Microbial profiling identifies potential key drivers in gastric cancer patients

Gastric cancer (GC) is the fifth most commonly diagnosed cancer and the third leading cause of cancer-related death in the world. Microbiota is believed to be associated with GC. Growing evidences showed Helicobacter pylori played a key role in GC development. However, little was known about the microbiota in gastric juices and tissues in GC patients, and thus it was difficult to understand other potential microbial causation for GC. Here, we collected the gastric juice and surgically removed gastric tissues from GC patients to give insight into GC microbiota. Most microbes identified in the gastric samples were opportunistic pathogens or resident flora of the human microbiota. Further network analyses identified five opportunistic pathogens as keystone species. H. pylori is the direct cause of GC, but other opportunistic microbes might also function in GC development. The microbiota in the gastric juice and gastric tissue of the GC patients were complex, and some dominant opportunistic pathogens contributed to the GC development. This study introduces microbiota in gastric juice, gastric normal tissue and gastric cancer tissue of GC patients, and highlights the potential keystone microbes functioned during GC development

The Role of EjSOC1s in Flower Initiation in Eriobotrya japonica

The MADS-box transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates environmental and endogenous signals to promote flowering in Arabidopsis. However, the role of SOC1 homologs in regulating flowering time in fruit trees remains unclear. To better understand the molecular mechanism of flowering regulation in loquat (Eriobotrya japonica Lindl.), two SOC1 homologs (EjSOC1-1 and EjSOC1-2) were identified and characterized in this work. Sequence analysis showed that EjSOC1-1 and EjSOC1-2 have conserved MADS-box and K-box domains. EjSOC1-1 and EjSOC1-2 were clearly expressed in vegetative organs, and high expression was detected in flower buds. As observed in paraffin-embedded sections, expression of the downstream flowering genes EjAP1s and EjLFYs started to increase at the end of June, a time when flower bud differentiation occurs. Additionally, high expression of EjSOC1-1 and EjSOC1-2 began 10 days earlier than that of EjAP1s and EjLFYs in shoot apical meristem (SAM). EjSOC1-1 and EjSOC1-2 were inhibited by short-day (SD) conditions and exogenous GA3, and flower bud differentiation did not occur after these treatments. EjSOC1-1 and EjSOC1-2 were found to be localized to the nucleus. Moreover, ectopic overexpression of EjSOC1-1 and EjSOC1-2 in wild-type Arabidopsis promoted early flowering, and overexpression of both was able to rescue the late flowering phenotype of the soc1-2 mutant. In conclusion, the results suggest that cultivated loquat flower bud differentiation in southern China begins in late June to early July and that EjSOC1-1 and EjSOC1-2 participate in the induction of flower initiation. These findings provide new insight into the artificial regulation of flowering time in fruit trees

Expression of aspartyl protease and C3HC4-type RING zinc finger genes are responsive to ascorbic acid in Arabidopsis thaliana

Ascorbate (AsA) is a redox buffer and enzyme cofactor with various proposed functions in stress responses and growth. The aim was to identify genes whose transcript levels respond to changes in leaf AsA. The AsA-deficient Arabidopsis mutant vtc2-1 was incubated with the AsA precursor L-galactono-1,4-lactone (L-GalL) to increase leaf AsA concentration. Differentially expressed genes screened by DNA microarray were further characterized for AsA responsiveness in wild-type plants. The analysis of 14 candidates by real-time PCR identified an aspartyl protease gene (ASP, At1g66180) and a C3HC4-type RING zinc finger gene (AtATL15, At1g22500) whose transcripts were rapidly responsive to increases in AsA pool size caused by L-GalL and AsA supplementation and light. Transgenic Arabidopsis plants expressing an AtATL15 promoter::luciferase reporter confirmed that the promoter is L-GalL, AsA, and light responsive. The expression patterns of ASP and AtATL15 suggest they have roles in growth regulation. The promoter of AtATL15 is responsive to AsA status and will provide a tool to investigate the functions of AsA in plants further

