Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp A11-2, reveal potential for expanding its substrate selectivity

Sulfur compounds in fossil fuels are a major source of environmental pollution, and microbial desulfurization has emerged as a promising technology for removing sulfur under mild conditions. The enzyme TdsC from the thermophile Paenibacillus sp. A11-2 is a two-component flavin-dependent monooxygenase that catalyzes the oxygenation of dibenzothiophene (DBT) to its sulfoxide (DBTO) and sulfone (DBTO2) during microbial desulfurization. The crystal structures of the apo and flavin mononucleotide (FMN)-bound forms of DszC, an ortholog of TdsC, were previously determined, although the structure of the ternary substrate–FMN–enzyme complex remains unknown. Herein, we report the crystal structures of the DBT–FMN–TdsC and DBTO–FMN–TdsC complexes. These ternary structures revealed many hydrophobic and hydrogen-bonding interactions with the substrate, and the position of the substrate could reasonably explain the two-step oxygenation of DBT by TdsC. We also determined the crystal structure of the indole-bound enzyme because TdsC, but not DszC, can also oxidize indole, and we observed that indole binding did not induce global conformational changes in TdsC with or without bound FMN. We also found that the two loop regions close to the FMN-binding site are disordered in apo-TdsC and become structured upon FMN binding. Alanine substitutions of Tyr-93 and His-388, which are located close to the substrate and FMN bound to TdsC, significantly decreased benzothiophene oxygenation activity, suggesting their involvement in supplying protons to the active site. Interestingly, these substitutions increased DBT oxygenation activity by TdsC, indicating that expanding the substrate-binding site can increase the oxygenation activity of TdsC on larger sulfur-containing substrates, a property that should prove useful for future microbial desulfurization applications

Analysis of the Optimum Tapering Angle in Microanastomosis Using Computational Fluid Dynamics

Background: In free flap transfer, size discrepancy between the vascular pedicle and recipient vessel can create a problem for microsurgeons and sometimes induces postoperative thrombus formation. When there is a major difference between the diameters of the vascular pedicle and the recipient vessel, the larger vessel is often tapered to perform the anastomosis properly. However, the decision on the tapering angle used depends mostly on the operator’s experience. In this study, computational fluid dynamics (CFD) was used to investigate the optimum tapering angle. Methods: Using ANSYS ICEM 16.0 (ANSYS Japan, Tokyo, Japan), simulated vessels of diameters 1.5 mm and 3.0 mm were designed and then used to produce four anastomosis models with the 3.0-mm vessel tapered at angles of 15º, 30º, 60º, and 90º (no tapering). Venous perfusion with a mean value of 13.0 mL/min was simulated, and this was passed through the four anastomosis models in both the forward direction (F), from the smaller to the larger vessel, and the retrograde direction (R), from the larger to the smaller vessel. The velocity, wall shear stress (WSS), and oscillatory shear index (OSI) were measured in these eight patterns and then analyzed using OpenFOAM version 5. Results: The decrease in velocity was limiting. The WSS was greater in the R direction than the F direction at every tapering angle. The OSI also tended to be almost the same in the F direction, and lower at smaller tapering angles in the R direction. And, it was greater in the F direction than in the R direction at every tapering angle. The OSI values for 15º and 30º were almost identical in the R direction. Conclusion: The risk of thrombus formation is thought to be lower when tapering is used for anastomosis if the direction of flow is from the larger to the smaller vessel, rather than vice versa. These results also suggest that the optimum tapering angle is approximately 30º in both directions

Effect of dapagliflozin on 24-hour glycemic variables in Japanese patients with type 2 diabetes mellitus receiving basal insulin supported oral therapy (DBOT) : a multicenter, randomized, open-label, parallel-group study

Introduction: This study aimed to evaluate the impacts of dapagliflozin on 24-hour glucose variability and diabetes-related biochemical variables in Japanese patients with type 2 diabetes who had received basal insulin supported oral therapy (BOT). Research design and methods: Changes in mean daily blood glucose level before and after 48–72 hours of add-on or no add-on of dapagliflozin (primary end point) and diabetes-related biochemical variables and major safety variables during the 12 weeks (secondary end point) were evaluated in the multicenter, randomized, two-arm, open-label, parallel-group comparison study. Results: Among 36 participants, 18 were included in the no add-on group and 18 were included in the dapagliflozin add-on group. Age, gender, and body mass index were comparable between the groups. There were no changes in continuous glucose monitoring metrics in the no add-on group. In the dapagliflozin add-on group, mean glucose (183–156mg/dL, p=0.001), maximum glucose (300–253, p<0.01), and SD glucose (57–45, p<0.05) decreased. Time in range increased (p<0.05), while time above the range decreased in the dapagliflozin add-on group but not in the no add-on group. After 12-week treatment with dapagliflozin add-on, 8-hydroxy-2’-deoxyguanosine (8OHdG), as well as hemoglobin A1c (HbA1c), decreased. Conclusions: This study showed that the mean daily blood glucose and other daily glucose profiles were amended after 48–72 hours of dapagliflozin add-on in Japanese patients with type 2 diabetes who received BOT. The diabetes-related biochemical variables such as HbA1c and urinary 8OHdG were also obtained during the 12 weeks of dapagliflozin add-on without major adverse events. A preferable 24-hour glucose profile in ‘time in ranges’ and an improvement in reactive oxygen species by dapagliflozin warrant us to evaluate these benefits in larger clinical studies

