Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower

Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.

Value of long non-coding RNA HAS2-AS1 as a diagnostic and prognostic marker of glioma

BACKGROUND

Glioma presents high incidence and poor prognosis, and therefore more effective treatments are needed. Studies have confirmed that long non-coding RNAs (lncRNAs) basically regulate various human diseases including glioma. It has been theorized that HAS2-AS1 serves as an lncRNA to exert an oncogenic role in varying cancers. This study aimed to assess the value of lncRNA HAS2-AS1 as a diagnostic and prognostic marker for glioma.

METHODS

The miRNA expression data and clinical data of glioma were downloaded from the TCGA database for differential analysis and survival analysis. In addition, pathological specimens and specimens of adjacent normal tissue from 80 patients with glioma were used to observe the expression of HAS2-AS1. The receiver operating characteristic (ROC) curve was used to analyze the diagnostic ability and prognostic value of HAS2-AS1 in glioma. Meanwhile, a Kaplan-Meier survival curve was plotted to evaluate the survival of glioma patients with different HAS2-AS1 expression levels.

RESULTS

HAS2-AS1 was significantly upregulated in glioma tissues compared with normal tissue. The survival curves showed that overexpression of HAS2-AS1 was associated with poor overall survival (OS) and progression-free survival (PFS). Several clinicopathological factors of glioma patients, including tumor size and WHO grade, were significantly correlated with HAS2-AS1 expression in tissues. The ROC curve showed an area under the curve (AUC) value of 0.863, indicating that HAS2-AS1 had good diagnostic value. The ROC curve for the predicted OS showed an AUC of 0.906, while the ROC curve for predicted PFS showed an AUC of 0.88. Both suggested that overexpression of HAS2-AS1 was associated with poor prognosis.

CONCLUSIONS

Normal tissues could be clearly distinguished from glioma tissues based on HAS2-AS1 expression. Moreover, overexpression of HAS2-AS1 indicated poor prognosis in glioma patients. Therefore, HAS2-AS1 could be used as a diagnostic and prognostic marker for glioma.

Strictureplasty may lead to increased preference in the surgical management of Crohn's disease: a case-matched study

BACKGROUND

Resection and strictureplasty are the two surgical modalities used in the management of Crohn's disease (CD). The objective of this study was to compare morbidity and clinical recurrence between patients who underwent strictureplasty and patients who underwent resection.

METHODS

Patients with CD who underwent strictureplasty between January 2012 and December 2022 were enrolled. The patients were well matched with patients who underwent resection without strictureplasty. Patient- and disease-specific characteristics, postoperative morbidity, and clinical recurrence were also analyzed.

RESULTS

A total of 118 patients who underwent a total of 192 strictureplasties were well matched to 118 patients who underwent resection. The strictureplasty group exhibited significantly less blood loss (30 ml versus 50 ml, p < 0.001) and stoma creation (2.5% versus 16.9%, p < 0.001). No significant difference was found regarding postoperative complications or length of postoperative stay. At the end of the follow-up, the overall rate of clinical recurrence was 39.4%, and no difference was observed between the two groups. Postoperative prophylactic use of biologics (odds ratio = 0.2, p < 0.001) was the only protective factor against recurrence.

CONCLUSION

Strictureplasty does not increase the risk of complications or recurrence compared with resection. It represents a viable alternative to resection in selected patients, and as such, it should have a broader scope of indications and greater acceptance among surgeons.

Distinguishment between high-grade gliomas and solitary brain metastases in peritumoural oedema: quantitative analysis using synthetic MRI at 3 T

AIM

To investigate the efficacy of synthetic magnetic resonance imaging (MRI) in distinguishing high-grade gliomas (HGGs) from solitary brain metastases (SBMs) in peritumoural oedema.

MATERIALS AND METHODS

Thirty-five patients with HGGs and 25 patients with SBMs were recruited and scanned using synthetic MRI using a 3 T scanner. Two radiologists measured synthetic MRI-derived relaxation values independently (T1, T2, proton density [PD]) in the peritumoural oedema, which was used to generate quantitative metrics before (T1native, T2native, and PDnative) and after (T1post, T2post, and PDpost) contrast agent injection. Student's t-test or the Mann-Whitney U-test was performed to detect statistically significant differences in the aforementioned metrics in peritumoural oedema between HGGs and SBMs. The receiver operating characteristic (ROC) curves were plotted to evaluate the efficacy of each metric in distinguishing the two groups, and the areas under the curves (AUCs) were compared pairwise by performing the Delong test.

RESULTS

The mean T1native, T2native, and T1post values in the peritumoural oedema of HGGs were significantly lower compared with SBMs (all p<0.05). The T1post value had a higher AUC (0.843) in differentiating HGGs and SBMs than all other individual metrics (all p<0.05). The combined T1native, T2native, and T1post model had the best distinguishing performance with an AUC, sensitivity, and specificity of 0.987, 94.3%, and 100%, respectively.

CONCLUSIONS

Synthetic MRI may be a potential supplement to the preoperative diagnosis of HGGs and SBMs in clinical practice, as the synthetic MRI-derived tri-parametric model in the peritumoural oedema showed significantly improved diagnostic performance in distinguishing HGGs from SBMs.

Functional genomics of Brassica napus: Progresses, challenges, and perspectives

Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.

Paternal chromosome elimination of inducer triggers induction of double haploids in Brassica napus

A synthetic octoploid rapeseed, Y3380, induces maternal doubled haploids when used as a pollen donor to pollinate plant. However, the mechanism underlying doubled haploid formation remains elusive. We speculated that double haploid induction occurs as the inducer line's chromosomes pass to the maternal egg cell, and the zygote is formed through fertilization. In the process of zygotic mitosis, the paternal chromosome is specifically eliminated. Part of the paternal gene might have infiltrated the maternal genome through homologous exchange during the elimination process. Then, the zygote haploid genome doubles (early haploid doubling, EH phenomenon), and the doubled zygote continues to develop into a complete embryo, finally forming doubled haploid offspring. To test our hypothesis, in the current study, the octoploid Y3380 line was back bred with the 4122-cp4-EPSPS exogenous gene used as a marker into hexaploid Y3380-cp4-EPSPS as paternal material to pollinate three different maternal materials. The fertilization process of crossing between the inducer line and the maternal parent was observed 48 h after pollination, and the fertilization rate reached 97.92% and 98.72%. After 12 d of pollination, the presence of cp4-EPSPS in the embryo was detected by in situ PCR, and at 13-23 d after pollination, the probability of F1 embryos containing cp4-EPSPS gene was up to 97.27%, but then declined gradually to 0% at 23-33 d. At the same time, the expression of cp4-EPSPS was observed by immunofluorescence in the 3rd to 29th day embryo. As the embryos developed, cp4-EPSPS marker genes were constantly lost, accompanied by embryonic death. After 30 d, the presence of cp4-EPSPS was not detected in surviving embryos. Meanwhile, SNP detection of induced offspring confirmed the existence of double haploids, further indicating that the induction process was caused by the loss of specificity of the paternal chromosome. The tetraploid-induced offspring showed infiltration of the induced line gene loci, with heterozygosity and homozygosity. Results indicated that the induced line chromosomes were eliminated during embryonic development, and the maternal haploid chromosomes were synchronously doubled in the embryo. These findings support our hypothesis and lay a theoretical foundation for further localization or cloning of functional genes involved in double haploid induction in rapeseed.

