Application of upscaling methods for fluid flow and mass transport in multi-scale heterogeneous media : A critical review

Physical and biogeochemical heterogeneity dramatically impacts fluid flow and reactive solute transport behaviors in geological formations across scales. From micro pores to regional reservoirs, upscaling has been proven to be a valid approach to estimate large-scale parameters by using data measured at small scales. Upscaling has considerable practical importance in oil and gas production, energy storage, carbon geologic sequestration, contamination remediation, and nuclear waste disposal. This review covers, in a comprehensive manner, the upscaling approaches available in the literature and their applications on various processes, such as advection, dispersion, matrix diffusion, sorption, and chemical reactions. We enclose newly developed approaches and distinguish two main categories of upscaling methodologies, deterministic and stochastic. Volume averaging, one of the deterministic methods, has the advantage of upscaling different kinds of parameters and wide applications by requiring only a few assumptions with improved formulations. Stochastic analytical methods have been extensively developed but have limited impacts in practice due to their requirement for global statistical assumptions. With rapid improvements in computing power, numerical solutions have become more popular for upscaling. In order to tackle complex fluid flow and transport problems, the working principles and limitations of these methods are emphasized. Still, a large gap exists between the approach algorithms and real-world applications. To bridge the gap, an integrated upscaling framework is needed to incorporate in the current upscaling algorithms, uncertainty quantification techniques, data sciences, and artificial intelligence to acquire laboratory and field-scale measurements and validate the upscaled models and parameters with multi-scale observations in future geo-energy research.© 2021 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)This work was jointly supported by the National Key Research and Development Program of China (No. 2018YFC1800900 ), National Natural Science Foundation of China (No: 41972249 , 41772253 , 51774136 ), the Program for Jilin University (JLU) Science and Technology Innovative Research Team (No. 2019TD-35 ), Graduate Innovation Fund of Jilin University (No: 101832020CX240 ), Natural Science Foundation of Hebei Province of China ( D2017508099 ), and the Program of Education Department of Hebei Province ( QN219320 ). Additional funding was provided by the Engineering Research Center of Geothermal Resources Development Technology and Equipment , Ministry of Education, China.fi=vertaisarvioitu|en=peerReviewed

In Vitro Inhibition of Acetylcholinesterase, Alphaglucosidase, and Xanthine Oxidase by Bacteria Extracts from Coral Reef in Hainan, South China Sea

Acetylcholinesterase is one of the most important enzymes in living organisms, which is responsible for the synapse cholinergic and other nervous processes. However, its inhibiting effects have proven to have pharmacological applications in the treatment of different diseases, as well as in the control of insect pests; thus, the search for inhibitors is a matter of interest for biomedical and agrochemical fields. Alzheimer’s is a progressive neurodegenerative disease, which can be seen as a wide degeneration of synapses, as well as neurons, in the cerebral cortex, hippocampus, and subcortical structures. Acetylcholinesterase inhibition is an important target for the management of Alzheimer’s. Additionally, diabetes mellitus is a chronic disease with clinical manifestation of hyperglycemia, due to the ineffective production of insulin that controls the level of blood glucose. Alphaglucosidaseinhibitors could retard the uptake of dietary carbohydrates and have shown significant therapeutic effects in clinical application. Fifty-five ethyl acetate extracts from nine bacterial families from Hainan (China) were evaluated to observe their acetylcholinesterase, alphaglucosidase, and xanthine oxidase inhibitory activity. Moreover, a screening of inhibitory activity against the pathogens fungi Fusarium oxysporum and Colletotrichum gloeosporioides was performed. The best acetylcholinesterase and alphaglucosidase inhibitory activity was shown by Vibrio neocaledonicus (98.95%). This is the first report of inhibition of both enzymes by ethyl acetate extract from this strain

Identificación de dianas moleculares del cáncer de mama que interactúan con moléculas presentes en los frutos de Antidesma bunius: análisis basado en farmacología de red in silico

