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A self-propelled object coupled with an enzyme reaction between urease and urea was investigated at the air/aqueous interface. A plastic object that was fixed to a urease-immobilized filter paper was used as a self-propelled object, termed a urease motor, placed on an aqueous urea solution. The driving force of the urease motor is the difference in the surface tension around the object. Oscillatory motion or no motion was triggered depending on the initial pH of the urea solution. Both the frequency and maximum speed of the oscillatory motion varied depending on the initial pH of the water phase. The mechanisms underlying the oscillatory motion and no motion were discussed in relation to the bell-shaped enzyme activity of urease in the enzyme reaction and the surface tension around the urease motor.

Cerebrospinal fluid drainage (CSFD) is recommended as a spinal cord protective strategy in open and endovascular thoracic aortic repair. Although small studies support the use of CSFD, systematic reviews have not suggested definite conclusion and a large-scale study is needed. Therefore, we reviewed medical records of patients who had undergone descending and thoracoabdominal aortic repair (both open and endovascular repair) at multiple institutions to assess the association between CSFD and postoperative motor deficits. Patients included in this study underwent descending or thoracoabdominal aortic repair between 2000 and 2013 at 12 hospitals belonging to the Japanese Association of Spinal Cord Protection in Aortic Surgery. We conducted a retrospective study to investigate whether motor-evoked potential monitoring is effective in reducing motor deficits in thoracic aortic aneurysm repair. We use the same dataset to examine whether CSFD reduces motor deficits after propensity score matching. We reviewed data from 1214 patients [open surgery, 601 (49.5%); endovascular repair, 613 (50.5%)]. CSFD was performed in 417 patients and not performed in the remaining 797 patients. Postoperative motor deficits were observed in 75 (6.2%) patients at discharge. After propensity score matching (n = 700), mixed-effects logistic regression performed revealed that CSFD is associated with postoperative motor deficits at discharge [adjusted odds ratio (OR), 3.87; 95% confidence interval (CI), 2.30–6.51]. CSFD may not be effective for postoperative motor deficits at discharge.

Post-translational modifications (PTMs) of histone N-terminal tails in nucleosome core particle (NCP), such as acetylation, play crucial roles in regulating gene expression. To unveil the regulation mechanism, atomic-level structural analysis of in-vitro modified NCP is effective with verifying the PTMs of histones. So far, identification of PTMs of NCP originating from living cells has mainly been performed using mass spectrometry (MS) techniques, such as bottom-up approach. The bottom-up approach is the most established method for protein characterization, but it does not always provide sufficient information on the acetylated sites of lysine residues in the histone tails if trypsin digestion is carried out. For histone proteins, which have many basic amino acids, trypsin generates too many short fragments that cannot be perfectly analyzed by tandem MS. In this study, we investigated the in vitro acetylation sites in the histone H3 tail using a top-down sequence analysis, matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) experiment, in combination with aminopeptidase digestion. Aminopeptidase can cleave peptide bonds one-by-one from the N-terminus of peptides or proteins, generating N-terminally truncated peptides and/or proteins. As a result, it was identified that this method enables sequence characterization of the entire region of the H3 tail. Also, application of this method to H3 in in-vitro acetylated NCP enabled assigning acetylation sites of H3. Thus, this method was found to be effective for obtaining information on in-vitro acetylation of NCP for structural biology study.

A procedure for the determination of iron in mice urine using graphite furnace atomic absorption spectrometry was developed. The mice urinary samples contain many organic compounds in the matrix, whose concentrations are approximately 20%, and the value is 30-fold higher compared to those found in human urine. Moreover, only 0.2 mL or less of urine was obtained as a sample volume per urination event. It was difficult to decompose the organic materials in the samples by wet digestion using mineral acids and oxidising agents, because of the tiny volumes. In this experiment, raw urinary samples were placed directly into the graphite tube furnace for analysis. The organic contents were simply ashed during the preheating stages. To facilitate ashing in the furnace, air was invaded from the surroundings by interrupting the stream of argon gas. Atomic absorption was measured at 248.3270 nm (wavelength for atomic absorption), with the background monitored at 247.0658 nm (wavelength for background correction). The optimised instrument operating conditions precluded the use of chemical modification technique. The analytical procedures used are quite simple, i.e. an aliquot of raw urine sample was injected directly into the graphite tube furnace and was followed by a suitable heating programme with no chemical modifier. Therefore, this method is useful for scientists who are not familiar with delicate chemical experiments. The proposed analytical method was applied as a kind of biomarker by determining iron concentrations in urinary samples of mice, which were irradiated with 4 Gy of gamma irradiation to their whole body. The time dependence of the iron concentration was determined, and the iron concentrations increased within 1 day of irradiation exposure, then decreased to ordinal values after several days.

Microarrays containing 45 different lectins were analyzed to identify global changes in the glycosylation of serum glycoproteins from mice exposed to whole-body γ-radiation. The results showed that radiation exposure increased and decreased the relative amounts of α-2,3- and α-2,6-sialic acids, respectively. The expression of α-2,3- and α-2,6-sialyltransferase genes in the liver was analyzed to determine whether changes in their expression were responsible for the sialic acid changes. The increase in α-2,3-sialic acid correlated with St3gal5 upregulation after radiation exposure; however, a decrease in St6gal1 expression was not observed. Analysis of a PCR array of genes expressed in irradiated mouse livers revealed that irradiation did not alter the expression of most of the included genes. These results suggest that glycomic screening of serum glycoproteins using lectin microarrays can be a powerful tool for identifying radiation-induced changes in the post-translational addition of sugar moieties to proteins. In addition, the results indicate that altered sialylation of glycoproteins may be an initial response to acute radiation exposure.

