Synthesis and characterization of a practically better DEPMPO-type spin trap, 5-(2,2-dimethyl-1,3-propoxy cyclophosphoryl)-5-methyl-1-pyrrolineN-oxide (CYPMPO)

5-(2,2-dimethyl-1,3-propoxy cyclophosphoryl)-5-methyl-1-pyrroline N-oxide (CYPMPO), a new cyclic DEPMPO-type nitrone was evaluated for spin-trapping capabilities toward hydroxyl and superoxide radicals. CYPMPO is colorless crystalline and freely soluble in water. Both the solid and diluted aqueous solution did not develop electron spin resonance (ESR) signal for at least 1 month at ambient conditions. CYPMPO can spin-trap superoxide and hydroxyl radicals in both chemical and biological systems, and the ESR spectra are readily assignable. Half life for the superoxide adduct of CYPMPO produced in UV-illuminated hydrogen peroxide solution was approximately 15 min, and in biological systems such as hypoxanthine (HX)/xanthine oxidase (XOD) the half-life of the superoxide adduct was approximately 50 min. In UV-illuminated hydrogen peroxide solution, there was no conversion from the superoxide adduct to the hydroxyl adduct. Although overall spin-trapping capabilities of CYPMPO are similar to DEPMPO, its high melting point, low hygroscopic property, and the long shelf-life would be highly advantageous for the practical use.

Enhancement of Radiation-induced Apoptosis by 6-Formylpterin

Radiation-induced apoptosis and its possible enhancement in the presence of 6-formylpterin (6-FP), a metabolite of folic acid, were examined in human myelomonocytic lymphoma U937 cells. When cells were treated with 6-FP at a nontoxic concentration of 300 microM, and then exposed to X-rays at a dose of 10 Gy, significant enhancement of radiation-induced apoptosis as determined by nuclear morphological change, phosphatidylserine (PS) externalization and DNA fragmentation were observed. Flow cytometry for the detection of intracellular hydrogen peroxide (H2O2) revealed that 6-FP increased the formation of intracellular H2O2, which further increased when the cells were irradiated. Decrease of mitochondria trans-membrane potential (MMP), release of cytochrome c from mitochondria, and activation of caspase-3 were enhanced after the combined treatment. Remarkable activation of protein kinase C delta (PKC delta) and its translocation from cytosol to mitochondria were detected in combined treatment. Increase of intracellular Ca2+ concentrations ([Ca2+]i) was also observed, however, neither calpain I nor calpain II could inhibit the apoptosis. In addition, c-Jun NH2-terminal kinase (JNK) activation was not enhanced in the combined treatment. A protein involved in a caspase-independent apoptosis pathway, apoptosis inducing factor (AIF), remained unchanged even 3 h after treatment. These results indicate that intracellular H2O2 generated by 6-FP enhances radiation-induced apoptosis via the mitochondria-mediated caspase-dependent pathway, with the active involvement of PKC delta.

Gene expression in enhanced apoptosis of human lymphoma U937 cells treated with the combination of different free radical generators and hyperthermia

The effects of various free radicals derived from 6-formylpterin (6-FP), alpha-phenyl-tert-butyl nitrone (PBN) and 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH) combined with hyperthermia, on gene expression in similarly enhanced apoptosis of human lymphoma U937 cells were investigated using cDNA microarrays containing approximately 16,600 genes and computational gene expression analysis tools. When the cells were treated for 10 min at 44 degrees C (15% apoptosis level), 39 up-regulated and 3 down-regulated genes were identified. In the up-regulated genes, apoptosis- and unfolded protein response-associated genes were contained. The combined treatment with heat and either chemical enhanced apoptosis level (approximately 30%) and showed a chemical-specific gene expression pattern. Furthermore, the expression levels of selected genes were confirmed by a real-time quantitative PCR. The present results will provide a basis for further understanding the molecular mechanisms in enhancement of heat-induced apoptosis by different intracellular oxidative stress.

Stabilization of the immobilized linkers and DNA probes for DNA microarray fabrication by end-capping of the remaining unreacted silanol on the glass

High stability of the oligonucleotides immobilized on the glass is essential for the reliable DNA microarray analysis. In the present study, effect of end-capping of the unreacted silanol, remaining after the surface amine-functionalization, was explored: (1) Cy3-NHS (N-hydorxysuccinincimide) dye was spotted on the surface and change in the fluorescent intensity was measured. (2) DNA probes were immobilized by the reactivity of oxanine linked at the 5'-end, the complementary oligonucleotides with Cy5-fluorescence at the 5'-end was hybridized, and the time-dependence of the fluorescence intensity was observed. Both the systems showed improved stability of the immobilized molecules, indicative of the stabilization by end-capping.

