• Journal of Genetic Medicine
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• 제12권1호
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• pp.57-60
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• 2015

CHARGE syndrome (coloboma, heart defects, atresia choanae, retarded growth and development, genital hypoplasia, and ear abnormalities) is characterized by multiple malformations and is diagnosed using distinct consensus criteria. Mutations in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7) are the major cause of CHARGE syndrome. Clinical features of CHARGE syndrome considerably overlap those of 22q11.2 deletion syndrome. Of these features, immunodeficiency and hypocalcemia are frequently reported in patients with 22q11.2 deletion syndrome but are rarely reported in patients with CHARGE syndrome. In this report, we have described the case of a patient with typical phenotypes of 22q11.2 deletion syndrome but without the proven chromosome microdeletion. Mutation analysis of CHD7 identified a pathogenic mutation (c.2238+1G>A) in this patient. To our knowledge, this is the first case of CHARGE syndrome with immunodeficiency and hypocalcemia in Korea. Our observations suggest that mutation analysis of CHD7 should be performed for patients showing the typical phenotypes of 22q11.2 deletion syndrome but lacking the proven chromosome microdeletion.

• BMB Reports
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• 제52권2호
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• pp.133-138
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• 2019

Upon viral infection, the 2', 5'-oligoadenylate synthetase (OAS)-ribonuclease L (RNaseL) system works to cleave viral RNA, thereby blocking viral replication. However, it is unclear whether OAS proteins have a role in regulating gene expression. Here, we show that OAS1 and OAS3 act as negative regulators of the expression of chemokines and interferon-responsive genes in human macrophages. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) technology was used to engineer human myeloid cell lines in which the OAS1 or OAS3 gene was deleted. Neither OAS1 nor OAS3 was exclusively responsible for the degradation of rRNA in macrophages stimulated with poly(I:C), a synthetic surrogate for viral double-stranded (ds)RNA. An mRNA sequencing analysis revealed that genes related to type I interferon signaling and chemokine activity were increased in $OAS1^{-/-}$ and $OAS3^{-/-}$ macrophages treated with intracellular poly(I:C). Indeed, retinoic-acid-inducible gene (RIG)-I- and interferon-induced helicase C domain-containing protein (IFIH1 or MDA5)-mediated induction of chemokines and interferon-stimulated genes was regulated by OAS3, but Toll-like receptor 3 (TLR3)- and TLR4-mediated induction of those genes was modulated by OAS1 in macrophages. However, stimulation of these cells with type I interferons had no effect on OAS1- or OAS3-mediated chemokine secretion. These data suggest that OAS1 and OAS3 negatively regulate the expression of chemokines and interferon-responsive genes in human macrophages.

• The Plant Pathology Journal
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• 제35권5호
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• pp.538-542
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• 2019

In 2017, two new tomato mosaic virus (ToMV) isolates were collected from greenhouses in Buyeo, Chungcheongnam-do, South Korea. Full-length cDNAs of the new ToMV isolates were cloned into dual cauliflower mosaic virus 35S and T7 promoter-driven vectors, sequenced and their pathogenicities investigated. The nucleotide sequences of isolates GW1 (MH507165) and GW2 (MH507166) were 99% identical, resulting in only two amino acid differences in nonconserved region II and the helicase domain, Ile668Thr and Val834Ile. The two isolates were most closely related to a ToMV isolate from Taiwan (KJ207374). Isolate GW1 (Ile668, Val834) induced a systemic hypersensitive response in Nicotiana benthamiana compared with the isolate GW2, which a single residue substitution showed was due to Val834.

