• 제목, 요약, 키워드: Phenotype

검색결과 1,246건 처리시간 0.04초

Improved Prediction of Coreceptor Usage and Phenotype of HIV-1 Based on Combined Features of V3 Loop Sequence Using Random Forest

  • Xu, Shungao;Huang, Xinxiang;Xu, Huaxi;Zhang, Chiyu
    • 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.

Phenotypes of allergic diseases in children and their application in clinical situations

  • Lee, Eun;Hong, Soo-Jong
    • Clinical and Experimental Pediatrics
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    • v.62 no.9
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    • pp.325-333
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    • 2019
  • Allergic diseases, including allergic rhinitis, asthma, and atopic dermatitis, are common heterogeneous diseases that encompass diverse phenotypes and different pathogeneses. Phenotype studies of allergic diseases can facilitate the identification of risk factors and their underlying pathophysiology, resulting in the application of more effective treatment, selection of better treatment responses, and prediction of prognosis for each phenotype. In the early phase of phenotype studies in allergic diseases, artificial classifications were usually performed based on clinical features, such as triggering factors or the presence of atopy, which can result in the biased classification of phenotypes and limit the characterization of heterogeneous allergic diseases. Subsequent phenotype studies have suggested more diverse phenotypes for each allergic disease using relatively unbiased statistical methods, such as cluster analysis or latent class analysis. The classifications of phenotypes in allergic diseases may overlap or be unstable over time due to their complex interactions with genetic and encountered environmental factors during the illness, which may affect the disease course and pathophysiology. In this review, diverse phenotype classifications of allergic diseases, including atopic dermatitis, asthma, and wheezing in children, allergic rhinitis, and atopy, are described. The review also discusses the applications of the results obtained from phenotype studies performed in other countries to Korean children. Consideration of changes in the characteristics of each phenotype over time in an individual's lifespan is needed in future studies.

Enhanced macrophage uptake of radiolabeled liposome triggered by ginseng extracts

  • Lee, Woonghee;Rhee, Man Hee;Yoo, Jeongsoo
    • 대한방사성의약품학회지
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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.

장기간 과량의 마늘투여가 HK phenotype 진도견의 혈액상에 미치는 영향 (The Effect of Long-term Administration of Excessive Amount of Garlic on Hematology in HK Phenotype Jindo-Dog)

  • 진태원;김홍태;장우석;오태호;송재찬;정규식;박승춘;이근우
    • 한국임상수의학회지
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    • v.18 no.3
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    • pp.237-242
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    • 2001
  • The garlic has been eaten widely regardless of easten and westen countries to cure the various disease like cancer, tuberculosis, dentalgia, toxemia and leprosy from ancient times. Even now it is reported that they lower the level of triglycerides and cholesterol in blood and that they also affect on the cohesive power of the platelets. In addition, it is also known that it lowers the glucose level in blood. Especially, the sulfur containing amine acid and the derivatives of the garlic has the counteracting effect to heavy metals. Nowadays, the garlic is known for its efficiency for the various kinds of cancer, neoplasms, hypertension, arteriosclerosis and apoplexy. However, it is reported that the intake of the excessive amount of garlic causes hemolytic anemia recently. The hemolytic anemia is more severe especially in HK phenotype dogs which has Na-K-ATPase activity. Therefore, this study was performed to examine the effect on the blood of the HK phenotype Jindo dogs when administered the excessive amount of garlic. HK phenotype group showed the significant decrease on RBC, WBC, PCV, Hb, MCV, MCHC, GSH, Met-Hb but LK phenotype group didn's show the significant decrease. AST, ALT, BUN, creatinine, CPK, glucose, and total protein values were within normal ranges during the period.

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단기간 과량의 마늘투여가 HK phenotype 진도견의 혈액상에 미치는 영향 (The Effect of Short-Term Administration of Excessive Amount of Garlic on Hematology in HK Phenotype Jindo-Dog)

  • 진태원;김홍태;장우석;오태호;송재찬;정규식;박승춘;이근우
    • 한국임상수의학회지
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    • v.18 no.3
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    • pp.232-236
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    • 2001
  • It has been known that garlic, one of the essential ingredient in korean food, has a hypotensive effect. and it is reported that they lower the level of triglycerides, cholesterol and glucose in blood. Especially, the sulfur containing amine acid and the derivatives of the garlic has the counteracting effect to heavy metals. Nowadays, the garlic is known for its efficiency for the various kinds of cancer, neoplasms, hypertension, arteriosclerosis and apoplexy. But, it is reported that the intake of the excessive amount of garlic causes hemolytic anemia recently. The hemolytic anemia is more severe especially in HK phenotype dogs which has a Na-K-ATPase activity. Therefore, this study was performed to examine the effect on the blood of the HK phenotype Jindo dogs when administered the excessive amount of garlic. HK phenotype group showed the significant decrease on RBC, WBC, PCV, Hb, MCV, MCHC, GSH, Met-Hb but LK phenotype group didn't show the significant decrease.