Translocation and the alternative D-galacturonate pathway contribute to increasing the ascorbate level in ripening tomato fruits together with the D-mannose/L-galactose pathway

The D-mannose/L-galactose pathway for the biosynthesis of vitamin C (L-ascorbic acid; AsA) has greatly improved the understanding of this indispensable compound in plants, where it plays multifunctional roles. However, it is yet to be proven whether the same pathway holds for all the different organs of plants, especially the fruit-bearing plants, at different stages of development. Micro-Tom was used here to elucidate the mechanisms of AsA accumulation and regulation in tomato fruits. The mRNA expression of the genes in the D-mannose/L-galactose pathway were inversely correlated with increasing AsA content of Micro-Tom fruits during ripening. Feeding L-[6-14C]AsA to Micro-Tom plants revealed that the bulk of the label from AsA accumulated in the source leaf was transported to the immature green fruits, and the rate of translocation decreased as ripening progressed. L-Galactose feeding, but neither D-galacturonate nor L-gulono-1,4-lactone, enhanced the content of AsA in immature green fruit. On the other hand, L-galactose and D-galacturonate, but not L-gulono-1,4-lactone, resulted in an increase in the AsA content of red ripened fruits. Crude extract prepared from insoluble fractions of green and red fruits showed D-galacturonate reductase- and aldonolactonase-specific activities, the antepenultimate and penultimate enzymes, respectively, in the D-galacturonate pathway, in both fruits. Taken together, the present findings demonstrated that tomato fruits could switch between different sources for AsA supply depending on their ripening stages. The translocation from source leaves and biosynthesis via the D-mannose/L-galactose pathway are dominant sources in immature fruits, while the alternative D-galacturonate pathway contributes to AsA accumulation in ripened Micro-Tom fruits

Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe

Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees. Here, we reveal how WGD laid the foundation for co-option and differentiation of medicinally important ursane triterpene pathway duplicates, generating distinct chemotypes between species and between developmental stages in the apple tribe. After generating chromosome-level assemblies of a widely cultivated loquat variety and Gillenia trifoliata, we define differentially evolved, duplicated gene pathways and date the WGD in the apple tribe at 13.5 to 27.1 Mya, much more recent than previously thought. We then functionally characterize contrasting metabolic pathways responsible for major triterpene biosynthesis in G. trifoliata and loquat, which pre- and postdate the Maleae WGD, respectively. Our work mechanistically details the metabolic diversity that arose post-WGD and provides insights into the genomic basis of medicinal properties of loquat, which has been used in both traditional and modern medicines

Assessment of global shipping risk caused by maritime piracy

Due to the frequent occurrence of piracy incidents, normal trade, and transportation activities have been hindered. This paper uses the Piracy and Armed Robbery dataset in the Global Integrated Shipping Information System to analyze the types and evolutionary characteristics of shipping risk caused by piracy and the piracy behavior patterns in different seas. This study found that there are three regions with high incidence of piracy in the world, and their gathering centers change dynamically over time. Piracy incidents can be divided into four categories based on the quantitative assessment of shipping risk caused by piracy. Shipping risk caused by piracy shows different evolution characteristics in different seas, affected by factors such as the evolution of national political situations and anti-piracy measures. Based on the qualitative assessment of the shipping risk caused by piracy, the piracy corpus reflects the diverse patterns of piracy in different seas. In the process of pirate attacks, the diversity is mainly manifested in violence and selectivity. In the consequences of pirate attacks, the targets that pirates pay attention to vary significantly in different seas. This research will help to strengthen the dynamic monitoring of shipping risk caused by piracy, and further contribute to the research on maritime transport safety

Analysis of major triterpene acids and total polysaccharides in the leaves of 11 species of

