Biomedical subjects

H Tsuruta

Publications and source records attributed to H Tsuruta.

At least 19 recordsLinked to original sources

PubMed2004

Regional inventory of soil surface nitrogen balances in Indian agriculture (2000-2001).

Nitrogen regulates several ecological and biogeochemical processes and excess reactive nitrogen in the environment can lead to pollution problems, including the deterioration of air quality, disruption of forest processes, acidification of lakes and streams, and degradation of coastal waters. Much of the excess nitrogen inputs are related to food and energy production. An important step to understanding the sources of nitrogen and ultimately defining solutions to excess nitrogen is to describe the geographic distribution of agricultural nitrogen contributions from different regions. In this study, soil surface nitrogen loads were quantified for different states of India for the period 2000-2001. Nearly 35.4 Tg of nitrogen has been estimated as inputs from different sources, with output nitrogen from harvested crops of about 21.20 Tg. The soil surface nitrogen balance, estimated as inputs minus outputs, is found to be about 14.4 Tg surplus from the agricultural land of India. Livestock manure constituted a major percentage of total inputs (44.06%), followed by inorganic fertilizer (32.48%), atmospheric deposition (11.86%) and nitrogen fixation (11.58%). Nitrogen balance varied from deficit to surplus for different states. The highest nitrogen surplus was found in Uttar Pradesh (2.50 Tg) followed by Madhya Pradesh (1.83 Tg), Andhra Pradesh (1.79 Tg), etc. A negative nitrogen balance was found in Orissa (-0.01 Tg), Andaman Nicobar Islands (-0.32 Tg) and for some of the northeastern states. Major fertilizer consumption states were found to be Tamilnadu (204 kg/ha), Haryana (132 kg/ha), Punjab (148 kg/ha), followed by others. Similarly, nitrogen inputs from total livestock excretions were found to be high for Kerala (616 kg/ha), Jammu and Kashmir (389 kg/ha), Tamil Nadu (338 kg/ha), etc. The average nitrogen surplus of about 54 kg/ha observed for the agricultural land of the entire country of India is comparatively higher than the average surplus of about 31 kg/ha reported for European countries. These results, obtained from nutrient mass balance calculations, will be useful to formulate nutrient management plans relating to fertilizer usage, livestock management and for adopting some best management strategies at a state level in India.

Agriculture↗

PubMed2003

Nutrient regulation of epothilone biosynthesis in heterologous and native production strains.

Fermentation media with different initial concentrations of ammonium and phosphate salts were used to study the inhibitory effects of those ions on growth and production of epothilone in Sorangium cellulosum and Myxococcus xanthus. The native epothilone producer, S. cellulosum was more sensitive to ammonium and phosphate than the heterologous producer, M. xanthus. An ammonium concentration of 12 mM reduced epothilone titers by 90% in S. cellulosum but by only 40% in M. xanthus. When 5 mM phosphate was added to the medium, production in both strains was 60% lower. Higher phosphate concentrations had little additional effect on M. xanthus titers, but epothilone production with 17 mM extra-cellular phosphate in S. cellulosum was 95% lower than in the control condition. The effect of iron supplementation to the fermentation medium was also investigated. Both strains showed best production with 20 microM iron added to the medium.

Antineoplastic Agents↗

PubMed2003

Seasonal changes of CO(2), CH(4) and N(2)O fluxes in relation to land-use change in tropical peatlands located in coastal area of South Kalimantan.

Tropical peatland could be a source of greenhouse gases emission because it contains large amounts of soil carbon and nitrogen. However these emissions are strongly influenced by soil moisture conditions. Tropical climate is characterized typically by wet and dry seasons. Seasonal changes in the emission of carbon dioxide (CO(2)), methane (CH(4)) and nitrous oxide (N(2)O) were investigated over a year at three sites (secondary forest, paddy field and upland field) in the tropical peatland in South Kalimantan, Indonesia. The amount of these gases emitted from the fields varied widely according to the seasonal pattern of precipitation, especially methane emission rates were positively correlated with precipitation. Converting from secondary forest peatland to paddy field tended to increase annual emissions of CO(2) and CH(4) to the atmosphere (from 1.2 to 1.5 kg CO(2)-C m(-2)y(-1) and from 1.2 to 1.9 g CH(4)-C m(-2)y(-1)), while changing land-use from secondary forest to upland tended to decrease these gases emissions (from 1.2 to 1.0 kg CO(2)-C m(-2)y(-1) and from 1.2 to 0.6 g CH(4)-C m(-2)y(-1)), but no clear trend was observed for N(2)O which kept negative value as annual rates at three sites.

