Development of a novel titration and off-gas analysis (TOGA) sensor for study of biological processes in wastewater treatment systems

The development of the new TOGA (titration and off-gas analysis) sensor for the detailed study of biological processes in wastewater treatment systems is outlined. The main innovation of the sensor is the amalgamation of titrimetric and off-gas measurement techniques. The resulting measured signals are: hydrogen ion production rate (HPR), oxygen transfer rate (OTR), nitrogen transfer rate (NTR), and carbon dioxide transfer rate (CTR). While OTR and NTR are applicable to aerobic and anoxic conditions, respectively, HPR and CTR are useful signals under all of the conditions found in biological wastewater treatment systems, namely, aerobic, anoxic and anaerobic. The sensor is therefore a powerful tool for studying the key biological processes under all these conditions. A major benefit from the integration of the titrimetric and off-gas analysis methods is that the acid/base buffering systems, in particular the bicarbonate system, are properly accounted for. Experimental data resulting from the TOGA sensor in aerobic, anoxic, and anaerobic conditions demonstrates the strength of the new sensor. In the aerobic environment, carbon oxidation (using acetate as an example carbon source) and nitrification are studied. Both the carbon and ammonia removal rates measured by the sensor compare very well with those obtained from off-line chemical analysis. Further, the aerobic acetate removal process is examined at a fundamental level using the metabolic pathway and stoichiometry established in the literature, whereby the rate of formation of storage products is identified. Under anoxic conditions, the denitrification process is monitored and, again, the measured rate of nitrogen gas transfer (NTR) matches well with the removal of the oxidised nitrogen compounds (measured chemically). In the anaerobic environment, the enhanced biological phosphorus process was investigated. In this case, the measured sensor signals (HPR and CTR) resulting from acetate uptake were used to determine the ratio of the rates of carbon dioxide production by competing groups of microorganisms, which consequently is a measure of the activity of these organisms. The sensor involves the use of expensive equipment such as a mass spectrometer and requires special gases to operate, thus incurring significant capital and operational costs. This makes the sensor more an advanced laboratory tool than an on-line sensor. (C) 2003 Wiley Periodicals, Inc.

Robust model-order reduction of complex biological processes

This paper addresses robust model-order reduction of a high dimensional nonlinear partial differential equation (PDE) model of a complex biological process. Based on a nonlinear, distributed parameter model of the same process which was validated against experimental data of an existing, pilot-scale BNR activated sludge plant, we developed a state-space model with 154 state variables in this work. A general algorithm for robustly reducing the nonlinear PDE model is presented and based on an investigation of five state-of-the-art model-order reduction techniques, we are able to reduce the original model to a model with only 30 states without incurring pronounced modelling errors. The Singular perturbation approximation balanced truncating technique is found to give the lowest modelling errors in low frequency ranges and hence is deemed most suitable for controller design and other real-time applications. (C) 2002 Elsevier Science Ltd. All rights reserved.

The removal of xenobiotic compounds from wastewater through the use of biological processes and advanced oxidation technologies

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Química e Bioquímica pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

The state of art of biological processes in paternal care

This review of the state of art aimed to present the most recent data on neuronal, neurochemical, hormonal and genetic bases of paternal care using MEDLINE and PsycInfo databases (1970-2013). An integrated model of biological substrates that assist men in the transition to fatherhood is presented. Guided by a genetic background, hypothalamic-midbrain-limbic-paralimbic-cortical circuits were found to be activated in fathers when infant stimuli are presented. A set of specifi c neuropeptides and steroid hormones are produced and seem to be related to brain activation, potentiating the paternal phenotype. Together, genetic, brain and hormonal processes suggest the existence of biological bases of paternal care in humans, activated and enhanced by infant stimuli and responsive to variations in the father-infant relationship.

Metallopeptidase inhibitors arrest vital biological processes in the fungal pathogen Scedosporium apiospermum

P>Scedosporium apiospermum is an emerging agent of opportunistic mycoses in humans. Previously, we showed that mycelia of S. apiospermum secreted metallopeptidases which were directly linked to the destruction of key host proteins. In this study, we analysed the effect of metallopeptidase inhibitors on S. apiospermum development. As germination of inhaled conidia is a crucial event in the infectious process of S. apiospermum, we studied the morphological transformation induced by the incubation of conidia in Sabouraud-dextrose medium at 37 degrees C. After 6 h, some conidia presented a small projection resembling a germ-tube. A significant increase, around sixfold, in the germ-tube length was found after 12 h, and hyphae were exclusively observed after 24 h. Three distinct metallopeptidase inhibitors were able to arrest the transformation of conidia into hyphae in different ways; for instance, 1,10-phenanthroline (PHEN) completely blocked this process at 10 mu mol l-1, while ethylenediamine tetraacetic acid (EDTA) and ethylene glycol-bis (beta-aminoethyl ether; EGTA) only partially inhibited the differentiation at up to 10 mmol l-1. EGTA did not promote any significant reduction in the conidial growth, while PHEN and EDTA, both at 10 mmol l-1, inhibited the proliferation around 100% and 65%, respectively. The secretion of polypeptides into the extracellular environment and the metallopeptidase activity secreted by mycelia were completely inhibited by PHEN. These findings suggest that metallo-type enzymes could be potential targets for future therapeutic interventions against S. apiospermum.

