The MdMYB44-MdTPR1 repressive complex inhibits MdCCD4 and MdCYP97A3 expression through histone deacetylation to regulate carotenoid biosynthesis in apple.

Carotenoids are photosynthetic pigments and antioxidants that contribute to different plant colors. However, the involvement of TOPLESS (TPL/TPR)-mediated histone deacetylation in the modulation of carotenoid biosynthesis through ethylene-responsive element-binding factor-associated amphiphilic repression (EAR)-containing transcription factors (TFs) in apple (Malus domestica Borkh.) is poorly understood. MdMYB44 is a transcriptional repressor that contains an EAR repression motif. In the present study, we used functional analyses and molecular assays to elucidate the molecular mechanisms through which MdMYB44-MdTPR1-mediated histone deacetylation influences carotenoid biosynthesis in apples. We identified two carotenoid biosynthetic genes, MdCCD4 and MdCYP97A3, that were confirmed to be involved in MdMYB44-mediated carotenoid biosynthesis. MdMYB44 enhanced ß-branch carotenoid biosynthesis by repressing MdCCD4 expression, whereas MdMYB44 suppressed lutein level by repressing MdCYP97A3 expression. Moreover, MdMYB44 partially influences carotenoid biosynthesis by interacting with the co-repressor TPR1 through the EAR motif to inhibit MdCCD4 and MdCYP97A3 expression via histone deacetylation. Our findings indicate that the MdTPR1-MdMYB44 repressive cascade regulates carotenoid biosynthesis, providing profound insights into the molecular basis of histone deacetylation-mediated carotenoid biosynthesis in plants. These results also provide evidence that the EAR-harboring TF/TPL repressive complex plays a universal role in histone deacetylation-mediated inhibition of gene expression in various plants.

Abscisic acid activates transcription factor module MdABI5-MdMYBS1 during carotenoid-derived apple fruit coloration.

Carotenoids are major pigments contributing to fruit coloration. We previously reported that the apple (Malus domestica Borkh.) mutant fruits of 'Beni Shogun' and 'Yanfu 3' show a marked difference in fruit coloration. However, the regulatory mechanism underlying this phenomenon remains unclear. In this study, we determined that carotenoid is the main factor influencing fruit flesh color. We identified an R1-type MYB transcription factor, MdMYBS1, which was found to be highly associated with carotenoids and abscisic acid (ABA) contents of apple fruits. Overexpression of MdMYBS1 promoted, and silencing of MdMYBS1 repressed, ß-branch carotenoids synthesis and ABA accumulation. MdMYBS1 regulates carotenoid biosynthesis by directly activating the major carotenoid biosynthetic genes encoding phytoene synthase (MdPSY2-1) and lycopene ß-cyclase (MdLCYb). 9-cis-epoxycarotenoid dioxygenase 1 (MdNCED1) contributes to ABA biosynthesis, and MdMYBS1 enhances endogenous ABA accumulation by activating the MdNCED1 promoter. In addition, the basic leucine zipper domain transcription factor ABSCISIC ACID-INSENSITIVE5 (MdABI5) was identified as an upstream activator of MdMYBS1, which promotes carotenoid and ABA accumulation. Furthermore, ABA promotes carotenoid biosynthesis and enhances MdMYBS1 and MdABI5 promoter activities. Our findings demonstrate that the MdABI5-MdMYBS1 cascade activated by ABA regulates carotenoid-derived fruit coloration and ABA accumulation in apple, providing avenues in breeding and planting for improvement of fruit coloration and quality.

A time-consistent stabilized finite element method for fluids with applications to hemodynamics.

