• Korean Journal of Medicinal Crop Science
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• v.26 no.2
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• pp.113-118
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• 2018

Background: Gastrodia elata Blume is a saprophytic perennial plant in the Orchidaceae family, because of its agricultural and medicinal effectiveness, researchers focus on its genome and chemical components. However, cytogenetic information based on the chromosome structure and composition to construct chromosomal backbone for genome sequencing research and for the development and breeding of plants is very limited. Methods and Results: We determined the metaphase chromosome composition of the G. elata genome by fluorescence in situ hybridization (FISH) using 5S and 45S rDNAs and telomeric repeat probes. The nuclear genome of G. elata was organized into 2 n = 36, with relatively small ($2.71-5.50{\mu}m$)chromosomes that showed gradual decrease in size. Conglutination phenomenon was observed among the metaphase chromosomes, and it was distinguished from that in other plant metaphase chromosome spreads. One pair of signal was detected for each 5S and 45S rDNA in the pericentromeric region and interstitial region on the short arm of chromosomes 10 and 4, respectively, and telomeric DNA signals were detected in the terminal region of most chromosomes. Conclusions: To our knowledge, this is the first FISH chromosome composition result in G. elata and could be useful in more comprehensive molecular cytogenetic and genomic analyses as well as breeding programs of the medicinal plant G. elata.

• Journal of Genetic Medicine
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• v.10 no.2
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• pp.117-119
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• 2013

Double trisomy mosaicism of two different cell lines is extremely rare, particularly those that involve constitutional trisomy 8. We report a case of 47,XXX/47,XX,+8 in a 12-year-old female presenting with several skeletal anomalies. She exhibited distinct phenotypic features such as tall stature, deviation of the left middle finger, webbing of both thumbs and flexion deformities of the both third and fifth distal intermediate phalanges. A mild impulse-control disorder was observed, without mental retardation. Chromosomal and fluorescence in situ hybridization analysis demonstrated double trisomy mosaicism both on lymphocytes and buccal epithelial cells.

• Journal of Korean Society on Water Environment
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• v.24 no.3
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• pp.383-390
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• 2008

Recently, the interests on economical nitrogen removal from wastewater are growing. As a method of the novel nitrogen removal technology, nitrogen removal via nitrite pathway by selective inhibition of free ammonia and free nitrous acid on nitrite oxidizing bacteria have been intensively studied. The inhibition effects of free ammonia and free nitrous acid are low when domestic wastewater is used, however, because of its relatively lower nitrogen concentration than the wastewater from industry and landfill, etc. In this study, a sequencing batch reactor (SBR) is proposed for nitrogen removal to investigate the effect of the low nitrogen concentration on nitrite accumulation. Nitrification efficiency reached almost 100% during the aerobic cycle and the maximum specific nitrification rate ($V_{max,nit}$) reached $17.8mg\;NH_4{^+}-N/g\;MLVSS{\bullet}h$. During the anoxic cycle, average denitrification efficiency reached 87% and the maximum specific denitrification rate ($V_{max,den}$) reached $9.8mg\;NO_3{^-}-N/g\;MLVSS{\bullet}h$. From the analysis the main reason of nitrite accumulation in the SBR was free nitrous acid rather than free ammonia. Nitrite accumulation increased with the decrease of organic content in the wastewater and the mechanism is not well understood yet. From the result of fluorescent in situ hybridization, the distribution of nitrite oxidizing bacteria was in equilibrium with ammonium oxidizing bacteria when nitrite accumulation did not occur.

