Structure, genomic DNA typing, and kinetic characterization of the D allozyme of placental alkaline phosphatase (PLAP/ALPP)

The D allozyme of placental alkaline phosphatase (PLAP) displays enzymatic properties at variance with those of the common PLAP allozymes. We have deduced the amino acid sequence of the PLAP D allele by PCR cloning of its gene, ALPP Two coding substitutions were found in comparison With the cDNA of the common PLAP F allele, i.e., 692C>G and 1352A>G, which translate into a P209R and E429G substitution. A single nucleotide primer extension (SNuPE) assay was developed using PCR primers that enable the amplification of a 1.9 kb PLAP fragment. Extension primers were then used on this PCR fragment to detect the 692C>G and 1352A>G substitution. The SNuPE assay on these two nucleotide substitutions enabled us to distinguish the PLAP F and D alleles from the PLAP S/I alleles. Functional studies on the D allozyme were made possible by constructing and expressing a PLAP D cDNA, i.e., [Arg209, Gly429] PLAP, into wildtype Chinese hamster ovary cells. We determined the k(cat) and K-m, of the PLAP S, F. and D allozymes using the non,physiological substrate p-nitrophenylphosphate at an optimal pH (9.8) as well as two physiological substrates, i.e., pyridoxal-5'-phosphate and inorganic pyrophosphate at physiological pH (7.5). We found that the biochemical properties of the D allozyme of PLAP are significantly different from those of the common PLAP allozymes. These biochemical findings suggest that a suboptimal enzymatic function by the PLAP D allozyme may be the basis for the apparent negative selective pressure of the PLAP D allele. The development of the SNuPE assay will enable us to test the hypothesis that the PLAP D allele is subjected to intrauterine selection by examining genomic DNA from statistically informative population samples. Hum Mutat 19:258-267, 2002. (C) 2002 Wiley-Liss, Inc.

Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

Changes in physiological and stroking parameters during interval swims at the slope of the d-t relationship

The slope of the distance-time relationship from maximal 200 and 400 in bouts (S(200-400)) has been increasingly employed for setting training intensities in swimming. However, physiological and mechanical responses at this speed are poorly understood. Thus, this study investigated blood lactate, heart rate (HR), stroke rate (SR), stroke length (SL) and RPE responses to an interval swimming set at S(200-400) in trained swimmers. In a 50-m pool, twelve athletes (16.5 +/- 1.2 yr, 176 +/- 7 cm, 68.4 +/- 5.4 kg, and 7.8 +/- 2.5% body fat) performed maximal 200 and 400 m crawl trials for S(200-400) determination (1.28 +/- 0.05 m/s). Thereafter, swimmers were instructed to perform 5 x 400 in at this speed with 1.5 min rest between repetitions. Three athletes Could not complete the set (exhaustion at 21.0 +/- 3.1 min). For the remaining swimmers (total set duration = 32.0 +/- 1.3 min) significant increases) (p < 0.05) in blood lactate (5.7 +/- 0.8-7.9 +/- 2.4 mmol/l), SR (29.6 +/- 3.2-32.1 +/- 4.1 cycles/min), HR (169 +/- 11-181 +/- 8 bpm) and RPE (13.3 +/- 1.6-16.3 +/- 2.6) were observed through the IS. Conversely, SL decreased significantly (p < 0.05) from the first to the fifth repetition (2.48 +/- 0.22-2.31 +/- 0.24 m/cycle). These results suggest that interval swimming at S(200-400) represents an intense physiological, mechanical and perceptual stimulus that can be sustained for a prolonged period by most athletes. (C) 2008 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Downregulation of nuclear factor-kappa B (NF-kappa B) pathway by silibinin in human monocytes challenged with Paracoccidioides brasiliensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Increased Levels of NOTCH1, NF-kappa B, and Other Interconnected Transcription Factors Characterize Primitive Sets of Hematopoietic Stem Cells

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The Effects of N Helix Deletion and Mutant F29W on the Ca2+ Binding and Functional Properties of Chicken Skeletal Muscle Troponin C

To assess the structural and functional significance of the N helix (residues 3-13) of avian recombinant troponin C (rTnC), we have constructed NHdel, in which residues 1-11 have been deleted, both in rTnC and in the spectral probe mutant F29W (Pearlstone, J. R., Borgford, T., Chandra, M., Oikawa, K., Kay, C. M., Herzberg, O., Moult, J., Herklotz, A., Reinach, F. C., and Smillie, L.B. (1992) Biochemistry 31, 6545-6553). Comparison of the far- and near-UV CD spectra (±Ca2+) of F29W and F29W/ NHdel and titration of the Ca2+-induced ellipticity and fluorescence changes indicates that the deletion has little effect on the global fold of the molecule but reduces the Ca2+ affinity of the N domain, but not the C domain, by 1.6-1.8-fold. Comparisons of the mutants NHdel, F29W, and F29W/NHdel with rTnC have been made using several functional assays. In reconstituted troponin-tropomyosin actomyosin subfragment 1 and myofibrillar ATPase systems, both F29W and NHdel have significantly reduced Ca2+-activated enzymic activities. These effects are cumulative in the double mutant F29W/ NHdel. On the other hand, maximal isometric tension development in Ca2+-activated reconstituted skinned fibers is not affected with F29W and NHdel, although the Ca2+ sensitivity of NHdel in this system is markedly reduced. We conclude that both mutations, NHdel and F29W, are functionally deleterious, possibly affecting interactions of the N domain with troponin I and/or T.

