• Journal of Energy Engineering
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• v.22 no.3
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• pp.250-261
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• 2013

In order to overcome the 21st century's challenges such as national energy supply security, global warming, and resource depletion, we are struggling to accelerate the paradigm shift in our life style from fossil fuel-based economy to biomass-based economy. In the context of sustainable bioeconomy revitalization, we comprehensively review the development status of the biorefinery as a system for bioenergy/biochemicals co-products on the basis of the various categories according to six criteria.

• Journal of Ginseng Research
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• v.19 no.2
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• pp.127-133
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• 1995

The complete open reading frame (ORF) of o-subunit of the $F_1$ ATP synthase (atPA) in Korean ginseng mitochondria was identified by the sequence similarity with atPA genes in other plant mitochondria. The sequence alignment showed that the common translation initiation codon, ATG, in plant genes was replaced with GTG valid codon in Korean ginseng. The atPA gene from GTG to TGA termination codon was 1524 nucleotides long, and the sequence homology of nucleotides and deduced amino acids revealed high values of 92~97%. A deletion event of 6 nucleotides was observed at the 1468th nucleotide from the GTG in Korean ginseng, in contrast to that at the 1450th in other plants such as pea, common bean, soybean, sugar beet, and radish. An unidentified open reading frame (on7) was observed upstream of atmA ORF. No other ATG as an initiation codon was detected in the region between off and atmA ORF in Korean ginseng, although a pyrimidine cluster "TTTTCTTTT" was located in this region as in Oenothera and maize genes. It could be supposed that GTG codon in atpA gene of Korean ginseng mitochondria would act as an initiation codon as in microbial genes.ial genes.

• Journal of Veterinary Science
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• v.21 no.6
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• pp.73.1-73.10
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• 2020

Background: Bovine papilloma is a neoplastic disease caused by bovine papillomaviruses (BPVs), which were recently divided into 5 genera and at least 24 genotypes. Objectives: The complete genome sequence of BPV type 15 (BPV Aks-02), a novel putative BPV type from skin samples from infected cows in Southern Xinjiang China, was determined by collecting warty lesions, followed by DNA extraction and amplicon sequencing. Methods: DNA was analyzed initially by polymerase chain reaction (PCR) using the degenerate primers FAP59 and FAP64. The complete genome sequences of the BPV Aks-02 were amplified by PCR using the amplification primers and sequencing primers. Sequence analysis and phylogenetic analysis were performed using bio-informatic software. Results: The nucleotide sequence of the L1 open reading frame (ORF) of BPV Aks-02 was 75% identity to the L1 ORF of BPV-9 reference strain from GenBank. The complete genome consisted of 7,189 base pairs (G + C content of 42.50%) that encoded 5 early (E8, E7, E1, E2, and E4) and 2 late (L1 and L2) genes. The E7 protein contained a consensus CX₂CX₂₉CX₂C zinc-binding domain and a LxCxE motif. Among the different members of this group, the percentages of the complete genome and ORFs (including 5 early and 2 late ORFs) sequence identity of BPV Aks-02 were closer to the genus Xipapillomavirus 1 of the Xipapillomavirus genus. Phylogenetic analysis and sequence similarities based on the L1 ORF of BPV Aks-02 revealed the same cluster. Conclusions: The results suggest that BPV type (BPV Aks-02) clustered with members of the Xipapillomavirus genus as BPV 15 and were closely related to Xipapillomavirus 1.

• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.258-263
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• 2000

2-Hydroxy-6-oxo-6phenylhexa-2,4-dienoate (HOPDA) hydrolase catalyzes the hydrolytic cleavage of HOPDA to bemzpate and 2-hydroxypenta-2, 4-dienoate (HPD) during microbial catabolism of biphenyl and polychlorinated biphenyls. A HOPDA hydrolase gene (pcbD) was isolated from the genomic library of Pseudomonas sp. P20 and designated as pCNUO1201; a 7.5-kb XbaI DNA fragment from Pseudomonas sp. P20 was inserted into the pBluescript SK(+) XbaI site. E. coli HB101 harboring pCNU1201 exhibited HOPDA hydrolase activity. The open reading frame (ORF) corresponding to the pcbD gene consisted of 855 base pairs with an ATG initiation codon and a TGA termination codon. The ORF was preceded by a rebosome-binding sequence of 5'-TGGAGC-3' and its G+C content was 55 mol%. The pcbD gene of Pseudomonas sp. P20 was located immedeately downstream of the pcbC gene encoding 2,3- dihydroxybiphenyl 1,2-dioxygenase, and approximately 4-kb upstream of the pcbE gene encoding HPD hydratase. The pcbK gene was able to encode a polypeptide with a molecular weight of 31,732 containing 284 amino acid residues. The deduced amino acid sequence of the HOPDA hydrolase of Pseudomonas sp. P20 exhibited high identity (62%) with those of the HOPDA hydrolases of P. putida KF715, P. pseudoalcaligenes KF707, and Burkholderia cepacia LB400, and also significant homology with those of other hydrolytic enzymes including esterase, transferase, and peptidase.