Measuring the Shock Stage of Asteroid Regolith Grains by Electron Back-Scattered Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction. These techniques would then be available for samples returned from other asteroid regoliths

Measuring Shock Stage of ltokawa Regolith Grains by Electron Back-Scattered Diffraction and Synchrotron X-Ray Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction techniques. We are making measurements of olivine crystal structures and using these to elucidate critical regolith impact processes. We use electron back-scattered diffraction (EBSD) and synchrotron X-ray diffraction (SXRD). We are comparing the Itokawa samples to L and LL chondrite meteorites chosen to span the shock scale experienced by Itokawa, specifically Chainpur (LL3.4, Shock Stage 1), Semarkona (LL3.00, S2), Kilabo (LL6, S3), NWA100 (L6, S4) and Chelyabinsk (LL5, S4). In SXRD we measure the line broadening of olivine reflections as a measure of shock stage. In this presentation we concentrate on the EBSD work. We employed JSC's Supra 55 variable pressure FEG-SEM and Bruker EBSD system. We are not seeking actual strain values, but rather indirect strain-related measurements such as extent of intra-grain lattice rotation, and determining whether shock state "standards" (meteorite samples of accepted shock state, and appropriate small grain size) show strain measurements that may be statistically differentiated, using a sampling of particles (number and size range) typical of asteroid regoliths. Using our system we determined that a column pressure of 9 Pa and no C-coating on the sample was optimal. We varied camera exposure time and gain to optimize mapping performance, concluding that 320x240 pattern pixilation, frame averaging of 3, 15 kV, and low extractor voltage yielded an acceptable balance of hit rate (>90%), speed (11 fps) and map quality using an exposure time of 30 ms (gain 650). We found that there was no strong effect of step size on Grain Orientation Spread (GOS) and Grain Reference Orientation Deviation angle (GROD-a) distribution; there was some effect on grain average Kernel Average Misorientation (KAM) (reduced with smaller step size for the same grain), as expected. We monitored GOS, Maximum Orientation Spread (MOS) and GROD-a differences between whole olivine grains and sub-sampled areas, and found that there were significant differences between the whole grain dataset and subsets, as well as between subsets, likely due to sampling-related "noise". Also, in general (and logically) whole grains exhibit greater degrees of cumulative lattice rotation. Sampling size affects the apparent strain character of the grain, at least as measured by GOS, MOS and GROD-a. There were differences in the distribution frequencies of GOS and MOS between shock stages, and in plots of MOS and GOS vs. grain diameter. These results are generally consistent with those reported this year. However, it is unknown whether the differences between samples of different shock states exceeds the clustering of these values to the extent that shock stage determinations can still be made with confidence. We are investigating this by examination of meteorites with higher shock stage 4 to 5. Our research will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results will directly enrich the ongoing asteroid and comet exploration missions by NASA and JAXA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith

人総研シンポジウム抄録 : 福島原発事故12年の経験から学ぶ -当時小学生だった若者達との対話から(第2回)-

departmental bulletin pape

Evaluation of [¹⁸F]pitavastatin as a positron emission tomography tracer for in vivo organic transporter polypeptide function

Introduction: To understand the pathways involved in drug clearance from the body, quantitative evaluations of the hepatobiliary transport of drugs are important. The organic anion transporting polypeptide (OATP) family transporter, particularly OATP1B1 and 1B3, are considered to play an important role in hepatic uptake of organic anion compounds. Pitavastatin is a substrate of OATP, and it includes a fluorine group. Therefore, it represents an acceptable positron-emission tomography (PET) tracer using fluorine-18 to image in vivo hepatic transporter functions. Method: [¹⁸F]Pitavastatin was synthesized using the method we previously reported. To evaluate the potential of [¹⁸F]pitavastatin in PET imaging of in vivo OATP functions, we investigated the hepatic uptake with/without rifampicin as an OATP inhibitor after administration in normal SD rats. [¹⁸F]Pitavastatin metabolite was evaluated using reverse-phase thin-layer chromatography (TLC) autoradiography. We subsequently analyzed the PET image results and demonstrated that [¹⁸F]pitavastatin selectively accumulated in the liver post-administration. Result and discussion: In metabolite analysis using reverse-phase TLC, we found that the radioactivity detected in the plasma, liver (>90% intact), and bile mostly originated from the parent pitavastatin of the PET study (~40 min). [¹⁸F]pitavastatin's hepatic uptake decreased (approximately 76%) with rifampicin co-administration in PET analysis. Because [¹⁸F]pitavastatin has lower clearance in rats than other previously reported OATP1B PET s, it holds the potential of an imaging tracer that has a higher sensitivity in monitoring hepatic OATP1B function's changes. Conclusion: Compared with the previously reported OATP imaging tracers, [¹⁸F]pitavastatin is more suitable for the sensitive detection of functional changes in OATP transporters. We believe that [¹⁸F]pitavastatin enables quantitative analysis of the hepatobiliary transport system for organic anion compounds