Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Nutritional composition, quality and spoilage capacity of orange roughy (Hoplostethus atlanticus) from the North East Atlantic

The nutritional composition o f orange roughy (collected from the Northeast Atlantic near the Rockall Trough) was studied on a seasonal basis. In addition samples were aged and stability assessed. Protein levels (16.68-16.21% w/w) were found to be slightly higher than those recorded for the N ew Zealand species o f orange roughy and compared favourably with protein values for fish muscle in general. Statistically results show a significant seasonal variation with no variation from fish to fish or in the location within the fish. Lipid content (3.6-4.5% w/w) was found to be much lower than that recorded for New Zealand. As with protein statistically results show a significant seasonal variation and no variation from fish to fish or in the location within the fish. Moisture levels (77.3_79.6%w/w) compared favourably with values obtained from other studies. Again statistically results show a significant seasonal variation with no variation from fish to fish or within the fish. Iodine values (74.63-79.54) indicate the likely presence o f a high level o f mono unsaturated fatty acids. Statistically results show no significant seasonal variation and no sample variation or variation within fish. Thin layer chromatography o f the extracted fat showed the major type to be wax esters with a much lower amount o f triglycerides and smaller amounts of polar lipids, free sterols and free fatty acids. Total fatty acid composition was found to be very similar to that recorded from other studies and showed that most o f the oils extracted from the fish muscle contained a high percentage o f mono unsaturates namely 16:1,18:1, 20:1 and 22:1 (85.63 - 91.14% ) with 16:1 present in the smallest amounts and 18:1 the major one. The only saturated fatty M.Sc. in Biochemistry III Nutritional Composition, Quality and Spoilage Capacity of Specific Deep Sea Fish acids present in significant quantities were 14:0, 16:0 and 18:0, the total varied from a seasonal average high o f 4.05 % to an average low o f 2.27%. The polyunsaturated fatty acids linoleic and arachidonic acid were present in small quantities varying in total from 0.89% to 1.50%. Docosapentaenoic acid (D P A ) was found only in trace quantities in spring, autumn and winter samples and undetected in summer. Levels o f Eicosapentaenoic acid (EPA ) and Docosahexaenoic acid (D H A ) were also found in very low percentages and varied on a seasonal basis with average values ranging from 0.41% in summer to 1.03 % in autumn for EPA and from 1.44 % in summer to3.20 % in autumn for D H A . Again statistically results show a significant seasonal variation with no variation from fish to fish or location within the fish. Levels o f freshness were measured using the Thiobarbituric acid (T B A ), Total volatile base nitrogen (T V B -N ) and Trimethylamine (T M A ) techniques. The quality o f the fish upon arrival was excellent and well below legal/acceptable lim its.T V B -N values ranged from 6.88-8.91 mg/lOOg and T M A values from 4.82-6.46 mg/lOOg Values for T B A ranged from 0.18-0.35 mg Malonaldehyde/kg fish. The summer values were higher than the other seasons. Seasonal variation was significant for all methods with no variation from fish to fish or within the fish. Fish aged at +4°C in air did not exceed the T V B N lim it o f 35mg/100g until day 6 whereas the T V B N lim it was extended to 8 days for fish aged at +4°C in vacuum. However the T M A lim it o f 12mg/100g was reached on day 4 for fish stored at +4°C in air and on day 5 for vacuum packed samples stored at +4°C . Fish stored at -5°C in air and vacuum packed did not reach the T V B N lim it until day 61 but the T M A limit was reached on day 24 for fish stored at -5°C in air and was extended to 31 days for vacuum packed fish stored at-5°C. Prolonged storage at -18°C caused some deterioration o f the frozen fish muscle. Upon thawing the shelf life o f fish stored for 12 months was much shorter than that stored for 6 M.Sc. in Biochemistry IV Nutritional Composition, Quality and Spoilage Capacity of Specific Deep Sea Fish months. This in turn deteriorated faster than fresh fish held at refridgeration temperature in air. Orange roughy were found to be a good source of protein with moisture levels similar to that o f other fish. They were o f medium fat content but have a very poor content o f the essential omega 3 and omega 6 fatty acids. Orange roughy can be stored at -18°C but its subsequent refridgerated shelf life will be shorter than that o f unfrozen orange roughy stored at refridgeration temperature. Orange roughy are a very important part o f the ecosystem. Their composition is less nutritionally beneficial than more readily available fish for human consumption and therefore should not be fished at all

