[Survey of Helicobacter pylori levofloxacin and clarithromycin resistance rates and drug resistance genes in Ningxia, 2020-2022]

Objective: To explore the rate of Helicobacter pylori (Hp) resistance to levofloxacin and clarithromycin and the common mutation patterns of resistance genes in Ningxia, and to assess the concordance between phenotypic resistance and genotypic resistance. Methods: Cross-sectional study. Patients diagnosed with Hp infection in 14 hospitals in Ningxia region from February 2020 to May 2022 were retrospectively selected. Hp strains were isolated from gastric biopsy specimens of Hp-infected patients and subjected to phenotypic drug sensitivity testing and detection of resistance genes to analyze the rate of Hp resistance to levofloxacin and clarithromycin and the common mutation patterns of resistance genes in Ningxia region; and the concordance rate and Kappa concordance test were used to assess the concordance between phenotypic resistance and genotypic resistance. Results: A total of 1 942 Hp strains were isolated and cultured, and among the infections, 1 069 cases (55.0%) were male and 873 cases (45.0%) were female, aged (50.0±12.5) years (15-86 years). The rates of Hp resistance to levofloxacin and clarithromycin in Ningxia were 42.1% (818/1 942) and 40.1% (779/1 942), respectively, and the rate of dual resistance to both was 22.8% (443/1 942). The rate of resistance to levofloxacin and clarithromycin of Hp strains from female patients was higher than in male patients (levofloxacin: 50.4%(440/873) vs 35.4%(378/1 069); clarithromycin: 44.4%(388/873) vs 36.6%(391/1 069), both P<0.001). Among the GyrA gene mutations associated with levofloxacin resistance, the differences in mutation rate of amino acid at positions 87 and 91 were statistically significant in both drug-resistant and sensitive strains(both P<0.001), except for Asn87Thr. Hp strains were statistically significant for levofloxacin (Kappa=0.834, P<0.001) and clarithromycin (Kappa=0.829, P<0.001) had good concordance in resistance at the phenotypic and genotypic levels. Conclusion: The resistance of Hp to levofloxacin and clarithromycin in Ningxia region is severe, and there is good consistency between genotypic and phenotypic resistance.

Polysaccharides from Hemerocallis citrina Baroni Inhibit the Growth of Hepatocellular Carcinoma Cells by Regulating the Wnt/β-Catenin Pathway

Hemerocallis citrina Baroni is an edible plant with anti-inflammatory, antidepressant, and anticancer activities. However, studies on H. citrina polysaccharides are limited. In this study, a polysaccharide named HcBPS2 was isolated and purified from H. citrina. Monosaccharide component analysis showed that HcBPS2 was composed of rhamnose, arabinose, galactose, glucose, xylose, mannose, galacturonic acid, and glucuronic acid. Notably, HcBPS2 significantly inhibited human hepatoma cell proliferation, but had little effect on human normal liver cells (HL-7702). Mechanism investigations indicated HcBPS2 suppressed human hepatoma cell growth through the induction of G2/M phase arrest and mitochondria-dependent apoptosis in human hepatoma cells. In addition, the data revealed that HcBPS2 treatment led to the inactivation of Wnt/β-catenin signaling, which then gave rise to cell cycle arrest and apoptosis in human hepatoma cancer cells. Collectively, these findings suggested that HcBPS2 may serve as a therapeutic agent against liver cancer.

Bioinspired Anti-demineralization Enamel Coating for Orthodontics

White spot lesions and enamel cracks are the 2 most prominent diseases that occur after orthodontic treatment and are caused by enamel demineralization from accumulated bacterial biofilms and/or enamel damage caused by the removal of residual adhesive after bracket debonding. Inspired by the self-assembled amelogenin nanoribbons in enamel, we developed an enamel coating with a self-assembling antimicrobial peptide, D-GL13K, to simultaneously reduce demineralization and residual adhesive. The self-assembled amphiphilic nanoribbons significantly increased the hydrophobicity of the etched enamel, which reduced the permeability of the coated enamel surfaces as desired. The antimicrobial activity of this coating was evaluated against Streptococcus mutans by colony-forming unit counting and live/dead assays. The anti-demineralization effect was demonstrated by the reduced demineralization depth analyzed by optical coherence tomography and the increased Vickers hardness. The coatings did not reduce the shear bond strength but significantly reduced the adhesive remnant index score. This bioinspired enamel coating may provide a new strategy for preventing white spot lesions and enamel cracks after orthodontic treatment.

