Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity.

Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.

Adenocarcinoma arising in an ectopic enterogenous cyst: A rare case report and review of literature.

Enterogenous cyst (EC) is a rare congenital lesion generally located in the central nervous system, such as in the cerebral hemispheres, posterior fossa, or spinal canal. They are usually benign lesions, and malignant transformation is rare. A 42-year-old woman felt an obvious pain in the lump and went to a local hospital for local lumpectomy. After 7 months, she again felt pain in the buttocks and difficulty in urinating and defecation. The computed tomography (CT) scan showed a mass in the pelvis. Sacrococcygeal cyst excision was performed 10 days later, and postoperative pathology showed epidermoid cyst. Shortly after, the patient recovered and was discharged from the hospital; the pain in the buttocks continued to recur. Puncture and drainage were performed five times. Later, the patient went to our hospital for treatment, and pelvic MRI showed multiple abnormal signal shadows in the presacral and sacrococcygeal regions, some of which were considered abscesses, and some were cystic lesions. She underwent tumor resection and was diagnosed with EC with locally moderately differentiated adenocarcinoma. Four months later, the patient's symptoms of swelling and pain recurred. MRI examination showed multiple high-signal T2 shadows in the anterior sacral and subcutaneous tissues of the buttocks, and enhanced scan showed partial marginal enhancement. After assessment, the patient was given a radiation dose of 60 Gy/25F. ECs in the anterior sacral and soft tissue of the buttocks are very rare, and the case of carcinomatous transformation has never been reported. Therefore, we discussed the clinicopathological features of ectopic ECs and reviewed the literature.

The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice.

RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNA-directed DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues.

Reinforcement of CHH methylation through RNA-directed DNA methylation ensures sexual reproduction in rice.

DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well studied in Arabidopsis (Arabidopsis thaliana), most mutations in RdDM genes cause no remarkable developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 (OsRDR2) in rice (Oryza sativa). Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH (H = A, C, or T) methylation. Moreover, male and female reproductive development was disturbed, which led to sterility in osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation may regulate the expression of multiple key genes involved in stamen development, meiosis, and pollen viability. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of CHH methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity, which includes OsRDR2 activity. Our results, which revealed a global increase in CHH methylation through enhancement of RdDM activity in reproductive organs, suggest a crucial role for OsRDR2 in the sexual reproduction of rice.

Ding's herbal enema treats dextran sulfate sodium-induced colitis in mice by regulating the gut microbiota and maintaining the Treg/Th17 cell balance.

Ding's herbal enema (DHEP) is a traditional Chinese medicinal therapy that has been used to treat ulcerative colitis (UC) in China. The present study determined the molecular mechanism of the effect of DHEP in UC treatment. C57BL/6J mice were treated with 3.5% (w/v) dextran sulfate sodium (DSS) for 7 days to establish an animal model of colitis. The mice were divided into five groups (n=5): Control, vehicle, DHEP, mesalazine and ß-sitosterol. After oral administration for 7 days, the body weight, disease activity index, histopathology and inflammatory factors were analyzed. The fractions of CD4+Foxp3+ regulatory T (Treg) cells and CD4+IL-17A+ T helper (Th) cells were determined by flow cytometry. Gut microbiota composition was analyzed by next-generation sequencing. The results revealed that DHEP and ß-sitosterol could significantly alleviate the symptoms of DSS-induced UC. Furthermore, the levels of IL-6, cyclooxygenase-2, TNF-α and p65 were reduced after administration of DHEP. Additionally, the data indicated that DHEP could increase the abundance of seven operational taxonomic units (OTUs) and decrease the abundance of 12 OTUs in the gut microbiota. The content of short-chain fatty acids in the colon remodeled the balance of Treg/Th17 cells in DSS-induced UC in mice. The present study preliminarily defined the mechanism of action of DHEP in UC that may be associated with the regulation of the gut microbiota composition, and maintenance of the balance between Treg and Th17 cells. Furthermore, ß-sitosterol exhibited the same effects with DHEP and it could be a possible substitute for DHEP in UC treatment.

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice.

RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

Autologous adipose-derived stem cells for the treatment of Crohn's fistula-in-ano: an open-label, controlled trial.

