Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation.

BACKGROUND: Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS: Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the ß-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS: The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.

Temporal and spatial variation of domoic acid along Canada's coast.

Shellfish poisonings have posed severe risks to human health globally. The Canadian Shellfish Sanitation Program was established in 1948 to monitor the toxin levels at shellfish harvesting sites along the coast of six provinces in Canada. Domoic acid has been a causal toxin for amnesic shellfish poisoning, and a macro-scale analysis of the temporal and spatial variation of domoic acid along Canada's coast was conducted in this study. We aggregated the toxin levels by week in blue mussel (Mytilus edulis) and soft-shell clam (Mya arenaria) samples, respectively, over a one-year scale. The subsequent application of Functional Principal Component Analysis unveiled that magnitudes of seasonal variation and peaked DA levels around early summer, spring, or mid-fall formed the largest variation in the toxin levels in blue mussels along the coastlines of British Columbia and Prince Edward Island and in soft-shell calms along those of New Brunswick and Nova Scotia. In Quebec, the DA levels were low and varied mostly in terms of the overall magnitude from spring to fall. Downstream correlation analyses in British Columbia further discovered that, at most sites, the strongest correlations were negative between precipitation as well as inorganic nutrients (including nitrate, nitrite, phosphate, and silicate) on one side and DA a few weeks afterward on the other. These findings indicated associations between amnesic shellfish poisoning and environmental stresses.

Longitudinal study of paralytic shellfish toxins along Canada's coast.

Paralytic shellfish toxins (PST) in shellfish products have led to severe risks to human health. To monitor the risk, the Canadian Shellfish Sanitation Program has been collecting longitudinal PST measurements in blue mussel (Mytilus edulis) and soft-shell clam (Mya arenaria) samples in six coastal provinces of Canada. The spatial distributions of major temporal variation patterns were studied via Functional Principal Component Analysis. Seasonal increases in PST contamination were found to vary the most in terms of magnitude along the coastlines, which provides support for location-specific management of the time-sensitive PST contamination. In British Columbia, the first functional principal component (FPC1) indicated the variance among the magnitudes, while FPC2 indicated the seasonality of the PST levels. The temporal variations tended to be positively correlated with the abundance of dianoflagellates Alexandrium spp., and negatively with precipitation and inorganic nutrients. These findings indicate the underlying mechanism of PST variation in various geographical settings. In New Brunswick, Prince Edward, and Nova Scotia, the top FPCs indicated that the PST contamination differed mostly in the seasonal increase of the PST level during summer.

Astroglial Hmgb1 regulates postnatal astrocyte morphogenesis and cerebrovascular maturation.

Astrocytes are intimately linked with brain blood vessels, an essential relationship for neuronal function. However, astroglial factors driving these physical and functional associations during postnatal brain development have yet to be identified. By characterizing structural and transcriptional changes in mouse cortical astrocytes during the first two postnatal weeks, we find that high-mobility group box 1 (Hmgb1), normally upregulated with injury and involved in adult cerebrovascular repair, is highly expressed in astrocytes at birth and then decreases rapidly. Astrocyte-selective ablation of Hmgb1 at birth affects astrocyte morphology and endfoot placement, alters distribution of endfoot proteins connexin43 and aquaporin-4, induces transcriptional changes in astrocytes related to cytoskeleton remodeling, and profoundly disrupts endothelial ultrastructure. While lack of astroglial Hmgb1 does not affect the blood-brain barrier or angiogenesis postnatally, it impairs neurovascular coupling and behavior in adult mice. These findings identify astroglial Hmgb1 as an important player in postnatal gliovascular maturation.

RNA-Seq Data Processing in Plant-Pathogen Interaction System: A Case Study.

