Quantifying the impact of upscaled parameters on radionuclide transport in three-dimensional fracture-matrix systems.

Assessing the long-term safety of geological repositories for high-level radioactive waste is critically dependent on understanding radionuclide transport in multi-scale fractured rocks. This study explores the influence of upscaled parameters on radionuclide movement within a three-dimensional fracture-matrix system using a discrete fracture-matrix (DFM) model. The developed numerical simulation workflow includes creating a random discrete fracture network, meshing of the fractures and matrix, assigning upscaled parameters, and conducting finite element simulations. We simulated the spatiotemporal evolution of radionuclide concentrations in the fractures and matrix over a century, revealing significant spatial heterogeneity driven by a heterogeneous seepage field. Employing geostatistics-based upscaling methods, we predicted the effective ranges of crucial solute transport parameters at the field scale. The matrix diffusion coefficient, matrix distribution coefficient, and longitudinal dispersivity were upscaled by factors of 2.0-3.0, 2.5-4.0, and 10-104, respectively, based on laboratory-scale measurements. Incorporating these upscaled parameters into the DFM model, we analyzed their impact on radionuclide transport. Our findings demonstrate that an upscaled matrix diffusion coefficient and matrix distribution coefficient result in a delayed transport of radionuclides in fractures by enhancing mass transfer between the fractures and rock matrix, while an upscaled longitudinal dispersivity accelerates transport by advancing the positions of concentration peaks. Sensitivity analysis revealed that the matrix distribution coefficient is the most impactful, followed by dispersivity and matrix diffusion coefficient. These insights are important for minimizing parameter uncertainties and enhancing the accuracy of predictions concerning radionuclide transport in multi-scale fractured rocks.

WRKY transcription factors in passion fruit analysis reveals key PeWRKYs involved in abiotic stress and flavonoid biosynthesis.

WRKY transcription factors (TFs) are a superfamily of regulators involved in plant responses to pathogens and abiotic stress. Passion fruit is famous for its unique flavor and nutrient-rich juice, but its growth is limited by environmental factors and pathogens. In this study, 55 WRKY genes were identified from the Passiflora edulis genome. The structure and evolutionary characteristics of PeWRKYs were analyzed using a bioinformatics approach. PeWRKYs were classified into seven subgroups (I, IIa, IIb, IIc, IId, IIe, III) according to their homologs in Arabidopsis thaliana. Group IIa PeWRKY48 gene was highly up-regulated under cold stress by RNA expression analysis, and transgenic PeWRKY48 in yeast and Arabidopsis showed resistance exposure to cold, salt, and drought stress. Metabolome and transcriptome co-expression analysis of two different disease resistance genotypes of P. edulis identified PeWRKY30 as a key TF co-expressed with flavonoid accumulation in yellow fruit P. edulis, which may contribute to biotic or abiotic resistance. The qRT-PCR verified the expression of key genes in different tissues of P. edulis and in different species of Passiflora. This study provides a set of WRKY candidate genes that will facilitate the genetic improvement of disease and abiotic tolerance in passion fruit.

Characterization of Dof Transcription Factors and the Heat-Tolerant Function of PeDof-11 in Passion Fruit (Passiflora edulis).

Abiotic stress is the focus of passion fruit research since it harms the industry, in which high temperature is an important influencing factor. Dof transcription factors (TFs) act as essential regulators in stress conditions. TFs can protect against abiotic stress via a variety of biological processes. There is yet to be published a systematic study of the Dof (PeDof) family of passion fruit. This study discovered 13 PeDof family members by using high-quality genomes, and the members of this characterization were identified by bioinformatics. Transcriptome sequencing and qRT-PCR were used to analyze the induced expression of PeDofs under high-temperature stress during three periods, in which PeDof-11 was significantly induced with high expression. PeDof-11 was then chosen and converted into yeast, tobacco, and Arabidopsis, with the findings demonstrating that PeDof-11 could significantly respond to high-temperature stress. This research lays the groundwork for a better understanding of PeDof gene regulation under high-temperature stress.

