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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Journal DOI :
Korean Society for Biochemistry and Molecular Biology
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Volume & Issues
Volume 39, Issue 6 - Nov 2006
Volume 39, Issue 5 - Sep 2006
Volume 39, Issue 4 - Jul 2006
Volume 39, Issue 3 - May 2006
Volume 39, Issue 2 - Mar 2006
Volume 39, Issue 1 - Jan 2006
Selecting the target year
A New Approach to Managing Oral Manifestations of Sjogren's Syndrome and Skin Manifestations of Lupus
Hsu, Stephen ; Dickinson, Douglas ;
BMB Reports , volume 39, issue 3, 2006, Pages 229~239
DOI : 10.5483/BMBRep.2006.39.3.229
gren's syndrome (SS) is an autoimmune disorder that affects the salivary glands, leading to xerostomia, and the lacrimal glands, resulting in xerophthalmia. Secondary SS is associated with other autoimmune disorders such as systemic rheumatic diseases and systemic lupus erythematosis (SLE), which can affect multiple organs, including the epidermis. Recent studies have demonstrated that green tea polyphenols (GTPs) possess both anti-inflammatory and anti-apoptotic properties in normal human cells. Epidemiological evidence has indicated that, in comparison to the United States, the incidence of SS, clinical xerostomia and lupus is considerably lower in China and Japan, the two leading green tea-consuming countries. Thus, GTPs might be responsible, in part, for geographical differences in the incidence of xerostomia by reducing the initiation or severity of SS and lupus. Consistent with this, molecular, cellular and animal studies indicate that GTPs could provide protective effects against autoimmune reactions in salivary glands and skin. Therefore, salivary tissues and epidermal keratinocytes could be primary targets for novel therapies using GTPs. This review article evaluates the currently available research data on GTPs, focusing on their potential application in the treatment of the oral manifestations of SS and skin manifestations of SLE.
Compositional Correlations in Canine Genome Reflects Similarity with Human Genes
Joy, Faustin ; Basak, Surajit ; Gupta, Sanjib Kumar ; Das, Pranab Jyoti ; Ghosh, Shankar Kumar ; Ghosh, Tapash Chandra ;
BMB Reports , volume 39, issue 3, 2006, Pages 240~246
DOI : 10.5483/BMBRep.2006.39.3.240
The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of
composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of
composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.
Array-based Nano-amplification Technique Was Applied in Detection of Hepatitis E Virus
Liu, Hui-Hui ; Cao, Xuan ; Yang, Yong ; Liu, Ming-Gui ; Wang, Ye-Fu ;
BMB Reports , volume 39, issue 3, 2006, Pages 247~252
DOI : 10.5483/BMBRep.2006.39.3.247
A rapid method for the detection of Hepatitis E Virus (HEV) was developed by utilizing nano-gold labeled oligonucleotide probes, silver stain enhancement and the microarray technique. The 5'-end -
modified oligonucleotide probes were immobilized on the surface of the chip base as the capture probe. The detection probe was made of the 3'-end -SH modified oligonucleotide probe and nano-gold colloid. The optimal concentrations of these two probes were determined. To test the detection sensitivity and specificity of this technique, a conservative fragment of the virus RNA was amplified by the RT-PCR/PCR one step amplification. The cDNA was hybridized with the capture probes and the detection probes on microarray. The detection signal was amplified by silver stain enhancement and could be identified by naked eyes. 100 fM of amplicon could be detected out on the microarray. As the results, preparation of nano-gold was improved and faster. Development time also was shortened to 2 min. Thus, considering high efficiency, low cost, good specificity and high sensitivity, this technique is alternative for the detection of HEV.
