Crystallization and preliminary X-ray diffraction analysis of human IL-22 bound to its soluble decoy receptor IL-22BP

Interleukin-22 (IL-22) is a pleiotropic cytokine that is involved in inflammatory responses. Human IL-22 was incubated with its soluble decoy receptor IL-22BP (IL-22 binding protein) and the IL-22 -IL-22BP complex was crystallized in hanging drops using the vapour-diffusion method. Suitable crystals were obtained from polyethylene glycol solutions and diffraction data were collected to 2.75 angstrom resolution. The crystal belonged to the tetragonal space group P41, with unit-cell parameters a = b = 67.9, c = 172.5 angstrom, and contained two IL-22-IL- 22BP complexes per asymmetric unit.

Density functional theory and ab initio molecular dynamics study of NO adsorption on Pd(111) and Pt(111) surfaces

The origin of the unique geometry for nitric oxide (NO) adsorption on Pd(111) and Pt(111) surfaces as well as the effect of temperature were studied by density functional theory calculations and ab initio molecular dynamics at finite temperature. We found that at low coverage, the adsorption geometry is determined by electronic interactions, depending sensitively on the adsorption sites and coverages, and the effect of temperature on geometries is significant. At coverage of 0.25 monolayer (ML), adsorbed NO at hollow sites prefer an upright configuration, while NO adsorbed at top sites prefer a tilting configuration. With increase in the coverage up to 0.50 ML, the enhanced steric repulsion lead to the tilting of hollow NO. We found that the tilting was enhanced by the thermal effects. At coverage of 0.75 ML with p(2 x 2)-3NO(fcc+hcp+top) structure, we found that there was no preferential orientation for tilted top NO. The interplay of the orbital hybridization, thermal effects, steric repulsion, and their effects on the adsorption geometries were highlighted at the end.

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale

This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than similar to 10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.

Interference with Hemozoin Formation Represents an Important Mechanism of Schistosomicidal Action of Antimalarial Quinoline Methanols

Background: The parasitic trematode Schistosoma mansoni is one of the major causative agents of human schistosomiasis, which afflicts 200 million people worldwide. Praziquantel remains the main drug used for schistosomiasis treatment, and reliance on the single therapy has been prompting the search for new therapeutic compounds against this disease. Our group has demonstrated that heme crystallization into hemozoin (Hz) within the S. mansoni gut is a major heme detoxification route with lipid droplets involved in this process and acting as a potential chemotherapeutical target. In the present work, we investigated the effects of three antimalarial compounds, quinine (QN), quinidine (QND) and quinacrine (QCR) in a murine schistosomiasis model by using a combination of biochemical, cell biology and molecular biology approaches. Methodology/Principal Findings: Treatment of S. mansoni-infected female Swiss mice with daily intraperitoneal injections of QN, and QND (75 mg/kg/day) from the 11(th) to 17(th) day after infection caused significant decreases in worm burden (39%-61%) and egg production (42%-98%). Hz formation was significantly inhibited (40%-65%) in female worms recovered from QN- and QND-treated mice and correlated with reduction in the female worm burden. We also observed that QN treatment promoted remarkable ultrastructural changes in male and female worms, particularly in the gut epithelium and reduced the granulomatous reaction to parasite eggs trapped in the liver. Microarray gene expression analysis indicated that QN treatment increased the expression of transcripts related to musculature, protein synthesis and repair mechanisms. Conclusions: The overall significant reduction in several disease burden parameters by the antimalarial quinoline methanols indicates that interference with Hz formation in S. mansoni represents an important mechanism of schistosomicidal action of these compounds and points out the heme crystallization process as a valid chemotherapeutic target to treat schistosomiasis.

Direct evidence of singlet molecular oxygen generation from peroxynitrate, a decomposition product of peroxynitrite