[Application of synthetic MRI in predicting isocitrate dehydrogenase 1 genotypes in gliomas]

This study analyzed the clinical and imaging data of 81 glioma patients who underwent brain synthetic MRI and diffusion weighted imaging (DWI) examination in the General Hospital of Ningxia Medical University from August 2020 to September 2021 to explore the value of synthetic MRI relaxation quantitative value in predicting the genotype of isocitrate dehydrogenase 1 (IDH1) in gliomas. There were 44 males and 37 females, those patients with an aged 50.0 (36.5, 59.0) years. The tumor pre-T1, pre-T2, pre-PD, post-T1 and ADC values were obtained by outlining the region of interest (ROI). Univariate analysis was used to compare the differences of parameter values between groups, and the receiver operating characteristic was used to evaluate the diagnostic efficacy of each parameter value in predicting glioma IDH1 genotype. The results showed that the pre-T1 and pre-PD values [M (Q1, Q3)] of IDH1m glioma were lower than those of IDH1w glioma [1 462.75 (1 306.41, 1 567.75) ms vs 1 532.83 (1 434.67, 1 617.67) ms, 84.18 (82.28, 86.41) pu vs 85.85 (84.65, 86.90) pu] (all P<0.05). The post-T1 and ADC values of IDH1m glioma were higher than those of IDH1w glioma [1 054.50 (631.92, 1 262.63) ms vs 669.67 (535.17, 823.33) ms, 1.20 (0.86, 1.35) ×10-3 mm2/s vs 0.80 (0.76, 0.93) ×10-3 mm2/s] (all P<0.05). The AUC of the combined model (pre-T1+pre-PD+post-T1+ADC+Age) is 0.828 (95%CI:0.729-0.903). Synthetic MRI relaxation quantitative values are helpful to distinguish IDH1 genotypes in glioma. The diagnostic efficacy of the multi-parameter combined model based on pre-T1, pre-PD, post-T1, ADC, and age is better than that of the single parameter, and it can be used as an effective strategy to improve the differential diagnosis ability of gliomas molecular markers.

[Single-cell RNA sequencing deciphers transcriptional profiles of hepatocytes in mouse with hepatic alveolar echinococcosis]

OBJECTIVE

To investigate the cell composition and the transcriptional characteristics in microenvironments of hepatic tissues in mice at late stage of Echinococcus multilocularis infection at a single-cell level.

METHODS

Peri-lesion and paired distal hepatic specimens were collected from two BALB/c mice (6 to 8 weeks old) infected with E. multilocularis for single-cell RNA sequencing. The Seurat package in the R software was employed for quality control of data, multi-sample integration and correction of batch effects, and uniform manifold approximation and projection (UMAP) algorithm was used for cell clustering. Cell types were annotated using classical marker genes. Differentially expressed genes were screened in each cell type through differential gene expression analysis, and the biological roles of cells were predicted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

RESULTS

A total of 43 710 cells from peri-lesion and distal hepatic tissues of E. multilocularis-infected mice were analyzed, and were classified into 11 cell types, including neutrophils, T cells, macrophages, granulocyte-monocyte progenitor cells, B cells, plasma cells, basophils, hepatic stellate cells, endothelial cells, hepatocytes, and platelets. T cells were the largest population of immune cells in the microenvironment of hepatic tissues, including five CD4⁺ T cell subsets, two CD8⁺ T cell subsets and phosphoantigen-reactive γδT cells. The proportions of CD4⁺ helper T cells and cytotoxic CD4⁺ T cells decreased and the proportion of T helper 2 (Th2) cells increased in peri-lesion tissues relative to distal hepatic tissues. In addition, the differentially expressed genes in Th2 cells were associated with negative regulation of the immune system, and the highly expressed genes in cytotoxic CD4⁺ T cells correlated with activation of the immune system.

CONCLUSIONS

Single-cell RNA sequencing deciphers the cell composition and distribution in microenvironments of hepatic tissues from mice infected with E. multilocularis, and the increased proportion of Th2 cells in peri-lesion hepatic tissues may be associated with formation of immunosuppressive microenvironments.

Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines

Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available Brassica oleracea-nigra MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived B. oleracea plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental B. oleracea, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived B. oleracea plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to B. nigra, in all five MAALs more DEGs were downregulated than upregulated. Trans-effects were likely more prevailing than cis-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that cis- and trans-mechanisms synergistically regulated alien gene transcriptions after distant hybridization.

Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism

Orychophragmus violaceus is a Brassicaceae species widely cultivated in China, particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand. Recently, O. violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids (diOH-FAs), which contribute to superior high-temperature lubricant properties. In this study, we performed de novo assembly of the O. violaceus genome. Whole-genome synteny analysis of the genomes of its relatives demonstrated that O. violaceus is a diploid that has undergone an extra whole-genome duplication (WGD) after the Brassicaceae-specific α-WGD event, with a basic chromosome number of x = 12. Formation of diOH-FAs is hypothesized to have occurred after the WGD event. Based on the genome and the transcriptome data from multiple stages of seed development, we predicted that OvDGAT1-1 and OvDGAT1-2 are candidate genes for the regulation of diOH-FA storage in O. violaceus seeds. These results may greatly facilitate the development of heat-tolerant and eco-friendly plant-based lubricants using O. violaceus seed oil and improve our understanding of the genomic evolution of Brassicaceae.

Fine mapping of genes controlling pigment accumulation in oilseed rape (Brassica napus L.)