[Cone-beam CT evaluation of the effect of indirect anchorage of mini-screw assisted clear aligner on molar distalization]

Objective: To evaluate the effect of indirect anchorage with mini-screw assisted clear aligner on molar distalization. Methods: Twenty-six adult patients [12 males and 14 females, aged 19 to 31 years, mean age (26.4±4.2) years], who were treated in the Department of Orthodontics, the Affiliated Stomatological Hospital of Nanchang University between January 2018 and September 2021, were included. All the patients were treated with clear aligner and mini-screw indirect anchorage to distalize maxillary molars. In the stage of molar distalization, the mini-implants were implanted between the buccal roots of the maxillary first molar and the second premolar, and rigidly connected to the maxillary second premolar as anchorage reenforcement. Until the first molar had distally moved to the designated position, the mini-implants were transferred to the buccal area between the first and the second molars and similar device was connected to the first molar. Cone-beam CT (CBCT) images were taken before the treatment (T0), at the maxillary first molar distally moved to the designated position (T1), and at the anterior teeth alignment finished (T2). The CBCT data were imported into Mimics 20.0 software for three-dimensional reconstruction. After correcting the head position, each reference point was determined in the multi-plane reconstruction view. The bilateral porion, the right orbitale, the nasion, and the anterior nasal spine were selected as reference points to construct the three-dimensional space coordinate system. The positions of the first molar, the second premolar, and the incisor were analyzed three-dimensionally. The three-dimensional position changes of maxillary first molars and maxillary second premolars during the stages of T0-T1, T1-T2, T0-T2, and the mesiodistal and vertical position changes of maxillary central incisors were analyzed. The statistical analysis was carried out using a one-way repeated measures ANOVA. Results: There was a significant difference in the sagittal position changes of the root and cusp of the maxillary central incisors among three time points (F=24.84, P<0.001; F=27.66, P=0.001), but no difference was observed between T0 and T1 (P>0.05). There was a significant difference in lingual retraction of the maxillary central incisor root [(2.17±0.42) mm] and cusp [(1.81±0.28) mm] between T1 and T2 (P<0.05). A significant difference was noted in the sagittal position changes of the root and crown of the maxillary second premolars among three time points (F=17.16, P=0.001; F=57.99, P<0.001). However, no statistical difference was detected between T0 and T1 (P>0.05) and the difference in maxillary second premolar distalization [root (1.95±0.42) mm, cusp (2.53±0.33) mm] was observed between T1 and T2 (P<0.05). There was a statistically significant difference in the sagittal position changes of the root and the crown of the maxillary first molar among three time points (F=9.37, P=0.002; F=140.26, P<0.001). The difference in the maxillary first molar distalization [crown (3.51±0.30) mm, root (1.98±0.25) mm] between T0 and T1 was significant (P<0.05). However, no significant difference in the sagittal position of the maxillary first molars was observed between T1 and T2 (P>0.05). There was a statistically significant difference in the vertical position of the center point of the root in maxillary first molar among three time points (F=59.06, P<0.001), while (2.28±0.24) mm of intrusion between T0 and T1 was exhibited (P<0.05). However, no significant difference was found in the vertical position of the maxillary first molars between T1 and T2 (P>0.05). There was no significant difference in other measurements among three time points (P>0.05). Conclusions: The effect of indirect anchorage with mini-screw-assisted clear aligner on molar distalization was positive.

