The H1/H5 domain contributes to OsTRBF2 phase separation and gene repression during rice development.

Transcription factors (TFs) tightly control plant development by regulating gene expression. The phase separation of TFs plays a vital role in gene regulation. Many plant TFs have the potential to form phase-separated protein condensates; however, little is known about which TFs are regulated by phase separation and how it affects their roles in plant development. Here, we report that the rice (Oryza sativa) single Myb TF TELOMERE REPEAT-BINDING FACTOR 2 (TRBF2) is highly expressed in fast-growing tissues at the seedling stage. TRBF2 is a transcriptional repressor that binds to the transcriptional start site of thousands of genes. Mutation of TRBF2 leads to pleiotropic developmental defects and misexpression of many genes. TRBF2 displays characteristics consistent with phase separation in vivo and forms phase-separated condensates in vitro. The H1/H5 domain of TRBF2 plays a crucial role in phase separation, chromatin targeting, and gene repression. Replacing the H1/H5 domain by a phase-separated intrinsically disordered region from Arabidopsis (Arabidopsis thaliana) AtSERRATE partially recovers the function of TRBF2 in gene repression in vitro and in transgenic plants. We also found that TRBF2 is required for trimethylation of histone H3 Lys27 (H3K27me3) deposition at specific genes and genome wide. Our findings reveal that phase separation of TRBF2 facilitates gene repression in rice development.

PICKLE and HISTONE DEACETYLASE6 coordinately regulate genes and transposable elements in Arabidopsis.

Chromatin dynamics play essential roles in transcriptional regulation. The chromodomain helicase DNA-binding domain 3 chromatin remodeler PICKLE (PKL) and HISTONE DEACETYLASE6 (HDA6) are required for transcriptional gene silencing, but their coordinated function in gene repression requires further study. Through a genetic suppressor screen, we found that a point mutation at PKL could partially restore the developmental defects of a weak Polycomb repressive complex 1 (PRC1) mutant (ring1a-2 ring1b-3), in which RING1A expression is suppressed by a T-DNA insertion at the promoter. Compared to ring1a-2 ring1b-3, the expression of RING1A is increased, nucleosome occupancy is reduced, and the histone 3 lysine 9 acetylation (H3K9ac) level is increased at the RING1A locus in the pkl ring1a-2 ring1b-3 triple mutant. HDA6 interacts with PKL and represses RING1A expression similarly to PKL genetically and molecularly in the ring1a-2 ring1b-3 background. Furthermore, we show that PKL and HDA6 suppress the expression of a set of genes and transposable elements (TEs) by increasing nucleosome density and reducing H3K9ac. Genome-wide analysis indicated they possibly coordinately maintain DNA methylation as well. Our findings suggest that PKL and HDA6 function together to reduce H3K9ac and increase nucleosome occupancy, thereby facilitating gene/TE regulation in Arabidopsis (Arabidopsis thaliana).

CircDiaph3 aggravates H/R-induced cardiomyocyte apoptosis and inflammation through miR-338-3p/SRSF1 axis.