BACKGROUND: Crohn's fistula-in-ano is a refractory disease in colorectal and anal surgery. Although autologous adipose-derived stem cell (ADSC) has been used in the treatment of Crohn's fistula-in-ano because of its convenience, non-incision of normal tissue, good tolerance, repeatability, quick recovery, less pain, less damage to anal function, and high quality of life during the perioperative period, there are no reports of its use in China. This is the first clinical trial in China on the treatment of Crohn's fistula-in-ano with ADSC to evaluate its efficacy and safety. METHODS: A total of 22 patients with Crohn's fistula-in-ano were enrolled in this study from January 2018 to October 2018 in the Colorectal Disease Center of Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine. Patients were divided (1:1) into an observation group (ADSC) and a control group (incision-thread-drawing procedure). Primary efficacy endpoint evaluated at months 3, 6, and 12 was the closure of fistulas (closure of all treated fistulas at baseline, confirmed by doctor's clinical assessment and magnetic resonance imaging or transrectal ultrasonography). The patients additionally completed some scoring scales at each follow-up including simplified Crohn's Disease Activity Index (CDAI), Perianal Disease Activity Index (PDAI), Inflammatory Bowel Disease Questionnaire (IBDQ), pain scores with visual analog score (VAS), and Wexner score. The data of inflammatory indexes were also collected. RESULTS: The healing rates of the observation group and the control group at months 3, 6, and 12 were as follows: 10/11(90.9%) vs 5/11(45.5%), 8/11(72.7%) vs 6/11(54.5%), and 7/11(63.6%) vs 6/11(54.5%), respectively. There was no statistical difference between the two groups. In addition, the improvement in simplified CDAI, PDAI, IBDQ, VAS, and Wexner score of the observation group were better than that of the control group at each follow-up. The inflammatory indexes decreased in both the observation group and the control group at 3 months follow-up. And there were no significant differences in the changes of inflammatory indexes between two groups at month 3 compared with the baseline. Safety was maintained throughout month 12, and adverse events occurred in 63.6% of patients in the observation group and 100% patients in the control group. And no adverse event associated with ADSC injection was observed in the study. CONCLUSION: ADSC is a feasible and effective treatment for Crohn's fistula-in-ano, compared with traditional incision and thread-drawing. It can protect anal function of patients, relieve pain, allow quick recovery, be well-tolerated, and improve the quality of life during perioperative period. TRIAL REGISTRATION: China Clinical Trials Registry, No. ChiCTR1800014599. Registered 23 January 2018.

ß-Sitosterol improves experimental colitis in mice with a target against pathogenic bacteria.

In this article, we aim to examine the novel effects of ß-sitosterol on murine experimental colitis. ß-Sitosterol significantly reduces the weight loss, colon length, and alleviated microscopic appearances of colitis induced by dextran sulfate sodium. This compound also decreases the levels of TNF-α, IL-6, and IL-1ß in intestinal tissue of mice with experimental colitis in a concentration-dependent manner. ß-Sitosterol treatment to intestinal epithelial cells significantly increases expression of antimicrobial peptides and reduces survival of intracellular Salmonella typhimurium. These results showed the multiple effects of ß-sitosterol against pathogenic bacteria for a novel approach to the treatment of colonic inflammation.

Nitrogen topdressing timing modifies free amino acids profiles and storage protein gene expression in wheat grain.

BACKGROUND: Nitrogen is one basic element of amino acids and grain protein in wheat. In field experiments, wheat plants were subjected to different timing of nitrogen topdressing treatments: at the stages of emergence of the top fifth leaf (TL5), top third leaf (TL3) and top first leaf (TL1) to test the regulatory effects of nitrogen topdressing timing on grain protein quality. The underlying mechanisms were elucidated by clarifying the relationship between proteolysis in vegetative organs and accumulation of amino acids in the endosperm cavity, conversion of amino acids, and storage protein synthesis in endosperm of wheat grain. RESULTS: Delayed nitrogen topdressing up-regulated gene expression related to nitrogen metabolism and protease synthesis in the flag leaf, followed by more free amino acids being transported to both the cavity and the endosperm from 7 days after anthesis (DAA) to 13 DAA in TL1. TL1 enhanced the conversion between free amino acids in endosperm and upregulated the expression of genes encoding high molecular weight (HMW) and low molecular weight (LMW) subunits and protein disulfide isomerases-like (PDIL) proteins, indicating that the synthesis and folding of glutenin were enhanched by delayed nitrogen topdressing. As a consequense, the content of glutenin macropolymers (GMP) and glutenin increased with delaying nitrogen topdressing. CONCLUSIONS: The results highlight the relationship between nitrogen remobilization and final grain protein production and suggest that the nitrogen remobilization processes could be a potential target for improving the quality of wheat grain. Additionally, specific gene expression related to nitrogen topdressing was identified, which conferred more detailed insights into underlying mechanism on the modification protein quality.

Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis.

DNA methylation is a conserved epigenetic mark that is critical for many biological processes in plants and mammals. In Arabidopsis, the antagonistic activities of RNA-directed DNA methylation (RdDM) and ROS1-dependent active DNA demethylation are key for the dynamic regulation of locus-specific DNA methylation. However, the molecular factors that coordinate RdDM and active demethylation are largely unknown. Here we report that CLSY4 and its three paralogous SWI2/SNF2-type chromatin-remodeling proteins function in both RdDM and DNA demethylation in Arabidopsis. We initially identified CLSY4 in a genetic screen for DNA demethylation factors and subsequently demonstrated that it also is important in RdDM. Comprehensive genetic analyses using single and high order mutants of CLSY family proteins revealed their roles as double agents in the balance between methylation and demethylation reactions. The four CLSY proteins collectively are necessary for the canonical RdDM pathway; at the same time, each CLSY likely mediates DNA demethylation at specific loci where DNA methylation depends on RdDM. These results indicate that the four chromatin-remodeling proteins have dual functions in regulating genomic DNA methylation, and thus provide new insights into the dynamic regulation of DNA methylation in a model multicellular eukaryotic organism.

DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana.

Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4 Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.

Calcium Pumps and Interacting BON1 Protein Modulate Calcium Signature, Stomatal Closure, and Plant Immunity.

Calcium signaling is essential for environmental responses including immune responses. Here, we provide evidence that the evolutionarily conserved protein BONZAI1 (BON1) functions together with autoinhibited calcium ATPase10 (ACA10) and ACA8 to regulate calcium signals in Arabidopsis. BON1 is a plasma membrane localized protein that negatively regulates the expression of immune receptor genes and positively regulates stomatal closure. We found that BON1 interacts with the autoinhibitory domains of ACA10 and ACA8, and the aca10 loss-of-function (LOF) mutants have an autoimmune phenotype similar to that of the bon1 LOF mutants. Genetic evidences indicate that BON1 positively regulates the activities of ACA10 and ACA8. Consistent with this idea, the steady level of calcium concentration is increased in both aca10 and bon1 mutants. Most strikingly, cytosolic calcium oscillation imposed by external calcium treatment was altered in aca10, aca8, and bon1 mutants in guard cells. In addition, calcium- and pathogen-induced stomatal closure was compromised in the aca10 and bon1 mutants. Taken together, this study indicates that ACA10/8 and BON1 physically interact on plasma membrane and function in the generation of cytosol calcium signatures that are critical for stomatal movement and impact plant immunity.

[Dynamic three-dimensional ultrasound study on levator ani muscle fissures for female pelvic floor relaxation syndrome].

OBJECTIVE: To explore the value of dynamic three-dimensional ultrasound in detecting the levator ani muscle fissures morphological changes of female pelvic floor relaxation syndrome after biofeedback and acupuncture treatments. METHODS: Forty female constipation patients with pelvic floor relaxation syndrome were screened from the Constipation Designed Disease Clinic in our hospital between October 2011 and September 2012. Cleveland Constipation Score (CCS) scale was used. Anteroposterior and transverse diameters of the levator ani muscle fissures were measured by dynamic three-dimensional ultrasound in Valsalva maneuver. After a course (10 days) of biofeedback and acupuncture treatments, CCS scale was filled, and dynamic three-dimensional ultrasound was performed in Valsalva maneuver as well. Associated data before and after treatment were compared. RESULTS: Twenty-five patients completed the trial. As compared to pre-treatment, the longitudinal axes of levator ani muscle fissure [(4.89±0.89) cm vs. (5.13±0.82) cm, P<0.01], the horizontal axes of the levator ani muscle fissure [(4.62±0.75) cm vs. (4.86±0.74) cm, P<0.01], and the area of the levator ani muscle fissure [(18.16±6.42) cm(2) vs. (19.92±6.33) cm(2), P<0.01] decreased significantly after treatment, while CCS scale (9.52±2.50 vs. 15.80±3.42, P<0.01) declined significantly as well. CONCLUSIONS: The dynamic three-dimensional ultrasound is an effective, simple and non-invasive method for the determination of levator ani muscle fissure in female patients with pelvic floor relaxation syndrome.