Association between gut microbiota and Hirschsprung disease: a bidirectional two-sample Mendelian randomization study

Background

Several studies have pointed to the critical role of gut microbiota (GM) and their metabolites in Hirschsprung disease (HSCR) pathogenesis. However, the detailed causal relationship between GM and HSCR remains unknown.

Methods

In this study, we used two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between GM and HSCR, based on the MiBioGen Consortium's genome-wide association study (GWAS) and the GWAS Catalog's HSCR data. Reverse MR analysis was performed subsequently, and the sensitivity analysis, Cochran's Q-test, MR pleiotropy residual sum, outlier (MR-PRESSO), and the MR-Egger intercept were used to analyze heterogeneity or horizontal pleiotropy. 16S rDNA sequencing and targeted mass spectrometry were developed for initial validation.

Results

In the forward MR analysis, inverse-variance weighted (IVW) estimates suggested that Eggerthella (OR: 2.66, 95%CI: 1.23-5.74, p = 0.01) was a risk factor for HSCR, while Peptococcus (OR: 0.37, 95%CI: 0.18-0.73, p = 0.004), Ruminococcus2 (OR: 0.32, 95%CI: 0.11-0.91, p = 0.03), Clostridiaceae1 (OR: 0.22, 95%CI: 0.06-0.78, p = 0.02), Mollicutes RF9 (OR: 0.27, 95%CI: 0.09-0.8, p = 0.02), Ruminococcaceae (OR: 0.16, 95%CI: 0.04-0.66, p = 0.01), and Paraprevotella (OR: 0.45, 95%CI: 0.21-0.98, p = 0.04) were protective factors for HSCR, which had no heterogeneity or horizontal pleiotropy. However, reverse MR analysis showed that HSCR (OR: 1.02, 95%CI: 1-1.03, p = 0.049) is the risk factor for Eggerthella. Furthermore, some of the above microbiota and short-chain fatty acids (SCFAs) were altered in HSCR, showing a correlation.

Conclusion

Our analysis established the relationship between specific GM and HSCR, identifying specific bacteria as protective or risk factors. Significant microbiota and SCFAs were altered in HSCR, underlining the importance of further study and providing new insights into the pathogenesis and treatment.

The impact of probiotics on gut microbiota in the eradication of Helicobacter pylori infection: a systematic review

OBJECTIVE

The effect of probiotics supplementation on the gut microbiota in Helicobacter pylori (H. pylori) eradication therapy is controversial. Therefore, this review aimed to illustrate changes in the gut microbiota after standard eradication therapy with probiotics supplements.

MATERIALS AND METHODS

A computerized literature search in PubMed, Cochrane Library, Web of Science, and Embase database was performed up to February 1st, 2022, with English language restriction. The extracted outcomes were analyzed, including gut microbiota, adverse effects, and eradication rate.

RESULTS

13 studies reported data on 777 participants who were finally eligible for this systematic review. All of them are randomized controlled trials investigating the effect of H. pylori eradication with probiotics supplementation therapy on gut microbiota. Probiotics supplementation seems to play a positive role in restoring the gut microbiota during H. pylori eradication therapy. However, the changes in the gut microbiota are still controversial. The included studies had significant heterogeneity in the study population, diagnostic methods of H. pylori infection, and detection techniques of the gut microbiota and probiotics species.

CONCLUSIONS

The results provided a basis for the rational selection of probiotics in the H. pylori eradication process. Probiotic supplementation might keep the balance of gut microbiota and reduce the gastrointestinal adverse effects of antibiotics, but whether it could improve the eradication rate or not is a debatable point. Therefore, more research is needed to provide evidence.

Fecal microbiota transplantation enhances cell therapy in a rat model of hypoganglionosis by SCFA-induced MEK1/2 signaling pathway

Hirschsprung disease (HSCR), one of several neurocristopathies in children, is characterized by nerve loss in the large intestine and is mainly treated by surgery, which causes severe complications. Enteric neural crest-derived cell (ENCC) transplantation is a potential therapeutic strategy; however, so far with poor efficacy. Here, we assessed whether and how fecal microbiota transplantation (FMT) could improve ENCC transplantation in a rat model of hypoganglionosis; a condition similar to HSCR, with less intestinal innervation. We found that the hypoganglionosis intestinal microenvironment negatively influenced the ENCC functional phenotype in vitro and in vivo. Combining 16S rDNA sequencing and targeted mass spectrometry revealed microbial dysbiosis and reduced short-chain fatty acid (SCFA) production in the hypoganglionic gut. FMT increased the abundance of Bacteroides and Clostridium, SCFA production, and improved outcomes following ENCC transplantation. SCFAs alone stimulated ENCC proliferation, migration, and supported ENCC transplantation. Transcriptome-wide mRNA sequencing identified MAPK signaling as the top differentially regulated pathway in response to SCFA exposure, and inhibition of MEK1/2 signaling abrogated the SCFA-mediated effects on ENCC. This study demonstrates that FMT improves cell therapy for hypoganglionosis via short-chain fatty acid metabolism-induced MEK1/2 signaling.

Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets

Objective

Hirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR.

Methods

Based on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)-target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF-miRNA-mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method.

Results

We identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell-substrate adhesion, PI3K-Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53 and TWIST1), 4 miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and 4 mRNAs (PIM3, CHUK, F2RL1, and CA1) were identified to construct the TF-miRNA-mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8).

Conclusion

This study suggests a potential role of the TF-miRNA-mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.

Total arterial revascularization is associated with long-term survival benefit in coronary artery bypass grafting: systematic review with meta-analysis

Importance

Total arterial revascularization (TAR), the complete avoidance of saphenous vein grafting (SVG) in coronary artery bypass grafting (CABG), is advocated based on the superior conduit durability and resistance against atherosclerosis. However, the low adoption rate of TAR indicates a high level of controversy.

Objective

To compare long-term survival between TAR and conventional CABG involving SVG.

Data sources

A comprehensive literature search was conducted through digital databases including MEDLINE, Embase, and Cochrane Central Register of Controlled Trials from the inception to May 2021.

Study selection

The inclusion criteria were randomized clinical trials, or propensity-score balanced or multivariable-adjusted observational studies with a sample size of at least 100 patients in each arm, isolated CABG, comparing TAR (SVG=0) vs. non-TAR (SVG≥1), and inclusion of all-cause mortality.

