Development of cDNA-derived SSR markers and their efficiency in diversity assessment of Cymbidium accessions

Abstract Cymbidium spp. are popular flowering plants. Assessment of the genetic diversity in cultivated Cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. Thus, it is important to develop more efficient polymorphic DNA markers. Although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cDNA library, a larger number of successful primers were obtained from the cDNA library (59.9%) than from genomic DNA library (51.1%). However, higher PIC and gene diversity were identified in genomic SSRs. The average allele number per locus was also higher in genomic SSRs (7.3) than EST-SSRs (5.2), among the 24 evaluated Cymbidium accessions. AT/TA was comparatively high in EST-SSRs, while this motif was not as common in genomic SSRs. The CTT/AAG/TCT/AGA/TTC/GAA and TGC/GCA/GCT/AGC/CTG/CAG motifs were the most abundant tri-nucleotide sequences in EST-SSRs, while GTT/AAC/TGT/ACA/TTG/CAA was the most frequent in genomic SSRs. The number of repeats ranged from 3 to 12 in EST-SSRs. Currently, 52 novel polymorphic SSR markers have been evaluated, which will be useful for germplasm assessments, core set construction, evaluation of genetic diversity, and marker assisted selection (MAS) based Cymbidium breeding

Enhancement of phase separation in the InGaN layer for self-assembled In-rich quantum dots

The enhancement of phase separation in the InGaN layer grown on a GaN layer with a rough surface was investigated for the formation of self-assembled In-rich quantum dots(QDs) in the InGaN layer. Transmission electron microscopy images showed that In-rich QDs with a size of 2–5 nm were formed even in an InGaN layer with a low indium content, and a layer thickness less than the critical thickness. The room-temperature photoluminescence(PL) spectrum of this layer showed emission peaks corresponding to In-rich QDs. The temperature-dependent PL spectra showed dominant peak shifts to the lower energy side, indicating that the self-assembled In-rich QDs are formed in the InGaN layer grown on a rough GaNsurface and that the carriers are localized in In-rich QDs

Prefoldin 5 and Anti-prefoldin 5 Antibodies as Biomarkers for Uveitis in Ankylosing Spondylitis

Objective: Uveitis is the most common extra-articular manifestation of ankylosing spondylitis (AS), for which no diagnostic biomarkers have been identified. This study was conducted to identify biomarker for uveitis in AS.Methods: To identify autoantibodies associated with uveitis in AS, we performed human protein microarray analysis using sera derived from various autoimmune diseases and ELISA analysis of sera derived from AS and rheumatoid arthritis patients. In the curdlan-induced SKG mice model, ophthalmic examination was performed at week 8 post-immunization and histologic examination of the ocular lesions performed at week 16 post-immunization. Serum levels of target antibodies were assessed at various time-points. To evaluate the functional role of specific autoantibodies, an in vitro apoptosis assay using ARPE-19 cells was performed.Results: Reactivity against prefoldin subunit 5 (PFDN5) was identified in AS with uveitis. Levels of anti-PFDN5 antibodies and PFDN5 in sera from AS with uveitis patients were significantly higher than those in AS without uveitis. At week 8, half of curdlan-treated SKG mice developed anterior uveitis, while all of them developed histologically confirmed uveitis at week 16. The levels of anti-PFDN5 antibodies increased over time in the sera of curdlan-treated SKG mice along with increased expression of PFDN5 and apoptosis in the ocular lesions. Knockdown of PFDN5 in ARPE19 cells resulted in increased apoptosis, suggesting a protective role of PFDN5 against cell death in uveitis.Conclusion: AS patients with uveitis have increased levels of anti-PFDN5 antibodies, and our findings suggest that anti-PFDN5 antibodies could provide a biomarker for uveitis in AS

Decision tree-based approach for online management of PEM fuel cells for residential application

This thesis demonstrates a new intelligent technique for the online optimal management of PEM fuel cells units for onsite energy production to supply residential utilizations. Classical optimization techniques are based on offline calculations and cannot provide the necessary computational speed for online performance. In this research, a Decision Tree (DT) algorithm is employed to obtain the optimal, or quasioptimal, settings of the fuel cell online and in a general framework. The main idea is to employ a classification technique, trained on a sufficient subset of data, to produce an estimate of the optimal setting without repeating the optimization process. A database is extracted from a previously-performed Genetic Algorithm (GA)-based optimization has been used to create a suitable decision tree, which was intended for generalizing the optimization results. The approach provides the flexibility of adjusting the settings of the fuel cell online according to the observed variations in the tariffs and load demands. Results at different operating conditions are presented to confirm the high accuracy of the proposed generalization technique. The accuracy of the decision tree has been tested by evaluating the relative error with respect to the optimized values. Then, the possibility of pruning the tree has been investigated in order to simplify its structure without affecting the accuracy of the results. In addition, the accuracy of the DTs to approximate the optimal performance of the fuel cell is compared to that of the Artificial Neural Networks (ANNs) used for the same purpose. The results show that the DTs can somewhat outperform the ANNs with certain pruning levels

