• Molecules and Cells
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• v.24 no.1
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• pp.76-82
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• 2007

By combining in situ hybridization (ISH) and immunocytochemistry (IC), microscopic topological localization of mRNAs and proteins can be determined. Although this technique can be applied to a variety of tissues, it is particularly important for use on neuronal cells which are morphologically complex and in which specific mRNAs and proteins are located in distinct subcellular domains such as dendrites and dendritic spines. One common technical problem for combined ISH and IC is that the signal for immunocytochemical localization of proteins often becomes much weaker after conducting ISH. In this manuscript, we report a simplified but robust protocol that allows immunocytochemical localization of proteins after ISH. In this protocol, we fix cultured cortical or hippocampal neurons with 4% paraformaldehyde (PFA), rinse briefly in PBS, and then further fix the cells with $-20^{\circ}C$ methanol. Our method has several major advantages over previously described ones in that (1) it is simple, as it is just consecutive routine fixation procedures, (2) it does not require any special alteration to the fixation procedures such as changes in salt concentration, and (3) it can be used with antibodies that are compatible with either methanol (MeOH-) or PFA-fixed target proteins. To our best knowledge, we are the first to employ this fixation method for fluorescence ISH + IC.

• Microbiology and Biotechnology Letters
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• v.34 no.3
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• pp.257-264
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• 2006

An aerobic submerged membrane bioreactor (MBR) treating ammonium wastewater was studied in respect of nitrification characteristics and distribution of nitrification bacteria over a period of 350 days. MBR was fed with ammonium concentration of 500-1000 mg $NH_4-N/L$ at a nitrogen load of $1-2kg\;N/m^3{\cdot}d$. Overall ammonium oxidation rate increased with dissolved oxygen (DO) concentration, temperature, and sludge retention time (SRT). Under a higher concentration of free ammonia ($NH_3-N$) due to the decrease of ammonium oxidation rate, the nitrite ratio ($NO_2-N/NO_x-N$) in the effluent increased. The sudden collapse of nitrification efficiency accompanied by sludge foaming and the increase of sludge volume index (SVI) was observed unexpectedly during the operation. At the later stage of operation, additional carbon source was fed to the MBR and resulted in twice higher value of SVI and the decrease of ammonium oxidation rate. In fluorescence in situ hybridization (FISH) analysis, genus Nitrosomonas which is specifically hybridized with probe NSM156 was initially the dominant ammonia oxidizing bacteria and the amount of Nitrosospira gradually increased. Nitrospira was the dominant nitrite oxidizing bacteria during whole operational period. Significant amount of Nitrobacter was also detected which might due to the high concentration of nitrite maintained in the reactor.

• Journal of Hydrogen and New Energy
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• v.25 no.1
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• pp.11-18
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• 2014

This study was conducted to investigate the effect of thermal pre-treatment on bio-hydrogen from food waste. Two continuous reactors operated and VFAs(volatile fatty acids) production and microbial communities were analyzed. The average hydrogen yield was 0.50 and 0.33mol $H_2/mol$ $hexose_{added}$ in thermally treated food added reactor(R1) and control(R2), respectively. Butyrate concentration was similarly 7,500mg/L in both reactors, but two times higher lactate concentration was observed in R2(3,800mg/L). The results of FISH(fluorescence in situ hybridization) showed that the relative microorganism to hydrogen producing bacteria was 78 and 27% in R1 and R2, respectively.

• Animal Bioscience
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• v.35 no.9
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• pp.1289-1302
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• 2022

The next generation sequencing has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the male-specific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in Bos taurus, 5 and 7 in Bubalus bubalis, 5 and 24 in Ovis aries, 5 and 19 in Capra hircus, 10 and 16 in Sus scrofa, 46 and 18 in Equus caballus. While in Vicugna pacos only 10 loci are reported in the PAR region. The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.

• Journal of Korean Society on Water Environment
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• v.23 no.6
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• pp.920-926
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• 2007

The upflow Biobead$^{(R)}$ process, one of biological aerated filters (BAF), which was used commercially, invented for removal of organic materials and nitrification. This process was modified to enhance the ability of denitrification through the induction of pre-anoxic tank. In this research, we investigated the effects of hydraulic retention time (HRT) and backwashing period in aerobic tank. The characteristics of nitrifying bacteria, which are composed of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), also investigated using fluorescence in situ hybridization (FISH). Even though the HRT was shortened, the efficiency of nitrification was not decreased when the organic loading rate and ammonium-nitrogen loading rate were $2.10kg/m^3/day$ and $0.25kg/m^3/day$, respectively. And then the distribution ratios of AOB and NOB showed the similar patterns. However, when the backwashing period was lengthened from 12 hours to 24 hours in aerobic 1 tank, the nitrification efficiency was decreased to 63.9% from 89.2%. The results of FISH explained that this decrease of nitrification efficiency was caused by the decrease of distribution ratio of AOB in aerobic 1 tank. The nitrification efficiencies of aerobic 1 and aerobic 2 tank were increased when the backwashing period was lengthened because of relative high distribution ratios of nitrifying bacteria.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2004.11a
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• pp.13-15
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• 2004