Bioethanol production from xylose by recombinant Saccharomyces cerevisiae expressing xylose reductase, NADP(+)-dependent xylitol dehydrogenase, and xylulokinase

We constructed a set of recombinant Saccharomyces cerevisiae strains with xylose-fermenting ability. A recombinant S. cerevisiae strain D-XR/ARSdR/XK, in which protein engineered NADP(+)-dependent XDH was expressed, showed 40% increased ethanol production and 23% decrease in xylitol excretion as compared with the reference strain D-XR/XDH/XK expressing the wild-type XDH.

Anticancer photodynamic and non-photodynamic effects of pterin derivatives on a pancreatic cancer cell line

To evaluate the feasibility of two kinds of pterin derivatives, 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-pivaloylpteridin-4-one (DFP) and 2-(N,N-dimethylaminomethyleneamino)-3-pivaloylpteridin-4-one (DP), as anticancer drugs, their photodynamic and non-photodynamic effects on pancreatic cancer cell line Panc-1 cells were examined. For photodynamic effects, cell death 48 h after UV-A irradiation was more prominent in cells preloaded with DP than DFP. When cells were simply incubated for 96 h without irradiation, DFP induced cell death, while DP suppressed cell proliferation. Furthermore, DP was much more soluble in water than DFP. These findings collectively indicated that DP is more feasible as an anticancer drug than DFP.

Absolute calibration of imaging plate for GeV electrons

An imaging plate has been used as a useful detector of energetic electrons in laser electron acceleration and laser fusion studies. The absolute sensitivity of an imaging plate was calibrated at 1 GeV electron energy using the injector Linac of SPring-8. The sensitivity curve obtained up to 100 MeV in a previous study was extended successfully to GeV range.

Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism

The Entner-Doudoroff (ED) pathway is a classic central pathway of d-glucose metabolism in all three phylogenetic domains. On the other hand, Archaea and/or bacteria possess several modified versions of the ED pathway, in which nonphosphorylated intermediates are involved. Several fungi, including Pichia stipitis and Debaryomyces hansenii, possess an alternative pathway of L-rhamnose metabolism, which is different from the known bacterial pathway. Gene cluster related to this hypothetical pathway was identified by bioinformatic analysis using the metabolic enzymes involved in analogous sugar pathways to the ED pathway. Furthermore, the homologous gene cluster was found not only in many other fungi but also several bacteria, including Azotobacter vinelandii. Four putative metabolic genes, LRA1-4, were cloned, overexpressed in Escherichia coli, and purified. Substrate specificity and kinetic analysis revealed that nonphosphorylated intermediates related to L-rhamnose are significant active substrates for the purified LRA1-4 proteins. Furthermore, L-2-keto-3-deoxyrhamnonate was structurally identified as both reaction products of dehydration by LRA3 and aldol condensation by LRA4. These results suggested that the LRA1-4 genes encode L-rhamnose 1-dehydrogenase, L-rhamnono-gamma-lactonase, L-rhamnonate dehydratase, and L-KDR aldolase, respectively, by which L-rhamnose is converted into pyruvate and L-lactaldehyde through analogous reaction steps to the ED pathway. There was no evolutionary relationship between L-KDR aldolases from fungi and bacteria.

Functional reactivity of oxanine: its biological meanings and biotechnological applications

Oxanine (Oxa), generated as one of the major products from guanine by nitrosative oxidation, has been focused as a mutagenic lesion. Here, Oxa was explored in terms of its unique property to react with - NH2 or -SH group since Oxa possesses O-acylisourea conformation in the base-ring structure. In particular, Oxa has been characterized in terms of its formation and mechanism of DNA-protein cross-link (DPC). In addition, Oxa was testified as a new carboxy-linker for activation-free covalent bonding with NH2-molecules, which can be usefully employed for the design of biotechnological or nano/biotechnological systems.