The decomposition of peroxynitrite to nitrite and dioxygen at neutral pH follows complex kinetics, compared to its isomerization to nitrate at low pH. Decomposition may involve radicals or proceed by way of the classical peracid decomposition mechanism. Peroxynitrite (ONOOH/ONOO(-)) decomposition has been proposed to involve formation of peroxynitrate (O(2)NOOH/O(2)NOO(-)) at neutral pH (D. Gupta, B. Harish, R. Kissner and W. H. Koppenol, Dalton Trans., 2009, DOI: 10.1039/b905535e, see accompanying paper in this issue). Peroxynitrate is unstable and decomposes to nitrite and dioxygen. This study aimed to investigate whether O(2)NOO(-) formed upon ONOOH/ONOO(-) decomposition generates singlet molecular oxygen [O(2) ((1)Delta(g))]. As unequivocally revealed by the measurement of monomol light emission in the near infrared region at 1270 nm and by chemical trapping experiments, the decomposition of ONOO(-) or O(2)NOOH at neutral to alkaline pH generates O(2) ((1)Delta(g)) at a yield of ca. 1% and 2-10%, respectively. Characteristic light emission, corresponding to O(2) ((1)Delta(g)) monomolecular decay was observed for ONOO(-) and for O(2)NOOH prepared by reaction of H(2)O(2) with NO(2)BF(4) and of H(2)O(2) with NO(2)(-) in HClO(4). The generation of O(2) ((1)Delta(g)) from ONOO(-) increased in a concentration-dependent manner in the range of 0.1-2.5 mM and was dependent on pH, giving a sigmoid pro. le with an apparent pK(a) around pD 8.1 (pH 7.7). Taken together, our results clearly identify the generation of O(2) ((1)Delta(g)) from peroxynitrate [O(2)NOO(-) -> NO(2)(-) + O(2) ((1)Delta(g))] generated from peroxynitrite and also from the reactions of H(2)O(2) with either NO(2)BF(4) or NO(2)(-) in acidic media.

Singlet molecular oxygen trapping by the fluorescent probe diethyl-3,3 '-(9,10-anthracenediyl)bisacrylate synthesized by the Heck reaction

Singlet molecular oxygen O(2)((1)Delta(g)) is a potent oxidant that can react with different biomolecules, including DNA, lipids and proteins. Many polycyclic aromatic hydrocarbons have been studied as O(2)((1)Delta(g)) chemical traps. Nevertheless, a suitable modification in the polycyclic aromatic ring must be made to increase the yield of O(2)((1)Delta(g)) chemical trapping. With this goal, an anthracene derivative, diethyl-3,3 '-(9,10-anthracenediyl)bisacrylate (DADB), was obtained from the reaction of 9,10-dibromoanthracene and ethyl acrylate through the Heck coupling reaction. The coupling of ethyl acrylate with the anthracene ring produced a new lipophilic, esterified, fluorescent probe reactive toward O(2)((1)Delta(g)). This compound reacts with O(2)((1)Delta(g)) at a rate of k(r) = 1.69 x 10(6) M(-1) s(-1) forming a stable endoperoxide (DADBO(2)), which was characterized by UV-Vis, fluorescence, HPLC/MS and (1)H and (13)C NMR techniques. The photophysical, photochemical and thermostability features of DADB were also evaluated. Furthermore, this compound has the potential for great application in biological systems because it is easily synthetized in large amount and generates specific endoperoxide (DADBO(2)), which can be easily detected by HPLC tandem mass spectrometry (HPLC/MS/MS).

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624408]

Polarization effects in molecular dynamics simulations of glass-formers Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8

Thermodynamics, equilibrium structure, and dynamics of glass-forming liquids Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8, have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H(2)O and NO(3)- on the basis of previous fluctuating charge models for pure water and the molten salt 2Ca(NO(3))(2)center dot 3KNO(3). Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature, T(g), estimated from MD simulations was dependent on polarization, in particular the dependence of T(g) with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation, cation-anion, and water-water structures. Polarization increases the diffusion coefficient of H(2)O, but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization, but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

Fragility and glassy dynamics of 2Ca(NO(3))(2)center dot 3KNO(3) under pressure: Molecular dynamics simulations

Molecular dynamics simulations of the glass-forming liquid 2Ca(NO(3))(2)center dot 3KNO(3) (CKN) were performed from high temperature liquid states down to low temperature glassy states at six different pressures from 10(-4) to 5.0 GPa. The temperature dependence of the structural relaxation time indicates that the fragility of liquid CKN changes with pressure. In line with recent proposal [Scopigno , Science 302, 849 (2003)], the change on liquid fragility is followed by a proportional change of the nonergodicity factor of the corresponding glass at low temperature. (c) 2008 American Institute of Physics.

Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies

Background: Mutations in TP53 are common events during carcinogenesis. In addition to gene mutations, several reports have focused on TP53 polymorphisms as risk factors for malignant disease. Many studies have highlighted that the status of the TP53 codon 72 polymorphism could influence cancer susceptibility. However, the results have been inconsistent and various methodological features can contribute to departures from Hardy-Weinberg equilibrium, a condition that may influence the disease risk estimates. The most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or via a separate method. Results: We developed two new genotyping methods for TP53 codon 72 polymorphism detection: Denaturing High Performance Liquid Chromatography (DHPLC) and Dot Blot hybridization. These methods were compared with Restriction Fragment Length Polymorphism (RFLP) using two different restriction enzymes. We observed high agreement among all methodologies assayed. Dot-blot hybridization and DHPLC results were more highly concordant with each other than when either of these methods was compared with RFLP. Conclusions: Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required.

