Optimizing cost, growth performance, and nutrient absorption with a bio-emulsifier based on lysophospholipids for broiler chickens.

Two experiments (Exp.) were conducted to evaluate effects of a lysophospholipid-based bio-emulsifier (LPL) on growth performance, nutrient digestibility and energy utilization of broilers as well as the return on investment (ROI). In Exp. 1, 392 chicks were housed in battery cages in a completely randomized design with 8 treatments and 7 replicates of 7 birds each from d 0 to 21 posthatch. In Exp. 2, 1,400 chicks were allocated in floor pens and fed the same 8 treatments, with 7 replicates and 25 birds each from d 0 to 43 posthatch. Treatments consisted of 6 degummed soybean oil-based diets: positive control (PC1); PC1 formulated with 500 g/ton LPL (PC1+LPL on top); PC1 formulated with 60 kcal LPL matrix (PC1+LPL60); PC1 formulated with 100 kcal LPL matrix (PC1+LPL100); and two negative controls NC-60 and NC-100 with reductions of 60 and 100 kcal/kg ME, respectively. Two other diets were formulated with acid soybean oil: positive control (PC2) and PC2 formulated with 60 kcal LPL matrix (PC2+LPL60). In Exp. 1, performance was evaluated from d 0 to 21, ME and ileal digestibility of DM, CP and energy were determined on d 21. In Exp. 2, growth performance was evaluated from d 0 to 42, and on d 43 carcass and abdominal fat yields were calculated. There were no effects of soybean oil sources in any parameter. Inclusion of LPL increased (P < 0.05) BW gain and ileal digestibility of DM, fat and CP. Broilers fed the PC1+LPL on top diet had increased (P < 0.05) performance, ileal digestibility and energy utilization as well as decreased abdominal fat compared to NC-60 or NC-100. The use of LPL on top had a ROI of 8:1 vs. PC1, considering the gains in revenue of the slaughtered broilers in relation to the investment with LPL in feed. In conclusion, a lysophospholipid-based bio-emulsifier increased performance, digestibility and return on investment of broilers fed standard or reformulated diets.

Spatial distribution of triatomines (Reduviidae: Triatominae) in urban areas of the city of Salvador, Bahia, Brazil.

Environmental changes have a strong influence on the emergence and/or reemergence of infectious diseases. The city of Salvador, Brazil--currently the focus of a housing boom linked to massive deforestation--is an example in point as the destruction of the remaining areas of the Atlantic Forest around the city has led to an increased risk for Chagas disease. Human domiciles have been invaded by the triatomine vectors of Trypansoma cruzi, the flagellate protozoan causing Chagas disease, a problem of particular concern in urban/suburban areas of the city such as the Patamares sector in the north-east, where numbers of both the vector and human cases of the disease have increased lately. To control and prevent further deterioration of the situation, the control programme for Chagas disease, developed by the Bahia Center for Zoonosis Control, has divided the area into a grid of designated surveillance units (ZIs) that are subjected to vector examination. In six out of 98 of these ZIs, 988 triatomes were collected and georeferenced during the 3-year period between 2006 and 2009. The hottest months, that are also generally the driest, showed the highest numbers of triatomines with Triatoma tibiamaculata being the predominant species (98.3%) with Panstrongylus geniculatus present only occasionally (0.6%). Fifty-four percent of all triatomines captured were found inside the homes, and 48.6% out of 479 individuals in the affected ZIs selected for analysis tested positive for T. cruzi infection. The study presented here is a pioneering initiative to map the spatial distribution of triatomines based on geographical information systems with the additional aim of contributing to an expanded knowledge-base about T. cruzi and its vectors in urban areas and raise public health awareness of the risks involved.

Ab initio 3-D structure prediction of an artificially designed three-alpha-helix bundle via all-atom molecular dynamics simulations.

The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three- alpha -helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-alpha-helix bundle.

Ab initio 3-D structure prediction of an artificially designed three-alpha-helix bundle via all-atom molecular dynamics simulations

The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three-alpha-helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-alpha-helix bundle.

