• BMB Reports
• /
• v.53 no.10
• /
• pp.521-526
• /
• 2020

Endogenous retroviruses (ERVs) are retrotransposons present in various metazoan genomes and have been implicated in metazoan evolution as well as in nematodes and humans. The long terminal repeat (LTR) retrotransposons contain several regulatory sequences including promoters and enhancers that regulate endogenous gene expression and thereby control organismal development and response to environmental change. ERVs including the LTR retrotransposons constitute 8% of the human genome and less than 0.6% of the Caenorhabditis elegans (C. elegans) genome, a nematode genetic model system. To investigate the evolutionarily conserved mechanism behind the transcriptional activity of retrotransposons, we generated a transgenic worm model driving green fluorescent protein (GFP) expression using Human endogenous retroviruses (HERV)-K LTR as a promoter. The promoter activity of HERV-K LTR was robust and fluorescence was observed in various tissues throughout the developmental process. Interestingly, persistent GFP expression was specifically detected in the adult vulva muscle. Using deletion constructs, we found that the region from positions 675 to 868 containing the TATA box was necessary for promoter activity driving gene expression in the vulva. Interestingly, we found that the promoter activity of the LTR was dependent on che-1 transcription factor, a sensory neuron driver, and lin-15b, a negative regulator of RNAi and germline gene expression. These results suggest evolutionary conservation of the LTR retrotransposon activity in transcriptional regulation as well as the possibility of che-1 function in non-neuronal tissues.

• Molecules and Cells
• /
• v.43 no.4
• /
• pp.331-339
• /
• 2020

Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.

• Korean Journal of Poultry Science
• /
• v.39 no.4
• /
• pp.311-315
• /
• 2012

The increasing demand for Korean native chicken meat indicates that the discovery of haplotypes is very important from both economic and conservation points of view. In this study, mtDNA D-loop sequences from two crossbred Korean native chicken populations of 138 individuals were investigated. Twenty six nucleotide substitutions were identified from sequence analysis and were classified into 12 haplotypes. The haplotype H_8 represents 73.47% of Woorimatdag (chicken population) sequences, which were identified in all five Woorimatdag chicken populations investigated. The H_7 haplotype (Dhap1) for D population covers 45% sequences, which indicate maternal inheritance from black Korean native chicken. On the other hand, Chap3 and Chap4 for C population are specific haplotypes, as H_5 and H_2, respectively. Based on the network profiles, six SNPs (C199T, A239G, G242A, A291G, T330C and C391A) of the D-loop region are effective markers for discrimination between Woorimatdag and Hanhyup chicken populations. Also, the phylogenetic analyses of Woorimatdag and Hanhyup chicken populations were used to identify the genetic relationships among the haplotypes. The results presented here can be used for developing molecular markers to discriminate between two commercial Korean native chickens.

• Korean Journal of Plant Taxonomy
• /
• v.46 no.3
• /
• pp.273-282
• /
• 2016

The establishment of a DNA barcode database at the regional scale and assessments of the utility of DNA barcodes are crucial for conservation biology and for the sustainable utilization of biological resources. Schisandraceae is a small family consisting of ca. 45 species. It contains many economically important species, such as Schisandra chinensis, which is widely used as a source in tonic beverages and in oriental medicine. In Korea, three species, S. chinensis, S. repanda, and Kadsura japonica, are distributed. We evaluated the level of variation of the DNA sequences of rbcL, matK, and the ITS regions from 13 accessions representing the distributional range of the three species. The three DNA barcode regions were easily amplified and sequenced. The minimum values of the interspecific genetic distances among S. chinensis, S. repanda, and K. japonica either separately or in combination are 4- to 23-fold higher than the maximum value of the intraspecific distance, showing that there is a clear DNA barcoding gap in the regions for Korean Schisandraceae. Phylogenetic analyses of the three DNA barcode regions, separately and simultaneously, indicate that all of the DNA barcode regions are useful for identifying a species of Schisandraceae in Korea. The distinctiveness of the three species of Schisandraceae was also supported at the species level when Chinese and Japanese populations were added. The results of this study indicate that three concatenated regions constitute the best option for DNA barcoding in Schisandraceae in Korea.