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Biological Characterization of HIV-1 Isolates from Long-term non-progressors (LTNP) and Rapid Progressors (RP) in Korea

  • Nam, Jeong-Gu;Kang, Chun;Lee, Sung-Rae;Lee, Joo-Shil
    • 대한바이러스학회지
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    • v.28 no.4
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    • pp.347-358
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    • 1998
  • To analyze the correlation between biological phenotypes of HIV-1 isolates and disease progression, we selected 9 long-term non-progressors (LTNP) and 12 rapid progressors (RP) from HIV-1 infected Korean. We isolated HIV-1 isolates by culture of PBMC of LTNP and RP with normal PBMC and measured HIV-1 p24 antigen production. The HIV-1 isolation rate from LTNP was 55.6% (5/9). And 4 HIV-1 LTNP isolates were non-syncytium inducing (NSI) phenotype and showed slow/low replication. The HIV-1 isolation rate from RP was 91.7% (11/12) which was higher than that from LTNP. Besides 3 RP HIV-1 isolates which showed syncytium inducing (SI) phenotype, 8 RP HIV-1 isolates showed NSI phenotype in normal PBMC and MT-2 cell line. All RP HIV-1 isolates replicated more rapidly than LTNP HIV-1 isolates. Comparing the replication kinetics and syncytium forming capacity of HIV-1 isolates from LTNP and RP, we suggest that the difference of biological phenotype of HIV-1 isolates could be related with disease progression of HIV-1 infected persons.

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Choosing preferable labels for the Japanese translation of the Human Phenotype Ontology

  • Ninomiya, Kota;Takatsuki, Terue;Kushida, Tatsuya;Yamamoto, Yasunori;Ogishima, Soichi
    • Genomics & Informatics
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    • v.18 no.2
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    • pp.23.1-23.6
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    • 2020
  • The Human Phenotype Ontology (HPO) is the de facto standard ontology to describe human phenotypes in detail, and it is actively used, particularly in the field of rare disease diagnoses. For clinicians who are not fluent in English, the HPO has been translated into many languages, and there have been four initiatives to develop Japanese translations. At the Biomedical Linked Annotation Hackathon 6 (BLAH6), a rule-based approach was attempted to determine the preferable Japanese translation for each HPO term among the candidates developed by the four approaches. The relationship between the HPO and Mammalian Phenotype translations was also investigated, with the eventual goal of harmonizing the two translations to facilitate phenotype-based comparisons of species in Japanese through cross-species phenotype matching. In order to deal with the increase in the number of HPO terms and the need for manual curation, it would be useful to have a dictionary containing word-by-word correspondences and fixed translation phrases for English word order. These considerations seem applicable to HPO localization into other languages.

CDe 표현형의 환자에서 항-E와 항-E/-c 항체 생성 특이성의 차이 (Difference in Characteristics in the Formation of Anti-E and Anti-E/-c in Patients with the CDe Phenotype)

  • 안규대;김경희;임현호;정인화
    • 대한수혈학회지
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    • v.29 no.3
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    • pp.282-290
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    • 2018
  • 배경: CDe 표현형 환자에서 수혈에 의해 항-E 또는 항-E/-c 항체가 생길 수 있다. CDe 표현형 환자에서 항-E 또는 항-E/-c 항체의 생성에 따른 특성의 차이를 조사해 보고자 하였다. 방법: 2014년에 실시된 비예기항체 동정 검사결과를 후향적으로 검토하였다. Rh 표현형과 항체 특이성을 조사하였고, CDe 표현형 환자의 수혈 및 의무 기록을 조사 하였다. 결과: 총 76명의 환자가 포함되었다. 76명의 환자 중 38명(50.0%)이 CDe 표현형이었다. 항-E 항체 양성군은 23명(60.5%)이었고, 항-E/-c 양성군은 9명(23.7%) 이었다. 총 수혈 단위와 혈소판 수혈 단위는 항-E/-c 항체 양성군에서 유의하게 높았다(P=0.028, P=0.01). 분류된 질병군의 분포는 항-E 및 항-E/-c 항체 양성군간에 차이가 없었다. 수혈의 빈도가 4회 이상을 차지하는 비율은 간담도계 질환 환자군에서 85.7%로 가장 높았다. 결론: CDe 표현형 환자에서 항-E 양성군보다 항-E/-c 양성군에서 혈소판 수혈이 의미 있게 높아 적혈구 동종면역에 혈소판의 역할이 있음을 알 수 있었다. 한국인에서 E 항원 면역원성이 가장 높기 때문에 CDe 표현형 환자들에게 E 항원과 c 항원 음성 혈액의 수혈이 요구되는 질환군을 향 후 정의할 필요가 있다.

MAP: Mutation Arranger for Defining Phenotype-Related Single-Nucleotide Variant

  • Baek, In-Pyo;Jeong, Yong-Bok;Jung, Seung-Hyun;Chung, Yeun-Jun
    • Genomics & Informatics
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    • v.12 no.4
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    • pp.289-292
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    • 2014
  • Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

Linkage Analysis of the Three Loci Determining Rind Color and Stripe Pattern in Watermelon

  • Yang, Hee-Bum;Park, Sung-woo;Park, Younghoon;Lee, Gung Pyo;Kang, Sun-Cheol;Kim, Yong Kwon
    • 원예과학기술지
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    • v.33 no.4
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    • pp.559-565
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    • 2015
  • The rind phenotype of watermelon fruits is an important agronomic characteristic in the watermelon market. Inheritance and linkage analyses were performed for three rind-related traits that together determine the rind phenotype: foreground stripe pattern, rind background color, and depth of rind color. The inheritance of the foreground stripe pattern was analyzed using three different $F_2$ populations, showing that the striped pattern is dominant over the non-striped pattern. The inheritance analysis of the rind background color was performed using $F_2$ populations of the '10909' and '109905', and the depth of rind color was analyzed using $F_2$ populations of the '90509' and '109905'. Yellow color was found to be dominant over green color, and a deep color was dominant over the standard color. Linkage analysis of the three traits was conducted using three $F_2$ populations in which two traits were segregating. Each pair of traits was inherited independently, which demonstrated that the three traits are not linked. Therefore, we propose a three-locus model for the determination of rind phenotype, providing novel insight that rind phenotype is determined by the combination of three genetically independent loci.