• Journal of Microbiology
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• v.45 no.5
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• pp.441-446
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• 2007

HIV-1 coreceptor usage and phenotype mainly determined by V3 loop are associated with the disease progression of AIDS. Predicting HIV-1 coreceptor usage and phenotype facilitates the monitoring of R5-to-X4 switch and treatment decision-making. In this study, we employed random forest to predict HIV-1 biological phenotype, based on 37 random features of V3 loop. In comparison with PSSM method, our RF predictor obtained higher prediction accuracy (95.1% for coreceptor usage and 92.1% for phenotype), especially for non-B non-C HIV-l subtypes (96.6% for coreceptor usage and 95.3% for phenotype). The net charge, polarity of V3 loop and five V3 sites are seven most important features for predicting HIV-1 coreceptor usage or phenotype. Among these features, V3 polarity and four V3 sites (22, 12, 18 and 13) are first reported to have high contribution to HIV-1 biological phenotype prediction.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.5 no.2
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• pp.113-119
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• 2019

During tumor progression various immunosuppressive cells are recruited to a tumor microenvironment (TME). Tumor-associated macrophages (TAMs) are particularly abundant in TME. Based on their function, macrophages are categorized into two phenotypes: tumoricidal M1 and tumor-supportive M2. Generally, TAMs closely resemble M2-macrophages and lead to tumor growth. However, their phenotype can be changed by immune activator from M2 to M1 and thus promote tumor immunotherapy. Ginseng extracts are well known for its anti-tumor and anti-inflammatory effects from numerous reported studies. However, the mechanism of their effects is still not clear. Recently, some studies suggested that ginseng extracts induced immune activation as well as anti-tumor activities by a repolarization of activated macrophage from M2 phenotype to M1 phenotype. But, further verification about the mechanism as to how ginseng extracts can stimulate the immune response is still needed. In this study, we investigated whether ginseng extracts can alter the phenotype from M2 macrophages to M1 macrophages in mice by using a radiolabeled liposome. And we also evaluated the potential of radiolabeled liposome as a nuclear imaging agent to monitor the transition of phenotype of TAMs. In conclusion, the ginseng extracts seem to change the phenotype of macrophages from M2 to M1 like as lipopolysaccharide (LPS) in mice.

• BMB Reports
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• v.43 no.2
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• pp.79-90
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• 2010

Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.

• Journal of Microbiology and Biotechnology
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• v.1 no.3
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• pp.169-175
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• 1991

Pediococcus acidilactici strain M produced a bacteriocin which was proteinaceous, heat stable, and exhibited antimicrobial activity against lactic acid bacteria, variety of food spoilage and pathogenic bacteria. The antimicrobial activity was not caused by $H_2$$O_2$ and organic acid, and was remained between pHs of 4.0 to 9. Molecular weight of crude bacteriocin was approximately 2, 500. Phenotypic assignment after plasmid cruing experiment demonstrated that a 53.7 kilobase (kb) plasmid, designated as pSUC53, was responsible for the sucrose fermentation phenotype ($Suc^+$) and a 11.1 kb plasmid, designated as pBAC11, was associated with bacteriocin production phenotype ($Bac^+$). Neither of the two plasmids were linked to antibiotic resistance.

• BMB Reports
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• v.50 no.1
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• pp.31-36
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• 2017

High-dose caffeine uptake is a developmental stressor and causes food-avoidance behavior (aversion phenotype) in C. elegans, but its mode of action is largely unknown. In this study, we investigated the molecular basis of the caffeine-induced aversion behavior in C. elegans. We found that aversion phenotype induced by 30 mM caffeine was mediated by JNK/MAPK pathway, serotonergic and dopaminergic neuroendocrine signals. In this process, the dopaminergic signaling appears to be the major pathway because the reduced aversion behavior in cat-2 mutants and mutants of JNK/MAPK pathway genes was significantly recovered by pretreatment with dopamine. RNAi depletion of hsp-16.2, a cytosolic chaperone, and cyp-35A family reduced the aversion phenotype, which was further reduced in cat-2 mutants, suggesting that dopaminergic signal is indeed dominantly required for the caffeine-induced food aversion. Our findings suggest that aversion behavior is a defense mechanism for worms to survive under the high-dose caffeine conditions.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2004.10a
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• pp.48-52
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• 2004

We have found the role of rice mitogen-activated protein kinase kinase kinase (MAPKKK), OsEDR1, as controling hypersensitive response (HR) and increased disease resistance to rice blast fungus Magnaporthe grisea. Generation of transgenic rice plants through introduction of the over-expression construct of OsEDR1 using Agrobacterium-mediated transformation results in lesion mimic phenotype. Up-regulation of defense mechanism was detected through detection of increased transcription level of rice PBZ1 and PR1a. Inoculation of rice blast fungus on the lesion mimic transgenic lines displayed significantly increased resistance. The disease symptoms were arrested like HR responses which are commonly detected in the incompatible interactions. High accumulation of phenolic compounds around developing lesions was detected under UV light. There was variation among transgenic lines on the timing of lesion progression as well as the lesion numbers on the rice leaves. Transgenic lines with few lesions also show increased resistance as well as equal amount of grain yields compared to that of wild type rice cultivar Nipponbare. This is the first report of the MAPKKK as a positive regulator molecule on defense mechanism through inducing HR-like cell death lesion mimic phenotype. The application of OsEDR1 is highly expected for the development of resistant cultivars against rice pathogens.