Acute myocardial infarction (AMI) is one of the most prevalent cardiovascular diseases, accounting for a high incidence rate and high mortality worldwide. Hypoxia/reoxygenation (H/R)-induced myocardial cell injury is the main cause of AMI. Several studies have shown that circular RNA contributes significantly to the pathogenesis of AMI. Here, we established an AMI mouse model to investigate the effect of circDiaph3 in cardiac function and explore the functional role of circDiaph3 in H/R-induced cardiomyocyte injury and its molecular mechanism. Bioinformatics tool and RT-qPCR techniques were applied to detect circDiaph3 expression in human patient samples, heart tissues of AMI mice, and H/R-induced H9C2 cells. CCK-8 was used to examine cell viability, while annexin-V/PI staining was used to assess cell apoptosis. Myocardial reactive oxygen species (ROS) levels were detected by immunofluorescence. Western blot was used to detect the protein expression of anti-apoptotic Bcl-2 while pro-apoptotic Bax and cleaved-Caspase-3. Furthermore, ELISA was used to detect inflammatory cytokines production. While bioinformatics tool and RNA pull-down assay were used to verify the interaction between circDiaph3 and miR-338-3p. We found that circDiaph3 expression was high in AMI patients and mice, as well as in H/R-treated H9C2 cells. CircDiaph3 silencing ameliorated apoptosis and inflammatory response of cardiomyocytes in vivo. Moreover, the knockdown of cirDiaph3 mitigated H/R-induced apoptosis and the release of inflammatory mediators like IL-1ß, IL-6, and TNF-α in H9C2 cells. Mechanistically, circDiaph3 induced cell apoptosis and inflammatory responses in H/R-treated H9C2 cells by sponging miR-338-3p. Overexpressing miR-338-3p in H/R-treated cells prominently reversed circDiaph3-induced effects. Notably, miR-338-3p inhibited SRSF1 expression in H/R-treated H9C2 cells. While overexpressing SRSF1 abrogated miR-338-3p-mediated alleviation of apoptosis and inflammation after H/R treatment. To summarize, circDiaph3 aggravates H/R-induced cardiomyocyte apoptosis and inflammation through the miR-338-3p/SRSF1 axis. These findings suggest that the circDiaph3/miR-338-3pp/SRSF1 axis could be a potential therapeutic target for treating H/R-induced myocardial injury.

Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis.

A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.

Using Natural Language Processing (GPT-4) for Computed Tomography Image Analysis of Cerebral Hemorrhages in Radiology: Retrospective Analysis.

BACKGROUND: Cerebral hemorrhage is a critical medical condition that necessitates a rapid and precise diagnosis for timely medical intervention, including emergency operation. Computed tomography (CT) is essential for identifying cerebral hemorrhage, but its effectiveness is limited by the availability of experienced radiologists, especially in resource-constrained regions or when shorthanded during holidays or at night. Despite advancements in artificial intelligence-driven diagnostic tools, most require technical expertise. This poses a challenge for widespread adoption in radiological imaging. The introduction of advanced natural language processing (NLP) models such as GPT-4, which can annotate and analyze images without extensive algorithmic training, offers a potential solution. OBJECTIVE: This study investigates GPT-4's capability to identify and annotate cerebral hemorrhages in cranial CT scans. It represents a novel application of NLP models in radiological imaging. METHODS: In this retrospective analysis, we collected 208 CT scans with 6 types of cerebral hemorrhages at Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, between January and September 2023. All CT images were mixed together and sequentially numbered, so each CT image had its own corresponding number. A random sequence from 1 to 208 was generated, and all CT images were inputted into GPT-4 for analysis in the order of the random sequence. The outputs were subsequently examined using Photoshop and evaluated by experienced radiologists on a 4-point scale to assess identification completeness, accuracy, and success. RESULTS: The overall identification completeness percentage for the 6 types of cerebral hemorrhages was 72.6% (SD 18.6%). Specifically, GPT-4 achieved higher identification completeness in epidural and intraparenchymal hemorrhages (89.0%, SD 19.1% and 86.9%, SD 17.7%, respectively), yet its identification completeness percentage in chronic subdural hemorrhages was very low (37.3%, SD 37.5%). The misidentification percentages for complex hemorrhages (54.0%, SD 28.0%), epidural hemorrhages (50.2%, SD 22.7%), and subarachnoid hemorrhages (50.5%, SD 29.2%) were relatively high, whereas they were relatively low for acute subdural hemorrhages (32.6%, SD 26.3%), chronic subdural hemorrhages (40.3%, SD 27.2%), and intraparenchymal hemorrhages (26.2%, SD 23.8%). The identification completeness percentages in both massive and minor bleeding showed no significant difference (P=.06). However, the misidentification percentage in recognizing massive bleeding was significantly lower than that for minor bleeding (P=.04). The identification completeness percentages and misidentification percentages for cerebral hemorrhages at different locations showed no significant differences (all P>.05). Lastly, radiologists showed relative acceptance regarding identification completeness (3.60, SD 0.54), accuracy (3.30, SD 0.65), and success (3.38, SD 0.64). CONCLUSIONS: GPT-4, a standout among NLP models, exhibits both promising capabilities and certain limitations in the realm of radiological imaging, particularly when it comes to identifying cerebral hemorrhages in CT scans. This opens up new directions and insights for the future development of NLP models in radiology. TRIAL REGISTRATION: ClinicalTrials.gov NCT06230419; https://clinicaltrials.gov/study/NCT06230419.