Several finite element methods for simulating incompressible flows rely on the streamline upwind Petrov-Galerkin stabilization (SUPG) term, which is weighted by [Formula: see text]. The conventional formulation of [Formula: see text] includes a constant that depends on the time step size, producing an overall method that becomes exceedingly less accurate as the time step size approaches zero. In practice, such method inconsistency introduces significant error in the solution, especially in cardiovascular simulations, where small time step sizes may be required to resolve multiple scales of the blood flow. To overcome this issue, we propose a consistent method that is based on a new definition of [Formula: see text]. This method, which can be easily implemented on top of an existing streamline upwind Petrov-Galerkin and pressure stabilizing Petrov-Galerkin method, involves the replacement of the time step size in [Formula: see text] with a physical time scale. This time scale is calculated in a simple operation once every time step for the entire computational domain from the ratio of the L2-norm of the acceleration and the velocity. The proposed method is compared against the conventional method using four cases: a steady pipe flow, a blood flow through vascular anatomy, an external flow over a square obstacle, and a fluid-structure interaction case involving an oscillatory flexible beam. These numerical experiments, which are performed using linear interpolation functions, show that the proposed formulation eliminates the inconsistency issue associated with the conventional formulation in all cases. While the proposed method is slightly more costly than the conventional method, it significantly reduces the error, particularly at small time step sizes. For the pipe flow where an exact solution is available, we show the conventional method can over-predict the pressure drop by a factor of three. This large error is almost completely eliminated by the proposed formulation, dropping to approximately 1% for all time step sizes and Reynolds numbers considered.

Preparation of NiS/Ti3C2Tx co-doped with N and P at the covalent interface and its electromagnetic wave absorption properties.

The harm of electromagnetic waves on human daily life has gradually received attention, and electromagnetic waves absorption materials have been used to address this issue. MXene, as a new type of 2D material, is a very promising electromagnetic wave absorption material. In this study, NiS nanoparticles were grown on the surface of S terminated Ti3C2Tx, and -S group acted as sulfur sources to construct Ti-S-Ni covalent interface directly in NiS/Ti3C2Tx composites. To further regulate the interface structure and electromagnetic properties, -P and -NH2 groups were also introduced onto the surface of MXene to achieve the N, P co-doping NiS/Ti3C2Tx composites with covalent interface. By investigating the electromagnetic wave absorption performance of the composites, it was found that N and P doping could effectively enhance the electron transfer rate at the interface and optimize the conduction loss, resulting in a significant improvement in performance. The minimum reflection loss was -50.6 dB at a frequency of 15.6 GHz, and the matching thickness was only 1.14 mm with an effective absorption bandwidth of 3.6 GHz. These results provide an important references and guidance for further research and development of high-performance electromagnetic wave absorption materials.

An apple (Malus domestica) AP2/ERF transcription factor modulates carotenoid accumulation.

Color is an important trait for horticultural crops. Carotenoids are one of the main pigments for coloration and have important implications for photosynthesis in plants and benefits for human health. Here, we identified an APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factor named MdAP2-34 in apple (Malus domestica Borkh.). MdAP2-34 expression exhibited a close correlation with carotenoid content in 'Benin Shogun' and 'Yanfu 3' fruit flesh. MdAP2-34 promotes carotenoid accumulation in MdAP2-34-OVX transgenic apple calli and fruits by participating in the carotenoid biosynthesis pathway. The major carotenoid contents of phytoene and ß-carotene were much higher in overexpressing MdAP2-34 transgenic calli and fruit skin, yet the predominant compound of lutein showed no obvious difference, indicating that MdAP2-34 regulates phytoene and ß-carotene accumulation but not lutein. MdPSY2-1 (phytoene synthase 2) is a major gene in the carotenoid biosynthesis pathway in apple fruit, and the MdPSY2-1 gene is directly bound and transcriptionally activated by MdAP2-34. In addition, overexpressing MdPSY2-1 in apple calli mainly increases phytoene and total carotenoid contents. Our findings will advance and extend our understanding of the complex molecular mechanisms of carotenoid biosynthesis in apple, and this research is valuable for accelerating the apple breeding process.

Simulation of a vacuum helmet to contain pathogen-bearing droplets in dental and otolaryngologic outpatient interventions.

