industrial waste discharged into the water body due to human activities;this waste caused serious heavy metal pollution,and NF substantially contributed to heavy metal pollution inputs to Lake Chaohu.Several subbasins in the southern part of Lake Chaohu Basin exhibited high concentrations of Cu in surface sediments,mainly from mining and agriculture.This study identified the main contamination areas,revealed the possible sources of each heavy metal,and can serve as a reference for the remediation and management of Lake Chaohu Basin to ensure the water safety of Lake Chaohu.
BreedingEIS:An Efficient Evaluation Information System for Crop Breeding

Crop breeding programs generate large datasets.Thus,it is difficult to ensure the accuracy and integrity of all the collected data in the breeding process.To improve breeding efficiency,we established an open source and free breeding evaluation information system (BreedingEIS).The full system is composed of a web client and a mobile client.The web client is used to name the individual breeding offspring plants and analyze data.The mobile client is based on the technology of widely used smartphones and is suitable for Android and iOS systems.Its functions focus on field evaluation,including quick response code recognition,evaluation data entry,and real-time viewing.In addition,near-field communication technology and portable label machines are introduced to enable breeders to quickly locate each individual plant and accurately label any samples collected from it.Generally,BreedingEIS enables users to accurately and conveniently register phenotypic data and quickly lock target individual plants from large volumes of data.The system provides a low-cost and highly efficient solution for crop information evaluation and enables breeders to better collect,manage,and use breeding data for decision making,which is a valuable resource for crop breeding.
Mapping and validation of the epistatic D and P genes controlling anthocyanin biosynthesis in the peel of eggplant (Solanum melongena L.) fruit

Fruit color is an important trait influencing the commercial value of eggplant fruits.Three dominant genes (D,P and Y) cooperatively control the anthocyanin coloration in eggplant fruits,but none has been mapped.In this study,two white-fruit accessions (19 141 and 19 147) and their F2 progeny,with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits,were used for mapping the D and P genes.A high-density genetic map was constructed with 5270 SNPs spanning 1997.98 cM.Three QTLs were identified,including two genes on chromosome 8 and one on chromosome 10.Gene expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D,respectively.We further identified (1) a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19 141,(2) a G base InDel in the promoter region leading to an additional cis-regulatory element and (3) a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1,in 19 147.Subsequently,these three variations were validated by PARMS technology as related to phenotypes in the F2 population.Moreover,silencing of SmANS or SmMYB1 in the purple red fruits of F1 (E3316) led to inhibition of anthocyanin biosynthesis in the peels.Conversely,overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19 141 and 19 147 respectively.Our findings demonstrated the epistatic interactions underlying the white color of eggplant fruits,which can be potentially applied to breeding of eggplant fruit peel color.
The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis

Fallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a wholegenome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.
Raman spectroscopy in crop quality assessment: focusing on sensing secondary metabolites: a review

As a crop quality sensor, Raman spectroscopy has been consistently proposed as one of the most promising and non-destructive methods for qualitative and quantitative analysis of plant substances, because it can measure molecular structures in a short time without requiring pretreatment along with simple usage. The sensitivity of the Raman spectrum to target chemicals depends largely on the wavelength, intensity of the laser power, and exposure time. Especially for plant samples, it is very likely that the peak of the target material is covered by strong fluorescence effects. Therefore, methods using lasers with low energy causing less fluorescence, such as 785 nm or near-infrared, are vigorously discussed. Furthermore, advanced techniques for obtaining more sensitive and clear spectra, like surface-enhanced Raman spectroscopy, time-gated Raman spectroscopy or combination with thin-layer chromatography, are being investigated. Numerous interpretations of plant quality can be represented not only by the measurement conditions but also by the spectral analysis methods. Up to date, there have been attempted to optimize and generalize analysis methods. This review summarizes the state of the art of micro-Raman spectroscopy in crop quality assessment focusing on secondary metabolites, from in vitro to in vivo and even in situ, and suggests future research to achieve universal application.
PsERF1B-PsMYB10.1-PsbHLH3 module enhances anthocyanin biosynthesis in the flesh-reddening of amber-fleshed plum (cv.Friar) fruit in response to cold storage

