Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome.

Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.

Theoretical insights into the intercalation mechanism of Li, Na, and Mg ions in a metallic BN/VS2 heterostructure.

Layered VS2 has been widely used as a battery anode material owing to its large specific surface area and controllable ion-transport channel. However, its semiconductor properties and poor cycling stability seriously limit its further applications. Herein, a two-dimensional BN/VS2 heterostructure (BVH) was constructed as an anode material for rechargeable metal-ion batteries (RMIBs). Demonstrated using first principles calculations, BVH exhibits a metallic property due to lattice stress between monolayer BN and VS2. BVH displays low ion diffusion energy barriers (0.13, 0.43, and 0.56 eV) and high theoretical capacities (447, 553.5, and 340.7 mA h g-1) for Li+, Na+, and Mg2+ storage. In BVH, the VS2 layer as the main redox center supports charge transfer, while the inactive BN layer enables high structural stability. This synergistic effect is expected to simultaneously achieve a high rate, high capacity, and long life. This design provides an important insight into developing new anode materials for RMIBs.

A two-dimensional VO2/VS2 heterostructure as a promising cathode material for rechargeable Mg batteries: a first principles study.

Rechargeable magnesium batteries (RMBs) are considered as highly promising energy storage systems. However, the lack of cathode materials with fast Mg2+ diffusion kinetics and high energy density severely hinders the development of RMBs. Herein, a two-dimensional (2D) VO2/VS2 heterostructure as a RMB cathode material is proposed by introducing an O-V-O layer in VS2 to improve the discharge voltage and specific capacity while keeping the fast Mg2+ diffusion kinetics. Based on first principle calculations, the geometric structures, electronic characteristics of the VO2/VS2 heterostructure, and the adsorption properties and diffusion behaviors of Mg2+ in VO2/VS2 are systematically studied. The metallic properties of VO2/VS2 and a relatively low diffusion barrier of Mg2+ (0.6 eV) in VO2/VS2 enable a large potential in delivering high rate performance in actual RMBs. Compared with traditional VS2 materials (1.25 V), the average discharge platform of VO2/VS2 could be increased to 1.7 V. The theoretical capacities of the layered VS2 and VO2/VS2 are calculated as 233 and 301 mA h g-1, respectively. Thus, the VO2/VS2 heterostructure exhibits a high theoretical energy density of 511.7 W h kg-1, significantly surpassing that of VS2 (291.3 W h kg-1). This work provides important guidance for designing high-energy and high-rate 2D heterostructure cathode materials for RMBs and other multivalent ion batteries.

Precise Measurement of the Thickness of Vaginal Intraepithelial Neoplasia.

OBJECTIVES: Although carbon dioxide laser vaporization is frequently used for treating vaginal intraepithelial neoplasia (VaIN), the optimal depth of epithelial destruction with laser vaporization requires elucidation. We aimed to evaluate VaIN depth and better illustrate epithelial destruction during laser vaporization. MATERIALS AND METHODS: We included 246 women diagnosed with VaIN (low-grade VaIN [VaIN 1], 123 women; high-grade VaIN [VaIN 2/3], 123 women) using colposcopy-directed biopsy at our hospital from January 1, 2019, to April 30, 2020. The thickness of the noninvolved epithelium, if available, was determined. All available data, including cytology and histological information, were recorded. The t test and Pearson χ 2 test were used for statistical analysis. Statistical significance was set at p < .05. RESULTS: The involved epithelial thicknesses in VaIN 2/3 and VaIN 1 were 0.41 ± 0.21 and 0.40 ± 0.19 mm, respectively, which were both greater than their noninvolved epithelial thickness values (0.17 ± 0.10 and 0.17 ± 0.08 mm, p < .01 and p < .01, respectively). In subgroup comparisons between the VaIN 2/3 and VaIN 1 groups, the involved epithelial thickness did not differ between premenopausal patients, postmenopausal women receiving estrogen, and postmenopausal women who did not receive estrogen ( p > .05). In the VaIN 2/3 group, the lesion thickness in premenopausal was greater than that in postmenopausal women receiving estrogen ( p = .016) and those who were not receiving estrogen ( p = .017). CONCLUSIONS: The thickness of VaIN is generally less than 1 mm for women of all ages, except in rare cases of visible lesions with papillary hyperplasia.

Impaired Autophagy in Intestinal Epithelial Cells Alters Gut Microbiota and Host Immune Responses.

