Cytochrome c-promoted cardiolipin oxidation generates singlet molecular oxygen

The interaction of cytochrome c (cyt c) with cardiolipin (CL) induces protein conformational changes that favor peroxidase activity. This process has been correlated with CL oxidation and the induction of cell death. Here we report evidence demonstrating the generation of singlet molecular oxygen [O-2((1)Delta(g))] by a cyt c-CL complex in a model membrane containing CL. The formation of singlet oxygen was directly evidenced by luminescence measurements at 1270 nm and by chemical trapping experiments. Singlet oxygen generation required cyt c-CL binding and occurred at pH values higher than 6, consistent with lipid-protein interactions involving fully deprotonated CL species and positively charged residues in the protein. Moreover, singlet oxygen formation was specifically observed for tetralinoleoyl CL species and was not observed with monounsaturated and saturated CL species. Our results show that there are at least two mechanisms leading to singlet oxygen formation: one with fast kinetics involving the generation of singlet oxygen directly from CL hydroperoxide decomposition and the other involving CL oxidation. The contribution of the first mechanism was clearly evidenced by the detection of labeled singlet oxygen [O-18(2)((1)Delta(g))] from liposomes supplemented with 18-oxygen-labeled CL hydroperoxides. However quantitative analysis showed that singlet oxygen yield from CL hydroperoxides was minor (<5%) and that most of the singlet oxygen is formed from the second mechanism. Based on these data and previous findings we propose a mechanism of singlet oxygen generation through reactions involving peroxyl radicals (Russell mechanism) and excited triplet carbonyl intermediates (energy transfer mechanism).

Morphological and molecular evidences within Osmundea (Ceramiales, Rhodophyta) from the Canary Islands, eastern Atlantic Ocean

The genus Osmundea is a strongly supported monophyletic group within the Laurencia complex and shows a disjunct distribution occurring in the North-East and South-West Pacific, the Indian and Atlantic oceans and the Mediterranean Sea. Its phenotypic plasticity on the Canary Islands may be the result of the high ecological variability partially due to the particular oceanographic characteristics in this region. The combination of molecular analyses based on the comparison of the chloroplast-encoded rbcL sequences and morphological data allowed us to delimit three distinct taxa from the coasts of the Canarian Archipelago: Osmundea pinnatifida, Osmundea truncata and an unidentified species, Osmundea sp. Moreover, the high value of genetic divergence between Osmundea sp. and the rest of the Osmundea species suggests that this taxon should be assigned to a new species within the Osmundea genus. Occurrence of O. hybrida and O. oederi (synonym: O. ramosissima) has not been confirmed. Our results also suggest a possibly questionable record of the taxa O. hybrida and O. oederi on the Canary Islands.

Molecular phylogeny of the New World Dipsadidae (Serpentes: Colubroidea): a reappraisal

We present a phylogenetic analysis of the New World dipsadids based on an expanded data matrix that includes 246 terminal taxa including 196 dipsadids. The species are sampled for eight genes (12S, 16S, cytb, nd2, nd4, bdnf, c-mos, rag2). The data are explored using two distinct optimality proceduresmaximum parsimony and maximum likelihoodand two alignment strategiesdynamic homology and static homology. Two previously unsampled dipsadid genera, Sordellina and Rhachidelus, are now included in the analysis. The definitions of the genera, Erythrolamprus, Clelia, Hypsirhynchus, Philodryas and Phimophis, and the tribes Alsophiini, Echinantherini and Conophiini, are revised. In order to maintain monophyly, the genus Umbrivaga is synonymized with Erythrolamprus, and two new genera are erected to accommodate Phimophis iglesiasi and Clelia rustica, as well as their closely related species. The West Indian genera Schwartzophis, Darlingtonia, Antillophis and Ocyophis are resurrected. (c) The Willi Hennig Society 2012.