Feasibility of direct venous inoculation of the radiation-attenuated Plasmodium falciparum whole sporozoite vaccine in children and infants in Siaya, western Kenya

PfSPZ Vaccine, composed of radiation-attenuated, aseptic, purified, cryopreserved Plasmodium falciparum sporozoites, is administered by direct venous inoculation (DVI) for maximal efficacy against malaria. A critical issue for advancing vaccines that are administered intravenously is the ability to efficiently administer them across multiple age groups. As part of a pediatric safety, immunogenicity, and efficacy trial in western Kenya, we evaluated the feasibility and tolerability of DVI, including ease of venous access, injection time, and crying during the procedure across age groups. Part 1 was an age de-escalation, dose escalation trial in children aged 13 months-5 years and infants aged 5-12 months; part 2 was a vaccine efficacy trial including only infants, using the most skilled injectors from part 1. Injectors could use a vein viewer, if needed. A total of 1222 injections (target 0.5 mL) were initiated by DVI in 511 participants (36 were 5-9-year-olds, 65 were 13-59-month-olds, and 410 infants). The complete volume was injected in 1185/1222 (97.0%) vaccinations, 1083/1185 (91.4%) achieved with the first DVI. 474/511 (92.8%) participants received only complete injections, 27/511 (5.3%) received at least one partial injection (<0.5 mL), and in 10/511 (2.0%) venous access was not obtained. The rate of complete injections by single DVI for infants improved from 77.1% in part 1 to 92.8% in part 2. No crying occurred in 51/59 (86.4%) vaccinations in 5-9-year-olds, 25/86 (29.1%) vaccinations in 13-59-month-olds and 172/1067 (16.1%) vaccinations in infants. Mean administration time ranged from 2.6 to 4.6 minutes and was longer for younger age groups. These data show that vaccination by DVI was feasible and well tolerated in infants and children in this rural hospital in western Kenya, when performed by skilled injectors. We also report that shipping and storage in liquid nitrogen vapor phase was simple and efficient. (Clinicaltrials.gov NCT02687373).

[Three-dimensional changes in condylar position in skeletal class Ⅲ patients with mandibular deviation after bilateral sagittal split ramus osteotomy]

Objective: To investigage the three-dimensional changes in condylar position after bilateral sagittal split ramus osteotomy (BSSRO) in skeletal class Ⅲpatients with mandibular deviation using cone-beam CT (CBCT). Methods: Twenty-five skeletal class Ⅲ patients with mandibular deviation were included. The patients (12 males and 13 females, aged 19-25 years, average age 22.4 years) were treated in the Department of Orthodontics, Affiliated Stomatological Hospital, Nanchang University from October 2013 to March 2017. The patients were divided into T1, T2 and T3 groups (T1 group: CBCT taken within 1 week before operation; T2 group: CBCT taken within 1 week after operation; T3 group: CBCT taken 6-8 months after surgery). Three sets of image data of condyles on both sides (deviation side and contralateral side) were obtained. After the DICOM data collection, the software of Mimics 17.0 was used to perform three-dimensional reconstruction and condylar position measurements: the distance from the condylar top (CoT) to the standard horizontal plane (SHP), the middle sagittal plane (MSP) and the sella coronal plane (SCP) (CoT-SHP, CoT-MSP, CoT-SCP); the distance from the condylar center (CoC) to SHP, MSP and SCP (CoC-SHP, CoC-MSP, CoC-SCP); the angle from the condyle cella plane (CCP) to SHP, MSP and SCP (CCP-SHP, CCP-MSP, CCP-SCP); the angle from the condyle sagittal plane (CSP) to SHP, MSP and SCP (CSP-SHP, CSP-MSP, CSP-SCP) and the distance of the anterior, superior, posterior, medial, central and lateral joint space. One-way ANOVA and LSD-t test were used to compare the changes in condylar position at different periods (T1, T2, and T3). Results: Within 1 week before operation on the deviation side, CoT-SHP [(2.5±1.3) mm], CSP-MSP (41.2°±8.4°) and the posterior joint space [(2.0±0.6) mm] were obviously increased (P<0.05), and CoT-SCP [(9.1±3.3) mm], CCP-MSP (78.2°±5.2°) were decreased significantly (P<0.05); on the contralateral side, CoT-MSP [(50.4±3.1) mm], CCP-MSP (80.6°±6.0°), the anterior joint space [(2.2±0.6) mm] and the medial joint space [(2.6±0.6) mm] were obviously increased (P<0.05), and CCP-SCP (11.4°±8.8°) were decreased significantly (P<0.05). Six to eight months after surgery, CoT-SHP [(2.2±1.0) mm] and the posterior joint space [(1.9±0.5) mm] on deviation side and CoT-SCP [(8.4±2.8) mm] on the contralateral side were increased significantly (P<0.05). No significant difference was found in other measurements (P>0.05). Conclusions: The condylar position in skeletal class Ⅲ patients with mandibular deviation was asymmetrical. Within 1 week after the operation of BSSRO, the condyle on the deviation side was moved forward, downward and inward. Meanwhile, the condyle on the contralateral side was moved backward and outward. Six to eight months after surgery, the condylar position on both sides was gradually restored to the pre-operative condylar position.