In RNA-seq data processing, short reads are usually aligned from one species against its own genome sequence; however, in plant-pathogen interaction systems, reads from both host and pathogen samples are blended together. In contrast with single-genome analyses, both pathogen and host reference genomes are involved in the alignment process. In such circumstances, the order in which the alignment is carried out, whether the host or pathogen is aligned first, or if both genomes are aligned simultaneously, influences the read counts of certain genes. This is a problem, especially at advanced infection stages. It is crucial to have an appropriate strategy for aligning the reads to their respective genomes, yet the existing strategies of either sequential or parallel alignment become problematic when mapping mixed reads to their corresponding reference genomes. The challenge lies in the determination of which reads belong to which species, especially when homology exists between the host and pathogen genomes. This chapter proposes a combo-genome alignment strategy, which was compared with existing alignment scenarios. Simulation results demonstrated that the degree of discrepancy in the results is correlated with phylogenetic distance of the two species in the mixture which was attributable to the extent of homology between the two genomes involved. This correlation was also found in the analysis using two real RNA-seq datasets of Fusarium-challenged wheat plants. Comparisons of the three RNA-seq processing strategies on three simulation datasets and two real Fusarium-infected wheat datasets showed that an alignment to a combo-genome, consisting of both host and pathogen genomes, improves mapping quality as compared to sequential alignment procedures.

Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis.

In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many research projects, and among these, we demonstrate the strength of DEFE in a case study on RNA-sequencing (RNA-seq) data analysis of wheat challenged with the phytopathogenic fungus, Fusarium graminearum. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB.

Dynamics of fecal coliform bacteria along Canada's coast.

The vast coastline provides Canada with a flourishing seafood industry including bivalve shellfish production. To sustain a healthy bivalve molluscan shellfish production, the Canadian Shellfish Sanitation Program was established to monitor the health of shellfish harvesting habitats, and fecal coliform bacteria data have been collected at nearly 15,000 marine sample sites across six coastal provinces in Canada since 1979. We applied Functional Principal Component Analysis and subsequent correlation analyses to find annual variation patterns of bacteria levels at sites in each province. The overall magnitude and the seasonality of fecal contamination were modelled by functional principal component one and two, respectively. The amplitude was related to human and warm-blooded animal activities; the seasonality was strongly correlated with river discharge driven by precipitation and snow melt in British Columbia, but such correlation in provinces along the Atlantic coast could not be properly evaluated due to lack of data during winter.

Computational genomics insights into cold acclimation in wheat.

Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Fusarium graminearum Infection in Wheat.

RNA/DNA difference (RDD) is a post-transcriptional modification playing a crucial role in regulating diverse biological processes in eukaryotes. Although it has been extensively studied in plant chloroplast and mitochondria genomes, RDDs in plant nuclear genomes are not well studied at present. Here, we investigated the RDDs associated with fusarium head blight (FHB) through a novel method by comparing the RNA-seq data between Fusarium-infected and control samples of four wheat genotypes. A total of 187 high-confidence unique RDDs in 36 genes were identified, representing the first landscape of the FHB-responsive RDD in wheat. The majority (26) of these 36 RDD genes were correlated either positively or negatively with FHB levels. Effects of these RDDs on RNA and protein sequences have been identified, their editing frequency and the expression level of the corresponding genes provided, and the prediction of the effect on the minimum folding free energy of mRNA, miRNA binding, and colocation of RDDs with conserved domains presented. RDDs were predicted to induce modifications in the mRNA and protein structures of the corresponding genes. In two genes, TraesCS1B02G294300 and TraesCS3A02G263900, editing was predicted to enhance their affinity with tae-miR9661-5p and tae-miR9664-3p, respectively. To our knowledge, this study is the first report of the association between RDD and FHB in wheat; this will contribute to a better understanding of the molecular basis underlying FHB resistance, and potentially lead to novel strategies to improve wheat FHB resistance through epigenetic methods.

A computational analysis of potential aortic dilation induced by the hemodynamic effects of bicuspid aortic valve phenotypes.

