Embryonic gene expression of Coregonus palaea (whitefish) under pathogen stress as analyzed by high-throughput RNA-sequencing.

Most fishes produce free-living embryos that are exposed to environmental stressors immediately following fertilization, including pathogenic microorganisms. Initial immune protection of embryos involves the chorion, as a protective barrier, and maternally-allocated antimicrobial compounds. At later developmental stages, host-genetic effects influence susceptibility and tolerance, suggesting a direct interaction between embryo genes and pathogens. So far, only a few host genes could be identified that correlate with embryonic survival under pathogen stress in salmonids. Here, we utilized high-throughput RNA-sequencing in order to describe the transcriptional response of a non-model fish, the Alpine whitefish Coregonus palaea, to infection, both in terms of host genes that are likely manipulated by the pathogen, and those involved in an early putative immune response. Embryos were produced in vitro, raised individually, and exposed at the late-eyed stage to a virulent strain of the opportunistic fish pathogen Pseudomonas fluorescens. The pseudomonad increased embryonic mortality and affected gene expression substantially. For example, essential, upregulated metabolic pathways in embryos under pathogen stress included ion binding pathways, aminoacyl-tRNA-biosynthesis, and the production of arginine and proline, most probably mediated by the pathogen for its proliferation. Most prominently downregulated transcripts comprised the biosynthesis of unsaturated fatty acids, the citrate cycle, and various isoforms of b-cell transcription factors. These factors have been shown to play a significant role in host blood cell differentiation and renewal. With regard to specific immune functions, differentially expressed transcripts mapped to the complement cascade, MHC class I and II, TNF-alpha, and T-cell differentiation proteins. The results of this study reveal insights into how P. fluorescens impairs the development of whitefish embryos and set a foundation for future studies investigating host pathogen interactions in fish embryos.

Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases.

Treatment of micropollutants in municipal wastewater: study of a sequential batch biofilter

All the experimental part of this final project was done at Laboratoire de Biotechnologie Environnementale (LBE) from the École Polytechnique Fédérale de Lausanne (EPFL), Switzerland, during 6 months (November 2013- May 2014). A fungal biofilter composed of woodchips was designed in order to remove micropollutants from the effluents of waste water treatment plants. Two fungi were tested: Pleurotus ostreatus and Trametes versicolor in order to evaluate their efficiency for the removal of two micropollutants: the anti-inflammatory drug naproxen and the antibiotic sulfamethoxazole,. Although Trametes versicolor was able to degrade quickly naproxen, this fungus was not any more active after one week of operation in the filter. Pleurotus ostreatus was, on contrary, able to survive more than 3 months in the filter, showing good removal efficiencies of naproxen and sulfamethoxazole during all this period, in tap water but also in real treated municipal wastewater. Several other experiments have provided insight on the removal mechanisms of these micropollutants in the fungal biofilter (degradation and adsorption) and also allowed to model the removal trend. Fungal treatment with Pleurotus ostreatus grown on wood substrates appeared to be a promising solution to improve micropollutants removal in wastewater.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Copy number variations of colorectal cancer by whole exome sequencing data

Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer death worldwide. About 85% of the cases of CRC are known to have chromosomal instability, an allelic imbalance at several chromosomal loci, and chromosome amplification and translocation. The aim of this study is to determine the recurrent copy number variant (CNV) regions present in stage II of CRC through whole exome sequencing, a rapidly developing targeted next-generation sequencing (NGS) technology that provides an accurate alternative approach for accessing genomic variations. 42 normal-tumor paired samples were sequenced by Illumina Genome Analyzer. Data was analyzed with Varscan2 and segmentation was performed with R package R-GADA. Summary of the segments across all samples was performed and the result was overlapped with DEG data of the same samples from a previous study in the group1. Major and more recurrent segments of CNV were: gain of chromosome 7pq(13%), 13q(31%) and 20q(75%) and loss of 8p(25%), 17p(23%), and 18pq(27%). This results are coincident with the known literature of CNV in CRC or other cancers, but our methodology should be validated by array comparative genomic hybridisation (aCGH) profiling, which is currently the gold standard for genetic diagnosis of CNV.