P2838The impact of anesthesia depth on catheter ablation for atrial fibrillation: a systematic review and meta-analysis of observational studies

Objectives

This meta-analysis and systematic review seeks to compare both characteristic parameters and procedural outcomes of catheter ablation in patients under GA/deep sedation and mild/moderate sedation.

Background

Catheter ablation has become a widely applied intervention for treating symptomatic AF and arrhythmias that are refractory to medical therapy. It can be conducted through from mild sedation to general anesthesia.

Methods

PubMed and Embase were searched up to July 2018 for randomized controlled trials, cohort and observational studies that assessed the outcomes of catheter ablation under GA/deep sedation or mild/moderate sedation. 12 studies were included in this meta-analysis after screening with the inclusion and exclusion criteria. Heterogeneity between studies and publication bias was evaluated by I2 index and Egger's regression, respectively.

Results

Our meta-analysis found catheter AF ablation with GA/deep sedation to be associated with reduced risk of recurrence (RR: 0.79, 95% CI: 0.56 to 1.13, P=0.20) and complications (RR: 0.95, 95% CI: 0.64 to 1.42, P=0.82), though statistically insignificant. In terms of procedural parameters, there was non-significant difference between the two groups when both procedural time (SMD: −0.13, 95% CI: −0.90 to 0.63, P=0.74) and fluoroscopy time (SMD: −0.41, 95% CI: −1.40 to 0.58, P=0.41) were considered. Multivariate meta-regression demonstrated hypertension as an independent moderating factor for complication risk.

Complications Comparison

Conclusion

Apart from an increased likelihood of procedural success, ablation by GA/deep sedation was found to be non-significantly different from the mild/moderate sedation approach in both procedural parameters and outcome measures.

[A cone-beam CT investigation on condylar growth in beagle dog treated with Herbst appliance and prostaglandin E2 during late stage of growth]

Objective: To assess the mandibular condylar growth using cone-beam CT (CBCT) in beagle dogs treated with Herbst appliance and exogenous prostaglandin E2 (PGE2) during late stage of growth. Methods: Twenty-four male beagle dogs aged 8 months were divided into four groups according to the random number table (n=6 in each group): natural growth group, mandibular protraction group (Herbst group), injected prostaglandin E2 group (PGE2 group), mandibular protraction plus injected prostaglandin E2 group (Herbst+PGE2 group). The beagle dogs in Herbst+PGE2 group and PGE2 group were injected 0.1 ml of prostaglandin E2 (dose of 0.05 mg) into bilateral temporomandibular joint articular cavity. The dogs in natural growth group and Herbst group were injected 0.1 ml of saline into bilateral temporomandibular joint articular cavity as control. PGE2 and saline were injected once every 3 days for 60 days, respectively. CBCT was taken before the application of Herbst appliance and after removal of the appliance for all beagle dogs in four groups at the same time. The CBCT images were reconstructed using Invivo5 software and the relevant parameters of temporomandibular joint were measured. Results: No significant difference was found in natural growth group before and after the experiment (P>0.05). After the treatment, the condylar height and condylar size in Herbst group ([0.19+0.04] and [0.18+0.30] mm), PGE2 group ([0.38+0.14] and [0.51+0.24] mm) and Herbst+PGE2 group ([0.65+0.08] and [0.70+0.24] mm) slightly increased (P<0.05). The condylar changes in all experimental groups were greater than the natural growth group (P<0.05), and the ranges of change, in descending order, were Herbst+PGE2 group, PGE2 group and Herbst group (P<0.05). However, the condylar longitudinal distances, condyle width, condylar transverse diameter, glenoid fossa width and glenoid fossa depth had no statistically significant difference among the four groups (P>0.05). Conclusions: Injection of exogenous PGE2 into the temporomandibular joint articular cavity, or using Herbst appliance separately, a certain amount of growth was observed on the mandibular condyle in beagle dogs during late stage of growth. The combination of Herbst appliance and exogenous PGE2 injection made the condylar growth more obviously.