Data extraction and synthesis

Two reviewers performed independent extraction following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Pooled hazard ratios (HR) and 95% confidence intervals (CI) were estimated with random-effect and fixed-effect models using generic inverse variance weighting. Individual patient time-to-event data were reconstructed to create an overall Kaplan-Meier survival function for matched studies. Sensitivity analyses were performed according to the risk of bias, matching status, and source of HR.

Main outcomes and measures

The primary endpoint was all-cause mortality.

Results

A total of 23 studies (100,314 patients), all with a retrospective observational design, were identified. The weighted mean follow-up time was 8.8 years post-operatively. Total arterial revascularization was associated with greater freedom from all-cause mortality than non-TAR (HR, 0.77, 95% CI, 0.71 to 0.84, p<0.001). There was evidence of low heterogeneity (I2=45%) across studies. Low publication bias was observed. Leave-one-out influence analysis and sensitivity analyses produced consistent results. Cochrane Collaboration signaling domains showed no critical risk of bias.

Conclusions and relevance

This meta-analysis found superior late survival associated with total arterial revascularization. Further randomized clinical trials are needed.

Funding Acknowledgement

Type of funding sources: None.

[Long-term outcomes of 328 patients with of autism spectrum disorder after fecal microbiota transplantation]

Objective: To evaluate the efficacy and safety of fecal microbiota transplantation (FMT) in the treatment of autism spectrum disorder (ASD). Methods: A longitudinal study was conducted. Clinical data from ASD patients with gastrointestinal symptoms and who underwent FMT in the Tenth People's Hospital affiliated to Tongji University or Jinling Hospital between May 2012 to May 2021 were retrospectively collected. Scores derived from the autism behavior checklist (ABC), the childhood autism rating scale (CARS), the Bristol stool form scale (BSFS), and the gastrointestinal symptom rating scale (GSRS) were analyzed at baseline and at the 1st, 3rd, 6th, 12th, 24th, 36th, 48th and 60th month after FMT. Records of any adverse reactions were collected. Generalized estimating equations were used for analysis of data on time points before and after FMT. Results: A total of 328 patients met the inclusion criteria for this study. Their mean age was 6.1±3.4 years old. The cohort included 271 boys and 57 girls. The percentage of patients remaining in the study for post-treatment follow-up at the 1st, 3rd, 12th, 24th, 36th, 48th and 60th month were as follows: 303 (92.4%), 284 (86.7%), 213 (64.9%), 190 (57.9%), 143 (43.6%), 79 (24.1%), 46 (14.0%), 31 (9.5%). After FMT, the average ABC score was significantly improved in the first 36 months and remained improved at the 48th month. However, the average score was not significantly different from baseline by the 60th month (1st-36th month, P<0.001; 48th month, P=0.008; 60th month, P=0.108). The average CARS score improved significantly during the first 48 months and remained improved at the 60th month (1st-48th month, P<0.001; 60th month, P=0.010). The average BSFS score was also significantly improved in the first 36 months (with an accompanying stool morphology that resembled type 4). This improvement was maintained at the 48th month. However, the average score was similar to baseline at the 60th month (1st-36th month, P<0.001; 48th month, P=0.008; 60th month, P=0.109). The average GSRS score was significantly improved during the first 24 months, but not afterwards (1st-24th month, P<0.001; 36th month, P=0.209; 48th month, P=0.996; 60th month, P=0.668). The adverse events recorded during treatment included abdominal distension in 21 cases (6.4%), nausea in 14 cases (4.3%), vomiting in 9 cases (2.7%), abdominal pain in 15 cases (4.6%), diarrhea in 18 cases (5.5%), fever in 13 cases (4.0%), and excitement in 24 cases (7.3%). All adverse reactions were mild to moderate and improved immediately after suspension of FMT or on treatment of symptoms. No serious adverse reactions occurred. Conclusion: FMT has satisfactory long-term efficacy and safety for the treatment of ASD with gastrointestinal symptoms.

Pharmacological inhibition of eIF2alpha phosphorylation by integrated stress response inhibitor (ISRIB) ameliorates vascular calcification in rats

Vascular calcification (VC) is an independent risk factor for cardiovascular events and all-cause mortality with the absence of current treatment. This study aimed to investigate whether eIF2alpha phosphorylation inhibition could ameliorate VC. VC in rats was induced by administration of vitamin D3 (3×10(5) IU/kg, intramuscularly) plus nicotine (25 mg/kg, intragastrically). ISRIB (0.25 mg/kg·week), an inhibitor of eIF2alpha phosphorylation, ameliorated the elevation of calcium deposition and ALP activity in calcified rat aortas, accompanied by amelioration of increased SBP, PP, and PWV. The decreased protein levels of calponin and SM22alpha, and the increased levels of RUNX2 and BMP2 in calcified aorta were all rescued by ISRIB, while the increased levels of the GRP78, GRP94, and C/EBP homologous proteins in rats with VC were also attenuated. Moreover, ISRIB could prevent the elevation of eIF2alpha phosphorylation and ATF4, and partially inhibit PERK phosphorylation in the calcified aorta. These results suggested that an eIF2alpha phosphorylation inhibitor could ameliorate VC pathogenesis by blocking eIF2alpha/ATF4 signaling, which may provide a new target for VC prevention and treatment.

Novel AVPR2 mutations and clinical characteristics in 28 Chinese families with congenital nephrogenic diabetes insipidus

AIMS

To investigate genotype and phenotype of congenital nephrogenic diabetes insipidus caused by AVPR2 mutations, which is rare and limitedly studied in Chinese population.

METHODS

88 subjects from 28 families with NDI in a department (Beijing, PUMCH) were screened for AVPR2 mutations. Medical records were retrospectively reviewed and characterized. Genotype and phenotype analysis was performed.