Investigating the influence of bentonite colloids on strontium sorption in granite under various hydrogeochemical conditions.

The disposal of high-level radioactive waste in deep geological repositories is a critical environmental issue. The presence of bentonite colloids generated in the engineering barrier can significantly impact the transport of radionuclides, but their effect on radionuclide sorption in granite remains poorly understood. This study aimed to investigate the sorption characteristics of strontium (Sr) on granite as well as on the coexistence system of granite and colloids under various hydrogeochemical conditions, through batch experiments. Fourier transform infrared spectroscopy was employed to analyze the sorption forms of Sr on granite before and after sorption. Several hydrogeochemical factors were examined, including contact time, pH, ionic strength, coexisting ions, and bentonite and humic acid colloid concentration. Among these factors, the concentration of bentonite colloids exhibited a significant effect on Sr sorption. Within a specific range of colloid concentration, the sorption of Sr on the solid system increased linearly with the bentonite colloid concentration. pH and ionic strength were also found to play crucial roles in the sorption process. At low pH, Sr sorption primarily occurred through the outer sphere's surface complexation and Na+/H+ ion exchange. However, at high pH, inner sphere surface complexation dominated the process. As the ionic strength increased, electrostatic repulsion gradually increased, resulting in fewer binding sites for particle aggregation and Sr sorption on bentonite colloids. The results also indicate that with increasing pH, the predominant forms of Sr in the solution transitioned from SrHCO3+ and SrCl+ to SrCO3 and SrCl+. This was mainly due to the ion exchange of Ca2+/Mg2+ in plagioclase and biotite, forming SrCO3 precipitation. These findings provide valuable insights into the transport behavior of radionuclides in the subsurface environment of the repository and highlight the importance of considering bentonite colloids and other hydrogeochemical factors when assessing the environmental impact of high-level radioactive waste disposal.

WITHDRAWN: Monochasma savatieri Inhibits the Migration of the Breast Cancer Cell Line MDA-MB-231

This article has been withdrawn from the journal Anti-Cancer Agents in Medicinal Chemistry due to a Conflict of Interest between the authors.Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused.The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorialpoliciesmain. php. BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

Comprehensive analysis of bZIP transcription factors in passion fruit.

The bZIP transcription factors are well-known transcriptional regulators that are essential for regulating resistance to biotic and abiotic stresses in plants. In this study, a total of 56 putative bZIP members were identified in passion fruit (Passiflora edulis). An integrative analysis was performed using bioinformatics. Transcriptome analysis revealed that most PebZIPs respond to drought, salt, cold and heat stress. By combining the transcriptome results of two different resistant genotypes, four representative members were finally selected for differential expression validation in different tissues and cultivars. Furthermore, transcriptome and metabolome association analysis revealed consistent expression trends of PeZIP20 and PeZIP21, with only one difference at 63aa, with different metabolites including flavonoids, lipids and amino acids. This work will contribute to further studies of the functions of bZIPs and their resistance properties, as well as to the development of novel germplasm.

Identification of the passion fruit (Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses.

Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.

Characterization of the NAC Transcription Factor in Passion Fruit (Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress.

The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.

Genome-Wide Association and Expression Analysis of the Lipoxygenase Gene Family in Passiflora edulis Revealing PeLOX4 Might Be Involved in Fruit Ripeness and Ester Formation.