[Clinical characteristics of neonatal fungal sepsis in neonatal intensive care unit]

OBJECTIVE

To study the characteristics of neonatal fungal sepsis and the difference between bacterial sepsis and fungal sepsis. To improve the understanding of neonatal fungal sepsis.

METHODS

Clinical data of neonatal fungal sepsis in neonatal intensive care unit (NICU) were collected from 2011 to 2016 in Peking University first Hospital. The clinical characteristics were analyzed retrospectively. The difference between neonatal fungal sepsis and bacterial sepsis was also analyzed.

RESULTS

Fifteen cases of neonatal fungal sepsis were recruited. Over the study period, the incidence of neonatal fungal sepsis was 0.52%, while it was 2.5% in very low birth weight infants. Clinical characteristics were nonspeci-fic. All the infants were treated with parenteral nutrition and broad spectrum antibiotics. Peripheral inserted central catheter (PICC) was placed in thirteen patients. Pathogenic analyses indicated Candida glabrata was the main pathogen in our study. All the pathogens were sensitive to amphotericin B. Only one Candida glabrata was resistant to fluconazole. Thirty-four cases of bacterial sepsis were included. The clinical characteristics and laboratory examination results were compared. The platelet count was 61×10⁹/L in fungal group, while the platelet count was 178×10⁹/L in bacterial group. There was statistical difference between the fungal group and bacterial group (P=0.004). The rate of thrombocytopenia was 80.0% in fungal group, while it was 29.4% in bacterial group. It was much higher in fungal group than in bacterial group (P=0.001). The rate of PICC placement was 86.7% in fungal group, while it was 55.7% in bacterial group. It was much higher in fungal group than in bacterial group (P=0.037). Receiver operating characteristic (ROC) curve analysis showed that the cut-off value of the platelet count for the diagnosis of neonatal fungal sepsis was 145×10⁹/L (sensitivity 61.8%, specificity 92.9%). All the patients were cured after standardized antifungal therapy. The indicators of liver and renal function were also measured before and after antifungal therapy. No significant difference was observed before and after treatment.

CONCLUSION

The clinical characteristics of neonatal fungal sepsis was nonspecific. Candida glabrata was the main pathogen in our NICU. It can be cured as the result of standardized treatment. Decreased platelet count and PICC placement may indicate the possibility of fungal sepsis in neonates.

[A cone-beam CT investigation on the effect of two-phase treatment and fixed appliance treatment only on temporomandibular joint]

OBJECTIVE

To assess the effects of two phase treatment(Herbst and fixed appliance) and fixed appliance treatment only(edgewise appliance) on temporomandibular joint in Cass Ⅱ patients with mandibular retrusion using cone-beam CT(CBCT) analysis.

METHODS

Thirty Class Ⅱ patients with mandibular retrusion in the permanent dentition were divided into two groups. Group A consisted of 15 patients with two phase treatment. Group B consisted of 15 patients with fixed appliance treatment only. CBCT was taken before(T1) and after(T2) treatment. The Invivo Dental software was used to calculate the relevant parameters of temporomandibular joint. Wilcoxon analysis was carried out.