• 한국미생물·생명공학회지
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• 제50권4호
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• pp.563-573
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• 2022

Xanthomonas arboricola pv. juglandis (Xaj) is a globally important bacterial pathogen of walnut trees that causes substantial economic losses in commercial walnut production. Although prophages are common in bacterial plant pathogens and play important roles in bacterial diversity and pathogenicity, there has been limited investigation into the distribution and function of prophages in Xaj. In this study, we identified and characterized 13 predicted prophages from the genomes of 12 Xaj isolates from around the globe. These prophages ranged in length from 11.8 kb to 51.9 kb, with between 11-75 genes and 57.82-64.15% GC content. The closest relatives of these prophages belong to the Myoviridae and Siphoviridae families of the Caudovirales order. The phylogenetic analysis allowed the classification of the prophages into five groups. The gene constitution of these predicted prophages was revealed via Roary analysis. Amongst 126 total protein groups, the most prevalent group was only present in nine prophages, and 22 protein groups were present in only one prophage (singletons). Also, bioinformatic analysis of the 13 identified prophages revealed the presence of 431 genes with an average length of 389.7 bp. Prokka annotation of these prophages identified 466 hypothetical proteins, 24 proteins with known function, and six tRNA genes. The proteins with known function mainly comprised prophage integrase IntA, replicative DNA helicase, tyrosine recombinase XerC, and IS3 family transposase. There was no detectable insertion site specificity for these prophages in the Xaj genomes. The identified Xaj prophage genes, particularly those of unknown function, merit future investigation.

• The Plant Pathology Journal
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• 제39권2호
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• pp.191-206
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• 2023

Ground cherry (Physalis pubescens) is the most prominent species in the Solanaceae family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on P. pubescens in China that caused by both BLS pathogens Xanthomonas euvesicatoria pv. euvesicatoria resulted in substantial monetary losses. Here, we compared whole genome sequences of X. euvesicatoria to other Xanthomonas species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect X. euvesicatoria on P. pubescens using recQ, hrpB1, and hrpB2 genes for efficient and precise identification. For rapid molecular detection of X. euvesicatoria, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of X. euvesicatoria was more closely relative to X. perforans than X. vesicatoria, and X. gardneri with 98%, 84%, and 86% ANI, respectively. All infected leaves of P. pubescens found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the X. euvesicatoria. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of X. euvesicatoria using the unique target recQ gene through advance molecular approaches.

• Clinical and Experimental Reproductive Medicine
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• 제50권4호
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• pp.253-261
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• 2023

Objective: Azoospermia (the total absence of sperm in the ejaculate) affects approximately 10% of infertile males. Despite diagnostic advances, azoospermia remains the most challenging issue associated with infertility treatment. Our study evaluated transition nuclear protein 2 (TNP2) and synaptonemal complex protein 3 (SYCP3) polymorphisms, azoospermia factor a (AZFa) microdeletion, and gene expression levels in 100 patients with azoospermia. Methods: We investigated a TNP2 single-nucleotide polymorphism through polymerase chain reaction (PCR) restriction fragment length polymorphism analysis using a particular endonuclease. An allele-specific PCR assay for SYCP3 was performed utilizing two forward primers and a common reverse primer in two PCR reactions. Based on the European Academy of Andrology guidelines, AZFa microdeletions were evaluated by multiplex PCR. TNP2, SYCP3, and the AZFa region main gene (DEAD-box helicase 3 and Y-linked [DDX3Y]) expression levels were assessed via quantitative PCR, and receiver operating characteristic curve analysis was used to determine the diagnostic capability of these genes. Results: The TNP2 genotyping and allelic frequency in infertile males did not differ significantly from fertile volunteers. In participants with azoospermia, the allelic frequency of the SYCP3 mutant allele (C allele) was significantly altered. Deletion of sY84 and sY86 was discovered in patients with azoospermia and oligozoospermia. Moreover, SYCP3 and DDX3Y showed decreased expression levels in the azoospermia group, and they exhibited potential as biomarkers for diagnosing azoospermia (area under the curve, 0.722 and 0.720, respectively). Conclusion: These results suggest that reduced SYCP3 and DDX3Y mRNA expression profiles in testicular tissue are associated with a higher likelihood of retrieving spermatozoa in individuals with azoospermia. The homozygous genotype TT of the SYCP3 polymorphism was significantly associated with azoospermia.