Influence of the environment on behavior patterns of laying hens kept in cages

The aim of this paper is to verify the correlation between environmental indicators and behaviors expressed by laying hens kept in cages. The birds react to a severe environment through their behaviors, end the behaviors can be monitored to identify the birds' welfare conditions. The behaviors birds display ere the result of stress caused by the combination of environmental temperature, relative humidity, radiant heat, and air speed (environmental temperature being the most important). In order to check the influence of the environment, an experiment was carried out on a commercial poultry farm, located in the city of Bastos. The study was initiated in March 2007, during four non-consecutive weeks. The birds' behaviors were recorded using video, by cameras installed in the cages. The birds behaviors were identified and noted for the frequency of occurrence for each bird, and the average duration of each behavior (in seconds), using video samples of 15 minutes recorded from 1 PM to 4 PM. The environmental variables collected were: air temperature, concentration of ammonia, relative air humidity, velocity of the air, noise, roof temperature, and light intensity. The observed behaviors were: opening wings, stretching, threatening, ruffling feathers, drinking water, aggressive pecking, eating, running, lying down, stretching head out of the cage, preening, mounting and prostrating. Principal Components Analysis was used to determine associations between the behavior variables and environmental variables described above. In this experiment, there were no significant correlations between behavioral variables and environmental variables.

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Studies of jet mass in dijet and W/Z + jet events

Invariant mass spectra for jets reconstructed using the anti-k T and CambridgeAachen algorithms are studied for different jet grooming techniques in data corresponding to an integrated luminosity of 5 fb-1, recorded with the CMS detector in proton-proton collisions at the LHC at a center-of-mass energy of 7 TeV. Leading-order QCD predictions for inclusive dijet and W/Z+jet production combined with parton-shower Monte Carlo models are found to agree overall with the data, and the agreement improves with the implementation of jet grooming methods used to distinguish merged jets of large transverse momentum from softer QCD gluon radiation. © 2013 CERN for the benefit of the CMS collaboration.

O A.B.C. de Lima Barreto (1916-1922)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Efficacy of the d-phenothrin/pyriproxyfen association against mites in naturally co-infested rabbits

O objetivo do presente estudo foi avaliar a eficácia da associação de d-fenotrina e piriproxifen no controle de infestações simultâneas por Psoroptes ovis, Cheyletiella parasitivorax e Leporacarus gibbus em coelhos naturalmente co-infestados. Vinte coelhos mestiços (Nova Zelândia Branco x Califórnia) infestados simultaneamente pelas três espécies de ácaros foram divididos aleatoriamente em dois grupos. Todos os coelhos infestados por apresentavam eritema, hiperemia e formação de crostas nas orelhas, causados por P. ovis. Infestações simultâneas por C. parasitivorax e L. gibbus foram considerados assintomáticas em todos os animais. Dez animais foram tratados com uma formulação spray contendo d-fenotrina a 4,4% e piriproxifen a 0,148%, pulverizando toda a superfície corporal de forma uniforme, incluindo a face interna das orelhas. Os outros 10 coelhos não foram t ratados, sendo mantidos como grupo controle. Os animais foram avaliados nos dias 7, 14, 21, 28 e 35 pós-tratamento. A associação de d-fenotrina e piriproxifen foi 100% eficaz no controle das três espécies de ácaros e foi responsável pela remissão das lesões de sarna psoróptica nos animais tratados. Não foram observados sinais de intoxicação. Os resultados indicam que a formulação spray de d-fenotrina e piriproxifen em uma única aplicação é uma opção clinicamente segura e eficaz no controle de infestações por ácaros em coelhos.

Chromosomal Mapping of Repetitive DNA and Cytochrome C Oxidase I Sequence Analysis Reveal Differentiation among Sympatric Samples of Astyanax fasciatus (Characiformes, Characidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The NINJA-2 project: detecting and characterizing gravitational waveforms modelled using numerical binary black hole simulations

The Numerical INJection Analysis (NINJA) project is a collaborative effort between members of the numerical relativity and gravitational-wave (GW) astrophysics communities. The purpose of NINJA is to study the ability to detect GWs emitted from merging binary black holes (BBH) and recover their parameters with next-generation GW observatories. We report here on the results of the second NINJA project, NINJA-2, which employs 60 complete BBH hybrid waveforms consisting of a numerical portion modelling the late inspiral, merger, and ringdown stitched to a post-Newtonian portion modelling the early inspiral. In a 'blind injection challenge' similar to that conducted in recent Laser Interferometer Gravitational Wave Observatory (LIGO) and Virgo science runs, we added seven hybrid waveforms to two months of data recoloured to predictions of Advanced LIGO (aLIGO) and Advanced Virgo (AdV) sensitivity curves during their first observing runs. The resulting data was analysed by GW detection algorithms and 6 of the waveforms were recovered with false alarm rates smaller than 1 in a thousand years. Parameter-estimation algorithms were run on each of these waveforms to explore the ability to constrain the masses, component angular momenta and sky position of these waveforms. We find that the strong degeneracy between the mass ratio and the BHs' angular momenta will make it difficult to precisely estimate these parameters with aLIGO and AdV. We also perform a large-scale Monte Carlo study to assess the ability to recover each of the 60 hybrid waveforms with early aLIGO and AdV sensitivity curves. Our results predict that early aLIGO and AdV will have a volume-weighted average sensitive distance of 300 Mpc (1 Gpc) for 10M circle dot + 10M circle dot (50M circle dot + 50M circle dot) BBH coalescences. We demonstrate that neglecting the component angular momenta in the waveform models used in matched-filtering will result in a reduction in sensitivity for systems with large component angular momenta. This reduction is estimated to be up to similar to 15% for 50M circle dot + 50M circle dot BBH coalescences with almost maximal angular momenta aligned with the orbit when using early aLIGO and AdV sensitivity curves.