Composition and construction of embedded software families

Feature modeling, embebbed software, software product lines, tool support

Towards flexible feature composition : static and dynamic binding in software product lines

Magdeburg, Univ., Fak. für Informatik, Diss., 2011

Impact of casting parameters and chemical composition on the solidification behaviour of Al-Si-Cu hypoeutectic alloy

Magdeburg, Univ., Fak. für Maschinenbau, Diss., 2010

Impact of cultivation conditions on N-glycosylation of influenza A virus hemagglutinin, on quasispecies composition, and on immunogenicity of virus preparations

Magdeburg, Univ., Fak. für Verfahrens- und Systemtechnik, Diss., 2014

Doses and methods of distribution of potassium chloride on soybean crop (Glycine max (L.) Merrill) in a red latosol, affecting soil salinity, grain production and chemical composition of leaves

The present work deal t wi th an experiment under field conditions and a laboratory test of soil incubation the objectives were as follows: a. to study effects on soybean grain product ion and leaf composition of increasing doses of potassium chloride applied into the soil through two methods of distribution; b. to observe chemical modifications in the soils incubated with increasing doses of potassium chloride; and, c. to correlate field effects with chemical alterations observed in the incubation test, The field experiment was carried out in a Red Latosol (Haplustox) with soybean cultivar UFV - 1. Potassium chloride was distributed through two methods: banded (5 cm below and 5 cm aside of the seed line) and broadcasted and plowed-down. Doses used were: 0; 50; 100 and 200 kg/ha of K2O. Foliar samples were taken at flowering stage. Incubation test were made in plastic bags with 2 kg of air dried fine soil, taken from the arable layer of the field experiment, with the following doses of KC1 p,a. : 0; 50; 100; 200; 400; 800; 1,600; 3.200; 6,400 and 12,800 kg/ha of K(2)0. In the conditions observed during the present work, results allowed the following conclusions: A response by soybean grain production for doses of potassium chloride, applied in both ways, banded or broadcasted, was not observed. Leaf analysis did not show treatment influence over the leaf contents for N, P, K, Ca, Mg, and CI, Potassium chloride salinity effects in both methods of distribution for all the tested closes were not observed.

Influence of boron on growth and mineral composition of bean (Phaseolus vulgaris L.)

Nine cultivars of Phaseolus vulgaris L. were grown in nutrient solution to study the effect of boron on growth and mineral composition. Data obtained in thie study allowed for the following conclusions: (1) high levels of boron affected plant height, root length, dry weight of tops, dry weight of root, and total dry weight; (2) regression analysis was used to point out differential behaviour among cultivars in relation to boron concentration in nutrient solution; (3) the best mineral concentration in the plant tissue was obtained with application of 0,5 ppm of boron in the nutrient solution.

Influence of aluminum on growth and mineral composition of bean (Phaseolus vulgaris L.)

Seven cultivars of Phaseolus vulgaris L. were grown in nutrient solution in the presence and absence of aluminum. Da ta obtained herewith allowed for the following conclusions to be drawn: (1) plant height, root lenght and total dry weight decreased with increase of aluminum levels in the nutrient solution; (2) aluminum concentration in plant tissue increased with higher levels of aluminum in the substrate; decreases pf calcium and magnesium concentration in the dry matter in the presence of higher aluminum concentration in the nutrient solution were observed.

effect of the extracellular environment on the composition and function of synapses

Otto-von-Guericke-Universität magdeburg, Fakultät für Naturwissenschaften, Dissertation, 2015

Fish assemblage composition in a tributary of the Mogi Guaçu river basin, southeastern Brazil

Fish assemblage composition and seasonal patterns of species abundance were studied in Cabaceiras stream, a tributary of the Mogi Guaçu river in São Paulo State, Brazil. Three stations were sampled monthly from June 1999 to May 2000 using sieves and small trawl net and gill nets. Fifteen fish families, 37 genera and 45 species were captured. Characiformes (27 spp.) and Siluriformes (13 spp.) were the most species-rich orders. Gymnotiformes and Perciformes were represented by two species each, and Synbranchiformes had only a single species. One group of species (approximately 75 %) persisted in the stream throughout the year. A second group (approximately 25 %) contained species that only occupy the stream for a limited period of their life cycle, and overall fish assemblage composition was associated with the seasonal flood cycle.