Convergence in the variation of local and regional galling species richness / Convergence in the variation of local and regional galling species richness

We investigate the local and regional determinants of galling insect richness on the dioecious shrub Baccharis concinna Barroso (Asteraceae) in the southeastern portion of the Espinhaço Mountains in Brazil. The total number of galling species and the richness of galling Cecidomyiidae (Diptera) were influenced by plant gender. Male plants supported a higher richness of galling insects than female plants, supporting the hypothesis of sex-biased herbivory at the community level. The total number of galling species and the richness of galling cecidomyiids showed a peak at intermediate altitudes. The richness of all galling species and galling cecidomyiids were strongly influenced by habitat. Plants in xeric habitats supported more galling species than plants in mesic habitats, corroborating the hypothesis of hygrothermal/nutritional stress. Our results indicate that local factors may be the most important factors structuring the galling insect community on B. concinna.

Foram investigados os determinantes locais e regionais da riqueza de insetos indutores de galhas sobre o arbusto dióico Baccharis concinna Barroso (Asteraceae) na porção sudeste da Cadeia do Espinhaço, MG. O número total de espécies de insetos indutores de galhas e a riqueza de Cecidomyiidae (Diptera) foram influenciados pelo sexo da planta. Plantas masculinas apresentaram maior riqueza de insetos indutores de galhas do que plantas femininas, corroborando a hipótese da herbivoria mediada pelo sexo na comunidade. O número total de espécies de insetos galhadores e a riqueza de Cecidomyiídeos mostraram um pico em altitudes intermediárias. A riqueza de todas as espécies de insetos galhadores e de cecidomiideos foi fortemente influenciada pelo habitat. Plantas no habitat xérico apresentaram mais espécies de insetos galhadores do que plantas no habitat mésico, corroborando a hipótese do estresse higrotérmico/nutricional. Os resultados indicam que os fatores locais podem ser importantes estruturadores da comundade de insetos galhadores em B. concinna.

Molecular dynamics simulations of a protein-protein dimer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model.

In this article we present two 1000 ps molecular dynamics simulations on the rat micro-glutathione S-transferase dimeric enzyme in complex with the product 1-(S-glutathionyl)-2,4-dinitrobenzene, in a periodic box with explicit solvent molecules, and investigate the effect of long-range electrostatics models on the structure and dynamics of the dimer and its components. One simulation used the standard cutoff method (10A), whilst the other used the particle-mesh Ewald (PME) method. We monitored the root mean-square atomic deviation (RMSD) from the initial crystal structure to examine the convergence of both simulations, as well as several other structural parameters such as the distance between active sites, rigid body rotation between domains in subunits, radius of gyration, B-factors, number of hydrogen bonds and salt bridges and solvent-accessible surface area. For example, with the PME method, the dimer structure remains much closer to the initial crystallographic structure with an average RMSD of 1.3A +/- 0.1A and 1.0A +/- 0.1A for all heavy and backbone atoms, respectively, in the last 200 ps; the respective values for the cutoff simulation are 4.7A +/- 0.3A and 4.2A +/- 0.3A. The large deviations observed in the cutoff simulation severely affected the stability of the enzyme dimer and its complex with the bound product. This finding is contrary to that found in a similar study of the monomeric protein ubiquitin [Fox, T. & Kollman, P. A. Proteins Struct. Func. Genet. 25, 315-334 (1996)]. Unlike the earlier published work, the present study provides evidence that the standard cutoff method is not generally valid for the study of protein complexes, or their subunits.

Inherent DNA curvature and flexibility correlate with TATA box functionality.

Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG).d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation.

The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model.

DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X-ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable and remains in an intermediate state between the canonical A and B forms of the duplex. The magnitude of global curvature (75 degrees) agrees well with the experimental estimate (72 degrees) available. Analysis of local (every base triplet) and sublocal (every helix turn) curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature. We further characterize the flexibility of individual nucleotides in the molecule and find the sugar flexibility within the A-tracts to be strongly correlated with the pattern of A-tract cleavage by the hydroxyl radical. Differential curvature and flexibility at the 5' and 3'junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K-DNA fragment.

Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method.