Carbon Dioxide↗

PubMed2002

Modulation of epothilone analog production through media design.

Recently, the epothilone polyketide synthase (PKS) was successfully introduced into a heterologous production host for the large-scale production of epothilone D. We have found that at least three other epothilones can also be produced as the major fermentation product of this recombinant strain by supplementation of specific substrates to the production media. Addition of acetate or propionate to the media results in modulation of the epothilone D:C ratio, whereas addition of L-serine with either acetate or propionate yields epothilone H(1) or H(2) as the major product. This strategy permits production of at least four novel epothilones by culturing a single host with a genetically modified epothilone PKS in various media.

Acetates↗

PubMed2002

Surface flux measurements of CO2 and N2O from a dried rice paddy in Japan during a fallow winter season.

The CO2 and N2O soil emissions at a rice paddy in Mase, Japan, were measured by enclosures during a fallow winter season. The Mase site, one of the AsiaFlux Network sites in Japan, has been monitored for moisture, heat, and CO2 fluxes since August 1999. The paddy soil was found to be a source of both CO2 and N2O flux from this experiment. The CO2 and N2O fluxes ranged from -27.6 to 160.4 microg CO2/m2/sec (average of 49.1 +/- 42.7 microg CO2/m2/sec) and from -4.4 to 129.5 ng N2O/m2/sec (average of 40.3 +/- 35.6 ng N2O/m2/ sec), respectively. A bimodal trend, which has a sub-peak in the morning around 10:00 a.m. and a primary peak between 2:00 and 3:00 p.m., was observed. Gas fluxes increased with soil temperature, but this temperature dependency seemed to occur only on the calm days. Average CO2 and N2O fluxes were 27.7 microg CO2/m2/sec and 13.4 ng N2O/m2/sec, with relatively small fluctuation during windy days, while averages of 69.3 microg CO2/m2/sec and 65.8 ng N2O/m2/sec were measured during calm days. This relationship was thought to be a result of strong surface winds, which enhance gas exchange between the soil surface and the atmosphere, thus reducing the gas emissions from soil surfaces.

Agriculture↗

PubMed2002

Simulation of potassium extraction by continuous haemodiafiltration.

Prediction of potassium extraction rates by continuous haemodiafiltration (CHDF) is useful for safe management of potassium levels in patients with hyperkalaemia. For this purpose, we developed a formula to predict the quantity of potassium extracted by CHDF. We hypothesized that potassium concentration in efflux dialysate was completely saturated by the influx blood, and potassium concentration in efflux blood was calculated based on this hypothesis. To check the accuracy of the calculation, potassium concentration was measured in efflux blood, and values were compared to predicted concentrations. Predicted potassium concentrations demonstrated good correlation to the measured values (95% confidence range, -0.32 to 0.58 mmol/l). These results confirmed that our hypothesis is applicable to clinical use of CHDF. Based on our observations, we created a formula to accurately predict the amount of potassium (dK) extracted by CHDF: dK=(Cb-Cd)xQd+CbxQf-CsxQs (Cb: plasma potassium concentration; Cd: potassium concentration in a dialysate; Cs: potassium concentration in the replacement fluid; Qd: dialysis rate; Qf: filtration rate and Qs: infusion rate of replacement fluid).

Acute Kidney Injury↗

PubMed2001

Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation.

Time-resolved small-angle X-ray scattering (TR-SAXS) was used to study the kinetics of a large conformational change that occurs during the maturation of an icosahedral virus. Virus-like particles (VLPs) of the T=4 non-enveloped RNA virus Nudaurelia capensis omega virus (NomegaV) were shown to undergo a large pH-dependent conformational change. Electron cryo-microscopy (cryoEM) and X-ray solution scattering were used to show that the precursor VLP (procapsid) was 16 % larger in diameter than the resulting capsid, which was shown by the cryoEM study to closely resemble the infectious mature virion. The procapsid form of the VLPs was observed at pH 7.5 and was converted to the capsid form at pH 5.0. Static SAXS measurements of the VLPs in solutions ranging between these pH values determined that the half-titration point of the transition was pH 6.0. Time-resolved SAXS experiments were performed on VLP solutions by initiating a pH change from 7.5 to 5.0 using a stopped-flow device, and the time-scale of the conformational change occurred in the subsecond range. Using a less drastic pH change (lowering the pH to 5.8 or 5.5), the conformational change occurred more slowly, on the subminute or minute time-scale, with the detection of a fast-forming intermediate in the transition. Further characterization using static SAXS measurements showed that the conformational change was initially reversible but became irreversible after autoproteolytic maturation was about 15 % complete. In addition to characterizing the large quaternary conformational change, we have been able for the first time to demonstrate that it takes place on the subsecond time-scale, a regime comparable to that observed in other multisubunit assemblies.