BACKGROUND AND OBJECTIVES: The bicuspid aortic valve (BAV) is a major risk factor for the progression of aortic dilation (AD) because of the induced abnormal blood flow environment in aorta. The differences in the development of AD induced by BAV phenotypes remains unclear. Therefore, the objective of this study was to assess the potential locations of AD induced by different phenotypes of BAV. The different effects of opening orifice area and leaflet orientation on ascending aortic hemodynamics in Type-1 BAV was investigated by means of numerical simulation. METHODS: Finite element dynamic analysis was performed on tricuspid aortic valve (TAV) and BAV models to simulate the motion of the leaflets and obtain the geometrical characteristics of AV at peak systole as a reference, which were used for aortic models. Then, four sets of aortic fluid models were designed according to the leaflet fusion types [TAV; BAV (left-right-coronary cusp fusion, LR; right-non-coronary cusp fusion, RN; left-non-coronary cusp fusion, LN)], and the computational fluid dynamics method was applied to compare the hemodynamic differences within the aorta at peak systole. RESULTS: The maximum opening area of BAV was significantly reduced, resulting in alterations in aortic hemodynamics compared with TAV. The velocity streamlines were essentially parallel to the aortic wall in TAV. The average pressure and wall shear stress in aorta tend to be stable. In contrary, the eccentricity of BAV orifice jet resulted in high-velocity flow directed toward the ascending aorta (AA) wall and aortic arch for LR and LN; RN features an asymmetrical velocity distribution toward the outer bend of the middle AA, and eccentric flow tends to impact the distal AA. As the flow angle is associated with distinct flow impingement locations, different degrees of WSS and pressure concentration occur along the aortic wall from the AA to the aortic arch in three BAV types. CONCLUSIONS: The BAV morphotype affects the aortic hemodynamics, and the abnormal blood flow associated with BAV may play a role in AD. The different BAV phenotypes determine the direction of blood flow jet and change the expression of dilation. LR is likely to cause dilation of the tubular AA; RN results in dilation of the middle AA to proximal aortic arch; and LN causes an increased incidence of the tubular AA and the proximal aortic arch.

Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge.

BACKGROUND: Treatment of wheat with the phytohormones abscisic acid (ABA) and gibberellic acid (GA) has been shown to affect Fusarium head blight (FHB) disease severity. However, the molecular mechanisms underlying the elicited phenotypes remain unclear. Toward addressing this gap in our knowledge, global transcriptomic profiling was applied to the FHB-susceptible wheat cultivar 'Fielder' to map the regulatory responses effected upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge. RESULTS: Spike treatments resulted in a total of 30,876 differentially expressed genes (DEGs) identified in 'Fielder' (26,004) and the Fg (4872) pathogen. Topology overlap and correlation analyses defined 9689 wheat DEGs as Fg-related across the treatments. Further enrichment analyses demonstrated that these included expression changes within 'Fielder' defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Dysregulation of ABA and GA crosstalk arising from repression of 'Fielder' FUS3 was noted. As well, expression of a putative Fg ABA-biosynthetic cytochrome P450 was detected. The co-applied condition of Fg + ABA elicited further up-regulation of phytohormone biosynthesis, as well as SA and ET signaling pathways and cell wall/polyphenolic metabolism. In contrast, co-applied Fg + GA mainly suppressed phytohormone biosynthesis and signaling, while modulating primary and secondary metabolism and flowering. Unexpectedly, co-applied Fg + AS6 did not affect ABA biosynthesis or signaling, but rather elicited antagonistic responses tied to stress, phytohormone transport, and FHB disease-related genes. CONCLUSIONS: Observed exacerbation (misregulation) of classical defense mechanisms and cell wall fortifications upon ABA treatment are consistent with its ability to promote FHB severity and its proposed role as a fungal effector. In contrast, GA was found to modulate primary and secondary metabolism, suggesting a general metabolic shift underlying its reduction in FHB severity. While AS6 did not antagonize traditional ABA pathways, its impact on host defense and Fg responses imply potential for future investigation. Overall, by comparing these findings to those previously reported for four additional plant genotypes, an additive model of the wheat-Fg interaction is proposed in the context of phytohormone responses.

Effect of Valve Height on the Opening and Closing Performance of the Aortic Valve Under Aortic Root Dilatation.