Transduced Tat-α-Synuclein Protects against Oxidative Stress In vitro and In vivo
Choi, Hee-Soon ; Lee, Sun-Hwa ; Kim, So-Young ; An, Jae-Jin ; Hwang, Seok-Il ; Kim, Dae-Won ; Yoo, Ki-Yeon ; Won, Moo-Ho ; Kang, Tae-Cheon ; Kwon, Hyung-Joo ; Kang, Jung-Hoon ; Cho, Sung-Woo ; Kwon, Oh-Shin ; Choi, Jin-Hi ; Park, Jin-Seu ; Eum, Won-Sik ; Choi, Soo-Young ;
BMB Reports , volume 39, issue 3, 2006, Pages 253~262
DOI : 10.5483/BMBRep.2006.39.3.253
Parkinson's disease (PD) is a common neurodegenerative disorder and is characterized by the progressive loss of dopaminergic neurons in the substantia nigra. Although many studies showed that the aggregation of
-synuclein might be involved in the pathogenesis of PD, its protective properties against oxidative stress remain to be elucidated. In this study, human wild type and mutant
-synuclein genes were fused with a gene fragment encoding the nine amino acid trans activator of transcription (Tat) protein transduction domain of HIV-l in a bacterial expression vector to produce a genetic in-frame WT Tat-
-synuclein (wild type) and mutant Tat-a-synucleins (mutants; A30P and A53T), respectively, and we investigated the protective effects of wild type and mutant Tat-
-synucleins in vitro and in vivo. WT Tat-
-synuclein rapidly transduced into an astrocyte cells and protected the cells against paraquat induced cell death. However, mutant Tat-
-synucleins did not protect at all. In the mice models exposed to the herbicide paraquat, the WT Tat-
-synuclein completely protected against dopaminergic neuronal cell death, whereas mutants failed in protecting against oxidative stress. We found that these protective effects were characterized by increasing the expression level of heat shock protein 70 (HSP70) in the neuronal cells and this expression level was dependent on the concentration of transduced WT Tat-
-synuclein. These results suggest that transduced Tat-
-synuclein might protect cell death from oxidative stress by increasing the expression level of HSP70 in vitro and in vivo and this may be of potential therapeutic benefit in the pathogenesis of PD.
Characterization of ORF39 from Helicoverpa armigera Single-nucleocapsid Nucleopolyhedrovirus, the Gene Containing RNA Recognition Motif
Xu, Hai-Jun ; Liu, Yan-He ; Yang, Zhang-Nv ; Zhang, Chuan-Xi ;
BMB Reports , volume 39, issue 3, 2006, Pages 263~269
DOI : 10.5483/BMBRep.2006.39.3.263
In the genome of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus, open reading frame 39 (Ha39) is the only gene predicted to encode an RNA recognition protein. Computer analysis revealed that Ha39 homologues were found in 15 NPVs, but not in GVs. Its transcripts were detected from 3 through 72 hours post infection (h p.i.) using RT-PCR and Northern blot analysis. The protein was detected in infected-cell lysates from 6 h p.i. Western blot assay of ODV and BV preparations revealed that Ha39 encodes a structural protein associated with BVs. Additionally, immunofluorescence microscopy demonstrated that the protein was present within cytoplasm in virus-infected cells, but not in the nuclear region.
Novel Preparation and Characterization of the α4-loop-α5 Membrane-perturbing Peptide from the Bacillus thuringiensis Cry4Ba δ-endotoxin
Leetachewa, Somphob ; Katzenmeier, Gerd ; Angsuthanasombat, Chanan ;
BMB Reports , volume 39, issue 3, 2006, Pages 270~277
DOI : 10.5483/BMBRep.2006.39.3.270
Helices 4 and 5 of the Bacillus thuringiensis Cry4Ba
-endotoxin have been shown to be important determinants for mosquito-larvicidal activity, likely being involved in membrane-pore formation. In this study, the Cry4Ba mutant protein containing an additional engineered tryptic cleavage site was used to produce the
hairpin peptide by an efficient alternative strategy. Upon solubilization of toxin inclusions expressed in Escherichia coli and subsequent digestion with trypsin, the 130-kDa mutant protoxin was processed to protease-resistant fragments of ca. 47, 10 and 7 kDa. The 7-kDa fragment was identified as the
hairpin via N-terminal sequencing and mass spectrometry, and was successfully purified by size-exclusion FPLC and reversed-phase HPLC. Using circular dichroism spectroscopy, the 7-kDa peptide was found to exist predominantly as an
-helical structure. Membrane perturbation studies by using fluorimetric calcein-release assays revealed that the 7-kDa helical hairpin is highly active against unilamellar liposomes compared with the 65-kDa activated full-length toxin. These results directly support the role of the
hairpin in membrane perturbation and pore formation of the full-length Cry4Ba toxin.