Aroma is an important factor in fruit quality. Passiflora edulis (passion fruit) is popular among consumers because of its rich flavor and nutritional value. Esters are the main components of the volatile aroma of passion fruit. Lipoxygenase (LOX), as the first key enzyme upstream of esters, may play an important role in the formation of passion fruit aroma. In this study, a total of 12 passion fruit LOX (PeLOX) members were screened out based on the Passiflora edulis genome database, which were distributed unevenly on 6 chromosomes, all containing the highly conserved lipoxygenase domain and some containing the PLAT domain. The gene structure, evolutionary analysis and cis-acting elements of the family members were predicted in this study. Transcriptome analysis showed that 12 PeLOX genes had different degrees of response to different abiotic stresses (drought stress, salt stress, cold stress, and high temperature). PeLOX1, PeLOX2, PeLOX7, PeLOX11, and PeLOX12 responded significantly to various abiotic stresses, while PeLOX8 and PeLOX9 had little change in expression in all stresses. Quantitative real-time PCR (qRT-PCR) in six tissues revealed that the 12 PeLOX genes exhibited tissue expression specificity, and the relative expression of most genes were particularly high in the roots, stems, and fruits. Focusing on passion fruit ripening and ester synthesis, the transcriptomic analysis showed that with the increase in fruit development and fruit maturity, the expression levels of PeLOX1, PeLOX9, PeLOX11, and PeLOX12 showed downregulated expression, while PeLOX2 and PeLOX4 showed upregulated expression. In particular, the upregulation trend of PeLOX4 was the most obvious, and the qRT-PCR results were consistent with the transcriptome result. Pearson correlation analysis showed that with the development and ripening of fruit, the expression level of PeLOX4, LOX enzyme activity and total ester content all showed an increasing trend, in particular during the period when the peel was red and shrank (from T2 to T3 stage), the esters' contents increased by 37.4 times; the highest expression levels were all in the T3 period. The results indicated that PeLOX4 may be a candidate gene involved in fruit ripeness and the formation of volatile aroma compounds, with the increase in fruit ripening, the expression level of PeLOX4 increased and the LOX enzyme activity increased accordingly, thereby promoting the synthesis of volatile esters in fruit pulp. Our discovery lays the foundation for the functional study of LOX in passion fruit.

Plutonium reactive transport in fractured granite: Multi-species experiments and simulations.

Plutonium (Pu) in the subsurface environment can transport in different oxidation states as an aqueous solute or as colloidal particles. The transport behavior of Pu is affected by the relative abundances of these species and can be difficult to predict when they simultaneously exist. This study investigates the concurrent transport of Pu intrinsic colloids, Pu(IV)(aq) and Pu(V-VI)(aq) through a combination of controlled experiments and semi-analytical dual-porosity transport modeling. Pu transport experiments were conducted in a fractured granite at high and low flow rates to elucidate sorption processes and their scaling behavior. In the experiments, Pu(IV)(aq) was the least mobile of the Pu species, Pu(V-VI)(aq) had intermediate mobility, and the colloidal Pu, which consisted mainly of precipitated and/or hydrolyzed Pu(IV), was the most mobile. The semi-analytical modeling revealed that the sorption of each Pu species was rate-limited, as the sorption could not be described by assuming local equilibrium in the experiments. The model was able to describe the sorption of the different Pu species that occurring either on fracture surfaces, in the pores of the rock matrix, or simultaneously in both locations. While equally good fits to the data could be achieved using any of these assumptions, a fracture-dominated process was considered to be the most plausible because it provided the most reasonable estimates of sorption rate constants. Importantly, a key result of this work is that the sorption rate constant of all Pu species tends to decrease with increasing time scales, which implies that Pu will tend to be more mobile at longer time scales than observations at shorter time scales suggest. This result has important implications for predicting the environmental impacts of Pu in the safety assessments of geologic repositories for radioactive waste disposal, and we explore potential mechanistic bases for upscaling the sorption rate constants to time and distance scales that cannot be practically evaluated in experiments.

Genome-Wide Identification and Expression Analyses of the Aquaporin Gene Family in Passion Fruit (Passiflora edulis), Revealing PeTIP3-2 to Be Involved in Drought Stress.

