Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida is a key enzyme in the Entner-Doudoroff pathway which catalyses the cleavage of KDPG via a class I Schiff-base mechanism. The crystal structure of this enzyme has been refined to a crystallographic residual R = 17.1% (R-free = 21.4%). The N-terminal helix caps one side of the torus of the (betaalpha)(8)-barrel and the active site is located on the opposite, carboxylic side of the barrel. The Schiff-base-forming Lys145 is coordinated by a sulfate (or phosphate) ion and two solvent water molecules. The interactions that stabilize the trimer are predominantly hydrophobic, with the exception of the cyclically permuted bonds formed between Glu132 OE1 of one molecule and Thr129 OG1 of a symmetry-equivalent molecule. Except for the N-terminal helix, the structure of KDPG aldolase from P. putida closely resembles the structure of the homologous enzyme from Escherichia coli.

The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.

CMS physics technical design report, volume II: Physics performance

CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider ( LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking - through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start- up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb(-1) or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, B-s production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb(-1) to 30 fb(-1). The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z(0) boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing E-T, B-mesons and tau's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model.

The CMS experiment at the CERN LHC

The Compact Muon Solenoid (CMS) detector is described. The detector operates at the Large Hadron Collider (LHC) at CERN. It was conceived to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1) (10(27)cm(-2)s(-1)). At the core of the CMS detector sits a high-magnetic-field and large-bore superconducting solenoid surrounding an all-silicon pixel and strip tracker, a lead-tungstate scintillating-crystals electromagnetic calorimeter, and a brass-scintillator sampling hadron calorimeter. The iron yoke of the flux-return is instrumented with four stations of muon detectors covering most of the 4 pi solid angle. Forward sampling calorimeters extend the pseudo-rapidity coverage to high values (vertical bar eta vertical bar <= 5) assuring very good hermeticity. The overall dimensions of the CMS detector are a length of 21.6 m, a diameter of 14.6 m and a total weight of 12500 t.

Sistemas de cultivo e uso de diferentes adubos na produção de silagem e grãos de milho

O presente trabalho teve por objetivo avaliar o desempenho do milho para produção de silagem e grãos, cultivado em diferentes sistemas e adubações. O delineamento experimental adotado foi de blocos inteiramente casualizados, em esquema fatorial 2 x 3, composto por dois sistemas de cultivo (sucessão e rotação de culturas) e três fontes de adubação (orgânica, mineral e organomineral), com quatro repetições. Para produção de silagem de planta inteira, os sistemas e as adubações não diferiram estatisticamente entre si (p < 0,05). Para produção de silagem de grão úmido, o sistema em sucessão e a adubação mineral mostraram-se superiores aos demais, produzindo 10.823 e 10.815 kg ha-1, respectivamente, não incrementando, contudo, qualidade à silagem. Já na colheita dos grãos, o sistema em sucessão produziu em média 6.820 kg ha-1 e foi superior ao sistema em rotação. A adubação mineral foi superior às demais, produzindo em média 7.277 kg ha-1, contudo apresentou 54,62% de plantas acamadas, fato este que resultaria em perdas significativas na produtividade, caso a colheita tivesse sido mecanizada.

Nutrição e produtividade da cultura do milho em sistemas de culturas e fontes de adubação

A utilização de esterco animal na agricultura, aliada ao cultivo de plantas de cobertura, pode conferir sustentabilidade ao sistema agrícola. Com o objetivo de avaliar o efeito de dois sistemas de culturas e de três fontes de nutrientes, na cultura do milho, conduziu-se um experimento, em Latossolo Vermelho, no município de Marechal Cândido Rondon (PR). O delineamento experimental utilizado foi de blocos casualizados, com quatro repetições, e, os tratamentos, dispostos em esquema fatorial 2 x 3, compostos por dois sistemas de culturas (sucessão trigo/milho e consórcio aveia+ervilhaca+nabo/milho) e três fontes de nutrientes (mineral, orgânica e organomineral). em junho de 2006, implantou-se a cultura do trigo e o consórcio de plantas de cobertura. em outubro de 2006, semeou-se milho sob os dois sistemas. As adubações orgânica e organomineral consistiram na aplicação de dejetos de suínos, unicamente, e combinada com fertilizante mineral, respectivamente. O consórcio de aveia preta, ervilhaca peluda e nabo forrageiro mostrou-se capaz de fornecer a quantidade adequada de biomassa, concretizando sua viabilidade para produção de cobertura vegetal ao solo, durante o inverno. O cultivo de milho em sucessão ao trigo proporcionou a maior absorção de N e K e a maior produtividade. A adubação mineral proporcionou maior absorção de N e maior produtividade de milho, em comparação com as adubações orgânica e organomineral com dejetos de suínos.

