• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1525-1531
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• 2015

Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.

• Journal of Microbiology and Biotechnology
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• 제8권2호
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• pp.146-151
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• 1998

The aminoglycoside multiple-resistance determinant from Streptoalloteichus hindustanus was cloned into Streptomyces lividans and named nbrB. The 1.2-kb ApaI- BclI fragment encompassing nbrB was located within a 2.6-kb ApaI fragment by successive subcloning experiments. The complete DNA nucleotide sequence of 1.2-kb containing nbrB was determined. The sequence contains an open reading frame that putatively encodes a polypeptide of 281 amino acids with a predicted molecular weight of 30,992. The deduced amino acid sequence of nbrB shows identities of 85.1% to kgmB of S. tenebrarius, 59.6% to sgm of Micromonospora zionensis, and 57.7% to grm of M. rosea. The similarity of nbrB to kgmB suggests that nbrB encodes a 16S rRNA methylase similar to that encoded by kgmB and that both genes might be derived from a common ancestral gene.

• 한국환경농학회지
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• 제41권4호
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• pp.335-343
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• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• BMB Reports
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• 제42권12호
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• pp.834-839
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• 2009

DNA methyltransferase (DNMT) 1 is the key enzyme responsible for DNA methylation, which often occurs in CpG islands located near the regulatory regions of genes and affects transcription of specific genes. In this study, we examined the possible association of DNMT1 polymorphisms with HBV clearance and the risk of hepatocellular carcinoma (HCC). Seven common polymorphic sites were selected by considering their allele frequencies, haplotype-tagging status and LDs for genotyping in larger-scale subjects (n = 1,100). Statistical analysis demonstrated that two intron polymorphisms of DNMT1, +34542G > C and +38565G > T, showed significant association with HBV clearance in a co-dominant model (OR = 1.30, $P^{corr}$ = 0.03) and co- dominant/recessive model (OR = 1.34-1.74, $P^{corr}$ = 0.01-0.03), respectively. These results suggest that two intron polymorphisms of DNMT1, +34542G > C and +38565G > T, might affect HBV clearance.

• Molecules and Cells
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• 제25권1호
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• pp.30-42
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• 2008

The disease-specific (dsp) region and the hypersensitive response and pathogenicity (hrp) genes, including the hrpW, $hrpN_{Ep}$, and hrpC operons have previously been sequenced in Erwinia pyrifoliae WT3 [Shrestha et al. (2005a)]. In this study, the remaining hrp genes, including the hrpC, hrpA, hrpS, hrpXY, hrpL and hrpJ operons, were determined. The hrp genes cluster (ca. 38 kb) was comprised of eight transcriptional units and contained nine hrc (hrp conserved) genes. The genetic organization of the hrp/hrc genes and their orientation for the transcriptions were also similar to and collinear with those of E. amylovora, showing ${\geq}80%$ homologies. However, ORFU1 and ORFU2 of unknown functions, present between the hrpA and hrpS operons of E. amylovora, were absent in E. pyrifoliae. To determine the HR active domains, several proteins were prepared from truncated fragments of the N-terminal and the C-terminal regions of $HrpN_{Ep}$ protein of E. pyrifoliae. The proteins prepared from the N-terminal region elicited HR, but not from those of the C-terminal region indicating that HR active domains are located in only N-terminal region of the $HrpN_{Ep}$ protein. Two synthetic oligopeptides produced HR on tobacco confirming presence of two HR active domains in the $HrpN_{Ep}$. The HR positive N-terminal fragment ($HN{\Delta}C187$) was further narrowed down by deleting C-terminal amino acids and internal amino acids to investigate whether amino acid insertion region have role in faster and stronger HR activity in $HrpN_{Ep}$ than $HrpN_{Ea}$. The $HrpN_{Ep}$ mutant proteins $HN{\Delta}C187$ (D1AIR), $HN{\Delta}C187$ (D2AIR) and $HN{\Delta}C187$ (DM41) retained similar HR activation to that of wild-type $HrpN_{Ep}$. However, the $HrpN_{Ep}$ mutant protein $HN{\Delta}C187$ (D3AIR) lacking third amino acid insertion region (102 to 113 aa) reduced HR when compared to that of wild-type $HrpN_{Ep}$. Reduction in HR elicitation could not be observed when single amino acids at different positions were substituted at third amino acids insertion region. But, substitution of amino acids at L103R, L106K and L110R showed reduction in HR activity on tobacco suggesting their importance in activation of HR faster in the $HrpN_{Ep}$ although it requires further detailed analysis.

• Journal of Korean Neurosurgical Society
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• 제59권6호
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• pp.650-654
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• 2016

Intrathoracic meningoceles are relatively rare entities found in patients with neurofibromatosis type I (NF1). Given that both the BRCA1 and NF-1 genes are located on the same long arm of chromosome 17, one would expect concurrence of neurofibromatosis and breast cancer. However, incidence of such co-disorders is very rare in the literature. Here, the authors report a case of a 50-year-old female patient with NF-1 and concurrent cancer of the left breast, who had a huge bilobulated intrathoracic meningocele with thoracic dystrophic scoliosis, treated surgically via a posterior-only approach for the meningocele and spinal deformity in the same setting.

• Genomics & Informatics
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• 제8권2호
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• pp.86-89
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• 2010

Closely related species share large genomic segments called syntenic regions, where the genomic elements such as genes are arranged co-linearly among the species. While synteny is an important criteria in establishing orthologous regions between species, non-syntenic regions may display species-specific features. As the first step in cataloging human- or primate- specific genomic elements, we surveyed human genomic regions that are not syntenic with any other non-primate mammalian genomes sequenced so far. Based on the data compiled in Ensembl databases, we were able to identify 10 such regions located in eight different human chromosomes. Interestingly, most of these highly human- or primate- specific loci are concentrated in subtelomeric or pericentromeric regions. It has been reported that subtelomeric regions in human chromosomes are highly plastic and filled with recently shuffled genomic elements. Pericentromeric regions also show a great deal of segmental duplications. Such genomic rearrangements may have caused these large human- or primate- specific genome segments.

• International Journal of Industrial Entomology and Biomaterials
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• 제2권1호
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• pp.87-89
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• 2001

The nucleotide sequence of the domestic silkworm (Bombyx mori) mitochondrial (mt) control region and its flanking genes was determined from PCR clones. The control region of the silkworm mt genome was located between the small ribosomal RNA gene and transfer RN $A^{Met}$. This 499 bp control region hale 95.4% A+T content. Extensive comparative analysis studies performed with similar control region of other insect genomes could not reveal a highly conserved region containing conserved motifs of animal mito-chondrial genome. The remarkable feature that found in this control region was the presence of tandem motifs containing nine repetitive sequences. The potential usefulness of this motif sequences for Bombyx species or their taxonomically related species is enhanced by its unique localization in the maternally inheritance mitochondrial molecule.e.

• Journal of Microbiology and Biotechnology
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• 제32권12호
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• pp.1527-1536
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• 2022

Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA-ylbE-ylbF-ybcF that is located downstream of the allDCE-operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA, ylbE, ylbF, and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The V_max is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the K_M value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK.

• KSBB Journal
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• 제26권2호
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• pp.131-138
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• 2011

Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.