Chemical natures of 6-formylpterin nucleoside analogs

Pterin is an electron transfer compound in biological systems. Among the analogs, 6-formylpterin (6FP) has been demonstrated to have many marked physiological activities. In the present study, we have developed the synthetic procedure for nucleoside analogs of 6FP and prepared 1-(beta-D-ribofuranosyl)-2-(N,N-diethylaminomethyleneamino)-6-formylpteridin-4-one (RDEF) and 1-(beta-D-ribofuranosyl)-2-(piperidine-1-ylmethyleneamino)-6-formylpteridin-4-one (RPIF) in which the 1-position is glycosylated. By electron paramagnetic resonance analysis coupled with the DMPO spin trapping technique, it has been elucidated that O2 was converted to H2O2 by RDEF at pH 7.4 in the presence of NADH in the dark. This result indicates that marked reactive oxygen species (ROS) generation activities of 6FP occurring under light illumination, which gives rise to the particular physiological activities such as induction of apoptosis, can be reproduced in the cellular and living systems by such derivatives and gives suggestion for designing pharmaceutical compounds that generate appropriate and controllable amounts of ROS in vivo.

Repair mechanism of DNA-protein cross-link damage in Escherichia coli

DNA-protein cross-link (DPC) damage is produced by varieties of genotoxic agents such as ionizing radiation, UV light, aldehydes, and some chemotherapeutic compounds. DPCs would be harmful to cells since proteins immobilized on DNA strands could hamper DNA transactions in cells. However, it has not been clarified how DPCs are repaired in cells. In the present study, we prepared DNA substrates containing defined DPCs and tested them for repair enzymes. We also examined the sensitivity of Escherichia coli to DPC-inducing agents.

Biophysical stability and enzymatic recognition of oxanine in DNA

Oxanine (Oxa), which is one of the major products generated from guanine by nitrosative oxidation and is as long-lived as Gua in DNA, has been thought to be one of the major causes for NO-induced DNA damage. In the present study, using several synthetic Oxa-containing oligodeoxynucleotides, biophysical stability and enzymatic recognition of Oxa was investigated in DNA strands. It was found that Oxa did not mediate marked distortion in the whole DNA structure although Oxa pairing with 4 normal bases decreased thermal stability of the DNA duplexes compared to Gua:Cyt base pair. Regarding the responses of the DNA-relevant enzymes to Oxa, it was determined that Oxa was recognized as Gua except that DNA polymerases incorporated Thy as well as Cyt opposite Oxa. These results imply that Oxa tends to behave as a kind of naturally occurring base, Gua and therefore, would be involved in the genotoxic and cytotoxic threats of NO in cellular system.

Reactivity of oxanine: efficient fabrication of DNA microarray by using oxanine-containing DNA oligomer as probe molecule

Oxanine (Oxa), a mutagenic lesion generated from guanine by nitrosative oxidation, can make a covalent bonding with -NH(2) or -SH group since Oxa possesses O-acylisourea conformation in the base-ring structure. We employed such unique reactive functionality of Oxa for fabrication of DNA-immobilized system. When DNA oligomer with Oxa at 5'-end (Oxa-end DNA) is spotted on amine-functionalized surface, the DNA probe can be immobilized without any involvement of activation step or any treatment of chemical linker. We further optimized the fabrication conditions for efficient immobilization of Oxa-end DNA.

Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein-engineered NADH-preferring xylose reductase from Pichia stipitis

A recombinant Saccharomyces cerevisiae strain transformed with xylose reductase (XR) and xylitol dehydrogenase (XDH) genes from Pichia stipitis (PsXR and PsXDH, respectively) has the ability to convert xylose to ethanol together with the unfavourable excretion of xylitol, which may be due to intercellular redox imbalance caused by the different coenzyme specificity between NADPH-preferring XR and NAD(+)-dependent XDH. In this study, we focused on the effect(s) of mutated NADH-preferring PsXR in fermentation. The R276H and K270R/N272D mutants were improved 52- and 146-fold, respectively, in the ratio of NADH/NADPH in catalytic efficiency [(k(cat)/K(m) with NADH)/(k(cat)/K(m) with NADPH)] compared with the wild-type (WT), which was due to decrease of k(cat) with NADPH in the R276H mutant and increase of K(m) with NADPH in the K270R/N272D mutant. Furthermore, R276H mutation led to significant thermostabilization in PsXR. The most positive effect on xylose fermentation to ethanol was found by using the Y-R276H strain, expressing PsXR R276H mutant and PsXDH WT: 20 % increase of ethanol production and 52 % decrease of xylitol excretion, compared with the Y-WT strain expressing PsXR WT and PsXDH WT. Measurement of intracellular coenzyme concentrations suggested that maintenance of the of NADPH/NADP(+) and NADH/NAD(+) ratios is important for efficient ethanol fermentation from xylose by recombinant S. cerevisiae.