Abundance and species composition of planktonic Ciliophora from the wastewater discharge zone in the Bahía Blanca Estuary, Argentina

The specific composition and abundance variation of the ciliate community from a wastewater discharge zone in the Bahía Blanca estuary, Argentina, were studied all throughout a year, from June 1995 to May 1996. The polluted area exhibited high values of particulate organic matter and nutrients, particularly phosphates. Aloricate ciliates were represented by 15 species belonging to the genera Strombidium Claparède & Lachmann, 1859; Strombidinopsis Kent, 1881; Cyrtostrombidium Lynn & Gilron, 1993; Strobilidium Schewiakoff, 1983; Lohmmanniella Leegaard, 1915 and Tontonia Fauré-Fremiet, 1914. Tintinnids were represented by nine species belonging to the genera Tintinnidium Kent, 1881, Tintinnopsis Stein, 1867 and Codonellopsis Jörgensen, 1924. The total abundance of aloricate ciliates reached a peak of 1,800 ind. 1-1 and the total abundance of tintinnids reached a peak of 9,400 ind. 1-1. Tintinnidium balechi Barría de Cao, 1981 was the most abundant ciliate in the community. Considerations on the presence and abundance of ciliates are made in relation to physicochemical and biochemical parameters.

Sewage impact on the composition and distribution of Polychaeta associated to intertidal mussel beds of the Mar del Plata rocky shore, Argentina

The polychaete composition and distribution within mussel beds were studied in order to assess organic pollution due to domestic sewage in a rocky shore of Mar del Plata (Argentina) during 1997. Four stations and a control site were randomly sampled around the local effluent. Quantitative data on polychaetes, as well as sediment accumulated among mussels and its organic carbon content were measured. Polychaete distribution patterns are related to the organic matter gradient, being Capitella cf. capitata, Neanthes succinea (Frey & Leuckart, 1847) and Boccardia polybranchia (Haswell, 1885) the dominant indicator species close to the effluent. At medial distances, the cirratulids Caulleriella alata (Southern, 1914) and Cirratulus cirratus (Müller, 1776) are very important in abundance. The syllids Syllis prolixa Ehlers, 1901 and S. gracilis Grube, 1840 are distributed along the study area, but dominate at the medial stations and at the control site. The orbiniid Protoariciella uncinata Hartmann-Schröder, 1962 is subdominant at the control station.

Composition of the family Didelphidae Gray, 1821 (Didelphoidea:Marsupialia), with a review of the morphology and behavior of the included four-eyed pouched opossums of the genus Philander Tiedemann, 1808 /

n.s. no.86(1997)

Composition and diversity of Trichoptera (Insecta) larvae communities in the middle section of the Jacuí river and some tributaries, State of Rio Grande do Sul, Brazil

The taxonomic composition and diversity of Trichoptera larvae communities were studied in four lotic sites in central region of State of Rio Grande do Sul. Sampling was done monthly from June, 2001 to May, 2002 in four sites located at the middle section of Jacuí River (Point 4) and in three tributaries (Carijinho River - Point 1; Lajeado da Gringa - Point 2 and Lajeado do Gringo - Point 3), with a Surber sampler. The total number of larvae collected was 29,143, belonging to 25 genera distributed in nine families; twenty of these genera are new records for the State. The highest abundance was found at Point 2 (n = 12,547). The highest standardized richness, for a 1,177 specimens sample chosen by chance, was recorded at Point 1, followed by Point 4 (17.7 and 16 genera, respectively). The highest diversity was found at Point 1, and the lowest at Point 3 (H' = 1.31 and H' = 0.77, respectively). Point 1 had the lowest anthropic influence and the best preserved riparian vegetation, while Point 3 presented the highest anthropic impact, and a very reduced riparian vegetation. The diversity of Trichoptera observed in this study is low, compared to the estimated maximum theoretical diversity. Low diversity values are related to the low evenness, since the richness was relatively high. The Trichoptera larvae communities seem to be related to the food availability and physical features (riparian vegetation and anthropic influence) of the study sites.