Capsid↗

PubMed2001

Structure and mechanism of the RuvB Holliday junction branch migration motor.

The RuvB hexamer is the chemomechanical motor of the RuvAB complex that migrates Holliday junction branch-points in DNA recombination and the rescue of stalled DNA replication forks. The 1.6 A crystal structure of Thermotoga maritima RuvB together with five mutant structures reveal that RuvB is an ATPase-associated with diverse cellular activities (AAA+-class ATPase) with a winged-helix DNA-binding domain. The RuvB-ADP complex structure and mutagenesis suggest how AAA+-class ATPases couple nucleotide binding and hydrolysis to interdomain conformational changes and asymmetry within the RuvB hexamer implied by the crystallographic packing and small-angle X-ray scattering in solution. ATP-driven domain motion is positioned to move double-stranded DNA through the hexamer and drive conformational changes between subunits by altering the complementary hydrophilic protein- protein interfaces. Structural and biochemical analysis of five motifs in the protein suggest that ATP binding is a strained conformation recognized both by sensors and the Walker motifs and that intersubunit activation occurs by an arginine finger motif reminiscent of the GTPase-activating proteins. Taken together, these results provide insights into how RuvB functions as a motor for branch migration of Holliday junctions.

Adenosine Diphosphate↗

PubMed2001

Domain bridging interactions. A necessary contribution to the function and structure of Escherichia coli aspartate transcarbamoylase.

Aspartate transcarbamoylase undergoes a domain closure in the catalytic chains upon binding of the substrates that initiates the allosteric transition. Interdomain bridging interactions between Glu(50) and both Arg(167) and Arg(234) have been shown to be critical for stabilization of the R state. A hybrid version of the enzyme has been generated in vitro containing one wild-type catalytic subunit, one catalytic subunit in which Glu(50) in each catalytic chain has been replaced by Ala (E50A), and wild-type regulatory subunits. Thus, the hybrid enzyme has one catalytic subunit capable of domain closure and one catalytic subunit incapable of domain closure. The hybrid does not behave as a simple mixture of the constituent subunits; it exhibits lower catalytic activity and higher aspartate affinity than would be expected. As opposed to the wild-type enzyme, the hybrid is inhibited allosterically by CTP at saturating substrate concentrations. As opposed to the E50A holoenzyme, the hybrid is not allosterically activated by ATP at saturating substrate concentrations. Small angle x-ray scattering showed that three of the six interdomain bridging interactions in the hybrid is sufficient to cause the global structural change to the R state, establishing the critical nature of these interactions for the allosteric transition of aspartate transcarbamoylase.

Aspartate Carbamoyltransferase↗

PubMed2001

Characterization of subunit structural changes accompanying assembly of the bacteriophage P22 procapsid.

P22 serves as a model for the assembly and maturation of icosahedral double-stranded DNA viruses. The viral capsid precursor, or procapsid, is assembled from 420 copies of a 47 kDa coat protein subunit (gp5) that is rich in beta-strand secondary structure. Maturation to the capsid, which occurs in vivo upon DNA packaging, is accompanied by shell expansion and a large increase in the level of protection against deuterium exchange of amide NH groups. Accordingly, shell maturation resembles the final step in protein folding, wherein domain packing and an exchange-protected core become more fully developed [Tuma, R., Prevelige, P. E., Jr., and Thomas, G. J., Jr. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9885-9890]. Here, we exploit recent advances in Raman spectroscopy to investigate the P22 coat protein subunit under conditions which stabilize the monomeric state, viz., in solution at very low concentrations. Under these conditions, the monomer exhibits an elongated shape, as demonstrated by small-angle X-ray scattering. Raman spectra allow the identification of conformation-sensitive marker bands of the monomer, as well as the characterization of NH exchange dynamics for comparison with procapsid and capsid shell assemblies. We show that procapsid assembly involves significant ordering of the predominantly beta-strand backbone. We propose that such ordering may mediate formation of the distinct subunit conformations required for assembly of a T = 7 icosahedral lattice. However, the monomer, like the subunit within the procapsid lattice, exhibits a moderate level of protection against low-temperature NH exchange, indicative of a nascent folding core. The environments and exchange characteristics of key side chains are also similar for the monomeric and procapsid subunits, and distinct from corresponding characteristics of the capsid subunit. The monomer thus represents a compact but metastable folding intermediate along the pathway to assembly of the procapsid and capsid.

