• Genomics & Informatics
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• 제21권3호
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• Fisheries and Aquatic Sciences
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• 제20권10호
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• pp.26.1-26.9
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• 2017

Fishes in genus Sardinella are small pelagic species, which plays an important role in marine ecosystem as the first consumer. Those species are also commercially important, whose total catch reaches 278,600 tons in 2011 in Indonesia, but their identification has been difficult for their morphological similarity. In this study, we reported Sardinella jussieu for the first time in Indonesian coastal area (Banten Bay, Indonesia, $6^{\circ}\;0^{\prime}\;50.00^{{\prime}{\prime}}\;S-106^{\circ}\;10^{\prime}\;21.00^{{\prime}{\prime}}\;E$). We were able to confirm the species by both its morphological characteristics including the black spot at dorsal fin origin, the dusky pigmentation at caudal fin, 31 total scute numbers, and DNA sequence identity in the GenBank database by the molecular analysis. Its total mitochondrial genome was determined by the combination of next-generation sequencing and typical PCR strategy. The total mitochondrial genome of Sardinella jussieu (16,695 bp) encoded 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and the putative control region. All protein-coding genes started with ATG and typical stop codon and ended with TAA or TAG except for ND4 in which AGA is used. Phylogenetic analyses of both COI region and full mitochondrial genome showed that S. jussieu is most closely related to Sardinella albella and Sardinella gibbosa

• 한국축산식품학회지
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• 제35권1호
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• pp.86-90
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• 2015

In this study, we reported the morphogenetic analysis and genome sequence by genomic analysis of the newly isolated staphylococcal phage SMSAP5 from soil of slaughterhouses for cattle. Based on transmission electron microscopy evident morphology, phage SMSAP5 belonged to the Siphoviridae family. Phage SMSAP5 had a double-stranded DNA genome with a length of 45,552 bp and 33 % G+C content. Bioinformatics analysis of the phage genome revealed 43 open reading frames. A blastn search revealed that its nucleotide sequence shared a high degree of similarity with that of the Staphylococcus phage tp310-2. In conclusion, this study is the first report to show the morphological features and the complete genome sequence of the phage SMSAP5 from soil of slaughterhouses for cattle.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2004년도 The 13th Korea Genome Conference
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• pp.47.2-47.2
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• 2004

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.815-820
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• 2003

A huge database resulted from whole genome sequencing has provided a possibility of new information that is likely to extent the scope and thus changes the way of approach for the functional assigning of putative open reading frames annotated by whole genome sequence analyses. These are mainly realized by ease, one-step identification of putative genes using genomics or proteomics tools. A major challenge remained in biotechnology may translate these informations into better ways to screen or select a gene as a representative sequence. Further attempts to mine the related whole genes or partial DNA fragment from whole genome treasure, and then the incorporation of these sequences into a representative template, will result in the use of putative genes that can be translated into functional proteins or allowed the generation of new lineages as a valuable pool. Such screens enable rapid biochemical analysis and easy isolation of the target activity, thereby accelerating the screening of novel enzymes from the expanded library with related sequences. Information-based PCR amplification of whole genes and reconstitution of functional DNA fragments will provide a platform for expanding the functional spaces of potential enzymes, especially when used mixed- or metagenome as gene resources.

• BMB Reports
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• 제54권2호
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• pp.98-105
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• 2021

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a family of DNA sequences originally discovered as a type of acquired immunity in prokaryotes such as bacteria and archaea. In many CRISPR systems, the functional ribonucleoproteins (RNPs) are composed of CRISPR protein and guide RNAs. They selectively bind and cleave specific target DNAs or RNAs, based on sequences complementary to the guide RNA. The specific targeted cleavage of the nucleic acids by CRISPR has been broadly utilized in genome editing methods. In the process of genome editing of eukaryotic cells, CRISPR-mediated DNA double-strand breaks (DSB) at specific genomic loci activate the endogenous DNA repair systems and induce mutations at the target sites with high efficiencies. Two of the major endogenous DNA repair machineries are non-homologous end joining (NHEJ) and homology-directed repair (HDR). In case of DSB, the two repair pathways operate in competition, resulting in several possible outcomes including deletions, insertions, and substitutions. Due to the inherent stochasticity of DSB-based genome editing methods, it was difficult to achieve defined single-base changes without unanticipated random mutation patterns. In order to overcome the heterogeneity in DSB-mediated genome editing, novel methods have been developed to incorporate precise single-base level changes without inducing DSB. The approaches utilized catalytically compromised CRISPR in conjunction with base-modifying enzymes and DNA polymerases, to accomplish highly efficient and precise genome editing of single and multiple bases. In this review, we introduce some of the advances in single-base level CRISPR genome editing methods and their applications.

• 미생물학회지
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• 제55권1호
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• pp.58-60
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• 2019

혐기성 그람 음성 세균인 Prevotella intermedia는 사람의 구강 내 정상세균총의 하나이고 다양한 구강 및 전신 질환과 관련이 있다. 본 논문에서는 경부안면형 방선균증으로부터 분리된 P. intermedia ATCC 15032 균주의 유전체 염기서열을 분석하여 보고한다. 이 균주의 유전체는 2,848,426 bp의 크기로 GC 함량은 43.45%이다. 이 유전체 서열 정보는 P. intermedia 종 내에서의 균주 간 유전체 다양성 및 표현형 차이의 유전적 기초를 이해하는데 중요한 정보를 제공할 것이다.

• Genomics & Informatics
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• 제1권1호
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• pp.50-54
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• 2003

Genome of an extreme thermophile, Thermus caldophilus GK24 has been analyzed to construct the genomic map. The genomic DNAs encapsulated in agarose gel were digested with SspI, EcoRI, SpeI, and HpaI restriction endonucleases, and then the resulting genomic DNA fragments were analyzed by pulsed-field gel electrophoresis. Its restriction map has been constructed by analyzing sizes of the restriction fragments obtained from both complete and partial digestions. The circular form of its genome was composed of about 1.98 Mbp and a megaplasmid. The genomic loci for the genes of xylose isomerase, thioredoxin, tRNA-16S rRNA, 23S rRNA, L5 ribosomal protein, ADP-glucose pyrophosphorylase, DNA-ligase, and Tca DNA polymerase were determined by both Southern hybridization and PCR.

• Journal of Microbiology and Biotechnology
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• 제33권7호
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• pp.875-885
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• 2023

Volatile organic compounds such as benzene, toluene, ethylbenzene, and isomers of xylenes (BTEX) constitute a group of monoaromatic compounds that are found in petroleum and have been classified as priority pollutants. In this study, based on its newly sequenced genome, we reclassified the previously identified BTEX-degrading thermotolerant strain Ralstonia sp. PHS1 as Cupriavidus cauae PHS1. Also presented are the complete genome sequence of C. cauae PHS1, its annotation, species delineation, and a comparative analysis of the BTEX-degrading gene cluster. Moreover, we cloned and characterized the BTEX-degrading pathway genes in C. cauae PHS1, the BTEX-degrading gene cluster of which consists of two monooxygenases and meta-cleavage genes. A genome-wide investigation of the PHS1 coding sequence and the experimentally confirmed regioselectivity of the toluene monooxygenases and catechol 2,3-dioxygenase allowed us to reconstruct the BTEX degradation pathway. The degradation of BTEX begins with aromatic ring hydroxylation, followed by ring cleavage, and eventually enters the core carbon metabolism. The information provided here on the genome and BTEX-degrading pathway of the thermotolerant strain C. cauae PHS1 could be useful in constructing an efficient production host.