A mathematical model has been proposed for the batch culture of Agaricus blazei with mixed carbon sources of glucose and dextrin. In the proposed model, the metabolism of A. blazei was divided into three parts: cell growth, exopolysaccharides (EPS) production, and another EPS production pathway activated by dextrin hydrolysis. Each pathway was described mathematically and incorporated into the mechanistic model structure. Batch cultures were carried out with six different carbon source compositions. Although parameters were estimated by using the experimental data from the two extreme cases such as glucose only and dextrin only, the model represented well the profiles of glucose, cell mass, and EPS concentrations for all the six different carbon source mixtures, showing a good interpolation capability. Of note, the lag in EPS production could be quite precisely predicted by assuming that the glucose-to-cell mass ratio was the governing factor for EPS production.

Ansamitocin P-3 is a potent antitumor agent produced by A. pretiosum. A deletion mutant of A. pretiosum was constructed by deleting the asm2 gene, a putative transcriptional repressor. The deletion mutant showed a 9-fold enhanced ansamitocin P-3 productivity. The response surface method with central composite design was employed to further optimize the culture medium composition for ansamitocin P-3 production by the deletion mutant. The concentrations of four medium ingredients, dextrin, maltose, cotton seed flour, and yeast extract, which have been reported as major components for ansamitocin production, were optimized through a series of flask culture experiments. The optimum concentrations of the selected factors were found to be dextrin 6.0%; maltose 3.0%; cotton seed flour 0.53%; and yeast extract 0.45%. The maximum titer of ansamitocin P-3 was 78.3 mg/l with the optimized composition, about 15-folds higher than the unoptimized titer of 5.0 mg/l obtained with YMG medium.

The aims of this study were to establish a simple and effective method for isolating male germline stem cells (GSCs), and to test the possibility of using these cells as a new approach for male infertility treatment. Testes obtained from neonatal and adult mice were manually decapsulated. GSCs were collected from seminiferous tubules by a two-step enzyme digestion method and plated on gelatin-coated dishes. Over 5-7 days of culture, GSCs obtained from neonates and adults gave rise to large multicellular colonies that were subsequently grown for 10 passages. During in vitro proliferation, oct-4 and two immunological markers (Integrin ${\beta}1,\;{\alpha}6$) for GSCs were highly expressed in the cell colonies. During another culture period of 6 weeks to differentiate to later stage germ cells, the expression of oct-4 mRNA decreased in GSCs and Sertoli cells encapsulated with calcium alginate, but the expression of c-kit and testis-specific histone protein 2B(TH2B) mRNA as well as the localization of c-kit protein was increased. Expression of transition protein (TP-l) and localization of peanut agglutinin were not seen until 3 weeks after culturing, and appeared by 6 weeks of culture. The putative spermatids derived from GSCs supported embryonic development up to the blastocyst stage with normal chromosomal ploidy after chemical activation. Thus, GSCs isolated from neonatal and adult mouse testes were able to be maintained and proliferated in our simple culture conditions. These GSCs have the potential to differentiate into haploid germ cells during another long-term culture.

The simultaneous saccharification and fermentation (SSF) process consists of concurrent enzymatic saccharification and fermentation. In the present cybernetic model, the saccharification process, which is based on the modified Michaelis-Menten kinetics and enzyme inhibition kinetics, was combined with the fermentation process, which is based on the Monod equation. The cybernetic modeling approach postulates that cells adapt to utilize the limited resources available to them in an optimal way. The cybernetic modeling was suitable for describing sequential growth on multiple substrates by Brettanomyces custersii, which is a glucose- and cellobiose-fermenting yeast. The proposed model was able to elucidate the SSF process in a systematic manner, and the performance was verified by previously published data.

A new constitutive episomal expression vector, pGAPZ-E, was constructed and used for initial screening of eukaryotic target gene expression in Pichia pastoris. Two reporter genes such as beta-galactosidase gene and GFPuv gene were overexpressed in P. pastoris. The expression level of the episomal pGAPZ-E strain was higher than that of the integrated form when the beta-galactosidase gene was used as the reporter gene in P. pastoris X33. The avoiding of both the integration procedure and an induction step simplified the overall screening process for eukaryotic target gene expression in P. pastoris. Nine human protein targets from the Core 50, family of Northeast Structural Genomics Consortium (http://www.nesg.org), which were intractable when expressed in E. coli, were subjected to rapid screening for soluble expression in P. pastoris. HR547, HR919, and HR1697 human proteins, which had previously been found to express poorly or to be insoluble in E. coli, expressed in soluble form in P. pastoris. Therefore, the new episomal GAP promoter vector provides a convenient and alternative system for high-throughput screening of eukaryotic protein expression in P. pastoris.