RESULTS

23 AVPR2 mutations were identified, including six novel mutations (p.Y117D, p.W208R, p.L313R, p.S127del, p.V162Sfs*30 and p.G251Pfs*96). The onset-age ranged from 1 week to 3 years. Common presentations were polydipsia and polyuria (100%) and intermittent fever (57%). 21% and 14% of patients had short stature and mental impairment. Urine SG and osmolality were decreased, while serum osmolality and sodium were high. Urological ultrasonography results showed hydronephrosis of the kidney (52%), dilation of the ureter (48%), and thickened bladder wall or increased residual urine (32%), led to intermittent urethral catheterization (7%), cystostomy (11%) and binary nephrostomy (4%). Urological defects were developed in older patients. Genotype and phenotype analysis revealed patients with non-missense mutations had higher levels of serum sodium than missense mutations.

CONCLUSION

In the first and largest case series of NDI caused by AVPR2 mutations in Chinese population, we established genetic profile and characterized clinical data, reporting six novel mutations. Further, we found genotype was associated with phenotype. This knowledge broadens genotype and phenotype spectrum of rare congenital NDI caused by AVPR2 mutations, and provides basis for studying molecular biology of AVPR2.

Manganese promoted wheat straw decomposition by regulating microbial communities and enzyme activities

AIMS

This study investigated the dose-effect of manganese (Mn) addition on wheat straw (WS) decomposition, and explored the potential mechanisms of Mn involved in the acceleration of WS decomposition in regards to the soil microbial communities and enzyme activities.

METHODS AND RESULTS

A 180-day incubation experiment was performed to examine the decomposition of WS under four Mn levels, that is, 0, 0.25, 1 and 2 mg g^-1 . The effects of microbial communities and enzyme activities were evaluated using control (0 mg g^-1 ) and Mn (0.25 mg g^-1 ) treatments. Our results revealed that Mn (0.25 mg g^-1 ) addition significantly increased WS decomposition, and enhanced the release of carbon and nitrogen. Optimal Mn addition (0.25 mg g^-1 ) also caused significant increases in the activity of neutral xylanase (NEX), laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP) within the incubation period. Mn (0.25 mg g^-1 ) addition also enriched some operational taxonomic units (OTUs) that, in turn, had the potential ability to decompose crop straw, such as secreting lignocellulolytic enzymes.

CONCLUSIONS

Mn (0.25 mg g^-1 ) could promote WS decomposition through enrichment of the microbial species involved in biomass decomposition, which enhanced the lignocellulose-degrading enzyme activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence for Mn to promote WS biodegradation after Mn application, opening new windows to improve the utilization efficiency of crop residues.

NEAT1 Negatively Regulates Cell Proliferation and Migration of Neuroblastoma Cells by miR-183-5p/FOXP1 Via the ERK/AKT Pathway

Neuroblastoma, a malignant tumor of the sympathetic nervous system, is an aggressive extracranial tumor in childhood. Long noncoding RNAs (lncRNAs) have been discovered to play a key role in the eukaryotic regulatory gene network and be involved in a wide variety of biological processes. We observed that the expression of lncRNA nuclear-enriched abundant transcript-1 (NEAT1) was significantly decreased in human neuroblastoma tissues and cell lines, compared with the normal. We observed cell proliferation, migration, and invasion with Cell Counting Kit-8 assay, colony formation assay, and Transwell assay to investigate the effects of NEAT1, miR-183-5p, or FOXP1 on neuroblastoma cells. And we also used StarBase and luciferase reporter gene assay to predict and confirm the interaction of NEAT1, miR-183-5p, and FOXP1 in neuroblastoma cells. First, overexpression of NEAT1 suppressed cell proliferation and played a key role in cell migration and invasion. In addition, NEAT1 was demonstrated to directly interact with miR-183-5p and exerted its antioncogenic role in neuroblastoma by negatively regulating miR-183-5p expression. miR-183-5p suppressed the expression of FOXP1 and regulated cell proliferation and migration by directly targeting FOXP1 mRNA 3′-untranslated region. Moreover, FOXP1 antagonized the effect of miR-183-5p on the phosphorylation of extracellular-regulated kinase/protein kinase B (ERK/AKT), while FOXP1 siRNA increased the reduced phosphorylation of ERK/AKT caused by miR-183-5p inhibitor in neuroblastoma cells. Taken together, these data showed that NEAT1 negatively regulated cell proliferation and migration of neuroblastoma by the miR-183-5p/FOXP1 axis via suppression of the ERK/AKT pathway. Our findings may provide a new target for the study of pathogenesis and treatment of neuroblastoma.

Involvement of the lncRNA AFAP1-AS1/microRNA-195/E2F3 axis in proliferation and migration of enteric neural crest stem cells of Hirschsprung's disease

NEW FINDINGS

What is the central question of this study? Long non-coding RNAs (lncRNAs) are widely involved in the progression of Hirschsprung's disease (HSCR), but the role of actin filament associated protein 1 antisense RNA1 (AFAP1-AS1), an lncRNA, in HSCR has not been explored before. What is the main finding and its importance? Downregulation of AFAP1-AS1 blocks enteric neural crest stem cell proliferation, differentiation, migration and invasion and promotes the occurrence of HSCR via the miR-195/E2F3 axis, indicating thatAFAP1-AS might be a potential biomarker for HSCR patients.

ABSTRACT

Long non-coding RNAs (lncRNAs) are involved in several human disorders. Nevertheless, it remains unclear whether they are implicated in the phenotypes of enteric neural crest stem cells (ENCSCs) in Hirschsprung's disease (HSCR). Therefore, we designed this study to explore the pathogenicity of AFAP1-AS1 for HSCR. Microarray analysis and bioinformatic tools were used to screen out the differentially lncRNAs and microRNAs (miRNAs) in patients with HSCR. Small interference RNA transfection was applied to carry out functional experiments in ENCSCs. Cellular activities were detected by cell counting kit-8, 5-ethynyl-2'-deoxyuridine, Transwell assays and flow cytometry. Finally, rescue experiments were performed to examine the cofunction of AFAP1-AS1 and miR-195 and of miR-195 and E2F transcription factor 3 (E2F3). AFAP1-AS1 was reduced in HSCR patients. Meanwhile, knockdown of AFAP1-AS1 reduced the cell migratory and proliferative capacities and facilitated cell apoptosis along with G0/G1 phase arrest. E2F3 was diminished when miR-195 was upregulated, and AFAP1-AS1 inhibition reduced its ability to bind to miR-195. Altogether, AFAP1-AS1 silencing acts as an endogenous RNA by interacting with miR-195 to alter E2F3 expression, thus conferring repressive effects on ENCSC activity and promoting HSCR progression.