• Journal of Gastric Cancer
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• v.21 no.2
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• pp.213-219
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• 2021

Plexiform fibromyxoma (PF) of the stomach is a very rare mesenchymal tumor of the gastrointestinal tract. We report the first case of PF with 2 different growth patterns pathologically confirmed after surgical resection. The tumor was characterized microscopically as infiltrative; it demonstrated diffuse growth into the smooth muscle bundles of the muscularis propria and was also multinodular and plexiform within the myxoid stroma. Immunohistochemical analysis revealed that the tumor cells were positive or weakly positive for smooth muscle actin, vimentin, and H-caldesmon and negative for desmin, CD117, CD34, CK-20, Pan-CK, Dog1, S100, ER, PR, and CD10. No mutations of C-kit and platelet-derived growth factor receptor alpha were detected. No genetic disruption of glioma-associated oncogene homolog 1 was detected by fluorescence in situ hybridization. The final diagnosis of PF was mainly based on the morphological and immunohistochemical findings.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.971-977
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• 2015

Malignant glioblastoma multiforme (GBM) is the most malignant brain tumor and despite recent advances in diagnostics and treatment prognosis remains poor. In this retrospective study, we assessed the clinical and radiological parameters, as well as fluorescence in situ hybridization (FISH) of 1p19q deletion, in a series of cases. A total of 816 patients with GBM who received surgery and radiation between January 2010 and May 2014 were included in this study. Kaplan-Meier survival analysis and Cox regression analysis were used to find the factors independently influencing patient progression free survival (PFS) and overall survival (OS). Age at diagnosis, preoperative Karnofsky Performance Scale (KPS) score, KPS score change at 2 weeks after operation, neurological deficit symptoms, tumor resection extent, maximal tumor diameter, involvement of eloquent cortex or deep structure, involvement of brain lobe, Ki-67 and MMP9 expression level and adjuvant chemotherapy were statistically significant factors (p<0.05) for both PFS and OS in the univariate analysis. Cox proportional hazards modeling revealed that age ${\leq}50$ years, preoperative KPS score ${\geq}80$, KPS score change after operation ${\geq}0$, involvement of single frontal lobe, deep structure involvement, low Ki-67 and MMP9 expression and adjuvant chemotherapy were independent favorable factors (p<0.05) for patient clinical outcomes.

• Journal of Genetic Medicine
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• v.4 no.1
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• pp.64-71
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• 2007

Purpose : The purpose of this study was to evaluate the clinical utility of rapid detection of Down syndrome and Edward syndrome by Interphase Fluorescence in Situ Hybridization (FISH) analysis. Methods : Aretrospective study in 309 cases of amniotic fluid samples, analysed by interphase FISH with DNA probes specific to chromosome 18 and 21, was performed. All FISH results w ere compared with conventional cytogenetic karyotypings. Results : The results were considered as informative and they were obtained within 48 hrs. A case of Down syndrome and a case of Edward syndrome were diagnosed by FISH and confirmed by subsequent cytogenetic analysis. In 12 cases with normal FISH results, the cytogenetic analysis showed a case of partial trisomy 22, three cases of sex chromosomal aneuploidy, two cases of mosaicism, two cases of microdeletion, and four cases of structural rearrangement. Conclusion : FISH is a rapid and effective diagnostic method, which can be used as an adjunctive test to cytogenetic analysis, for prenatal identification of chromosome aneuploidies. For the more genome-wide screening with variety of probes, the technique of FISH is both expensive and labor-intensive.

• Journal of Genetic Medicine
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• v.10 no.2
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• pp.99-103
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• 2013

Purpose: This study was designed to determine the frequency and echocardiographic findings of 22q11.2 deletions in fetuses with cardiac defects on fetal ultrasound or familial backgrounds of 22q11.2 deletions. Materials and methods: We retrospectively reviewed the medical and ultrasonographic records of 170 fetuses that underwent fluorescence in situ hybridization (FISH) analysis for chromosome 22q11.2 deletions between February 2001 and April 2013. Results: Among 145 fetuses with cardiac defects, six (4.1%) had 22q11.2 deletions. Deletions of 22q11.2 were detected in 6 (5%) of the 120 fetuses with conotruncal defects: 5 (8.9%) of 56 with tetralogy of Fallot (TOF) and 1 (5.9%) of 17 with double outlet right ventricle (DORV). No deletions were found in cases of pulmonary atresia, truncus arteriosus, right aortic arch, or transposition of the great arteries. No 22q11.2 deletions were found in non-conotruncal cardiac malformations. Among 25 fetuses with familial backgrounds of 22q11.2 deletions, one (4%) had a maternally inherited 22q11.2 deletion with no cardiac findings. Conclusion: Knowledge of the frequency and echocardiographic findings of 22q11.2 deletions might be helpful for prenatal genetic counseling. It is advisable to perform FISH analysis for 22q11.2 deletions in pregnancies exhibiting conotruncal cardiac defects such as TOF or DORV.