Cloning, Characterization and Antifungal Activity of Defensin Tfgd1 from Trigonella foenum-graecum L.
Olli, Sudar ; Kirti, P.B. ;
BMB Reports , volume 39, issue 3, 2006, Pages 278~283
DOI : 10.5483/BMBRep.2006.39.3.278
Defensins are small cysteine rich peptides with a molecular mass of 5-10 kDa and some of them exhibit potent antifungal activity. We have cloned the coding region of a cDNA of 225 bp cysteine rich defensin, named as Tfgd1, from the legume Trigonella foenum-graecum. The amino acid sequence deduced from the coding region comprised 74 amino acids, of which the N-terminal 27 amino acids constituted the signal peptide and the mature peptide comprised 47 amino acids. The protein is characterized by the presence of eight cysteine resisdues, conserved in the various plant defensins forming four disulphide bridges, which stabilize the mature peptide. The recombinant protein expressed in E coli exhibited antifungal activity against the broad host range fungus, Rhizoctonia solani and the peanut leaf spot fungus, Phaeoisariopsis personata.
cDNA Cloning, Sequence Analysis and Molecular Modeling of a New Peptide from the Scorpion Buthotus saulcyi Venom
Nikkhah, Maryam ; Naderi-Manesh, Hossein ; Taghdir, Majid ; Talebzadeh, Mehdi ; Sadeghi-Zadeh, Majid ; Schaller, Janatan ; Sarbolouki, Mohamad N. ;
BMB Reports , volume 39, issue 3, 2006, Pages 284~291
DOI : 10.5483/BMBRep.2006.39.3.284
In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the
-strand1 to the
-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of
-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a
-toxin that competes with the depressant insect toxins for binding to
channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded
-sheet and a stretch of
-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.
2-D Graphical Representation for Characteristic Sequences of DNA and its Application
Li, Chun ; Hu, Ji ;
BMB Reports , volume 39, issue 3, 2006, Pages 292~296
DOI : 10.5483/BMBRep.2006.39.3.292
DNA sequencing has resulted in an abundance of data on DNA sequences for various species. Hence, the characterization and comparison of sequences become more important but still difficult tasks. In this paper, we first give a 2-D ladderlike graphical representation for the characteristic sequences of a DNA sequence, and then construct a 3-component vector, in which the normalized ALE-indices extracted from such three 2-D graphs via D/D matrices are individual components, to characterize the DNA sequence. The examination of similarities/dissimilarities among sequences of the
-globin genes of different species illustrates the utility of the approach.
Isolation and Expression Analysis of a GDSL-like Lipase Gene from Brassica napus L.
Ling, Hua ; Zhao, Jingya ; Zuo, Kaijing ; Qiu, Chengxiang ; Yao, Hongyan ; Qin, Jie ; Sun, Xiaofen ; Tang, Kexuan ;
BMB Reports , volume 39, issue 3, 2006, Pages 297~303
DOI : 10.5483/BMBRep.2006.39.3.297
As lipolytic enzymes, GDSL lipases play an important role in plant growth and development. In order to identify their functions and roles, the full-length cDNA of a GDSL lipase gene, designated BnLIP2, was isolated from Brassica napus L. BnLIP2 was 1,300 bp long, with 1,122 bp open reading frame (ORF) encoding 373 amino acid residues. Sequence analysis indicated that BnLIP2 belonged to GDSL family. Southern blot analysis indicated that BnLIP2 belonged to a small gene family in rapeseed genome. RT-PCR analysis revealed that BnLIP2 was a tissue-specific expressing gene during reproductive growth and strongly expressed during seed germination. BnLIP2 expression could not be detected until three days after germination, and it subsequently became stronger. The transcript of this gene was deficient in root of seedlings growing at different stages. When juvenile seedlings were treated by methyl jasmonate (MeJ), salicylic acid (SA) and naphthalene acetic acid (NAA), BnLIP2 expression could not be induced in root. Our study implicates that BnLIP2 probably plays an important role in rapeseed germination, morphogenesis, flowering, but independent of root growth and development.