A novel set of ss-N-biaryl ether sulfonamide hydroxamates as potential MMPs inhibitors: Molecular dynamics simulations and molecular properties evaluation

Matrix metalloproteinases (MMPs) constitute a family of zinc-dependent proteases involved in the extracellular matrix degradation. MMP-2 and MMP9 are overexpressed in several human cancer types, including melanoma, thus the development of new compounds to inhibit MMPs' activity is desirable. Molecular dynamic simulation and molecular properties calculations were performed on a set of novel beta-N-biaryl ether sulfonamide-based hydroxamates, reported as MMP-2 and MMP-9 inhibitors, for providing data to develop an exploratory analysis. Thermodynamic, electronic, and steric descriptors have significantly discriminated highly active from moderately and less active inhibitors of MMP-2 whereas apparent partition coefficient at pH 1.5 was also significant for the MMP-9 data set. Compound 47 was considered an outlier in all analysis, indicating the presence of a bulky substituent group in R3 is crucial to this set of inhibitors for the establishment of molecular interactions with the S1 subsite of both enzymes, but there is a limit. (C) 2012 Wiley Periodicals, Inc.

Molecular features of sexual steroids on cartilage and bone

In Brazil, the increase in the reported cases of degenerative diseases of articular cartilage is 20% per year, meaning that 200,000 Brazilians develop degenerative joint diseases every year, which have a negative impact on bone mass. This study shows evidence that hormone production of sexual steroids (estrogens, progestogens, and androgens) have an influence on cartilage quality, as well as on bone mass. Therefore, this review aimed to analyze literature data on the molecular and genic action of sexual steroids on hyaline cartilage and bone physiology, as well as osteoarthritis interference on the quality of these structures.

Clinical, epidemiological and molecular features of the HIV-1 subtype C and recombinant forms that are circulating in the city of Sao Paulo, Brazil

Background: The city of Sao Paulo has the highest AIDS case rate, with nearly 60% in Brazil. Despite, several studies involving molecular epidemiology, lack of data regarding a large cohort study has not been published from this city. Objectives: This study aimed to describe the HIV-1 subtypes, recombinant forms and drug resistance mutations, according to subtype, with emphasis on subtype C and BC recombinants in the city of Sao Paulo, Brazil. Study design: RNA was extracted from the plasma samples of 302 HIV-1-seropositive subjects, of which 211 were drug-naive and 82 were exposed to ART. HIV-1 partial pol region sequences were used in phylogenetic analyses for subtyping and identification of drug resistance mutations. The envelope gene of subtype C and BC samples was also sequenced. Results: From partial pol gene analyses, 239 samples (79.1%) were assigned as subtype B, 23 (7.6%) were F1, 16 (5.3%) were subtype C and 24 (8%) were mosaics (3 CRF28/CRF29-like). The subtype C and BC recombinants were mainly identified in drug-naive patients (72.7%) and the heterosexual risk exposure category (86.3%), whereas for subtype B, these values were 69.9% and 57.3%, respectively (p = 0.97 and p = 0.015, respectively). An increasing trend of subtype C and BC recombinants was observed (p < 0.01). Conclusion: The HIV-1 subtype C and CRFs seem to have emerged over the last few years in the city of Sao Paulo, principally among the heterosexual population. These findings may have an impact on preventive measures and vaccine development in Brazil.

Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

Molecular organization and doping in poly(2-methoxyaniline)/Ni(dmit)(2) films obtained with the Langmuir-Blodgett technique

The control of the properties of materials at the molecular level is pursued for many applications, especially those associated with nanostructures. In this paper, we show that the coordination compound [Ni(dmit)(2)], where (dmit) is the 1,3-dithiole-2-thione-4,5-dithiolate ligand, can induce doping of poly(2-methoxyaniline) (POMA) in molecularly ordered Langmuir and Langmuir-Blodgett (LB) films. Doping was associated with interactions between the components and the compression of the Langmuir film at the air-water interface, according to polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS) data. Taking these results together with in situ UV-Vis absorption measurements, we could identify the molecular groups involved in the interaction, including the way they were reoriented upon film compression. The Langmuir films were sufficiently stable to be transferred as Y-type LB films, while the hybrid POMA/[Ni(dmit)(2)] films remain doped in the solid state. As expected, the molecular charges affected the film morphology, as observed from combined atomic and electric force microscopy measurements. In summary, with adequate spectroscopy and microscopy tools we characterized molecular-level interactions, which may allow one to design molecular electronic devices with controlled electrical properties.