Self-organized nanogels were prepared from pullulan/biotin conjugates (PU/Bio) for the development of an effective anticancer drug delivery system. The degree of biotin substitution was 11, 19, and 24 biotin groups per 100 anhydroglucose units of pullulan. The physicochemical properties of the nanogels (PU/Bio1, 2 and 3) in aqueous media were characterized by dynamic light scattering, transmission electron microscopy, and fluorescence spectroscopy. The mean diameter of all the samples was less than 300 nm with a unimodal size distribution. The critical aggregation concentrations (CACs) of the nanoparticles in distilled water were $2.8{\times}10^{-2},\;1.6{\times}10^{-2}$, and $0.7{\times}10^{-2}mg/ml$ for the PU/Bio1, 2, and 3, respectively. The aggregation behavior of the nanogels indicated that biotin can perform as a hydrophobic moiety. To observe the specific interaction with a hepatic carcinoma cell line (HepG2), the conjugates were labeled with rhodamine B isothiocyanate (RITC) and their intensities measured using a fluorescence microplate reader. The HepG2 cells treated with the fluorescence-labeled PU/Bio nanoparticles were strongly luminated compared with the control (pullulan). Confocal laser microscopy also confirmed internalization of the PU/Bio nanogels into the cancer cells. Such results demonstrated that the biotin in the conjugate acted as both a hydrophobic moiety for self-assembly and a tumor-targeting moiety for specific interaction with tumor cells. Consequently, PU/Bio nanogels would appear to be a useful drug carrier for the treatment of liver cancer.

Among 46 Acinetobacter baumannii isolates collected in 2004, two imipenem-resistant isolates were obtained from clinical specimens taken from patients hospitalized in Busan, Republic of Korea. Two carbapenemase-producing isolates were further investigated to determine the mechanism of resistance. These isolates were analyzed by antibiotic susceptibility testing, microbiological tests of carbapenemase activity, determination of pI, transconjugation test, enterobacterial repetitive consensus (ERIC)-PCR, and DNA sequencing. Two cases of infection by A. baumannii producing the IMP-1 ${\beta}$-lactamase were detected. The isolates were characterized by a modified cloverleaf synergy test and EDTA-disk synergy test. Isoelectric focusing of crude bacterial extracts revealed nitrocefin-positive bands with a pI value of 9.0. PCR amplification and characterization of the amplicons by direct sequencing indicated that the isolates carried a $bla_{IMP-l}$ determinant. The isolates were characterized by a multidrug resistance phenotype, including penicillins, extended-spectrum cephalosporins, carbapenems, and aminoglycosides. These results indicate that the observed imipenem resistance of two Korean A. baumannii isolates was due to the spread of an IMP-1-producing clone. Our microbiological test of carbapenemase activity is simple to screen class B metallo-${\beta}$-lactamase-producing clinical isolates to determine their clinical impact and to prevent further spread. This study shows that the $bla_{IMP-l}$ resistance determinant, which is emerging in Korea, may become an emerging therapeutic problem, since clinicians are advised not to use extended-spectrum cephalosporins, imipenem, and aminoglycosides. This observation emphasizes the importance of having effective control measures in Asian hospitals, such as early detection of colonized patients, isolation procedures, and a judicious use of antibiotics.