Regulation of Nrf2 Transactivation Domain Activity by p160 RAC3/SRC3 and Other Nuclear Co-Regulators
Lin, Wen ; Shen, Guoxiang ; Yuan, Xiaoling ; Jain, Mohit R. ; Yu, Siwang ; Zhang, Aihua ; Chen, J. Don ; Kong, Ah-Ng Tony ;
BMB Reports , volume 39, issue 3, 2006, Pages 304~310
DOI : 10.5483/BMBRep.2006.39.3.304
Transcription factor NF-E2-related factor 2 (Nrf2) regulates the induction of Phase II detoxifying enzymes and antioxidant enzymes in response to many cancer chemopreventive compounds. In this study, we investigated the role of receptor associated coactivator (RAC3) or steroid receptor coactivator-3 (SRC3) and other nuclear co-regulators including CBP/p300 (CREB-binding protein), CARM1 (Coactivator-associated arginine methyltransferase), PRMT1 (Protein arginine methyl-transferase 1), and p/CAF (p300/CBP-associated factor) in the transcriptional activation of a chimeric Gal4-Nrf2-Luciferase system containing the transactivation domain (TAD) of Nrf2 in HepG2 cells. The results indicated that RAC3 up-regulated the transactivation activity of Gal4-Nrf2-(1-370) in a dose-dependent manner. The enhancement of transactivation domain activity of Gal4-Nrf2-(1-370) by RAC3 was dampened in the presence of dominant negative mutants of RAC3. Next we studied the effects of other nuclear co-regulators including CBP/p300, CARM1, PRMT1 and p/CAF, and the results showed that they had different level of positive effects on this transactivation domain activity of Gal4-Nrf2-(1-370). But importantly, synergistic effects of these co-regulators in the presence of RAC3/SRC3 on the transactivation activity of Gal4-Nrf2-(1-370) were observed. In summary, our present study showed for the first time that the 160 RAC3/SRC3 is involved in the functional transactivation of TAD of Nrf2 and that the other nuclear co-regulators such as CBP/p300, CARM1, PRMT1 and p/CAF can also transcriptionally activate this TAD of Nrf2 and that they could further enhance the transactivation activity mediated by RAC3/SRC3.
Yeast Elf1 Factor Is Phosphorylated and Interacts with Protein Kinase CK2
Kubinski, Konrad ; Zielinski, Rafal ; Hellman, Ulf ; Mazur, Elzbieta ; Szyszka, Ryszard ;
BMB Reports , volume 39, issue 3, 2006, Pages 311~318
DOI : 10.5483/BMBRep.2006.39.3.311
One of the biggest group of proteins influenced by protein kinase CK2 is formed by factors engaged in gene expression. Here we have reported recently identified yeast transcription elongation factor Elf1 as a new substrate for both monomeric and tetrameric forms of CK2. Elf1 serves as a substrate for both the recombinant CK2
) and holoenzyme (
). By MALDI-MS we identified the two serine residues at positions 95 and 117 as the most probable in vitro phosphorylation sites. Co-immunoprecypitation experiments show that Elf1 interacts with catalytic (
') as well as regulatory (
') subunits of CK2. These data may help to elucidate the role of protein kinase CK2 and Elf1 in the regulation of transcription elongation.