Flesh-reddening usually occurs in the amber-fleshed plum (Prunus salicina Lindl.) fruit during cold storage but not during ambient storage direct after harvest.It is not clear how postharvest cold signal is mediated to regulate the anthocyanin biosynthesis in the forming of flesh-reddening yet.In this study,anthocyanins dramatically accumulated and ethylene produced in the ‘Friar' plums during cold storage,in comparison with plums directly stored at ambient temperature.Expression of genes associated with anthocyanin biosynthesis,as well as transcription factors of PsMYB10.1,PsbHLH3,and PsERF1B were strongly stimulated to upregulated in the plums in the period of cold storage.Suppression of ethylene act with 1-methylcyclopropene greatly suppressed flesh-reddening and downregulated the expression of these genes.Transient overexpression and virus-induced gene silencing assays in plum flesh indicated that PsMYB10.1 encodes a positive regulator of anthocyanin accumulation.The transient overexpression of PsERF1B,coupled with PsMYB10.1 and PsbHLH3,could further prompt the anthocyanin biosynthesis in a tobacco leaf system.Results from yeast two-hybrid and luciferase complementation assays verified that PsERF1B directly interacted with PsMYB10.1.PsERF1B and PsMYB10.1 enhanced the activity of the promoter of PsUFGT individually,and the enhancement was prompted by the co-action of PsERF1B and PsMYB10.1.Overall,the stimulation of the PsERF1B-PsMYB10.1-PsbHLH3 module mediated cold signal in the transcriptomic supervision of the anthocyanin biosynthesis in the ‘Friar' plums.The results thereby revealed the underlying mechanism of the postharvest alteration of the flesh phenotype of ‘Friar' plums subjected to low temperature.
Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics

Carrot (Daucus carota) is an Apiaceae plant with multi-colored fleshy roots that provides a model system for carotenoid research. In this study, we assembled a 430.40 Mb high-quality gapless genome to the telomere-to-telomere (T2T) level of “Kurodagosun” carrot. In total, 36 268 genes were identified and 34 961 of them were functionally annotated. The proportion of repeat sequences in the genome was 55.3%, mainly long terminal repeats. Depending on the coverage of the repeats, 14 telomeres and 9 centromeric regions on the chromosomes were predicted. A phylogenetic analysis showed that carrots evolved early in the family Apiaceae. Based on the T2T genome, we reconstructed the carotenoid metabolic pathway and identified the structural genes that regulate carotenoid biosynthesis. Among the 65 genes that were screened, 9 were newly identified. Additionally, some gene sequences overlapped with transposons, suggesting replication and functional differentiation of carotenoid-related genes during carrot evolution. Given that some gene copies were barely expressed during development, they might be functionally redundant. Comparison of 24 cytochrome P450 genes associated with carotenoid biosynthesis revealed the tandem or proximal duplication resulting in expansion of CYP gene family. These results provided molecular information for carrot carotenoid accumulation and contributed to a new genetic resource.
Functional characterization of two flavone synthase II members in citrus