In in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS), 1,5-diaminonaphthalene (1,5-DAN) is a most frequently used matrix probably due to the highly sensitive detection of fragment ions. 1,5-DAN is a reducing matrix generating c- and z-series ions by N–Cα bond cleavage. However, it is difficult for reducing matrices to distinguish leucine and isoleucine, and generate c(n-1)-series ions owing to proline (Pro) at residues n. Oxidizing matrices providing a- and x-series ions accompanied by d-series ions by Cα–C bond cleavage solve the problem, but their sensitivity of the ISD fragment ions has been lower than reducing matrices such as 1,5-DAN. Recently, 3-hydroxy-4-nitrobenzoic acid (3H4NBA) had been reported as an oxidizing matrix generating a-series ions with higher intensity compared with conventional oxidizing matrices such as 5-nitrosalicylic acid, but a little lower intensity compared with 1,5-DAN (Anal Chem 88, 8058–8063, 2016). In this study, 3H4NBA isomers (2H3NBA, 2H4NBA, 2H5NBA, 2H6NBA, 3H2NBA, 3H5NBA, 4H2NBA, 4H3NBA, 5H2NBA, and 3H4NBA) were evaluated. All the isomers generated a-series ions accompanied by d-series ions, wherein 3H2NBA, 3H5NBA, 4H2NBA, 4H3NBA, and 5H2NBA were first confirmed as oxidizing matrices for ISD. Among the isomers, 3H2NBA and 4H3NBA generated a-series ions with higher peak intensity compared with 3H4NBA for several peptides. Especially, 3H2NBA generated a-series ions with almost the same or higher intensity, and clearly higher peak resolution compared with c-series ions using 1,5-DAN in several cases. 3H2NBA was expected to contribute to ISD analyses in MALDI-MS as one of the most effective oxidizing matrices.

Postoperative motor dysfunction can develop after spinal surgery, neurosurgery and aortic surgery, in which there is a risk of injury of motor pathway. In order to prevent such devastating complication, intraoperative monitoring of motor evoked potentials (MEP) has been conducted. However, to prevent postoperative motor dysfunction, proper understanding of MEP monitoring and proper anesthetic managements are required. Especially, a variety of anesthetics and neuromuscular blocking agent are known to attenuate MEP responses. In addition to the selection of anesthetic regime to record the baseline and control MEP, the measures to keep the level of hypnosis and muscular relaxation at constant are crucial to detect the changes of MEP responses after the surgical manipulation. Once the changes of MEP are observed based on the institutional alarm criteria, multidisciplinary team members should share the results of MEP monitoring and respond to check the status of monitoring and recover the possible motor nerve injury. Prevention of MEP-related adverse effects is also important to be considered. The Working Group of Japanese Society of Anesthesiologists (JSA) developed this practical guide aimed to help ensure safe and successful surgery through appropriate anesthetic management during intraoperative MEP monitoring.

Self-propelled droplets can spontaneously move using chemical energy. In several reports of self-propelled droplets, interfacial chemical reactions occur at the oil/aqueous interface to induce the Marangoni flow. While the dynamics of interfacial tension is essential to the droplet motion, there are few reports that quantitatively discuss the moving mechanism based on interfacial tension measurements. In this study, we focused on the self-propelled motion of an aqueous droplet in the oil phase, where the surfactant monoolein reacts with bromine at the interface, and estimated the physicochemical parameters related to the droplet motion based on the time series of interfacial tension. These results may reveal the general mechanism for the self-propelled motion of aqueous/oil droplets driven by the interfacial chemical reaction.

A self-propelled motor driven by the enzymatic reaction of catalase adsorbed onto a filter paper floating on an aqueous solution of H2 O2 was used to study nonlinear behavior in the motor's motion. An increase in the concentration of H2 O2 resulted in a change from no motion to irregular oscillatory motion, periodic oscillatory motion, and continuous motion. The mechanisms underlying oscillation and mode bifurcation are discussed based on experimental results on O2 bubble formation and growth on the underside of the motor.

In-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) is a rapid sequencing method for peptides. 1,5-Diaminonaphthalene (1,5-DAN) is a most frequently used matrix for ISD. However, using 1,5-DAN generates mainly c- and z-series ions by N-Cα bond cleavage, which makes it difficult to distinguish leucine (Leu) and isoleucine (Ile), and frequently lacks c(n-1)-series ions owing to proline (Pro) at residues n. Several oxidizing matrices generating a- and x-series ions accompanied by d-series ions by Cα-C bond cleavage have been reported, but an issue remained concerning their sensitivity. 3-Hydroxy-4-nitrobenzoic acid (3H4NBA) has been reported as a matrix for 2-nitrobenzenesulfenyl-labeled peptides by Matsuo et al. (Proteomics 2006, 6, 2042-2049). Here, we used 3H4NBA as an oxidizing matrix for ISD. As a result, numerous a- and d-series ions for amyloid β 1-40 were generated with high sensitivity using 3H4NBA. Each of the two Leu and two Ile was identified by the d-series ions. The sensitivity of the a-series ions using 3H4NBA was a little lower than that of c-series ions using 1,5-DAN. The same tendency was observed for N-acetyl renin substrate and ACTH 18-39. The a-series ions were detected, even at the left side of Pro. The sensitivity of the a-series ions using 3H4NBA was higher than with other existing oxidizing matrices, such as 5-nitrosalicylic acid and 5-formyl salycilic acid. The ions were detected over the entire area of the matrix-analyte spot using 3H4NBA. 3H4NBA was confirmed to be a useful oxidizing matrix for ISD, leading to higher sequence coverage of peptides.

The authors investigated the association between intraoperative motor-evoked potential (MEP) changes and the severity of spinal cord infarction diagnosed with magnetic resonance imaging (MRI) to clarify the discrepancy between them, which was observed in patients with postoperative motor deficits after thoracic and thoracoabdominal aortic surgery.A multicenter retrospective study.Motor-evoked potential25% of control values was deemed positive for spinal cord ischemia. The severity of spinal cord infarction was categorized into grades A to D based on previous studies using the most severe axial MRI slices. The associations between MRI grade, MEP changes, and motor deficits were examined using logistic regression.Twenty-three of 1,245 patients (from 1999 to 2013, at 12 hospitals in Japan) were extracted from medical records of patients who underwent thoracic and thoracoabdominal aortic repair, with intraoperative MEP examinations and postoperative spinal MRI.No intervention (observational study).Motor-evoked potential25% of control value was associated significantly with motor deficits at discharge (adjusted odds ratio [OR], 130.0; p = 0.041), but not with severity of spinal cord infarction (adjusted OR, 0.917; p = 0.931). Motor deficit at discharge was associated with severe spinal cord infarction (adjusted OR, 4.83; p = 0.043), MEP25% (adjusted OR, 13.95; p = 0.031), and combined deficits (motor and sensory, motor and bowel or bladder, or sensory and bowel or bladder deficits; adjusted OR, 31.03; p = 0.072) in stepwise logistic regression analysis.Motor-evoked potential25% was associated significantly with motor deficits at discharge, but not with the severity of spinal cord infarction.