• BMB Reports
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• v.37 no.2
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• pp.206-212
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• 2004

The genes that are located within the odvp-6e/odv-e56 region of the Choristoneura fumiferana granulovirus (ChfuGV) were identified by sequencing the 11 kb BamHI restriction fragment on the ChfuGV genome. The global GC content that was calculated from the data obtained from this genomic region was 34.96%. The open-reading frames (ORFs), located within the odvp-6e/odv-e56 region, are presented and compared to the equivalent ORFs that are located at the same region in other GVs. This region is composed of 14 ORFs, including three ORFs that are unique to ChfuGV with no obvious homologues in other baculoviruses as well as eleven ORFs with homologues to granuloviral ORFs, such as granulin, CfORF2, pk-1, ie-1, odv-e18, p49, and odvp-6e/odv-e56. In this study, the conceptual products of seven major conserved ORFs (granulin, CfORF2, IE-1, ODV-E18, p49 and ODVP-6E/ODV-E56) were used in order to construct phylogenetic trees. Our results show that granuloviruses can be grouped in 2 distinct groups as follows: Group I; Choristoneura fumiferana granulovirus (ChfuGV), Cydia pomonella granulovirus (CpGV), Phthorimaea operculella granulovirus (PhopGV), and Adoxophyes orana granulovirus (AoGV). Group II; Xestia c-nigrum granulovirus (XcGV), Plutella xylostella granulovirus (PxGV), and Trichoplusia ni granulovirus (TnGV). The ChfuGV conserved proteins are most closely related to those of CpGV, PhopGV, and AoGV. Comparative studies, performed on gene arrangements within this region of genomes, demonstrated that three GVs from group I maintain similar gene arrangements.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.748-755
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• 2014

In the genome annotation of Escherichia coli MG1655, the orf382 (1,149 bp) is designated as a gene encoding an alcohol dehydrogenase that may be Fe-dependent. In this study, the gene was amplified from the genome by PCR and overexpressed in Escherichia coli BL21(DE3). The recombinant $6{\times}$His-tag protein was then purified and characterized. In an enzymatic assay using different hydroxyl-containing substrates (n-butanol, $\small{L}$-threonine, ethanol, isopropanol, glucose, glycerol, $\small{L}$-serine, lactic acid, citric acid, methanol, or $\small{D}$-threonine), the enzyme showed the highest activity on $\small{L}$-threonine. Characterization of the mutant constructed using gene knockout of the orf382 also implied the function of the enzyme in the metabolism of $\small{L}$-threonine into glycine. Considering the presence of tested substrates in living E. coli cel ls and previous literature, we believed that the suitable nomenclature for the enzyme should be an $\small{L}$-threonine dehydrogenase (LTDH). When using $\small{L}$-threonine as the substrate, the enzyme exhibited the best catalytic performance at $39^{\circ}C$ and pH 9.8 with $NAD^+$ as the cofactor. The determination of the Km values towards $\small{L}$-threonine (Km = $11.29{\mu}M$), ethanol ($222.5{\mu}M$), and n-butanol ($8.02{\mu}M$) also confirmed the enzyme as an LTDH. Furthermore, the LTDH was shown to be an ion-containing protein based on inductively coupled plasma-atomic emission spectrometry with an isoelectronic point of pH 5.4. Moreover, a circular dichroism analysis revealed that the metal ion was structurally and enzymatically essential, as its deprivation remarkably changed the ${\alpha}$-helix percentage (from 12.6% to 6.3%).

