Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Effect of NaCl additive on solute-solvent interactions in aqueous polyethylene glycol-sodium sulfate two-phase systems

Abstract Partition behavior of eight small organic compounds and six proteins was examined in poly(ethylene glycol)-8000-sodium sulfate aqueous two-phase systems containing 0.215 M NaCl and 0.5 M osmolyte (sorbitol, sucrose, TMAO) and poly(ethylene glycol)-10000-sodium sulfate-0.215 M NaCl system, all in 0.01 M sodium phosphate buffer, pH 6.8. The differences between the solvent properties of the coexisting phases (solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were characterized with solvatochromic dyes using the solvatochromic comparison method. Differences between the electrostatic properties of the phases were determined by analysis of partitioning of sodium salts of dinitrophenylated (DNP-) amino acids with aliphatic alkyl side-chain. The partition coefficients of all compounds examined (including proteins) were described in terms of solute-solvent interactions. The results obtained in the study show that solute-solvent interactions of nonionic organic compounds and proteins in polyethylene glycol-sodium sulfate aqueous two-phase system change in the presence of NaCl additive.

Interactions between carpenter bees and orchid bees (Hymenoptera: Apidae) in flowers of Bertholletia excelsa Bonpl. (Lecythidaceae)

Competition between two species of bees for the same type of floral resource may generate antagonistic behavior between them, especially in cultivated areas where food resources are limited, seasonally and locally. In this study, was tested the hypothesis of antagonism between two solitary bee species of the family Apidae, Eulaema mocsaryi (Euglossini) and Xylocopa frontalis (Xylocopini), visiting the Brazil nut flowers (Bertholletia excelsa: Lecythidaceae) in a central Amazonia agricultural area. The visitation time was analyzed to detect the possible temporal overlap in the foraging of these bees. Furthermore, was analyzed their interspecific interactions for manipulating flower species visited by an opponent species, as well as attempts to attack this opponent. The individuals of Xylocopa frontalis visited the Brazil nut flowers before Eulaema mocsaryi, although the peak visitation of both did not presented significant differences. Neither of the species manipulated flowers recently visited by opponent species, and there were practically no antagonistic interactions between them. Thus, X. frontalis and E. mocsaryi shared the same food source in the flowers of B. excelsa due to differences in their time of visits and non-aggressive way of interacting with the opponent. This result has important implications for pollinating the Brazil nut, and a possible management of X. frontalis and E. mocsaryi, since these two were the most abundant pollinators in the studied locality.

Indoor biological agents: evaluation of primary schools environments

Dissertação de mestrado em Human Engineering

Biological markers in noninvasive brain stimulation trials in major depressive disorder: a systematic review

Objectives: The therapeutic effects of transcranial magnetic stimulation (TMS) and transcranial direct current stimulation in patients with major depression have shown promising results; however, there is a lack of mechanistic studies using biological markers (BMs) as an outcome. Therefore, our aim was to review noninvasive brain stimulation trials in depression using BMs. Methods: The following databases were used for our systematic review: MEDLINE, Web of Science, Cochrane, and SCIELO. We examined articles published before November 2012 that used TMS and transcranial direct current stimulation as an intervention for depression and had BM as an outcome measure. The search was limited to human studies written in English. Results: Of 1234 potential articles, 52 articles were included. Only studies using TMS were found. Biological markers included immune and endocrine serum markers, neuroimaging techniques, and electrophysiological outcomes. In 12 articles (21.4%), end point BM measurements were not significantly associated with clinical outcomes. All studies reached significant results in the main clinical rating scales. Biological marker outcomes were used as predictors of response, to understand mechanisms of TMS, and as a surrogate of safety. Conclusions: Functional magnetic resonance imaging, single-photon emission computed tomography, positron emission tomography, magnetic resonance spectroscopy, cortical excitability, and brain-derived neurotrophic factor consistently showed positive results. Brain-derived neurotrophic factor was the best predictor of patients’ likeliness to respond. These initial results are promising; however, all studies investigating BMs are small, used heterogeneous samples, and did not take into account confounders such as age, sex, or family history. Based on our findings, we recommend further studies to validate BMs in noninvasive brain stimulation trials in MDD.

Abnormal interactions between context, memory structure, and mood in schizophrenia: an ERP investigation

This study used event-related potentials to examine interactions between mood, sentence context, and semantic memory structure in schizophrenia. Seventeen male chronic schizophrenia and 15 healthy control subjects read sentence pairs after positive, negative, or neutral mood induction. Sentences ended with expected words (EW), within-category violations (WCV), or between-category violations (BCV). Across all moods, patients showed sensitivity to context indexed by reduced N400 to EW relative to both WCV and BCV. However, they did not show sensitivity to the semantic memory structure. N400 abnormalities were particularly enhanced under a negative mood in schizophrenia. These findings suggest abnormal interactions between mood, context processing, and connections within semantic memory in schizophrenia, and a specific role of negative mood in modulating semantic processes in this disease.