The Present State and a Development Plan of Cost Accounting in Batch Production of Wind Turbine Gears

The aim of this master’s thesis was to document the present state and to create a development plan for Moventas Wind’s cost accounting. The current cost accounting system was evaluated and most fundamental problems were chosen as areas of focus in development work. The development plan includes both short- and long-term development proposals for problems identified. This report presents two alternative models for product costing. Benchmarking of cost accounting practices and modern cost accounting theories were used in development of cost accounting. It was found that the current cost accounting system functions quite well and the adjustments in unit cost rate calculation have only a minor influence on costs of goods sold. An OEE-based standard cycle concept was also developed and it was found that the implementation of this new system is worthwhile in the long-term.

Retrieval of kinetic rates in reactions with semi batch liquid phase using ill-posed inverse problem theory

A neural network procedure to solve inverse chemical kinetic problems is discussed in this work. Rate constants are calculated from the product concentration of an irreversible consecutive reaction: the hydrogenation of Citral molecule, a process with industrial interest. Simulated and experimental data are considered. Errors in the simulated data, up to 7% in the concentrations, were assumed to investigate the robustness of the inverse procedure. Also, the proposed method is compared with two common methods in nonlinear analysis; the Simplex and Levenberg-Marquardt approaches. In all situations investigated, the neural network approach was numerically stable and robust with respect to deviations in the initial conditions or experimental noises.

Imobilização de lacase de Aspergillus sp. em quitosana e sua aplicação na bioconversão de fenóis em reatores de leito fixo

The immobilization of laccase on chitosan by cross-linking and application of the immobilized laccase in the bioconversion of phenolic compounds in batch and fixed bed reactors were studied. The process for immobilization of enzyme was optimized using a rotational central composite design. The optimized conditions to generate immobilized laccase with maximal activity were determined to be a glutaraldehyde concentration of 1.0% (v/v), a pH of 6.0, an immobilization time of 5.0 hours and an enzyme concentration of 5.2 g L-1. In packed bed reactors, the activity of the immobilized enzyme is maintained for a longer time in the bioconversion of 2,6-dimethoxyphenol than in the bioconversion of syringaldazine.

Flow-batch analyser for preparation of calibration standard mixtures in simultaneous multicomponent spectrometric analysis

The application of multivariate calibration techniques to multicomponent analysis by UV-VIS molecular absorption spectrometry is a powerful tool for simultaneous determination of several chemical species. However, when this methodology is accomplished manually, it is slow and laborious, consumes high amounts of reagents and samples, is susceptible to contaminations and presents a high operational cost. To overcome these drawbacks, a flow-batch analyser is proposed in this work. This analyser was developed for automatic preparation of standard calibration and test (or validation) mixtures. It was applied to the simultaneous determination of Cu2+, Mn2+ and Zn2+ in polyvitaminic and polymineral pharmaceutical formulations, using 4-(2-piridilazo) resorcinol as reagent and a UV-VIS spectrophotometer with a photodiode array detector. The results obtained with the proposed system are in good agreement with those obtained by flame atomic absorption spectrometry, which was employed as reference method. With the proposed analyser, the preparation of calibration and test mixtures can be accomplished about four hours, while the manual procedure requires at least two days. Moreover, it consumes smaller amounts of reagents and samples than the manual procedure. After the preparation of calibration and test mixtures, 60 samples h-1 can be carried out with the proposed flow-batch analyser.

