GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site

BACKGROUND:. In all species examined, GDP-fucose is synthesized from GDP-mannose in a three-step reaction catalyzed by two enzymes, GDP-mannose 4,6 dehydratase and a dual function 3, 5-epimerase-4-reductase named GDP-fucose synthetase. In this latter aspect fucose biosynthesis differs from that of other deoxy and dideoxy sugars, in which the epimerase and reductase activities are present as separate enzymes. Defects in GDP-fucose biosynthesis have been shown to affect nodulation in bacteria, stem development in plants, and are associated with the immune defect leukocyte adhesion deficiency type II in humans. RESULTS:. We have determined the structure of GDP-fucose synthetase from Escherichia coli at 2.2 A resolution. The structure of GDP-fucose synthetase is closely related to that of UDP-galactose 4-epimerase and more distantly to other members of the short-chain dehydrogenase/reductase family. We have also determined the structures of the binary complexes of GDP-fucose synthetase with its substrate NADPH and its product NADP+. The nicotinamide cofactors bind in the syn and anti conformations, respectively. CONCLUSIONS:. GDP-fucose synthetase binds its substrate, NADPH, in the proper orientation (syn) for transferring the 4-pro-S hydride of the nicotinamide. We have observed a single binding site in GDP-fucose synthetase for the second substrate, GDP-4-keto,6-deoxy-mannose. This implies that both the epimerization and reduction reactions occur at the same site in the enzyme. As is the case for all members of the short-chain family of dehydrogenase/reductases, GDP-fucose synthetase retains the Ser-Tyr-Lys catalytic triad. We propose that this catalytic triad functions in a mechanistically equivalent manner in both the epimerization and reduction reactions. Additionally, the X-ray structure has allowed us to identify other residues that are potentially required for substrate binding and catalysis.     

Contribution of semi-quantum dielectric function models to the analysis of infrared spectra

A new approach to modeling using semi-quantum dielectric function models is proposed for the retrieval of the optical functions from infrared spectra. The powerful points of the method are shown throughout the analysis of two semitransparent materials, MgO and KBr. All the results are discussed in light of those obtained with classical techniques. This type of model is able to retrieve, for example, the extinction index in a range that covers at least six orders of magnitude and gives access to highly valuable information about high-order phonon processes.     

Voluntary food intake during prolonged exercise in obese women

The effect of 57 days of moderate physical activity on the energy intake and balance of three obese women (187% of ideal weight) was investigated in a metabolic balance study. Food was offered in extra quantity, prepared in a palatable but simple fashion, and intake was covertly monitored. Expenditure was measured using the factorial method and indirect calorimetry done every 3 to 4 days. After a 5-day evaluation phase which no exercise was done, individual treadmill assignments were given to subjects to increase daily expenditure to 125% of sedentary levels. Mean dialy intake (1903 kcal/day) and expenditure (2882 kcal/day) did not change with time. As a result, negative energy balance was obtained and sustained. A consistent rate of weight loss (0.12 kg/day) at a reasonable cost (8200 kcal/kg)occurred. Therefore, obese women doing long-term moderate exercise do not compensate by an increase in caloric intake. This can produce a negative caloric balance when exercise is coupled with ad libitum selection of ordinary foods.     

Learning to Match the Schemas of Data Sources: A Multistrategy Approach

The problem of integrating data from multiple data sources—either on the Internet or within enterprises—has received much attention in the database and AI communities. The focus has been on building data integration systems that provide a uniform query interface to the sources. A key bottleneck in building such systems has been the laborious manual construction of semantic mappings between the query interface and the source schemas. Examples of mappings are element location maps to address and price maps to listed-price. We propose a multistrategy learning approach to automatically find such mappings. The approach applies multiple learner modules, where each module exploits a different type of information either in the schemas of the sources or in their data, then combines the predictions of the modules using a meta-learner. Learner modules employ a variety of techniques, ranging from Naive Bayes and nearest-neighbor classification to entity recognition and information retrieval. We describe the LSD system, which employs this approach to find semantic mappings. To further improve matching accuracy, LSD exploits domain integrity constraints, user feedback, and nested structures in XML data. We test LSD experimentally on several real-world domains. The experiments validate the utility of multistrategy learning for data integration and show that LSD proposes semantic mappings with a high degree of accuracy.     

Increase of critical current density and voltage for triggering avalanche injection through use of graded collector doping

In this paper it is shown that both critical current density and voltage of an epitaxial bipolar power transistor with an inductive load, which are taken as a measure of its susceptibility to avalanche injection, can be significantly increased by using double graded collector doping profiles. The first graded portion gives the required current protection level and the steeper second graded profile can be used to increase the voltage protection level. Calculations are carried out for optimum collector parameters to achieve minimum resistance for the required open base breakdown voltage. Results are compared with uniformly doped profile for the same collector resistance and open base voltage. It is shown that a device with graded collector is less prone to failure due to avalanche injection.     

