• BMB Reports
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• v.38 no.4
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• pp.500-506
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• 2005

HOX11 encodes a homeodomain-containing transcription factor which directs the development of the spleen during embryogenesis. While HOX11 expression is normally silenced through an unknown mechanism in all tissues by adulthood, the deregulation of HOX11 expression is associated with leukemia, such as T-cell acute lymphoblastic leukemia. The elucidation of regulatory elements contributing to the molecular mechanism underlying the regulation of HOX11 gene expression is of great importance. Previous reports of HOX11 regulatory elements mainly focused on the 5'-flanking region of HOX11 on the chromosome related to transcriptional control. To expand the search of putative cis-elements involved in HOX11 regulation at the post-transcriptional level, we analyzed HOX11 mRNA 3'-untranslated region (3'UTR) and found an AU-rich region. To characterize this AU-rich region, in vitro analysis of HOX11 mRNA 3'UTR was performed with human RNA-binding protein HuR, which interacts with AU-rich element (ARE) existing in the 3'UTR of many growth factors' and cytokines' mRNAs. Our results showed that the HOX11 mRNA 3'UTR can specifically bind with human HuR protein in vitro. This specific binding could be competed effectively by typical ARE containing RNA. After the deletion of the AU-rich region present in the HOX11 mRNA 3'UTR, the interaction of HOX11 mRNA 3'UTR with HuR protein was abolished. These findings suggest that HOX11 mRNA 3'UTR contains cis-acting element which shares similarity in the action pattern with RE-HuR interactions and may involve in the post-transcriptional regulation of the HOX11 gene.

• Journal of Microbiology and Biotechnology
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• v.30 no.6
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• pp.804-810
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• 2020

The profitability of the dairy and beef industries is largely affected by the actually achieved reproductive efficiency. Although a large proportion of cows worldwide are bred by artificial insemination (AI) services, many potential factors affecting the outcome of pregnancy by AI remain to be addressed. In the present study, we investigated the vaginal microbiota by high-throughput sequencing of 16S rRNA gene and analyzed their association with differential pregnancy outcomes (i.e., pregnant vs. nonpregnant) of multiple AI services in dairy cows. Sequencing of the V3-V4 region totally produced 512,046 high-quality sequences that were computationally clustered into 2,584 operational taxonomic units (OTUs). All OTUs were taxonomically assigned to 10 bacterial phyla. There were statistically significant differences among the three AI service times (T1, T2 and T3) with respect to the Shannon index and number of observed OTUs (p < 0.05). Bray-Curtis distance-based PCoA analysis also revealed that T2 group could be significantly distinguished from T1 and T3. However, no significant difference between the pregnant and nonpregnant cows was found in confidence regarding both alpha diversity and beta diversity. These results could help us better understand the possible influence of vaginal microbial community on pregnancy outcomes of AI service in cows.

• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.888-897
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• 2014

A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.

• Mycobiology
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• v.50 no.6
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• pp.439-447
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• 2022

Two strains, YP344 and YP579 were isolated from soil samples in Pocheon City, Gyeonggi Province, South Korea. The strains YP344 and YP579 belong to the genus Vishniacozyma and Dioszegia, respectively. The molecular phylogenetic analysis showed that the strain YP344 was closely related to Vishniacozyma peneaus. Strain YP344T differed by four nucleotide substitutions with no gap (0.70%) in the D1/D2 domain of the LSU rRNA gene and 16 nucleotide substitutions with 8 gaps (5.76%) in the ITS region. On the other hand, the strain YP579^T varied from the type strain of the most closely related species, Dioszegia zsoltii var. zsoltii, by 6 nucleotide substitutions with four gaps (1.64%) in the D1/D2 domain of LSU rRNA gene and 26 nucleotide substitutions with 14 gaps (8.16%) in the ITS region. Therefore, the name Vishniacozyma terrae sp. nov. and Dioszegia terrae sp. nov. are proposed, with type strains YP344T (KCTC27988^T) and YP579^T (KCTC 27998^T), respectively.

• IMMUNE NETWORK
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• v.11 no.5
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• pp.227-244
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• 2011

MicroRNAs (miRNAs) are small noncoding RNA molecules that negatively regulate gene expression via degradation or translational repression of their target messenger RNAs (mRNAs). Recent studies have clearly demonstrated that miRNAs play critical roles in several biologic processes, including cell cycle, differentiation, cell development, cell growth, and apoptosis and that miRNAs are highly expressed in regulatory T (Treg) cells and a wide range of miRNAs are involved in the regulation of immunity and in the prevention of autoimmunity. It has been increasingly reported that miRNAs are associated with various human diseases like autoimmune disease, skin disease, neurological disease and psychiatric disease. Recently, the identification of miRNAs in skin has added a new dimension in the regulatory network and attracted significant interest in this novel layer of gene regulation. Although miRNA research in the field of dermatology is still relatively new, miRNAs have been the subject of much dermatological interest in skin morphogenesis and in regulating angiogenesis. In addition, miRNAs are moving rapidly center stage as key regulators of neuronal development and function in addition to important contributions to neurodegenerative disorder. Moreover, there is now compelling evidence that dysregulation of miRNA networks is implicated in the development and onset of human neruodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, Tourette's syndrome, Down syndrome, depression and schizophrenia. In this review, I briefly summarize the current studies about the roles of miRNAs in various autoimmune diseases, skin diseases, psychoneurological disorders and mental stress.

