Can arsenic-phytochelatin complex formation be used as an indicator for toxicity in Helianthus annuus?

The formation of arsenic-phytochelatin (As-PC) complexes is thought to be part of the plant detoxification strategy for arsenic. This work examines (i) the arsenic (As) concentration-dependent formation of As-PC complex formation and (ii) redistribution and metabolism of As after arrested As uptake in Helianthus annuus. HPLC with parallel ICP-MS/ES-MS detection was used to identify and quantify the species present in plant extracts exposed to arsenate (As(V)) (between 0 and 66.7 micromol As l-1 for 24 h). At As concentrations below the EC50 value for root growth (22 micromol As l-1) As uptake is exponential, but it is reduced at concentrations above. Translocation between root and shoot seemed to be limited to the uptake phase of arsenic. No redistribution of As between root and shoot was observed after arresting As exposure. The formation of As-PC complexes was concentration-dependent. The amount and number of As-PC complexes increased exponentially with concentration up to 13.7 micromol As l-1. As(III)-PC3 and GS-As(III)-PC2 complexes were the dominant species in all samples. The ratio of PC-bound As to unbound As increased up to 1.3 micromol As l-1 and decreased at higher concentrations. Methylation of inorganic As was only a minor pathway in H. annuus with about 1% As methylated over a 32 d period. The concentration dependence of As-PC complex formation, amount of unbound reduced and oxidized PC2, and the relative uptake rate showed that As starts to influence the cellular metabolism of H. annuus negatively at As concentrations well below the EC50 value determined by more traditional means. Generally, As-PC complexes and PC-synthesis rate seem to be the more sensitive parameters to be studied when As toxicity values are to be estimated.

TLM2.0 based timing accurate modeling method for complex NoC systems

Scalability and efficiency of on-chip communication of emerging Multiprocessor System-on-Chip (MPSoC) are critical design considerations. Conventional bus based interconnection schemes no longer fit for MPSoC with a large number of cores. Networks-on-Chip (NoC) is widely accepted as the next generation interconnection scheme for large scale MPSoC. The increase of MPSoC complexity requires fast and accurate system-level modeling techniques for rapid modeling and veri-fication of emerging MPSoCs. However, the existing modeling methods are limited in delivering the essentials of timing accuracy and simulation speed. This paper proposes a novel system-level Networks-on-Chip (NoC) modeling method, which is based on SystemC and TLM2.0 and capable of delivering timing accuracy close to cycle accurate modeling techniques at a significantly lower simulation cost. Experimental results are presented to demonstrate the proposed method. ©2010 IEEE.

Complex Interactions between Dioxin-Like and Non-Dioxin-Like Compounds for in Vitro Cellular Responses: Implications for the Identification of Dioxin Exposure Biomarkers

Despite considerable advances in reducing the production of dioxin-like toxicants in recent years, contamination of the food chain still occasionally occurs resulting in huge losses to the agri-food sector and risk to human health through exposure. Dioxin-like toxicity is exhibited by a range of stable and bioaccumulative compounds including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs), produced by certain types of combustion, and man-made coplanar polychlorinated biphenyls (PCBs), as found in electrical transformer oils. While dioxinergic compounds act by a common mode of action making exposure detection biomarker based techniques a potentially useful tool, the influence of co-contaminating toxicants on such approaches needs to be considered. To assess the impact of possible interactions, the biological responses of H4IIE cells to challenge by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in combination with PCB-52 and benzo-a-pyrene (BaP) were evaluated by a number of methods in this study. Ethoxyresorufin-O-deethylase (EROD) induction in TCDD exposed cells was suppressed by increasing concentrations of PCB-52, PCB-153, or BaP up to 10 mu M. BaP levels below 1 mu M suppressed TCDD stimulated EROD induction, but at higher concentrations, EROD induction was greater than the maximum observed when cells were treated with TCDD alone. A similar biphasic interaction of BaP with TCDD co-exposure was noted in the AlamarBlue assay and to a lesser extent with PCB-52. Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF) profiling of peptidomic responses of cells exposed to compound combinations was compared. Cells co-exposed to TCDD in the presence of BaP or PCB-52 produced the most differentiated spectra with a substantial number of non-additive interactions observed. These findings suggest that interactions between dioxin and other toxicants create novel, additive, and non-additive effects, which may be more indicative of the types of responses seen in exposed animals than those of single exposures to the individual compounds.