Amides↗

PubMed2001

Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination.

Several factors, including spatial and temporal coherence of the electron microscope, specimen movement, recording medium, and scanner optics, contribute to the decay of the measured Fourier amplitude in electron image intensities. We approximate the combination of these factors as a single Gaussian envelope function, the width of which is described by a single experimental B-factor. We present an improved method for estimating this B-factor from individual micrographs by combining the use of X-ray solution scattering and numerical fitting to the average power spectrum of particle images. A statistical estimation from over 200 micrographs of herpes simplex virus type-1 capsids was used to estimate the spread in the experimental B-factor of the data set. The B-factor is experimentally shown to be dependent on the objective lens defocus setting of the microscope. The average B-factor, the X-ray scattering intensity of the specimen, and the number of particles required to determine the structure at a lower resolution can be used to estimate the minimum fold increase in the number of particles that would be required to extend a single particle reconstruction to a specified higher resolution. We conclude that microscope and imaging improvements to reduce the experimental B-factor will be critical for obtaining an atomic resolution structure.

Capsid↗

PubMed2001

Synthesis and sweetness characteristics of L-aspartyl-D-alanine fenchyl esters.

Four isomers of the L-aspartyl-D-alanine fenchyl esters were prepared as potential peptide sweeteners. L-Aspartyl-D-alanine (+)-alpha-fenchyl ester and L-aspartyl-D-alanine (-)-beta-fenchyl ester showed sweetness with potencies 250 and 160 times higher than that of sucrose, respectively. In contrast, L-aspartyl-D-alanine (+)-beta-fenchyl ester and L-aspartyl-D-alanine (-)-alpha-fenchyl ester had the highest sweetness potencies at 5700 and 1100 times that of sucrose, respectively. In particular, L-aspartyl-D-alanine (-)-alpha-fenchyl ester had an excellent sweetness quality; but L-aspartyl-D-alanine (+)-beta-fenchyl ester did not have an excellent quality of sweetness because it displayed an aftertaste caused by the strong sweetness.

Dipeptides↗

PubMed2001

Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase.

Regulation of protein function, often achieved by allosteric mechanisms, is central to normal physiology and cellular processes. Although numerous models have been proposed to account for the cooperative binding of ligands to allosteric proteins and enzymes, direct structural support has been lacking. Here, we used a combination of X-ray crystallography and small angle X-ray scattering in solution to provide direct structural evidence that the binding of ligand to just one of the six active sites of Escherichia coli aspartate transcarbamoylase induces a concerted structural transition from the T to the R state.

Allosteric Regulation↗

PubMed2000

Crystal and solution structures of an HslUV protease-chaperone complex.

HslUV is a "prokaryotic proteasome" composed of the HslV protease and the HslU ATPase, a chaperone of the Clp/Hsp100 family. The 3.4 A crystal structure of an HslUV complex is presented here. Two hexameric ATP binding rings of HslU bind intimately to opposite sides of the HslV protease; the HslU "intermediate domains" extend outward from the complex. The solution structure of HslUV, derived from small angle X-ray scattering data under conditions where the complex is assembled and active, agrees with this crystallographic structure. When the complex forms, the carboxy-terminal helices of HslU distend and bind between subunits of HslV, and the apical helices of HslV shift substantially, transmitting a conformational change to the active site region of the protease.

ATP-Dependent Proteases↗

PubMed2000

Topologically linked protein rings in the bacteriophage HK97 capsid.

The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.

Asparagine↗

PubMed2000

Maturation dynamics of a viral capsid: visualization of transitional intermediate states.

Typical of DNA bacteriophages and herpesviruses, HK97 assembles in two stages: polymerization and maturation. First, capsid protein polymerizes into closed shells; then, these precursors mature into larger, stabler particles. Maturation is initiated by proteolysis, producing a metastable particle primed for expansion-the major structural transition. We induced expansion in vitro by acidic pH and monitored the resulting changes by time-resolved X-ray diffraction and cryo-electron microscopy. The transition, which is not synchronized over the population, proceeds in a series of stochastically triggered subtransitions. Three distinct intermediates were identified, which are comparable to transitional states in protein folding. The intermediates' structures reveal the molecular events occurring during expansion. Integrated into a movie (see Dynamic Visualization below), they show capsid maturation as a dynamic process.