The signal transduction system is one of the most important devices involved in maintaining life, and many protein kinases are included in the cellular signal transduction system. Finding a protein kinase inhibitor is very valuable, as it can be used to study cell biology and applied to pharmaceuticals. For the efficient and rapid screening of protein kinase inhibitors, two assay systems were combined; the nonradioactive protein kinase assay system that uses an FITC-labeled IRS-2 peptide and the cell-based paper disc assay system that uses Streptomyces griseus as the indicator strain. Among 330 kinds of herb extracts tested, the extract of Dalbergia odorifera exhibited the strongest inhibitory activity in the two assay systems and was selected for further isolation. Based on solvent extraction and many steps of chromatography, seven compounds were finally separated to homogeneity and their structures determined by $^{1}H$ and $^{13}C$ NMR spectroscopies. Four were to be flavonoids and identified as butin ($C_{15}H_{12}O_5$, Mw=272.07), 3'-hydroxymelanetin ($C_{16}H_{12}O_6$, Mw=300.06), liquiritigenin ($C_{15}H_{12}O_4$, Mw=256.07), and 2'-hydroxyformononetin ($C_{16}H_{12}O_{5}$, Mw=284.07). 3'-Hydroxymelanetin inhibited the phosphorylation of the GSK3 protein by Akt to 37% at a concentration of $10{\mu}g/ml$ and showed the strongest cytotoxicity ($ED_{50}<50{\mu}g/ml$) against the human cancer cell line HCT116. Under the same conditions, liquiritigenin also inhibited the phosphorylation of GSK3 by Akt to 26%, and its cytotoxicity against the HCT116 cell line was lower than $100{\mu}g/ml$.

We investigated a possible coordination between the biosyntheses of two polyketides in the cereal head blight fungus Gibberella zeae, zearalenone (ZEA) and aurofusarin (AUR), which are catalyzed by the polyketide synthases (PKS) PKS4/PKS13 and PKS12, respectively. To determine if the production of one polyketide influences that of the other, we used four different transgenic strains of G zeae; three were deficient for either ZEA or AUR or both, and one was an AUR-overproducing strain. The mycelia of both the wild-type and ${\Delta}PKS4$ strain deficient for ZEA produced AUR normally, whereas the mycelia of both the ${\Delta}PKS12$ and ${\Delta}PKS4::{\Delta}PKS12$ strain showed no AUR accumulation. All the examined deletion strains caused necrotic spots on the surface of com kernels and were found to produce the nonpolyketide mycotoxins trichothecenes to the same amount as the wild-type strain. In contrast, the AUR-deficient ${\Delta}PKS12$ strains produced greater quantities of ZEA and its derivatives than the wild-type progenitor on both a rice substrate and a liquid medium; the AUR-overproducing strain did not produce ZEA on either medium. Furthermore, the expression of both PKS4 and PKS13 was induced earlier in the ${\Delta}PKS12$ strains than in the wild-type strain, and there was no difference in the transcription of PKS12 between the two strains. Therefore, these results indicate that the ZEA biosynthetic pathway is negatively regulated by the accumulation of another polyketide (AUR) in G zeae.

The roots of Aralia continentalis (AC) have been used traditionally in Korean as a folk medicine for anti-inflammation and as an anti-rheumatic. In this study, we report that the ethyl acetate-soluble traction (ACE) of the methanolic extract of AC root inhibited the cell growth of various human cancer cell lines and induced apoptosis of HL-60, human promyelocytic leukemia cells. Its $IC_{50}$ values on growth inhibition were estimated to be $56.3{\mu}g/ml$ on HL-60, $87.2{\mu}g/ml$ on HepG2, $93.2{\mu}g/ml$ on HeLa, $135.5{\mu}g/ml$ on DU-145, and $135.8{\mu}g/ml$ on HT-29 cells. Interestingly, ACE showed no antiproliferative effect on normal lymphocyte cells used as control. Furthermore, nuclear DAPI staining revealed the typical nuclear features of apoptosis in the HL-60 cells exposed to $80{\mu}g/ml$ ACE, and a flow cytometric analysis of the HL-60 cells using propidium iodide showed that the apoptotic cell population increased gradually from 5% at 0 h to 16% at 12 h and 20% at 24 h after treated with $50{\mu}g/ml$ of ACE. TUNEL assay also revealed the apoptotic induction of the HL-60 cells treated with ACE. To obtain further information on the ACE-induced apoptosis, the expression level of certain apoptosis-associated proteins was examined using a Western blot analysis. Treatment of the HL-60 cells with ACE resulted in the activation of caspase-3, and subsequent proteolytic cleavage of poly(ADP-ribose) polymerase (PARP). The above results confirmed that the apoptosis in the HL-60 cells was induced by ACE, and that caspase-3-mediated PARP cleavage was involved in the process.