Establishing and maintaining beneficial interactions between the host and associated gut microbiota are pivotal requirements for host health. Autophagy is an important catabolic recycling pathway that degrades long-lived proteins and some organelles by lysosome to maintain cellular homeostasis. Although impaired autophagy is thought to be closely correlated with Crohn's disease (CD), the functional role of autophagy in the maintenance of gut microbiota is poorly understood. As autophagy-related 5 (Atg5) is a key gene associated with the extension of the phagophoric membrane in autophagic vesicles, we established a gut-specific Atg5 knockout mouse model, and we found that the disruption of autophagic flux in the intenstinal epithelium cells dramatically altered the composition of the gut microbiota and reduced alpha diversity. Microbial function prediction indicated that the pathway allocated for infectious diseases was enriched in Atg5-/- mice. "Candidatus Arthromitus" and the Pasteurellaceae family were increased in Atg5-/- mice, whereas Akkermansia muciniphila and the Lachnospiraceae family were reduced. Transcriptome analysis revealed that two key inflammatory bowel disease (IBD)-related transcription factors, RORC and TBX21, of host cells were upregulated in Atg5-/- mice, thus elevating the Muc2-related immunological response. The findings suggest that intestinal autophagy plays a vital role in modulating the diversity and composition of gut microbiota.IMPORTANCE The homeostasis of host-microbiota interactions is of great importance to host health. Previous studies demonstrated that disruption of autophagy was linked to inflammatory bowel disease. However, the interaction mechanism of gut microbiota regulated by autophagy was obscure. In an intestinal epithelium-specific autophagy-related 5 (Atg5) knockout mouse model, we observed a significant alteration and decreased diversity in the gut microbiota of Atg5-deficient mice compared with that of wild-type mice. Although the numbers of some organisms (e.g., Akkermansia muciniphila and members of the Lachnospiraceae family) associated with the control of inflammation decreased, those of proinflammationory bacteria (e.g., "Candidatus Arthromitus") and potential pathogens (the Pasteurellaceae family) increased in Atg5-/- mice. Differential gene expression analysis revealed that two key genes, RORC and TBX21, involved in inflammatory bowel disease were upregulated in Atg5-/- mice. Our study suggests that Atg5 deficiency results in an imbalance of the host-microbe interaction and deterioration of the gut microenvironment.

Value of loop electrosurgical excision procedure conization and imaging for the diagnosis of papillary squamous cell carcinoma of the cervix.

Background: Loop electrosurgical excision procedure (LEEP) conization and hysterectomy are performed for some patients with papillary squamous cell carcinoma (PSCC), whereas only hysterectomy is performed for others. We aimed to determine the optimal management for PSCC. Methods: Patients diagnosed with PSCC by colposcopy-directed biopsy between June 2008 and January 2020 who underwent LEEP conization and hysterectomy or only hysterectomy at our hospital were enrolled. Results of cervical cytology, high-risk human papillomavirus testing, transvaginal sonography, pelvic magnetic resonance imaging, LEEP, hysterectomy, and pathology testing of colposcopy-directed biopsy samples were analyzed. Results: A total of 379 women were diagnosed with PSCC by colposcopy-directed biopsy; 174 underwent LEEP before hysterectomy and 205 underwent only hysterectomy. Patients underwent and did not undergo LEEP were aged 47 ± 11 years and 52 ± 11 years, respectively. Among women who underwent LEEP, the agreement between LEEP and hysterectomy pathology was 85.1%. For women who underwent only hysterectomy, the agreement between preoperative clinical staging and pathological staging after hysterectomy was 82.4%. For patients with preoperative imaging indicative of malignancy, the accuracy of LEEP for diagnosing and staging PSCC was 88.5%, whereas for the hysterectomy-only group, it was 86.2%. For patients without malignancy detected with imaging, the accuracy of LEEP for diagnosing and staging PSCC was 81.6%; however, for those who did not undergo LEEP, it was 70.0%. Conclusion: For women diagnosed with PSCC by colposcopy-directed biopsy, LEEP conization is necessary for an accurate diagnosis when imaging does not indicate cancer; however, LEEP is not necessary when imaging indicates cancer.

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome.

Multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts and variation in DNA methylation, mRNA expression, and microRNA profiles in the ceca. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by the upregulation of expression of gga-miR-2128 and a methylated region near its transcription start site (388 bp). Correlation analysis showed that IGF2BP1 expression was associated with an abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in adapting to long-term artificial selection for body weight. Our study provides evidence that adaptation of the holobiont can occur in the microbiome as well as in the epigenetic profile of the host. IMPORTANCE The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts, and variation in DNA methylation, mRNA expression, and microRNA profiles in ceca. The insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by a methylated region near its transcription start site and the upregulation of expression of gga-miR-2128. Correlation analysis also showed that IGF2BP1 expression was associated with the abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in response to long-term artificial selection for body weight. Our study shows that the holobiont may adapt in both the microbiome and the host's epigenetic profile.