We used high-performance liquid chromatography to separate urine obtained from whole-body gamma-irradiated mice (4 Gy) before analyzing each fraction with matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry to identify radiation-responsive molecules. We identified two candidates: hepcidin antimicrobial peptide 2 (hepcidin-2) and peptide fragments of kidney androgen-regulated protein (KAP). We observed that peak increases of hepcidin-2 in urine were delayed in a dose-dependent manner (1 Gy and above); however, the amount of KAP peptide fragments showed no correlation with radiation dose. In addition, an increase in hepcidin-2 after exposure to relatively low radiation doses (0.25 and 0.5 Gy, respectively) was biphasic (at 8–48 h and 120–168 h, respectively, after irradiation). The increase in hepcidin-2 paralleled an increase in hepcidin-2 gene (Hamp2) mRNA levels in the liver. These results suggest that radiation exposure directly or indirectly induces urinary excretion of hepcidin-2 at least in part by the upregulation of Hamp2 mRNA in the liver.

Protein tyrosine nitration is a selective process, as revealed in studies of animals. However, evidence for selective protein nitration in plants is scarce. In this study, Arabidopsis plants were exposed to air with or without nitrogen dioxide at 40 ppm for 8 h in light. Proteins extracted from whole leaves or isolated chloroplasts were subjected to 2D PAGE followed by SYPRO Ruby staining and immunoblotting using an anti-3-nitrotyrosine antibody. We determined the relative intensity of a spot on an immunoblot (designated RISI), and relative intensity of the corresponding spot on SYPRO Ruby gel (designated RISS). Proteins that exhibited a high RISI value and/or a high RISI/RISS ratio were considered selectively nitrated. In whole leaf proteins from exposed plants, all immunopositive spots were identified as PsbO1, PsbO2 or PsbP1 by PMF. Thus, nitration was exclusive to PsbO and PsbP, extrinsic proteins of photosystem II (PSII). Their RISI/RISS ratio was ≤1.5. Non-exposed plants showed very faint nitration. In purified chloroplast proteins, PsbO and PsbP accounted for >80% of the total RISI values, while four non-PSII proteins, including peroxiredoxin II E, exhibited high RISI/RISS ratios (2.5∼6.6). Tyr(9) of PsbO1 was identified as a nitration site. Thus, nitration is selective for two PSII and four non-PSII proteins in Arabidopsis.

The interaction between camphor and sodium dodecyl sulfate (SDS) was experimentally investigated to understand restoration of Marangoni flow around a camphor disk on water under the addition of SDS. With an increase in the concentration of SDS, the flow velocity decreased to almost zero up to the critical micelle concentration (cmc), but increased above the cmc. Speed of Marangoni flow around the camphor disk increased with an increase in the scale of the aqueous channel. 13C NMR, NOE experiments, and mass spectrometry were used to evaluate the interaction between camphor and SDS molecules, which increased the dissolution rate of camphor into the SDS aqueous solution. The experimental results suggest that an increase in the dissolution of camphor into SDS micelles induces the restoration of Marangoni flow.

In previous studies, we found that stimulation of Toll-like receptor 5 (TLR5) by flagellin induced the activation of mitogen-activated protein kinase (MAPK)-activated protein kinase-2 (MAPKAPK-2) through activation of the p38 MAPK pathway in cultured alveolar epithelial A549 cells. Our studies strongly suggested that MAPKAPK-2 phosphorylated epidermal growth factor receptor (EGFR) at Ser1047. It has been reported that phosphorylation of Ser1047 after treatment with tumor necrosis factor α (TNFα) induced the internalization of EGFR. In the present study, we first found that treatment of A549 cells with hydrogen peroxide induced the activation of MAPKAPK-2 and phosphorylation of EGFR at Ser1047 within 30 min. This was different from flagellin treatment because hydrogen peroxide treatment induced the phosphorylation of EGFR at Tyr1173 as well as Ser1047, indicating the activation of EGFR. We also found that KN93, an inhibitor of CaM kinase II, inhibited the hydrogen peroxide-induced phosphorylation of EGFR at Ser1047 through inhibition of the activation of the p38 MAPK pathway. Furthermore, we examined the internalization of EGFR by three different methods. Flow cytometry with an antibody against the extracellular domain of EGFR and biotinylation of cell surface proteins revealed that flagellin, but not hydrogen peroxide, decreased the amount of cell-surface EGFR. In addition, activation of extracellular signal-regulated kinase by EGF treatment was reduced by flagellin pre-treatment. These results strongly suggested that hydrogen peroxide activated the p38 MAPK pathway via activation of CaM kinase II and that flagellin and hydrogen peroxide regulate the functions of EGFR by different mechanisms.

Spinal cord ischemic injury is the most devastating sequela of descending and thoracoabdominal aortic surgery. Motor-evoked potentials (MEPs) have been used to intraoperatively assess motor tract function, but it remains unclear whether MEP monitoring can decrease the incidence of postoperative motor deficits. Therefore, we reviewed multicenter medical records of patients who had undergone descending and thoracoabdominal aortic repair (both open surgery and endovascular repair) to assess the association of MEP monitoring with postoperative motor deficits.Patients included in the study underwent descending or thoracoabdominal aortic repair at 12 hospitals belonging to the Japanese Association of Spinal Cord Protection in Aortic Surgery between 2000 and 2013. Using multivariable mixed-effects logistic regression analysis, we investigated whether intraoperative MEP monitoring was associated with postoperative motor deficits at discharge after open and endovascular aortic repair.We reviewed data from 1214 patients (open surgery, 601 [49.5%]; endovascular repair, 613 [50.5%]). MEP monitoring was performed in 631 patients and not performed in the remaining 583 patients. Postoperative motor deficits were observed in 75 (6.2%) patients at discharge. Multivariable logistic regression analysis revealed that postoperative motor deficits at discharge did not have a significant association with MEP monitoring (adjusted odds ratio [OR], 1.13; 95% confidence interval [CI], 0.69-1.88; P = .624), but with other factors: history of neural deficits (adjusted OR, 6.08; 95% CI, 3.10-11.91; P.001), spinal drainage (adjusted OR, 2.14; 95% CI, 1.32-3.47; P = .002), and endovascular procedure (adjusted OR, 0.45; 95% CI, 0.27-0.76; P = .003). The sensitivity and specificity of MEP25% of control value for motor deficits at discharge were 37.8% (95% CI, 26.5%-49.5%) and 95.5% (95% CI, 94.7%-96.4%), respectively.MEP monitoring was not significantly associated with motor deficits at discharge.