• Genomics & Informatics
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• v.19 no.1
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• pp.2.1-2.10
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• 2021

BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.

• Clinical and Experimental Pediatrics
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• v.50 no.9
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• pp.835-840
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• 2007

Any infant noted to be jaundiced at 2 weeks of age should be evaluated for cholestasis with measurement of total and direct serum bilirubin. With the insight into the clinical phenotype and the genotype-phenotype correlations, it is now possible to evaluate more precisely the neonate who presents with conjugated hyperbilirubinemia. Testing should be performed for the specific treatable causes of neonatal cholestasis, specifically sepsis, galactosemia, tyrosinemia, citrin deficiency and endocrine disorders. Biliary atresia must be excluded. Low levels of serum gamma-glutamyl transferase in the presence of cholestasis should suggest progressive familial intrahepatic cholestasis type 1, 2, or arthrogryposis- renal dysfunction-cholestasis syndrome. If the serum bile acid level is low, a bile acid synthetic defect should be considered. Molecular genetic testing and molecular-based diagnostic strategies are in evolution.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.290-290
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• 2022

Powdery mildew is known to be one of the serious diseases in C. moschata cultivation. Plants infected with powdery mildew cause damage to cultivation areas such as occurrence of deformity fruit and decrease in quantity. also, it has been reported that many farms have difficulties in controlling powdery mildew due to the outbreak under various conditions throughout the year. Therefore, this study intends to perform a phenotype test and a genotype test for C. moschata 60 lines grown in Jenong S&T. Podospareaxanthii, known as a pathogen that causes powder mildew disease in pumpkins in Korea, was collected and used as an inoculation source, phenotype test was performed by examining the infection area rate(%) of powdery mildew disease that occurred in leaves 25 days after inoculation. It was determined that 0% of the infection area rate was in the first stage, 1 to 5% in the second stage, 6 to 15% in the third stage, 16 to 30% in the fourth stage, and 31% or more in the fifth stage, The first and second stages were judged as resistance, the third as moderate resistance, and the fourth and fifth stages as sensitivity. As a result of the phenotype test, it was confirmed that the resistance was 21 points, moderate resistance was 14 points, and sensitivity was 25 points. After searching for the genes related to powdery mildew resistance resistance, pm-0, CmbHLH87, and LOC111453072, 21 points of resistance and 9 points of moderate resistance identified through phenotype tests were identified through gel electrophoresis after polymerase chain reaction(PCR) using 5 primers related to 3 genes. As a result of genotype testing of a total 30 points, the CmbHLH87 and LOC111453072 gene were found to be resistant bands in all points, PMR1 was identified as 20 points for resistance, 4 points for moderate resistance, and 6 points for sensitivity, PMR2 was not identified in the entire band, and PMR5 was identified as 18 point for resistance, 3 points for moderate resistance, and 9 points for sensitivity. As a result, when comparing the phenotype test results and genotype test results, CmbHLH87 and LOC111453072 genes was 100% consistent in resistance and moderate resistance, PMR1 was 95.2% in resistance, 44.4% in moderate resistance, and PMR5 was 90% in resistance and 33.3% in moderate resistance, PMR2 was not consistent in resistance and moderate resistance. Therefore, it is expected that more accurate PMR test will be possible by using molecular markers(PMR1, PMR5) and by developing CmbHLH87 and LOC111453072 gene-related molecular markers.

• The Korean Journal of Physiology and Pharmacology
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• v.26 no.6
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• pp.479-499
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• 2022

The lack of a clonal renin-secreting cell line has greatly hindered the investigation of the regulatory mechanisms of renin secretion at the cellular, biochemical, and molecular levels. In the present study, we investigated whether it was possible to induce phenotypic switching of the renin-expressing clonal cell line As4.1 from constitutive inactive renin secretion to regulated active renin secretion. When grown to postconfluence for at least two days in media containing fetal bovine serum or insulin-like growth factor-1, the formation of cell-cell contacts via N-cadherin triggered downstream cellular signaling cascades and activated smooth muscle-specific genes, culminating in phenotypic switching to a regulated active renin secretion phenotype, including responding to the key stimuli of active renin secretion. With the use of phenotype-switched As4.1 cells, we provide the first evidence that active renin secretion via exocytosis is regulated by phosphorylation/dephosphorylation of the 20 kDa myosin light chain. The molecular mechanism of phenotypic switching in As4.1 cells described here could serve as a working model for full phenotypic modulation of other secretory cell lines with incomplete phenotypes.