• Journal of Microbiology and Biotechnology
• /
• v.17 no.1
• /
• pp.29-36
• /
• 2007

The xynA gene encoding the xylanase A of Paenibacillus sp. DG-22 was isolated with a DNA probe obtained by PCR amplification, using degenerated primers deduced from the amino acid residues of the known N-terminal region of the purified enzyme and the conserved region in the family 11 xylanases. The positive clones were screened on the LB agar plates supplemented with xylan, by the Congo-red staining method. The xynA gene consists of a 630-bp open reading frame encoding a protein of 210 amino acids, and the XynA preprotein contains a 28-residues signal peptide whose cleavage yields a l82-residues mature protein of a calculated molecular weight of 20,000Da and pI value of 8.77. The cloned DNA fragment also has another ORF of 873 nucleotides that showed 76% identity to the putative transcriptional activator of Bacillus halodurans C-125. Most of the xylanase activity was found in the periplasmic space of E. coli. The xynA gene was subcloned into pQE60 expression vector to fuse with six histidine-tag. The recombinant xylanase A was purified by heating and immobilized metal affinity chromatography. The optimum pH and temperature of the purified enzyme were 6.0 and $60^{\circ}C$, respectively. This histidine-tagged xylanase A was less thermostable than the native enzyme.

• Journal of Microbiology and Biotechnology
• /
• v.4 no.4
• /
• pp.256-263
• /
• 1994

The aceB gene, encoding for malate synthase, one of the key enzymes of glyoxylate bypass, was isolated from a pMT1-based Corynebacterium glutamicum gene library via complementation of an Escherichia coli aceB mutant on an acetate minimal medium. The aceB gene was closely linked to aceA, separated by 598 base pairs, and transcribed in divergent direction. The aceB expressed a protein product of Mr 83, 000 in Corynebacterium glutamicum which was unusually large compared with those of other malate synthases. A DNA-sequence analysis of the cloned DNA identified an open-reading frame of 2, 217 base pairs which encodes a protein with the molecular weight of 82, 311 comprising 739 aminoo acids. The putative protein product showed only limited amino acid-sequence homology to its counteliparts in other organisms. The N-terminal region of the protein, which shows no apparent homology with the known sequences of other malate synthases, appeared to be responsible for the protein s unusually large size. A potential calciumbinding domain of EF-hand structure found among eukaryotes was detected in the N-terminal region of the deduced protein.

• Journal of Microbiology and Biotechnology
• /
• v.10 no.2
• /
• pp.221-226
• /
• 2000

Cephalosporin-C deacetylase (CAH) catalyzes the deacetylation of cephalosporin derivatives. A novel gene encoding the CAH from Bacillus sp. KCCM10143 was cloned and sepuenced. The uncleotide sequence contained an open reading frame encoding a polypeptide consisting of 217 amino acids and a molecular weight of 24 kDa which was in good agreement with the value obtained by sodium dodecylsulfate-polyacrylamide gel electrophoresis. An expression plasmid was constructed by inserting the CAH gene into the region of the pTrc99A expression vector. An active from of the CAH protein was expressed in the soluble fraction obtained after cell disruption. in fermentation using a 5-1 jar fementer, the transformant E. coli JM109 (pDST654) produced 4.12 U of CAH per ml of culture during 16 h of incubation.

• Journal of Aquaculture
• /
• v.17 no.1
• /
• pp.62-68
• /
• 2004

A cDNA encoding the masu salmon, Oncorhynchus masou, estrogen receptor $\alpha$ (msER$\alpha$) was cloned from the pituitary gland by polymerase chain reaction (PCR). This cDNA contains an open reading frame encoding 513 amino acid residues, and the calculated molecular weight of this protein is about 56,430 Dalton. The amino acid sequences of the DNA binding and ligand binding domains of msER$\alpha$ showed high homology to those of other fish species (84-100%). Reverse transcription PCR analysis showed that the mRNA level of msER$\alpha$ in the pituitary was slightly higher in estradiol-17$\beta$(E2) injected masu salmon than that of control fish. To test the biological activity of msER$\alpha$, the cDNA was ligated to a mammalian expression vector and transfected into a gonadotrope-derived cell line, L$\beta$T2, with a reporter plasmid including estrogen responsive element. Expression of the reporter protein, luciferase, was E2 and msER$\alpha$-dependent. The masu salmon ER$\alpha$ is structurally conserved among teleost species and functions as a transcriptional activator in the pituitary cells.

• ALGAE
• /
• v.27 no.1
• /
• pp.55-62
• /
• 2012

A novel lectin specific to N-acetyl-D-galactosamine as well as N-acetyl-D-glucosamine was isolated from Bryopsis plumosa and named as BPL-4. Sodium dodecyl sulfate polyacrylamide gel electrophorese (SDS-PAGE) and matrix-assisted laser desorption / ionization-time of flight (MALDI-TOF) mass spectrometry data showed that this lectin was a monomeric protein with molecular weight 12.9 kDa. The N-terminal amino acid sequences of the lectin were determined by Edman degradation and the full cDNA sequence encoding this lectin was obtained using the degenerate primers designed from the amino acid sequence. The size of the cDNA was 414 bp containing single open reading frame (ORF) encoding the lectin precursor. The homology analysis showed that this lectin might belong to H lectin group. BPL-4 showed high sequence similarity (60.6%) to BPL-3, which is a previously reported lectin from the same species. The comparative analysis on the lectin's primary structure showed two conserved domains including one possible active domain of H lectin group.