Hydrophobic peptides are difficult to detect in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), because of the hydrophilic properties of conventional matrices and the low affinity for hydrophobic peptides. Recently, we reported on alkylated dihydroxybenzoic acid (ADHB) as a matrix additive for hydrophobic peptides; however, the peptides were detected in the rim of the matrix-analyte dried spot. Here, we report on a novel matrix, alkylated trihydroxyacetophenone (ATHAP), which is a 2,4,6-trihydroxyacetophenone derivative incorporating a hydrophobic alkyl chain on the acetyl group and thus is expected to have an affinity for hydrophobic peptides. ATHAP increased the sensitivity of hydrophobic peptides 10-fold compared with α-cyano-4-hydroxycinnamic acid (CHCA), in which the detection of hydrophilic peptides was suppressed. The peptides were detected throughout the entire matrix-analyte dried spot using ATHAP, overcoming the difficulty of finding a "sweet spot" when using ADHB. In addition, ATHAP functioned alone as a matrix, unlike ADHB as an additive. In phosphorylase b digests analysis, hydrophobic peptides, which were not detected with CHCA for 1 pmol, were detected with this matrix, confirming that ATHAP led to increased sequence coverage and may extend the range of target analytes in MALDI-MS.

Accumulating evidence indicates that epidermal growth factor receptor (EGFR) is desensitized by phosphorylation of serine 1047 (Ser1047). We and other groups have reported that stimulation of a receptor of tumor-necrosis factor α (TNFα) and Toll-like receptor 5 (TLR5) induced the phosphorylation of Ser1047 through activation of p38 mitogen-activated protein kinase (p38 MAPK) in cultured lung alveolar epithelial A549 cells. However, phosphorylation of EGFR at Ser1047 by stimulation of any G-protein coupled receptors (GPCRs) has not been reported in any cultured cells. In the present study, we first confirmed that A549 cells expressed bradykinin (BK) B2 receptor, and then, we examined whether BK treatment of A549 cells activated MAPKs and induced the phosphorylation of EGFR at Ser1047. Immunoblotting analysis and reporter gene assays indicated that BK activated the pathways of extracellular signal-regulated kinase (ERK) and p38 MAPK. Inhibitor studies suggested that Gq/11 was mainly involved in the activation of ERK and p38 MAPK. We found that stimulation of the BK B2 receptor, but not the BK B1 receptor, induced phosphorylation of EGFR at Ser1047. Pharmacological experiments indicated that both ERK and p38 MAPK were involved in the phosphorylation of EGFR. These results strongly suggested that BK regulates EGFR functions in lung alveolar epithelial cells. In addition, we found that BK treatment increased the mRNA level of dual specificity MAPK phosphatase 5 (DUSP5) in an ERK-dependent manner, which suggested that a negative feedback mechanism of ERK existed in the cells.

The mode change of a simple autonomous motor depending on the nature of an N-acyl-p-nitroaniline, (CnANA, CH3(CH2)n−2CONHφNO2, n = 8, 14, 16, 18, or 22) monolayer on water was investigated. A camphor disk was floated on a molecular layer of CnANA, which gave a characteristic surface pressure (Π) vs area (A) isotherm. The nature of the camphor motion changed depending on the Π vs A isotherm, and in particular reciprocating motion was observed for C14ANA, C16ANA, and C18ANA, which gave a Π vs A isotherm with a local minimum and a local maximum. The characteristic motion of a camphor disk is discussed in relation to the Π vs A isotherm of CnANA and the influence of the interaction between molecules on the driving force of motion. Reciprocating motion was qualitatively reproduced by numerical calculation.

Nitric oxide (NO) exerts a ubiquitous influence on cellular signaling, largely through S-nitrosylation/denitrosylation of cysteines in proteins. The ability to analyze S-nitrosylation directly by mass spectrometry (MS) would be highly useful in understanding the action of NO in various biological processes. However, S-nitrosylation has never been detected by ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) MS because the NO group completely dissociates during the ionization process. In this study, tetraphenylporphyrin (TPP) was used as matrix additive with 2,5-dihydroxybenzoic acid (DHB) to evaluate its suppressive effect on the NO group dissociation of S-nitrosylated peptides. Samples were subjected to MS and MS/MS analysis by MALDI-TOF MS and MALDI-QIT-TOF MS, respectively. In MS analysis using TPP as a matrix additive, the presumably intact molecular ion [M+H]+ peak was also observed, although the NO-dissociated ions [M−NO+H]+ were mainly detected. In contrast, in the absence of TPP, this [M+H]+ peak was not observed. MS/MS analysis of this ion indicated that the peptides contained S-nitrosylated cysteines. Furthermore, other reagents with radical scavenging activity (retinoic acid, α-tocopherol, ascorbic acid, naringenin, and 3,5-di-tert-butyl-4-hydroxytoluene) were tested to examine the possibility of their use as matrix additives for S-nitrosylation detection. As with TPP, these additives showed a suppressive effect on NO group dissociation. In conclusion, radical scavenging reagents are effective additive candidates for detecting S-nitrosylation directly with UV-MALDI MS.

The demand for establishment of high-throughput biodosimetric methods is increasing. Our aim in this study was to identify low-molecular-weight urinary radiation-responsive molecules using electrospray ionization Fourier transform mass spectrometry (ESI-FT MS), and our final goal was to develop a sensitive biodosimetry technique that can be applied in the early triage of a radiation emergency medical system. We identified nine metabolites by statistical comparison of mouse urine before and 8 h after irradiation. Time-course analysis showed that, of these metabolites, thymidine and either thymine or imidazoleacetic acid were significantly increased dose-dependently 8 h after radiation exposure; these molecules have already been reported as potential radiation biomarkers. Phenyl glucuronide was significantly decreased 8 h after radiation exposure, irrespective of the dose. Histamine and 1-methylhistamine were newly identified by MS/MS and showed significant, dose-dependent increases 72 h after irradiation. Quantification of 1-methylhistamine by enzyme-linked immunosorbent assay (ELISA) analysis also showed a significant increase 72 h after 4 Gy irradiation. These results suggest that urinary metabolomics screening using ESI-FT MS can be a powerful tool for identifying promising radiation-responsive molecules, and that urinary 1-methylhistamine is a potential radiation-responsive molecule for acute, high-dose exposure.

