The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea (Rosaceae): investigation of intraspecific variations on its chloroplast genomes.

The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea is 155,125 bp long (GC ratio is 36.9%) and has four subregions: 84,458 bp of large single copy (34.9%) and 18,737 bp of small single copy (30.4%) regions are separated by 25,965 bp of inverted repeat (42.6%) regions including 129 genes (84 protein-coding genes, eight rRNAs, and 37 tRNAs). 258 SNPs and 542 INDELs were identified as intraspecific variations against the partial genome (KY419942). Phylogenetic trees show that our chloroplast genome was clustered with the previous A. pilosa chloroplast genome.

Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus.

Understanding the evolutionary history of a virus and the mechanisms influencing the direction of its evolution is essential for the development of more durable strategies to control the virus in crop fields. While the deployment of host resistance in crops is the most efficient means to control various viruses, host resistance itself can act as strong selective pressure and thus play a critical role in the evolution of virus virulence. Cucumber mosaic virus (CMV), a plant RNA virus with high evolutionary capacity, has caused endemic disease in various crops worldwide, including pepper (Capsicum annuum L.), because of frequent emergence of resistance-breaking variants. In this study, we examined the molecular and evolutionary characteristics of recently emerged, resistance-breaking CMV variants infecting pepper. Our population genetics analysis revealed that the high divergence capacity of CMV RNA1 might have played an essential role in the host-interactive evolution of CMV and in shaping the CMV population structure in pepper. We also demonstrated that nonsynonymous mutations in RNA1 encoding the 1a protein enabled CMV to overcome the deployed resistance in pepper. Our findings suggest that resistance-driven selective pressures on RNA1 might have contributed in shaping the unique evolutionary pattern of CMV in pepper. Therefore, deployment of a single resistance gene may reduce resistance durability against CMV and more integrated approaches are warranted for successful control of CMV in pepper.

The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae).

Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.

Urodynamic study for distinguishing multiple system atrophy from Parkinson disease.

OBJECTIVE: To evaluate the differences in urodynamic findings between multiple system atrophy (MSA) and Parkinson disease (PD) and to identify the differential diagnostic ability of urodynamic study. METHODS: We reviewed patients with MSA or PD who underwent urodynamic studies between January 2011 and August 2018. Patients with probable MSA and PD determined by movement disorder specialists at our center were included. Patients with alleged MSA or PD from outside hospitals, atypical or secondary parkinsonism, and any history of pelvic operation or radiation therapy were excluded. RESULTS: A total of 219 patients, 107 with MSA (male:female 50:57) and 112 with PD (male:female 57:55), were included. Patients with MSA had shorter disease duration and were referred for urologic evaluation earlier (p < 0.001). Detrusor overactivity and associated urine leakage were prominent in PD (p < 0.001). Patients with MSA showed lower maximal flow rate (4.0 ± 5.8 vs 9.1 ± 8.3 mL/s, p < 0.001) and larger postvoid residual (290.8 ± 196.7 vs 134.0 ± 188.1 mL, p < 0.001) with decreased compliance (44.9% vs 10.7%, p < 0.001) and impaired contractility (24.9 ± 33.8 vs 65.7 ± 51.1, p < 0.001). Postvoid residual from a pressure-flow study had the highest sensitivity and specificity (74.8% and 75.9%), followed by detrusor pressure at maximal uroflow (72.6% and 70.5%), bladder contractility index, and postvoid residual from uroflowmetry (71.0% and 70.5%, respectively). CONCLUSIONS: Patients with MSA showed lower maximal flow rate, larger postvoid residual with decreased compliance, and impaired contractility, whereas patients with PD had higher incidence of detrusor overactivity and associated leakage. For differential diagnosis, postvoid residual from a pressure-flow study provided the best sensitivity and specificity. CLASSIFICATION OF EVIDENCE: This study provides Class III evidence that urodynamic measures can distinguish patients with MSA from those with PD.

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Typica' (Rubiaceae).

We presented complete chloroplast genome of Coffea arabica L. 'Typica' which is 155,187 bp long and has four subregions: 85,159 bp of large single copy (LSC) and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4%, 31.3%, and 43.0%, respectively. Interestingly, almost most of sequence variations identified against five coffee chloroplast genomes are insertions and deletions.

The complete chloroplast genome of Potentilla Freyniana Bornm. (Rosaceae).

Potentilla freyniana Bornm. has radical leaves with petioles and trifoliolate distinguished from Potentilla fragarioides and Duchesnea indica. In this study, we presented first complete chloroplast genome of P. freyniana to understand its phylogenetic position. Its length is 156,381 bp long and has four subregions: 85,724 bp of large single copy (LSC) and 18,617 bp of small single copy (SSC) regions are separated by 26,020 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC, and IR regions are 34.8%, 30.7%, and 42.7%, respectively. Phylogenetic trees show that phylogenetic position of P. freyniana disagrees with three phylogenetic studies, showing that more Potentilla chloroplast genomes are required for clarifying Potentilla phylogeny.

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae).

Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Blue Mountain' (Rubiaceae).

We presented complete chloroplast genome of Coffea arabica BM1 which is 155,189 bp long and has four subregions: 85,159 bp of large single copy (LSC), and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4, 31.3, and 43.0%, respectively. Low level of cultivar specific sequence variations was found among seven coffee chloroplast genomes.

Complete chloroplast genome sequence of the Pseudostellaria longipedicellata S. Lee, K. Heo & S. C. Kim (Caryophyllaceae).