The particle-mesh Ewald (PME) method is considered to be both efficient and accurate for the evaluation of long-range electrostatic interactions in large macromolecular systems being studied by molecular dynamics simulations. This method assumes "infinite" periodic boundary conditions resembling the symmetry of a crystal environment. Can such a "solid-state" method accurately portray a macromolecular solute such as DNA in solution? To address this issue, we have performed three 1500-ps PME molecular dynamics (MD) simulations, each with a different box size, on the d(CGCGA6CG)-(CGT6CGCG) DNA dodecamer. The smallest box had the DNA solvated by a layer of water molecules of at least 5 A along each orthogonal direction. The intermediate size box and the largest box had the DNA solvated by a layer of water molecules of at least 10 A and 15 A, respectively, along each orthogonal direction. The intermediate size box in the present study is similar to the box size currently chosen by most workers in the field. Based on a comparison of RMSDs and curvature for this single DNA dodecamer sequence, the larger two box sizes do not appear to afford any extra benefit over the smallest box. The implications of this finding are briefly discussed.

Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using AMBER 4.1 and particle-mesh Ewald method.

This report describes one 3000 ps and two 1500 ps molecular dynamic simulations on a TATA box containing dodecamer DNA duplex in a periodic box of TIP3P water molecules, using the AMBER 4.1 implementation of the particle-mesh Ewald method. We compare the effect of warmup protocol and simulation time length on the root-mean square deviation (RMSD) parameter. For the longer simulation, the RMSD computed for the 500-1000 ps time interval is representative of longer time intervals, including 500-3000 ps. The various warmup protocols do not appear to have a significant effect on the simulation results. Based on the present results, DNA sequence-dependent differences in RMSD, or related properties, should exceed two standard deviations before being attributed to non-simulation factors, such as warmup protocol and sampling time effects; we recommend a minimum criterion of at least a three standard deviation difference with a sampling period of at least 500-1000 ps. In addition, while end effects appear negligible there is a consistent dependence of RMSD on DNA helix length.

Inhibition of experimental proliferative vitreoretinopathy in rabbits by suramin.

Proliferative vitreoretinopathy (PVR) is the most common cause for failure of retinal reattachment surgery. In a search for better pharmacologic treatment of PVR, we investigated the effect of intravenous injections of suramin on an experimental rabbit model of PVR. PVR was induced in rabbits by intravitreal injection of autologous fibroblasts. The experimental group (7 eyes) received intravenous injections of suramin (100 mg/kg body weight) every 3 days for 15 days, beginning 3 days before fibroblast injection. The control group (5 eyes) was treated similarly but received intravenous saline solution in place of suramin. A third group (4 eyes) received suramin according to the protocol above but did not receive intravitreal fibroblasts. The animals were examined by indirect ophthalmoscopy every 3 days and were sacrificed 14 days after the injection of fibroblasts. The serum levels of suramin were evaluated by high-performance liquid chromatography. The PVR was classified as stages I-V, based upon clinical findings. PVR developed in both experimental and control animals but was less severe in those treated with suramin. On day 14, the average stage of PVR in the control group was 3.8; in the suramin-treated group, however, the average stage was 2.4, which was significantly less than in the control group (p < 0.02). None of the rabbits in the third group showed pathologic changes. Serum levels of suramin were maintained at an average of 280.2 micrograms/ml and no apparent toxicity was found in the retina by histologic study.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA structure, hydration and dynamics.

Although the double helical model of DNA structure is now 40 years old, there is still considerable effort being made to elucidate the range of conformations that can be adopted by this flexible molecule. We review the current state of our knowledge of DNA structure which is available from both experimental and computational approaches.

Molecular dynamics simulations of oligonucleotides in solution: visualization of intrinsic curvature.

We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG- and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).

[Cardiac memory in patients with permanent artificial pacemakers]. / Memória cardíaca em pacientes com marcapasso artificial definitivo.