Purple/red appearance is one of the common phenotypic variations in leaves, stems, and siliques of oilseed rape (Brassica napus L.) but very rare in flowers. In this study, the causal genes for the purple/red traits in stems and flowers in two accessions of oilseed rape (DH_PR and DH_GC001, respectively) derived from the wide hybridization were fine mapped, and candidate genes were determined by methods combined with bulked segregant analysis (BSA) and RNA-seq analysis. Both traits of purple stem and red flowers were mapped to the locus as AtPAP2 homologous genes (BnaPAP2.C6a and BnaPAP2.A7b, respectively) belonging to the R2R3-MYB family. Sequence comparisons of full-length allelic genes revealed several InDels and SNPs in intron 1 as well as exons, and completely different promoter region of BnaPAP2.C6a and a 211 bp insertion was identified in the promoter region of BnaPAP2.A7b of DH_GC001. Our results not only contribute to a better understanding of anthocyanin inheritance in B. napus, but also provide a useful toolbox for future breeding of cultivars with purple/red traits through the combination of different functional alleles and homologs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01365-5.

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.

Sinapis genomes provide insights into whole-genome triplication and divergence patterns within tribe Brassiceae

Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra, S. alba, and S. arvensis, and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole-genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole-genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba diverged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the divergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea. Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.

Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type

To improve 'bench-to-bedside' translation, it is integral that knowledge flows bidirectionally-from animal models to humans, and vice versa. This requires common analytical frameworks, as well as open software and data sharing practices. We share a new pipeline (and test dataset) for the preprocessing of wide-field optical fluorescence imaging data-an emerging mode applicable in animal models-as well as results from a functional connectivity and graph theory analysis inspired by recent work in the human neuroimaging field. The approach is demonstrated using a dataset comprised of two test-cases: (1) data from animals imaged during awake and anesthetized conditions with excitatory neurons labeled, and (2) data from awake animals with different genetically encoded fluorescent labels that target either excitatory neurons or inhibitory interneuron subtypes. Both seed-based connectivity and graph theory measures (global efficiency, transitivity, modularity, and characteristic path-length) are shown to be useful in quantifying differences between wakefulness states and cell populations. Wakefulness state and cell type show widespread effects on canonical network connectivity with variable frequency band dependence. Differences between excitatory neurons and inhibitory interneurons are observed, with somatostatin expressing inhibitory interneurons emerging as notably dissimilar from parvalbumin and vasoactive polypeptide expressing cells. In sum, we demonstrate that our pipeline can be used to examine brain state and cell-type differences in mesoscale imaging data, aiding translational neuroscience efforts. In line with open science practices, we freely release the pipeline and data to encourage other efforts in the community.

Transposon insertions within alleles of BnaFT.A2 are associated with seasonal crop type in rapeseed

We identified two new transposon insertions within the promoter of BnaFT.A2 in addition to an existing 288 bp MITE within the second intron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. Florigen, encoded by FLOWERING LOCUS T (FT), plays key roles not only as a flowering hormone, but also a universal growth factor affecting several aspects of plant architecture. In rapeseed, BnaFT.A2 has been revealed as one of the major loci associated with flowering time and different ecotypes. However, it is unclear how allelic variations of BnaFT.A2 affect its function in flowering time regulation and beyond. In this study, we confirmed an existing 288 bp miniature inverted-repeat transposable element (MITE) insertion within the second intron and identified two new insertions within the promoter of BnaFT.A2-a 3971 bp CACTA and a 1079 bp Helitron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. These alleles have similar tissue-specific expression patterns but discrete transcriptional patterns tightly associated with rapeseed flowering time and ecotype. RNAi lines and mutants of BnaFT.A2 flowered significantly later than controls. Differentially expressed genes (DEGs), identified in transcriptomic profiling of seedling leaves from two loss-of-function mutants (Bnaft.a2-L1 and Bnaft.a2-L2) compared with controls, indicated significant enrichment for hormone metabolic genes and roles related to plant cell wall synthesis and photosynthesis. Plants with loss-of-function BnaFT.A2 had smaller leaves and lower net photosynthetic rate compared to controls. These findings not only further clarify the genetic basis of flowering time variation and ecotype formation in B. napus, but also provide an additional toolbox for genetic improvement of seasonal adaptation and production.

Test of a multi-gigawatt, 800 ns high power microwave driver based on Marx generator and metal-oxide varistors

High power microwave (HPM) sources usually require a well-defined rectangular pulse waveform, which is especially true for the case of long pulse (>100 ns), stable, and high efficiency operation. Most long pulse HPM drivers are realized with pulse forming networks. This paper presents a long pulse driver composed of a conventional Marx generator and metal-oxide varistors (MOVs), utilizing the MOV's nonlinear V-I characteristic. This method is easy to implement, and it has an additional benefit that the voltage can be stabilized even if the load's impedance changes slightly. A low inductance zig-zag folding structure of the MOV is designed to decrease its size and self-inductance. An LC filter is used to reduce the energy loss in the MOV. In the experiment, a 400 kV, 800 ns long pulse is achieved at a foil-less electron diode, and longer than 300 ns HPM generation is obtained.

Production and cytology of Brassica autoallohexaploids with two and four copies of two subgenomes

Different digenomic Brassica autoallohexaploids were produced from the crosses of three allotetraploids and ancestral diploids and characterized for the cytological behavior of two subgenomes with two and four copies. Interspecific hybridization and allopolyploidization present an important pathway for plant evolution and breeding. In this study, different types of digenomic autoallohexaploids with two or four copies of two subgenomes (AAAACC, AACCCC, AAAABB, BBBBCC, BBCCCC) were synthesized by the crosses between three Brassica allotetraploids and their diploid progenitors and the chromosome doubling, and their meiotic behaviors were analyzed by fluorescence in situ hybridization (FISH). These autoallohexaploids showed some variations in pollen fertility and seed-sets and produced both euploid and aneuploid progenies with some chromosomes lost. Two subgenomes in these autoallohexaploids showed some aberrant pairings and segregations, and the degrees of meiotic regularity were negatively associated with the genome affinities. The chromosomes of the subgenome with four copies formed few quadrivalents with the average number < 2, and mainly paired as bivalents, and majority of the chromosomes from the subgenome with two copies gave the expected bivalents. The different extents of the equal and unequal segregations corresponded to the chromosome pairings. The development and cytological investigation of these autoallohexaploids provide not only the new germplasm for genetic research and breeding but also the new clues for the genome behavior and interplay between these subgenomes with different copies.

RNA sequencing and iTRAQ proteomic data from an experiment examining the influence of conceptus presence and preovulatory estradiol on endometrial gene transcripts and proteins around maternal recognition of pregnancy in beef cattle

RNA sequencing reads and isobaric tags for a relative and absolute quantification (iTRAQ)-Based Proteomic Data were used to determine the impact of conceptus presence and preovulatory estradiol concentration on function of the d16 uterus in beef cattle. Conceptuses and endometrial biopsies were collected from the uterine horn ipsilateral to the corpus luteum. Total cellular RNA was extracted from endometrium for RNA sequencing across two lanes of a NovaSeq S2, 2 × 50-bp run. Two independent uterine luminal fluid pools (ULF) were made for each group: highE2/conceptus, highE2/noconceptus, lowE2/conceptus, and lowE2/noconceptus. Peptides were labeled with iTRAQ reagents and analyzed using 2-dimensional liquid chromatography mass spectrometry. Transcript abundances were determined using DESeq2 (FDR <0.05, FC>2). Scaffold Q+ was used to quantitate peptide and protein identifications in ULF. Datasets include uterine transcript and protein abundances among highE2/conceptus vs highE2/noconceptus and lowE2/conceptus vs lowE2/noconceptus groups. This information can be useful for further investigating the role of specific transcripts and proteins in the maintenance of early pregnancy in beef cattle. This dataset is related to the article ‘Influence of conceptus presence and preovulatory estradiol exposure on uterine gene transcripts and proteins around maternal recognition of pregnancy in beef cattle’ by E.J. Northrop-Albrecht, J.J.J. Rich, R.A. Cushman, R. Yao, X. Ge, G.A. Perry. Molecular and Cellular Endocrinology.

Metabolic and RNA sequencing analysis of cauliflower curds with different types of pigmentation

Cauliflower (Brassica oleracea var. botrytis) is a popular vegetable worldwide due to its delicious taste, high nutritional value and anti-cancer properties. Cauliflower normally produces white curds, and natural spontaneous mutations lead to the production of orange, purple or green curds. However, some white cauliflowers show uneven purple pigmentation in their curds, which seriously affects the appearance quality and economic value of this crop. The underlying mechanism is still unclear. In this study, we performed comparative transcriptional and metabolic profiling analysis of light orange, white and purplish cauliflower curds. Metabolite analysis revealed that the pigments conferring purple colouration were delphinin and cyanin. Transcriptome analysis showed that the anthocyanin metabolism-related structural genes DFR, ANS and UGT and the transcription factor genes PAP2, TT8, GL3, EGL3 and TTG1 were upregulated in purplish versus white curds. These findings shed light on the formation of purplish curds, which could facilitate the breeding of purely white or red cauliflower.

[A case of communicating oncocytic carcinoma of the naso-orbit]

A patient with a left eyelid mass for more than 1 year was admitted. One year ago, the patient underwent left sinus mass resection in another hospital, and the postoperative histopathology showed oncocytic carcinoma. Imaging examination in our hospital revealed lesions in the left eyelid and inner canthus, involving the canalis nasolacrimalis and orbit. The orbital mass was removed under general anesthesia. The histopathological diagnosis was oncocytic carcinoma.

Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed

Two CO paralogs in Brassica napus were confirmed and shown distinct expression pattern and function in promoting flowering and allelic variation s within BnaCO.A10 were found closely associated with ecotype divergence. CONSTANS (CO) is a key gene that responds to photoperiod and in Arabidopsis can promote flowering under long-day (LD) conditions. Brassica napus L. is a major oil crop and close relative of Arabidopsis, and arose via allopolyploidization from the diploids B. rapa (A genome) and B. oleracea (C genome). In this study, we confirmed that B. napus has two CO genes located on the A10 (BnaCO.A10) and C9 (BnaCO.C9) chromosomes. Significant differences in level and temporal pattern of transcription, as well as in protein function, of these homoeologous may have resulted from sequence variation in the promoter as well as in the coding region. Apart from two insertions of 527 bp and 2002 bp in the promoter of BnaCO.C9 that function as transcriptional enhancers, this gene is otherwise highly conserved in both promoter and coding region. However, BnaCO.A10 was classified into two haplotypes and transgene analysis in Arabidopsis and backcross analysis in rapeseed indicated that the winter-type haplotype had a greater effect in promoting flowering than the spring type. We discuss the contribution of CO alleles to species evolution, and for eco-geographic radiation following crop domestication, alongside scope for managing this locus in future breeding.

Dosage-Dependent Gynoecium Development and Gene Expression in Brassica napus-Orychophragmus violaceus Addition Lines

Distant hybridization usually leads to female sterility of the hybrid but the mechanism behind this is poorly understood. Complete pistil abortion but normal male fertility was shown by one Brassica napus-Orychophragmus violaceus monosomic alien addition line (MA, AACC + 1 IO, 2n = 39) produced previously. To study the effect of a single O. violaceus chromosome addition on pistil development in different genetic backgrounds, hybrids between the MA and B. carinata (BBCC), B. juncea (AABB), and two synthetic hexaploids (AABBCC) were firstly produced in this study which show complete female sterility. A microspore culture was further performed to produce the haploid monosomic alien addition line (HMA, AC + 1 IO, 2n = 20) and disomic addition line (DA, AACC + 2 IO, 2n = 40) together with haploid (H, AC, 2n = 19) and double haploid (DH, AACC, 2n = 38) plants of B. napus from MA to investigate the dosage effect of the alien O. violaceus chromosome on pistil development and gene expression. Compared to MA, the development of the pistils of DA and HMA was completely or partially recovered, in which the pistils could swell and elongate to a normal shape after open pollination, although no seeds were produced. Comparative RNA-seq analyses revealed that the numbers of the differentially expressed genes (DEGs) were significantly different, dosage-dependent, and consistent with the phenotypic difference in pairwise comparisons of HMA vs. H, DA vs. DH, MA vs. DH, MA vs. DA, and MA vs. HMA. The gene ontology (GO) enrichment analysis of DEGs showed that a number of genes involved in the development of the gynoecium, embryo sac, ovule, and integuments. Particularly, several common DEGs for pistil development shared in HMA vs. H and DA vs. DH showed functions in genotoxic stress response, auxin transport, and signaling and adaxial/abaxial axis specification. The results provided updated information for the molecular mechanisms behind the gynoecium development of B. napus responding to the dosage of alien O. violaceus chromosomes.