Stability of biomass-derived black carbon in soils

Black carbon (BC) may play ail important role in the global C budget, due to its potential to act as a significant sink of atmospheric CO(2). In order to fully evaluate the influence of BC oil the global C cycle, in understanding of the stability of BC is required. The biochemical stability of BC was assessed in a chronosequence of high-BC-containing Anthrosols from the central Amazon, Brazil, using a range of spectroscopic and biological methods. Results revealed that the Anthrosols had 61-80% lower (P < 0.05) CO(2) evolution per unit C over 532 days compared to their respective adjacent soils with low BC contents. No significant (P > 0.05) difference in CO(2) respiration per unit C was observed between Anthrosols with contrasting ages of BC (600-8700 years BP) Lind soil textures (0.3-36% clay). Similarly, the molecular composition of the core regions of micrometer-sized BC particles quantified by synchrotron-based Near-Edge X-ray Fine Structure (NEXAFS) spectroscopy coupled to Scanning Transmission X-ray Microscopy (STXM) remained similar regardless of their ages and closely resembled the spectral characteristics or fresh BC. BC decomposed extremely slowly to ail extent that it was not possible to detect chemical changes between Youngest and oldest samples, as also confirmed by X-ray Photoelectron Spectroscopy (XPS). Deconvolution of NEXAFS spectra revealed greater oxidation oil the surfaces of BC particles with little penetration into the core of the particles. The similar C mineralization between different BC-rich soils regardless of soil texture underpins the importance of chemical recalcitrance for the stability of BC, in contrast to adjacent soils which showed the highest mineralization in the sandiest soil. However, the BC-rich Anthrosols had higher proportions (72-90%) of C in the more stable organo-mineral fraction than BC-poor adjacent soils (2-70%), Suggesting some degree of physical stabilization. (c) 2008 Elsevier Ltd. All rights reserved.

Molecular and morphological characterization of Amathia distans Busk and Amathia brasiliensis Busk (Bryozoa: Ctenostomata) from the tropical and subtropical Western Atlantic

Morphological and molecular analyses have proven to be complementary tools of taxonomic information for the redescription of the ctenostome bryozoans Amathia brasiliensis Busk, 1886 and Amathia distans Busk, 1886. The two species, originally described from material collected by the `Challenger` expedition but synonymized by later authors, now have their status fixed by means of the selection of lectotypes, morphological observations and analyses of DNA sequences described here. The morphological characters allowing the identification of living and/or preserved specimens are (1) A. brasiliensis: whitish-pale pigment spots in the frontal surface of stolons and zooids, and a wide stolon with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it, the spirality direction being maintained from maternal to daughter stolons; and (2) A. distans: bright yellow pigment spots in stolonal and zooidal surfaces including lophophores, and a slender stolon, thickly cuticularized, with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it and the spirality direction not maintained from maternal to daughter stolons. Pairwise comparisons of DNA sequences of the mitochondrial genes cytochrome c oxidase subunit I and large ribosomal RNA subunit revealed deep genetic divergence between A. brasiliensis and A. distans. Finally, analyses of those sequences within a Bayesian phylogenetic context recovered their genealogical species status.

Characterization of feather-degrading bacteria from Brazilian soils

Studies on keratinolytic microorganisms have been mainly related to their biotechnological applications and association with animal pathologies. However, these organisms have an ecological relevance to recycling keratinous residues in nature. This work aimed to select and identify new culturable feather-degrading bacteria isolated from soils of Brazilian Amazon forest and Atlantic forest. Bacteria that were isolated from temperate soils and bacteria from Amazonian basin soil were tested for their capability to grow on feather meal agar (FMA). Proteolytic bacteria were tested for feather degradation and were further identified according to their morphological and biochemical characteristics. Also, molecular identification based on 165 rDNA gene sequencing was carried out. A total of 24 proteolytic and 20 feather-degrading isolates were selected; Most of the isolates were from the Bacillus genus (division Firmicutes), but one Aeromonas, two Serratia (gamma-Proteobacteria), and one Chryseobacterium (Cytophaga-Flavobacterium group). (C) 2010 Elsevier Ltd. All rights reserved.