Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton.

Cotton, an intriguing plant species shaped by polyploidization, evolution, and domestication, holds particular interest due to the complex mechanisms governing fiber traits across its two subgenomes. However, the regulatory elements or transcriptional networks between subgenomes during fiber elongation remain to be fully clarified. Here, we analyzed 1462 cotton fiber samples to reconstruct the gene-expression regulatory networks that influence fiber cell elongation. Inter-subgenome expression quantitative trait loci (eQTLs) largely dictate gene transcription, with a notable tendency for the D subgenome to regulate A-subgenome eGenes. This regulation reveals synchronized homoeologous gene expression driven by co-localized eQTLs and divergent patterns that diminish genetic correlations, thus leading to preferential expression in the A and D subgenomes. Hotspot456 emerged as a key regulator of fiber initiation and elongation, and artificial selection of trans-eQTLs in hotspot456 that positively regulate KCS1 has facilitated cell elongation. Experiments designed to clarify the roles of trans-eQTLs in improved fiber breeding confirmed the inhibition of GhTOL9 by a specific trans-eQTL via GhWRKY28, which negatively affects fiber elongation. We propose a model in which the GhWRKY28-GhTOL9 module regulates this process through the ESCRT (endosomal sorting complex required for transport) pathway. This research significantly advances our understanding of cotton's evolutionary and domestication processes and the intricate regulatory mechanisms that underlie significant plant traits.

Promotion of apoplastic oxidative burst by artificially selected GhCBSX3A enhances Verticillium dahliae resistance in upland cotton.

Verticillium wilt (VW) is a devasting disease affecting various plants, including upland cotton, a crucial fiber crop. Despite its impact, the genetic basis underlying cotton's susceptibility or defense against VW remains unclear. Here, we conducted a genome-wide association study on VW phenotyping in upland cotton and identified a locus on A13 that is significantly associated with VW resistance. We then identified a cystathionine ß-synthase domain gene at A13 locus, GhCBSX3A, which was induced by Verticillium dahliae. Functional analysis, including expression silencing in cotton and overexpression in Arabidopsis thaliana, confirmed that GhCBSX3A is a causal gene at the A13 locus, enhancing SAR-RBOHs-mediated apoplastic oxidative burst. We found allelic variation on the TATA-box of GhCBSX3A promoter attenuated its expression in upland cotton, thereby weakening VW resistance. Interestingly, we discovered that altered artificial selection of GhCBSX3A_R (an elite allele for VW) under different VW pressures during domestication and other improved processes allows specific human needs to be met. Our findings underscore the importance of GhCBSX3A in response to VW, and we propose a model for defense-associated genes being selected depending on the pathogen's pressure. The identified locus and gene serve as promising targets for VW resistance enhancement in cotton through genetic engineering.

Prospective observational study on biomarkers of response in pancreatic ductal adenocarcinoma.

Adjuvant chemotherapy benefits patients with resected pancreatic ductal adenocarcinoma (PDAC), but the compromised physical state of post-operative patients can hinder compliance. Biomarkers that identify candidates for prompt adjuvant therapy are needed. In this prospective observational study, 1,171 patients with PDAC who underwent pancreatectomy were enrolled and extensively followed-up. Proteomic profiling of 191 patient samples unveiled clinically relevant functional protein modules. A proteomics-level prognostic risk model was established for PDAC, with its utility further validated using a publicly available external cohort. More importantly, through an interaction effect regression analysis leveraging both clinical and proteomic datasets, we discovered two biomarkers (NDUFB8 and CEMIP2), indicative of the overall sensitivity of patients with PDAC to adjuvant chemotherapy. The biomarkers were validated through immunohistochemistry on an internal cohort of 386 patients. Rigorous validation extended to two external multicentic cohorts-a French multicentric cohort (230 patients) and a cohort from two grade-A tertiary hospitals in China (466 patients)-enhancing the robustness and generalizability of our findings. Moreover, experimental validation through functional assays was conducted on PDAC cell lines and patient-derived organoids. In summary, our cohort-scale integration of clinical and proteomic data demonstrates the potential of proteomics-guided prognosis and biomarker-aided adjuvant chemotherapy for PDAC.

Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1.