Comparação entre métodos para a avaliação do vigor de lotes de sementes de triticale

Dentro de um programa de controle de qualidade, a avaliação do vigor de sementes é fundamental e necessária para o sucesso da produção. Este trabalho teve como objetivo avaliar a eficiência de diferentes testes de vigor na avaliação da qualidade fisiológica de sementes de triticale (X. triticosecale Wittmack), buscando a diferenciação de lotes. Cinco lotes da cultivar 'IPR 111' foram submetidos ao teste de germinação, primeira contagem, teste de frio, condutividade elétrica (50 sementes 50mL-1 de água; 25°C 24h-1), lixiviação de potássio (50 sementes 75mL-1 de água; 25°C 3h-1), envelhecimento acelerado (43°C 48h-1) e teor de água. O teste de condutividade elétrica e lixiviação de potássio são eficientes na diferenciação do vigor de lotes de sementes de triticale.

Effect of boron and zinc fertilization on white oats grown in soil with average content of these nutrients

The objective of this study was to evaluate the effect of fertilization with zinc or boron on the growth and dry matter production, nutritional value and accumulation of nutrients in white oats. The study comprised two experiments conducted in glasshouses, the first consisting of the application of four doses of zinc (0, 0.2, 0.4 and 0.6 mg/dm³) in the form of zinc sulphate (20% Zn), and the second consisting of the application of four doses of boron (0, 0.2, 0.4 and 0.6 mg/dm³) in the form of Borax (11% B). The experimental design in each case was a randomized block design, with five replicates. Fertilization with zinc and boron increased the growth of white oats, but had no significant effect on the nutritional value of the forage. Higher levels of absorption and accumulation of nutrients in plant tissues were observed following the application of boron and zinc at rates of up to 0.60 mg/dm³ of soil.

Active and exo-site inhibition of human factor Xa: Structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum

Hookworms are hematophagous nematodes capable of growth, development and subsistence in living host systems such as humans and other mammals. Approximately one billion, or one in six, people worldwide are infected by hookworms causing gastrointestinal blood loss and iron deficiency anemia. The hematophagous hookworm Ancylostoma caninum produces a family of small, disulfide-linked protein anticoagulants (75-84 amino acid residues). One of these nematode anticoagulant proteins, NAP5, inhibits the amidolytic activity of factor Xa (fXa) with K-i = 43 pM, and is the most potent natural fXa inhibitor identified thus far. The crystal structure of NAP5 bound at the active site of gamma-carboxyglutamic acid domainless factor Xa (des-fXa) has been determined at 3.1 angstrom resolution, which indicates that Asp189 (fXa, S1 subsite) binds to Arg40 (NAP5, P1 site) in a mode similar to that of the BPTI/trypsin interaction. However, the hydroxyl group of Ser39 of NAP5 additionally forms a hydrogen bond (2.5 angstrom) with His57 NE2 of the catalytic triad, replacing the hydrogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has not been observed before. Furthermore, the C-terminal extension of NAP5 surprisingly interacts with the fXa exosite of a symmetry-equivalent molecule forming a short intermolecular beta-strand as observed in the structure of the NAPc2/fXa complex. This indicates that NAP5 can bind to fXa at the active site, or the exosite, and to fX at the exosite. However, unlike NAPc2, NAP5 does not inhibit fVIIa of the fVIIa/TF complex. (c) 2007 Elsevier Ltd. All rights reserved.

Prospective Evaluation of Laparoscopic Pancreatic Biopsies in 11 Healthy Cats

BackgroundDefinitive diagnosis of feline pancreatic disease is dependent on histologic examination of biopsies.HypothesisLaparoscopic punch biopsy of the pancreas does not significantly affect pancreatic health or clinical status of healthy cats, and provides an adequate biopsy sample for histopathology.AnimalsEleven healthy female domestic shorthair cats.MethodsEffects of laparoscopic pancreatic visualization alone in 5 cats compared with laparoscopic pancreatic visualization and punch biopsy in 6 cats were studied. Temperature, pulse, and respiratory rate, physical examination, and daily caloric intake were evaluated for 1 week before and 1 week after the procedure. Pain scores (simple descriptive score and dynamic interactive visual assessment score) were evaluated hourly during the 1st 6 hours postprocedure. Complete blood cell counts, serum biochemical profiles, serum feline pancreatic lipase immunoreactivity, and urine specific gravity were evaluated before the procedure and at 6, 24, and 72 hours postprocedure. One month postprocedure, during sterilization, the pancreas was reassessed visually in all cats, and microscopically in the biopsy group.ResultsFor all variables evaluated, there were no significant differences between biopsy and control cats. Re-evaluation of the pancreatic biopsy site 1 month later documented a normal tissue response to biopsy. The laparoscopic punch biopsy forceps provided high-quality pancreatic biopsy samples with an average size of 5 mm x 4 mm on 2-dimensional cut section.Conclusions and Clinical ImportanceLaparoscopic pancreatic biopsy is a useful and safe technique in healthy cats.