Inhibition of ROCK signaling pathway accelerates enteric neural crest cell-based therapy after transplantation in a rat hypoganglionic model

BACKGROUND

Hirschsprung's disease (HSCR) is a congenital gastrointestinal disorder, characterized by enteric ganglia absence in part or entire of the colon, due to abnormal colonization and migration of enteric neural crest cells (ENCCs) during development. Currently, besides surgery which is the main therapy for HSCR, the potential of stem cell-based transplantation was investigated as an alternative option. Although promising, it has limitations, including poor survival, differentiation, and migration of the grafted cells. We hypothesized that modulation of extracellular factors during transplantation could promote ENCCs proliferation and migration, leading to increased transplantation efficiency. Considering that the RhoA/ROCK pathway is highly involved in cytoskeletal dynamics and neurite growth, our study explored the effect of inhibition of this pathway to improve the success of ENCCs transplantation.

METHODS

Enteric neural crest cells were isolated from rat embryos and labeled with a GFP-tag. Cell viability, apoptosis, differentiation, and migration assays were performed with and without RhoA/ROCK inhibition. Labeled ENCCs were transplanted into the muscle layer of an induced hypoganglionic rat model followed by intraperitoneal injections of ROCK inhibitor. The transplanted segments were collected 3 weeks after for histological analysis.

KEY RESULTS

Our results showed that inhibition of ROCK increased viable cell number, differentiation, and migration of ENCCs in vitro. Moreover, transplantation of labeled ENCCs into the hypoganglionic model showed enhanced distribution of grafted ENCCs, upon treatment with ROCK inhibitor.

CONCLUSIONS AND INFERENCES

ROCK inhibitors influence ENCCs growth and migration in vitro and in vivo, and should be considered to improve the efficiency of ENCCs transplantation.

[A preliminary study on the evaluation of diaphragm function by ultrasound in patients with invasive mechanical ventilation]

Objectives: To study the feasibility of using ultrasound to evaluate diaphragm function in patients with invasive mechanical ventilation. Methods: From March to December 2017, 40 adult patients with acute respiratory distress syndrome who were admitted to the Department of Critical Care Medicine, Xiangya Hospital, Central South University for more than 48 hours were included. Diaphragmatic excursion and thickness of bilateral anterior, middle and posterior parts were measured by ultrasound for 5 consecutive days. Results: (1) Compared with the diaphragmatic excursion of the right [anterior: (11.05±3.04) mm; middle: (12.08±2.71) mm; posterior: (11.51±3.33) mm] and left [anterior: (13.63±7.52) mm; middle: (15.44±7.52) mm; posterior: (14.76±6.93) mm] sides on day 1, the diaphragmatic excursion of the right [anterior: (8.90±3.65) mm; middle: (10.02±4.24) mm; posterior: (10.25±4.38) mm] and left [anterior: (9.82±1.96) mm; middle: (11.60±1.13) mm; posterior: (11.52±1.98) mm] sides decreased significantly on day 3 (P<0.05). Bilateral anterior, middle and posterior diaphragmatic excursion recovered on day 5, and was higher than the baseline levels on day 1, with the left middle and posterior diaphragmatic excursion changing most significantly. (2) Compared with day 1, 2, 3, the thickening fraction of bilateral anterior, middle and posterior diaphragm were significantly decreased on day 4, with the left middle part [day 1: (33.87±14.34)%; day 2: (37.26±13.91)%; day 3: (30.56±14.27)%; day 4: (15.53±5.68)%] and the left posterior part [day 1: (35.50±15.69)%; day 2: (39.84±15.32)%; day 3: (29.06±14.96)%; day 4: (13.30±5.79)%] changing most significantly (P<0.05). The thickening fractions of left anterior, middle and posterior diaphragm recovered on day 5 compared with that on day 4, but still lower than those on day 1 (P<0.05). Conclusions: It is feasible to evaluate the diaphragm function in patients with invasive mechanical ventilation by ultrasound, which can provide guidance for preventing diaphragmatic atrophy and withdrawing from mechanical ventilation.

[Clinical features of 9 cases of Brucella endocarditis]

Objective: To explore the clinical characteristics of patients with Brucella endocarditis. Methods: The clinical data of 9 patients with Brucella endocarditis admitted to Beijing Ditan Hospital from October 2008 to August 2018 were retrospectively analyzed. Through the electronic medical record system of the hospital. Through assessing the electronic medical record system of the hospital, demographic data, main symptoms, vital signs, blood culture, Rose Bengal Plate Agglutination Test, echocardiography, electrocardiogram, chest imaging and other clinical data of included patients were inquired and recorded. Patients were followed up by telephone for medication, operation and outcome. Results: The 9 patients were all Han nationality, aged from 25 to 66 years, 7 out of 9 patients were male, and they came from Hebei, Shandong, Shanxi, Inner Mongolia and Beijing. Of the 9 patients, 5 were farmers, 2 were self-employed, 1 was a technician, and 1 was unemployed. Of the 9 cases, 8 had a history of close contact with cattle and sheep, and 5 had a history of eating beef and mutton. Rose-Bengal Plate Agglutination Test and blood culture were positive in all 9 patients. Aortic valve was involved in 7 out of 9 patients, mitral and tricuspid valve was involved in 1 patient, respectively, and aortic dissection occurred in 1 patient. Condition of 1 patient rapidly deteriorated after admission and finally died during hospitalization despite antibiotic therapy, the remaining patients received long-term antibiotic treatment. A total of 7 patients who underwent valve replacement were followed up. One patient died of cerebral hemorrhage 6 months after operation, and the remaining 6 patients recovered well after valve replacement. Heart failure occurred in all 9 patients, and pericardial effusion occurred in 8 patients. Electrocardiogram showed low voltage of the QRS complex in the limb in 3 cases and poor R-wave progression in V(1)-V(3) lead in 2 cases, and sinus tachycardia in 2 cases. One patient developed non-specific ST-T abnormalities. All patients had fever, 7 patients complained of weakness, and 6 patients complained of palpitations. Among the 9 patients, 7 cases had anemia, 7 patients had pneumonia, 6 had bilateral pleural effusion, 4 had thrombocytopenia. Creatinine was above normal in 4 patients, urine protein was positive in 3 patients, Delta Bilirubin was higher in 3 cases. Conclusions: Patients with Brucella endocarditis often suffer from heart failure and have severe complications. Adequate antibiotic therapy in combination with valve replacement is effective for the treatment of patients with Brucella endocarditis.