• Journal of Environmental Impact Assessment
• /
• v.23 no.3
• /
• pp.197-207
• /
• 2014

In this study, the functional priority of wetlands was determined through analysis of previous research. To determine relative importance, three processes were performed. First, quantitative values from the case studies were normalized. Second, non-quantitative values were prioritized based on standard criteria. Third, equal weight was applied as long as there was no special consideration regarding a particular value's disproportionate priority in the research. Finally, results were grouped into large, medium, and small classes.In this study, the functions of the medium class were found to be the most significant, in the following order of priority: water supply and ground water recharge; culture and recreation; biodiversity; product; water quality control; flood control; erosion control; moderation of climate change; and provision of biochemical matter. To verify these results, we compared our findings with those of an assessment that used the Rapid Assessment Method (RAM) on the same type of study area. Whereas this comparison indicated some correlations by the culture, water storage, and genetic sustainability functions, it suggested a lack of such relationship by the water purification and flood prevention functions.

• Journal of the Korean Society of Environmental Restoration Technology
• /
• v.21 no.2
• /
• pp.27-38
• /
• 2018

Environmental planning includes resource allocation and spatial planning process for the conservation and management of environment. Because the spatialization of the environmental planning is not specifically addressed in the relevant statutes, it actually depends on the qualitative methodology such as expert judgement. The results of the qualitative methodology have the advantage that the accumulated knowledge and intuition of the experts can be utilized. However, it is difficult to objectively judge whether it is enough to solve the original problem or whether it is the best of the possible scenarios. Therefore, this study proposed a methodology to quantitatively and objectively spatialize various environmental planning. At first, we suggested a quantitative spatial planning model based on an optimization algorithm. Secondly, we applied this model to two kinds of environmental planning and discussed about the model performance to present the applicability. Since the models were developed based on conceptual study site, there was a limitation in showing possibility of practical use. However, we expected that this study can contribute to the fields related to environmental planning by suggesting flexible and novel methodology.

• Genomics & Informatics
• /
• v.4 no.4
• /
• pp.147-160
• /
• 2006

GATA transcription factors are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif in the form $CX_{2}CX_{17-20}CX_{2}C$followed by a basic region. In fungi, they act as transcriptional activators or repressors in several different processes, ranging from nitrogen source utilization to mating-type switching. Using an in-house bioinformatics portal system, we surveyed 50 fungal and 9 out-group genomes and identified 396 putative fungal GATA transcription factors. The proportion of GATA transcription factors within a genome varied among taxonomic lineages. Subsequent analyses of phylogenetic relationships among the fungal GATA transcription factors, as well as a study of their domain architecture and gene structure, demonstrated high degrees of conservation in type IVa and type IVb zinc finger motifs and the existence of distinctive clusters at least at the level of subphylum. The SFH1 subgroup with a 20-residue loop was newly identified, in addition to six well-defined subgroups in the subphylum Pezizomycotina. Furthermore, a novel GATA motif with a 2f-residue loop ($CX_{2}CX_{21}CX_{2}C$, designated 'zinc finger type IVc') was discovered within the phylum Basidiomycota. Our results suggest that fungal GATA factors might have undergone multiple distinct modes of evolution resulting in diversified cellular modulation in fungi.