Histopathology of women with non-uniform endometrial echogenicity and risk factors for atypical endometrial hyperplasia and carcinoma.

OBJECTIVE: In sonography, homogeneous endometrium is defined as uniform endometrial echogenicity and heterogeneous, asymmetrical or cystic endometrium is defined as non-uniform. However, the relationship between the non-uniform endometrial echogenicity and the presence or absence of pathology is not known. A retrospective study of the patients with ultrasound non-uniform endometrium who underwent hysteroscopy-directed biopsy was performed to explore its clinical meaning in the diagnosis of endometrial lesions. MATERIALS AND METHODS: Patients with non-uniform endometrial echogenicity who underwent hysteroscopy-directed biopsy were enrolled in the Obstetrics and Gynecology Hospital of Fudan University from January 2015 to May 2018 as the primary cohort. In total, 692 patients with non-uniform endometrial echogenicity were diagnosed and underwent hysteroscopy-directed biopsy. Characteristics were assessed using univariate logistic regression between patients with and without atypical endometrial hyperplasia and carcinoma (atypical EH+). Multivariate analyses were used to develop the predicting model. We incorporated statistically significant variables and presented with nomogram. Internal validation was assessed. An independent validation cohort consisted of 237 consecutive patients from June 2018 to February 2019. RESULTS: Hysteroscopy-directed biopsy showed that 55.20% (382/692) of the patients with non-uniform endometrium had normal endometrium, while 44.80% (310/692) had endometrial lesions, including 39.31% (272/692) benign lesions and 5.49% (38/692) atypical EH+. Univariate logistic analysis showed that older age (P=0.027), abnormal uterine bleeding (AUB) before menopause (P=0.011), postmenopausal bleeding (P<0.001) and endometrial thickness ≥7 mm (P=0.013) were statistically significant for atypical EH+. Multivariate logistic regression analysis showed that age ≥50 years old (OR: 3.97, 95% CI: 1.17-13.43, P=0.027), endometrial thickness ≥7 mm (OR: 8.08, 95% CI: 1.86-35.08, P=0.005) and postmenopausal bleeding (OR: 8.98, 95% CI: 3.26-24.76, P<0.001) were risk factors for atypical EH+. Predictors in the individualized predicted nomogram included age ≥50 years old, AUB before menopause, postmenopausal bleeding and endometrial thickness ≥7 mm. The model showed good discrimination with area under curve (AUC) of 77.09%. With cutoff value of 0.0089267, the recall of atypical EH+ is 100% with precision 6.52% and 6.22% in both primary and validation cohort, respectively. Conclusion Non-uniform endometrial echogenicity is clinically meaningful in assessment of atypical EH+ with risk factors of age ≥50 years old, postmenopausal bleeding and endometrial thickness ≥7 mm. The model can help clinician to predicate the probability of atypical EH+ and make clinical decision.

Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant.

The common pheasant Phasianus colchicus, belonging to the order Galliformes and family Phasianidae, is the most widespread species. Despite a long history of captivity, the domestication of this bird is still at a preliminary stage. Recently, the demand for accelerating its transformation to poultry for meat and egg production has been increasing. In this study, we assembled high quality, chromosome scale genome of the common pheasant by using PacBio long reads, next-generation short reads, and Hi-C technology. The primary assembly has contig N50 size of 1.33 Mb and scaffold N50 size of 59.46 Mb, with a total size of 0.99 Gb, resolving most macrochromosomes into single scaffolds. A total of 23,058 genes and 10.71 Mb interspersed repeats were identified, constituting 30.31% and 10.71% of the common pheasant genome, respectively. Our phylogenetic analysis revealed that the common pheasant shared common ancestors with turkey about 24.7-34.5 million years ago (Ma). Rapidly evolved gene families, as well as branch-specific positively selected genes, indicate that calcium-related genes are potentially related to the adaptive and evolutionary change of the common pheasant. Interestingly, we found that the common pheasant has a unique major histocompatibility complex B locus (MHC-B) structure: three major inversions occurred in the sequence compared with chicken MHC-B. Furthermore, we detected signals of selection in five breeds of domestic common pheasant, several of which are production-oriented.

Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens.