EGFR tyrosine kinase inhibitor Almonertinib induces apoptosis and autophagy mediated by reactive oxygen species in non-small cell lung cancer cells

Almonertinib, a new third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, is highly selective to EGFR T790M-mutant non-small cell lung cancer (NSCLC). However, there is no available information on the form and molecular mechanism of Almonertinib-induced death in NSCLC cells. Herein, CCK-8 and colony formation assays, flow cytometry, electron microscopy, and western blots assay showed that Almonertinib inhibited NSCLC cells growth and proliferation by inducing apoptosis and autophagy which can be inhibited by a broad spectrum of caspase inhibitor Z-VAD-fmk or autophagy inhibitor chloroquine. Importantly, Almonertinib-induced autophagy was cytoprotective in NSCLC cells, and the blockade of autophagy improved cell apoptosis. In addition, Almonertinib increased reactive oxygen species (ROS) generation and clearance of ROS through pretreatment with N-acetyl-L-cysteine (NAC) inhibited the decrease of cell viability, apoptosis and increase of LC3-II induced by Almonertinib. The results of Western blot showed that both EGFR activity and downstream signaling pathways were inhibited by Almonertinib. Taken together, these findings indicated that Almonertinib induced apoptosis and autophagy by promoting ROS production in NSCLC cells.

POS0788 CIRCULATING EXOSOMES PROMOTE LUPUS NEPHRITIS IN MRL-LPR MICE

Background:

Systemic Lupus Erythematosus (SLE) is a prototypic autoimmune disease that characterized by the loss of self-tolerance and the production of autoantibodies (autoAbs) [1, 2]. Lupus nephritis (LN), the severe organ-threatening manifestations of SLE, could cause massive damage to patients[3, 4]. Currently, some exosomal microRNAs (miRNAs) are considered as potential biomarkers in SLE. However, the role of exosomal miRNAs in Lupus Nephritis (LN) remains unclear.

Objectives:

The purpose of this study was to investigate molecular mechanism of plasma exosomal miRNAs in the development of Lupus Nephritis.

Methods:

Circulating exosomes were isolated from plasma of patients with LN, SLE without LN (NLN). Plasma exosomes were authenticated by Western Blot, Nanosight Tracking Analysis (NTA) and transmission electron microscopy (TEM). Fluorescence microscopy of co-cultured plasma exosomes and podocytes demonstrated that exosomes were uptaken into podocytes. Moreover, cell apoptosis and the inflammation factors was assessed using Western Blot. We analyzed the expression profiles of miRNAs in LN and NLN exosomes and the expression profiles of mRNAs of podocytes stimulated with LN and NLN exosomes with the help of next generation sequencing (NGS).

Results:

We demonstrate that exosomes derived from LN plasma could be taken by neighboring podocytes and promote the apoptosis of podocytes and the expression of inflammation factors. In addition, the sequencing found that miRNAs were differentially expressed in LN and NLN exosomes and mRNAs were differentially expressed in podocytes stimulated with LN and NLN exosomes.

Conclusion:

LN plasma exosomes have a potency to stimulate the apoptosis of podocytes and the expression of inflammation factors. Moreover, differentially expressed miRNAs in exosomes play a potential role in the development of LN.

References:

[1]T. Colasanti, A. Maselli, F. Conti, M. Sanchez, C. Alessandri, C. Barbati, D. Vacirca, A. Tinari, F. Chiarotti, A. Giovannetti, F. Franconi, G. Valesini, W. Malorni, M. Pierdominici, E. Ortona, Autoantibodies to estrogen receptor α interfere with T lymphocyte homeostasis and are associated with disease activity in systemic lupus erythematosus, Arthritis and rheumatism, 64 (2012) 778-787.

[2]H.A. Al-Shobaili, A.A. Al Robaee, A.A. Alzolibani, Z. Rasheed, Antibodies against 4-hydroxy-2-nonenal modified epitopes recognized chromatin and its oxidized forms: role of chromatin, oxidized forms of chromatin and 4-hydroxy-2-nonenal modified epitopes in the etiopathogenesis of SLE, Disease markers, 33 (2012) 19-34.

[3]A. Kaul, C. Gordon, M.K. Crow, Z. Touma, M.B. Urowitz, R. van Vollenhoven, G. Ruiz-Irastorza, G. Hughes, Systemic lupus erythematosus, Nat Rev Dis Primers, 2 (2016) 16039.

[4]M.G. Tektonidou, A. Dasgupta, M.M. Ward, Risk of End-Stage Renal Disease in Patients With Lupus Nephritis, 1971-2015: A Systematic Review and Bayesian Meta-Analysis, Arthritis & rheumatology (Hoboken, N.J.), 68 (2016) 1432-1441.

Disclosure of Interests:

None declared

POS0401 THE APPLICATION OF MTX-LOADING DNA TETRAHEDRON IN TREATING COLLAGEN-INDUCED ARTHRITIS MICE VIA REGULATING MACROPHAGE

Background:

Rheumatoid arthritis (RA) is a systemic autoimmune disease which mainly affect joints. [1]. Macrophages often infiltrate in the inflammatory joints. Activated macrophages release TNF-α, IL-1β to accelerate tissue damage, is one of the most important targets for RA intervention. The traditional drugs currently used commonly have some disadvantages cannot be bypassed[2], while DNA nanostructure is a new type of drugs have precise design, and likewise takes biological effect together[3]. We synthesized a DNA tetrahedron loaded with MTX and conjugated with HA which targeted to macrophage.

Objectives:

To verify whether MTX-loading DNA tetrahedron can regulate the apoptosis and polarization of macrophage and finally improve the condition of CIA model mice by while decrease the side effect of MTX.

Methods:

DNA TET was synthesized by mixing signal strand DNA in TM buffer and heated to 95 °C for 10 min, then cooling to 4 °C. Electrophoresis was applied to confirm the formation of TET. The absorbance of MTX solution was detected by microplate reader to analyze the loading efficiency of MTX into TET. Fluorescence microscope was used to observe the intake of TET into cells. CCK8 experiment was applied to measure the vitality of cells. Flow cytometry was used to detect the apoptosis and polarization. CIA model was established based on DBA/1 mice. Mice were randomly divided into five groups: normal group injected with NS; after established CIA model, CIA group injected with NS, MTX group injected with MTX solution, MTX-TET group injected with MTX-TET NP.