The Histone Variant H3.3 Is Required for Plant Growth and Fertility in Arabidopsis.

Histones are the core components of the eukaryote chromosome, and have been implicated in transcriptional gene regulation. There are three major isoforms of histone H3 in Arabidopsis. Studies have shown that the H3.3 variant is pivotal in modulating nucleosome structure and gene transcription. However, the function of H3.3 during development remains to be further investigated in plants. In this study, we disrupted all three H3.3 genes in Arabidopsis. Two triple mutants, h3.3cr-4 and h3.3cr-5, were created by the CRISPR/Cas9 system. The mutant plants displayed smaller rosettes and decreased fertility. The stunted growth of h3.3cr-4 may result from reduced expression of cell cycle regulators. The shorter stamen filaments, but not the fertile ability of the gametophytes, resulted in reduced fertility of h3.3cr-4. The transcriptome analysis suggested that the reduced filament elongation of h3.3cr-4 was probably caused by the ectopic expression of several JASMONATE-ZIM DOMAIN (JAZ) genes, which are the key repressors of the signaling pathway of the phytohormone jasmonic acid (JA). These observations suggest that the histone variant H3.3 promotes plant growth, including rosette growth and filament elongation.

Replication protein RPA2A regulates floral transition by cooperating with PRC2 in Arabidopsis.

RPA2A is a subunit of the conserved heterotrimeric replication protein A (RPA) in Arabidopsis, which is an essential replisome component that binds to single-stranded DNA during DNA replication. RPA2A controls a set of developmental processes, but the underlying mechanism is largely unknown. Here we show that RPA2A represses key flowering genes including FLOWERING LOCUS T (FT), AGAMOUS (AG) and AGAMOUS LIKE 71 (AGL71) to suppress floral transition by cooperating with the PRC2 complex. RPA2A is vigorously expressed in dividing cells and required for correct DNA replication. Mutation of RPA2A leads to early flowering, which is dependent on ectopic expression of key flowering genes including FT molecularly and genetically. RPA2A and PRC2 have common target genes including FT, AG and AGL71 supported using genetic analysis, transcriptome profiling and H3K27me3 ChIP-seq analysis. Furthermore, RPA2A physically interacts with PRC2 components CLF, EMF2 and MSI1, which recruits CLF to the chromatin loci of FT, AG and AGL71. Together, our results show that the replication protein RPA2A recruits PRC2 to key flowering genes through physical protein interaction, thereby repressing the expression of these genes to suppress floral transition in Arabidopsis.

Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress.

Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.

[Peripheral blood albumin level in significantly correlated with the severity of atherosclerosis in hypertensive patients].