Amphiphilic fluoroalkyl end-capped N-(1,1-dimethyl-3-oxobutyl)acrylamide–acryloylmorpholine cooligomer/fluorescein nanocomposites afforded brilliant yellow-colored solutions in not only protic solvents such as methanol and ethanol but also protic-like solvents such as dichloromethane and 1,2-dichloroethane, respectively. However, the corresponding non-fluorinated cooligomer/fluorescein composites and parent fluorescein gave the colorless solutions under similar conditions. On the other hand, unexpectedly, such brilliant yellow-colored solutions provided by these fluorinated nanocomposites completely disappeared in aprotic solvents such as N,N-dimethylformamide, dimethyl sulfoxide, and tetrahydrofuran. Thus, these fluorinated fluorescein nanocomposites can exhibit a coloring–decoloring behavior through solvatochromic response.

Hydrophobic peptides are generally difficult to detect using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) because the majority of MALDI matrixes are hydrophilic and therefore have a low affinity for hydrophobic peptides. Here, we report on a novel matrix additive, o-alkylated dihydroxybenzoic acid (ADHB), which is a 2,5-dihydroxybenzoic acid (DHB) derivative incorporating a hydrophobic alkyl chain on a hydroxyl group to improve its affinity for hydrophobic peptides, thereby improving MALDI-MS sensitivity. The addition of ADHB to the conventional matrix α-cyano-4-hydroxycinnamic acid (CHCA) improved the sensitivity of hydrophobic peptides 10- to 100-fold. The sequence coverage of phosphorylase b digest was increased using ADHB. MS imaging indicated that hydrophobic peptides were enriched in the rim of a matrix/analyte dried spot when ADHB was used. In conclusion, the addition of ADHB to the standard matrix led to improved sensitivity of hydrophobic peptides by MALDI-MS.

We developed a catalytic propelled motor using the fuel source glucose, without the addition of hydrogen peroxide (H2O2), in an aqueous phase. The motor was composed of a Pt foil and a filter paper...

The topology and dynamics of melittin within the liposome were investigated by a mass spectrometry coupled with acetylation. The MALDI-TOF MS and MALDI-QIT-TOF MS/MS analyses revealed that only N-terminal amine of melittin was dominantly acetylated in the presence of liposome although all of four primary amines were completely and rapidly acetylated in aqueous solution. This result indicates that melittin adopts the N-terminal-outside transmembrane topology within the liposome. The time course of acetylation followed the first-order kinetics at any examined temperatures (6–30 °C). The rate constant was less than that of the acetylation of melittin in aqueous solution. The activation energy for acetylation (74 kJ mol −1 ) was comparable to that for dissociation of a lipid monomer from the membrane, suggesting a float-like longitudinal motion of melittin within the liposome. These results demonstrate that a mass spectrometry combined with chemical modification is very efficient way for clarifying the topology and dynamics of peptides bound to the membrane.

Cell surface heparan sulfate proteoglycans (HSPGs) play significant roles in the regulation of developmental signaling, including vascular endothelial growth factor (VEGF), fibroblast growth factor, Wnt and bone morphogenetic protein signaling, through modification of their sulfation patterns. Recent studies have revealed that one of the functions of heparan sulfate 6-O-endosulfatase (Sulf) is to remove the sulfate from the 6-O position of HSPGs at the cell surface, thereby regulating the binding activities of heparan sulfate (HS) chains to numerous ligands and receptors in animal species. In this study, we focused on the sea urchin Hemicentrotus pulcherrimus homolog of Sulf (HpSulf), and analyzed its expression pattern and functions during development. HpSulf protein was present throughout development and localized at cell surface of all blastomeres. In addition, the HS-specific epitope 10E4 was detected at the cell surface and partially colocalized with HpSulf. Knockdown of HpSulf using morpholino antisense oligonucleotides (MO) caused abnormal morphogenesis, and the development of MO-injected embryos was arrested before the hatched blastula stage, indicating that HpSulf is necessary for the early developmental process of sea urchin embryos. Furthermore, we found that injection of HpSulf mRNA suppressed the abnormal skeleton induced by overexpression of HpVEGF mRNA, whereas injection of an inactive form of HpSulf mRNA, containing mutated cysteines in the sulfatase domain, did not have this effect. Taken together, these results suggest that HpSulf is involved in the regulation of various signal transductions, including VEGF signaling, during sea urchin development.

We have previously demonstrated that RNA interference-mediated suppression of xanthine dehydrogenase (XDH), the rate-limiting enzyme in purine degradation, causes defects in the normal growth and development of Arabidopsis thaliana. Here, we investigated a possible role for XDH in drought tolerance, since this enzyme is also implicated in plant stress responses and acclimatization. When XDH-suppressed lines were subjected to drought stress, plant growth was markedly reduced in conjunction with significantly enhanced cell death and H2O2 accumulation. This drought-hypersensitive phenotype was reversed by pretreatment with exogenous uric acid, the catalytic product of XDH. These results suggest that fully functional purine metabolism plays a role in the Arabidopsis drought acclimatization.

We investigated the topology and dynamics of melittin within the liposomes using mass spectrometry combined with acetylation. According to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry/mass spectrometry (MALDI-QIT-TOF MS/MS) analyses, melittin within the liposomes was mono acetylated; with the acetylated position being the N-terminal of melittin. This acetylation followed first-order kinetics. The rate constant was less than that of the acetylation of melittin in aqueous solution. Thus, it is suggested that the observed rate constant is that for the release of the N-terminal region of melittin to a water phase from the hydrophobic core of the liposomes. This approach has opened a new method in the study of dynamics of transmembrane helices within the membranes using mass spectrometry.