The fruit of Antidesma bunius has both medicinal and edible properties. In previous studies, the fruit extract of A. bunius showed anti-proliferation activity on breast cancer cells, but its functional components and anti-tumor mechanism are still unclear. In this research, the main active components of A. bunius fruits (detected by UHPLC-MS/MS) and the corresponding targets were analyzed by network pharmacology method, and its interactions were verified by molecular docking to explore the possible tumor suppressor mechanisms. A total of 24 active chemical components were screened from fruits extract of A. bunius，and 44 targets genes were intersected with breast cancer, among them, AKT1, ESR1, EGFR, EP300, ERBB2 and AR were the top core targets．The GO enrichment of target genes mainly involved processes of cellular lipid metabolism, response to hormones, tube development, and KEGG pathway analysis centers in cancer pathways present in  breast, pancreatic and non-small cell lung cancer．The flavonoids in the fruits of A. bunius showed strong binding to the core targets by molecular docking analysis. These results strongly suggest that the flavonoids in the fruit of A. bunius can inhibit proliferation of breast cancer through multiple targets, mainly by ERK and PI3K-AKT pathways.El fruto de Antidesma bunius tiene propiedades medicinales y comestibles. En estudios anteriores, el extracto de fruta de A. bunius mostró actividad antiproliferativa en las células de cáncer de mama, pero sus componentes funcionales y mecanismo antitumoral aún no están claros. En esta investigación se analizaron los principales componentes activos de los frutos de A. bunius (detectados por UHPLC-MS / MS) y las dianas correspondientes mediante el método de farmacología en red, y se verificaron sus interacciones mediante acoplamiento molecular para explorar los posibles mecanismos supresores de tumores. Se seleccionaron un total de 24 componentes químicos activos del extracto de frutas de A. bunius, y 44 genes diana se cruzaron con el cáncer de mama, entre ellos, AKT1, ESR1, EGFR, EP300, ERBB2 y AR fueron los principales objetivos principales. de los genes diana involucraban principalmente procesos de metabolismo de lípidos celulares, respuesta a hormonas, desarrollo de tubos y centros de análisis de la vía KEGG en las vías del cáncer presentes en el cáncer de mama, páncreas y pulmón de células no pequeñas．Los flavonoides en los frutos de A. bunius mostraron fuertes unión a los objetivos centrales mediante análisis de acoplamiento molecular. Estos resultados sugieren fuertemente que los flavonoides en la fruta de A. bunius pueden inhibir la proliferación del cáncer de mama a través de múltiples dianas, principalmente por las vías ERK y PI3K-AKT

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

Characterization of the Passion Fruit (<i>Passiflora edulis</i> Sim) bHLH Family in Fruit Development and Abiotic Stress and Functional Analysis of <i>PebHLH56</i> in Cold Stress

Abiotic stress is the focus of research on passion fruit characters because of its damage to the industry. Basic helix-loop-helix (bHLH) is one of the Transcription factors (TFs) which can act in an anti-abiotic stress role through diverse biological processes. However, no systemic analysis of the passion fruit bHLH (PebHLH) family was reported. In this study, 117 PebHLH members were identified from the genome of passion fruit, related to plant stress resistance and development by prediction of protein interaction. Furthermore, the transcriptome sequencing results showed that the PebHLHs responded to different abiotic stresses. At different ripening stages of passion fruit, the expression level of most PebHLHs in the immature stage (T1) was higher than that in the mature stage (T2 and T3). Eight PebHLHs with differentially expressed under different stress treatments and different ripening stages were selected and verified by qRT-PCR. In this research, the expression of one member, PebHLH56, was induced under cold stress. Further, the promoter of PebHLH56 was fused to β-Galactosidase (GUS) to generate the expression vector that was transformed into Arabidopsis. It showed that PebHLH56 could significantly respond to cold stress. This study provided new insights into the regulatory functions of PebHLH genes during fruit maturity stages and abiotic stress, thereby improving the understanding of the characteristics and evolution of the PebHLH gene family

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

Transcriptome Sequencing of Different Avocado Ecotypes: <i>de novo</i> Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies

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&ndash;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 &times; Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan &times; West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated