Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens

Plasmodium falciparum, the causative agent of human malaria, invades host erythrocytes using several proteins on the surface of the invasive merozoite, which have been proposed as potential vaccine candidates. Members of the multi-gene PfRh family are surface antigens that have been shown to play a central role in directing merozoites to alternative erythrocyte receptors for invasion. Recently, we identified a large structural polymorphism, a 0.58 Kb deletion, in the C-terminal region of the PfRh2b gene, present at a high frequency in parasite populations from Senegal. We hypothesize that this region is a target of humoral immunity. Here, by analyzing 371 P. falciparum isolates we show that this major allele is present at varying frequencies in different populations within Senegal, Africa, and throughout the world. For allelic dimorphisms in the asexual stage antigens, Msp-2 and EBA-175, we find minimal geographic differentiation among parasite populations from Senegal and other African localities, suggesting extensive gene flow among these populations and/or immune-mediated frequency-dependent balancing selection. In contrast, we observe a higher level of inter-population divergence (as measured by F(st)) for the PfRh2b deletion, similar to that observed for SNPs from the sexual stage Pfs45/48 loci, which is postulated to be under directional selection. We confirm that the region containing the PfRh2b polymorphism is a target of humoral immune responses by demonstrating antibody reactivity of endemic sera. Our analysis of inter-population divergence suggests that in contrast to the large allelic dimorphisms in EBA-175 and Msp-2, the presence or absence of the large PfRh2b deletion may not elicit frequency-dependent immune selection, but may be under positive immune selection, having important implications for the development of these proteins as vaccine candidates. (C) 2009 Elsevier B.V. All rights reserved.

Worldwide sequence conservation of transmission-blocking vaccine candidate Pvs230 in Plasmodium vivax

Pfs230, surface protein of gametocyte/gamete of the human malaria parasite, Plasmodium falciparum, is a prime candidate of malaria transmission-blocking vaccine. Plasmodium vivax has an ortholog of Pfs230 (Pvs230), however, there has been no study in any aspects on Pvs230 to date. To investigate whether Pvs230 can be a vivax malaria transmission-blocking vaccine, we performed evolutionary and population genetic analysis of the Pvs230 gene (pvs230: PVX_003905). Our analysis of Pvs230 and its orthologs in eight Plasmodium species revealed two distinctive parts: an interspecies variable part (IVP) containing species-specific oligopeptide repeats at the N-terminus and a 7.5 kb interspecies conserved part (ICP) containing 14 cysteine-rich domains. Pvs230 was closely related to its orthologs, Pks230 and Pcys230, in monkey malaria parasites. Analysis of 113 pvs230 sequences obtained from worldwide, showed that nucleotide diversity is remarkably low in the non-repeat 8-kb region of pvs230 (theta pi = 0.00118) with 77 polymorphic nucleotide sites, 40 of which results in amino acid replacements. A signature of purifying selection but not of balancing selection was seen on pvs230. Functional and/or structural constraints may limit the level of polymorphism in pvs230. The observed limited polymorphism in pvs230 should ground for utilization of Pvs230 as an effective transmission-blocking vaccine. (C) 2011 Elsevier Ltd. All rights reserved.

Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum

Immune evasion by Plasmodium falciparum is favored by extensive allelic diversity of surface antigens. Some of them, most notably the vaccine-candidate merozoite surface protein (MSP)-1, exhibit a poorly understood pattern of allelic dimorphism, in which all observed alleles group into two highly diverged allelic families with few or no inter-family recombinants. Here we describe contrasting levels and patterns of sequence diversity in genes encoding three MSP-1-associated surface antigens of P. falciparum, ranging from an ancient allelic dimorphism in the Msp-6 gene to a near lack of allelic divergence in Msp-9 to a more classical multi-allele polymorphism in Msp-7 Other members of the Msp-7 gene family exhibit very little polymorphism in non-repetitive regions. A comparison of P. falciparum Msp-6 sequences to an orthologous sequence from P. reichenowi provided evidence for distinct evolutionary histories of the 5` and 3` segments of the dimorphic region in PfMsp-6, consistent with one dimorphic lineage having arisen from recombination between now-extinct ancestral alleles. In addition. we uncovered two surprising patterns of evolution in repetitive sequence. Firsts in Msp-6, large deletions are associated with (nearly) identical sequence motifs at their borders. Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi. (C) 2009 Elsevier B.V. All rights reserved.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Intraspecific sequence variation in 16S rRNA gene of Ureaplasma diversum isolates

Ureaplasma diversum infection in bulls may result in seminal vesiculitis, balanoposthitis and alterations in spermatozoids. In cows, it can cause placentitis, fetal alveolitis, abortion and the birth of weak calves. U. diversum ATCC 49782 (serogroups A), ATCC 49783 (serogroup C) and 34 field isolates were used for this study. These microorganisms were submitted to Polymerase Chain Reaction for 16S gene sequence determination using Tact High Fidelity and the products were purified and bi-directionally sequenced. Using the sequence obtained, a fragment containing four hypervariable regions was selected and nucleotide polymorphisms were identified based on their position within the 16S rRNA gene. Forty-four single nucleotide polymorphisms (SNP) were detected. The genotypic variability of the 16S rRNA gene of U. diversum isolates shows that the taxonomy classification of these organisms is likely much more complex than previously described and that 16S rRNA gene sequencing may be used to suggest an epidemiologic pattern of different origin strains. (c) 2011 Elsevier B.V. All rights reserved.

Partial spectral projected gradient method with active-set strategy for linearly constrained optimization

A method for linearly constrained optimization which modifies and generalizes recent box-constraint optimization algorithms is introduced. The new algorithm is based on a relaxed form of Spectral Projected Gradient iterations. Intercalated with these projected steps, internal iterations restricted to faces of the polytope are performed, which enhance the efficiency of the algorithm. Convergence proofs are given and numerical experiments are included and commented. Software supporting this paper is available through the Tango Project web page: http://www.ime.usp.br/similar to egbirgin/tango/.

Mass spectral characterization of submicron biogenic organic particles in the Amazon Basin

Submicron atmospheric particles in the Amazon Basin were characterized by a high-resolution aerosol mass spectrometer during the wet season of 2008. Patterns in the mass spectra closely resembled those of secondary-organic-aerosol (SOA) particles formed in environmental chambers from biogenic precursor gases. In contrast, mass spectral indicators of primary biological aerosol particles (PBAPs) were insignificant, suggesting that PBAPs contributed negligibly to the submicron fraction of particles during the period of study. For 40% of the measurement periods, the mass spectra indicate that in-Basin biogenic SOA production was the dominant source of the submicron mass fraction, contrasted to other periods (30%) during which out-of-Basin organic-carbon sources were significant on top of the baseline in-Basin processes. The in-Basin periods had an average organic-particle loading of 0.6 mu g m(-3) and an average elemental oxygen-to-carbon (O:C) ratio of 0.42, compared to 0.9 mu g m(-3) and 0.49, respectively, during periods of out-of-Basin influence. On the basis of the data, we conclude that most of the organic material composing submicron particles over the Basin derived from biogenic SOA production, a finding that is consistent with microscopy observations made in a concurrent study. This source was augmented during some periods by aged organic material delivered by long-range transport. Citation: Chen, Q., et al. (2009), Mass spectral characterization of submicron biogenic organic particles in the Amazon Basin, Geophys. Res. Lett., 36, L20806, doi: 10.1029/2009GL039880.

Spectral absorption properties of aerosol particles from 350-2500nm

The aerosol spectral absorption efficiency (alpha(a) in m(2)/g) is measured over an extended wavelength range (350-2500 nm) using an improved calibrated and validated reflectance technique and applied to urban aerosol samples from Sao Paulo, Brazil and from a site in Virginia, Eastern US, that experiences transported urban/industrial aerosol. The average alpha(a) values (similar to 3m(2)/g at 550 nm) for Sao Paulo samples are 10 times larger than a a values obtained for aerosols in Virginia. Sao Paulo aerosols also show evidence of enhanced UV absorption in selected samples, probably associated with organic aerosol components. This extra UV absorption can double the absorption efficiency observed from black carbon alone, therefore reducing by up to 50% the surface UV fluxes, with important implications for climate, UV photolysis rates, and remote sensing from space. Citation: Martins, J.V., P. Artaxo, Y.J. Kaufman, A.D. Castanho, and L.A. Remer (2009), Spectral absorption properties of aerosol particles from 350-2500nm, Geophys. Res. Lett., 36, L13810, doi: 10.1029/2009GL037435.

Study of Blood Porphyrin Spectral Profile for Diagnosis of Chronic Renal Failure

The progression to end-stage renal failure is independent of the initial pathogenic mechanism. Metabolic acidosis is a common consequence of chronic renal failure that results from inadequate ammonium excretion and decreased tubular bicarbonate reabsorption. Protoporphyrin IX (PpIX) is the immediate metabolic precursor of the heme molecule. The purpose of this study was to evaluate the levels of erythrocytes protoporphyrin IX at an animal model during progressive renal disease. A total of 36 eight-week-old male Wistar rats were divided into six groups: Normal, 4 and 8 weeks after 5/6 nephrectomy (NX). Renal function was evaluated by creatinine clearance and plasma creatinine levels. The autofluorescence of erythrocytes porphyrin of healthy and NX rats was analyzed using fluorescence spectroscopy. Emission spectra were obtained by exciting the samples at 405 nm. Significant differences between normal and NX rats autofluorescence shape occurred in the 600-700 nm spectral region. A correlation was observed between emission band intensity at 635 nm and progression of renal disease.