Patients with aortic valve disease can suffer from valve insufficiency after valve repair surgery due to aortic root dilatation. The paper investigates the effect of valve height (Hv) on the aortic valve opening and closing in order to select the appropriate range of Hv for smoother blood flow through the aortic valve and valve closure completely in the case of continuous aortic root dilatation. A total of 20 parameterized three-dimensional models of the aortic root were constructed following clinical surgical guidance. Aortic annulus diameter (DAA) was separately set to 26, 27, 28, 29, and 30 mm to simulate aortic root dilatation. HV value was separately set to 13.5, 14, 14.5, and 15 mm to simulate aortic valve alterations in surgery. Time-varying pressure loads were applied to the valve, vessel wall of the ascending aorta, and left ventricle. Then, finite element analysis software was employed to simulate the movement and mechanics of the aortic root. The feasible design range of the valve size was evaluated using maximum stress, geometric orifice area (GOA), and leaflet contact force. The results show that the valve was incompletely closed when HV was 13.5 mm and DAA was 29 or 30 mm. The GOA of the valve was small when HV was 15 mm and DAA was 26 or 27 mm. The corresponding values of the other models were within the normal range. Compared with the model with an HV of 14 mm, the model with an HV of 14.5 mm could effectively reduce maximum stress and had relatively larger GOA and less change in contact force. As a result, valve height affects the performance of aortic valve opening and closing. Smaller HV is adapted to smaller DAA and vice versa. When HV is 14.5 mm, the valve is well adapted to the dilatation of the aortic root to enhance repair durability. Therefore, more attention should be paid to HV in surgical planning.

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data.

Classification of tumors into subtypes can inform personalized approaches to treatment including the choice of targeted therapies. The two most common lung cancer histological subtypes, lung adenocarcinoma and lung squamous cell carcinoma, have been previously divided into transcriptional subtypes using microarray data, and corresponding signatures were subsequently used to classify RNA-seq data. Cross-platform unsupervised classification facilitates the identification of robust transcriptional subtypes by combining vast amounts of publicly available microarray and RNA-seq data. However, cross-platform classification is challenging because of intrinsic differences in data generated using the two gene expression profiling technologies. In this report, we show that robust gene expression subtypes can be identified in integrated data representing over 3500 normal and tumor lung samples profiled using two widely used platforms, Affymetrix HG-U133 Plus 2.0 Array and Illumina HiSeq RNA sequencing. We tested and analyzed consensus clustering for 384 combinations of data processing methods. The agreement between subtypes identified in single-platform and cross-platform normalized data was then evaluated using a variety of statistics. Results show that unsupervised learning can be achieved with combined microarray and RNA-seq data using selected preprocessing, cross-platform normalization, and unsupervised feature selection methods. Our analysis confirmed three lung adenocarcinoma transcriptional subtypes, but only two consistent subtypes in squamous cell carcinoma, as opposed to four subtypes previously identified. Further analysis showed that tumor subtypes were associated with distinct patterns of genomic alterations in genes coding for therapeutic targets. Importantly, by integrating quantitative proteomics data, we were able to identify tumor subtype biomarkers that effectively classify samples on the basis of both gene and protein expression. This study provides the basis for further integrative data analysis across gene and protein expression profiling platforms.

Novel Transcriptional and Translational Biomarkers of Tularemia Vaccine Efficacy in a Mouse Inhalation Model: Proof of Concept.

Francisella tularensis subspecies tularensis (Ftt) is extremely virulent for humans when inhaled as a small particle aerosol (<5 µm). Inhalation of ≥20 viable bacteria is sufficient to initiate infection with a mortality rate ≥30%. Consequently, in the past, Ftt became a primary candidate for biological weapons development. To counter this threat, the USA developed a live vaccine strain (LVS), that showed efficacy in humans against inhalation of virulent Ftt. However, the breakthrough dose was fairly low, and protection waned with time. These weaknesses triggered extensive research for better vaccine candidates. Previously, we showed that deleting the clpB gene from virulent Ftt strain, SCHU S4, resulted in a mutant that was significantly less virulent than LVS for mice, yet better protected them from aerosol challenge with wild-type SCHU S4. To date, comprehensive searches for correlates of protection for SCHU S4 ΔclpB among molecules that are critical signatures of cell-mediated immunity, have yielded little reward. In this study we used transcriptomics analysis to expand the potential range of molecular correlates of protection induced by vaccination with SCHU S4 ΔclpB beyond the usual candidates. The results provide proof-of-concept that unusual host responses to vaccination can potentially serve as novel efficacy biomarkers for new tularemia vaccines.

Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat.

In plant cells, phosphatidylglycerol (PG) in the chloroplast has a characteristic trans-∆3-hexadecenoic acid (t16:1) at the sn-2 position. The t16:1 content in wheat leaf tissues decreases during cold treatment, but the significance of this fatty acid compositional change and the underlying biochemical mechanism remains poorly understood. Using a large collection of wheat cultivars displaying a varying capacity of freezing tolerance, we show for the first time under field conditions that this low temperature induced t16:1 change is associated with winter hardiness. To explore the metabolic mechanism responsible for the reduction of t16:1, we performed detailed lipid analysis and comparative transcriptome study with four selected wheat lines under cold acclimation. Our results show that wheat leaf tissues experience a gradual decrease in chloroplast lipid pathway activity during cold acclimation and that the decline in chloroplast lipid synthesis manifests itself in the decrease of t16:1 in PG. Comparative RNA-seq analyses with leaf tissues further reveal concerted transcriptome shifts indicating a rebalancing of chloroplast and cytosolic lipid synthesis during cold acclimation. Our study, thus, provides mechanistic understanding on chloroplast lipid adjustments as a "molecular ideotype" and the t16:1 change as a specific metabolite marker for screening freezing tolerance in wheat.

Vascular contributions to 16p11.2 deletion autism syndrome modeled in mice.

While the neuronal underpinnings of autism spectrum disorder (ASD) are being unraveled, vascular contributions to ASD remain elusive. Here, we investigated postnatal cerebrovascular development in the 16p11.2df/+ mouse model of 16p11.2 deletion ASD syndrome. We discover that 16p11.2 hemizygosity leads to male-specific, endothelium-dependent structural and functional neurovascular abnormalities. In 16p11.2df/+ mice, endothelial dysfunction results in impaired cerebral angiogenesis at postnatal day 14, and in altered neurovascular coupling and cerebrovascular reactivity at postnatal day 50. Moreover, we show that there is defective angiogenesis in primary 16p11.2df/+ mouse brain endothelial cells and in induced-pluripotent-stem-cell-derived endothelial cells from human carriers of the 16p11.2 deletion. Finally, we find that mice with an endothelium-specific 16p11.2 deletion (16p11.2ΔEC) partially recapitulate some of the behavioral changes seen in 16p11.2 syndrome, specifically hyperactivity and impaired motor learning. By showing that developmental 16p11.2 haploinsufficiency from endothelial cells results in neurovascular and behavioral changes in adults, our results point to a potential role for endothelial impairment in ASD.

Characterization of QTL and eQTL controlling early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled haploid wheat population.

BACKGROUND: Fusarium head blight (FHB) is a major disease of cereal crops, caused by the fungal pathogen Fusarium graminearum and related species. Breeding wheat for FHB resistance contributes to increase yields and grain quality and to reduce the use of fungicides. The identification of genes and markers for FHB resistance in different wheat genotypes has nevertheless proven challenging. RESULTS: In this study, early infection by F. graminearum was analyzed in a doubled haploid population derived from the cross of the moderately resistant wheat genotypes Wuhan 1 and Nyubai. Three quantitative trait loci (QTL) were identified: 1AL was associated with lower deoxynivalenol content, and 4BS and 5A were associated with reduced F. graminearum infection at 2 days post inoculation. Early resistance alleles were inherited from Wuhan 1 for QTL 1AL and 4BS and inherited from Nyubai for the 5A QTL. Cis and trans expression QTL (eQTL) were identified using RNA-seq data from infected head samples. Hotspots for trans eQTL were identified in the vicinity of the 1AL and 4BS QTL peaks. Among differentially expressed genes with cis eQTL within the QTL support intervals, nine genes had higher expression associated with FHB early resistance, and four genes had higher expression associated with FHB early susceptibility. CONCLUSIONS: Our analysis of genotype and gene expression data of wheat infected by F. graminearum identified three QTL associated with FHB early resistance, and linked genes with eQTL and differential expression patterns to those QTL. These findings may have applications in breeding wheat for early resistance to FHB.