Characterization of a redox-modified clay mineral with respect to its suitability as a barrier in radioactive waste confinement

Engineered barriers for high-level nuclear waste (HLW) consist of excavated repositories in sub-surface rock formations where canisters holding the radionuclide are stored. Clay minerals, particularly the swelling 2:1 types, are used as backfill material, both in the canisters and in the bore hole, in order to prevent radionuclide transport to surrounding groundwater. One of the most important risks that can occur is the corrosion of the canister, which could be coupled with reduction of iron (Fe) in the clay structure. Such changes could greatly decrease the long-term stability of the clay and, consequently, of the barriers themselves. In order to test the potential effects of such redox interactions, an Fe-bearing clay mineral from a commercial source located in the Kutch region, India, was selected for study. This particular mineral is one of the candidate clay minerals to serve as such a barrier material, and is the one with the largest structural Fe content. Results from it should, therefore, provide maximum insight into the potential effects of redox interactions between the barrier and its surroundings. The unaltered clay was characterized by X-ray powder diffractometry (XRD), thermal gravimetric analysis (TGA/DTGA), Fourier-transform infrared (FTIR) spectroscopy, and variable-temperature Mössbauer spectroscopy. The chemically reduced and reoxidized forms of the clay were characterized by variable-temperature Mössbauer spectroscopy and chemical analysis. In the unaltered state the clay is comprised of smectite, maghemite, superparamagnetic goethite, and hematite, with a possible trace of kaolinite. In the reduced state the Fe (oxyhydr)oxides were dissolved. Upon reoxidation no six-line pattern was observed, indicating that the Fe remained only in the structure of the silicates. The final structure of the reduced–reoxidized clay contained more defects than the original clay, as revealed by greater quadrupole splitting values for structural Fe(III) in the clay. These findings indicate that upon exposure to natural redox cycles the Kutch clay could undergo permanent changes in its mineralogical composition and clay mineral structure, but further study is required to ascertain the effects that such changes would have on its long-term stability as a barrier material.     

Effects of initial climatic conditions on growth and accumulation of fluoride and nitrogen in leaves of two tropical tree species exposed to industrial air pollution

Saplings of Tibouchina pulchra and Psidium guajava, cultivated under standardized soil conditions, were placed in two sites at Cubat?o (state of S?o Paulo, southeast Brazil) to study the effects of air pollution on growth, biomass allocation and foliar nitrogen and fluoride concentrations. Thirty-six potted plants were maintained over two periods of one year (Jul/00 to Jun/01; Dec/00 to Nov/01) at each of two experimental sites with distinct levels of air pollution: Pil?es River Valley (PV) with vegetation virtually unaffected by air pollution; and Mogi River Valley (MV) severely affected by pollutants released mainly by chemical, fertilizer, iron and steel industries. For both species, saplings growing at MV showed alterations of growth and biomass allocation, as well as increased leaf concentrations of nitrogen and fluoride. Comparing both experimental periods, the one starting in winter (the driest season in Southeastern Brazil) seemed to affect the saplings more severely, the differences of the measured parameters between MV and PV being higher than in the second period. Multivariate analysis revealed two groups of data: one representing the MV and the other the PV saplings. For both species, saplings growing at MV showed differences in chemical composition, growth and biomass allocation, compared with the PV saplings. The results suggested that seasonal conditions of the first months of sapling exposure (summer or winter) modulate the intensity of responses to pollution stress.     

Chemical composition and physical properties of black liquors and their effects on liquor recovery operation in Brazilian pulp mills

Black liquor is the major by-product and fuel of pulp mills. In this work, effects of black liquor properties on its recovery unit operation are analyzed. Thus, an experimental methodology for characterizing the principal chemical and physical properties of eucalyptus Kraft and bamboo soda black liquors has been developed, including sample collections from six Brazilian mills. Based on results, eucalyptus and bamboo black liquors present higher contents of non-processing elements (NPEs), higher concentration and different molar mass of lignin than those reported by the pine Kraft black liquor. This leads to distinct rheological properties of these liquors. By comparing results obtained for the both liquors, the bamboo and the eucalyptus, the former has the lowest sulfur level, the highest silicon and lignin concentration and, consequently, the highest apparent viscosity.     

Hepatitis G and C viruses respond to interferon-alpha with different virologic kinetics

The aim of this work was to specify the time course of response to interferon (IFN) of hepatitis G virus (HGV) and hepatitis C virus (HCV) in coinfected individuals. A group of 33 patients, undergoing 12 months of IFN therapy for chronic hepatitis C, was screened for the presence of both HGV and HCV RNAs to select seven coinfected patients. Spontaneous recovery from HGV infection was excluded through the detection of antibodies to the envelope-2 protein of HGV and HCV isolates were genotyped. Within three months of treatment, we found that HGV RNA was transiently cleared in 6/7 patients, but the rate of long-term favorable response was very low (1/7). In addition, considering the same individuals separately, it was shown that HGV and HCV responded to IFN with different kinetics in 5/7 patients. Taken together, these results underscore the importance of the virological basis of the resistance to IFN treatment.     

Sub-Tenon's anaesthesia: an efficient and safe technique

AIM: To evaluate sub-Tenon's anaesthesia as an alternative to peribulbar anaesthesia. METHODS: 109 consecutive patients listed for various eye operations (including cataract, trabeculectomy, and vitrectomy) under peribulbar anaesthesia were operated on under sub-Tenon's anaesthesia instead. After topical anaesthesia a buttonhole was fashioned through the conjunctiva and Tenon's capsule 10 mm posterior to the limbus. 1.5 ml of lignocaine 2% was then delivered to the posterior sub-Tenon's space using a blunt cannula. The surgical procedure was performed immediately after the completion of the anaesthetic procedure. Chemosis, conjunctival haemorrhage, degree of akinesia, and pain scoring were analysed. RESULTS: There were no anaesthesia related complications. The administration of the block was painless for 99.1% of the patients. In all, 97.3% reported no pain during surgery. There was no akinesia when assessed just after the completion of the block and akinesia was limited when assessed after surgery. Chemosis and conjunctival haemorrhage were frequent but caused no intraoperative problems. CONCLUSION: Sub-Tenon's anaesthesia is an efficient and safe anaesthetic technique. It is a good alternative to peribulbar anaesthesia.