Results:

We synthesized DNA tetrahedron(A) and used 8% PAGE electrophoresis to confirmed the successfully synthesis(B). Then We found that when TET concentration fixed, the loading MTX concentration gradually increased and saturated at 190μM(C). While completely loading needed at least 4 hours(D). Fluorescence showed that single DNA strand cannot be taken by RAW, while TET can be easily taken by RAW(E). CCK8 showed that empty TET had no obvious effect on cells, while MTX and MTX-TET with equivalent concentration can obviously suppress the vitality(F). Similarly, the apoptosis trial showed that TET can slightly decrease the apoptosis of RAW, MTX and MTX-TET can significantly promote the apoptosis(G). Flow cytometry showed that the MTX-TET can decrease the expression of M1 marker CD80 (H).

At last, we treat mice with NS, TET, MTX and MTX-TET once a week after CIA model established, and found that TET have no significantly effect on mice, while MTX and MTX-TET can alleviate the inflammation symptom of paws(I).

Conclusion:

Conclusions: We synthesized MTX-loading DNA tetrahedron conjugated with HA, and found that the MTX-TET NP have the excellent ability of promote RAW apoptosis and relieve proinflammatory M1 polarization. while also can alleviate the symptom of CIA mice.

References:

[1]Aletaha D, Smolen JS: Diagnosis and Management of Rheumatoid Arthritis: A Review. JAMA 2018, 320(13):1360-1372.

[2]Smolen JS, Aletaha D, McInnes IB: Rheumatoid arthritis. Lancet 2016, 388(10055):2023-2038.

[3]Hu Q, Li H, Wang L, Gu H, Fan C: DNA Nanotechnology-Enabled Drug Delivery Systems. Chem Rev 2019, 119(10):6459-6506.

Figure 1.

Disclosure of Interests:

None declared

OP0016 IDENTIFICATION OF FUNCTIONAL VARIANTS IN THE RHEUMATOID ARTHRITIS ASSOCIATED JAZF1 LOCUS IN SYNOVIAL FIBROBLASTS

Background:

Over the past decade, genome wide association studies (GWAS) have identified the JAZF1 locus as a risk locus for several autoimmune diseases, including rheumatoid arthritis (RA)1. However, the exact causal variants in the JAZF1 locus and their underlying regulatory events contributing to RA are still not known. Here, we focus on the effect of these variants on gene expression in synovial fibroblasts (SF).

Objectives:

To characterize the functional consequences of RA-causal variants in the JAZF1 locus in SF.

Methods:

Genetic fine-mapping of RA loci was conducted by computing sets of credible variants driving GWAS signals. These credible variant sets were integrated with DNA architecture (ChIP-seq), 3D chromatin interactions (3C, HiC and capture HiC), DNA accessibility (ATAC-seq) and gene expression (RNA-seq and CAGE-seq) datasets to select putative RA-causal variants in SF. Selected variants in the JAZF1 locus were tested for regulatory function by luciferase reporter assays and electrophoretic mobility shift assays (EMSA) in the fibrosarcoma cell line HT1080. The JASPAR2020 database was used to identify putative transcription factors (TF) binding to the selected variants. The expression of HOTTIP was measured by quantitative PCR in hand SF (n=23). Genotyping was done by pyrosequencing.

Results:

Genetic fine mapping revealed 47 variants in the JAZF1 locus. Integration of these variants with the chromatin datasets prioritized rs2158624, rs57585717 and rs186735625 as the top candidates (posterior probability of causality >0.1) in the JAZF1 locus. We found that rs2158624 and rs186735625 are located in the vicinity of enhancer elements in SF as determined by ATAC-seq. In addition, the region of rs2158624 exhibited strong chromatin interactions with the genomic region of HOTTIP and HOXA13. Both these transcripts were previously shown to be specifically expressed in SF isolated from hands and feet2. Based on this, we selected rs2158624 as the most promising candidate in the JAZF1 locus. We found that the rs2158624-C allele (risk) is associated with lower expression of HOTTIP, but not HOXA13, in hand SF compared to the rs2158624-T allele (non-risk) (p=0.02). Luciferase assays in HT1080 cells demonstrated enhancer activity with both the rs2158624-C allele (p=0.006) and T allele (p=0.04), with no significant difference in enhancer activity between the rs2158624-C and T allele. EMSAs identified stronger specific binding of HT1080-cell nuclear extract for the rs2158624-T allele than for the C allele (risk). Based on the JASPAR2020 database, we identified NFAT5 as a potential TF that can bind to rs2158624 and may regulate the expression of HOTTIP.

Conclusion:

We were able to substantially narrow down the potential functional variants in the JAZF1 locus using our data integration approach and functional assays. We suggest that the risk allele of rs2158624 influences the binding of TFs controlling the expression of the long non-coding RNA HOTTIP in SF, which might confer specific risk to develop RA in hands.

References:

[1]Okada Y et al. Genetic of rheumatoid arthritis contributes to biology and drug discovery. Nature 2014;506:376.

[2]Frank-Bertoncelj M et al. Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions. Nat Commun 2017;8:14852.

Disclosure of Interests:

Miranda Houtman: None declared, Xiangyu Ge: None declared, Amanda McGovern: None declared, Kerstin Klein: None declared, Gisela Orozco: None declared, Mojca Frank Bertoncelj: None declared, Miriam Marks: None declared, Oliver Distler Speakers bureau: Bayer, Boehringer Ingelheim, iQone, Medscape, MSD, Novartis, Pfizer and Roche, Consultant of: Abbvie, Acceleron Pharma, Amgen, AnaMar, Arxx Therapeutics, Bayer, Baecon Discovery, Boehringer, CSL Behring, ChemomAb, Corbus Pharmaceuticals, Galapagos NV, GSK, Glenmark Pharmaceuticals, Horizon Pharmaceuticals, Inventiva, Italfarmaco, iQvia, Kymera, Lilly, Medac, Medscape, Mitsubishi Tanabe Pharma, MSD, Pfizer, Roche, Roivant Sciences, Sanofi and UCB, Grant/research support from: Kymera Therapeutics and Mitsubishi Tanabe, Paul Martin: None declared, Stephen Eyre: None declared, Caroline Ospelt: None declared

[Chaihu Guizhi decoction produces antidepressant-like effects via sirt1-p53 signaling pathway]

OBJECTIVE

To investigate the mechanism of the antidepressant-like effects of Chaihu Guizhi decoction (CGD).