Energy and carbon prices: a comparison of interactions in the European Union Emissions Trading Scheme and the Western Climate Initiative market

We provide a comparative analysis of how short-run variations in carbon and energy prices relate to each other in the emerging greenhouse gas market in California (Western Climate Initiative [WCI], and the European Union Emission Trading Scheme [EU ETS]). We characterize the relationship between carbon, gas, coal, electricity and gasoline prices and an indicator for economic activity, and present a first analysis of carbon prices in the WCI. We also provide a comparative analysis of the structures of the two markets. We estimate a vector autoregressive model and the impulse--response functions. Our main findings show a positive impact from a carbon shock toward electricity, in both markets, but larger in the WCI electricity price, indicating more efficiency. We propose that the widening of carbon market sectors, namely fuels transport and electricity imports, may contribute to this result. To conclude, the research shows significant and coherent relations between variables in WCI, which demonstrate some degree of success for a first year in operation. Reversely, the EU ETS should complete its intended market reform, to allow for more impact of the carbon price. Finally, in both markets, there is no evidence of carbon pricing depleting economic activity.

Biological and morphometric aspects and rearing of Syssphinx molina (Cramer) (Lepidoptera: Saturniidae), a defoliator of parica tree

The objective of this research was to describe the biological and morphometric aspects of the parica tree defoliator, Syssphinx molina (Cramer), and make recommendations about the insect rearing. The life cycle was 62.9 days with mean periods for the egg, larval, pre-pupal and pupal stages of 5.6, 31.1, 2.2 and 16.6 days respectively. The pupal viability was 60.5% for females and 48.6% for males. The sexual ratio was 0.5 with mean production of 182.3 ± 2.2 eggs per female and egg viability of 24.3%. The mean longevity was 7.9 ± 2 and 8.1 ± 3 days for females and males respectively. Other parameters were also observed and compared with description of other Saturniidae species.

The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy

The recent focus on the cystic fibrosis (CF) complex microbiome has led to the recognition that the microbes can interact between them and with the host immune system, affecting the disease progression and treatment routes. Although the main focus remains on the interactions between traditional pathogens, growing evidence supports the contribution and the role of emergent species. Understanding the mechanisms and the biological effects involved in polymicrobial interactions may be the key to improve effective therapies and also to define new strategies for disease control. This review focuses on the interactions between microbe-microbe and host-microbe, from an ecological point of view, discussing their impact on CF disease progression. There are increasing indications that these interactions impact the success of antimicrobial therapy. Consequently, a new approach where therapy is personalized to patients by taking into account their individual CF microbiome is suggested.

Polymicrobial interactions in infections: the case Pseudomonas aeruginosa and Candida albicans in ventilator-associated pneumonia

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clinica)

The effects of introducing the Amazonian squirrel monkey on the behavior of the northeast marmoset

The squirrel monkey Saimiri sciureus, an endemic primate of the Amazonian Basin, has been introduced in many localities of the Atlantic Forest biome. Introduced exotic species gain a competitive advantage in their new environment because of a lack of natural predators, competitors or diseases. This advantage can result in a reduction in the resources for the endemic species. The aims of this work were to evaluate the level of adaptation, and monitor the forms of interaction and the impact caused by S. sciureus on the behavior of the native species Callithrix jacchus in the Saltinho Biological Reserve, Tamandaré, Pernambuco, Brazil. The behavior was assessed by use of scan sampling method, every 5 min. A total of 382 h (191 h or 2,292 scans per group) of time sampling was performed. Sixteen interactions were recorded. The interaction index was low and represented 2.4% of the total observation time. Interactions were significantly higher during the dry season (58.5%) relative to the rainy season (41.5%). Callithrix jacchus was intolerant to the presence of S. sciureus and the last one was more tolerant during the interactions. In the presence of S. sciureus, C. jacchus eating, foraging, resting, socializing, and self-grooming behaviors were reduced while alertness was increased. Territorial behavior showed no significant difference. In the presence of S. sciureus, on average, the group of marmosets assembled at a higher layer of the forest stratum. The results might indicate a negative effect of S. sciureus on the native species, C. jacchus.

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70-50 ka into Eastern or Southern Africa, (2) postglacial movements (15-10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.

Biological behaviour of thin films consisting of Au nanoparticles dispersed in a TiO2 dielectric matrix

In this work it was studied the possible use of thin films, composed of Au nanoparticles (NPs) embedded in a TiO2 matrix, in biological applications, by evaluating their interaction with a well-known protein, Bovine Serum Albumin (BSA), as well as with microbial cells (Candida albicans). The films were produced by one-step reactive DC magnetron sputtering followed by heat-treatment. The samples revealed a composition of 8.3 at.% of Au and a stoichiometric TiO2 matrix. The annealing promoted grain size increase of the Au NPs from 3 nm (at 300 °C) to 7 nm (at 500 °C) and a progressive crystallization of the TiO2 matrix to anatase. A broad localized surface plasmon resonance (LSPR) absorption band (λ = 580–720 nm) was clearly observed in the sample annealed at 500 °C, being less intense at 300 °C. The biological tests indicated that the BSA adhesion is dependent on surface nanostructure morphology, which in turn depends on the annealing temperature that changed the roughness and wettability of the films. The Au:TiO2 thin films also induced a significant change of the microbial cell membrane integrity, and ultimately the cell viability, which in turn affected the adhesion on its surface. The microstructural changes (structure, grain size and surface morphology) of the Au:TiO2 films promoted by heat-treatment shaped the amount of BSA adhered and affected cell viability.

The relevance of bacterial interactions on oral health

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clínica)

Systems biology approaches for the design of novel Saccharomyces cerevisiae winemaking strains for enhanced flavour compounds synthesis

Tese de Doutoramento em Biologia Ambiental e Molecular