Polysaccharides from the starfish Asterina pectinifera were assessed in vitro for their chemopreventive potential in human breast cancer. The polysaccharides from A. pectinifera inhibited cell proliferation in the estrogen receptor-positive (MCF-7) and estrogen receptor-negative (MDA-MB-231) human breast carcinoma cell lines. In addition, the polysaccharides were found to be an inhibitor of cytochrome P450 1A1-mediated ethoxyresorufin O-deethylase activity, and caused a dose-dependent inhibition of aromatase activity in microsomes isolated from a human placenta. There was a significant reduction in the ornithine decarboxylase activity to 30.7% of the control in the polysaccharide-treated MCF-7 breast cancer cells. Therefore, the polysaccharides from A. pectinifera merit further investigation with respect to breast cancer chemoprevention.

Media components, including date juice, sodium acetate, peptone, and $K_{2}HPO_4$, which were screened by Plackett-Burman fractional factorial design, were optimized for lactic acid production from date juice using the response surface method (RSM). Sodium acetate, peptone (p<0.0001), and $K_{2}HPO_4$ (p=0.0029) were highly significant in influencing the lactic acid production. Close correlationship between predicted and experimental values was observed. When the optimum values of the parameters obtained through RSM (25.0 g/l date sugar, 15.0 g/l sodium acetate, 19.1 g/l peptone, and 4.7 g/l $K_{2}HPO_4$) were applied, lactic acid production (22.7 g/l) increased by 50.33%, compared with unoptimized media (15.1 g/l). The subsequent validation experiments confirmed the validity of the statistical model.

We identified a gene encoding the N-acetylmuramoyl L-alanine amidase (amiB) of Vibrio anguillarum, which catalyzes the degradation of peptidoglycan in bacteria. The entire open reading frame (ORF) of the amiB gene was composed of 1,722 nucleotides and 573 amino acids. The deduced amino acid sequence of AmiB showed a modular structure with two main domains; an N-terminal region exhibiting an Ami domain and three highly conserved, continuously repeating LysM domains in the C-terminal portion. An amiB mutant was constructed by homologous recombination to study the biochemical function of the AmiB protein in V. anguillarum. Transmission electron microscopy (TEM) revealed morphological differences, and that the mutant strain formed trimeric and tetrameric unseparated cells, suggesting that this enzyme is involved in the separation of daughter cells after cell division. Furthermore, inactivation of the amiB gene resulted in a marked increase of sensitivity to oxidative stress and organic acids.

An ABC transporter apparatus of the Gram-negative bacterial type I secretion pathway can be used as a secretory protein expression system in Escherichia coli. Four types of coexpression systems for the Pseudomonas fluorescens lipase gene, tliA, and its cognate ABC transporter gene cluster, tliDEF, were constructed. When the relative expression levels were changed by adding different concentrations of IPTG, the secretion (16.9 U/ml of culture) of TliA in E. coli [pTliDEFA-223+pACYC184] was significantly higher than E. coli [pKK223-3+pTliDEFA-184] secreting the lowest level of TliA (5.2 U/ml of culture). Maximal accumulation of the lipase secreted occurred in the mid-exponential phase, implying that the efficient protein secretion via an ABC transporter was restricted only to actively growing cells. Finally, the secretion level of TliA in E. coli [pTliDEFA-223+pACYC184] was increased to 26.4 U/ml by inducing gene expression at the culture initiation time. These results indicate that a significant increase in the ABC transporter-dependent protein secretion can be achieved by simply controlling the relative expression levels between the ABC transporter and its passenger protein, even in the recombinant E. coli cells.

Application of recombinant protein production and particularly their isotopic enrichment has stimulated development of a range of novel multidimensional heteronuclear NMR techniques. Peptides in most cases are amenable to assignment and structure determination without the need for isotopic labeling. However, there are many cases where the availability of $^{15}N$ and/or $^{13}C$ labeled peptides is useful to study the structure of peptides with more than 30 residues and the interaction between peptides and membrane. CRAMP (Cathelicidin-Related AntiMicrobial Peptide) was identified from a cDNA clone derived from mouse femoral marrow cells as a member of cathelicidin-derived antimicrobial peptides. CRAMP was successfully expressed as a GST-fused form in E. coli and purified using affinity chromatography and reverse-phase chromatography. The yield of the CRAMP was 1.5 mg/l 1. According to CD spectra, CRAMP adopted ${\alpha}$-helical conformation in membrane-mimetic environments. Isotope labeling of CRAMP is expected to make it possible to study the structure and dynamic properties of CRAMP in various membrane systems.