Identification of a BRCA1-mRNA Splicing Complex Required for Efficient DNA Repair and Maintenance of Genomic Stability

Mutations within BRCA1 predispose carriers to a high risk of breast and ovarian cancers. BRCA1 functions to maintain genomic stability through the assembly of multiple protein complexes involved in DNA repair, cell-cycle arrest, and transcriptional regulation. Here, we report the identification of a DNA damage-induced BRCA1 protein complex containing BCLAF1 and other key components of the mRNA-splicing machinery. In response to DNA damage, this complex regulates pre-mRNA splicing of a number of genes involved in DNA damage signaling and repair, thereby promoting the stability of these transcripts/proteins. Further, we show that abrogation of this complex results in sensitivity to DNA damage, defective DNA repair, and genomic instability. Interestingly, mutations in a number of proteins found within this complex have been identified in numerous cancer types. These data suggest that regulation of splicing by the BRCA1-mRNA splicing complex plays an important role in the cellular response to DNA damage.

Complex organic molecules in protoplanetary disks

Context. Protoplanetary disks are vital objects in star and planet formation, possessing all the material, gas and dust, which may form a planetary system orbiting the new star. Small, simple molecules have traditionally been detected in protoplanetary disks; however, in the ALMA era, we expect the molecular inventory of protoplanetary disks to significantly increase.

Aims. We investigate the synthesis of complex organic molecules (COMs) in protoplanetary disks to put constraints on the achievable chemical complexity and to predict species and transitions which may be observable with ALMA.

Methods. We have coupled a 2D steady-state physical model of a protoplanetary disk around a typical T Tauri star with a large gas-grain chemical network including COMs. We compare the resulting column densities with those derived from observations and perform ray-tracing calculations to predict line spectra. We compare the synthesised line intensities with current observations and determine those COMs which may be observable in nearby objects. We also compare the predicted grain-surface abundances with those derived from cometary comae observations.

Results. We find COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances similar to 10(-6)-10(-4) that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, similar to 10(-12)-10(-7). Including the irradiation of grain mantle material helps build further complexity in the ice through the replenishment of grain-surface radicals which take part in further grain-surface reactions. There is reasonable agreement with several line transitions of H2CO observed towards T Tauri star-disk systems. There is poor agreement with HC3(N) lines observed towards LkCa 15 and GO Tau and we discuss possible explanations for these discrepancies. The synthesised line intensities for CH3OH are consistent with upper limits determined towards all sources. Our models suggest CH3OH should be readily observable in nearby protoplanetary disks with ALMA; however, detection of more complex species may prove challenging, even with ALMA "Full Science" capabilities. Our grain-surface abundances are consistent with those derived from cometary comae observations providing additional evidence for the hypothesis that comets (and other planetesimals) formed via the coagulation of icy grains in the Sun's natal disk.

Isolating Informational Masking in Both Pure and Complex Tone Sequences

Objectives: Interference between a target and simultaneous maskers occurs both at the cochlear level through energetic masking and more centrally through informational masking (IM). Hence, quantifying the amount of IM requires a strict control of the energetic component. Presenting target and maskers on different sides (i.e., dichotically) reduces energetic masking but provides listeners with important lateralization cues that also drastically reduce IM. The main purpose of this study (Experiment 1) was to evaluate a "switch" manipulation aiming at restoring most of the IM despite dichotic listening. Experiment 2 was designed to investigate the source of the difficulty induced by this switching dichotic condition.

Design: In Experiment 1, the authors presented 60 normal-hearing young adults with a detection task in which a regularly repeating target was embedded in a randomly varying background masker. The authors evaluated spatial masking release induced by three different dichotic listening conditions in comparison with a diotic baseline. Dichotic stimuli were presented in either a nonswitching or a switching condition. In the latter case, the presentation sides of dichotic target and maskers alternated several times throughout 10 sec sequences. The impact of the number of switches on IM was investigated parametrically, with both pure and complex tone sequences. In Experiment 2, the authors compared performance of 13 young, normal-hearing listeners in a monotic and dichotic version of the rapidly switching condition, using pure-tone sequences.