OBJECTIVE

Chaihu Guizhi decoction at the daily dose of 17 g/kg and solvent vehicle were administered by gavage in 12 and 14 male C57BL/6J mice for 7 consecutive days, respectively. Forced swimming test (FST), elevated plus maze (EPM) test, open field test (OFT) and novelty-suppressed feeding test (NSF) were performed to assess the depression- and anxiety-like behaviors and motor ability of the mice. We further used chronic social defeat stress (CSDS) and social interaction test to evaluate the antidepressant-like effects of CGD in comparison with the solvent vehicle. Western blotting and RT-qPCR were performed to detect the expressions of sirt1, p53, acetylated p53, and the neuron plasticity-related genes including synapsin I (Syn1), Rab4B, SNAP25 and tubulin beta4b in the hippocampus of the mice.

OBJECTIVE

In FST, the immobility time of CGDtreated mice was decreased significantly (P < 0.05); no significant differences were found in the performances in EPM, NSF and OFT tests between the two groups. In social interaction test, the mouse models of CSDS treated with CGD showed significantly increased time in the interaction zone (P < 0.05). Compared with those in the vehicle group, the CGD-treated mouse models exhibited significantly increased protein level of SIRT1 and decreased p53 acetylation (P < 0.05) with up-regulated synapsin I mRNA expression in the hippocampus (P < 0.05); no significant difference were found in Rab (P=0.813), SNAP (P=0.820), or Tubb mRNA expressions (P=0.864) between the two groups.

OBJECTIVE

CGD produces antidepressant-like effects in mice possibly through the sirt1-p53 signaling pathway and synaptic plasticity.

Enhanced removal of Congo red dye from aqueous solution by surface modified activated carbon with bacteria

AIMS

The adsorption behaviour and mechanisms of the surface modified activated carbon with bacteria was evaluated.

METHODS AND RESULTS

16S rRNA was employed to identify the hydrocarbon-degrading bacteria. The bacteria was characterized by TEM and electron microscope. The surface modified activated carbon with bacteria was characterized by SEM. The adsorption behaviour was tested by static adsorption and dynamic adsorption.

CONCLUSION

The adsorption efficiency of the modified activated carbon was high when pH was weak acidic, and the adsorption capacity increased with the increase of temperature ranging from 20 to 35°C. The adsorption capacity peaked at 234·6 mg g^-1 at 25°C, which was sixfold higher than that of activated carbon. The pseudo-first-order kinetic can more accurately assess Congo red adsorption on the two adsorbents. The adsorption of Congo red by bacteria surface modified activated carbon fitted well with the Langmuir's model. The adsorption process was endothermic, and the biological floccules were formed during the adsorption. The physical adsorption is the main driving force.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results indicate that the bacteria surface-modified activated carbon can be used effectively as an adsorbent to eliminate Congo red from aqueous solutions.

A comparison between raltitrexed plus cisplatin and docetaxel plus cisplatin in concurrent chemoradiation for non-surgical esophageal squamous cell carcinoma

PURPOSE

Chemoradiotherapy (CRT) is considered as a standard treatment for unresectable and inoperable esophageal cancer (EC) patients. However, no consensus has been reached regarding the optimal synchronous chemotherapy regimen and the best combination of radiotherapy and chemotherapy. The aim of this study was to evaluate the efficacy and toxicity of raltitrexed plus cisplatin and docetaxel plus cisplatin to find a safe and effective concurrent chemotherapy schedule.

PATIENTS AND METHODS

Our retrospective study included 151 EC patients treated with raltitrexed and cisplatin (RP) (n=90) or docetaxel and cisplatin (DP) (n=61) from 2011 till 2018. Survival outcomes and treatment related toxicity were analyzed between the two groups.

RESULTS

PFS and OS were 18 and 34 months in the RP group, while 13 and 20 months in the DP group (P=0.118 and P=0.270). The 1-, 2-, 3-year survival rates of the RP group were 71.1, 55.4 and 46.4%. For the DP group, these were 63.9, 44.3 and 37.6%, respectively. Compared with DP group, RP group received a superior CR rate (68.9% versus 52.5%, P=0.041). There was a trend that the total number of toxic reactions in RP group was lower than that in DP group (P=0.058).

CONCLUSIONS

Even RP and DP groups have the similar survival outcomes and toxicity, raltitrexed/cisplatin get a higher complete response rate. Our study suggests that raltitrexed combined with cisplatin is a safe and effective concurrent chemotherapy regimen and it might be used as an alternative for cisplatin/5-FU and cisplatin/docetaxel in CCRT for EC patients.

Alternatively Spliced BnaPAP2.A7 Isoforms Play Opposing Roles in Anthocyanin Biosynthesis of Brassica napus L

Brassica napus L. (rapeseed, oilseed rape, and canola) and varieties of its two diploid parents, B. oleracea and B. rapa, display a large amount of variation in anthocyanin pigmentation of the leaf, stem, and fruit. Here, we demonstrate that BnaPAP2.A7, an ortholog of the B. oleracea anthocyanin activator BoMYB2 that confers purple traits, positively regulates anthocyanin biosynthesis in leaves of B. napus. Sequencing of BnaPAP2.A7 and transgenic analysis suggests that activation of this gene in purple rapeseed may result from a single nucleotide and/or 2bp insertion in its promoter region. BnaPAP2.A7 gives rise to three splice variants, designated BnaPAP2.A7-744, BnaPAP2.A7-910, and BnaPAP2.A7-395 according to the length of the transcripts. While BnaPAP2.A7-744 encodes a full-length R2R3-MYB, both BnaPAP2.A7-910 and BnaPAP2.A7-395 encode truncated proteins that lack both a partial R3 repeat and the complete C terminal domain, and so in vitro are unable to interact with the Arabidopsis bHLH protein AtTT8. Although expression of either BnaPAP2.A7-910 or BnaPAP2.A7-395 in green rapeseed does not result in purple leaves, both genes do modify genome-wide gene expression, with a strong repression of anthocyanin-related genes. We have demonstrated that BnaPAP.A7 regulates anthocyanin accumulation in leaves of B. napus and propose a potential mechanism for modulation of anthocyanin biosynthesis by alternative splicing.

Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed

In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.

Plasminogen improves lung lesions and hypoxemia in patients with COVID-19

BACKGROUND

Lungs from patients with coronavirus disease 2019 (COVID-19) have shown typical signs of acute respiratory distress syndrome (ARDS), formation of hyaline membrane mainly composed of fibrin and 'ground-glass' opacity. Previously, we showed plasminogen itself is a key regulator in fibrin degradation, wound healing and infection.

AIM

We aimed to investigate whether plasminogen can improve lung lesions and hypoxemia of COVID-19.

DESIGN

Thirteen clinically moderate, severe or critical COVID-19 patients were treated with atomization inhalation of freeze-dried plasminogen.