The La-Si binary phase diagram under a high pressure of 13.5 GPa was experimentally constructed. New superconducting silicides LaSi{sub 5} and LaSi{sub 10} were found, which have peritectic decomposition temperatures at 1000 and 750 deg. C, respectively. The single crystal X-ray structural analysis revealed that there are two polymorphs in LaSi{sub 5}. The alpha-form obtained by heating a molar mixture of LaSi{sub 2} and 3 Si at about 700 deg. C or by a rapid cooling from 1000 deg. C under pressure crystallizes with the space group C2/m and the lattice parameters a=15.11(3), b=4.032(6), c=8.26(1) A, and beta=109.11(1){sup o}. The beta-form obtained by a slow cooling from 800-950 deg. C to 600 deg. C under pressure has the same space group but with slightly different lattice parameters, a=14.922(7), b=3.906(2), c=8.807(4) A, and beta=107.19(1){sup o}. The beta-form is formed during the incomplete transformation of the alpha-form on cooling, and has always been obtained as a mixture with the alpha-form. The compound can be characterized as a Zintl phase with a polyanionic framework {sub i}nfinity{sup 3}[Si{sub 5}]{sup 3-} with large tunnels running along the b axis hosting lanthanum ions. In the beta-form, three of the five Si sites are disordered. The twomore » polymorphs contain one dimensional sila-polyacene ribbons, Si ladder polymer, running along the b axis. The alpha-form showed superconductivity with the transition temperature T{sub c} of 11.5 K. LaSi{sub 10} crystallizes with the space group 6{sub 3}/mmc and the lattice parameters a=9.623(4), c=4.723(3) A. It is composed of La containing Si{sub 18} polyhedra (La-Si{sub 18}) of hexagonal beer-barrel shape, which form straight columns by stacking along the c-axis via face sharing. One-dimensional columns of La-Si{sub 18} barrels are edge-shared, and bundled with infinite Si trigonal bipyramid chains via corner sharing. The Si atoms in the straight chains have a five-fold coordination. LaSi{sub 10} became a superconductor with T{sub c}=6.7 K. The ab initio calculation of the electric band structures showed that alpha-LaSi{sub 5} and LaSi{sub 10} are metallic, and the conduction electrons mainly come from Si-3p orbitals. - Graphical abstract: In the study of the phase diagram of the La-Si binary system under high pressure and high temperature conditions, new Si-rich superconducting LaSi{sub 5} (T{sub c}=11.5 K) and LaSi{sub 10} (T{sub c}=6.7 K) have been found. LaSi{sub 5} contain unique one-dimensional sila-polyacene ribbons, and LaSi{sub 10} has a hexagonal columnar structure formed by face shared La-Si{sub 18} polyhedra.« less

Glycogen synthase kinase-3beta (GSK-3beta) is known to play a role in the regulation of the dynamics of microtubule networks in cells. Here we show the role of GSK-3beta in the proper formation of the mitotic spindles through an interaction with GCP5, a component of the gamma-tubulin ring complex (gammaTuRC). GCP5 bound directly to GSK-3beta in vitro, and their interaction was also observed in intact cells at endogenous levels. Depletion of GCP5 dramatically reduced the GCP2 and gamma-tubulin in the gammaTuRC fraction of sucrose density gradients and disrupted gamma-tubulin localization to the spindle poles in mitotic cells. GCP5 appears to be required for the formation or stability of gammaTuRC and the recruitment of gamma-tubulin to the spindle poles. A GSK-3 inhibitor not only led to the accumulation of gamma-tubulin and GCP5 at the spindle poles but also enhanced microtubule nucleation activity at the spindle poles. Depletion of GCP5 rescued this disrupted organization of spindle poles observed in cells treated with the GSK-3 inhibitor. Furthermore, the inhibition of GSK-3 enhanced the binding of gammaTuRC to the centrosome isolated from mitotic cells in vitro. Our findings suggest that GSK-3beta regulates the localization of gammaTuRC, including GCP5, to the spindle poles, thereby controlling the formation of proper mitotic spindles.

Membrane proteins containing hydrophobic regions have been difficult to analyze using MALDI-MS, probably due to the use of conventional matrices with a low affinity for hydrophobic peptides. Recently, we reported 1-(2,4,6-trihydroxyphenyl)octan-1-one (alkylated trihydroxyacetophenone (ATHAP)) as a matrix for hydrophobic peptides. In this study, ATHAP was applied to analyze membrane proteins containing transmembrane domains. As a result, we detected intact molecular ions for bacteriorhodopsin (BR) containing seven transmembrane domains that are difficult to detect using 2,4,6-trihydroxyacetophenone or sinapinic acid, by using ATHAP. In addition, we detected digest ions containing all seven transmembrane domains that are difficult to detect using α-cyano-4-hydroxycinnamic acid (CHCA), by using ATHAP. Moreover, ions for hydrophobic digests containing a single transmembrane domain for cadherin 1 (CDH1), fibroblast growth factor receptor 4 (FGFR4), epithelial cell adhesion molecule (EPCAM) recombinant proteins, and human epidermal growth factor receptor type 2 (HER2) were detected with higher sensitivity using ATHAP than with CHCA, confirming that ATHAP improved the membrane protein analyses, especially for hydrophobic regions such as transmembrane domains.

We have quantified the photomovement behavior of a suspension of Euglena gracilis representing a behavioral response to a light gradient. Despite recent measurements of phototaxis and photophobicity, the details of macroscopic behavior of cell photomovements under conditions of light intensity gradients, which are critical to understand recent experiments on spatially localized bioconvection patterns, have not been fully understood. In this paper, the flux of cell number density under a light intensity gradient was measured by the following two experiments. In the first experiment, a capillary containing the cell suspension was illuminated with different light intensities in two regions. In the steady state, the differences of the cell numbers in the two regions normalized by the total number were proportional to the light difference, where the light intensity difference ranged from 0.5–2.0 μmol m−2 s−1. The proportional coefficient was positive (i.e., the bright region contained many microorganisms) when the mean light intensity was weak (1.25 μmol m−2 s−1), whereas it was negative when the mean intensity was strong (13.75 μmol m−2 s−1). In the second experiment, a shallow rectangular container of the suspension was illuminated with stepwise light intensities. The cell number density distribution exhibited a single peak at the position where the light intensity was about Ic ≃ 3.8 μmol m−2 s−1. These results suggest that the suspension of E. gracilis responded to the light gradient and that the favorable light intensity was Ic.