BACKGROUND: Cottonseed oil is a promising edible plant oil with abundant unsaturated fatty acids. However, few studies have been conducted to explore the characteristics of cottonseed oil. The molecular mechanism of cottonseed oil accumulation remains unclear. RESULTS: In the present study, we conducted comparative transcriptome and weighted gene co-expression network (WGCNA) analysis for two G. hirsutum materials with significant difference in cottonseed oil content. Results showed that, between the high oil genotype 6053 (H6053) and the low oil genotype 2052 (L2052), a total of 412, 507, 1,121, 1,953, and 2,019 differentially expressed genes (DEGs) were detected at 10, 15, 20, 25, and 30 DPA, respectively. Remarkably, a large number of the down-regulated DEGs were enriched in the phenylalanine metabolic processes. Investigation into the dynamic changes of expression profiling of genes associated with both phenylalanine metabolism and oil biosynthesis has shed light on a significant competitive relationship in substrate allocation during cottonseed development. Additionally, the WGCNA analysis of all DEGs identified eight distinct modules, one of which includes GhPXN1, a gene closely associated with oil accumulation. Through phylogenetic analysis, we hypothesized that GhPXN1 in G. hirsutum might have been introgressed from G. arboreum. Overexpression of the GhPXN1 gene in tobacco leaf suggested a significant reduction in oil content compared to the empty-vector transformants. Furthermore, ten other crucial oil candidate genes identified in this study were also validated using quantitative real-time PCR (qRT-PCR). CONCLUSIONS: Overall, this study enhances our comprehension of the molecular mechanisms underlying cottonseed oil accumulation.

Scalar thermal radiation using the adding-doubling method.

The scalar radiative transfer equation in the presence of thermal radiation source is solved in detail, using the adding-doubling method; Planck functions within any given layer are assumed to possess constant, linear, or exponential parameterizations with optical thickness. The radiance profile in any zenith direction is calculated directly in terms of matrix inversions. The inputs to the model are the inherent optical properties (layer total single-scattering albedos, scattering phase functions, and optical thickness) along with temperature and altitude profiles, and the top of the atmosphere and ground surface boundary conditions. The algorithm is implemented in a state-of-the-art MATLAB program, with the cosmic microwave background as the source at the upper boundary and a Lambertian surface reflection at the lower boundary. The simulations are validated against the VLIDORT discrete ordinate radiative transfer model. Results are compared in detail for cases with linear and exponential Planck function parameterizations.

Thermosonication Combined with Natural Antimicrobial Nisin: A Potential Technique Ensuring Microbiological Safety and Improving the Quality Parameters of Orange Juice.

Currently, thermal pasteurisation (TP) remains the most widely applied technique for commercial orange juice preservation; however, a high temperature causes adverse effects on the quality attributes of orange juice. In order to explore a novel non-thermal sterilization method for orange juice, the impacts of thermosonication combined with nisin (TSN) and TP treatments on the quality attributes including microbial and enzyme inactivation and the physicochemical, nutritional, functional, and sensory qualities of orange juice were studied. Both TP and TSN treatments achieved desirable bactericidal and enzyme inactivation effects, and nisin had a significant synergistic lethal effect on aerobic bacteria in orange juice (p < 0.05). Additionally, TSN treatment significantly improved the color attributes of orange juice and well maintained its physicochemical properties and sensory quality. More importantly, TSN treatment significantly increased the total polyphenols content (TPC) and total carotenoids (TC) by 10.03% and 20.10%, increased the ORAC and DPPH by 51.10% and 10.58%, and the contents of total flavonoids and ascorbic acid were largely retained. Correlation analysis of antioxidant activity showed that the ORAC and scavenging ability of DPPH radicals of orange juice are mainly attributed to TC and TPC. These findings indicate that TSN shows great potential application value, which could guarantee the microbiological safety and improve the quality attributes of orange juice.

Comparative Analysis of Physicochemical Characteristics, Nutritional and Functional Components and Antioxidant Capacity of Fifteen Kiwifruit (Actinidia) Cultivars-Comparative Analysis of Fifteen Kiwifruit (Actinidia) Cultivars.

Physicochemical characteristics, nutritional and functional components, and the antioxidant capacity of 15 kinds of domestic and imported kiwifruit in China were studied. Kiwifruit was classified according to flesh color or species, and the differences were analyzed and compared. Results demonstrated Ruiyu had the highest sugar-acid ratio, and Hongshi No.2 was an excellent cultivar with strong antioxidant capacity. TPC (total polyphenol content) and AAC (ascorbic acid content) showed a significant positive correlation. TPC was the greatest antioxidant contributor in the DPPH and FRAP assays. The sugar-acid ratio and TFC (total flavonoids content) in red-fleshed kiwifruit were significantly higher than those in yellow-fleshed and green-fleshed ones. The composition of free amino acids had a tendency to distinguish A. deliciosa and A. chinensis, but this needs further verification. In addition, the contents of mineral elements, folic acid and L-5-methyltetrahydrofolate were also analyzed. Generally, kiwifruit contains comprehensive nutrients and has strong antioxidant capacity. Cultivar is one of the main factors affecting nutritional and functional properties and antioxidant capacity.