Selection of radio transmitter and attachment method for post-release monitoring of captive-bred reintroduced Red-billed Curassow Crax blumenbachii, Brazil

Long-term monitoring of reintroduced individuals is a central component of many endangered species reintroduction programs. Radio-telemetry techniques are rarely used to monitor reintroduced captive-bred Cracids and few data exist regarding possible adverse effects of radio-tagging Cracids. In this study, we identify an appropriate radio transmitter design and develop a suitable attachment method that minimizes anthropogenic influence and enables long-term, post-release monitoring (2-3 years) of reintroduced captive-bred Red-billed Curassows in the Brazilian Atlantic Rainforest. We also review studies about the effects of different VHF radio transmitter models on survival, reproduction, behavior, and physiology of Galliformes.

Atributos físicos do solo e produtividade do milho sob sistemas de manejo e adubações

No-tillage system is an efficient technique in control of soil erosion, when compared with conventional tillage, however, some studies indicate higher compaction under no-tillage, mainly in the surface layer. Strategies that increase the organic matter content, as crop rotation and organic fertilization, can be used to solve the soil compaction. The aim of this study was to evaluate the effect of soil managements (crop succession and crop rotation) and fertilization (organic, mineral and organic-mineral) in the physical properties of the soil, under no-tillage system, from 2006 to 2008. The evaluations were carried out in February 2007, after the summer corn harvest, and in September 2008, after the winter corn harvest. Crop rotation decreased the soil density and soil resistance to penetration and increased the macroporosity and total porosity. The use of organic sources of fertilization did not affect any of the physical attributes of soil. The yield of summer corn was highest in succession crop and mineral fertilization, however, in the winter, there was no difference between the soil managements and among the fertilizations.

Estoque de carbono orgânico no solo afetado por adubação orgânica e sistemas de culturas no Sul do Brasil

Organic carbon is a major component of soil organic matter and its stock is influenced by the management system adopted. This study aimed to examine the effects of cropping systems and nutrient sources (mineral and organic) on the concentrations and storage of soil organic carbon in no-tillage system. The experiment was carried out in Mercedes, Parana, Brazil, in an Nitossolo Vermelho (Alfisol) from October 2007 to September 2009. The treatments consisted of four crop succession systems: (1) soybean/wheat/corn/wheat; (2) soybean/black oat/corn/black oat, (3) soybean/radish/corn/radish and (4) soybean/common vetch/corn/common vetch and by two sources of nutrients (mineral and organic), arranged in a to split plot randomized block design with four replications. Soil samples were collected in layers of 0.0-0.05, 0.05-0.10, 0.10-0.20 and 0.20 to 0.40 m deep in the first and the second years of cultivation. Different cropping systems does not affect the content and the stock of soil organic carbon in the first two years of adoption of the systems. The organic fertilization with manure increased soil organic carbon stock, with an annual contribution of C, layer 0.0 to 0.20 m, 1.15 Mg ha(-1) yr(-1). Cropping systems fertilized with mineral fertilizers provide the greatest losses of soil organic carbon, resulting in negative balance of C in soil.

Precision measurements of the ∧c + and D0 lifetimes

A measurement technique of charm baryons lifetimes from hadro-production data was presented. The measurement verified the lifetime analysis procedure in a sample with higher statistical precision. Other effects studied include mass reflections; effects of the presence of a second charm particle; and mismeasurement of charm decays. Monte carlo simulations were used for the detailed study of systematic effects using the charm data.

First measurement of π-e→π-eγ pion virtual compton scattering

Pion virtual compton scattering (VCS) via the reaction π-e→π-eγ was observed in the Fermilab E781 SELEX experiment. SELEX used a 600 GeV/c π- beam incident on target atomic electrons, detecting the incident π- and the final state π-, electron and γ. Theoretical predictions based on chiral perturbation theory are incorporated into a Monte Carlo simulation of the experiment and are compared to the data. The number of reconstructed events (=9) and their distribution with respect to the kinematic variables (for the kinematic region studied) are in reasonable accord with the predictions. The corresponding π- VCS experimental cross section is σ=38.8±13 nb, in agreement with the theoretical expectation of σ=34.7 nb.