Gene expression profiles displayed by peripheral blood mononuclear cells from patients with type 2 diabetes mellitus focusing on biological processes implicated on the pathogenesis of the disease

Patients with type 2 diabetes mellitus (T2DM) exhibit insulin resistance associated with obesity and inflammatory response, besides an increased level of oxidative DNA damage as a consequence of the hyperglycemic condition and the generation of reactive oxygen species (ROS). In order to provide information on the mechanisms involved in the pathophysiology of T2DM, we analyzed the transcriptional expression patterns exhibited by peripheral blood mononuclear cells (PBMCs) from patients with T2DM compared to non-diabetic subjects, by investigating several biological processes: inflammatory and immune responses, responses to oxidative stress and hypoxia, fatty acid processing, and DNA repair. PBMCs were obtained from 20 T2DM patients and eight non-diabetic subjects. Total RNA was hybridized to Agilent whole human genome 4x44K one-color oligo-microarray. Microarray data were analyzed using the GeneSpring GX 11.0 software (Agilent). We used BRB-ArrayTools software (gene set analysis - GSA) to investigate significant gene sets and the Genomica tool to study a possible influence of clinical features on gene expression profiles. We showed that PBMCs from T2DM patients presented significant changes in gene expression, exhibiting 1320 differentially expressed genes compared to the control group. A great number of genes were involved in biological processes implicated in the pathogenesis of T2DM. Among the genes with high fold-change values, the up-regulated ones were associated with fatty acid metabolism and protection against lipid-induced oxidative stress, while the down-regulated ones were implicated in the suppression of pro-inflammatory cytokines production and DNA repair. Moreover, we identified two significant signaling pathways: adipocytokine, related to insulin resistance; and ceramide, related to oxidative stress and induction of apoptosis. In addition, expression profiles were not influenced by patient features, such as age, gender, obesity, pre/post-menopause age, neuropathy, glycemia, and HbA(1c) percentage. Hence, by studying expression profiles of PBMCs, we provided quantitative and qualitative differences and similarities between T2DM patients and non-diabetic individuals, contributing with new perspectives for a better understanding of the disease. (C) 2012 Elsevier B.V. All rights reserved.

IDENTIFICATION OF GENES CONTROLLING BIOLOGICAL PROCESSES AND PATHWAYS THROUGH STATISTICAL ANALYSIS AND NETWORK RECONSTRUCTION

The developmental processes and functions of an organism are controlled by the genes and the proteins that are derived from these genes. The identification of key genes and the reconstruction of gene networks can provide a model to help us understand the regulatory mechanisms for the initiation and progression of biological processes or functional abnormalities (e.g. diseases) in living organisms. In this dissertation, I have developed statistical methods to identify the genes and transcription factors (TFs) involved in biological processes, constructed their regulatory networks, and also evaluated some existing association methods to find robust methods for coexpression analyses. Two kinds of data sets were used for this work: genotype data and gene expression microarray data. On the basis of these data sets, this dissertation has two major parts, together forming six chapters. The first part deals with developing association methods for rare variants using genotype data (chapter 4 and 5). The second part deals with developing and/or evaluating statistical methods to identify genes and TFs involved in biological processes, and construction of their regulatory networks using gene expression data (chapter 2, 3, and 6). For the first part, I have developed two methods to find the groupwise association of rare variants with given diseases or traits. The first method is based on kernel machine learning and can be applied to both quantitative as well as qualitative traits. Simulation results showed that the proposed method has improved power over the existing weighted sum method (WS) in most settings. The second method uses multiple phenotypes to select a few top significant genes. It then finds the association of each gene with each phenotype while controlling the population stratification by adjusting the data for ancestry using principal components. This method was applied to GAW 17 data and was able to find several disease risk genes. For the second part, I have worked on three problems. First problem involved evaluation of eight gene association methods. A very comprehensive comparison of these methods with further analysis clearly demonstrates the distinct and common performance of these eight gene association methods. For the second problem, an algorithm named the bottom-up graphical Gaussian model was developed to identify the TFs that regulate pathway genes and reconstruct their hierarchical regulatory networks. This algorithm has produced very significant results and it is the first report to produce such hierarchical networks for these pathways. The third problem dealt with developing another algorithm called the top-down graphical Gaussian model that identifies the network governed by a specific TF. The network produced by the algorithm is proven to be of very high accuracy.