Clinic encounters of dentists and otolaryngologists inherently expose these specialists to an enhanced risk of severe acute respiratory syndrome coronavirus 2 infection, thus threatening them, their patients, and their practices. In this study, we propose and simulate a helmet design that could be used by patients to minimize the transmission risk by retaining droplets created through coughing. The helmet has a port for accessing the mouth and nose and another port connected to a vacuum source to prevent droplets from exiting through the access port and contaminating the environment or clinical practitioners. We used computational fluid dynamics in conjunction with Lagrangian point-particle tracking to simulate droplet trajectories when a patient coughs while using this device. A range of droplet diameters and different operating conditions were simulated. The results show that 100% of the airborne droplets and 99.6% of all cough droplets are retained by the helmet.

Genetic variation in the promoter of an R2R3-MYB transcription factor determines fruit malate content in apple (Malus domestica Borkh.).

Deciphering the mechanism of malate accumulation in apple (Malus domestica Borkh.) fruits can help to improve their flavor quality and enhance their benefits for human health. Here, we analyzed malate content as a quantitative trait that is determined mainly by genetic effects. In a previous study, we identified an R2R3-MYB transcription factor named MdMYB44 that was a candidate gene in qtl08.1 (quantitative trait locus mapped to chromosome 8) of fruit malate content. In the present study, we established that MdMYB44 negatively regulates fruit malate accumulation by repressing the promoter activity of the malate-associated genes Ma1 (Al-Activated Malate Transporter 9), Ma10 (P-type ATPase 10), MdVHA-A3 (V-type ATPase A3), and MdVHA-D2 (V-type ATPase D2). Two single-nucleotide polymorphisms (SNPs) in the MdMYB44 promoter, SNP A/G and SNP T/-, were experimentally shown to associate with fruit malate content. The TATA-box in the MdMYB44 promoter in the presence of SNP A enhances the basal activity of the MdMYB44 promoter. The binding of a basic-helix-loop-helix transcription factor MdbHLH49 to the MdMYB44 promoter was enhanced by the presence of SNP T, leading to increased MdMYB44 transcript levels and reduced malate accumulation. Furthermore, MdbHLH49 interacts with MdMYB44 and enhances MdMYB44 activity. The two SNPs could be used in combination to select for sour or non-sour apples, providing a valuable tool for the selection of fruit acidity by the apple breeding industry. This research is important for understanding the complex molecular mechanisms of fruit malate accumulation and accelerating the development of germplasm innovation in apple species and cultivars.

An Efficient Assisted Bidirectional Glenn Design With Lowered Superior Vena Cava Pressure for Stage-One Single Ventricle Patients.

Recently, the assisted bidirectional Glenn (ABG) procedure has been proposed as an alternative to the modified Blalock-Taussig shunt (mBTS) operation for neonates with single-ventricle physiology. Despite success in reducing heart workload and maintaining sufficient pulmonary flow, the ABG also raised the superior vena cava (SVC) pressure to a level that may not be tolerated by infants. To lower the SVC pressure, we propose a modified version of the ABG (mABG), in which a shunt with a slit-shaped nozzle exit is inserted at the junction of the right and left brachiocephalic veins. The proposed operation is compared against the ABG, the mBTS, and the bidirectional Glenn (BDG) operations using closed-loop multiscale simulations. Both normal (2.3 Wood units-m2) and high (7 Wood units-m2) pulmonary vascular resistance (PVR) values are simulated. The mABG provides the highest oxygen saturation, oxygen delivery, and pulmonary flow rate in comparison to the BDG and the ABG. At normal PVR, the SVC pressure is significantly reduced below that of the ABG and the BDG (mABG: 4; ABG: 8; BDG: 6; mBTS: 3 mmHg). However, the SVC pressure remains high at high PVR (mABG: 15; ABG: 16; BDG: 12; mBTS: 3 mmHg), motivating an optimization study to improve the ABG hemodynamics efficiency for a broader range of conditions in the future. Overall, the mABG preserves all advantages of the original ABG procedure while reducing the SVC pressure at normal PVR.