Urachal Actinomycosis Mimicking a Urachal Tumor

A 26-year-old man presented with lower abdominal discomfort and a palpable mass in the right lower quadrant. An abdominal computed tomography (CT) scan revealed an abdominal wall mass that extended from the dome of the bladder. Fluorine-18 fluorodeoxyglucose (FDG) positron-emission tomography/CT (PET/CT) showed hypermetabolic wall thickening around the bladder dome area that extended to the abdominal wall and hypermetabolic mesenteric infiltration. Differential diagnosis included a urachal tumor with invasion into adjacent organs and chronic inflammatory disease. Partial cystectomy with abdominal wall mass excision was performed, and the final pathologic report was consistent with urachal actinomycosis

Impact of hypothyroidism on the development of non-alcoholic fatty liver disease: A 4-year retrospective cohort study

Background/AimsHypothyroidism is reported to contribute to the development of nonalcoholic fatty liver disease (NAFLD). We compared the risk of the development of NAFLD among three groups with different thyroid hormonal statuses (control, subclinical hypothyroidism, and overt hypothyroidism) in a 4-year retrospective cohort of Korean subjects.MethodsApparently healthy Korean subjects without NAFLD and aged 20-65 years were recruited (n=18,544) at health checkups performed in 2008. Annual health checkups were applied to the cohort for 4 consecutive years until December 2012. Based on their initial serum-free thyroxine (fT4) and thyroid-stimulating hormone (TSH) levels, they were classified into control, subclinical hypothyroidism (TSH >4.2 mIU/L, normal fT4), and overt hypothyroidism (TSH >4.2 mIU/L, fT4 <0.97 ng/dL) groups. NAFLD was diagnosed on the basis of ultrasonography findings.ResultsNAFLD developed in 2,348 of the 18,544 subjects, representing an overall incidence of 12.7%: 12.8%, 11.0%, 12.7% in the control, subclinical hypothyroidism, and overt hypothyroidism groups, respectively. The incidence of NAFLD did not differ significantly with the baseline thyroid hormonal status, even after multivariate adjustment (subclinical hypothyroidism group: hazard ratio [HR]=0.965, 95% confidence interval [CI]=0.814-1.143, P=0.67; overt hypothyroidism group: HR=1.255, 95% CI=0.830-1.899, P=0.28).ConclusionsOur results suggest that the subclinical and overt types of hypothyroidism are not related to an increased incidence of NAFLD

Optical and microstructural studies of atomically flat ultrathin In-rich InGaN/GaN multiple quantum wells

Optical and microstructural properties of atomically flat ultrathin In-rich (UTIR) InGaN/GaN multiple quantum well were investigated by means of photoluminescence (PL), time-resolved PL (TRPL), and cathodoluminescence (CL) experiments. The sample exhibits efficient trapping of the photoexcited carriers into quantum wells (QWs) and the effect of internal electric field in the QWs was found negligible by excitation power-dependent PL and TRPL. These phenomena were attributed to the nature of UTIR InGaN QWs, indicating the potential of this system for application in optoelectronic devices. Variation of TRPL lifetime across the PL band and spatially resolved monochromatic CL mapping images strongly suggest that there is micrometer-scale inhomogeneity in effective band gap in UTIR InGaN/GaN QWs, which is originated from two types of localized areas.open141

Grading system for periodontitis by analyzing levels of periodontal pathogens in saliva

Periodontitis is an infectious disease that is associated with microorganisms that colonize the tooth surface. Clinically, periodontal condition stability reflects dynamic equilibrium between bacterial challenge and host response. Therefore, periodontal pathogen assessment can assist in the early detection of periodontitis. Here we developed a grading system called the periodontal pathogen index (PPI) by analyzing the copy numbers of multiple pathogens both in healthy and chronic periodontitis patients. We collected 170 mouthwash samples (64 periodontally healthy controls and 106 chronic periodontitis patients) and analyzed the salivary 16S rRNA levels of nine pathogens using multiplex, quantitative real-time polymerase chain reaction. Except for Aggregatibacter actinomycetemcomitans, copy numbers of all pathogens were significantly higher in chronic periodontitis patients. We classified the samples based on optimal cut-off values with maximum sensitivity and specificity from receiver operating characteristic curve analyses (AUC = 0.91, 95% CI: 0.87-0.96) into four categories of PPI: Healthy (1-40), Moderate (41-60), At Risk (61-80), and Severe (81-100). PPI scores were significantly higher in all chronic periodontitis patients than in the controls (odds ratio: 31.7, 95% CI: 13.41-61.61) and were associated with age, scaling as well as clinical characteristics including clinical attachment level and plaque index. Our PPI grading system can be clinically useful for the early assessment of pathogenic bacterial burden and follow-up monitoring after periodontitis treatment