• ALGAE
• /
• v.31 no.2
• /
• pp.155-165
• /
• 2016

Green microalgae from the class Chlorophyceae represent a major biodiversity component of eukaryotic algae in continental water. Identification and classification of this group through morphology is a hard task, since it may present cryptic species and phenotypic plasticity. Despite the increasing use of molecular methods for identification of microorganisms, no single standard barcode marker is yet established for this important group of green microalgae. Some available studies present results with a limited number of chlorophycean genera or using markers that require many different primers for different groups within the class. Thus, we aimed to find a single marker easily amplified and with wide coverage within Chlorophyceae using only one pair of primers. Here, we tested the universality of primers for different genes (tufA, ITS, rbcL, and UCP4) in 22 strains, comprising 18 different species from different orders of Chlorophyceae. The ITS primers sequenced only 3 strains and the UCP primer failed to amplify any strain. We tested two pairs of primers for rbcL and the best pair provided sequences for 10 strains whereas the second one provided sequences for only 7 strains. The pair of primers for the tufA gene presented good results for Chlorophyceae, successfully sequencing 21 strains and recovering the expected phylogeny relationships within the class. Thus, the tufA marker stands out as a good choice to be used as molecular marker for the class.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.1
• /
• pp.3-12
• /
• 2018

Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates). The reference pig genome was annotated with 78.5% of the raw reads. A total of 33,506 putative methylated regions (PMR) were identified from methylated regions that overlapped at least two samples. Results: Of these, only 3.1% were commonly observed in all eight samples. DNA methylation patterns between two littermates were as diverse as between unrelated individuals (p = 0.47), indicating that maternal genetic effects have little influence on the variation in DNA methylation of porcine LDM. The highest density of PMR was observed on chromosome 10. A major proportion (47.7%) of PMR was present in the repeat regions, followed by introns (21.5%). The highest conservation of PMR was found in CpG islands (12.1%). These results show an important role for DNA methylation in species- and tissue-specific regulation of gene expression. PMR were also significantly related to muscular cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism. Conclusion: This study indicated the biased distribution and functional role of DNA methylation in gene expression of porcine LDM. DNA methylation was related to cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism (e.g., insulin signaling pathways). Nutritional and environmental management may have a significant impact on the variation in DNA methylation of porcine LDM.

• Journal of the Korean Society of Environmental Restoration Technology
• /
• v.16 no.3
• /
• pp.63-81
• /
• 2013

The vascular plants in the Ohseosan and the Bongsusan, Chungnam were listed 439 taxa (9.0% of all 4,881 taxa of vascular plants); 95 families, 268 genera, 339 species, 5 subspecies, 75 varieties and 20 forms. Furthermore, the Ohseosan were listed 339 taxa and the Bongsusan were listed 306 taxa. So, Hemicryptophytes (H) were 107 taxa (24.4%), Therophytes (Th), Geophytes (G) same as were 82 taxa (18.7%) showed high proportional ratio in life form. Based on the list of rare plants, 4 taxa; Aristolochia contorta, Viola albida, Scutellaria insignis (LC) and Scrophularia koraiensis (DD) and endemic plants, 8 taxa; Aconitum pseudolaeve, Ajuga spectabilis, etc. Based on the list of specific plants, 35 taxa; Wisteria floribunda for. floribunda in class IV, 5 taxa (Scutellaria insignis, Scrophularia koraiensis, etc.) in class III, 5 taxa (Acer triflorum, Cymopterus melanotilingia, etc.) in class II, 24 taxa (Pyrus ussuriensis var. ussuriensis, Campanula punctata, etc.) in class I. Based on the list of naturalized plants, 9 families, 20 genera, 24 taxa (Persicaria orientalis, Carduus crispus, etc.) and ecosystem disturbing plants were Rumex acetocella, Ambrosia artemisiifolia. Naturalization rate was 5.5% of all 439 taxa of vascular plants and urbanization index was 7.5% of all 321 taxa of naturalized plants. In particular, for rare plants, in and ex-situ conservation of genetic resources must surely be done, by preserving present natural habitats, discovering additional natural habitats and securing seeds. Moreover, ecosystem disturbing plants require long-term monitoring and consistent management, since not only do they disturb the ecosystem in competition with Korean native species, but damage humans, too.