PURPOSE: To correlate the direction of QRS complex of paced beats and postpacing T wave, in patients with artificial pacemaker. METHODS: Thirty five patients with spontaneous rhythm obtained by chest wall stimulation or by programmability of the automatic interval. It was correlated in all patients, the direction forces of QRS complexes of paced beats and postpacing T waves in all 12 ECG leads. It was considered as a cardiac memory phenomenon when QRS complexes of paced beats and postpacing T waves had the same polarity. The phenomenon was correlated with the 12 ECG leads and with specific variables like spontaneous rhythm, QRS complex duration, type and modality of artificial stimulation and chronicity of the implant. RESULTS: The artificial QRS complexes and spontaneous T waves had the same direction in 5 or more leads of the frontal plane in 77% of the patients and in 50% of the patients in the horizontal plane. In patients with supraventricular command, this correlation was found in 82% of the patients and in 50% of the patients with idioventricular rhythm. Regardless of the type of spontaneous command, the phenomenon was better observed with normal intraventricular conduction. It was not found correlation between type, modality of stimulation and chronicity of the implant and cardiac memory. It was better observed in aVF, D2, D3 and V3, V4. CONCLUSION: The phenomenon of cardiac memory in patients with artificial pacemaker is very frequent. The most important factor to develop the phenomenon seem to be a normal pattern of ventricular activation.

Comparison of aztreonam plus clindamycin with tobramycin plus clindamycin in the treatment of intra-abdominal infections.

The activity of aztreonam (a beta-lactam antibiotic with specific activity against gram-negative bacteria) was evaluated and compared with that of tobramycin in hospitalized patients with severe intra-abdominal infections due to gram-negative pathogens, either alone or in association with other bacteria. Of a total study population of 156 patients, 76 were assigned to treatment with aztreonam + clindamycin, and the remaining 80 were treated with tobramycin + clindamycin. Patients underwent a variety of surgical procedures involving the peritoneal cavity. The final clinical evaluation revealed similar percentages of satisfactory results: 86.8% for the patients in the aztreonam-treated group and 86.2% for the tobramycin-treated patients. Among the patients who had a poor therapeutic result, gram-negative bacteria, either alone or associated with gram-positive pathogens, were considered responsible for 50% of the infections in the aztreonam group; the percentage increased to 82% among those treated with tobramycin. The incidence of side effects and laboratory alterations was not significant and was similar in both groups. The results of this study suggest that aztreonam may be an effective and safe drug for the treatment of bacterial infections due to gram-negative pathogens.

Aztreonam plus clindamycin vs. tobramycin plus clindamycin for the treatment of intraabdominal infections.

Sixty-six patients with acute intraabdominal infections due to gram-negative aerobic organisms were treated with aztreonam plus clindamycin or with tobramycin plus clindamycin in a multicenter, comparative, randomized study. The patients had undergone a variety of surgical procedures; most of them had peritonitis. Thirty-three of the 36 patients in the aztreonam group and 26 of the 30 patients in the tobramycin group had satisfactory clinical responses. Only one gram-negative aerobic pathogen, a strain of Pseudomonas aeruginosa, persisted after treatment; the patient involved was in the tobramycin group. The incidences of adverse reactions, superinfections, and abnormal laboratory values were low in each treatment group. The difference between the efficacies of the two regimens was not statistically significant. This study suggests that aztreonam may be a useful alternative to the aminoglycosides in the treatment of gram-negative intraabdominal infections.

Surface antigenic determinant of epimastigote forms common to trypomastigote and amastigote forms of different strains of Trypanosoma cruzi.

A fraction (FA) has been isolated from the sediment obtained from Trypanosoma cruzi of epimastigote lysates centrifuged at 1500 x g, for 30 min. This fraction, obtained by extracting sediments, for 10 min, with ice-cold 0.1 N NaOH, exhibited a single component, a glycoprotein, when analysed by electrophoresis in 1% agarose gel and presented a single faint precipitation line in immunoelectrophoresis experiments. FA components were unable to penetrate polyacrylamide gel matrix, even when 1% SDS 4% polyacrylamide gels were used, unless previously hydrolyzed by parasite proteinase. Under this condition FA preparations presented at least four glycoproteins components as detected by electrophoresis in 1% SDS 15% polyacrylamide gels. FA obtained from Y strain was able to inhibit agglutination reactions between anti-epimastigote sera and epimastigote of either Y or Nic strains. Anti-FA antibodies, elicited in 4 out of 12 rabbits inoculated with this fraction, gave positive immunofluorescence and immunoperoxidase reactions with blood trypomastigota and tissue amastigota, obtained from mice infected with any of 6 different strains of T. cruzi. These reactions which were inhibited by FA preparations were completely abolished if antisera were absorbed with living epimastigota of Y or Nic strains.