A study of combustion phenomena in circulating fluidized beds by developing and applying experimental and modelling methods for laboratory-scale reactors

The results shown in this thesis are based on selected publications of the 2000s decade. The work was carried out in several national and EC funded public research projects and in close cooperation with industrial partners. The main objective of the thesis was to study and quantify the most important phenomena of circulating fluidized bed combustors by developing and applying proper experimental and modelling methods using laboratory scale equipments. An understanding of the phenomena plays an essential role in the development of combustion and emission performance, and the availability and controls of CFB boilers. Experimental procedures to study fuel combustion behaviour under CFB conditions are presented in the thesis. Steady state and dynamic measurements under well controlled conditions were carried out to produce the data needed for the development of high efficiency, utility scale CFB technology. The importance of combustion control and furnace dynamics is emphasized when CFB boilers are scaled up with a once through steam cycle. Qualitative information on fuel combustion characteristics was obtained directly by comparing flue gas oxygen responses during the impulse change experiments with fuel feed. A one-dimensional, time dependent model was developed to analyse the measurement data Emission formation was studied combined with fuel combustion behaviour. Correlations were developed for NO, N2O, CO and char loading, as a function of temperature and oxygen concentration in the bed area. An online method to characterize char loading under CFB conditions was developed and validated with the pilot scale CFB tests. Finally, a new method to control air and fuel feeds in CFB combustion was introduced. The method is based on models and an analysis of the fluctuation of the flue gas oxygen concentration. The effect of high oxygen concentrations on fuel combustion behaviour was also studied to evaluate the potential of CFB boilers to apply oxygenfiring technology to CCS. In future studies, it will be necessary to go through the whole scale up chain from laboratory phenomena devices through pilot scale test rigs to large scale, commercial boilers in order to validate the applicability and scalability of the, results. This thesis shows the chain between the laboratory scale phenomena test rig (bench scale) and the CFB process test rig (pilot). CFB technology has been scaled up successfully from an industrial scale to a utility scale during the last decade. The work shown in the thesis, for its part, has supported the development by producing new detailed information on combustion under CFB conditions.

Quali/quantitative characterization of biogas produced in batch digesters supplied with six distinct substrates

The present research was carried out at the DER/FCAV, São Paulo State University - Brazil, with the purpose of analyzing the quantity and quality of biogas produced by six types of substrates. The substrates used in the anaerobic digestion were characterized as: 1- Litter of broiler (LB); 2- Grinded broiler litter (GBL); 3- Broiler litter with wood shavings (BLWS); 4- Grinded broiler litter with wood shavings (GBLWS); 5- Broiler litter with peanut hulls (BLPH); 6- Grinded broiler litter with peanut hull (GBLPH). It was concluded from the collected data that: the (GBL) substrate showed a superior biogas accumulated production in relation to the other substrates, while the BLWS presented an inferior accumulated production; the grinded substrates showed higher quantities of accumulated biogas in relation to the non-grinded substrates, except for GBLPH, with 20.9 m³ inferior than BLPH; the period of maximum biogas production started from 45 to 60 days, declining after 120 days; at 57 days after filling up the digesters the biogas produced had levels of CH4 superior than 53%, and from 99 days all of them produced biogas with levels of CH4 superior than 70%; LB and GBL presented higher concentrations of CH4 in the biogas.

Kinetic behavior of nitrification in the post-treatment of poultry wastewater in a sequential batch reactor

A sequential batch reactor with suspended biomass and useful volume of 5 L was used in the removal of nutrients and organic matter in workbench scale under optimal conditions obtained by central composite rotational design (CCRD), with cycle time (CT) of 16 h (10.15 h, aerobic phase, and 4.35 h, anoxic phase) and carbon: nitrogen ratio (COD/NO2--N+NO3--N) equal to 6. Complete cycles (20), nitrification followed by denitrification, were evaluated to investigate the kinetic behavior of degradation of organic (COD) and nitrogenated (NH4+-N, NO2--N and NO3--N) matter present in the effluent from a bird slaughterhouse and industrial processing facility, as well as to evaluate the stability of the reactor using Shewhart control charts of individual measures. The results indicate means total inorganic nitrogen (NH4+-N+NO2- -N+NO3--N) removal of 84.32±1.59% and organic matter (COD) of 53.65±8.48% in the complete process (nitrification-denitrification) with the process under statistical control. The nitrifying activity during the aerobic phase estimated from the determination of the kinetic parameters had mean K1 and K2 values of 0.00381±0.00043 min-1 and 0.00381±0.00043 min-1, respectively. The evaluation of the kinetic behavior of the conversion of nitrogen indicated a possible reduction of CT in the anoxic phase, since removals of NO2--N and NO3--N higher than 90% were obtained with only 1 h of denitrification.