[Inhibition of the TGF-β/Smad3 signaling pathway by SB431542: A study of the intervention effect of SB431542 on silicotic fibrosis in rats]

Objective: To investigate the intervention effect of SB431542, which inhibits the TGF-β/Smad3 signaling pathway, on silicotic fibrosis in rats. Methods: A total of 40 specific pathogen-free Sprague-Dawley rats were divided into normal saline control group, model group, SB431542 inhibitor group, and SB431542 inhibitor control group using a random number table, with 10 rats in each group. All rats except those in the normal saline control group were given non-exposed single intratracheal instillation of free silicon dioxide dust suspension 1 mL (50 mg/mL) ; the rats in the SB431542 inhibitor group were given intraperitoneal injection of SB431542 (5 mg/kg) on days 7 and 30 after dust exposure, those in the SB431542 inhibitor control group were given intraperitoneal injection of SB431542 cosolvent (5 mg/kg) on days 7 and 30 after dust exposure, and those in the normal saline control group were given intratracheal instillation of an equal volume of normal saline (5 mg/kg). On day 60 after dust exposure, the paraffin-embedded section of the right upper lobe of lung was collected for HE staining; the left upper lobe of lung was collected to measure the mRNA levels of fibronectin (FN) , collagen type I (COL-I) , and collagen type III (COL-III) by quantitative real-time PCR; the right inferior lobe of lung was collected to measure the protein levels of FN, COL-I, COL-III, phosphorylated Smad3 (p-Smad3) , and Smad3. Results: Compared with the normal saline control group, the model group had nodules with various sizes in lung tissue, with rupture of some alveolar septa, emphysema changes, and pulmonary interstitial fibrosis, as well as significant increases in the mRNA expression of FN, COL-I, and COL-III and the protein expression of FN, COL-I, COL-III, p-Smad3, and Smad3 in lung tissue (P<0.05) . Compared with the SB431542 inhibitor control group, the SB431542 inhibitor group had a relatively complete structure of lung tissue without marked nodules and with a small amount of exudate in alveolar space and the lumen of bronchioles, as well as significant reductions in the mRNA expression of FN, COL-I, and COL-III and the protein expression of FN, COL-I, COL-III, p-Smad3, and Smad3 in lung tissue (P<0.05) . There were no significant differences in the mRNA expression of FN, COL-I, and COL-III and the protein expression of FN, COL-I, COL-III, p-Smad3, and Smad3 between the model group and the SB431542 inhibitor control group (P>0.05) . Conclusion: SB431542 exerts an intervention effect on silicotic fibrosis by blocking the TGF-β/Smad3 signaling pathway and reducing the expression of the downstream fibrosis factors FN, COL-I, and COL-III.

[Delay on care-seeking and related influencing factors among tuberculosis patients in Wuhan, 2008-2017]

Objective: To analyze the epidemiological characteristics, trend and related factors of tuberculosis patients that delayed for care, in Wuhan from 2008 to 2017. Methods: Data regarding tuberculosis (TB) patients was collected from the tuberculosis management information system (TMIS), a part of the China information system for disease control and prevention from 2008 to 2017. A total of 64 208 tuberculosis patients, aged 0 to 95 years were included for the analysis. Unconditional logistic regression method was used to estimate those factors that associated with this study. Results: Days of delay among TB patients appeared as M=10 (P(25)-P(75): 3-28) day, in Wuhan, 2008-2017. The prevalence of the delay was 52.5% (33 703/64 208), presenting a downward trend from 2008 to 2017 (trend χ(2)=10.64, P<0.001), but the proportions of women and ≥65 year-olds were gradually increasing. Results from the multivariate logistic regression analysis showed that factors as: patients living far away from the city vs. near the city (OR=1.29, 95%CI: 1.25-1.35), and age above 45 years vs. younger than 25 years (the age 45-64 years group vs. aged less than 25 years group, OR=1.22, 95%CI: 1.15-1.29; the age 65 or above group vs. aged less than 25 years group, the OR=1.30, 95%CI: 1.22-1.39) were under higher risk on the delay of seeking care. Occupation, way of case-finding and classification of tuberculosis patients also appeared as influencing factors on this issue. Conclusions: Prevalence on the delay of care was 52.5% among tuberculosis patients in Wuhan, 2008-2017, but with an annual decrease. Attention should be paid to female, wrinkly or elderly tuberculosis patients regarding the delay of care on TB, in Wuhan.

Neoadjuvant chemotherapy with irinotecan and nedaplatin in a single cycle followed by esophagectomy on cT4 resectable esophageal squamous cell carcinoma: a prospective nonrandomized trial for short-term outcomes

Neoadjuvant chemotherapy (NAC) significantly extends survival in advanced esophageal squamous cell carcinoma (ESCC), but the short-term outcomes for cT4 ESCC remain controversial. Many NAC regimens have been previously reported, although no study has reported a regimen of irinotecan and nedaplatin for cT4 potential resectable ESCC. We evaluated the short-term outcomes of NAC with irinotecan and nedaplatin in a single cycle followed by esophagectomy on cT4 resectable ESCC. A total of 51 patients with cT4 potentially resectable ESCC were eligible for this study. Twenty of these patients underwent NAC, and the other 31 patients underwent surgery alone. The toxicities and response of NAC were evaluated. The clinicopathologic characteristics, responses, toxicities, surgical outcomes, postoperative complications, and survival time between the two groups were analyzed. No significant differences were found in clinicopathologic characteristics between the groups (P > 0.05). The response rate of NAC was 75% (15/20). The differences in the long-axis diameter of the tumor and cT stage between pre- and post-NAC were significant (P < 0.05). Twenty-four toxic events occurred in 11 patients of the NAC group, and 20/24 of these were mild. The R0 resection rates in the NAC group and the surgery alone group were 85% and 64.5%, with no statistically significant difference (P > 0.05). Differences in the pathological T stage and pathological tumor-node-metastasis (TNM) stage were significant (P < 0.05). The overall survival (OS) time and mortality in the NAC group versus the surgery alone group were 31.57 ± 3.06 months versus 15.24 ± 1.46 months and 25% versus 61.3%, respectively. The differences in OS and mortality were significant (P < 0.05). The NAC group and R0 resection were significant and independent predictors of positive prognosis. NAC with irinotecan and nedaplatin in a single cycle followed by esophagectomy on cT4 resectable ESCC as a new NAC is safe and effective.