An updated synthesis of the observed and projected impacts of climate change on the chemical, physical and biological processes in the oceans

The 5th Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC) states with very high certainty that anthropogenic emissions have caused measurable changes in the physical ocean environment. These changes are summarized with special focus on those that are predicted to have the strongest, most direct effects on ocean biological processes; namely, ocean warming and associated phenomena (including stratification and sea level rise) as well as deoxygenation and ocean acidification. The biological effects of these changes are then discussed for microbes (including phytoplankton), plants, animals, warm and cold-water corals, and ecosystems. The IPCC AR5 highlighted several areas related to both the physical and biological processes that required further research. As a rapidly developing field, there have been many pertinent studies published since the cut off dates for the AR5, which have increased our understanding of the processes at work. This study undertook an extensive review of recently published literature to update the findings of the AR5 and provide a synthesized review on the main issues facing future oceans. The level of detail provided in the AR5 and subsequent work provided a basis for constructing projections of the state of ocean ecosystems in 2100 under two the Representative Concentration Pathways RCP4.5 and 8.5. Finally the review highlights notable additions, clarifications and points of departure from AR5 provided by subsequent studies.

Seawater carbonate chemistry and biological processes of Mytilus edulis during experiments, 2010

Marine organisms are exposed to increasingly acidic oceans, as a result of equilibration of surface ocean water with rising atmospheric CO2 concentrations. In this study, we examined the physiological response of Mytilus edulis from the Baltic Sea, grown for 2 months at 4 seawater pCO2 levels (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm). Shell and somatic growth, calcification, oxygen consumption and excretion rates were measured in order to test the hypothesis whether exposure to elevated seawater pCO2 is causally related to metabolic depression. During the experimental period, mussel shell mass and shell-free dry mass (SFDM) increased at least by a factor of two and three, respectively. However, shell length and shell mass growth decreased linearly with increasing pCO2 by 6-20 and 10-34%, while SFDM growth was not significantly affected by hypercapnia. We observed a parabolic change in routine metabolic rates with increasing pCO2 and the highest rates (+60%) at 243 Pa. excretion rose linearly with increasing pCO2. Decreased O:N ratios at the highest seawater pCO2 indicate enhanced protein metabolism which may contribute to intracellular pH regulation. We suggest that reduced shell growth under severe acidification is not caused by (global) metabolic depression but is potentially due to synergistic effects of increased cellular energy demand and nitrogen loss.

Seawater carbonate chemistry and Globigerinoides sacculifer biological processes during experiments, 2010

The effect of carbonate ion concentration ([CO3]) on calcification rates estimated from shell size and weight was investigated in the planktonic foraminifera Orbulina universa and Globigerinoides sacculifer. Experiments on G. sacculifer were conducted under two irradiance levels (35 and 335 µmol photons m-2 s-1). Calcification was ca. 30% lower under low light than under high light, irrespective of the [CO3]. Both O. universa and G. sacculifer exhibited reduced final shell weight and calcification rate under low [CO3]. For the [CO3] expected at the end of the century, the calcification rates of these two species are projected to be 6 to 13% lower than the present conditions, while the final shell weights are reduced by 20 to 27% for O. universa and by 4 to 6% for G. sacculifer. These results indicate that ocean acidification would impact on calcite production by foraminifera and may decrease the calcite flux contribution from these organisms.

Effects of seawater acidification on early development of the intertidal sea urchin Paracentrotus lividus, seawater carbonate chemistry and biological processes

The effect of pH ranging from 8.0 to 6.8 (total scale - pHT) on fertilization, cleavage and larval development until pluteus stage was assessed in an intertidal temperate sea urchin. Gametes were obtained from adults collected in two contrasting tide pools, one showing a significant nocturnal pH decrease (lowest pHT = 7.4) and another where pH was more stable (lowest pHT = 7.8). The highest pHT at which significant effects on fertilization and cleavage were recorded was 7.6. On the contrary, larval development was only affected below pHT 7.4, a value equal or lower than that reported for several subtidal species. This suggests that sea urchins inhabiting stressful intertidal environments produce offspring that may better resist future ocean acidification. Moreover, at pHT 7.4, the fertilization rate of gametes whose progenitors came from the tide pool with higher pH decrease was significantly higher, indicating a possible acclimatization or adaptation of gametes to pH stress.