• Journal of Veterinary Clinics
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• v.21 no.2
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• pp.102-108
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• 2004

Orf virus (ORFV), a member of genus Parapoxvirus (family-Poxviridae), a causative agent of contagious ecthyma in sheep and goat leading to a condition commonly known as vesicular dermatitis. Recently, twelve goats from Iksan in Jeonbuk province were observed with clinical signs like necrotic vesicular lesions around the mucosa of mouth, nasal cavity, eye, ear, teats, abdomen and groin. Based on these clinical symptoms, contagious ecthyma infection was suspected. The skin scrapping was collected from lesions for isolation of DNA and subsequent PCR amplification of ORFV specific 235 bp region of B2L gene. All of the samples were found positive by PCR analysis. Sequencing and further phylogenetic analysis of the PCR product revealed 100% identity to Japan isolate of ORFV (Okinawa, GenBank accession number AB080769), and showed 99.6% of similarity to New Zealand strain (NZ-2, GenBank accession number U06671). It was concluded that ORFV strain detected in the present study is homologous to Japan isolate and New Zealand strain. The PCR test based on amplification of B2L gene is a highly useful tools for rapid and specific diagnosis of contagious ecthyma.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.402-406
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• 2005

Lipomyces starkeyi produces a novel glucanhydrolase containing endo-dextranase and ${\alpha}-amylase$ activities. A cDNA from L. starkeyi encoding a dextranase was isolated and characterized. The 2,052 kb cDNA fragment (lsd1) carrying dextranase gene showed one open reading frame (ORF) composed of 1,824 bp flanked by a 41 bp 5'-UTR and a 184 bp 3'-UTR including a poly(A) tail of 27 bp. The ORF encodes for a 608 amino acid with a predicted molecular mass of 67.6 kDa. There was 77% deduced amino acid sequence identity between the LSD1 dextranase and the dextranase from Penicillium minioluteum. The primary structure of the dextranase from L. starkeyi has distant similarity with enzymes belonging to glycosyl hydrolase family 49. The lsd1 protein was expressed in the Saccharmyces cerevisiae under control of GAL1 promoter and active dextranase was produced.

• Journal of Plant Biology
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• v.36 no.4
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• pp.415-423
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• 1993

대두의 uricase II cDNA를 탐침으로 plaque 혼성화 방법에 의해 해녀콩의 뿌리를 cDNA library로부터의 두 개의 phage 클론(λCINUO-01, λCINUO-02)을 선별하였다. 두 phage 클론은 약 1.6 kb와 1.0 kb의 insert를 갖고 있었으며 이들의 염기서열을 결정하기 위하여 pUC19과 pBSKS vector에 subcloing(pcCLNUO-01, pcCLNUO-02)하였다. Sanger법에 의해 염기서열을 결정한 결과, 두 클론은 각각 1,611 bp와 1,024 bp로 이루어져 있었으며 pcCINUO-01은 308개의 아미노산, pcCINUO-02는 301개의 아미노산을 암호화하는 open reading frame(ORF)을 갖고 있었다. 두 클론의 ORF의 염기서열은 대두의 uricase II와 각각 88.9%, 89.3%의 상동성을 보여주었으며, 아미노산 서열은 84.1%, 85.4%의 상동성을 보여주었다. pcCINUO-01의 경우, 종결코돈으로부터 313 NT 하류쪽에 진핵생물의 poly(A) 첨가신호인 AATAAA 서열이 존재하였으며 이로부터 21 NT 하류쪽에 17 잔기의 poly(A)가 존재하였다. 두 클론의 염기서열에서 추정된 아미노산 서열의 카르복시 말단에는 세포질에서 합성된 몇몇 단백질들이 peroxisome으로 수송되는데 필요한 신호서열인 Ser-Lys-Leu-COOH 서열이 존재하고 있었다. 두 클론의 염기서열을 토대로 아미노산 조성을 살펴본 결과, 염기성 아미노산(Arg, His, Lys)과 산성 아미노산(Asp, Glu)이 각각 46 대 35, 47 대 35의 비를 보여주었는데 이는 uricase II 단백질의 염기성 성질을 보여주는 결과로 추정된다. Northern 혼성화 결과 해녀콩에서 uricase II는 뿌리혹에서만 특이적으로 발현됨을 알 수 있었고 게놈 혼성화 반응 결과는 uricase II 유전자가 해녀콩 게놈상에 유전자 가족으로는 존재할 수 있음을 보여주었다.

• Korean Journal of Microbiology
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• v.30 no.6
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• pp.456-459
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• 1992

The genes of Halohacteria. gvpD and gvpE. take part in formation of gas vesicle. These mRNA cause a lot of experimental prohlems due to its eharacteristic instahility in the analysis of transcripts. This study allowed easy cloning and sequencing of RNA hy substituting a stable complementary DNA for the mRNA of the genes for an analysis. The weak 111 RNA was reverse transcribed to DNA using reverse transcriptase. and was amplified using PCR method. The transcripts confirmed in this ~,tudy have not heen round in the northern hybridization covering almost all ranges of ORF of the gene. gvpD.