Results: When target and maskers switched rapidly within sequences, IM was significantly stronger than in nonswitching dichotic sequences and was comparable with the masking effect induced by diotic sequences. Furthermore, Experiment 2 suggests that rapidly switching target and maskers prevent listeners from relying on lateralization cues inherent to the dichotic condition, hence preserving important amounts of IM.

Conclusions: This paradigm thus provides an original tool to isolate IM in signal and maskers having overlapping spectra.

Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified. Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome-wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells. We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites. We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity. Collectively, this results in a global TP53-dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveal that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair.

Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

Magnetic Characteristics of a High-layer-number NiFe/FeMn Multilayer

We report the static & dynamic magnetic characteristics of a high-layer-number NiFe/FeMn multilayer test structure with potential applications in broadband absorber and filter devices. To allow fine control over the absorption linewidths and to understand the mechanisms governing the resonances in a tailored structure similar to that expected to be used in real world applications, the multilayer was intentionally designed to have layer thickness and interface roughness variations. Magnetometry measurements show the sample has complex hysteresis loops with features consistent with single ferromagnetic film reversals. Structural characterisation by transmission electron microscopy allows us to correlate the magnetic properties with structural features. Analysis of resonance frequencies from broadband ferromagnetic resonance measurements as a function of field magnitude and orientation provide values of the local exchange bias, rotatable anisotropy, and uniaxial anisotropy fields for specific layers in the stack and explain the observed mode softening. The linewidths of the multilayer are adjustable around the bias field, approaching twice that seen at larger fields, allowing control over the bandwidth of devices formed from the structure.

2P/Encke, the Taurid complex NEOs and the Maribo and Sutter's Mill meteorites

Aims. 2P/Encke is a short period comet that was discovered in 1786 and has been extensively observed and studied for more than 200years. The Taurid meteoroid stream has long been linked with 2P/Encke owing to a good match of their orbital elements, even thoughthe comet’s activity is not strong enough to explain the number of observed meteors. Various small near-Earth objects (NEOs) havebeen discovered with orbits that can be linked to 2P/Encke and the Taurid meteoroid stream. Maribo and Sutter’s Mill are CM typecarbonaceous chondrite that fell in Denmark on January 17, 2009 and April 22, 2012, respectively. Their pre-atmospheric orbits placethem in the middle of the Taurid meteoroid stream, which raises the intriguing possibility that comet 2P/Encke could be the parentbody of CM chondrites.
Methods. To investigate whether a relationship between comet 2P/Encke, the Taurid complex associated NEOs, and CM chondritesexists, we performed photometric and spectroscopic studies of these objects in the visible wavelength range. We observed 2P/Enckeand 10 NEOs on August 2, 2011 with the FORS instrument at the 8.2 m Very Large Telescope on Cerro Paranal (Chile).
Results. Images in the R filter, used to investigate the possible presence of cometary activity around the nucleus of 2P/Encke andthe NEOs, show that no resolved coma is present. None of the FORS spectra show the 700 nm absorption feature due to hydratedminerals that is seen in the CM chondrite meteorites. All objects show featureless spectra with moderate reddening slopes at λ < 800nm. Apart for 2003 QC10 and 1999 VT25, which show a flatter spectrum, the spectral slope of the observed NEOs is compatible withthat of 2P/Encke. However, most of the NEOs show evidence of a silicate absorption in lower S/N data at λ > 800 nm, which is notseen in 2P/Encke, which suggests that they are not related.
Conclusions. Despite similar orbits, we find no spectroscopic evidence for a link between 2P/Encke, the Taurid complex NEOs andthe Maribo and Sutter’s Mill meteorites. However, we cannot rule out a connection to the meteorites either, as the spectral differencesmay be caused by secondary alteration of the surfaces of the NEOs. 

Interacting agents on complex networks and stochastic processes in them

Nas últimas décadas, um grande número de processos têm sido descritos em termos de redes complexas. A teoria de redes complexas vem sendo utilizada com sucesso para descrever, modelar e caracterizar sistemas naturais, artificias e sociais, tais como ecossistemas, interações entre proteínas, a Internet, WWW, até mesmo as relações interpessoais na sociedade. Nesta tese de doutoramento apresentamos alguns modelos de agentes interagentes em redes complexas. Inicialmente, apresentamos uma breve introdução histórica (Capítulo 1), seguida de algumas noções básicas sobre redes complexas (Capítulo 2) e de alguns trabalhos e modelos mais relevantes a esta tese de doutoramento (Capítulo 3). Apresentamos, no Capítulo 4, o estudo de um modelo de dinâmica de opiniões, onde busca-se o consenso entre os agentes em uma população, seguido do estudo da evolução de agentes interagentes em um processo de ramificação espacialmente definido (Capítulo 5). No Capítulo 6 apresentamos um modelo de otimização de fluxos em rede e um estudo do surgimento de redes livres de escala a partir de um processo de otimização . Finalmente, no Capítulo 7, apresentamos nossas conclusões e perspectivas futuras.