RESULTS

In group A, the condylar anterior-posterior diameters(7.41[2.55]) and the condylar head height(3.58[0.86]) increased significantly after treatment(P<0.05). In group B, all skeletal measurements had no significant changes(P> 0.05) after treatment. The changes of condylar head height in group A(0.60[0.48]) showed greater than in group B(0.02[0.21]) (P<0.05). No significant differences in the temporomandibular joint spaces were found before and after treatment, and between the two groups(P>0.05).

CONCLUSIONS

Compared with fixed appliance treatment only, except for condylar growth changes, no significant changes of other skeletal morphology of the temporomandibular joint and the condyle position within the glenoid fossa were found between patients with two phase treatment and with fixed appliance treatment only.

Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.

Phylogenetic utility of the glycerol-3-phosphate acyltransferase gene: evolution and implications in Paeonia (Paeoniaceae)

The nuclear-encoded chloroplast-expressed glycerol-3-phosphate acyltransferase (GPAT) gene has been found to be single-copy in a number of angiosperm families. In this study we investigated the phylogenetic utility of the GPAT gene at the interspecific level using the genus Paeonia (Paeoniaceae) as an example. An approximately 2.3- to 2.6-kb fragment of the GPAT gene, containing a large intron of more than 2 kb, was amplified, cloned, and sequenced from 19 accessions representing 13 Paeonia species. The GPAT gene phylogeny inferred by parsimony analysis supported interspecific relationships that were previously unresolved, suggesting that large introns of low-copy nuclear genes are particularly informative in the resolution of close relationships at low taxonomic levels. Whereas the GPAT phylogeny is largely congruent with the previous phylogenetic hypothesis of Paeonia, it shows a significant discordance involving the paraphyly of section Paeonia. Given evidence of an ancient duplication and the subsequent silencing of one GPAT locus in P. anomala, this discordance is most likely the result of paralogy. Two distinct genomic clones containing partial GPAT genes were isolated from P. anomala. The GPAT sequence from one clone corresponded to the functional copy of the gene, and the second genomic clone was determined to contain a GPAT pseudogene. The insertion of a retrotransposon in an intron of this pseudogene may have been responsible for the silencing of this GPAT locus in P. anomala. This study suggests that, although it is unlikely that universal nuclear gene markers free from paralogy are usually available, low-copy nuclear genes can be very useful in plant phylogenetic reconstruction, especially at low taxonomic levels, as long as the evolutionary dynamics of the genes are carefully examined.

Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia)

Phylogenies of Adh1 and Adh2 genes suggest that a widespread Mediterranean peony, Paeonia officinalis, is a homoploid hybrid species between two allotetraploid species, Paeonia peregrina and a member of the Paeonia arietina species group. Three phylogenetically distinct types of Adh sequences have been identified from both accessions of P. officinalis, of which two types are most closely related to the two homoeologous Adh loci of the P. arietina group and the remaining type came from one of the two Adh homoeologs of P. peregrina. The other Adh homoeolog of P. peregrina was apparently lost from the hybrid genome, possibly through backcrossing with the P. arietina group. This is a documentation of homoploid hybrid speciation between allotetraploid species in nature. This study suggests that hybrid speciation between allotetraploids can occur without an intermediate stage of genome diploidization or a further doubling of genome size.

Testing hybridization hypotheses based on incongruent gene trees

Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Consider two incongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. After developing a bootstrap test to test these alternative hypotheses, we extended the model and test to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolved at a constant rate. The computer simulation also suggested that the model remained valid as long as the rate heterogeneity was occurring proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparing phylogenies of multiple unlinked genes.

