• Title/Summary/Keyword: Phenotype analysis

Search Result 476, Processing Time 0.032 seconds

Clinical Phenotype of a First Unprovoked Acute Pulmonary Embolism Associated with Antiphospholipid Antibody Syndrome

  • Na, Yong Sub;Jang, Seongsoo;Hong, Seokchan;Oh, Yeon Mok;Lee, Sang Do;Lee, Jae Seung
    • Tuberculosis and Respiratory Diseases
    • /
    • v.82 no.1
    • /
    • pp.53-61
    • /
    • 2019
  • Background: Antiphospholipid antibody syndrome (APS), an important cause of acquired thrombophilia, is diagnosed when vascular thrombosis or pregnancy morbidity occurs with persistently positive antiphospholipid antibodies (aPL). APS is a risk factor for unprovoked recurrence of pulmonary embolism (PE). Performing laboratory testing for aPL after a first unprovoked acute PE is controversial. We investigated if a specific phenotype existed in patients with unprovoked with acute PE, suggesting the need to evaluate them for APS. Methods: We retrospectively reviewed patients with PE and APS (n=24) and those with unprovoked PE with aPL negative (n=44), evaluated 2006-2016 at the Asan Medical Center. We compared patient demographics, clinical manifestations, laboratory findings, and radiological findings between the groups. Results: On multivariate logistic regression analysis, two models of independent risk factors for APS-PE were suggested. Model I included hemoptysis (odds ratio [OR], 12.897; 95% confidence interval [CI], 1.025-162.343), low PE severity index (OR, 0.948; 95% CI, 0.917-0.979), and activated partial thromboplastin time (aPTT; OR, 1.166; 95% CI, 1.040-1.307). Model II included age (OR, 0.930; 95% CI, 0.893-0.969) and aPTT (OR, 1.104; 95% CI, 1.000-1.217). Conclusion: We conclude that patients with first unprovoked PE with hemoptysis and are age <40; have a low pulmonary embolism severity index, especially in risk class I-II; and/or prolonged aPTT (above 75th percentile of the reference interval), should be suspected of having APS, and undergo laboratory testing for aPL.

Expression of Senescence-Associated Secretory Phenotype in Senescent Gingival Fibroblasts

  • Sangim Lee
    • Journal of dental hygiene science
    • /
    • v.23 no.2
    • /
    • pp.169-175
    • /
    • 2023
  • Background: Although microbial infection is direct cause of periodontal disease, various environmental factors influence the disease severity. Aging is considered a risk factor for oral diseases, with the prevalence of periodontal diseases increasing with age. Moreover, senescence-associated secretory phenotype (SASP) expressed in age-related diseases is a key marker of chronic inflammation and aging phenotypes. Therefore, this study aimed to understand the relevance of senescent cells to periodontal health and disease, investigate the possibility of regulating the expression of aging- and osteolysis-related factors in gingival fibroblasts, and investigate the effect of senescence induction in gingival fibroblasts on osteoclast differentiation in mouse bone marrow-derived macrophages (BMMs). Methods: After stimulation with 400 nM hydrogen peroxidase, human gingival fibroblasts (HGFs) were examined for senescence-associated β-galactosidase. Western blot and enzyme-linked immunosorbent assays were performed to assess the expression of SASP. Osteoclast formation was assessed in BMMs using a conditioned medium (CM) from hydrogen peroxide-stimulated HGFs. Osteoclastic differentiation was investigated using tartrate-resistant acid phosphatase (TRAP) staining and activity. Data analysis was performed using SPSS version 25.0. Results: The expression of senescence-related molecules, including p53, p16, and p21, and the expression of osteolytic factors, including IL-6, IL-8, and IL-17, were found to be significantly higher in the hydrogen peroxide-stimulated HGF than in the control group. Regarding the indirect effects of senescent gingival cells, the number of osteoclasts and TRAP activity increased according to the differentiation of BMM cultured in CM. Conclusion: Our results on the of between osteolytic factors and cellular senescence in gingival fibroblast cells helped to reveal evidence of pathological aging mechanisms. Furthermore, our results suggest that the development of novel therapies that target specific SASP factors could be an effective treatment strategy for periodontal disease.

