• Genomics & Informatics
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• 제20권4호
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• pp.40.1-40.8
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• 2022

The concepts of phylogeny and floral genetics play a crucial role in understanding the origin and diversification of flowers in angiosperms. Angiosperms evolved a great diversity of ways to display their flowers for reproductive success with variations in floral color, size, shape, scent, arrangements, and flowering time. The various innovations in floral forms and the aggregation of flowers into different kinds of inflorescences have driven new ecological adaptations, speciation, and angiosperm diversification. Evolutionary developmental biology seeks to uncover the developmental and genetic basis underlying morphological diversification. Advances in the developmental genetics of floral display have provided a foundation for insights into the genetic basis of floral and inflorescence evolution. A number of regulatory genes controlling floral and inflorescence development have been identified in model plants such as Arabidopsis thaliana and Antirrhinum majus using forward genetics, and conserved functions of many of these genes across diverse non-model species have been revealed by reverse genetics. Transcription factors are vital elements in systems that play crucial roles in linked gene expression in the evolution and development of flowers. Therefore, we review the sex-linked genes, mostly transcription factors, associated with the complex and dynamic event of floral development and briefly discuss the sex-linked genes that have been characterized through next-generation sequencing.

• The Plant Pathology Journal
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• 제40권2호
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• pp.225-232
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• 2024

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

• Journal of Genetic Medicine
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• 제2권1호
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• pp.41-47
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• 1998

Human uniparental gestations such as gynogenetic ovarian teratomas provide a model to evaluate the integrity of parent-specific gene expression - i.e. imprinting - in the absence of a complementary parental genetic contribution. The few imprinted genes characterized so far include the insulin-like growth factor-2 gene (IGF2) coding for a fetal growth factor and H19 gene whose normal function is unknown but it is likely to act as an mRNA. IGF2 is expressed by the paternal allele and H19 by the maternal allele. This reciprocal expression is quite interesting because both H19 and IGF2 genes are located close to each other on chromosome 11p15.5. In situ RNA hybridization analysis has shown variable expression of the H19 and IGF2 alleles according to the tissue origin in 11 teratomas. Especially, Skin, derivative of ectoderm, is expressed conspicuously. We examined imprinting of H19 and IGF2 in teratomas using PCR and RT-PCR of exonic polymorphism. H19 and IGF2 transcript could be expressed either biallelically or monoallelically in the teratomas. Biallelic expression (i.e., loss of imprinting) of IGF2 occurred in 5 out of 6 mature teratomas and 1 out of 1 immature teratoma. Biallelic expression of H19 occurred in 4 out of 10 mature teratomas and 1 out of 1 immature teratoma. Expression levels of H19 and IGF2 transcript using the semi-quantitative RT-PCR had no relation between monoallelic and biallelic expression. Moreover, IGF2 biallelic expression did not affect allele-specificity or levels of H19 expression. These results demonstrate that both genes, H19 and IGF2, can be imprinted, expressed and regulated independently and individually of each other in ovarian teratoma.

• Clinical and Experimental Pediatrics
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• 제50권10호
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• pp.931-937
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• 2007

The hemolytic uremic syndrome (HUS) is a rare disease of microangiopathic hemolytic anemia, low platelet count and renal impairment. HUS usually occurs in young children after hemorrhagic colitis by shigatoxin-producing enterohemorrhagic E. coli (D+HUS). HUS is the most common cause of acute renal failure in infants and young children, and is a substantial cause of acute mortality and morbidity; however, renal function recovers in most of them. About 10% of children with HUS do not reveal preceding diarrheal illness, and is referred to as D- HUS or atypical HUS. Atypical HUS comprises a heterogeneous group of thrombomicroangiopathy (TMA) triggered by non-enteric infection, virus, drug, malignancies, transplantation, and other underlying medical condition. Emerging data indicate dysregulation of alternative complement pathway in atypical HUS, and genetic analyses have identified mutations of several regulatory genes; i.e. the fluid phase complement regulator Factor H (CFH), the integral membrane regulator membrane cofactor protein (MCP; CD46) and the serine protease Factor I (IF). The uncontrolled activation of the complement alternative pathway results in the excessive consumption of C3. Plasma exchange or plasma infusion is recommended for treatment of, and has dropped the mortality rate. However, overall prognosis is poor, and many patients succumb to end-stage renal disease. Clinical presentations, response to plasma therapy, and outcome after renal transplantation are influenced by the genotype of the complement regulators. Thrombotic thrombocytopenic purpura (TTP), another type of TMA, occurs mainly in adults as an acquired disease accompanied by fever, neurologic deficits and renal abnormalities. However, less frequent cases of congenital or hereditary TTP associated with ADAMTS-13 (a disintegrin and metalloprotease, with thrombospondin 1-like domains 13) gene mutations have been reported, also. Recent advances in molecular genetics better allow various HUS to be distinguished on the basis of their pathogenesis. The genetic analysis of HUS is important in defining the underlying etiology, predicting the genotype-related outcome and optimizing the management of the patients.