The stable anchorage of pyridoxal 5'-phosphate (PLP) in the active site of D-amino acid transaminase (D-AT) is crucial for the enzyme catalysis. The three-dimensional structure of D-AT revealed that Glu32 is one of the active site groups that may playa role in PLP binding. To prove the role of Glu32 in PLP stability, we firstly checked the rate of the potential rate-limiting step. The kinetic analysis showed that the rate of the ${\alpha}$-deprotonation step reduced to 26-folds in E32A mutant enzyme. Spectral analyses of the reaction of D-AT with D-serine revealed that the E32A mutant enzyme failed to stabilize the key enzyme-substrate intermediate, namely a quinonoid intermediate (E-Q). Finally, analysis of circular dichroism (CD) on the wild-type and E32A mutant enzymes showed that the optical activity of PLP in the enzyme active site was lost by the removal of the carboxylic group, proving that Glu32 is indeed involved in the cofactor anchorage. The results suggested that the electrostatic interaction network through the groups from PLP, Glu32, His47, and Arg50, which was observed from the three-dimensional structure of the enzyme, plays a crucial role in the stable anchorage of the cofactor to give necessary torsion to the plane of the cofactor-substrate complex.

The light perception and phototransformation of phytochromes are the first process of the phytochrome-mediated light signal transduction. The chromophore ligation and its photochromism of various site-specific and deletion mutants of pea phytochrome A and bacterial phytochrome-like protein (Cph1) were analyzed in vitro. Serial truncation mutants from the N-terminus and C-terminus indicated that the minimal N-terminal domain for the chromophore ligation spans from the residue 78 to 399 of pea phytochrome A. Site-specific mutants indicated that several residues are critical for the chromophore ligation and/or photochromism. Histidine-324 appears to serve as an anchimeric residue for photochromism through its H-bonding function. Isoleucine-80 and arginine-383 playa critical role for the chromophore ligation and photochromism. Arginine-383 is presumably involved in the stabilization of the Pfr form of pea phytochrome A. Apparently, the amphiphilic ${\alpha}$-helix centered around the residue-391 is in the chromophore pocket and critical for the chromophore ligation.

The effects of amplifying the gluconeogenic phosphoenolpyruvate carboxykinase of Escherichia coli ($pck_{Ec}$) on succinic acid production in E. coli were examined under anaerobic condition. No significant increase in succinic acid production was observed in E. coli overexpressing the $pck_{Ec}$ gene without supplementing $NaHCO_{3}$ or $MgCO_{3}$. On the other hand, succinic acid production was enhanced as the $NaHCO_{3}$ concentration was increased. When 20 g/l of $NaHCO_{3}$ was added, succinic acid production in recombinant E. coli overexpressing PCK was 2.2-fold higher than that observed in the wild-type strain. It was concluded that the gluconeogenic $pck_{Ec}$ overexpression enabled E. coli to enhance succinic acid production only under the high bicarbonate supplementation condition.

PKR-like endoplasmic reticulum (ER) kinase (PERK) is a type I transmembrane ER-resident protein containing a cytoplasmic catalytic domain with a Ser/Thr kinase activity, which is most closely related to the eukaryotic translation initiation factor-$2{\alpha}$ ($eIF2{\alpha}$) kinase PKR involved in the antiviral defense pathway by interferon. We cloned and expressed the PERK C-terminal kinase domain (cPERK) in Escherichia coli. Like PERK activation in cells under ER stress, wild-type cPERK underwent autophosphorylation when overexpressed in E. coli, whereas the cPERK(K621M) with a methionine substitution for the lysine at amino acid 621 lost the autophosphorylation activity. The activated form cPERK which was purified to near homogeneity, formed an oligomer and was able to trans-phosphorylate specifically its cellular substrate $eIF2{\alpha}$. Two-dimensional phosphoamino acids analysis revealed that phosphorylation of cPERK occurs at the Ser and Thr residues. The functionally active recombinant cPERK, and its inactive mutant should be useful for the analysis of biochemical functions of PERK and for the determination of their three-dimensional structures.