Polymethoxylated flavones (PMFs), the main form of flavones in citrus, are derived from the flavone branch of the flavonoid biosynthesis pathway. Flavone synthases (FNSs) are enzymes that catalyze the synthesis of flavones from flavanones. However, the FNS in citrus has not been characterized yet. Here, we identified two type II FNSs, designated CitFNSII-1 and CitFNSII-2, based on phylogenetics and transcriptome analysis. Both recombinant CitFNSII-1 and CitFNSII-2 proteins directly converted naringenin, pinocembrin, and liquiritigenin to the corresponding flavones in yeast. In addition, transient overexpression of CitFNSII-1 and CitFNSII-2, respectively, in citrus peel significantly enhanced the accumulation of total PMFs, while virus-induced CitFNSII-1 and CitFNSII-2 genes silencing simultaneously significantly reduced the expression levels of both genes and total PMF content in citrus seedlings. CitFNSII-1 and CitFNSII-2 presented distinct expression patterns in different cultivars as well as different developmental stages. Methyl salicylate (MeSA) treatment reduced the CitFNSII-2 expression as well as the PMFs content in the peel of Citrus sinensis fruit but did not affect the CitFNSII-1 expression. These results indicated that both CitFNSII-1 and CitFNSII-2 participated in the flavone biosynthesis in citrus while the regulatory mechanism governing their expression might be specific. Our findings improved the understanding of the PMFs biosynthesis pathway in citrus and laid the foundation for further investigation on flavone synthesis regulation.
Cannabis sativa: origin and history, glandular trichome development, and cannabinoid biosynthesis

Is Cannabis a boon or bane? Cannabis sativa has long been a versatile crop for fiber extraction (industrial hemp), traditional Chinese medicine (hemp seeds), and recreational drugs (marijuana). Cannabis faced global prohibition in the twentieth century because of the psychoactive properties of △9-tetrahydrocannabinol; however, recently, the perspective has changed with the recognition of additional therapeutic values, particularly the pharmacological potential of cannabidiol. A comprehensive understanding of the underlying mechanism of cannabinoid biosynthesis is necessary to cultivate and promote globally the medicinal application of Cannabis resources. Here, we comprehensively review the historical usage of Cannabis, biosynthesis of trichome-specific cannabinoids, regulatory network of trichome development, and synthetic biology of cannabinoids. This review provides valuable insights into the efficient biosynthesis and green production of cannabinoids, and the development and utilization of novel Cannabis varieties.
Multifaceted roles of LhWRKY44 in promoting anthocyanin accumulation in Asiatic hybrid lilies (Lilium spp.)

The Asiatic hybrid lily (Lilium spp.) is a horticultural crop with high commercial value and diverse anthocyanin pigmentation patterns. However, the regulatory mechanism underlying lily flower color has been largely unexplored. Here, we identified a WRKY transcription factor from lily tepals, LhWRKY44, whose expression was closely associated with anthocyanin accumulation. Functional verification indicated that LhWRKY44 positively regulated anthocyanin accumulation. LhWRKY44 physically interacted with LhMYBSPLATTER and directly bound to the LhMYBSPLATTER promoter, which enhanced the effect of the LhMYBSPLATTER-LhbHLH2 MBW complex activator on anthocyanin accumulation. Moreover, EMSA and dual-luciferase assays revealed that LhWRKY44 activated and bound to the promoters of gene LhF3H and the intracellular anthocyanin-related glutathione S-transferase gene LhGST. Interestingly, our further results showed that LhWRKY44 participated in light and drought-induced anthocyanin accumulation, and improved the drought tolerance in lily via activating stress-related genes. These results generated a multifaceted regulatory mechanism for the LhWRKY44-meditaed enhancement by the environmental signal pathway of anthocyanin accumulation and expanded our understanding of the WRKY-mediated transcriptional regulatory hierarchy modulating anthocyanin accumulation in Asiatic hybrid lilies.
Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator?

Recognized as a pivotal developmental transition, flowering marks the continuation of a plant’s life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.
MaMADS1-MaNAC083 transcriptional regulatory cascade regulates ethylene biosynthesis during banana fruit ripening