• BMB Reports
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• 제33권6호
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• pp.519-524
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• 2000

NF1 proteins are a family of DNA binding proteins which consist of two separate domains, N-terminal DNA binding domain and C-terminal transcription activation domain. The N-terminal 220 amino acids are highly conserved and are also known to mediate dimerization of NF1 proteins. The C-terminal regions of different type of NF1 proteins are heterogeneous and responsible for transcriptional activation. In this study, we tested the interaction between different domains of rat NF1-A protein by yeast two hybrid analysis and observed the interaction between C-terminal regions of NF1-A which do not contain the N-terminal dimerization domain. Our results showed that the C-terminal region of rat NF1-A between residues 231 and 509 strongly interacted not only with itself, but also with human NF1/CTF1 which is a different type of NF1. When the C-terminal region was divided into two fragments, one from residue 231 to 447 and the other from 448 to 509, the two fragments were able to interact with the C-terminal region of NF1-A significantly. This indicates that both fragments contain independent interaction domains. Analysis of the interactions with alanine substituted fragments showed that substitutions of the heptasequence, SPTSPTY of NF1-A, affected interaction between NF1 proteins. Our results strongly suggest that C-terminal regions may also be important for the formation of homo- and heterodimers in addition to the N-terminal dimerization domain. Also, the heptasequence motif may play some roles in dimer formation.

• Journal of Ginseng Research
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• 제35권2호
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• pp.200-208
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• 2011

Ginsenoside (G) $Rp_1$ is a ginseng saponin derivative with anti-cancer and anti-inflammatory activities. In this study, we examined the mechanism by which G-$Rp_1$ inhibits inflammatory responses of cells. We did this using a strategy in which DNA constructs containing cyclooxygenase (COX)-2 and inducible nitric oxide synthase (iNOS) promoters were transfected into HEK293 cells. G-$Rp_1$ strongly inhibited the promoter activities of COX-2 and iNOS; it also inhibited lipopolysaccharide induced upregulation of COX-2 and iNOS mRNA levels in RAW264.7 cells. In HEK293 cells G-$Rp_1$ did not suppress TANK binding kinase 1-, Toll-interleukin-1 receptor-domain-containing adapter-inducing interferon-${\beta}$ (TRIF)-, TRIF-related adaptor molecule (TRAM)-, or activation of interferon regulatory factor (IRF)-3 and nuclear factor (NF)-${\kappa}$B by the myeloid differentiation primary response gene (MyD88)-induced. However, G-$Rp_1$ strongly suppressed NF-${\kappa}$B activation induced by I${\kappa}$B kinase (IKK)${\beta}$ in HEK293 cells. Consistent with these results, G-$Rp_1$ substantially inhibited IKK${\beta}$-induced phosphorylation of $I{\kappa}B{\alpha}$ and p65. These results suggest that G-$Rp_1$ is a novel anti-inflammatory ginsenoside analog that can be used to treat IKK${\beta}$/NF-${\kappa}$B-mediated inflammatory diseases.

• Genomics & Informatics
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• 제11권4호
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• pp.263-271
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• 2013

We investigated the contribution of genetic variations of KLF5 to basal metabolic rate (BMR) and resting metabolic rate (RMR) and the inhibition of obesity in Korean children. A variation of KLF5 (rs3782933) was genotyped in 62 Korean children. Using multiple linear regression analysis, we developed a model to predict BMR in children. We divided them into several groups; normal versus overweight by body mass index (BMI) and low BMR versus high BMR by BMR. There were no differences in the distributions of alleles and genotypes between each group. The genetic variation of KLF5 gene showed a significant correlation with several clinical factors, such as BMR, muscle, low-density lipoprotein cholesterol, and insulin. Children with the TT had significantly higher BMR than those with CC (p=0.030). The highest muscle was observed in the children with TT compared with CC (p=0.032). The insulin and C-peptide values were higher in children with TT than those with CC (p=0.029 vs. p=0.004, respectively). In linear regression analysis, BMI and muscle mass were correlated with BMR, whereas insulin and C-peptide were not associated with BMR. In the high-BMR group, we observed that higher muscle, fat mass, and C-peptide affect the increase of BMR in children with TT (p < 0.001, p < 0.001, and p=0.018, respectively), while Rohrer's index could explain the usual decrease in BMR (adjust $r^2$=1.000, p < 0.001, respectively). We identified a novel association between TT of KLF5 rs3782933 and BMR in Korean children. We could make better use of the variation within KLF5 in a future clinical intervention study of obesity.