Development of SNP Molecular Markers Related to Seed-hair Characteristic Based on EST Sequences in Carrot (당근 EST 염기서열을 이용한 종자모 형질 관련 SNP 분자표지 개발)

  • Oh, Gyu-Dong;Shim, Eun-Jo;Jun, Sang-Jin;Park, Young-Doo
    • Horticultural Science & Technology
    • /
    • v.31 no.1
    • /
    • pp.80-88
    • /
    • 2013
  • Carrot (Daucus carota L. var. sativa) is one of the most extensively used vegetable crops in the world and a significant source of nutrient because of its high content of ${\beta}$-carotene, well known as the precursor of vitamin A carotenoid. However, seed-hairs generated and elongated from the epidermal cell of seeds inhibit absorption and germination by various factors such as carotol and so on. Accordingly, mechanical hair removal process is essential before commercialization of carrot seeds. Because of this process, producers will have additional losses such as time consuming, manpower, capital and so on. Furthermore, physical damage of seeds causes irregular germination rate. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed and studies for molecular markers related to seed-hair characteristic is needed for a new breeding program. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-SMR 616 OP 659-1 line, hairy-seed phenotype CT-SMR 616 OP 677-14 line and short-hair seed phenotype CT-ATR 615 OP 666-13 line, hairy-seed phenotype CT-ATR 615 OP 671-9 were constructed, respectively. Furthermore, 1,248 ESTs in each line, total 4,992 ESTs were sequenced. As a result, 19 SNP sites and 14 SNP sites in each of 2 combinations were confirmed by analyzing these EST sequences from short-hair and hairy-seed lines. Then we designed SNP primer sets from EST sequences of SNP sites for high resolution melting (HRM) analysis. Designed HRM primers were analyzed using hairy seed phenotype CT-SMR 616 OP 1040 line and short-hair seed phenotype CT-SMR 616 OP 1024, 1025, 1026 lines. One set of HRM primers showed specific difference between the melting curves of hairy and short-hair seed phenotype lines. Based on this result, allele-specific (AS) PCR primers were designed for easier selection between hairy-seed carrot and hairless seed carrot. These results of HRM and AS-PCR are expected to be useful in breeding of hairless seed carrot cultivar as a molecular marker.

Comparative Transcriptomic Analysis of MAPK-Mediated Regulation of Sectorization in Cryphonectria parasitica

  • Chun, Jeesun;So, Kum-Kang;Ko, Yo-Han;Kim, Jung-Mi;Kim, Dae-Hyuk
    • Molecules and Cells
    • /
    • v.42 no.4
    • /
    • pp.363-375
    • /
    • 2019
  • Fungal sectorization is a complex trait that is still not fully understood. The unique phenotypic changes in sporadic sectorization in mutants of CpBck1, a mitogen-activated protein kinase kinase kinase (MAPKKK) gene, and CpSlt2, a mitogen-activated protein kinase (MAPK) gene, in the cell wall integrity pathway of the chestnut blight fungus Cryphonectria parasitica have been previously studied. Although several environmental and physiological factors cause this sectoring phenotype, genetic variants can also impact this complex morphogenesis. Therefore, RNA sequencing analysis was employed to identify candidate genes associated with sectorization traits and understand the genetic mechanism of this phenotype. Transcriptomic analysis of CpBck1 and CpSlt2 mutants and their sectored progeny strains revealed a number of differentially expressed genes (DEGs) related to various cellular processes. Approximately 70% of DEGs were common between the wild-type and each of CpBck1 and CpSlt2 mutants, indicating that CpBck1 and CpSlt2 are components of the same MAPK pathway, but each component governs specific sets of genes. Functional description of the DEGs between the parental mutants and their sectored progenies revealed several key pathways, including the biosynthesis of secondary metabolites, translation, amino acid metabolism, and carbohydrate metabolism; among these, pathways for secondary metabolism and translation appeared to be the most common pathway. The results of this comparative study provide a better understanding of the genetic regulation of sector formation and suggest that complex several regulatory pathways result in interplays between secondary metabolites and morphogenesis.

Fecal Calprotectin and Phenotype Severity in Patients with Cystic Fibrosis: A Systematic Review and Meta-Analysis

  • Talebi, Saeedeh;Day, Andrew S.;Rezaiyan, Majid Khadem;Ranjbar, Golnaz;Zarei, Mitra;Safarian, Mahammad;Kianifar, Hamid Reza
    • Pediatric Gastroenterology, Hepatology & Nutrition
    • /
    • v.25 no.1
    • /
    • pp.1-12
    • /
    • 2022
  • Inflammation plays an important role in the outcome of patients with cystic fibrosis (CF). It may develop due to cystic fibrosis transmembrane conductance regulator protein dysfunction, pancreatic insufficiency, or prolonged pulmonary infection. Fecal calprotectin (FC) has been used as a noninvasive method to detect inflammation. Therefore, the aim of the current meta-analysis was to investigate the relationship between FC and phenotype severity in patients with CF. In this study, searches were conducted in PubMed, Science Direct, Scopus, and Embase databases up to August 2021 using terms such as "cystic fibrosis," "intestine," "calprotectin," and "inflammation." Only articles published in English and human studies were selected. The primary outcome was the level of FC in patients with CF. The secondary outcome was the relationship between FC and clinical severity. Statistical analysis was performed using Comprehensive Meta-Analysis software. Of the initial 303 references, only six articles met the inclusion criteria. The mean (95% confidence interval [CI]) level of FC was 256.5 mg/dL (114.1-398.9). FC levels were significantly associated with pancreatic insufficiency (mean, 243.02; 95% CI, 74.3 to 411.6; p=0.005; I2=0), pulmonary function (r=-0.39; 95% CI, -0.58 to -0.15; p=0.002; I2=60%), body mass index (r=-0.514; 95% CI, 0.26 to 0.69; p<0.001; I2=0%), and Pseudomonas colonization (mean, 174.77; 95% CI, 12.5 to 337.02; p=0.035; I2=71%). While FC is a reliable noninvasive marker for detecting gastrointestinal inflammation, it is also correlated with the severity of the disease in patients with CF.