Development of stable DNA microarray platforms suitable for quantitative analysis

DNA microarray has become one of the most indispensable tools for genome analysis, medical diagnosis and molecular biological studies. In this study, to make DNA microarray more reliable and efficient, we employed additional silanization modification on aminoalkoxysilane-treated surface. In addition, oxanine was used as a linker of DNA probe, which does not require any chemical activation step in probe immobilization. These strategies were practically convenient in DNA microarray fabrication, and the newly developed system showed enhanced stability for the immobilized DNA probes that could be useful for quantitative analysis.

Comparison of enzymatic recognition of DNA-duplexes containing NO-induced lesions by DNA-relevant enzymes

Nitric oxide (NO) produced in inflamed tissues is known to cause DNA damage by nitrosation or oxidation of base moieties. For investigating the biophysical and biochemical properties of DNA lesions induced by nitric oxide, we prepared synthetic DNA oligomers and analyzed melting temperature (T(m)) or enzymatic recognition of DNA strands containing oxanine (Oxa) and hypoxanthine (Hyp), using guanine (Gua) or adenine (Ade) as control bases, respectively. For enzymatic reaction by DNA-relevant enzymes, we employed T4 polynucleotide kinase, T4 DNA ligase and DNA polymerase (Klenow fragment (exo-)). These analyses revealed that enzymatic recognition of Oxa:Cyt or Hyp:Thy were almost same as Gua:Cyt or Ade:Thy in DNA strands, respectively, indicative of similar molecular and biological recognition of DNA-lesions to normal DNA bases in the cell.

Synthesis of 6-formylpterin nucleoside analogs and their ROS generation activities in the presence of NADH in the dark

We demonstrated previously that 3-position-modified 6-formylpterin (6FP) derivatives produce reactive oxygen species (ROS) such as hydrogen peroxide (H(2)O(2)) from oxygen in the presence of NADH in the dark. It has been shown that 6FP derivatives markedly generate ROS, which gives rise to their particular physiological activities, such as induction of apoptosis in cellular and living systems, suggesting that such compounds provide a hint for the design of a ROS controlling agent in vivo. However, it is not well understood why such unique activities appear on chemical modification. In the present study, in order to see the effect on ROS generation activity in the dark by the modification of the 1-position in 6FP, we have developed a new synthetic procedure for nucleoside analogs of 6FP and prepared 1-(beta-d-ribofuranosyl)-2-(N,N-diethylaminomethyleneamino)-6-formylpteridin-4-one (RDEF) and 1-(beta-d-ribofuranosyl)-2-(piperidine-1-ylmethyleneamino)-6-formylpteridin-4-one (RPIF) in which the 1-position of 6FP is glycosylated. At pH 7.4, NADH was spontaneously oxidized to NAD(+) in the presence of RDEF in the dark. Using electron paramagnetic resonance analysis coupled with the spin trapping technique, we show that O(2) was converted to H(2)O(2)via superoxide anion radical ( O(2)(-)) during this reaction. The modification of the 1-position of 6FP did not cancel ROS generation activities, which were demonstrated in 3-position-modified 6FPs. Since the 6FP derivatives developed in the present study have a ribose moiety, these compounds can be subjected to further derivatization, such as incorporation into oligonucleotides, oligosaccharides, proteins, or any other compounds that recognize and interact with specific biomolecules, and therefore would be useful in pharmaceutical investigations that need generation of appropriate and controllable amounts of ROS in vivo.

Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine

Oxanine having an O-acylisourea structure was explored to see if its reactivity with amino group is useful in DNA microarray fabrication. By the chemical synthesis, a nucleotide unit of oxanine (Oxa-N) was incorporated into the 5′-end of probe DNA with or without the -(CH₂)_n- spacers (n = 3 and 12) and found to immobilize the probe DNA covalently onto the NH₂-functionalized glass slide by one-pot reaction, producing the high efficiency of the target hybridization. The methylene spacer, particularly the longer one, generated higher efficiency of the target recognition although there was little effect on the amount of the immobilized DNA oligomers. The post-spotting treatment was also carried out under the mild conditions (at 25 or 42°C) and the efficiencies of the immobilization and the target recognition were evaluated similarly, and analogous trends were obtained. It has also been determined under the mild conditions that the humidity and time of the post-spotting treatment, pH of the spotting solution and the synergistic effects with UV-irradiation largely contribute to the desired immobilization and resulting target recognition. Immobilization of DNA oligomer by use of Oxa-N on the NH₂-functionalized surface without any activation step would be employed as one of the advanced methods for generating DNA-conjugated solid surface.