• Journal of Acupuncture Research
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• 제24권1호
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• pp.137-159
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• 2007

Objectives: The purpose of this study is to examine the risk factors and the genetic polymorphism of TNF-alpha associated with rheumatoid arthritis by Sasang constitution Methods : This study was planned to detect the susceptibility of the patients diagnosed by rheumatoid arthritis to Sasang Constitution and to examine the risk factor such as life style and environmental stress (smoking, environmental tobacco smoke, alcohol intake and so on). The genetic polymorphism of TNF-alpha (G308A) were analyzed by PCR-RFLP in rheumatoid arthritis patients and controls. Rheumatoid arthritis patients and matched controls are assessed with QSCCII question for Sasang Typology. Then the genetic polymorphism of patients by Sasang constitution are compared to those of control, which are statistically analyzed and adjusted by age, sex, smoking status, alcohol intake, BMI, and econocmic status. Results: Differential effect of passive smoking on the association between Sasang constitution and rheumatoid arthritis risk was found. This study showed that the genetic polymorphism (TNF-${\alpha}$(G308A)) of rheumatoid arthritis patients and controls associated with the susceptibility to rheumatoid arthritis by sasang constitution was analyzed. Differential effects of TNF-${\alpha}$(G308) genetic polymorphism on the association between rheumatoid arthritis risk and Sasang constitution were found. Conclusion : It is suggested that the genetic polymorphism correlated with susceptibility to rheumatoid arthritis by specific sasang constitution used as its susceptibility marker and further as basic data to prevent the risk factors for rheumatoid arthritis. But larger studies will be needed to confirm these preliminary findings.

• The Plant Pathology Journal
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• 제26권4호
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• pp.313-320
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• 2010

Genetic instability of the rice blast fungus Magnaporthe oryzae has been suggested as a major factor underlying the rapid breakdown of host resistance in the field. However, little information is available on the mechanism of genetic instability. In this study, we assessed the stability of repetitive DNA elements and several key phenotypic traits important for pathogenesis after serially transferring two isolates though rice plants and an artificial medium. Using isolate 70-15, we obtained a total of 176 single-spore isolates from 10 successive rounds of culturing on artificial medium. Another 20 isolates were obtained from germ tubes formed at the basal and apical cells of 10 three-celled conidia. Additionally, 60 isolates were obtained from isolate KJ201 after serial transfers through rice plants and an artificial medium. No apparent differences in phenotypes, including mycelial growth, conidial morphologies, conidiation, conidial germination, appressorium formation, and virulence, or in DNA fingerprints using MGR586, MAGGY, Pot2, LINE, MG-SINE and PWL2 as probes were observed among isolates from the same parent isolate. Southern hybridization and sequence analysis of two avirulence genes, AVR-Pita1 and AVR-Pikm, showed that both genes were also maintained stably during 10 successive generations on medium and plants. However, one reversible loss of restriction fragments was found in the telomere-linked helicase gene (TLH1) family, suggesting some telomere regions may be more unstable than the rest of the genome. Taken together, our results suggest that phenotype and genotype of M. oryzae isolates do not noticeably change, at least up to 10 successive generations on a cultural medium and in host plants.

• International Journal of Fuzzy Logic and Intelligent Systems
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• 제13권1호
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• pp.73-82
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• 2013

In pattern classification, feature selection is an important factor in the performance of classifiers. In particular, when classifying a large number of features or variables, the accuracy and computational time of the classifier can be improved by using the relevant feature subset to remove the irrelevant, redundant, or noisy data. The proposed method consists of two parts: a wrapper part with an improved genetic algorithm(GA) using a new reproduction method and a filter part using mutual information. We also considered feature selection methods based on mutual information(MI) to improve computational complexity. Experimental results show that this method can achieve better performance in pattern recognition problems than other conventional solutions.