Anthocyanin Biosynthesis and Methylation of the MdMYB10 Promoter Are Associated with the Red Blushed-Skin Mutant in the Red Striped-Skin "Changfu 2" Apple.

The color of apple skin, particularly anthocyanin-based coloration, is a key factor determining market acceptance. The mechanisms of anthocyanin accumulation in apples with different skin color patterns (i.e., striped and blushed) were analyzed. In total, 14 anthocyanins and 5 procyanidins were simultaneously assayed in red blushed-skin mutants (CF-B1 and CF-B2) and red striped-skin parents (CF-S1 and CF-S2), and 13 significant differences were revealed. Anthocyanin accumulation was significantly higher in the red blushed-skin apples than it was in the parents. The transcript levels of anthocyanin biosynthesis genes and regulatory factors (MdMYB10, MdbHLH3, and MdWD40) were associated with different skin color patterns during the coloring period at 4, 6, and 8 days after the fruits were debagged. The methylation levels of the MdMYB10 promoter regions -1203 to -779 bp, -1667 to -1180 bp, and -2295 to -1929 bp were associated with different skin color patterns, and there was more methylation in red striped-skin apples. These results improve our understanding of anthocyanin accumulation and its underlying molecular mechanism in apples with different skin color patterns, thereby providing valuable information for apple breeding.

Genome-wide identification and transcript analysis of TCP transcription factors in grapevine.

BACKGROUND: The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. RESULTS: A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. CONCLUSIONS: Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

Image-Based Flow Simulations of Pre- and Post-left Atrial Appendage Closure in the Left Atrium.

PURPOSE: For patients with atrial fibrillation, the left atrial appendage (LAA) is often the site of thrombus formation due to low atrial ejection fraction that triggers strokes and other thromboembolic events. Recently introduced percutaneous LAA occlusion procedure is known to reduce LAA-induced strokes. Despite having the procedure, there are still 11% of the patients who continue to suffer from future strokes or transient ischemic attacks, not accounting for the procedural related complications. The high failure rate is largely due to the variabilities in LAA's shape, size, and contractility which may result in ineffectiveness of this procedure. To correctly identify the candidates and evaluate the effectiveness of the procedure, we rely on patient-specific CT scans which provides the exact LA and LAA geometries and predictive hemodynamic analysis to assist in evaluating quantitative flow parameters pre- and post-LAA occlusion procedures. Hemodynamic parameters are critical to predict adverse hemodynamic flow patterns in LAA as well as the effectiveness of LAA closure in individual patient. The aim of this paper is to establish an image-based patient-specific computational fluid dynamic (CFD) simulation framework specific to the prediction of treatment outcomes of LAA closure with atrial fibrillation. This framework utilizes automated LA/LAA image segmentation which yields significant reduction in image processing. One set of patient data with successful procedure outcome is used to illustrate the potential of the proposed framework. METHODS: The proposed LAA occlusion simulation framework is composed of several components: (1) a novel image segmentation procedure, which is fully-automated to identify LA/LAA geometries from CT images, (2) a finite-element mesh generation procedure which transforms the surface geometry into a 3-D volume mesh and properly identified boundary planes, (3) performing CFD simulations with atrial fibrillation flow boundary conditions, and (4) analyzing flow characteristics (velocity, flow patterns, streamlines, vortices) within the LA for before and after LAA closure. RESULTS: Based on the LA/LAA segmentation of a 65 year old female patient with chronic atrial fibrillation, a CFD analysis was pursued to examine flow characteristics upon LAA closure. The results showed that the flow velocity magnitudes were significantly reduced by a maximum factor of 2.21, flow streamlines were greatly stabilized, and mitral outflow appeared to be more organized. Vortices were dramatically reduced in size, number, intensity, as well as duration. During diastole, the peak vortex diameter was reduced from 2.8 to 1.5 cm, while the vortex duration was reduced from 0.210 to 0.135 s. These flow characteristics all indicated a reduced risk in future thrombus formation and strokes based on the established relationship between flow and thrombus formation. For the patient case under study, the effectiveness of the procedure is predicted and found to be consistent with the actual procedural outcome. CONCLUSIONS: This framework successfully predicted patient-specific outcome of a LAA closure procedure for one patient with atrial fibrillation. It can be further developed into a useful tool for pre-procedural planning and candidate selection. More patient data are necessary for further validation studies.