Structural property and enzymatic response of oxanine in DNA strands

Oxanine (Oxa, O), one of the major products generated from guanine (Gua) by nitrosative oxidation has been expected as mutagenic lesion involved in NO- or HNO(2) -induced genotoxicity. Here, to elucidate the biological meaning of Oxa in DNA strands, several kinds of Oxa-containing oligodeoxynucleotides (Oxa-ODNs) were synthesized and applied to biophysical and biochemical characterization. CD and NMR analyses revealed that the conformations of all the Oxa-containing duplexes are basically B-type without causing any severe distortion in the whole DNA structure. It was also determined that restriction endonucleases recognize and cleave the specific base-sequence even when Gua was substituted by Oxa in the sequence. When Oxa-ODN was testified as substrates for other DNA-relevant enzymes, the enzymatic functions were not largely affected by Oxa.

Construction of various mutants of xylose metabolizing enzymes for efficient conversion of biomass to ethanol

We applied protein engineering to construct an efficient biomass-ethanol conversion system using Saccharomyces cerevisiae. Intercellular redox imbalance caused by the different coenzyme specificity of xylose reductase (XR) and xylitol dehydrogenase (XDH) has been thought to be one of the main factors of xylitol excretion. Introduction of NADH-dependant XR generated in this study reduced the xylitol excretion probably because of maintaining the intercellular redox balance. Ethanol fermentation was measured in batch culture under anaerobic conditions. The best strain R276H produced a maximum of 5.94 g/l ethanol with yield of 0.43 g/g from 5 g glucose/l plus 15 g xylose/l.

Chemical natures and application of 6-formylpterin derivatives

Pterin, an analog of guanine, is an electron transfer compound in biological systems. Among the analogs, 6-formylpterin (6FP) has been demonstrated to have many marked physiological and pharmacological activities. In vitro, 6FP converts molecular oxygen to reactive oxygen species (ROS) in the presence of NADH or NADPH under light illumination, with the oxidation of NADH is to NAD(+). In the present study, it has been elucidated that some of 6FP derivatives in which the 3-position of 6FP is modified have such unique activities even in the dark where the most of in vivo biological events occur.

Chemical synthesis of oxanine-contained oligodeoxynucleotides

Oxanine, one of major damaged product from deamination of guanine base mediated by NO or HNO2-induced nitrosative reaction, has been considered as a genotoxic lesion. To analyze the biophysical properties of oxanine in context of oligodeoxynucleotide, the chemical incorporation of 2'-deoxyoxanosine (dOxo, nucleoside form of oxanine) into oligodeoxynucleotide is required. Here, we developed the chemical synthesis procedures of dimethoxytritylated dOxo-phosphoramidite (DMT-dOxo-amidite) and oxanine-contained oligonucleotide.

1H NMR study on equilibrium between parallel G-quartet structures

Structural transition of parallel G-quartet formed by d(TG4T) are induced by monovalent cations. In the presence of K+ ion, G-quartet takes a single conformation, while in the presence of Na+ ion, the equilibrium between more than three conformations were observed.

Various mutations by using yeast gene for protein-engineering

For construct an efficient-ethanol fermentation system from xylose by using yeast, several protein-engineering of xylitol dehydrogenase (XDH) were carried out. At first, we created a NADP+-dependent XDH by multiple site-directed mutagenesis. Furthermore, we succeeded to improve the thermostability by introduction of the structural zinc atom into XDH which does not possess a second zinc atom natively. Finally, the introduction of a structural zinc atom into the NADP+-dependent XDH mutant increased the thermostability of this mutant and improved further the catalytic efficiency with NADP+.