Detection of glucose and triglycerides using information visualization methods to process impedance spectroscopy data

In this paper we discuss the detection of glucose and triglycerides using information visualization methods to process impedance spectroscopy data. The sensing units contained either lipase or glucose oxidase immobilized in layer-by-layer (LbL) films deposited onto interdigitated electrodes. The optimization consisted in identifying which part of the electrical response and combination of sensing units yielded the best distinguishing ability. It is shown that complete separation can be obtained for a range of concentrations of glucose and triglyceride when the interactive document map (IDMAP) technique is used to project the data into a two-dimensional plot. Most importantly, the optimization procedure can be extended to other types of biosensors, thus increasing the versatility of analysis provided by tailored molecular architectures exploited with various detection principles. (C) 2012 Elsevier B.V. All rights reserved.

Functional Magnetic Resonance Imaging Data Analysis by Autoregressive Estimator

The autoregressive (AR) estimator, a non-parametric method, is used to analyze functional magnetic resonance imaging (fMRI) data. The same method has been used, with success, in several other time series data analysis. It uses exclusively the available experimental data points to estimate the most plausible power spectra compatible with the experimental data and there is no need to make any assumption about non-measured points. The time series, obtained from fMRI block paradigm data, is analyzed by the AR method to determine the brain active regions involved in the processing of a given stimulus. This method is considerably more reliable than the fast Fourier transform or the parametric methods. The time series corresponding to each image pixel is analyzed using the AR estimator and the corresponding poles are obtained. The pole distribution gives the shape of power spectra, and the pixels with poles at the stimulation frequency are considered as the active regions. The method was applied in simulated and real data, its superiority is shown by the receiver operating characteristic curves which were obtained using the simulated data.

Oral health profile in patients infected with HTLV-1: Clinical findings, proviral load, and molecular analysis from HTLV-1 in saliva

Human T-lymphotropic virus type 1 (HTLV-1) is associated with adult T-cell leukemia (ATL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) and has also been implicated in several disorders, including periodontal disease. The proviral load is an important biological marker for understanding HTLV-1 pathogenesis and elucidating whether or not the virus is related to the clinical manifestation of the disease. This study describes the oral health profile of HTLV-1 carriers and HAM/TSP patients in order to investigate the association between the proviral load in saliva and the severity of the periodontal disease and to examine virus intra-host variations from peripheral blood mononuclear cells and saliva cells. It is a cross-sectional analytical study of 90 individuals carried out from November 2006 to May 2008. Of the patients, 60 were HTLV-1 positive and 30 were negative. Individuals from the HTLV-1 positive and negative groups had similar mean age and social-economic status. Data were analyzed using two available statistical software packages, STATA 8.0 and SPSS 11.0 to conduct frequency analysis. Differences of P?<?0.05 were considered statistically significant. HTLV-1 patients had poorer oral health status when compared to seronegative individuals. A weak positive correlation between blood and saliva proviral loads was observed. The mean values of proviral load in blood and saliva in patients with HAM/TSP was greater than those in HTLV-1 carriers. The HTLV-1 molecular analysis from PBMC and saliva specimens suggests that HTLV-1 in saliva is due to lymphocyte infiltration from peripheral blood. A direct relationship between the proviral load in saliva and oral manifestations was observed. J. Med. Virol. 84:1428-1436, 2012. (c) 2012 Wiley Periodicals, Inc.

Synthesis, biological evaluation and molecular docking studies of 3-(triazolyl)coumarin derivatives: Effect on inducible nitric oxide synthase

A series of 3-(triazolyl)-coumarins were synthesized and tested as anti-inflammatory agents. It was possible to infer that these compounds do not alter the interaction of LPS with TLR-4 or TLR-2, as the intracellular pathways involved in the TNF-alpha secretion and COX-2 activity were not affected. Nevertheless, the compounds inhibited iNOS-derived NO production, without affecting the eNOS activity. The outcome of the docking studies showed that it pi center dot center dot center dot pi interactions with the heme group are important for the iNOS inhibition, thus making compound 3c a promising lead. Moreover, the efficacy of this compound was visualized by the reduced number of neutrophils in the LPS-inflamed subcutaneous tissue. Together, biological and docking data show that triazolyl-substituted coumarins, that can act on iNOS, are a good scaffold to be explored. (C) 2012 Elsevier Masson SAS. All rights reserved.

