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The continuous generation of multi-omics and phenotype data is propelling advancements in precision oncology. UCSCXenaShiny was developed as an interactive tool for exploring thousands of cancer datasets available on UCSC Xena. However, its capacity for comprehensive and personalized pan-cancer data analysis is being challenged by the growing demands. Here, we introduce UCSCXenaShiny v2, a milestone update through a variety of improvements. Firstly, by integrating multidimensional data and implementing adaptable sample settings, we create a suite of robust TPC (TCGA, PCAWG, CCLE) analysis pipelines. These pipelines empower users to conduct in-depth analyses of correlation, comparison, and survival in three modes: Individual, Pan-cancer and Batch screen. Additionally, the tool includes download interfaces that enable users to access diverse data and outcomes, several features also facilitate the joint analysis of drug sensitivity and multi-omics of cancer cell lines. UCSCXenaShiny v2 is an open-source R package and a web application, freely accessible at https://github.com/openbiox/UCSCXenaShiny. UCSCXenaShiny integrates multidimensional data for robust and personalized pan-cancer analysis pipelines, enabling in-depth cancer data exploration in diverse scenarios. [ABSTRACT FROM AUTHOR]

Most commercial banana cultivars are highly susceptible to Fusarium wilt caused by soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4). Biological control using antagonistic microorganism has been considered as an alternative method to fungicide. Our previous study showed that Streptomyces sp. SCA3-4 T had a broad-spectrum antifungal activity from the rhizosphere soil of Opuntia stricta in a dry hot valley. Here, the sequenced genome of strain SCA3-4 T contained 6614 predicted genes with 72.38% of G + C content. A polymorphic tree was constructed using the multilocus sequence analysis (MLSA) of five house-keeping gene alleles (atpD, gyrB, recA, rpoB, and trpB). Strain SCA3-4 T formed a distinct clade with Streptomyces mobaraensis NBRC 13819 T with 71% of bootstrap. Average nucleotide identity (ANI) values between genomes of strain SCA3-4 T and S. mobaraensis NBRC 13819 T was 85.83% below 95–96% of the novel species threshold, and named after Streptomyces sichuanensis sp. nov. The type strain is SCA3-4 T (= GDMCC 4.214 T = JCM 34964 T). Genomic analysis revealed that strain SCA3-4 T contained 36 known biosynthetic gene clusters of secondary metabolites. Antifungal activity of strain SCA3-4 T was closely associated with the production of siderophore and its extracts induced the apoptosis of Foc TR4 cells. A total of 12 potential antifungal metabolites including terpenoids, esters, acid, macrolides etc. were obtained by the gas chromatography-mass spectrometry (GC–MS). Greenhouse experiment indicated that strain SCA3-4 T could significantly inhibit infection of Foc TR4 in the roots and corms of banana seedlings and reduce disease index. Therefore, strain SCA3-4 T is an important microbial resource for exploring novel natural compounds and developing biopesticides to manage Foc TR4. Key points: • Strain SCA3-4 T was identified as a novel species of Streptomyces. • Siderophore participates in the antifungal regulation. • Secondary metabolites of strain SCA3-4 T improves the plant resistance to Foc TR4. [ABSTRACT FROM AUTHOR]

The irrigating winter wheat one or two times each season was practiced in Huanghuai Winter Wheat Region in order to reduce the over-exploitation of groundwater. In this study, plant height (PH) and its relationship with yield were analyzed in a field study conducted over three growing seasons with 102 wheat varieties irrigated zero to two times at different growth stages. Here, we found that irrigation at the jointing stage increased wheat PH by 6.60–9.70%. Whereas irrigation at the early milking stage had almost no effect on it. Against the wildtype alleles Rht-B1a and Rht-D1a, the genetic background of Rht-B1b and Rht-D1b significantly reduced PH by 14.40–15.50% and 16.90–19.10%, respectively. The combined Rht-B1b and Rht-D1b can reduce PH by 29.10–32.50%. PH was strongly, negatively correlated with grain yield in jointing irrigation (W1) or jointing + milking irrigation (W2) over three growing seasons. In contrast, a significant positive correlation was detected in no-irrigation (W0) in the 2012/2013 wheat growing season, yet no correlation was found in 2013/2014 and 2014/2015. PH was positively correlated with drought coefficient (DRC) in W1 and W2. These results augment our understanding of the relationship between PH and grain yield in different irrigation regimes and provide PH traits for wheat improvement on water saving. [ABSTRACT FROM AUTHOR]

Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton. Three cotton small RNA libraries: non-stressed Shizao1 (early-maturing cotton variety) library (NSS), drought-stressed Shizao1 library (DSS) and non-stressed Jimian958 (medium-maturing cotton variety) library (NSJ) were constructed for deep sequencing. As a result, we identified a total of 64 known and 67 novel miRNAs in the 3 libraries and 88 of them were dramatically differentially expressed (greater than twofold) during drought stress. In addition, we found the expression of 41 miRNAs increased or reduced more than twofold in early-maturing cotton variety compared with that in medium-maturing cotton variety. Our results significantly increased the number of miRNAs in cotton and revealed for the first time the expression profile of miRNAs for early-maturing cotton. [ABSTRACT FROM AUTHOR]

The accumulation and redistribution of the plant hormone auxin plays a crucial role in root development and patterning. Plants can alter their root system architecture (RSA) to adapt to different biotic and abiotic stresses. In addition, reactive oxygen species (ROS), such as HO, are known to increase in plants undergoing stress. Here, we present evidence that HO can regulate auxin accumulation and redistribution through modulating polar auxin transport, leading to changes in RSA. Plants exposed to different concentrations of HO formed a highly branched root system with abundant lateral roots and a shorter primary root. Monitoring of the auxin responsive DR5::GUS indicated that auxin accumulation decreased in lateral root primordia (LRP) and emerging lateral root tips. In addition, polar auxin transport, including both basipetal and acropetal transport modulated by AUX1 and PIN protein carriers, was involved in the process. Taken together, our results suggest that HO could regulate plastic RSA by perturbing polar auxin transport as a means of modulating the accumulation and distribution of auxin. [ABSTRACT FROM AUTHOR]

The root apical meristem (RAM) determines both RAM activity and the growth of roots. Plant roots are constantly exposed to adverse environmental stresses that can cause DNA damage or cell cycle arrest in the RAM; however, the mechanism linking root meristematic activity and RAM size to the DNA damage response (DDR) is unclear. Here, we demonstrate that a loss of function in RCC1/UVR8/GEF-Like 3 (RUG3) substantially augmented the DDR and produced a cell cycle arrest in the RAM in rug3 mutant, leading to root growth retardation. Furthermore, the mutation of RUG3 caused increased intracellular reactive oxygen species (ROS) levels, and ROS scavengers improved the observed cell cycle arrest and reduced RAM activity level in rug3 plants. Most importantly, we detected a physical interaction between RUG3 and ataxia telangiectasia mutated (ATM), a key regulator of the DDR, suggesting that they synergistically modulated the alternative splicing of nad2. Our findings reveal a novel synergistic effect of RUG3 and ATM on the regulation of mitochondrial function, redox homeostasis, and the DDR in the RAM, and outline a protective mechanism for DNA damage repair and the restoration of mitochondrial function that involves RUG3-mediated mitochondrial retrograde signaling and the activation of an ATM-mediated DDR pathway. [ABSTRACT FROM AUTHOR]