Mechanism of Nucleoside Triphosphate Diphosphohydrolase-1-Associated Imbalance in Adenosine Diphosphate Degradation, B-Cell Activation, and Related Injury During Acute Antibody-Mediated Rejection

OBJECTIVE

The objective of this study was to investigate the effect of nucleoside triphosphate diphosphohydrolase-1 (NTPDase1) during acute antibody-mediated rejection (AMR).

METHODS

NTPDase1 overexpression, NTPDase1 knockout, and wild-type nude mice skin graft models were used to induce acute AMR. NTPDase1 expression in B cells, NTPDase1 messenger RNA expression in skin grafts, extracellular adenosine diphosphate (ADP) concentration, B-cell volume and surface antigens expression, average platelet transport rate, and ultrastructure and apoptosis of skin graft cells were investigated.

RESULTS

During acute AMR in nude mice, higher NTPDase1 expression caused lower extracellular ADP concentration, smaller increase in B-cell volume, and major histocompatibility complex II surface antigen expression, suggesting a negative correlation between them; higher NTPDase1 expression also caused slower average platelet transport rate and less severe skin graft injury, suggesting a negative correlation between them. Pretreatment with high-dose exogenous NTPDase1 inhibited platelet activation and protected skin grafts, but it resulted in prolonged bleeding time (by 51.4%) and prolonged coagulation time (by 44.1%).

CONCLUSION

An NTPDase1-associated imbalance in extracellular ADP degradation may contribute to B-cell activation, platelet activation, and more severe skin graft injury in nude mice. Pretreatment with high-dose exogenous NTPDase1 effectively protected skin grafts in nude mice at 1 week, but it increased the risk of bleeding.

Vitamin A maintains the airway epithelium in a murine model of asthma by suppressing glucocorticoid-induced leucine zipper

BACKGROUND

The effects of glucocorticoids (GCs) on the repair of the airway epithelium in asthma are controversial, and we previously reported that the GC dexamethasone (Dex) inhibits the repair of human airway epithelial cells and that this process is mediated by glucocorticoid-induced leucine zipper (GILZ) through MAPK-ERK signaling in vitro. Vitamin A (VA) is involved in the regulation of the MAPK-ERK pathway but has not been widely supplied during asthma treatment. It is unclear whether VA attenuates the negative regulation of GILZ on the MAPK-ERK pathway and maintains airway epithelium integrity during asthma treatment.

METHODS

Female BALB/c mice were sensitized and challenged with ovalbumin (OVA) and subsequently treated with Dex, VA or intranasal inhalation of adenovirus sh-GILZ vectors. Indexes of airway epithelium integrity, including pathological alterations, pulmonary EGFR expression and airway hyperresponsiveness (AHR), were then measured. The expression of GILZ and key components of activated MAPK-ERK signals (p-Raf-1, p-MEK, and p-Erk1/2) were also detected.

RESULTS

Dex failed to relieve OVA-induced asthma airway epithelium injury, as assessed through H&E staining, EGFR expression and AHR. Moreover, in the OVA-challenged mice treated with Dex, GLIZ expression was increased, whereas the ratios of p-Raf-1/Raf-1, p-MEK/MEK and p-Erk1/2/Erk1/2 were significantly decreased. Further study indicated that GILZ expression was decreased and that the ratios of p-Raf-1/Raf-1, p-MEK/MEK and p-Erk1/2/Erk1/2 were up-regulated in the GILZ-silenced OVA-challenged mice and VA-fed OVA-challenged mice, independent of Dex treatment. The airway epithelium integrity of the OVA-challenged mice was maintained by treatment with both VA and Dex.

CONCLUSIONS

Vitamin A maintained the Dex-treated asthma airway epithelium via the down-regulation of GILZ expression and the activation MAPK-ERK signaling, and these effects might contribute to improving the effects of GC therapeutics on asthma.

Reconciling agriculture, carbon and biodiversity in a savannah transformation frontier

Rapidly rising populations and likely increases in incomes in sub-Saharan Africa make tens of millions of hectares of cropland expansion nearly inevitable, even with large increases in crop yields. Much of that expansion is likely to occur in higher rainfall savannas, with substantial costs to biodiversity and carbon storage. Zambia presents an acute example of this challenge, with an expected tripling of population by 2050, good potential to expand maize and soya bean production, and large areas of relatively undisturbed miombo woodland and associated habitat types of high biodiversity value. Here, we present a new model designed to explore the potential for targeting agricultural expansion in ways that achieve quantitatively optimal trade-offs between competing economic and environmental objectives: total converted land area (the reciprocal of potential yield); carbon loss, biodiversity loss and transportation costs. To allow different interests to find potential compromises, users can apply varying weights to examine the effects of their subjective preferences on the spatial allocation of new cropland and its costs. We find that small compromises from the objective to convert the highest yielding areas permit large savings in transportation costs, and the carbon and biodiversity impacts resulting from savannah conversion. For example, transferring just 30% of weight from a yield-maximizing objective equally between carbon and biodiversity protection objectives would increase total cropland area by just 2.7%, but result in avoided costs of 27-47% for carbon, biodiversity and transportation. Compromise solutions tend to focus agricultural expansion along existing transportation corridors and in already disturbed areas. Used appropriately, this type of model could help countries find agricultural expansion alternatives and related infrastructure and land use policies that help achieve production targets while helping to conserve Africa's rapidly transforming savannahs.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'.