Effects of Signal Peptide and Adenylate on the Oligomerization and Membrane Binding of Soluble SecA
Shin, Ji-Yeun ; Kim, Mi-Hee ; Ahn, Tae-Ho ;
BMB Reports , volume 39, issue 3, 2006, Pages 319~328
DOI : 10.5483/BMBRep.2006.39.3.319
SecA protein, a cytoplasmic ATPase, plays a central role in the secretion of signal peptide-containing proteins. Here, we examined effects of signal peptide and ATP on the oligomerization, conformational change, and membrane binding of SecA. The wild-type (WT) signal peptide from the ribose-binding protein inhibited ATP binding to soluble SecA and stimulated release of ATP already bound to the protein. The signal peptide enhanced the oligomerization of soluble SecA, while ATP induced dissociation of SecA oligomer. Analysis of SecA unfolding with urea or heat revealed that the WT signal peptide induces an open conformation of soluble SecA, while ATP increased the compactness of SecA. We further obtained evidences that the signal peptide-induced oligomerization and the formation of open structure enhance the membrane binding of SecA, whereas ATP inhibits the interaction of soluble SecA with membranes. On the other hand, the complex of membrane-bound SecA and signal peptide was shown to resume nucleotide-binding activity. From these results, we propose that the translocation components affect the degree of oligomerization of soluble SecA, thereby modulating the membrane binding of SecA in early translocation pathway. A possible sequential interaction of SecA with signal peptide, ATP, and cytoplasmic membrane is discussed.
A Simple and Economical Short-oligonucleotide-based Approach to shRNA Generation
Kim, Jin-Su ; Kim, Hyuk-Min ; Lee, Yoon-Soo ; Yang, Kyung-Bae ; Byun, Sang-Won ; Han, Kyu-Hyung ;
BMB Reports , volume 39, issue 3, 2006, Pages 329~334
DOI : 10.5483/BMBRep.2006.39.3.329
RNAi (RNA interference) has become a popular means of knocking down a specific gene in vivo. The most common approach involves the use of chemically synthesized short interfering RNAs (siRNAs), which are relatively easy and fast to use, but which are costly and have only transient effects. These limitations can be overcome by using short hairpin RNA (shRNA) expression vectors. However, current methods of generating shRNA expression vectors require either the synthesis of long (50-70 nt) costly oligonucleotides or multi-step processes. To overcome this drawback, we have developed a one-step short-oligonucleotides-based method with preparation costs of only 15% of those of the conventional methods used to obtain essentially the same DNA fragment encoding shRNA. Sequences containing 19 bases homologous to target genes were synthesized as 17- and 31-nt DNA oligonucleotides and used to construct shRNA expression vectors. Using these plasmids, we were able to effectively silence target genes. Because our method relies on the onestep ligation of short oligonucleotides, it is simple, less error-prone, and economical.
Oxidative Modification of Human Ceruloplasmin by Methylglyoxal: An in vitro study
Kang, Jung-Hoon ;
BMB Reports , volume 39, issue 3, 2006, Pages 335~338
DOI : 10.5483/BMBRep.2006.39.3.335
Methylglyoxal (MG) is an endogenous physiological metabolite which is present in increased concentrations in diabetics. MG reacts with the amino acids of proteins to form advanced glycation end products. In this in vitro study, we investigated the effect of MG on the structure and function of ceruloplasmin (CP) a serum oxidase carrier of copper ions in the human. When CP was incubated with MG, the protein showed increased electrophoretic mobility which represented the aggregates at a high concentration of MG (100 mM). MG-mediated CP aggregation led to the loss of enzymatic activity and the release of copper ions from the protein. Radical scavengers and copper ion chelators significantly prevented CP aggregation. CP is an important protein that circulates in plasma as a major copper transport protein. It is suggested that oxidative damage of CP by MG may induce perturbations of the copper transport system and subsequently lead to harmful intracellular condition. The proposed mechanism, in part, may provide an explanation for the deterioration of organs in the diabetic patient.