Telomeres are the end of chromosomes and consist of a tandem repeat sequence of (TTAGGG)n and associated proteins. Telomeres are essential for chromosome stability and are related with cell senescence and apoptosis. This study was carried out to analyze the amount of telomeric DNA of chicken lymphocytes, which is to considered as bio-marker. The amount of telomeric DNA of lymphocytes in Korean Native Chicken and White Leghorn was analyzed by quantitative-fluorescence in situ hybridization (Q-FISH) technique using the chicken telomeric DNA probe. Telomere quantifies were compared among breeds, ages and sex, and the relationship between the amount of telomeres and their productive trait was also analyzed. Comparing the amount of telomeric DNA on lymphocytes during growing period, the amount of telomeres was gradually decreased as growing older. The telomere quantity was also significantly different in breeds and sex. Estimating correlation coefficient, the amount of telomeres was positively correlated to sexual maturity and body weight but negatively correlated to hen day egg production and egg weight. These results implicate the telomere quantity is considered as an individual bio-marker.

• Korean Journal of Ecology and Environment
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• v.40 no.4
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• pp.553-559
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• 2007

The vertical distributions of sulfate reducing bacteria (SRB) in sediments of lakes in Korea (Lake Sihwa and Lake Soyang) and China (Lake Aha and Lake Erhai) were investigated by fluorescence in situ hybridization (FISH). SRB from sediment of Lakes of China were located to deeper layer than those in Lakes of Korea. SRB were not detected below 19 cm and 10 cm depth in sediments of Lake Sihwa and Lake Soyang, respectively. SRB numbers were, however, detected at all observed sediments in Lake Aha and Lake Erhai. In case of lakes in Korea, the proportion of SRB ranged from 2.9 to 25.6% (Lake Sihwa) and ranged from 0.6 to 7.1% (Lake Soyang). For lakes in China, the proportions of SRB were from 0.6 to 19.4% and from 2.9 to 11.2% within sediments from Lake Aha and from Lake Erhai, respectively. The high peaks of SRB numbers in sediments of all lakes were appearing at depths between 0 cm and 2 cm.

• Journal of Genetic Medicine
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• v.5 no.1
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• pp.47-54
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• 2008

Purpose : Fluorescence in situ hybridization (FISH) on uncultured amniotic fluid cells offers the opportunity for rapid screening of aneuploidies and has become an integral part of the current practice in many clinical cytogenetics laboratories. Here, we retrospectively analyzed the results of interphase FISH in 943 amniotic fluid samples and assessed the efficiency of FISH for rapid detection of aneuploidies. Methods : Interphase FISH for chromosome 13, 18, and 21 was performed in 943 consecutive amniotic fluid samples for rapid diagnosis of aneuploidies referred from 2004 to 2006. Karyotypes from standard cytogenetic analysis were compared to the FISH results. Results : A total of 45 chromosomal rearrangements (4.8%) were found after conventional cytogenetic analysis of the 943 amniotic fluid. After exclusion of known familiar chromosomal rearrangements and inversions (2.1%, 20/943), 2.7% (25/943) were found to have chromosomal abnormalities. Of this group, 0.7% (6/943) were chromosomal abnormalities not detectable by FISH and 2.0% (19/943) were numerical abnormalities detectable by FISH. All 14 cases of Down syndrome (Classic type, 13 cases; Robertsonian type, 1 case) and 5 cases of trisomy 18 were diagnosed and detected by FISH and there were no false-positive or -negative results (specificity and sensitivity=100%). Conclusion : The present study demonstrates that FISH can provide a rapid and sensitive clinical method for prenatal identification of chromosome aneuploidies. However, careful genetic counseling is essential to explain the limitations of FISH, including the inability to detect all chromosomal abnormalities and the possibilities of uninformative or false-negative results in some cases.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.04a
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• pp.126-126
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• 2005

• Clinical and Experimental Reproductive Medicine
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• v.47 no.4
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• pp.293-299
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• 2020

Objective: The goal of the present study was to investigate the rate of chromosomal aneuploidies in surplus embryos after sex determination at the cleavage stage. Then, the same chromosomal aneuploidies were evaluated in blastocysts after extended culture. Methods: Sixty-eight surplus embryos were biopsied at the cleavage stage and incubated for an additional 3 days to allow them to reach the blastocyst stage. The embryos were reanalyzed via fluorescence in situ hybridization (FISH) to examine eight chromosomes (13, 15, 16, 18, 21, 22, X, and Y) in both cleavage-stage embryos and blastocysts. Results: Although the total abnormality rate was lower in blastocysts (32.35%) than in cleavage-stage embryos (45.58%), the difference was not significant (p=0.113). However, when we restricted the analysis to autosomal abnormalities, we observed a significant difference in the abnormality rate between the cleavage-stage embryos (44.11%) and the blastocysts (17.64%, p=0.008). A higher rate of sex chromosomal abnormalities was also observed in cleavage-stage embryos (29.4%) than in blastocysts (14.70%, p=0.038). Conclusion: The data indicated that embryo biopsy should be conducted at the blastocyst stage rather than the cleavage stage. The results also emphasized that examination of common chromosomal aneuploidies apart from sex selection cycles can be conducted in the blastocyst stage with the FISH method.