External Manual Carotid Compression is Effective in Patients with Cavernous Sinus Dural Arteriovenous Fistulae

SUMMARY

External manual carotid compression is a non-invasive method to treat patients with cavernous sinus dural arteriovenous fistulae (CSDAVF). We studied a group of patients with CSDAVF to identify factors that made cure by compression therapy possible. We treated 23 patients with CS-DAVF without cortical venous drainage or a recent decline in visual acuity by compression therapy. All were followed up by magnetic resonance angiography (MRA) at one, three, six, and 12 months after treatment and the characteristics of the imaging findings, their neurological symptoms, and the patterns of symptom improvement were examined. In group A (n=8), cure was achieved by manual carotid compression; in the other 15 patients (group B), cure was not obtained. Group B manifested significantly higher ocular pressure and a significantly longer interval between symptom onset and treatment by manual carotid compression. In group A, venous drainage was via the superior orbital vein (SOV) with/without involvement of the inferior petrosal sinus (IPS); closure of the CS-DAVF occurred within 4.1 months after the start of treatment. In three patients symptom improvement progressed steadily and gradually. The other five cured patients experienced transient worsening of their symptoms at two to four months after the start of treatment, these resolved within four to seven months. Manual carotid compression was effective in patients without retrograde venous CS-DAVF drainage or a severe decline in visual acuity. The factors that rendered cure by compression therapy possible were lower ocular pressure and a shorter interval between symptom onset and the start of treatment. Venous drainage in those patients was exclusively via the SOV without involvement of the IPS.

Biophysical and biochemical properties of oxanine-containing oligodeoxynucleotide

Since oxanine (Oxa) was found as one of the major products from nitrosative oxidation of guanine, Oxa has been expected as mutagenic lesion related to NO-induced DNA damage. Here, to elucidate the mutagenic significance of Oxa in vitro, several Oxa-containing oligodeoxynucleotides (Oxa-ODNs) were synthesized and subjected to biophysical and biochemical characterization. Oxa-ODNs were analyzed in terms of their duplex stabilities and DNA polymerase responses. These results will be helpful in understanding the genotoxic pattern induced by Oxa.

The positive effect of the decreased NADPH-preferring activity of xylose reductase from Pichia stipitis on ethanol production using xylose-fermenting recombinant Saccharomyces cerevisiae

We focused on the effects of a mutation of xylose reductase from Pichia stipitis (PsXR) on xylose-to-ethanol fermentation using recombinant Saccharomyces cerevisiae transformed with PsXR and PsXDH (xylitol dehydrogenase from P. stipitis) genes. Based on inherent NADH-preferring XR and several site-directed mutagenetic studies using other aldo-keto reductase enzymes, we designed several single PsXR mutants. K270R showing decreased NADPH-preferring activity without a change in NADH-preferring activity was found to be a potent mutant. Strain Y-K270R transformed with K270R PsXR and wild-type PsXDH showed a 31% decrease in unfavorable xylitol excretion with 5.1% increased ethanol production as compared to the control in the fermentation of 15 g l(-1) xylose and 5 g l(-1) glucose.

Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism

l-2-Keto-3-deoxyarabonate dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method.

l-2-Keto-3-deoxyarabonate (l-KDA) dehydratase is a novel member of the dihydrodipicolinate synthase (DHDPS)/N-acetylneuraminate lyase (NAL) protein family and catalyzes the hydration of l-KDA to α-ketoglutaric semialdehyde. l-KDA dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. The crystal diffracts to 2.0 Å resolution using synchrotron radiation and belongs to the trigonal space group P3₁21 or its enantiomorph P3₂21, with unit-cell parameters a = b = 78.91, c = 207.71 Å.

Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein engineered NADP+-dependent xylitol dehydrogenase

Effects of reversal coenzyme specificity toward NADP+ and thermostabilization of xylitol dehydrogenase (XDH) from Pichia stipitis on fermentation of xylose to ethanol were estimated using a recombinant Saccharomyces cerevisiae expressing together with a native xylose reductase from P. stipitis. The mutated XDHs performed the similar enzyme properties in S. cerevisiae cells, compared with those in vitro. The significant enhancement(s) was found in Y-ARSdR strain, in which NADP+-dependent XDH was expressed; 86% decrease of unfavorable xylitol excretion with 41% increased ethanol production, when compared with the reference strain expressing the wild-type XDH.