Phylogeny and divergence times in Pinaceae: evidence from three genomes

In Pinaceae, the chloroplast, mitochondrial, and nuclear genomes are paternally, maternally, and biparentally inherited, respectively. Examining congruence and incongruence of gene phylogenies among the three genomes should provide insights into phylogenetic relationships within the family. Here we studied intergeneric relationships of Pinaceae using sequences of the chloroplast matK gene, the mitochondrial nad5 gene, and the low-copy nuclear gene 4CL. The 4CL gene may exist as a single copy in some species of Pinaceae, but it constitutes a small gene family with two or three members in others. Duplication and deletion of the 4CL gene occurred at a tempo such that paralogous loci are maintained within but not between genera. Exons of the 4CL gene have diverged approximately twice as fast as the matK gene and five times more rapidly than the nad5 gene. The partition-homogeneity test indicates that the three data sets are homogeneous. A combined analysis of the three gene sequences generated a well-resolved and strongly supported phylogeny. The combined phylogeny, which is topologically congruent with the three individual gene trees based on the Templeton test, is likely to represent the organismal phylogeny of Pinaceae. This phylogeny agrees to a certain extent with previous phylogenetic hypotheses based on morphological, anatomical, and immunological data. Disagreement between the previous hypotheses and the three-genome phylogeny suggests that morphology of both vegetative and reproductive organs has undergone convergent evolution within the pine family. The strongly supported monophyly of Nothotsuga longibracteata, Tsuga mertensiana, and Tsuga canadensis on all three gene phylogenies provides evidence against previous hypotheses of intergeneric hybrid origins of N. longibracteata and T. mertensiana. Divergence times of the genera were estimated based on sequence divergence of the matK gene, and they correspond well with the fossil record.

[Determination of protocatechuic acid in Blumea riparia (Bl.) DC. by RP-HPLC]

OBJECTIVE

To determine the content of protocatechuic acid in Blumea riparia by RP-HPLC.

METHOD

mu-Bondapak C18 column was used, mobile phase consisted of methanol-water-glacial acetic acid(19:80:1) and detection was performed at UV 260 nm.

RESULT

The standard curve was linear in the range of 3.31-41.8 micrograms.ml-1. The correlation coefficient was 0.9999. The average recovery rate and RSD were 98.05% and 1.94% (n = 6) respectively.

CONCLUSION

The method provides scientific indexes for quality control of riparia.

Phylogeny of rice genomes with emphasis on origins of allotetraploid species

The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

Physical mapping of ribosomal RNA genes in peonies (Paeonia, Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution

Physical maps of the 18S-5.8S-26S ribosomal RNA genes (rDNA) were generated by fluorescent in situ hybridization for five diploid Paeonia species, P. delavayi and P. rockii of section Moutan, and P. emodi, P. tenuifolia, and P. veitchii of section Paeonia. Of five pairs of mitotic chromosomes, rDNA loci were mapped near the telomeres of chromosomes 3, 4, and 5 of P. rockii and P. tenuifolia, chromosomes 2, 3, 4, and 5 of P. delavayi, and all five pairs of chromosomes of P. emodi and P. veitchii. Combining this information with the previously obtained rDNA maps of P. brownii and P. californica of section Oneapia, we hypothesized that the most recent common ancestor of extant peony species had three rDNA loci located on chromosomes 3, 4, and 5. Increase in number of rDNA loci occurred later in each of the three sections, and the increase from three to four loci represents a parallel gain of an rDNA locus on chromosome 2 in P. delavayi of section Moutan and P. brownii of section Oneapia. The increase in number of rDNA loci likely resulted from the translocation of rDNA repeats from chromosomes bearing rDNA loci to chromosomes without them; such translocation is probably facilitated by the telomeric location of rDNA loci. For allotetraploid peony species lacking polymorphism in sequences of the internal transcribed spacers (ITS) of rDNA, the rDNAs derived from divergent diploid parents may have been homogenized through concerted evolution among at least six rDNA loci in the allotetraploids. Chromosomal location of rDNA loci has a more substantial impact on the tempo of concerted evolution than the number of loci.

Chromosomal structural rearrangement of Paeonia brownii and P. californica revealed by fluorescence in situ hybridization