Start-up of horizontal anaerobic reactors with sludge blanket and fixed bed for wastewater treatment from coffee processing by wet method

In this study it was evaluated the start-up procedures of anaerobic treatment system with three horizontal anaerobic reactors (R1, R2 and R3), installed in series, with volume of 1.2 L each. R1 had sludge blanket, and R2 and R3 had half supporter of bamboo and coconut fiber, respectively. As an affluent, it was synthesized wastewater from mechanical pulping of the coffee fruit by wet method, with a mean value of total chemical oxygen demand (CODtotal) of 16,003 mg L-1. The hydraulic retention time (HRT) in each reactor was 30 h. The volumetric organic loading (VOL) applied in R1 varied from 8.9 to 25.0 g of CODtotal (L d)-1. The mean removal efficiencies of CODtotal varied from 43 to 97% in the treatment system (R1+R2+R3), stabilizing above 80% after 30 days of operation. The mean content of methane in the biogas were of 70 to 76%, the mean volumetric production was 1.7 L CH4 (L reactor d)-1 in the system, and the higher conversions were around at 0.20 L CH4 (g CODremoved)-1 in R1 and R2. The mean values of pH in the effluents ranged from 6.8 to 8.3 and the mean values of total volatile acids remained below 200 mg L-1 in the effluent of R3. The concentrations of total phenols of the affluent ranged from 45 to 278 mg L-1, and the mean removal efficiency was of 52%. The start-up of the anaerobic treatment system occurred after 30 days of operation as a result of inoculation with anaerobic sludge with active microbiota.

Performance of UASB reactors in two stages under different HRT and OLR treating residual waters of swine farming

In this study it was evaluated the effects of hydraulic retention time (HRT) and Organic Loading Rate (OLR) on the performance of UASB (Upflow Anaerobic Sludge Blanket) reactors in two stages treating residual waters of swine farming. The system consisted of two UASB reactors in pilot scale, installed in series, with volumes of 908 and 188 L, for the first and second stages (R1 and R2), respectively. The HRT applied in the system of anaerobic treatment in two stages (R1 + R2) was of 19.3, 29.0 and 57.9 h. The OLR applied in the R1 ranged from 5.5 to 40.1 kg CODtotal (m³ d)-1. The average removal efficiencies of chemical oxygen demand (COD) and total suspended solids (TSS) ranged, respectively, from 66.3 to 88.2% and 62.5 to 89.3% in the R1, and from 85.5 to 95.5% and 76.4 to 96.1% in the system (R1 + R2). The volumetric production of methane in the system (R1 + R2) ranged from 0.295 to 0.721 m³CH4 (m³ reactor d)-1. It was found that the OLR applied were not limiting to obtain high efficiencies of CODtotal and TSS removal and methane production. The inclusion of the UASB reactor in the second stage contributed to increase the efficiencies of CODtotal and TSS removal, especially, when the treatment system was submitted to the lowest HRT and the highest OLR.

Anaerobic reactors with biofilter and different diameter-length ratios in cassava starch industry wastewater treatment

The use of anaerobic reactors with media support in the treatment of wastewater from the cassava starch industry has emerged as a viable option because it allows the application of high organic loads and a significant reduction of the HDT needed for the treatment. This research aimed at studying the process of biodigestion in two anaerobic reactors with bamboo support, in the treatment of effluent of cassava starch, by evaluating their performance. The two reactors used present the following diameter: length ratio, 1:6 and 1:3. The organic loads applied to the systems were 0.519, 1.156, 1.471, 3.049, 4.347, 4.708 and 5.601g.L-1.d-1. Regarding the efficiency of removal of COD, TS and TVS, no statistically significant differences were obtained between the reactors. The two systems evaluated showed a stable behavior with respect to the VA/TA (volatile acidity/total alkalinity) for all submitted loads. The reactors tended to the maintenance of biogas production as a function of consumed COD for the last three organic loads applied, indicating an ability to withstand higher organic loads.