Pullorum disease is one of the most common diarrhea-related diseases caused by Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S Pullorum); it negatively affects the poultry industry. However, limited studies have explored the association between the gut microbiota and S Pullorum infection in chickens. In the present study, we performed a microbiome comparison and a microbiome genome-wide association study (mGWAS) to investigate the association among the host genetics, the gut microbiota, and pullorum disease in chickens. We found that S Pullorum infection in chickens could alter the abundance of 39 bacterial genera (P < 0.05). The altered structure and composition of the gut microbiota were also detected in the offspring. mGWAS results revealed host genetic variants to be prominently associated with gut microbial diversity and individual microbes. The pathogens Pelomonas and Brevundimonas, which had a high abundance in positive parent chickens and their offspring, were significantly associated with several genetic mutations in immunity-related genes, such as TGIF1, TTLL12, and CCR7 This finding explained why Pelomonas and Brevundimonas were heritable in S Pullorum-infected chickens. The heritable gut microbes and identified genetic variants could provide references for the selection of resistant chickens and the elimination of pullorum disease.IMPORTANCE The present study investigated the association among the host genome, the gut microbiome, and S Pullorum infection in chickens. The results suggested that the gut microbial structure is altered in S Pullorum-infected chickens. The diversity and abundance of the gut microbiota remarkably differed between the offspring coming from S Pullorum-positive and S Pullorum-negative chickens. Heritable gut microbiota were detected in the offspring. Moreover, host genetic variants were associated with microbial diversity and individual gut microbes. The pathogens Pelomonas and Brevundimonas, which exhibited a high heritability in S Pullorum-positive parents and their offspring, were associated with several genetic mutations in immunity-related genes.

Next-Generation Sequencing Panel Analysis of Clinically Relevant Mutations in Circulating Cell-Free DNA from Patients with Gestational Trophoblastic Neoplasia: A Pilot Study.

Gestational trophoblastic neoplasia (GTN) originates from placental tissue and exhibits the potential for invasion and metastasis. Gene alterations in GTN have not been extensively studied because of a lack of qualified tumor specimens after chemotherapy. GTN has a rapid growth rate and is highly metastatic, which makes circulating tumor DNA (ctDNA) sequencing a promising modality for gene profiling. Accordingly, in this study, we performed targeted next-generation sequencing (NGS) of 559 tumor-associated genes using circulating cell-free DNA (cfDNA) collected prior to chemotherapy from 11 patients with GTN. All sequenced genes were associated with oncogenesis, progression, and targeted therapy. The average cfDNA level was 0.43 ± 0.22 ng/µL. Significant correlations were found between cfDNA concentration and maximum lesion diameter (r = 0.625, p=0.040) and time for human chorionic gonadotropin beta subunit (ß-HCG) recovering to normal level (r = 0.609, p=0.047). There were no significant correlations between cfDNA concentrations and ß-HCG expression level or lung metastasis. ctDNA mutations were detected in all patients, and 73 mutant genes were detected in 11 patients. BMPR1A (27.3%), LRP1B (27.3%), ERCC4 (18.2%), FGF14 (18.2%), HSP90AA1 (18.2%), KAT6A (18.2%), KMT2D (18.2%), MAP3K1 (18.2%), RANBP2 (18.2%), and ZNF217 (18.2%) mutations were detected as overlapping mutations. The mRNA and protein levels of bone morphogenetic protein receptor type 1A were significantly downregulated in human JAR and JEG-3 choriocarcinoma cells (p < 0.0001), whereas mRNA and protein levels of mitogen-activated protein kinase kinase kinase 1 were upregulated in these two cell lines (p=0.0128, p=0.0012, respectively). These genes may play important roles in GTN initiation and progression and may be candidate targets for GTN treatment. These findings suggested that cfDNA levels could provide potential assessment value in disease severity of GTN and that ctDNA sequencing was a promising approach for identifying gene mutations in GTN.

Inheritance and Establishment of Gut Microbiota in Chickens.

In mammals, the microbiota can be transmitted from the placenta, uterus, and vagina of the mother to the infant. Unlike mammals, development of the avian embryo is a process isolated from the mother and thus in the avian embryo the gut microbial developmental process remains elusive. To explore the establishment and inheritance of the gut microbiome in the avian embryo, we used the chicken as the model organism to investigate the gut microbial composition in embryos, chicks, and maternal hens. We observed: (1) 28 phyla and 162 genera of microbes in embryos where the dominated genus was Halomonas (79%). (2) 65 genera were core microbiota in all stages with 42% and 62% gut microbial genera of embryo were found in maternal hen and chick, respectively. There was a moderate correlation (0.40) between the embryo and maternal, and 0.52 between the embryo and chick at the family level. (3) Gut microbes that are involved in substance metabolism, infectious disease, and environmental adaptation are enriched in embryos, chicks, and maternal hens, respectively. (4) 94% genera of gut microbial composition were similar among three different chicken breeds which were maintained under similar conditions. Our findings provide evidence to support the hypothesis that part of the microbial colonizers harbored in early embryos were inherited from maternal hens, and the gut microbial abundance and diversity were influenced by environmental factors and host genetic variation during development.