Chromosomal structural rearrangement in Paeonia brownii and P. californica (2n = 10) was studied by in situ hybridization using 18S rDNA probes. Six major rDNA sites were detected in mitotic cells of P. californica; six major and two minor rDNA sites were found in P. brownii. Two cytotypes (A and B), with different chromosomal morphology and (or) rDNA locations, were observed in the population of P. californica. Cytotype A, with rDNA sites only on the short arms of chromosomes, was considered to be the normal cytotype. Both translocation and pericentric inversion may have occurred to give rise to cytotype B, in which one homolog of chromosome 4 has rDNA sites on both arms while its homolog has no rDNA sites: one homolog of chromosome 3 has a rDNA site on the long arm. Two rearranged cytotypes, C and D, were observed in the population of P. brownii. Given that the normal cytotype of P. brownii is most likely to have six major rDNA sites on the short arms of chromosomes 3, 4, and 5, and two minor sites on the short arms of chromosome 2, cytotype C may have resulted from a translocation between the short arm of one homolog of chromosome 2 and the long arm of one homolog of chromosome 4, and cytotype D may have resulted from a translocation between the short arm of one homolog of chromosome 3 and the long arm of one homolog of chromosome 4. These results supported previous observations, based on meiotic configurations, that chromosomal structural rearrangement occurred frequently in P. brownii and P. californica.

Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species

Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an additional gene, Adh1B, is also present in section Moutan. Phylogenetic analyses of exon sequences of the Adh genes of Paeonia and a variety of other angiosperms imply that duplication of Adh1 and Adh2 occurred prior to the divergence of Paeonia species and was followed by a duplication resulting in Adh1A and Adh1B. Concerted evolution appears to be absent between these paralogous loci. Phylogenetic analysis of only the Paeonia Adh exon sequences, positioning the root of the tree between the paralogous genes Adh1 and Adh2, suggests that the first evolutionary split within the genus occurred between the shrubby section Moutan and the other two herbaceous sections Oneapia and Paeonia. Restriction of Adh1B genes to section Moutan may have resulted from deletion of Adh1B from the common ancestor of sections Oneapia and Paeonia. A relative-rate test was designed to compare rates of molecular change among lineages based on the divergence of paralogous genes, and the results indicate a slower rate of evolution within the shrubby section Moutan than in section Oneapia. This may be responsible for the relatively long branch length of section Oneapia and the short branch length between section Moutan and the other two sections found on the Adh, ITS (nrDNA), and matK (cpDNA) phylogenies of the genus. Adh1 and Adh2 intron sequences cannot be aligned, and we therefore carried out separate analyses of Adh1A and Adh2 genes using exon and intron sequences together. The Templeton test suggested that there is not significant incongruence among Adh1A, ITS, and matK data sets, but that these three data sets conflict significantly with Adh2 sequence data. A combined analysis of Adh1A, ITS, and matK sequences produced a tree that is better resolved than that of any individual gene, and congruent with morphology and the results of artificial hybridization. It is therefore considered to be the current best estimate of the species phylogeny. Paraphyly of section Paeonia in the Adh2 gene tree may be caused by longer coalescence times and random sorting of ancestral alleles.

Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)

The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information. The mat K coding region, evolving more rapidly than the trnL-trn F spacer and more slowly than the psb A-trn H spacer, produced the best resolved phylogenetic tree. The mat K phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution

The internal transcribed spacers (ITS) of nuclear ribosomal DNA of 33 species of genus Paeonia (Paeoniaceae) were sequenced. In section Paeonia, different patterns of nucleotide additivity were detected in 14 diploid and tetraploid species at sites that are variable in the other 12 species of the section, suggesting that reticulate evolution has occurred. Phylogenetic relationships of species that do not show additivity, and thus ostensibly were not derived through hybridization, were reconstructed by parsimony analysis. The taxa presumably derived through reticulate evolution were then added to the phylogenetic tree according to additivity from putative parents. The study provides an example of successfully using ITS sequences to reconstruct reticulate evolution in plants and further demonstrates that the sequence data could be highly informative and accurate for detecting hybridization. Maintenance of parental sequences in the species of hybrid origin is likely due to slowing of concerted evolution caused by the long generation time of peonies. The partial and uneven homogenization of parental sequences displayed in nine species of putative hybrid origin may have resulted from gradients of gene conversion. The documented hybridizations may have occurred since the Pleistocene glaciations. The species of hybrid origin and their putative parents are now distantly allopatric. Reconstruction of reticulate evolution with sequence data, therefore, provides gene records for distributional histories of some of the parental species.