Acids↗

PubMed2000

Three of the six possible intersubunit stabilizing interactions involving Glu-239 are sufficient for restoration of the homotropic and heterotropic properties of Escherichia coli aspartate transcarbamoylase.

A hybrid version of Escherichia coli aspartate transcarbamoylase was investigated in which one catalytic subunit has the wild-type sequence, and the other catalytic subunit has Glu-239 replaced by Gln. Since Glu-239 is involved in intersubunit interactions, this hybrid could be used to evaluate the extent to which T state stabilization is required for homotropic cooperativity and for heterotropic effects. Reconstitution of the hybrid holoenzyme (two different catalytic subunits with three wild-type regulatory subunits) was followed by separation of the mixture by anion-exchange chromatography. To make possible the resolution of the three holoenzyme species formed by the reconstitution, the charge of one of the catalytic subunits was altered by the addition of six aspartic acid residues to the C terminus of each of the catalytic chains (AT-C catalytic subunit). Control experiments indicated that the AT-C catalytic subunit as well as the holoenzyme formed with AT-C and wild-type regulatory subunits had essentially the same homotropic and heterotropic properties as the native catalytic subunit and holoenzyme, indicating that the addition of the aspartate tail did not influence the function of either enzyme. The control reconstituted holoenzyme, in which both catalytic subunits have Glu-239 replaced by Gln, exhibited no cooperativity, an enhanced affinity for aspartate, and essentially no heterotropic response identical to the enzyme isolated without reconstitution. The hybrid containing one normal and one mutant catalytic subunit exhibited homotropic cooperativity with a Hill coefficient of 1.4 and responded to the nucleotide effectors at about 50% of the level of the wild-type enzyme. Small angle x-ray scattering experiments with the hybrid enzyme indicated that in the absence of ligands it was structurally similar, but not identical, to the T state of the wild-type enzyme. In contrast to the wild-type enzyme, addition of carbamoyl phosphate induced a significant alteration in the scattering pattern, whereas the bisubstrate analog N-phosphonoacetyl-L-aspartate induced a significant change in the scattering pattern indicating the transition to the R-structural state. These data indicate that in the hybrid enzyme only three of the usual six interchain interactions involving Glu-239 are sufficient to stabilize the enzyme in a low affinity, low activity state and allow an allosteric transition to occur.

Adenosine Triphosphate↗

PubMed2000

The effect of a hemofilter during extracorporeal circulation on hemodynamics in patients with SIRS.

OBJECTIVE: To evaluate the hypothesis that extracorporeal hemopurification with a hemofilter contributes to the stabilization of hemodynamics in patients with systemic inflammatory response syndrome (SIRS) due to a mechanism other than the removal of cytokines. DESIGN: Prospective study. SETTING: Intensive care unit (ICU) in a university hospital. PATIENTS: Seven critically ill patients who met criteria for SIRS with unstable hemodynamics requiring vasopressors after emergency surgery. INTERVENTIONS: Before initiation of continuous hemofiltration (CHF) extracorporeal circulation through the hemofilter (ECC) with a hollow-fiber polyacrylonitrile hemofilter was performed for 6 h. MEASUREMENTS AND RESULTS: Vital signs were monitored continuously and hemodynamics were evaluated intermittently. The blood level of endotoxin and the plasma levels of cytokines were measured at 0 and 6 h. Changes in plasma levels of cytokines passing through the hemofilter were evaluated at 3 h. A significant decrease of body temperature (P < 0.05 at 3 and 6 h vs 0 h), a significant elevation of mean arterial pressure (P < 0.05 at 0.5 h, P < 0.01 at 3 and 6 h vs 0 h), and a significant increase of urinary flow rate (P < 0.05 at 0 to 3 h vs -3 to 0 h) were observed with ECC. Neither the blood level of endotoxin nor the plasma levels of cytokines decreased. A significant increase of plasma IL-6 as it passed through the hemofilter was noted. CONCLUSIONS: The beneficial effects of hemopurification with a hemofilter on SIRS patients are possibly due to mechanisms other than the elimination of cytokines with ultrafiltration, diffusion, or adsorption.

Aged↗