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII.

Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, using MapQTL and BSA-seq (bulk segregant analysis using next generation sequencing) with two independent pedigree-based populations, we identified four major genome-wide QTLs responsible for apple fruit acidity. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single-nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37 and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H+ -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on the MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the fundamental physiological basis of quantitative genetics.

POD1 regulates pollen tube guidance in response to micropylar female signaling and acts in early embryo patterning in Arabidopsis.

The pollen tube germinates from pollen and, during its migration, it perceives and responds to guidance cues from maternal tissue and from the female gametophyte. The putative female cues have recently been identified, but how the pollen tube responds to these signals remains to be unveiled. In a genetic screen for male determinants of the pollen tube response, we identified the pollen defective in guidance1 (pod1) mutant, in which the pollen tubes fail to target the female gametophyte. POD1 encodes a conserved protein of unknown function and is essential for positioning and orienting the cell division plane during early embryo development. Here, we demonstrate that POD1 is an endoplasmic reticulum (ER) luminal protein involved in ER protein retention. Further analysis shows that POD1 interacts with the Ca(2+) binding ER chaperone CALRETICULIN3 (CRT3), a protein in charge of folding of membrane receptors. We propose that POD1 modulates the activity of CRT3 or other ER resident factors to control the folding of proteins, such as membrane proteins in the ER. By this mechanism, POD1 may regulate the pollen tube response to signals from the female tissues during pollen tube guidance and early embryo patterning in Arabidopsis thaliana.

Mutations in the Arabidopsis nuclear-encoded mitochondrial phage-type RNA polymerase gene RPOTm led to defects in pollen tube growth, female gametogenesis and embryogenesis.

The mitochondrial genes in Arabidopsis thaliana are transcribed by a small family of nuclear-encoded T3/T7 phage-type RNA polymerases (RPOTs). At least two nuclear-encoded RPOTs (RPOTm and RPOTmp) are located in mitochondria in A. thaliana. Their genetic roles are largely unknown. Here we report the characterization of novel mutations in the A. thaliana RPOTm gene. The mutations did not affect pollen formation, but significantly retarded the growth of the rpoTm mutant pollen tubes and had an impact on the fusion of the polar nuclei in the rpoTm mutant embryo sacs. Moreover, development of the rpoTm/- mutant embryo was arrested at the globular stage. The rpoTm rpoTmp double mutation could enhance the rpoTm mutant phenotype. Expression of RPOTmp under control of the RPOTm promoter could not complement the phenotype of the rpoTm mutations. All these data indicate that RPOTm is important for normal pollen tube growth, female gametogenesis and embryo development, and has distinct genetic and molecular roles in plant development, which cannot be replaced by RPOTmp.

GNOM-LIKE 2, encoding an adenosine diphosphate-ribosylation factor-guanine nucleotide exchange factor protein homologous to GNOM and GNL1, is essential for pollen germination in Arabidopsis.

In flowering plants, male gametes are delivered to female gametophytes by pollen tubes. Although it is important for sexual plant reproduction, little is known about the genetic mechanism that controls pollen germination and pollen tube growth. Here we report the identification and characterization of two novel mutants, gnom-like 2-1 (gnl2-1) and gnl2-2 in Arabidopsis thaliana, in which the pollen grains failed to germinate in vitro and in vivo. GNL2 encodes a protein homologous to the adenosine diphosphate-ribosylation factor-guanine nucleotide exchange factors, GNOM and GNL1 that are involved in endosomal recycling and endoplasmic reticulum-Golgi vesicular trafficking. It was prolifically expressed in pollen grains and pollen tubes. The results of the present study suggest that GNL2 plays an important role in pollen germination.