The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development.

Modern wheat production comes from two polyploid species, Triticum aestivum and Triticum turgidum (var durum), which putatively arose from diploid ancestors Triticum urartu, Aegilops speltoides, and Aegilops tauschii How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid genomes through hybridization, polyploidization, and breeding selection is not well understood. This study describes the global landscape of gene activities during wheat embryogenesis and grain development. Using comprehensive transcriptomic analyses of two wheat cultivars and three diploid grasses, we investigated gene expression at seven stages of embryo development, two endosperm stages, and one pericarp stage. We identified transcriptional signatures and developmental similarities and differences among the five species, revealing the evolutionary divergence of gene expression programs and the contributions of A, B, and D subgenomes to grain development in polyploid wheats. The characterization of embryonic transcriptional programming in hexaploid wheat, tetraploid wheat, and diploid grass species provides insight into the landscape of gene expression in modern wheat and its ancestral species. This study presents a framework for understanding the evolution of domesticated wheat and the selective pressures placed on grain production, with important implications for future performance and yield improvements.plantcell;31/12/2888/FX1F1fx1.

[Effect of sinus diameter on the opening and closing performance of aortic valve under the expansion of aortic root].

This study aims to explore the effect of aortic sinus diameter on aortic valve opening and closing performance in the case of no obvious disease of aortic valve and annulus and continuous dilation of aortic root. A total of 25 three-dimensional aortic root models with different aortic sinus and root diameters were constructed according to the size of clinical surgical guidance. The valve sinus diameter DS is set to 32, 36, 40, 44 and 48 mm, respectively, and the aortic root diameter DA is set to 26, 27, 28, 29 and 30 mm, respectively. Through the structural mechanics calculation with the finite element software, the maximum stress, valve orifice area, contact force and other parameters of the model are analyzed to evaluate the valve opening and closing performance under the dilated state. The study found that aortic valve stenosis occurs when the DS = 32 mm, DA = 26, 27 mm and DS = 36 mm, DA = 26 mm. Aortic regurgitation occurs when the DS = 32, 36 and 40 mm, DA = 30 mm and DS = 44, 48 mm, DA = 29, 30 mm. The other 15 models had normal valve movement. The results showed that the size of the aortic sinus affected the opening and closing performance of the aortic valve. The smaller sinus diameter adapted with the larger root diameter and the larger sinus diameter adapted with the smaller root diameter. When the sinus diameter is 40 mm, the mechanical performance of the valve are good and it can well adapt with the relatively large range of aortic root dilation.

[Influence of valve height on the opening/closure performance of transplanted aortic valve].

Valve transplantation is often used in the treatment of aortic valve insufficiency. However, after surgery, the reconstructed aortic roots have an expansion phenomenon, in which the lack of valve height causes the aortic valve to close again. In this paper, the effects of different aortic valve height design on valve opening and closing performance were studied. The optimal surgical plan was obtained by in vitro numerical simulation, providing technical support and theoretical basis. In this paper, six groups of three-dimensional geometric models with a valve height increment of ± 0.5 mm were established with a root diameter of 26.0 mm and a valve height of 14.0 mm. Through the structural mechanics calculation and analysis of the parameters such as maximum stress, valve area and contact force of the model, reasonable geometrical dimensions are obtained. The study found that the maximum stress values of the six groups of models ranged from 640 to 690 kPa, which was consistent with the results of the literature; the three-group models with valve heights of 13.5 mm, 14.0 mm, and 14.5 mm were within a reasonable range. The contact force value of the 6 groups of leaflets increased with the increase of valve height. Studies have shown that the height of the aortic valve has an effect on the aortic valve closure performance. A valve height that is too small or too large will reduce the aortic systolic valve area and affect the aortic function.