Base sequence- and T m-dependent DNA oligomer separation by open tubular capillary columns carrying complementary DNA oligomers as probes

DNA chips prepared on a flat glass surface have unavoidable drawbacks when used for quantitative analysis. In an attempt to overcome this problem, we constructed an HPLC-type system suitable for quantitative analysis that enables base sequence- and T (m)-dependent DNA oligomer separation in a flow system. A small open tubular capillary column (300-mm x 100-microm I.D.) was used. The DNA oligomers used as probes had an amino group at the 5'-end and were immobilized on the inner silica surface of the capillary column which had been sequentially treated with 3-aminopropyltriethoxysilane, butyltrimethoxysilane, and disuccinimidylglutarate. Using the combination of probe-immobilized column placed in a column oven equipped with temperature gradient function, a nano-flow-controllable pump, a small sample-loading injector, and a capillary-fitted UV detector, we succeeded in separating complementary and non-complementary DNA oligomers in specific and quantitative modes. We also designed a temperature gradient strategy for efficient separation of target DNA oligomers in DNA mixture samples. Using a column carrying two different probes with similar T (m) values, their complementary target DNA oligomers were also separated and detected. The developed DNA open tubular capillary column system investigated in the present study could be further improved as an alternative tool to DNA chips to be used for the quantitative analysis of DNA or mRNA samples.

α-Ketoglutaric Semialdehyde Dehydrogenase Isozymes Involved in Metabolic Pathways of D-Glucarate, D-Galactarate, and Hydroxy-L-proline

Azospirillum brasilense possesses an alternative pathway of l-arabinose metabolism in which alpha-ketoglutaric semialdehyde (alphaKGSA) dehydrogenase (KGSADH) is involved in the last step, the conversion of alphaKGSA to alpha-ketoglutarate. In the preceding studies, we identified a set of metabolic genes of the l-arabinose pathway including the KGSADH gene (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623; Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888; Watanabe, S., Shimada, N., Tajima, K., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 33521-33536). Here, we describe that A. brasilense possesses two different KGSADH isozymes from l-arabinose-related enzyme (KGSADH-I); that is, d-glucarate/d-galactarate-inducible KGSADH-II and hydroxy-l-proline-inducible KGSADH-III. They were purified homogeneously from A. brasilense cells grown on d-galactarate or hydroxy-l-proline, respectively. When compared with KGSADH-I, amino acid sequences of KGSADH-II and KGSADH-III were significantly similar but not totally identical. Physiological characterization using recombinant enzymes revealed that KGSADH-II and KGSADH-III showed similar high substrate specificity for alphaKGSA and different coenzyme specificity; that is, NAD(+)-dependent KGSADH-II and NADP(+)-dependent KGSADH-III. In the phylogenetic tree of the aldehyde dehydrogenase (ALDH) superfamily, KGSADH-II and KGSADH-III were poorly related to the known ALDH subclasses including KGSADH-I. On the other hand, ALDH-like ycbD protein involved in d-glucarate/d-galactarate operon from Bacillus subtilis is closely related to the methylmalonyl semialdehyde dehydrogenase subclass but not A. brasilense KGSADH isozymes. To estimate the correct function, the corresponding gene was expressed, purified, and characterized. Kinetic analysis revealed the physiological role as NADP(+)-dependent KGSADH. We conclude that three different types of KGSADH appeared in the bacterial evolutional stage convergently. Furthermore, even the same pathway such as l-arabinose and d-glucarate/d-galactarate metabolism also evolved by the independent involvement of KGSADH.

Pediatric primary CNS lymphoma: longterm survival after treatment with radiation monotherapy

Primary central nervous system lymphoma (PCNSL) in childhood is very rare. We report a 5-year-old boy who presented with headache and nausea. Magnetic resonance imaging (MRI) showed a faintly enhanced lesion in the left cerebellar hemisphere. MRI-guided biopsy was returned with a histopathological diagnosis of lymphoma. Cranial radiotherapy alone with whole-brain irradiation (30 Gy) followed by a 20-Gy booster to the tumor bed was successful and the patient is alive, well, and in persistent complete remission 14 years post-treatment. This is the only pediatric PCNSL encountered at our institution between 1989 and 2004.

Thermostabilization of Pichia stipitis xylitol dehydrogenase by mutation of structural zinc-binding loop

Xylitol dehydrogenase from Pichia stipitis (PsXDH) is one of the key enzymes for the bio-ethanol fermentation system from xylose. Previously, we constructed the C4 mutant (S96C/S99C/Y102C) with enhanced thermostability by introduction of structural zinc. In this study, for further improvement of PsXDH thermostability, we constructed the appropriate structural zinc-binding loop by comparison with other polyol dehydrogenase family members. A high thermostability of PsXDH was obtained by subsequent site-directed mutagenesis of the structural zinc-binding loop. The best mutant in this study (C4/F98R/E101F) showed a 10.8 degrees C higher thermal transition temperature (T(CD)) and 20.8 degrees C higher half denaturation temperature (T(1/2)) compared with wild-type.