Protein tyrosine nitration is an important post-translational modification. A variety of nitrated proteins are reported in Arabidopsis leaves and seedlings, sunflower hypocotyls, and pea roots. The identities of nitrated proteins are species-/organ-specific, and chloroplast proteins are most nitratable in leaves. However, precise mechanism is unclear. Here, we investigated nitroproteome in tobacco leaves following exposure to nitrogen dioxide. Proteins were extracted, electrophoresed and immunoblotted using an anti-3-nitrotyrosine antibody. Mass spectrometry and FASTA search identified for the first time an exclusive nitration of pathogenesis-related proteins, PR-1, PR-3 and PR-5, which are reportedly located in the apoplast or the vacuole. Furthermore, Tyr36 of thaumatin-like protein E2 was identfied as a nitration site. The underlying mechanism and physiological relevance are discussed.

A sigmoid-type dependence on the inhibitor concentration was observed in the cytochrome c reductase activity for peptide inhibitors (mastoparan and melittin), calmodulin antagonists (W-7 and tamoxifen) and monobutyltin in a reconstituted system comprised of recombinant rat neuronal nitric-oxide synthase (nNOS) and calmodulin (CaM). The increase in the concentration of CaM in the system induced a decrease in the inhibitory effect, indicating that the inhibitors might interfere with the interaction between nNOS and CaM. The changes in the fluorescence spectra of dansylated CaM caused by the addition of mastoparan, melittin and monobutyltin indicated complex formation between CaM and those compounds, which led to the decrease in the effective concentration of CaM available to nNOS. The sigmoid-type inhibition of mastoparan and melittin fit the theoretical equations quite well, assuming that two CaM molecules bind cooperatively to one nNOS homodimer. Monobutyltin, tamoxifen and W-7 were found to inhibit nNOS activity by binding to the CaM binding site of the nNOS homodimer, in addition to the binding of the inhibitors to calmodulin. These compounds inhibited the l -citrulline formation of nNOS from l -arginine, and the inhibitory effects were abrogated by raising the concentration of calmodulin. It became clear that the binding of calmodulin to nNOS can be interfered with in two ways: (1) via a decrease in the effective concentration of calmodulin caused by complex formation between the inhibitor and calmodulin, and (2) via the inhibition of the binding of calmodulin to nNOS caused by the occupation of the binding site by the inhibitor.

Site-specific hydrogen/deuterium (H/D) exchange was investigated using a model protein, Escherichia coli dihydrofolate reductase, by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) coupled with two-step protease digestion by pepsin and carboxypeptidase P. Carboxypeptidase, which is generally inactive under quenching conditions (0°C and pH 2.9), produced some overlapping peptide sequences in the presence of 3.9 mM NaCl as a stabilizer. From differences in the masses of these peptides, we successfully determined the deuterium incorporation of backbone amide hydrogens of six residues—Met16 (M20 loop), Glu17 (M20 loop), Met92 (βE), Ala117 (βF-βG loop), Cys152 (βH), and Phe153 (βH)—at a higher resolution using the program Isotopica, which is capable of deconvoluting a complex isotope envelope associated with the isotope distribution of deuterated peptides. The H/D exchange kinetics data obtained were highly consistent with the local structure and fluctuation of these sites as revealed by nuclear magnetic resonance (NMR) and X-ray crystallography. These results demonstrate that MALDI MS coupled with two-step digestion is a useful tool for studying the site-specific H/D exchange of proteins without the deuterium scrambling that occurs in the gas-phase collision-induced dissociation method.

Many static protein structures have been determined by X-ray crystallography and nuclear magnetic resonance (NMR). Protein dynamics has also been studied. The structure and dynamics of proteins provide critical information about their functional mechanisms. Recently, mass spectrometry has become an essential method to analyze protein topological structures and protein dynamics. We performed topological analysis of membrane proteins using mass spectrometry coupled with chemical cross-linking. The combination of chemical cross-linking and mass spectrometry is a powerful method for analyzing the topological organization of protein structures, protein complexes, and the interface between interacting subunits. In this paper, we introduce our strategies for studying the membrane-protein and protein-protein interaction sites of P450 17α with its redox partners, NADPH-cytochrome P450 reductase and cytochrome b5.

Motor dysfunction following descending and thoracoabdominal aortic surgery including thoracic endovascular aortic repair remains as one of their devastating complications, although several interventions have tried to preserve spinal cord blood flow during and after aortic aneurysm surgery for the purpose of reducing the incidence of postoperative paraplegia. One of the main limitations of protective strategies is the inability to assess the adequacy of spinal cord perfusion and spinal cord function intraoperatively. Advances in stimulation technique using short train pulses could make intraoperative monitoring of functional integrity of motor pathways possible by recording myogenic motor evoked potentials (MEP), which is a highly sensitive technique to assess spinal cord integrity, identifying insufficient blood flow. To reduce the risk of neurologic injury, anesthesiologists are required to properly understand monitoring of MEP and to manage anesthesia and hemodynamics appropriately. Here, we summarize the strategies for spinal cord protection, including the functional monitoring of spinal cord and anesthetic techniques.

We construct cellular automaton models for the spatio-temporal pattern of Euglena gracilis bioconvection, which is generated when a suspension of Euglena gracilis is illuminated from the bottom with strong light intensity through a statistical construction method of cellular automata. The method of construction is introduced by Kawaharada and Iima (A. Kawaharada and M. Iima, “Constructing Cellular Automaton Models from Observation Data”, In 2013 First International Symposium on Computing and Networking, pp. 559–562 (2013)). Some features of the original patterns are reproduced by one dimensional deterministic CA with the nearest three neighbors and eight possible states for a site.

Steroidogenic acute regulatory (StAR) protein is an important regulatory protein in steroidogenesis and rapidly undergoes proteolysis after import into the mitochondria. In this study, we determined the proteolytic cleavage sites and investigated the effects on the stimulation of steroidogenic activity of the blockage of these sites by mutation. The cleaved StAR proteins, which were purified using an anti-StAR immobilized column, reacted with antiserum against the StAR C-terminal oligopeptide. The molecular weights of the purified proteins were determined by MALDI-TOF mass spectrometry, and were found to be identical to those of the 40-285 and 55-285 amino-acid-regions of the StAR protein. To confirm the identification of the cleavage sites, we constructed site-directed mutants of bovine StAR cDNA, which contained the amino acids R37A/R38A/L40A and/or R53A/R54A/R55A. These mutant StAR proteins expressed in COS-1 cells were not cleaved at positions 39-40 and 54-55, and were processed at sites different from those in the wild-type StAR protein. These mutant proteins stimulated pregnenolone formation at almost the same rate as the wild-type StAR protein in COS-1 cells, which suggests that the cholesterol transfer activity was not affected by the mutation.