This study explored yeast diauxic promoters using a green fluorescent protein (GFP) reporter to screen growth phase-controlled promoters applicable for foreign protein production. Twenty-five diauxic promoters were inserted into a yeast 2-micron vector in front of the reporter GFP gene. The expressed GFP signal intensity measurements showed that 23 out of the 25 promoters produced a significant fluorescent signal when the cells were in the diauxic growth phase. Among the two strongest promoters pYDL204W and pYLR258W, the former remained constantly active after its activation at the diauxic shift, whereas the latter was only transiently activated right after the deprivation of the medium glucose.

Artemisia princeps Pampanini, which is named as Sajabalssuk (SJ-1) in Korea, was fermented with lactic acid bacteria (LAB), and their antiallergic activities were investigated. When SJ-l was fermented with some LAB isolated from human feces, the inhibition of NO production in RAW264.7 cells and antioxidant activities of SJ-1 were not affected. However, the inhibitory activity of SJ-1 against degranulation of RBL-2H3 cells induced by IgE was increased by LAB fermentation. Among the LAB tested, Bifidobacterium infantis K-525 provided the most potent inhibitory effect of SJ-1 against degranulation of RBL-2H3 cells. SJ-1 extract fermented with B. infantis K-525 (F-SJ-1) potently inhibited the mouse passive cutaneous anaphylaxis reaction induced by IgE with antigen, skin dermatitis induced by 12-O-tetradecanoylphorbol-13-acetate, and scratching behaviors induced by compound 48/80. These inhibitory activities of F-SJ-1 were more potent than those of SJ-1. These findings suggest that the inhibition of SJ-1. extract against IgE-induced allergic diseases, such as rhinitis and asthma, can be enhanced by LAB fermentation.

The last step in L-carnitine biosynthesis in eukaryotic organisms is mediated by ${\gamma}$-butyrobetaine hydroxylase (EC1.14.11.1), a dioxygenase that converts ${\gamma}$-butyrobetaine to L-carnitine. This enzyme was previously identified from rat liver and humans, and the peptide sequence of human ${\gamma}$-butyrobetaine hydroxylase was used to search the Neurospora crassa genome database, which led to an identification of an open reading frame (ORF) consisting of 1,407 bp encoding a polypeptide of 468 amino acids. When this protein was expressed in Saccharomyces cerevisiae, the crude cell-free extract exhibited ${\gamma}$-butyrobetaine hydroxylase activity.

Previous study demonstrated that the restriction barrier of Streptomyces griseus is almost completely bypassed by the Streptomyces-E. coli shuttle vectors passed through the E. coli GM161 strain and methylated with AluI and HpaII methyltransferases. The same DNA methylation of the genomic DNA fragments cloned the nonreplicative vectors generated integrative transformation and gene disruption of their chromosomal counterparts at high efficiencies in S. griseus. This result indicated that the efficiency of gene disruption depends on the efficient transfer of the incoming DNA into bacterial hosts.

The 63-amino-acid-encoding afsR2 is a global antibiotics-stimulating regulatory gene identified from the chromosome of Streptomyces lividans. To dissect a putative functional domain in afsR2, several afsR2-derivative deletion constructs were generated and screened for the loss of actinorhodin-stimulating capability. The afsR2-derivative construct missing a 50-bp C-terminal region significantly lost its actinorhodin-stimulating capability in S. lividans. In addition, site-directed mutagenesis on amino acid positions of #57-#61 in a 50-bp C-terminal region, some of which are conserved among known Sigma 70 family proteins, significantly changed the AfsR2's activity. These results imply that the C-terminal region of AfsR2 is functionally important for antibiotics-stimulating capability and the regulatory mechanism might be somehow related to the sigma-like domain present in the C-terminal of AfsR2.

In this study, glucose and glutamate (copiotrophic conditions) were used to enrich electrochemically active bacteria (EAB) in a microbial fuel cell (MFC). The enriched population consisted primarily of ${\gamma}$-Proteobacteria (36.5%), followed by Firmicutes (27%) and O-Proteobacteria (15%). Accordingly, we compared our own enrichments done under many different conditions with those reported from the literature, all of which support the notion that electrochemically active bacteria are taxonomically very diverse. Enrichments with different types and levels of energy sources (fuels) have clearly yielded many different groups of bacteria.