Loquat (Eriobotrya japonica) is a subtropical tree with commercially important fruit and with leaves that have medicinal uses against cough and asthma. Leaves contain significant amounts of phenols, flavonoids, triterpene acids, and polysaccharides. However, information of the triterpene acids and polysaccharides in leaves is limited. In this study, the contents of five major triterpene acids and total polysaccharides in the leaves of 11 species of Eriobotrya were determined using RP-HPLC and phenol-sulfuric acid method, respectively. Total concentration of triterpene acids varied from 8.38 to 22.35 mg g-1 DW. The concentration of triterpene acids was greater than 20 mg g-1 DW in E. bengalensis, E. prinoides and E. fragrans, and it was less than 10.0 mg g-1 DW in E. elliptica. Different drying temperature (40-80°C) of leaves did not affect the content of polysaccharides with highest content (80.8 mg g-1 DW) from E. prinoides. The contents of triterpene acid in six wild species and polysaccharides in 5 wild species were higher than that in cultivated loquat

Augmented Grad-CAM++: Super-Resolution Saliency Maps for Visual Interpretation of Deep Neural Network

In recent years, deep neural networks have shown superior performance in various fields, but interpretability has always been the Achilles’ heel of deep neural networks. The existing visual interpretation methods for deep neural networks still suffer from inaccurate and insufficient target localization and low-resolution saliency maps. To address the above issues, this paper presents a saliency map generation method based on image geometry augmentation and super-resolution called augmented high-order gradient weighting class activation mapping (augmented grad-CAM++). Unlike previous approaches that rely on a single input image to generate saliency maps, this method first introduces the image geometry augmentation technique to create a set of augmented images for the input image and generate activation mappings separately. Secondly, the augmented activation mappings are combined to form the final saliency map. Finally, a super-resolution technique is introduced to add pixel points to reconstruct the saliency map pixels to improve the resolution of the saliency map. The proposed method is applied to analyze standard image data and industrial surface defect images. The results indicate that, in experiments conducted on standard image data, the proposed method achieved a 3.1% improvement in the accuracy of capturing target objects compared to traditional methods. Furthermore, the resolution of saliency maps was three times higher than that of traditional methods. In the application of industrial surface defect detection, the proposed method demonstrated an 11.6% enhancement in the accuracy of capturing target objects, concurrently reducing the false positive rate. The presented approach enables more accurate and comprehensive capture of target objects with higher resolution, thereby enhancing the visual interpretability of deep neural networks. This improvement contributes to the greater interpretability of deep learning models in industrial applications, offering substantial performance gains for the practical deployment of deep learning networks in the industrial domain

Characterization of Carotenoid Accumulation and Carotenogenic Gene Expression During Fruit Development in Yellow and White Loquat Fruit

Accumulation of carotenoids in peel and pulp of the yellow-fleshed loquat ‘Zaozhong 6’ (ZZ6) and the white-fleshed loquat ‘Baiyu’ (BY) were tracked during different fruit development stages, and the expression of 15 carotenogenic genes were analyzed. During loquat fruit ripening the fresh weight content of β-carotene in peel and pulp of ZZ6 increased gradually and peaked at the fully ripe stage, reaching 68.53 µg⋅g−1 FW in the peel and 11.92 µg⋅g−1 FW in the pulp. In BY, the content of β-carotene in the peel increased and peaked at the fully ripe stage, reaching 38.89 µg⋅g−1 FW, while it decreased in the pulp from the original 0.47 µg⋅g−1 FW and reduced to 0.29 µg⋅g−1 FW. The content of β-cryptoxanthin in the peel and pulp of ZZ6 and BY both increased steadily, and peaked at the fully ripe stage; however, the content of lutein decreased in the peel of ZZ6 and increased in the pulp, but in BY, it dropped and then rose in the peel. There was no significant change of β-cryptoxanthin in the pulp of BY. After the breaker stage, the mRNA levels of phytoene synthase (PSY) and chromoplast-specific lycopene β-cyclase (CYCB) were higher in the peel, while CYCB and β-carotene hydroxylase (BCH) mRNAs were higher in the flesh of ZZ6, compared with BY. The results showed that the expression level of PSY, CYCB, and BCH appeared to cooperatively regulate the accumulation of carotenoids