Gastrokine 1 Expression in the Human Gastric Mucosa Is Closely Associated with the Degree of Gastritis and DNA Methylation

  • Choi, Won Suk;Seo, Ho Suk;Song, Kyo Young;Yoon, Jung Hwan;Kim, Olga;Nam, Suk Woo;Lee, Jung Yong;Park, Won Sang
    • Journal of Gastric Cancer
    • /
    • v.13 no.4
    • /
    • pp.232-241
    • /
    • 2013
  • Purpose: Gastrokine 1 plays an important role in gastric mucosal defense. Additionally, the Gastrokine 1-miR-185-DNMT1 axis has been shown to suppress gastric carcinogenesis through regulation of epigenetic alteration. Here, we investigated the effects of Gastrokine 1 on DNA methylation and gastritis. Materials and Methods: Expression of Gastrokine 1, DNMT1, EZH2, and c-Myc proteins, and the presence of Helicobacter pylori CagA protein were determined in 55 non-neoplastic gastric mucosal tissue samples by western blot analysis. The CpG island methylation phenotype was also examined using six markers (p16, hMLH1, CDH1, MINT1, MINT2 and MINT31) by methylation-specific polymerase chain reaction. Histological gastritis was assessed according to the updated Sydney classification system. Results: Reduced Gastrokine 1 expression was found in 20 of the 55 (36.4%) gastric mucosal tissue samples and was closely associated with miR-185 expression. The Gastrokine 1 expression level was inversely correlated with that of DNMT1, EZH2, and c-Myc, and closely associated with the degree of gastritis. The H. pylori CagA protein was detected in 26 of the 55 (47.3%) gastric mucosal tissues and was positively associated with the expression of DNMT1, EZH2, and c-Myc. In addition, 30 (54.5%) and 23 (41.9%) of the gastric mucosal tissues could be classified as CpG island methylation phenotype-low and CpG island methylation phenotype-high, respectively. Reduced expression of Gastrokine 1 and miR-185, and increased expression of DNMT1, EZH2, and c-Myc were detected in the CpG island methylation phenotype-high gastric mucosa. Conclusions: Gastrokine 1 has a crucial role in gastric inflammation and DNA methylation in gastric mucosa.

Personalized Dietary SikdanOme Recommendation based on Obesity Related SNP Genotype and Phenotype (비만 관련 SNP genotype-phenotype 정보기반의 맞춤 식단옴 추천)

  • Shin, Ga-Hee;Lee, Sang-Min;Kang, Byeong-Chul;Jang, Dai-Ja;Kwon, Dae Young;Kim, Min-Jung;Kim, Ri-Rang;Kim, Jin-Hee;Yang, Hye Jeong
    • The Journal of the Korea Contents Association
    • /
    • v.16 no.10
    • /
    • pp.435-442
    • /
    • 2016
  • Obesity extends the global economic burden and it causes that the failure of a reduction of physical activity, and diet management. In this work, nutritional information and personalized diet based on calorie supply system and is discriminatory utilized the obesity-related SNP information in order to recommend a personalized functional foods. This study performed a GWAS analysis for the excavation of a Korean-specific and obesity-related SNP, which utilizes genetic information were recommended by entering a personalized diet in accordance with the SNP genotype-phenotype information. In addition, we integrated Database with relation of nutrient for utilizing the USDA Food information and it was applied to recommend with Sickdanome. As a result, the obesity-related SNP information was confirmed in the sample which has the normal value BMI. In this study, we have recognized that the phenotype information related obesity, BMI is inconsistent with the SNP genotype information. This result is shown that it is necessary to provide the personalized dietary SickdanOme recommendation based on the both pheotype-genotype information.