Pseudostellaria longipedicellata which belongs to Caryophyllaceae is endemic in South Korea. In this study, we presented first complete chloroplast genome of P. longipedicellata which is 149,626 bp and has four sub-regions: 81,292 bp of large single copy (LSC) and 16,984 bp of small single copy (SSC) regions are separated by 25,675 bp of inverted repeat (IRs) regions including 126 genes (81 CDS, eight rRNAs, and 37 tRNAs). The overall GC contents of the chloroplast genome were 36.5% and in the LSC, SSC and IR regions were 34.3%, 29.3%, and 42.4%, respectively.

Characterization of AprE176, a fibrinolytic enzyme from Bacillus subtilis HK176.

Bacillus subtilis HK176 with high fibrinolytic activity was isolated from cheonggukjang, a Korean fermented soyfood. A gene, aprE176, encoding the major fibrinolytic enzyme was cloned from B. subtilis HK176 and overexpressed in E. coli BL21(DE3) using plasmid pET26b(+). The specific activity of purified AprE176 was 216.8 ± 5.4 plasmin unit/mg protein and the optimum pH and temperature were pH 8.0 and 40°C, respectively. Error-prone PCR was performed for aprE176, and the PCR products were introduced into E. coli BL21(DE3) after ligation with pET26b(+). Mutants showing enhanced fibrinolytic activities were screened first using skim-milk plates and then fibrin plates. Among the mutants, M179 showed the highest activity on a fibrin plate and it had one amino acid substitution (A176T). The specific activity of M179 was 2.2-fold higher than that of the wild-type enzyme, but the catalytic efficiency (kcat/Km) of M179 was not different from the wild-type enzyme owing to reduced substrate affinity. Interestingly, M179 showed increased thermostability. M179 retained 36% of activity after 5 h at 45°C, whereas AprE176 retained only 11%. Molecular modeling analysis suggested that the 176(th) residue of M179, threonine, was located near the cation-binding site compared with the wild type. This probably caused tight binding of M179 with Ca(2+), which increased the thermostability of M179.

Characterization of a fibrinolytic enzyme secreted by Bacillus amyloliquefaciens CB1 and its gene cloning.

Bacillus amyloliquefaciens CB1 was isolated from cheonggukjang, a Korean fermented soy food. B. amyloliquefaciens CB1 secretes proteases with fibrinolytic activities. A gene homologous to aprE of Bacillus subtilis, aprECB1, was cloned from B. amyloliquefaciens CB1, and DNA sequencing showed that aprECB1 can encode a prepro-type serine protease consisting of 382 amino acids. When aprECB1 was introduced into B. subtilis WB600 using an E. coli-Bacillus shuttle vector, pHY300PLK, transformants showed fibrinolytic activity and produced a 28 kDa protein, the size expected for the mature enzyme. The 28 kDa fibrinolytic enzyme was purified from the culture supernatant of B. subtilis WB600 transformant. AprECB1 was completely inhibited by phenylmethylsulfonyl fluoride and almost completely inhibited by EDTA and EGTA, indicating that it is a serine metalloprotease. AprECB1 exhibited the highest specificity for N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, a known substrate for α-chymotrypsin. Aα and Bß chains of fibrinogen were quickly degraded by AprECB1, but the γ-chain was resistant.

Clinical utility of chimerism status assessed by lineage-specific short tandem repeat analysis: experience from four cases of allogeneic stem cell transplantation.

Chimerism testing permits early prediction and documentation of successful engraftment, and also facilitates detection of impending graft rejection. In this study, we serially monitored chimerism status by short tandem repeat-based PCR in nucleated cells (NC), T cells and natural killer (NK) cells after myeloablative allogeneic stem cell transplantation (SCT). Four patients with myeloid malignancies showed discrepant chimerism results among those three fractions. Three patients had mixed chimerism (MC) of donor/host T cells at a time point around the onset of chronic graft-versus-host disease (GVHD). In two patients with disease relapse, MC of NK cells preceded a morphological relapse or NK cells showed a higher percentage of patient cells compared to NC. Therefore, our study shows that chimerism analysis in lineage-specific cells might be useful in predicting clinical outcome after allogeneic SCT in certain patients.

Effects of bladder training and/or tolterodine in female patients with overactive bladder syndrome: a prospective, randomized study.

We compared the effects of bladder training and/or tolterodine as first line treatment in female patients with overactive bladder (OAB). One hundred and thirty-nine female patients with OAB were randomized to treatment with bladder training (BT), tolterodine (To, 2 mg twice daily) or both (Co) for 12 weeks. Treatment efficacy was measured by micturition diary, urgency scores and patients' subjective assessment of their bladder condition. Mean frequency and nocturia significantly decreased in all treatment groups, declining 25.9% and 56.1%, respectively, in the BT group; 30.2% and 65.4%, respectively, in the To group; and 33.5% and 66.3%, respectively in the Co group (p<0.05 for each). The decrease in frequency was significantly greater in the Co group than in the BT group (p<0.05). Mean urgency score decreased by 44.8%, 62.2% and 60.2% in the BT, To, and Co groups, respectively, and the improvement was significantly greater in the To and Co groups than in the BT group (p<0.05 for each). Although BT, To and their combination were all effective in controlling OAB symptoms, combination therapy was more effective than either method alone. Tolterodine alone may be instituted as a first-line therapy, but may be more effective when combined with bladder training.