Aquaporins (AQPs) in plants can transport water and small molecules, and they play an important role in plant development and abiotic stress response. However, to date, a comprehensive study on AQP family members is lacking. In this study, 27 AQP genes were identified from the passion fruit genome and classified into four groups (NIP, PIP, TIP, SIP) on the basis of their phylogenetic relationships. The prediction of protein interactions indicated that the AQPs of passion fruit were mainly associated with AQP family members and boron protein family genes. Promoter cis-acting elements showed that most PeAQPs contain light response elements, hormone response elements, and abiotic stress response elements. According to collinear analysis, passion fruit is more closely related to Arabidopsis than rice. Furthermore, three different fruit ripening stages and different tissues were analyzed on the basis of the transcriptome sequencing results for passion fruit AQPs under drought, high-salt, cold and high-temperature stress, and the results were confirmed by qRT-PCR. The results showed that the PeAQPs were able to respond to different abiotic stresses, and some members could be induced by and expressed in response to multiple abiotic stresses at the same time. Among the three different fruit ripening stages, 15 AQPs had the highest expression levels in the first stage. AQPs are expressed in all tissues of the passion fruit. One of the passion fruit aquaporin genes, PeTIP3-2, which was induced by drought stress, was selected and transformed into Arabidopsis. The survival rate of transgenic plants under drought stress treatment is higher than that of wild-type plants. The results indicated that PeTIP3-2 was able to improve the drought resistance of plants. Our discovery lays the foundation for the functional study of AQPs in passion fruit.

Radionuclide transport in multi-scale fractured rocks: A review.

Significant progress has been achieved on radionuclide transport in fractured rocks due to worldwide urgent needs for geological disposal of high-level radioactive waste (HLW). Transport models designed with accurately constrained parameters are a fundamental prerequisite to assess the long-term safety of repositories constructed in deep formations. Focusing on geological disposal systems of HLW, this study comprehensively reviews the behavoir of radionuclides and transport processes in multi-scale fractured rocks. Three issues in transport modeling are emphasized: 1) determining parameters of radionuclide transport models in various scales from laboratory- to field-scale experiments, 2) upscaling physical and chemical parameters across scales, and 3) characterizing fracture structures for radionuclide transport simulations. A broad spectrum of contents is covered relevant to radionuclide transport, including laboratory and field scale experiments, analytical and numerical solutions, parameter upscaling, and conceptual model developments. This paper also discusses the latest progress of radionuclide migration in multi-scale fractured rocks and the most promising development trends in the future. It provides valuable insights into understanding radionuclide transport and long-term safety assessment for HLW geological repository.

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims).

Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

Genome-Wide Assessment of Avocado Germplasm Determined from Specific Length Amplified Fragment Sequencing and Transcriptomes: Population Structure, Genetic Diversity, Identification, and Application of Race-Specific Markers.

Genomic data is a powerful tool. However, the phylogenetic relationships among different ecological races of avocado remain unclear. Here, we used the results from specific length amplified fragment sequencing (SLAF-seq) and transcriptome data to infer the population structure and genetic diversity of 21 avocado cultivars and reconstructed the phylogeny of three ecological races and two interracial hybrids. The results of the three analyses performed (unweighted pair-group methods with arithmetic means (UPGMA) cluster, Principal coordinate analysis (PCoA), and STRUCTURE) based on single nucleotide polymorphisms (SNPs) from SLAF-seq all indicated the existence of two populations based on botanical race: Mexican⁻Guatemalan and West Indian genotype populations. Our results based on SNPs from SLAF-seq indicated that the Mexican and Guatemalan races were more closely related to each other than either was to the West Indian race, which also was confirmed in the UPGMA cluster results based on SNPs from transcriptomic data. SNPs from SLAF-seq provided strong evidence that the Guatemalan, Mexican, and Guatemalan × Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan × West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated.

Diversity in S-layers.

Surface layers, referred simply as S-layers, are the two-dimensional crystalline arrays of protein or glycoprotein subunits on cell surface. They are one of the most common outermost envelope components observed in prokaryotic organisms (Archaea and Bacteria). Over the past decades, S-layers have become an issue of increasing interest due to their ubiquitousness, special features and functions. Substantial work in this field provides evidences of an enormous diversity in S-layers. This paper reviews and illustrates the diversity from several different aspects, involving the S-layer-carrying strains, the structure of S-layers, the S-layer proteins and genes, as well as the functions of S-layers.