OBJECTIVE: To investigate the relationship between peripheral blood albumin (Hb) level and the severity of arteriosclerosis in hypertensive patients. METHODS: This retrospective analysis was conducted among 419 randomly selected patients with hypertension. The pulse wave velocity (ba-PWV) of the bilateral limbs was measured using an arteriosclerosis tester. According to the ba-PWV value (the higher value of the two sides), the hypertensive patients were divided into 4 groups, namely normal arterial group [S0 group, ba-PWV < 1400 cm/s; 49 cases (11.7%)], mild arteriosclerosis group [S1 group, ba-PWV of 1400-1800 cm/s; 190 cases (45.3%)], moderate arteriosclerosis group [S2 group, ba-PWV of 1800-2000 cm/s); 69 cases (16.5%)], and severe arteriosclerosis group [S3 group, ba-PWV > 2 000 cm/s; 111 cases (26.5 %)]. The clinical data of the patients were collected and multivariate logistic regression was used to analyze the risk factors of arteriosclerosis. RESULTS: The patients' age, obesity, albumin, alanine aminotransferase (ALT), total bile acid, adenosine deaminase, urea nitrogen, serum creatinine, cystatin C, low-density lipoprotein, red blood cells, hemoglobin (Hb), fibrinogen, and FT3 all differed significantly between S0 group and the 3 arteriosclerosis groups (P < 0.05). Multivariate logistic regression analysis revealed that in hypertensive patients, age was an independent risk factor for severe arteriosclerosis (OR=1.094, 95% CI: 1.052-1.137, P < 0.05) and moderate arteriosclerosis (OR= 1.081, 95% CI: 1.039-1.125, P < 0.05); Hb was an independent risk factor for new-onset severe arteriosclerosis (OR= 1.025, 95% CI: 1.003-1.045, P < 0.05) and moderate arteriosclerosis (OR=1.035, 95% CI: 1.008-1.056, P < 0.05), and an increase of Hb levels by 1 standard deviation was associated with a doubled risk in hypertensive patients. CONCLUSIONS: Peripheral Hb level is significantly correlated with the severity of arteriosclerosis and may serve as a new predictor for arteriosclerosis in hypertensive patients.

The Nuclear-Localized RxLR Effector PvAvh74 From Plasmopara viticola Induces Cell Death and Immunity Responses in Nicotiana benthamiana.

Downy mildew is one of the most serious diseases of grapevine (Vitis spp). The causal agent of grapevine downy mildew, Plasmopara viticola, is an obligate biotrophic oomycete. Although oomycete pathogens such as P. viticola are known to secrete RxLR effectors to manipulate host immunity, there have been few studies of the associated mechanisms by which these may act. Here, we show that a candidate P. viticola RxLR effector, PvAvh74, induces cell death in Nicotiana benthamiana leaves. Using agroinfiltration, we found that nuclear localization, two putative N-glycosylation sites, and 427 amino acids of the PvAvh74 carboxyl terminus were necessary for cell-death-inducing activity. Using virus-induced gene silencing (VIGS), we found that PvAvh74-induced cell death in N. benthamiana requires EDS1, NDR1, SGT1, RAR1, and HSP90, but not BAK1. The MAPK cascade components MEK2, WIPK, and SIPK were also involved in PvAvh74-induced cell death in N. benthamiana. Transient expression of PvAvh74 could suppress Phytophthora capsici colonization of N. benthamiana, which suggests that PvAvh74 elicits plant immune responses. Suppression of P. capsici colonization also was dependent on nuclear localization of PvAvh74. Additionally, PvAvh74-triggered cell death could be suppressed by another effector, PvAvh8, from the same isolate. This work provides a framework to further investigate the interactions of PvAvh74 and other RxLR effectors with host immunity.

Pre-operatively misdiagnosed undifferentiated embryonal sarcoma of the liver: analysis of 16 cases.

BACKGROUND: To investigate the clinical features of undifferentiated embryonal sarcoma of the liver (UESL) to improve its preoperative diagnostic accuracy. METHODS: The clinical, imaging, and histopathologic findings of 16 UESL patients whose disease was pathologically confirmed but preoperatively misdiagnosed were retrospectively analyzed. RESULTS: Among these 16 patients, 9 were clinically misdiagnosed as primary liver cancer, 3 as hepatoblastoma, and 4 as malignant hepatic mass. In 12 patients who were presented due to abdominal discomfort, ultrasound showed that predominantly solid lesions, whereas computed tomography (CT) and magnetic resonance imaging (MRI) demonstrated predominantly cystic masses within irregular soft tissue. Contrast-enhanced imaging showed enhancement intralesional foci, multiple internal septations, and edges. The postoperative pathology showed the cutting surface of tumors was variegated, with solid and cystic gelatinous areas, hemorrhage, and necrosis. Intracytoplasmic hyaline globules were commonly present among cancer cells. CONCLUSIONS: UESL is a rare clinical condition without specific clinical manifestations. The inconsistencies between ultrasound and CT/MRI findings may be helpful to improve the preoperative diagnosis accuracy.