The hormone ethylene is crucial in the regulation of ripening in climacteric fruit, such as bananas. The transcriptional regulation of ethylene biosynthesis throughout banana fruit ripening has received much study, but the cascaded transcriptional machinery of upstream transcriptional regulators implicated in the ethylene biosynthesis pathway is still poorly understood. Here we report that ethylene biosynthesis genes, including MaACS1, MaACO1, MaACO4, MaACO5, and MaACO8, were upregulated in ripening bananas. NAC (NAM, ATAF, CUC) transcription factor, MaNAC083, a ripening and ethylene-inhibited gene, was discovered as a potential binding protein to the MaACS1 promoter by yeast one-hybrid screening. Further in vitro and in vivo experiments indicated that MaNAC083 bound directly to promoters of the five ethylene biosynthesis genes, thereby transcriptionally repressing their expression, which was further verified by transient overexpression experiments, where ethylene production was inhibited through MaNAC083-modulated transcriptional repression of ethylene biosynthesis genes in banana fruits. Strikingly, MaMADS1, a ripening-induced MADS (MCM1, AGAMOUS, DEFICIENS, SRF4) transcription factor, was found to directly repress the expression of MaNAC083, inhibiting trans-repression of MaNAC083 to ethylene biosynthesis genes, thereby attenuating MaNAC083-repressed ethylene production in bananas. These findings collectively illustrated the mechanistic basis of a MaMADS1-MaNAC083-MaACS1/MaACOs regulatory cascade controlling ethylene biosynthesis during banana fruit ripening. These findings increase our knowledge of the transcriptional regulatory mechanisms of ethylene biosynthesis at the transcriptional level and are expected to help develop molecular approaches to control ripening and improve fruit storability.
Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression

Cassava is a crucial crop that makes a significant contribution to ensuring human food security.However,high-quality telomere-totelomere cassava genomes have not been available up to now,which has restricted the progress of haploid molecular breeding for cassava.In this study,we constructed two nearly complete haploid resolved genomes and an integrated,telomere-to-telomere gap-free reference genome of an excellent cassava variety,‘Xinxuan 048',thereby providing a new high-quality genomic resource.Furthermore,the evolutionary history of several species within the Euphorbiaceae family was revealed.Through comparative analysis of haploid genomes,it was found that two haploid genomes had extensive differences in linear structure,transcriptome features,and epigenetic characteristics.Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway.The high heterozygosity of cassava ‘Xinxuan 048' leads to rapid trait segregation in the first selfed generation.This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.
Mathematical Analysis on a General Delayed HBV Model with Capsids and Two Infection Routes

Considering that HBV belongs to the DNA virus family and is hepatotropic, we model the HBV DNA-containing capsids as a compartment. In this paper, a delayed HBV infection model is established, where the general incidence function and two infection routes including cell-virus infection and cell-cell infection are introduced. According to some preliminaries, including well-posedness, basic reproduction number and existence of two equilibria, we obtain the threshold dynamics for the model. We illustrate numerical simulations to verify the above theoretical results, and furthermore explore the impacts of intracellular delay and cell-cell infection on the global dynamics of the model.
On Hamiltonian Property of Cayley Digraphs

Let G be a finite group generated by S and C(G, S)the Cayley digraphs of G with connection set S. In this paper, we give some sufficient conditions for the existence of hamiltonian circuit in C(G, S), where G = Z_m ⋊ H is a semiproduct of Z_m by a subgroup H of G. In particular, if m is a prime, then the Cayley digraph of G has a hamiltonian circuit unless G = Z_m × H. In addition, we introduce a new digraph operation, called φ-semiproduct of Γ_1 by Γ_2 and denoted by Γ_1 ⋊_φ Γ_2, in terms of mapping φ: V(Γ_2)→ {1,-1}. Furthermore we prove that C(Z_m, fag)⋊_φ C(H, S)is also a Cayley digraph if φ is a homomorphism from H to {1,-1} ≤ Z_m~*, which produces some classes of Cayley digraphs that have hamiltonian circuits.
THE SPARSE REPRESENTATION RELATED WITH FRACTIONAL HEAT EQUATIONS

This study introduces a pre-orthogonal adaptive Fourier decomposition(POAFD)to obtain approximations and numerical solutions to the fractional Laplacian initial value problem and the extension problem of Caffarelli and Silvestre(generalized Poisson equation). As a first step, the method expands the initial data function into a sparse series of the fundamental solutions with fast convergence, and, as a second step, makes use of the semigroup or the reproducing kernel property of each of the expanding entries. Experiments show the effectiveness and efficiency of the proposed series solutions.