PLZF+ Innate T Cells Support the TGF-β-Dependent Generation of Activated/Memory-Like Regulatory T Cells

  • Kang, Byung Hyun;Park, Hyo Jin;Park, Hi Jung;Lee, Jae-Il;Park, Seong Hoe;Jung, Kyeong Cheon
    • Molecules and Cells
    • /
    • v.39 no.6
    • /
    • pp.468-476
    • /
    • 2016
  • PLZF-expressing invariant natural killer T cells and CD4 T cells are unique subsets of innate T cells. Both are selected via thymocyte-thymocyte interaction, and they contribute to the generation of activated/memory-like CD4 and CD8 T cells in the thymus via the production of IL-4. Here, we investigated whether $PLZF^+$ innate T cells also affect the development and function of $Foxp3^+$ regulatory CD4 T cells. Flow cytometry analysis of the thymus and spleen from both CIITA transgenic C57BL/6 and wild-type BALB/c mice, which have abundant $PLZF^+$ CD4 T cells and invariant natural killer T cells, respectively, revealed that $Foxp3^+$ T cells in these mice exhibited a $CD103^+$ activated/memorylike phenotype. The frequency of $CD103^+$ regulatory T cells was considerably decreased in $PLZF^+$ cell-deficient $CIITA^{Tg}Plzf^{lu/lu}$ and $BALB/c.CD1d^{-/-}$ mice as well as in an IL-4-deficient background, such as in $CIITA^{Tg}IL-4^{-/-}$ and $BALB/c.IL-4^{-/-}$ mice, indicating that the acquisition of an activated/ memory-like phenotype was dependent on $PLZF^+$ innate T cells and IL-4. Using fetal thymic organ culture, we further demonstrated that IL-4 in concert with TGF-${\beta}$ enhanced the acquisition of the activated/memory-like phenotype of regulatory T cells. In functional aspects, the activated/ memory-like phenotype of Treg cells was directly related to their suppressive function; regulatory T cells of $CIITA^{Tg}PIV^{-/-}$ mice more efficiently suppressed ovalbumin-induced allergic airway inflammation compared with their counterparts from wild-type mice. All of these findings suggest that $PLZF^+$ innate T cells also augmented the generation of activated/memory-like regulation via IL-4 production.

Proteomic analysis of differentially expressed skin proteins in iRhom2Uncv mice

  • Liu, Bing;Xu, Yuan;Li, Wen-Long;Zeng, Lin
    • BMB Reports
    • /
    • v.48 no.1
    • /
    • pp.19-24
    • /
    • 2015
  • A mouse homozygous for the spontaneous mutation uncovered (Uncv) has a hairless phenotype. A 309-bp non-frameshift deletion mutation in the N-terminal cytoplasmic domain of iRhom2 was identified in Uncv mice ($iRhom2^{Uncv}$) using target region sequencing. The detailed molecular basis for how the iRhom2 mutation causes the hairless phenotype observed in the homozygous $iRhom2^{Uncv}$ mouse remains unknown. To identify differentially expressed proteins in the skin of wild-type and homozygous $iRhom2^{Uncv}$ littermates at postnatal day 5, proteomic approaches, including two-dimensional gel electrophoresis and mass spectrometry were used. Twelve proteins were differentially expressed in the skin in a comparison between wild-type and homozygous $iRhom2^{Uncv}$ mice. A selection of the proteomic results were tested and verified using qRT-PCR, western blot and immunohistochemistry. These data indicate that differentially expressed proteins, especially KRT73, MEMO1 and Coro-1, might participate in the mechanism by which iRhom2 regulates the development of murine skin.

Functional Analysis of the marB gene of Escherichia coli K-12

  • Lee, Chang-Mi;Park, Byung-Tae
    • Biomedical Science Letters
    • /
    • v.10 no.2
    • /
    • pp.153-161
    • /
    • 2004
  • Antibiotic resistance is often associated with the production of inner membrane proteins (for example, AcrAB/TolC efflux pump) that are capable to extrude antibiotics, detergents, dyes and organic solvents. In order to evaluate the unknown MarB function of Escherichia coli, especially focused on the function of OmpF porin, several mutants were construted by T4GT7 transduction. MarA plays a major roles in mar (multiple antibiotic resistance) phenotype with AcrAB/TolC efflux pump in E. coli K-12. Futhermore, MarA decreases OmpF porin expression via micF antisense RNA. Expression of acrAB is increased in strains containing mutation in marR, and in those carrying multicopy plasmid expressing marA. MarB protein of E. coli K-12 showed its activity at OmpF porin & TolC protein as target molecule. Some paper reported MarB positively regulates OmpF function. MarA shows mar phenotype, and MarB along with MarA show decreased MIC through OmpF function. By this experiment, MarB could decrease MIC through the OmpF porin & TolC protein as target.

  • PDF