[Determination of relative elements of hard metal in workplace air and urine by inductive coupled plama]

Objective: To establish a rapid detection method regarding the air conditions of workplace and the workers' urine included Tungsten, Cobalt, Nickel, Titanium, Cadmium, Manganese, Lead and its compounds based on inductively coupled plasma mass spectrometry (ICP-MS) . Methods: The experiment adopts ICP-MS to deter-mine those metals in workshop air and workers urine, evaluate the detection's limitation, the precision and accuracy of the method. Using the membrane filter and urine freeze - dried metal standard material to verify this method. Results: Each element of correlation coefficient was greater than 0.999. The recovery rate of air samples was 91.6%~104.6%, within-batch RSD precision was 1.41%~3.50%, between-run precision was 1.28%~4.31%, urine samples recovery rate was 93.0%~102.6%, within - batch RSD precision was 1.25%~3.56%, between - run precision was 1.58%~4.67%, According to the method every element was within the scope of the standard reference, it was also showed that the established method is accurate and reliable. Conclusion: ICP-MS is an effective and feasible method to detect the workshop air and the workers' urine which included Tungsten, Cobalt, Nickel, Titanium, Cadmium, Manganese, Lead and its compounds.

A porcine reproductive and respiratory syndrome virus candidate vaccine based on the synthetic attenuated virus engineering approach is attenuated and effective in protecting against homologous virus challenge

Current porcine reproductive and respiratory syndrome virus (PRRSV) vaccines sometimes fail to provide adequate immunity to protect pigs from PRRSV-induced disease. This may be due to antigenic differences among PRRSV strains. Rapid production of attenuated farm-specific homologous vaccines is a feasible alternative to commercial vaccines. In this study, attenuation and efficacy of a codon-pair de-optimized candidate vaccine generated by synthetic attenuated virus engineering approach (SAVE5) were tested in a conventional growing pig model. Forty pigs were vaccinated intranasally or intramuscularly with SAVE5 at day 0 (D0). The remaining 28 pigs were sham-vaccinated with saline. At D42, 30 vaccinated and 19 sham-vaccinated pigs were challenged with the homologous PRRSV strain VR2385. The experiment was terminated at D54. The SAVE5 virus was effectively attenuated as evidenced by a low magnitude of SAVE5 viremia for 1-5 consecutive weeks in 35.9% (14/39) of the vaccinated pigs, lack of detectable nasal SAVE5 shedding and failure to transmit the vaccine virus from pig to pig. By D42, all vaccinated pigs with detectable SAVE5 viremia also had detectable anti-PRRSV IgG. Anti-IgG positive vaccinated pigs were protected from subsequent VR2385 challenge as evidenced by lack of VR2385 viremia and nasal shedding, significantly reduced macroscopic and microscopic lung lesions and significantly reduced amount of PRRSV antigen in lungs compared to the non-vaccinated VR2385-challenged positive control pigs. The nasal vaccination route appeared to be more effective in inducing protective immunity in a larger number of pigs compared to the intramuscular route. Vaccinated pigs without detectable SAVE5 viremia did not seroconvert and were fully susceptible to VR2385 challenge. Under the study conditions, the SAVE approach was successful in attenuating PRRSV strain VR2385 and protected against homologous virus challenge. Virus dosage likely needs to be adjusted to induce replication and protection in a higher percentage of vaccinated pigs.

[HER-2 expression and clinical significance in esophagogastric junction adenocarcinoma (Siewert type Ⅱ)]

OBJECTIVE

To investigate the human epidermal growth factor receptor-2 (HER-2) expression in esophagogastirc junction adenocarcinoma(Siewert type Ⅱ)and its clinical significance.

METHODS

A total of 180 patients with esophagogastric junction adenocarcinoma (Siewert type Ⅱ) were included in this study. The HER-2 expression was detected by immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) analysis was performed to assess the HER-2 gene amplification in the IHC-positive and IHC-weak positive cases.

RESULTS

HER-2 overexpression (3+ ), weak positive (2+ ) and negative (1+ /0) was 11.7%(21/180), 8.9%(16/180), and 79.4%(143/180), respectively. The FISH analysis showed HER-2 gene amplification in 95.2%(20/21) of HER-2(3+ ) cases and 18.8% (3/16) of HER-2(2+ ) cases. The concordance rate between IHC and FISH was 95.2%. Overexpression of HER-2(3+ ) was associated with the tumor differentiation (P<0.05), and irrelevant to age, sex, pT stage, pN stage, pM stage and pTNM stage (P>0.05). The median overall survival time (OS) was 13 months in HER-2(3+ ) patients, significantly shorter than the 21 months in HER-2(2+ ) and HER-2(+ /-) cases (P<0.01).

CONCLUSIONS

Approximately 11.7% of the patients with esophagogastric junction adenocarcinoma (Siewert type Ⅱ) are HER-2-positive on IHC. HER-2 overexpression is associated with the tumor differentiation. IHC can be used as a screening test for the positive expression of HER-2 in the esophagogastirc junction adenocarcinoma (Siewert type Ⅱ). However, FISH detection can be used as a more reliable detection method.

Kinetics of serological responses in influenza A(H7N9)-infected patients correlate with clinical outcome in China, 2013

The novel avian influenza A(H7N9) infection has recently emerged to cause severe respiratory illness in China. The objectives of this study were to define the kinetics of the antibody responses in patients with influenza A(H7N9) disease and to correlate these kinetics with clinical outcome. Serial serum samples were obtained at intervals of three to four days from 18 patients with virologically confirmed A(H7N9) disease in Shanghai. We determined the kinetics of the haemagglutination inhibition (HI) and A(H7H9) pseudotype neutralisation antibody (Nab) responses and correlated these with clinical outcomes. Most patients had robust serological responses by both HI and Nab tests. Taking into account censoring due to time of testing and death, the median time from onset of illness to Nab titre ≥1:40 was 14 days (95% confidence interval (CI): 11–18 days) in the fatal cases and 10.5 days (95% CI: 7–12) in the survivors (p=0.003). The two groups did not differ in initial Nab titres, but the rate of increase in Nab titres was significantly faster for survivors by approximately 10-fold per 15 days (p=0.007). Early and rapid induction of Nab was correlated significantly with better clinical outcome.

Reduction of angiocidin contributes to decreased HepG2 cell proliferation

BACKGROUND

Angiocidin plays a key role in angiogenesis and tumor progression. High angiocidin expression is detected in some kind of solid tumors and tumor vascular endothelial cells. Several reports have shown the inhibition of angiogenesis and tumor growth caused by angiocidin. However, the role of angiocidin in liver cancers growth is still unclear.