• Journal of Information Processing Systems
• /
• v.16 no.6
• /
• pp.1407-1423
• /
• 2020

A graph is a data structure consisting of nodes and edges between these nodes. Graph embedding is to generate a low dimensional vector for a given graph that best represents the characteristics of the graph. Recently, there have been studies on graph embedding, especially using deep learning techniques. However, until now, most deep learning-based graph embedding techniques have focused on unweighted graphs. Therefore, in this paper, we propose a graph embedding technique for weighted graphs based on long short-term memory (LSTM) autoencoders. Given weighted graphs, we traverse each graph to extract node-weight sequences from the graph. Each node-weight sequence represents a path in the graph consisting of nodes and the weights between these nodes. We then train an LSTM autoencoder on the extracted node-weight sequences and encode each nodeweight sequence into a fixed-length vector using the trained LSTM autoencoder. Finally, for each graph, we collect the encoding vectors obtained from the graph and combine them to generate the final embedding vector for the graph. These embedding vectors can be used to classify weighted graphs or to search for similar weighted graphs. The experiments on synthetic and real datasets show that the proposed method is effective in measuring the similarity between weighted graphs.

• BMB Reports
• /
• v.38 no.6
• /
• pp.668-675
• /
• 2005

A full-length cDNA encoding taxadiene synthase (designated as TmTXS), which catalyzes the first committed step in the Taxol biosynthetic pathway, was isolated from young leaves of Taxus media by rapid amplification of cDNA ends (RACE). The full-length cDNA of TmTXS had a 2586 bp open reading frame (ORF) encoding a protein of 862 amino acid residues. The deduced protein had isoelectric point (pI) of 5.32 and a calculated molecular weight of about 98 kDa, similar to previously cloned diterpene cyclases from other Taxus species such as T. brevifolia and T. chinenisis. Sequence comparison analysis showed that TmTXS had high similarity with other members of terpene synthase family of plant origin. Tissue expression pattern analysis revealed that TmTXS expressed strongly in leaves, weak in stems and no expression could be detected in fruits. This is the first report on the mRNA expression profile of genes encoding key enzymes involved in Taxol biosynthetic pathway in different tissues of Taxus plants. Phylogenetic tree analysis showed that TmTXS had closest relationship with taxadiene synthase from T. baccata followed by those from T. chinenisis and T. brevifolia. Expression profiles revealed by RT-PCR under different chemical elicitor treatments such as methyl jasmonate (MJ), silver nitrate (SN) and ammonium ceric sulphate (ACS) were also compared for the first time, and the results revealed that expression of TmTXS was all induced by the tested three treatments and the induction effect by MJ was the strongest, implying that TmTXS was high elicitor responsive.

• Microbiology and Biotechnology Letters
• /
• v.25 no.1
• /
• pp.23-29
• /
• 1997

The nucleotide sequence of the estI gene encoding acetylxylan esterase I of Bacillus stearothermophilus was determined and analyzed. The estI gene was found to consist of a 810 base pair open reading frame coding for a polypeptide of 270 amino acids with a deduced molecular weight of 30 kDa. This was in well agreement with the molecular weight (29 kDa) estimated by SDS-PAGE of the purified esterase. The coding sequence was preceded by a putative ribo some binding site 10 bp upsteam of the ATG codon. Further 53 bp upstream, the transcription initiation signals were identified. The putative $_{-}$10 sequence (TCCAAT) and $_{-}$35 seqence (TTGAAT) corresponded closely to the respective consensus sequences for the Bacillus subtiis major RNA polymerase. The G+C content of the coding region of the estI was 51% whereas that of the third position of codone was 60.2%. The N-terminal amino acid sequence of the EstI deduced from the nucleotide sequence perfectly matched the corresponding region of the purified esterase described previously. Comparison with the amino acid sequence of other esterases and lipases reported so far allowed us to identify a sequence, GLSMG at positions 123 to 127 of the EstI which was reported to be the highly conserved active site sequence for those enzymes. The nucleotide sequence of the estI revealed 55.7% homology to that of the xylC coding for the acetylxylan esterase of Caldocellum saccharolyticum.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
• /
• 2018.05a
• /
• pp.501-502
• /
• 2018

Traditional miniature micro-controllers focus on communication only because of memory capacity is low due to small size. Due to this, it is difficult to mount the UI for user convenience in the control system and a lot of functions cannot be added. To solve this problem, this paper proposes a weight reduction and encoding method for the control system. In addition, it is increased user convenience by overcoming the problem of difficulty in Korean system in the existing system. Also, we can add various functions to the memory space secured by system weight reduction.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.12 no.7
• /
• pp.3455-3474
• /
• 2018

As a unique form of signed-digit representation, non-adjacent form (NAF) minimizes Hamming weight by removing a stream of non-zero bits from the binary representation of positive integer. Thanks to this strong point, NAF has been used in various applications such as cryptography, packet filtering and so on. In this paper, to improve the NAF conversion speed of the $NAF_w$ algorithm, we propose a new NAF conversion algorithm, called w-bit Shifting Non-Adjacent Form($SNAF_w$), where w is width of scanning window. By skipping some unnecessary bit comparisons, the proposed algorithm improves the NAF conversion speed of the $NAF_w$ algorithm. To verify the excellence of the $SNAF_w$ algorithm, the $NAF_w$ algorithm and the $SNAF_w$ algorithm are implemented in the 8-bit microprocessor ATmega128. By measuring CPU cycle counter for the NAF conversion under various input patterns, we show that the $SNAF_2$ algorithm not only increases the NAF conversion speed by 24% on average but also reduces deviation in the NAF conversion time for each input pattern by 36%, compared to the $NAF_2$ algorithm. In addition, we show that $SNAF_w$ algorithm is always faster than $NAF_w$ algorithm, regardless of the size of w.