We investigated the differential protein expression patterns of retinal pigment epithelial (RPE) cells exposed to increased glucose concentrations. Cultured human RPE cells (ARPE-19) were exposed for 4 days with normal blood glucose concentration (5.5 mM D-glucose), followed by exposure to either normal (5.5 mM) or high (33 mM) concentrations of D-glucose for 48h. Protein extracts of glucose-treated RPE cells were then subjected to comparative proteome analysis based on 2-D gel electrophoresis. Protein spots were visualized by silver staining. The differentially expressed proteins were excised and digested in-gel with trypsin, then analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The expression levels of cathepsin B, glutathione peroxidase and heat shock protein 27 were increased, and that of protein disulfide isomerase decreased in high glucose treated RPE compared to normal glucose. The isoelectric point of copper/zinc-containing superoxide dismutase (Cu/Zn-SOD) shifted toward acidic region in response to high glucose. Cu/Zn-SOD activity in high glucose group was significantly lower than that in normal glucose group (P

The 2-nitrobenzenesulfenyl (NBS) method, which is useful for quantitative proteome analysis, is based on stable isotope labeling of tryptophan residues with NBS chloride ((12)C(6)-NBSCl or (13)C(6)-NBSCl). We found that 3-hydroxy-4-nitrobenzoic acid (3H4NBA) is a more suitable matrix than 2,5-dihydroxybenzoic acid (DHB) for detecting NBS-labeled peptides by MALDI-quadrupole IT (QIT)-TOF MS . Furthermore, NBS-labeled peptides were selectively ionized and detected in a mixture of NBS-labeled and unlabeled peptides. Labeled paired peaks were easily detected without enrichment, nonpaired labeled peaks were clearly distinguished from unlabeled contaminating peptides, and nitrotyrosine-containing peptides were also selectively detected on the 3H4NBA matrix, while by-product-peaks arising from nitrobenzene moieties were suppressed. The use of 3H4NBA as a comatrix with CHCA improved the sensitivity of detection while substantially retaining the selectivity of 3H4NBA. The 3H4NBA matrix offers great advantages in terms of simplicity, sensitivity, and usability when used for the NBS method and for MALDI-TOF MS analysis applied to compounds having a nitrobenzene ring.

vitamin D is 25-hydroxylated in the liver, before being activated by 1α-hydroxylation in the kidney. Recently, the rat cytochrome P450 2J3 (CYP2J3) has been identified as a principal vitamin D 25-hydroxylase in the rat [Yamasaki T, Izumi S, Ide H, Ohyama Y. Identification of a novel rat microsomal vitamin D3 25-hydroxylase. J Biol Chem 2004;279(22):22848-56]. In this study, we examine whether human CYP2J2 that exhibits 73 0x1.39bf8p-890mino acid homology to rat CYP2J3 has similar catalytic properties. Recombinant human CYP2J2 was overexpressed in Escherichia coli, purified, and assayed for vitamin D 25-hydroxylation activity. We found significant 25-hydroxylation activity toward vitamin D3 (turnover number, 0.087 min-1), vitamin D2 (0.16 min-1), and 1α-hydroxyvitamin D3 (2.2 min-1). Interestingly, human CYP2J2 hydroxylated vitamin D2, an exogenous vitamin D, at a higher rate than it did vitamin D3, an endogenous vitamin D, whereas, rat CYP2J3 hydroxylated vitamin D3 (1.4 min-1) more efficiently than vitamin D2 (0.86 min-1). Our study demonstrated that human CYP2J2 exhibits 25-hydroxylation activity as well as rat CYP2J3, although the activity of human CYP2J2 is weaker than rat CYP2J3. CYP2J2 and CYP2J3 exhibit distinct preferences toward vitamin D3 and D2. c 2006 Elsevier Inc. All rights reserved.

Morphological changes of DMPC, DLPC, and DPPC bilayers containing melittin (lecithin/melittin molar ratio of 10:1) around the gel-to-liquid crystalline phase transition temperatures (Tc) were examined by a variety of biophysical methods. First, giant vesicles with the diameters of approximately 20 microm were observed by optical microscopy for melittin-DMPC bilayers at 27.9 degrees C. When the temperature was lowered to 24.9 degrees C (Tc = 23 degrees C for the neat DMPC bilayers), the surface of vesicles became blurred and dynamic pore formation was visible in the microscopic picture taken at different exposure times. Phase separation and association of melittin molecules in the bilayers were further detected by fluorescent microscopy and mass spectrometry, respectively. These vesicles disappeared completely at 22.9 degrees C. It was thus found that the melittin-lecithin bilayers reversibly undergo their fusion and disruption near the respective Tcs. The fluctuation of lipids is, therefore, responsible for the membrane fusion above the Tc, and the association of melittin molecules causes membrane fragmentation below the Tc. Subsequent magnetic alignments were observed by solid-state (31)P NMR spectra for the melittin-lecithin vesicles at a temperature above the respective Tcs. On the other hand, additional large amplitude motion induced by melittin at a temperature near the Tc breaks down the magnetic alignment.

Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1), previously thought to be a backup enzyme for uracil-DNA glycosylase, has recently been shown to excise 5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU) bearing an oxidized group at ring C5 as well as an uracil. In the present study, we used site-directed mutagenesis to construct a series of mutants of human SMUG1 (hSMUG1), and tested their activity for uracil, hoU, hmU, fU and other bases to elucidate the catalytic and damage-recognition mechanism of hSMUG1. The functional analysis of the mutants, together with the homology modeling of the hSMUG1 structure based on that determined recently for Xenopus laevis SMUG1, revealed the crucial residues for the rupture of the N-glycosidic bond (Asn85 and His239), discrimination of pyrimidine rings through pi-pi stacking to the base (Phe98) and specific hydrogen bonds to the Watson-Crick face of the base (Asn163) and exquisite recognition of the C5 substituent through water-bridged (uracil) or direct (hoU, hmU and fU) hydrogen bonds (Gly87-Met91). Integration of the present results and the structural data elucidates how hSMUG1 accepts uracil, hoU, hmU and fU as substrates, but not other oxidized pyrimidines such as 5-hydroxycytosine, 5-formylcytosine and thymine glycol, and intact pyrimidines such as thymine and cytosine.