Efficient preparation of amine-modified oligodeoxynucleotide using modified H-phosphonate chemistry for DNA microarray fabrication

Amine-modified oligodeoxynucleotides (AMO) are commonly used probe oligodeoxynucleotides for DNA microarray preparation. Two methods are currently used for AMO preparation--use of amine phosphoramidites protected by acid-labile monomethoxytrityl (MMT) groups or alkali-labile trifluoroacetyl (TFA) groups. Because conventional AMO preparation procedures have defects, for example stringent acidic conditions are required for deprotection of MMT and hydrophobic purification cannot be used for TFA-protected amino groups, conventional preparation of AMO is unlikely to result in the expected outcome. In this paper a method of AMO synthesis using modified H-phosphonate chemistry is suggested. An aliphatic diamine is coupled with a phosphonate group forming a phosphoramidate linkage to the last internucleotide phosphate of oligodeoxynucleotides. In this method dimethoxytrityl (DMT) purification steps are used and stringent acid deprotection is not required to obtain the AMO. Although the method could lead to formation of AMO diastereomers, melting-temperature and CD analysis showed for two AMO that DNA duplex formation was the same as when normal oligodeoxynucleotides were used. Also, when these AMO were used as probes for DNA microarrays the immobilization efficiency was similar to that for AMO probes prepared by conventional means using an amino-modifier unit. The hybridization performance of these AMO was better than for those prepared conventionally. The procedures suggested would be useful for preparation of efficient AMO for fabrication of DNA microarrays and DNA-based nanoparticle systems.

Effects of Edaravone on Singlet Oxygen Released From Activated Human Neutrophils

The effects of edaravone, a curative agent for acute brain infarction, on singlet oxygen ((1)O2) released from activated human neutrophils were examined, and the effects were compared to those of histidine, a (1)O2 singlet oxygen scavenger. The neutrophils, stimulated with opsonized zymosan, released (1)O2 that was detected by chemiluminescence using a (1)O2 specific probe, trans-1-(2'-methoxyvinyl)pyrene. Edaravone dose-dependently suppressed the (1)O2 release with an IC(50) of approximately 0.3 microM, while the IC(50) of histidine was approximately 1 mM. This (1)O2 scavenging activity of edaravone might be involved in its curative effects on acute brain infarction.

Reactive oxygen species generation through NADH oxidation by 6-formylpterin derivatives in the dark

6-formylpterin (6FP) has been reported to produce reactive oxygen species (ROS) such as *O2- and H2O2 from O2 in the presence of NADH under light condition. In the present study, we prepared a variety of 6FP derivatives and found that 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-pivaloylpteridin-4-one and 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-methylpteridin-4-one, in which the 2-amino groups are modified by a dimethylaminomethylene group and the 3-positions by pivaloyl and methyl groups and 2-amino-6-formyl-3-methylpteridin-4-one in which the amino group at the 2-position is free and the 3-position is modified by a methyl group generated H2O2 from O2 on oxidation of NADH to NAD+ in the dark. However, 6FP and 2-(N,N-dimethylaminomethyleneamino)-6-formylpteridin-4-one, in which the 3-position is free did not yield H2O2. These results indicate that modification of the 3-position is essential to make the activities of 6FP available in the dark and would be suggestive for designing pharmaceutical compounds that generate appropriate and controllable amounts of ROS in vivo.

A novel method for synthesis of silica nanoparticles

A sequential method has been used, for the first time, to prepare monodisperse and uniform-size silica nanoparticles using ultrasonication by sol-gel process. The silica particles were obtained by hydrolysis of tetraethyl orthosilicate (TEOS) in ethanol medium and a detailed study was carried out on the effect of different reagents on particle sizes. Various-sized particles in the range 20-460 nm were synthesized. The reagents ammonia (2.8-28 mol L(-1)), ethanol (1-8 mol L(-1)), water (3-14 mol L(-1)), and TEOS (0.012-0.12 mol L(-1)) were used and particle size was examined under scanning electron microscopy and transmission electron microscopy. In addition to the above observations, the effect of temperature on particle size was studied. The results obtained in the present study are in agreement with the results observed for the electronic absorption behavior of silica particles, which was measured by UV-vis spectrophotometry.