• Plant Resources
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• v.7 no.1
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• pp.39-46
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• 2004

To demonstrate the importance of transformation efficiency in independent event, molecular and cytogenetic analysis were conducted with genomic DNA and chromosome of transgenic plants produced by Agrobacterium tumefeciens LBA4404 (pSBM-PPGN: gusA and bar). Selection ratios of putative transgenic calli were similar in independent experiments, however, transformation efficiencies were critically influenced by the type of regeneration media. MSRK5SS-Pr regeneration mediun, which contains 5 mgL$^{-1}$ kinetin, 2% (w/v) sucrose in combination with 3% (w/v) sorbitol, and 500 mgL$^{-1}$ proline, was efficient to produce transgenic plant of rice from putative transgenic callus in the presence of L-phosphinotricin (PPT). With MSRK5SS-Pr medium, transformation efficincies of Nagdongbyeo were significantly enhanced from 3.7% to 6.3% in independent callus lines arid from 7.3% to 19.7% in plants produced, respectively. Stable integration and expression of bar gene were confirmed by basta herbicide assay, PCR amplification and Southern blotting of bar gene, and fluorescence in situ hybridization (FISH) analysis using pSBM-PPGN as a probe. In Southern blot analysis, diverse band patterns were observed in total 44 transgenic plants regenerated from 20 independent PPT resistant calli showing from one to five copies of T-DNA segments, however, the transformants obtained from one callus line showed the same copy numbers with the same fractionized band patterns.

• Food Science and Industry
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• v.50 no.1
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• pp.2-10
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• 2017

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

• Clinical and Experimental Reproductive Medicine
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• v.38 no.3
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• pp.126-134
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• 2011

Preimplantation genetic diagnosis (PGD) is gradually widely used in prevention of gene diseases and chromosomal abnormalities. Much improvement has been achieved in biopsy technique and molecular diagnosis. Blastocyst biopsy can increase diagnostic accuracy and reduce allele dropout. It is cost-effective and currently plays an important role. Whole genome amplification permits subsequent individual detection of multiple gene loci and screening all 23 pairs of chromosomes. For PGD of chromosomal translocation, fluorescence $in-situ$ hybridization (FISH) is traditionally used, but with technical difficulty. Array comparative genomic hybridization (CGH) can detect translocation and 23 pairs of chromosomes that may replace FISH. Single nucleotide polymorphisms array with haplotyping can further distinguish between normal chromosomes and balanced translocation. PGD may shorten time to conceive and reduce miscarriage for patients with chromosomal translocation. PGD has a potential value for mitochondrial diseases. Preimplantation genetic haplotyping has been applied for unknown mutation sites of single gene disease. Preimplantation genetic screening (PGS) using limited FISH probes in the cleavage-stage embryo did not increase live birth rates for patients with advanced maternal age, unexplained recurrent abortions, and repeated implantation failure. Polar body and blastocyst biopsy may circumvent the problem of mosaicism. PGS using blastocyst biopsy and array CGH is encouraging and merit further studies. Cryopreservation of biopsied blastocysts instead of fresh transfer permits sufficient time for transportation and genetic analysis. Cryopreservation of embryos may avoid ovarian hyperstimulation syndrome and possible suboptimal endometrium.