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Abstract Objectives To investigate the feasibility of a deep learning-constrained compressed sensing (DL-CS) method in non-contrast-enhanced modified DIXON (mDIXON) coronary magnetic resonance angiography (MRA) and compare its diagnostic accuracy using coronary CT angiography (CCTA) as a reference standard. Methods Ninety-nine participants were prospectively recruited for this study. Thirty healthy subjects (age range: 20–65 years; 50% female) underwent three non-contrast mDIXON-based coronary MRA sequences including DL-CS, CS, and conventional sequences. The three groups were compared based on the scan time, subjective image quality score, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). The remaining 69 patients suspected of coronary artery disease (CAD) (age range: 39–83 years; 51% female) underwent the DL-CS coronary MRA and its diagnostic performance was compared with that of CCTA. Results The scan time for the DL-CS and CS sequences was notably shorter than that of the conventional sequence (9.6 ± 3.1 min vs 10.0 ± 3.4 min vs 13.0 ± 4.9 min; p

PurposeTo compare the ability of diffusion parameters obtained by stretched-exponential and kurtosis models of diffusion-weighted imaging (DWI) to distinguish between patients with primary aldosteronism (PA) and healthy controls (HCs) in renal assessment.Materials and methodsA total of 44 participants (22 patients and 22 HCs) underwent renal MRI with an 11 b-value DWI sequence and a 3 b-value diffusion kurtosis imaging (DKI) sequence from June 2021 to April 2022. Binary logistic regression was used to construct regression models combining different diffusion parameters. Receiver-operating characteristic (ROC) curve analysis and comparisons were used to evaluate the ability of single diffusion parameters and combined diffusion models to distinguish between the two groups.ResultsA total of six diffusion parameters (including the cortical anomalous exponent term [α_Cortex], medullary fractional anisotropy [FA_Medulla], cortical FA [FA_Cortex], cortical axial diffusivity [Da_Cortex], medullary mean diffusivity [MD_Medulla] and medullary radial diffusivity [Dr_Medulla]) were included, and 10 regression models were studied. The area under the curve (AUC) of Dr_Medulla was 0.855, comparable to that of FA_Cortex and FA_Medulla and significantly higher than that of α_Cortex, Da_Cortex and MD_Medulla. The AUC of the Model_all parameters was 0.967, comparable to that of Model_FA (0.946) and Model_DKI (0.966) and significantly higher than that of the other models. The sensitivity and specificity of Model_all parameters were 87.2% and 95%, respectively.ConclusionThe Model_all parameters, Model_FA and Model_DKI were valid for differentiating between PA patients and HCs with similar differentiation efficacy and were superior to single diffusion parameters and other models.

Leaf senescence is an important biological process that contributes to grain yield in crops. To study the molecular mechanisms underlying natural leaf senescence, we harvested three different developmental ear leaves of maize, mature leaves (ML), early senescent leaves (ESL), and later senescent leaves (LSL), and analyzed transcriptional changes using RNA-sequencing. Three sets of data, ESL vs. ML, LSL vs. ML, and LSL vs. ESL, were compared, respectively. In total, 4,552 genes were identified as differentially expressed. Functional classification placed these genes into 18 categories including protein metabolism, transporters, and signal transduction. At the early stage of leaf senescence, genes involved in aromatic amino acids (AAAs) biosynthetic process and transport, cellular polysaccharide biosynthetic process, and the cell wall macromolecule catabolic process, were up-regulated. Whereas, genes involved in amino acid metabolism, transport, apoptosis, and response to stimulus were up-regulated at the late stage of leaf senescence. Further analyses reveals that the transport-related genes at the early stage of leaf senescence potentially take part in enzyme and amino acid transport and the genes upregulated at the late stage are involved in sugar transport, indicating nutrient recycling mainly takes place at the late stage of leaf senescence. Comparison between the data of natural leaf senescence in this study and previously reported data for Arabidopsis implies that the mechanisms of leaf senescence in maize are basically similar to those in Arabidopsis. A comparison of natural and induced leaf senescence in maize was performed. Athough many basic biological processes involved in senescence occur in both types of leaf senescence, 78.07% of differentially expressed genes in natural leaf senescence were not identifiable in induced leaf senescence, suggesting that differences in gene regulatory network may exist between these two leaf senescence programs. Thus, this study provides important information for understanding the mechanism of leaf senescence in maize.

It is difficult to derive all qualitative proteomic and metabolomic experimental data in male (pollen tube) and female (pistil) reproductive tissues during pollination because of the limited sensitivity of current technology. In this study, genome-scale enzyme correlation network models for plants (Arabidopsis/maize) were constructed by analyzing the enzymes and metabolic routes from a global perspective. Then, we developed a data-driven computational pipeline using the "guilt by association" principle to analyze the transcriptional coexpression profiles of enzymatic genes in the consecutive steps for metabolic routes in the fast-growing pollen tube and stigma during pollination. The analysis identified an inferred pattern of pollen tube-stigma ethanol coupling. When the pollen tube elongates in the transmitting tissue (TT) of the pistil, this elongation triggers the mobilization of energy from glycolysis in the TT cells of the pistil. Energy-rich metabolites (ethanol) are secreted that can be taken up by the pollen tube, where these metabolites are incorporated into the pollen tube's tricarboxylic acid (TCA) cycle, which leads to enhanced ATP production for facilitating pollen tube growth. In addition, our analysis also provided evidence for the cooperation of kaempferol, dTDP-alpha-L-rhamnose and cell-wall-related proteins; phosphatidic-acid-mediated Ca2+ oscillations and cytoskeleton; and glutamate degradation IV for γ-aminobutyric acid (GABA) signaling activation in Arabidopsis and maize stigmas to provide the signals and materials required for pollen tube tip growth. In particular, the "guilt by association" computational pipeline and the genome-scale enzyme correlation network models (GECN) developed in this study was initiated with experimental "omics" data, followed by data analysis and data integration to determine correlations, and could provide a new platform to assist inachieving a deeper understanding of the co-regulation and inter-regulation model in plant research.

Diseases caused by begomoviruses such as tomato yellow leaf curl disease (TYLCD) are major constraints in agriculture. While the interactions between plants and monopartite begomoviruses during TYLCD pathogenesis have been explored extensively, how bipartite begomoviruses interact with tomato plants are understudied. Here we first found that a bipartite begomovirus tomato yellow leaf curl Thailand virus (TYLCTHV) induced stunted growth, leaf curl and yellowing in tomato plants. We then profiled the tomato transcriptomic changes in response to TYLCTHV infection. In total, we identified 2322 upregulated and 1377 downregulated genes. KEGG enrichment analysis of the differentially expressed genes (DEGs) revealed that many KEGG pathways regulating plant photosynthesis processes and defenses were enriched. Specifically, TYLCTHV infection disrupted the expression of DEGs that function in the light-harvesting chlorophyll protein complex, photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase. Additionally, the expression of many DEGs regulating plant defenses including pathogen-associated molecular pattern (PAMP)-triggered immunity, effector-triggered immunity and hypersensitive response was upregulated upon TYLCTHV infection. Taken together, we found that during the pathogenesis of TYLCD induced by TYLCTHV, the virus actively disrupts plant photosynthesis processes and induces defense responses. Our findings add to our knowledge of TYLCD pathogenesis and plant–virus interactions in general.

Background: Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available. Results: A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework. Conclusions: Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies. [ABSTRACT FROM AUTHOR]

Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins. [ABSTRACT FROM AUTHOR]