• Korean Journal Plant Pathology
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• v.11 no.1
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• pp.73-79
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• 1995

Complementary DNAs (cDNAs) to the coat protein gene of an ordinary Korean strain of potato virus Y (PVY-OK) isolated from potato (cv. Superior) were synthesized and cloned into a plasmid pUC119 and sequenced. The RNA of the virus propagated in tobacco (Nicotinaa sylvestris) was extracted by the method of phenol extraction. The first strand of cDNAs to the coat protein penomic RNA of the virus was made by Moloney murine leukemia virus reverse transcriptase. The cDNA were synthesized and amplified by the method of polymerase chain reaction (PCR) using a pair of oligonucleotide primers. PVYCP3P and PVYCP3M. The size of cDNAs inserted in pUC119 plasmid was estimated as about 840 bp upon agarose gel electrophoresis. Double stranded cDNAs were transformed into the competent cell of E. coli JM109. Sequence analysis of cDNAs was conducted by the dideoxynucleotide chain termination method. Homology of cDNAs of the PVY-OK coat protein genomic RNA with those of PVY-O (Japan), PVY-T (Japan), PVY-TH (Japan), PVYN (The Netherlands),and PVYY (France) was represented as 97.3%, 88.9%, 89.3%, 89.6% and 98.5%, respectively. Homology at the amino acid level turned out to the be 97.4%, 92.5%, 92.9%, 92.9% and 98.5%, respectively.

• Journal of Species Research
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• v.7 no.2
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• pp.151-160
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• 2018

Seven bacterial strains, 15J4M-1, 15J13-8, 16MFM10, 15J1-8, SR1-5-4, 15J13-6, and 15J8-11 assigned to the phylum Actinobacteria, Bacteroidetes, and Firmicutes were isolated from soil samples collected from Jeju, Korea. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains 15J4M-1, 15J13-8, 16MFM10, 15J1-8, SR1-5-4, 15J13-6, and 15J8-11 were most closely related to Bacillus selenatarsenatis $SF-1^T$ (with 99.4% similarity), Brevibacterium luteolum $CF87^T$ (99.5%), Carnobacterium iners CCUG $62000^T$ (99.6%), Exiguobacterium profundum $10C^T$ (99.3%), Larkinella insperata LMG $22510^T$ (99.3%), Pseudokineococcus lusitanus CECT $7306^T$ (99.4%), and Spirosoma endophyticum $EX36^T$ (99.3%), respectively. This is the first report of these seven species in Korea.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• Biomedical Science Letters
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• v.12 no.3
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• pp.131-137
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• 2006

RGS is a negative regulator of G-protein signaling and can be identified by the presence of a conserved $120{sim}125$ amino acid motif, which is referred to as the RGS box. A number of RGSs are induced in response to a wide variety of stimuli. Increased levels of RGSs lead to significant decreases in GPCR responsiveness. To obtain further evidence of a role of RGS proteins in rat C6 astrocytoma cells, we first determined the expression profile of RGS-specific mRNA in C6 cells using reverse transcription-polymerase chain reaction (RT-PCR) with a poly dT18 primer and transcript-specific primers. We found that RGS2, RGS3, RGS6, RGS9, RGS10, RGS12, and RGS16 were differentially expressed in C6 astrocytoma cells. The highest expression rate was found for RGS3, followed by RGS16, RGS10 and RGS9, whereas the expression level for RGS2 was barely detectable. We next assessed whether forskolin regulated the expression of RGSs expressed in C6 astrocytoma cells. The present study found that forskolin dose-dependently stimulated the expression of RGS2 transcripts. This up-regulation of RGS2 gene was abrogated by H-89, potent and broad-spectrum protein kinase A (PKA) inhibitors. Actinomycin D completely inhibited the up-regulation of RGS2 gene induced by forskolin $(10{\mu}M)$, indicating that the regulation of RGS2 gene is controlled at the transcriptional level. In addition, forskolin did significantly activate transcriptional cAMP response element (CRE) in either HEK 293 cells or C6 cells and did not modulate the $NF-{\kappa}B$ and AP-l activity as measured by luciferase reporter gene assay. Finally, forskolin induced the expression of RGS2 mRNA in C6 astrocytoma cells, which depend on the PKA pathway and CRE transcriptional pathways.

• International Journal of Stem Cells
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• v.16 no.2
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• pp.145-155
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• 2023

Background and Objectives: Embryologically, mesodermal development is closely related to the development of various organs such as muscles, blood vessels, and hearts, which are the main organs that make up the body. However, treatment for mesoderm developmental disorders caused by congenital or acquired factors has so far relied on surgery and drug treatment for symptom relief, and more fundamentally, treatment for mesoderm developmental disorders is needed. Methods and Results: In our study, microRNA (miRNA), which plays an important role in the mesoderm development process, was identified and the developmental function was evaluated. miRNAs consist of small nucleotides, which act as transcription factors that bind to the 3' untranslated region and suppressed target gene expression. We constructed the human embryonic stem cell (hESC) knockout cell line and analyzed the function and characteristics of miR-5739, which plays an important role in mesoderm lineage. miR-5739 acts as a transcription factor targeting SMA, Brachyury T, Hand1, which controls muscle proliferation and differentiation, and KDR gene, which regulates vessel formation in vitro. In vivo results suggest a role in regulating muscle proliferation and differentiation. Gene ontology analysis confirmed that the miR-5739 is closely related to genes that regulate muscle and vessel proliferation and differentiation. Importantly, abnormal expression of miR-5739 was detected in somatic cells derived from patients with congenital muscle disease. Conclusions: Our study demonstrate that miR-5739 gene function significantly affects transcriptional circuits that regulate muscle and vascular differentiation during embryonic development.