OBJECTIVES

To examine angiocidin expression in SMMC-7221 and HepG2 cells and the role of angiocidin in liver cancer cell growth.

METHODS

RT-PCR and western blot are used in this study to detect angiocidin expression. SiRNA and MTT experiments are used in exploring the role of angiocidin in tumor cell growth.

RESULTS

Our study showed high angiocidin expression in two kinds of liver cancer cells. Angiocidin protein production in HepG2 cells were reduced significantly by siRNA. When HepG2 cells were transfected with siRNA-angiocidin, these cells showed very low proliferation activity compared with control cells. Our study suggests that reduction of angiocidin may contribute to decreased proliferation activity in liver cancer cells.

CONCLUSION

Angiocidin is highly expressed in liver cancer cells, and it may play a key role in tumor growth of liver cancers.

Longitudinal spin Seebeck effect free from the proximity Nernst effect

This Letter provides evidence for intrinsic longitudinal spin Seebeck effects (LSSEs) that are free from the anomalous Nernst effect (ANE) caused by an extrinsic proximity effect. We report the observation of LSSEs in Au/Y(3)Fe(5)O(12) (YIG) and Pt/Cu/YIG systems, showing that the LSSE appears even when the mechanism of the proximity ANE is clearly removed. In the conventional Pt/YIG structure, furthermore, we separate the LSSE from the ANE by comparing the voltages in different magnetization and temperature-gradient configurations; the ANE contamination was found to be negligibly small even in the Pt/YIG structure.

Grammatical Immune System Evolution for reverse engineering nonlinear dynamic Bayesian models

An artificial immune system algorithm is introduced in which nonlinear dynamic models are evolved to fit time series of interacting biomolecules. This grammar-based machine learning method learns the structure and parameters of the underlying dynamic model. In silico immunogenetic mechanisms for the generation of model-structure diversity are implemented with the aid of a grammar, which also enforces semantic constraints of the evolved models. The grammar acts as a DNA repair polymerase that can identify recombination and hypermutation signals in the antibody (model) genome. These signals contain information interpretable by the grammar to maintain model context. Grammatical Immune System Evolution (GISE) is applied to a nonlinear system identification problem in which a generalized (nonlinear) dynamic Bayesian model is evolved to fit biologically motivated artificial time-series data. From experimental data, we use GISE to infer an improved kinetic model for the oxidative metabolism of 17beta-estradiol (E(2)), the parent hormone of the estrogen metabolism pathway.

Facial onset sensory and motor neuronopathy (FOSMN syndrome): a novel syndrome in neurology

A 'syringomyelia-like' syndrome has been infrequently reported in neurological disorders such as Tangiers disease and lepromatous leprosy. This study reports a novel 'syringomyelia-like' syndrome in four adult male patients, which we have termed facial onset sensory and motor neuronopathy, or FOSMN syndrome, that appears to have a neurodegenerative aetiology. Clinical, neurophysiological and pathological data of four patients were reviewed, including the autopsy in one patient. Four male patients (mean age at onset 43), initially developed paraesthesiae and numbness in a trigeminal nerve distribution, which slowly progressed to involve the scalp, neck, upper trunk and upper limbs in sequential order. Motor manifestations, including cramps, fasciculations, dysphagia, dysarthria, muscle weakness and atrophy developed later in the course of the illness. Neurophysiological findings revealed a generalized sensory motor neuronopathy of caudally decreasing severity in all four patients. Autopsy in one patient disclosed loss of motoneurons in the hypoglossal nucleus and cervical anterior horns, along with loss of sensory neurons in the main trigeminal sensory nucleus and dorsal root ganglia. FOSMN syndrome appears to be a slowly progressive neurodegenerative disorder, whose pathogenesis remains to be determined.

Excision of a selectable marker in transgenic rice (Oryza sativa L.) using a chemically regulated Cre/loxP system

Removal of a selectable marker gene from genetically modified (GM) crops alleviates the risk of its release into the environment and hastens the public acceptance of GM crops. Here we report the production of marker-free transgenic rice by using a chemically regulated, Cre/loxP-mediated site-specific DNA recombination in a single transformation. Among 86 independent transgenic lines, ten were found to be marker-free in the T0 generation and an additional 17 lines segregated marker-free transgenic plants in the T1 generation. Molecular and genetic analyses indicated that the DNA recombination and excision in transgenic rice were precise and the marker-free recombinant T-DNA was stable and heritable.

Host Range of Phytophthora capsici from Pumpkin and Pathogenicity of Isolates

This study was conducted to determine the host range of Phytophthora capsici isolates from pumpkin and virulence of the isolates on pumpkin cultivars. The pathogenicity of P. capsici isolates from pumpkin was evaluated on 45 species of herbaceous plants, including 36 species of crops grown in rotation sequences with pumpkin and nine species of weeds that commonly grow in pumpkin fields in Illinois. Plants were grown in the greenhouse, and 4-week-old seedlings were inoculated by adding 5 ml of a zoospore suspension (2 × 10⁵ spores per ml of water) onto the soil surface around the stem of each plant in the pot. Twenty-two crop species and two weed species became infected with P. capsici and developed symptoms. P. capsici was reisolated from all of the symptomatic plants by culturing tissues onto a semiselective medium (PARP). Also, P. capsici was detected in 87.5% of symptomatic plants by a polymerase chain reaction (PCR) method using PCAP and IT5 primers. Cucurbits and pepper were the most susceptible hosts of P. capsici. Five crop species or varieties, beet (Beta vulgaris), Swiss-chard (Beta vulgaris var. cicla), lima beans (Phaseolus lunatus), turnip (Brassica rapa), and spinach (Spinacia oleracea), and one weed species, velvet-leaf (Abutilon theophrasti), were found to be hosts of P. capsici for the first time. Six isolates of P. capsici were inoculated onto six pumpkin cultivars (three processing and three jack-o-lantern pumpkins) in the greenhouse and resulted in significant interactions between pathogen isolates and pumpkin types. P. capsici isolates were more virulent on jack-o-lantern pumpkins than on processing pumpkins.

Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes

A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativaL. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.)