METHODS

Levels of their lung lesions, oxygen saturation and heart rates were compared before and after treatment by computed tomography scanning images and patient monitor.

RESULTS

After plasminogen inhalation, conditions of lung lesions in five clinically moderate patients have quickly improved, shown as the decreased range and density of 'ground glass' opacity. Improvements of oxygen saturation were observed in six clinically severe patients. In the two patients with critical conditions, the oxygen levels have significantly increased from 79-82% to 91% just about 1 h after the first inhalation. In 8 of 13 patients, the heart rates had slowed down. For the five clinically moderate patients, the difference is even statistically significant. Furthermore, a general relief of chest tightness was observed.

CONCLUSION

Whereas it is reported that plasminogen is dramatically increased in adults with ARDS, this study suggests that additional plasminogen may be effective and efficient in treating lung lesions and hypoxemia during COVID-19 infections. Although further studies are needed, this study highlights a possible hope of efficiently combating this rapid epidemic emergency.

Effect of reference region size on strain measurements using geometrical phase analysis

Geometrical phase analysis (GPA) is typically a powerful tool to investigate the deformation in high resolution transmission electron microscopy images and has been used in various fields. During GPA, strain components are calculated relative to an undistorted reference region. In the present work, the effect of reference region size on strain measurements has been investigated. Experimental measurements on a locally distorted gold nanoparticle exhibited that a small reference region below the GPA spatial resolution can introduce an inaccuracy in the measured displacement field, which appears as a significant increase in measured strains and severe fluctuation in phase images. The inaccuracy may be ascribed to an error of insufficient sampling. Our results suggest that a small reference region below the GPA spatial resolution should be avoided during GPA. This prerequisite should be paid more attention to during strain measurement on nanoparticles.

Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus

Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, A_eA_e, 2n = 20) obtained from Brassica napus (A_nA_nC_nC_n, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (A_rA_r), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the A_n-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between A_n and C_n subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the A_n and C_n subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus

Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromosome number and normal meiosis behavior. Moreover, the metabolome analysis showed multiple important secondary metabolites, including flavonoids and glucosinolates, were significantly upregulated in the hybrid. Furthermore, transcriptome data revealed that the expression level of the important genes involved in phenylpropanoid and flavonoid pathways was significantly upregulated in the hybrid. Ultimately, our data indicate the intergeneric hybrid will be a valuable bioengineering resource and promise to become a new-type hybrid vegetable with great medicinal value in future.

Integrated impedance bridge for absolute capacitance measurements at cryogenic temperatures and finite magnetic fields

We developed an impedance bridge that operates at cryogenic temperatures (down to 60 mK) and in perpendicular magnetic fields up to at least 12 T. This is achieved by mounting a GaAs HEMT amplifier perpendicular to a printed circuit board containing the device under test and thereby parallel to the magnetic field. The measured amplitude and phase of the output signal allows for the separation of the total impedance into an absolute capacitance and a resistance. Through a detailed noise characterization, we find that the best resolution is obtained when operating the HEMT amplifier at the highest gain. We obtained a resolution in the absolute capacitance of 6.4 aF/Hz at 77 K on a comb-drive actuator while maintaining a small excitation amplitude of 15 k_BT/e. We show the magnetic field functionality of our impedance bridge by measuring the quantum Hall plateaus of a top-gated hBN/graphene/hBN heterostructure at 60 mK with a probe signal of 12.8 k_BT/e.

Association of Fractional Flow on 3D-TOF-MRA with Cerebral Perfusion in Patients with MCA Stenosis

BACKGROUND AND PURPOSE

Fractional flow measured on 3D-TOF-MRA was proposed to quantify cerebral hemodynamic changes in patients with artery stenosis. We investigated the association between fractional flow and cerebral perfusion changes in patients with symptomatic MCA stenosis.

MATERIALS AND METHODS

This prospective study was approved by the institutional review board, and all participants provided written informed consent. From June 2015 to May 2018, four hundred twenty-nine patients with symptomatic intracranial arterial stenosis were consecutively recruited and underwent conventional brain MR imaging, 3D-TOF-MRA, and brain CTP. A total of 91 patients with unilateral M1 segment stenosis of the MCA and a stenosis degree of 50%∼99% were included in the analysis. Fractional flow was measured by comparing distal and proximal signal intensity changes across the stenosis on 3D-TOF-MRA. The cutoff value for fractional flow for discriminating between normal perfusion and hypoperfusion was obtained from the receiver operating characteristic curve. Associations between fractional flow and hypoperfusion were assessed using univariate and multivariate analyses.

RESULTS

The receiver operating characteristic curve showed a significant fractional flow threshold value at 0.90 (sensitivity, 70.1%; 95% CI, 55.9%-81.2%; specificity, 69.6%; 95% CI, 47.6%-84.1%). Participants with a fractional flow of ≤0.90 were independently associated with cerebral hypoperfusion downstream from the stenosis site (adjusted OR, 3.68; 95% CI, 1.63-11.62; P = .027).

CONCLUSIONS

Fractional flow measured on 3D-TOF-MRA may serve as a noninvasive and practical tool for determining the cerebral hypoperfusion in patents with symptomatic MCA stenosis.

Development of a Fertility Restorer for inap CMS (Isatis indigotica) Brassica napus Through Genetic Introgression of One Alien Addition

Novel Brassica napus cytoplasmic male sterility (CMS) with carpelloid stamens (inap CMS) was produced by intertribal somatic hybridization with Isatis indigotica (Chinese woad), but its RF (restorer of fertility) gene(s) existed in one particular woad chromosome that was carried by one fertile monosomic alien addition line (MAAL) of rapeseed. Herein, the selfed progenies of this MAAL were extensively selected and analyzed to screen the rapeseed-type plants (2n = 38) with good male fertility and to produce their doubled haploid (DH) lines by microspore culture. From the investigation of fertility restoration in the F₁ hybrids with inap CMS, one DH line (RF 39) was identified to adequately restore male fertility and likely carried one dominant RF gene. Specifically, this restorer produced brown pollen grains, similar to the woad and the MAAL, suggesting that this trait is closely linked with the RF gene(s) and serves as one phenotypic marker for the restorer. This restorer contained 38 chromosomes of rapeseed and no intact chromosomes of woad, but some DNA fragments of woad origin were detected at low frequency. This restorer was much improved for pollen and seed fertility and for low glucosinolate content. The successful breeding of the restorer for inap CMS rendered this new pollination control system feasible for rapeseed hybrid production.