From Amazonia to the Atlantic forest: Molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges

Documenting the Neotropical amphibian diversity has become a major challenge facing the threat of global climate change and the pace of environmental alteration. Recent molecular phylogenetic studies have revealed that the actual number of species in South American tropical forests is largely underestimated, but also that many lineages are millions of years old. The genera Phyzelaphryne (1 sp.) and Adelophryne (6 spp.), which compose the subfamily Phyzelaphryninae, include poorly documented, secretive, and minute frogs with an unusual distribution pattern that encompasses the biotic disjunction between Amazonia and the Atlantic forest. We generated >5.8 kb sequence data from six markers for all seven nominal species of the subfamily as well as for newly discovered populations in order to (1) test the monophyly of Phyzelaphryninae, Adelophryne and Phyzelaphryne, (2) estimate species diversity within the subfamily, and (3) investigate their historical biogeography and diversification. Phylogenetic reconstruction confirmed the monophyly of each group and revealed deep subdivisions within Adelophryne and Phyzelaphryne, with three major clades in Adelophryne located in northern Amazonia, northern Atlantic forest and southern Atlantic forest. Our results suggest that the actual number of species in Phyzelaphryninae is, at least, twice the currently recognized species diversity, with almost every geographically isolated population representing an anciently divergent candidate species. Such results highlight the challenges for conservation, especially in the northern Atlantic forest where it is still degraded at a fast pace. Molecular dating revealed that Phyzelaphryninae originated in Amazonia and dispersed during early Miocene to the Atlantic forest. The two Atlantic forest clades of Adelophryne started to diversify some 7 Ma minimum, while the northern Amazonian Adelophryne diversified much earlier, some 13 Ma minimum. This striking biogeographic pattern coincides with major events that have shaped the face of the South American continent, as we know it today. (C) 2012 Elsevier Inc. All rights reserved.

Molecular phylogeny and phenotypic variability of clinical and environmental strains of Aspergillus flavus

Aspergillus flavus is the second most common cause of aspergillosis infection in immunocompromised patients and is responsible for the production of aflatoxins. Little is known about the population structure of A. flavus, although recent molecular and phenotypic data seem to demonstrate that different genetic lineages exist within this species. The aim of this study was to carry out a morphological, physiological, and molecular analysis of a set of clinical and environmental isolates to determine whether this variability is due to species divergence or intraspecific diversity, and to assess whether the clinical isolates form a separate group. The amdS and omtA genes were more phylogenetically informative than the other tested genes and their combined analysis inferred three main clades, with no clear distinction between clinical and environmental isolates. No important morphological and physiological differences were found between the members of the different clades, with the exception of the assimilation of D-glucosamine, which differentiates the members of the clade II from the others. (C) 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Recoupled separated-local-field experiments and applications to study intermediate-regime molecular motions

A specific separated-local-field NMR experiment, dubbed Dipolar-Chemical-Shift Correlation (DIPSHIFT) is frequently used to study molecular motions by probing reorientations through the changes in XH dipolar coupling and T-2. In systems where the coupling is weak or the reorientation angle is small, a recoupled variant of the DIPSHIFT experiment is applied, where the effective dipolar coupling is amplified by a REDOR-like pi-pulse train. However, a previously described constant-time variant of this experiment is not sensitive to the motion-induced T-2 effect, which precludes the observation of motions over a large range of rates ranging from hundreds of Hz to around a MHz. We present a DIPSHIFT implementation which amplifies the dipolar couplings and is still sensitive to T-2 effects. Spin dynamics simulations, analytical calculations and experiments demonstrate the sensitivity of the technique to molecular motions, and suggest the best experimental conditions to avoid imperfections. Furthermore, an in-depth theoretical analysis of the interplay of REDOR-like recoupling and proton decoupling based on Average-Hamiltonian Theory was performed, which allowed explaining the origin of many artifacts found in literature data. (C) 2012 Elsevier Inc. All rights reserved.