Polarization and Spectral Shift of Benzophenone in Supercritical Water

Monte Carlo simulation and quantum mechanics calculations based on the INDO/CIS and TD-DFT methods were utilized to study the solvatochromic shift of benzophenone when changing the environment from normal water to supercritical (P = 340.2 atm and T = 673 K) condition. Solute polarization increases the dipole moment of benzophenone, compared to gas phase, by 88 and 35% in normal and supercritical conditions, giving the in-solvent dipole value of 5.8 and 4.2 D, respectively. The average number of solute-solvent hydrogen bonds was analyzed, and a large decrease of 2.3 in normal water to only 0.8 in the supercritical environment was found. By using these polarized models of benzophenone in the two different conditions of water, we performed MC simulations to generate statistically uncorrelated configurations of the solute surrounded by the solvent molecules and subsequent quantum mechanics calculations on these configurations. When changing from normal to supercritical water environment, INDO/CIS calculations explicitly considering all valence electrons of the 235 solvent water molecules resulted in a solvatochromic shift of 1425 cm(-1) for the most intense transition of benzophenone, that is, slightly underestimated in comparison with the experimentally inferred result of 1700 cm(-1). TD-B3LYP/6-311+G(2d,p) calculations on the same configurations but with benzophenone electrostatically embedded in the 320 water molecules resulted in a solvatochromic shift of 1715 cm(-1) for this transition, in very good agreement with the experimental result. When using the unpolarized model of the benzophenone, this calculated solvatochromic shift was only 640 cm(-1). Additional calculations were also made by using BHandHLYP/6-311+G(2d,p) to analyze the effect of the asymptotic decay of the exchange functional. This study indicates that, contrary to the general expectation, there is a sizable solute polarization even in the low-density regime of supercritical condition and that the inclusion of this polarization is important for a reliable description of the spectral shifts considered here.

Decomposition of spectral density in individual eigenvalue contributions

The eigenvalue densities of two random matrix ensembles, the Wigner Gaussian matrices and the Wishart covariant matrices, are decomposed in the contributions of each individual eigenvalue distribution. It is shown that the fluctuations of all eigenvalues, for medium matrix sizes, are described with a good precision by nearly normal distributions.

Self-adjoint extensions and spectral analysis in the Calogero problem

In this paper, we present a mathematically rigorous quantum-mechanical treatment of a one-dimensional motion of a particle in the Calogero potential alpha x(-2). Although the problem is quite old and well studied, we believe that our consideration based on a uniform approach to constructing a correct quantum-mechanical description for systems with singular potentials and/or boundaries, proposed in our previous works, adds some new points to its solution. To demonstrate that a consideration of the Calogero problem requires mathematical accuracy, we discuss some `paradoxes` inherent in the `naive` quantum-mechanical treatment. Using a self-adjoint extension method, we construct and study all possible self-adjoint operators (self-adjoint Hamiltonians) associated with a formal differential expression for the Calogero Hamiltonian. In particular, we discuss a spontaneous scale-symmetry breaking associated with self-adjoint extensions. A complete spectral analysis of all self-adjoint Hamiltonians is presented.

Self-adjoint extensions and spectral analysis in the generalized Kratzer problem

We present a mathematically rigorous quantum-mechanical treatment of a one-dimensional non-relativistic motion of a particle in the potential field V(x) = g(1)x(-1) + g(2)x(-2), x is an element of R(+) = [0, infinity). For g(2) > 0 and g(1) < 0, the potential is known as the Kratzer potential V(K)(x) and is usually used to describe molecular energy and structure, interactions between different molecules and interactions between non-bonded atoms. We construct all self-adjoint Schrodinger operators with the potential V(x) and represent rigorous solutions of the corresponding spectral problems. Solving the first part of the problem, we use a method of specifying self-adjoint extensions by (asymptotic) self-adjoint boundary conditions. Solving spectral problems, we follow Krein`s method of guiding functionals. This work is a continuation of our previous works devoted to the Coulomb, Calogero and Aharonov-Bohm potentials.

Two-photon absorption of perylene derivatives: Interpreting the spectral structure

This work investigates the two-photon absorption spectrum of perylene tetracarboxylic derivatives using the white-light continuum Z-scan technique. Perylene derivatives present relatively high two-photon absorption cross-section, which makes them attractive for applications in photonics. Because of the spectral resolution of the white-light continuum Z-scan, we were able to observe a well defined structure in the two-photon absorption spectrum, composed by two distinct peaks. These peaks, as well as the resonant enhancement of the nonlinearity, were modeled using the sum-over-states approach considering a four-level energy diagram with two final two-photon states. The existence of such states was confirmed using the response function formalism within the DFT framework. (C) 2009 Elsevier B.V. All rights reserved.

Control of Two-Photon Absorption in Organic Compounds by Pulse Shaping: Spectral Dependence

In this work, we investigate the control of the two-photon absorption process of a series of organic compounds via spectral phase modulation of the excitation pulse. We analyzed the effect of the pulse central wavelength on the control of the two-photon absorption process for each compound. Depending on the molecules` two-photon absorption position relative to the excitation pulse wavelength, different levels of coherent control were observed. By simulating the two-photon transition probability in molecular systems, taking into account the band structure and its positions, we could explain the experimental results trends. We observed that the intrapulse coherent interference plays an important role in the nonlinear process control besides just the pulse intensity modulation.