• 생명과학회지
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• 제26권11호
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• pp.1336-1340
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• 2016

최근에 장수풍뎅이(Allomyrina dichotoma)는 관상용으로 인기가 높으며, 애벌레는 건강보조식품으로 주목을 받고 있다. 장수풍뎅이의 대량사육 시 발생하는 질병의 원인이 Oryctes rhinoceros nudivirus (OrNV)인 것이 2015년에 처음 보고되었다. 그러나 아직 정확한 진단, 발병기전과 치료방법을 찾지 못하고 있으며 곤충 사육농가에 매년 심각한 경제적 손실을 입고 있다. 본 연구는 장수풍뎅이의 대량사육 시 발생하는 OrNV질병의 조기진단과 치료에 실마리를 제공하기 위하여 OrNV에 감염된 장수풍뎅이의 장(intestine)에서 유전자발현이 조절되는 Klf15, ERAP2, Snrnp200, mbnl2a, MIMI_L93를 보고한다.

• 한국환경과학회지
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• 제23권8호
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• pp.1447-1453
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• 2014

The differentiation of sex is important for species preservation. However, Fairy Pitta is sexually monomorphic and sex of an individual is indistinguishable with its external characteristics. We determined the sex of Fairy Pitta through DNA analysis and investigated the causes and time of injury and mortality and the size based on sex. We collected 21 samples at Jeju Island, Korean Peninsula from 2004 to 2013 and extracted DNA from them and amplified chromo helicase DNA-binding gene from Z and W chromosomes through Polymerase Chain Reaction (PCR). We confirmed their sex with the banding pattern through Agarose gel electrophoresis, i.e. male (ZZ): one banded and female (ZW) two banded. We distinguished the sex of 17 of 21 samples resulting in 9 males and 8 females. Most casualties were recorded in adult of both sexes. Causes of injury and mortality proved that female casualties occurred from window strikes, dehydration, car accident, predation by natural enemies, and male occurred from window strikes, car accident and dehydration. The time of injury and mortality in adults differ by sex. There was no difference between sexes in any of the six size parameters. As the time of injury and mortality differ by sex, the survey on the role and ecological nature by sex in breeding season must be carried out in the future. External measurements may not be reliable for sexing of Fairy Pitta and other traits such as vocal or characteristics are required to identify the sex of individuals in the field.

• 생명과학회지
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• 제14권2호
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• pp.325-330
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• 2004

효모에 있어 자외선에 의한 절제회복 관여 DNA회복유전자가 많이 알려져 있으나, 이들이 어떤 기능을 하는지는 아직 잘 알려져 있지 않다. 본 연구에서는 자외선 조사 시 절제회복의 초기 단계에 절대적으로 필요한 RAD3 유전자와 유사한 유전자인 HRD3 유전자를 분열형 효모인 Schizosaccharomyces pombe에서 분리하여 그 특성을 연구하였다. 이 결과 분리한 유전자는 효모 RAD3 유전자와 염기서열에서 약 70%이상의 유사성을 보였다. 이 유전자의 염기서열 결과 유전자 산물의 분자량은 75 kDa였다. 2-D gel 결과 과잉발현 시 HRD3 단백질은 숙주 단백질의 합성 억제 또는 분해 촉진을 유발하여 숙주세포인 대장균에 독성초과를 나타내었다. HRD3 유전자와 lacZ 유전자를 융합시킨 여러 가지 재조합 vector를 만들어 이들 융합단백질을 분리, 연구 한 결과 HRD3 단백질의 카르복실 말단부분이 효모에 있어서 DNA회복기능과 대장균에서의 독성효과를 나타내는 중요부위임이 확인되었다.

• 생명과학회지
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• 제19권8호
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• pp.1159-1163
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• 2009

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOX04, AP-1, FOX03, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다.