Detection of quasi-periodic processes in complex systems: how do we quantitatively describe their properties?

It has been shown that in reality at least two general scenarios of data structuring are possible: (a) a self-similar (SS) scenario when the measured data form an SS structure and (b) a quasi-periodic (QP) scenario when the repeated (strongly correlated) data form random sequences that are almost periodic with respect to each other. In the second case it becomes possible to describe their behavior and express a part of their randomness quantitatively in terms of the deterministic amplitude–frequency response belonging to the generalized Prony spectrum. This possibility allows us to re-examine the conventional concept of measurements and opens a new way for the description of a wide set of different data. In particular, it concerns different complex systems when the ‘best-fit’ model pretending to be the description of the data measured is absent but the barest necessity of description of these data in terms of the reduced number of quantitative parameters exists. The possibilities of the proposed approach and detection algorithm of the QP processes were demonstrated on actual data: spectroscopic data recorded for pure water and acoustic data for a test hole. The suggested methodology allows revising the accepted classification of different incommensurable and self-affine spatial structures and finding accurate interpretation of the generalized Prony spectroscopy that includes the Fourier spectroscopy as a partial case.

Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

A simple genetic basis for complex social behaviour mediates widespread gene expression differences.

A remarkable social polymorphism is controlled by a single Mendelian factor in the fire ant Solenopsis invicta. A genomic element marked by the gene Gp-9 determines whether workers tolerate one or many fertile queens in their colony. Gp-9 was recently shown to be part of a supergene with two nonrecombining variants, SB and Sb. SB/SB and SB/Sb queens differ in how they initiate new colonies, and in many physiological traits, for example odour and maturation rate. To understand how a single genetic element can affect all these traits, we used a microarray to compare gene expression patterns between SB/SB and SB/Sb queens of three different age classes: 1-day-old unmated queens, 11-day-old unmated queens and mated, fully reproductive queens collected from mature field colonies. The number of genes that were differentially expressed between SB/SB and SB/Sb queens of the same age class was smallest in 1-day-old queens, maximal in 11-day-old queens and intermediate in reproductive queens. Gene ontology analysis showed that SB/SB queens upregulate reproductive genes faster than SB/Sb queens. For all age classes, genes inside the supergene were overrepresented among the differentially expressed genes. Consistent with the hypothesized greater number of transposons in the Sb supergene, 13 transposon genes were upregulated in SB/Sb queens. Viral genes were also upregulated in SB/Sb mature queens, consistent with the known greater parasite load in colonies headed by SB/Sb queens compared with colonies headed by SB/SB queens. Eighteen differentially expressed genes between reproductive queens were involved in chemical signalling. Our results suggest that many genes in the supergene are involved in regulating social organization and queen phenotypes in fire ants.

Soft tissue sarcomas with complex genomic profiles.

Soft tissue sarcomas (STS) with complex genomic profiles (50% of all STS) are predominantly composed of spindle cell/pleomorphic sarcomas, including leiomyosarcoma, myxofibrosarcoma, pleomorphic liposarcoma, pleomorphic rhabdomyosarcoma, malignant peripheral nerve sheath tumor, angiosarcoma, extraskeletal osteosarcoma, and spindle cell/pleomorphic unclassified sarcoma (previously called spindle cell/pleomorphic malignant fibrous histiocytoma). These neoplasms show, characteristically, gains and losses of numerous chromosomes or chromosome regions, as well as amplifications. Many of them share recurrent aberrations (e.g., gain of 5p13-p15) that seem to play a significant role in tumor progression and/or metastatic dissemination. In this paper, we review the cytogenetic, molecular genetic, and clinicopathologic characteristics of the most common STS displaying complex genomic profiles. Features of diagnostic or prognostic relevance will be discussed when needed.