Development of principle culture medium formulations for Saccharomyces cerevisiae

Saccharomyces cerevisiae as well as other microorganisms are frequently used in industry with the purpose of obtain different kind of products that can be applied in several areas (research investigation, pharmaceutical compounds, etc.). In order to obtain high yields for the desired product, it is necessary to make an adequate medium supplementation during the growth of the microorganisms. The higher yields are typically reached by using complex media, however the exact formulation of these media is not known. Moreover, it is difficult to control the exact composition of complex media, leading to batch-to-batch variations. So, to overcome this problem, some industries choose to use defined media, with a defined and known chemical composition. However these kind of media, many times, do not reach the same high yields that are obtained by using complex media. In order to obtain similar yield with defined media the addition of many different compounds has to be tested experimentally. Therefore, the industries use a set of empirical methods with which it is tried to formulate defined media that can reach the same high yields as complex media. In this thesis, a defined medium for Saccharomyces cerevisiae was developed using a rational design approach. In this approach a given metabolic network of Saccharomyces cerevisiae is divided into a several unique and not further decomposable sub networks of metabolic reactions that work coherently in steady state, so called elementary flux modes. The EFMtool algorithm was used in order to calculate the EFM’s for two Saccharomyces cerevisiae metabolic networks (amino acids supplemented metabolic network; amino acids non-supplemented metabolic network). For the supplemented metabolic network 1352172 EFM’s were calculated and then divided into: 1306854 EFM’s producing biomass, and 18582 EFM’s exclusively producing CO2 (cellular respiration). For the non-supplemented network 635 EFM’s were calculated and then divided into: 215 EFM’s producing biomass; 420 EFM’s producing exclusively CO2. The EFM’s of each group were normalized by the respective glucose consumption value. After that, the EFMs’ of the supplemented network were grouped again into: 30 clusters for the 1306854 EFMs producing biomass and, 20 clusters for the 18582 EFM’s producing CO2. For the non-supplemented metabolic network the respective EFM’s of each metabolic function were grouped into 10 clusters. After the clustering step, the concentrations of the other medium compounds were calculated by considering a reasonable glucose amount and by accounting for the proportionality between the compounds concentrations and the glucose ratios. The approach adopted/developed in this thesis may allow a faster and more economical way for media development.

Enumerating constrained elementary flux vectors of metabolic networks

The concept of elementary vector is generalised to the case where the steady-state space of the metabolic network is not a flux cone but is a general polyhedron due to further inhomogeneous constraints on the flows through some of the reactions. On one hand, this allows to selectively enumerate elementary modes which satisfy certain optimality criteria and this can yield a large computational gain compared with full enumeration. On the other hand, in contrast to the single optimum found by executing a linear program, this enables a comprehensive description of the set of alternate optima often encountered in flux balance analysis. The concepts are illustrated on a metabolic network model of human cardiac mitochondria.

An elementary treatise on logic : comprising the essential principles and different modes of reasoning, in the form of question and answer /

Mode of access: Internet.

Hoyle's games : illustrated edition. Embracing all the most modern modes of play, and the rules practised at the present time, in billiards, whist, draughts, cribbage, backgammon, and all other fashionable games; together with sixteen games adapted to the new Yankee-notion cards. Also the whole of Frer̀e's chess hand-book. Containing, besides elementary instruction and the laws of chess, about fifty select games by the first players, endings of games, and the defeat of the muzio gambit. Also, thirty-six of the choicest chess problems, and a description of, and rules for, four-handed chess /

Classified for chess; Frère's chess hand-book, p. 229-324.

Elementary Excitations at Magnetic Surfaces and Their Spin Dependence

The elementary surface excitations are studied by spin-polarized electron energy loss spectroscopy on a prototype oxide surface [an oxygen passivated Fe(001)-p(1 x 1) surface], where the various excitations coexist. For the first time, the surface phonons and magnons are measured simultaneously and are distinguished based on their different spin nature. The dispersion relation of all excitations is probed over the entire Brillouin zone. The different phonon modes observed in our experiment are described by means of ab initio calculations.

Density modes in spherical 4He shells

We compute the density-fluctuation spectrum of spherical 4HeN shells adsorbed on the outer surface of Cn fullerenes. The excitation spectrum is obtained within the random-phase approximation, with particle-hole elementary excitations and effective interaction extracted from a density-functional description of the shell structure. The presence of one or two solid helium layers adjacent to the adsorbing fullerene is phenomenologically accounted for. We illustrate our results for a selection of numbers of adsorbed atoms on C20, C60, and C120. The hydrodynamical model that has proven successful to describe helium excitations in the bulk and in restricted geometries permits to perform a rather exhaustive analysis of various fluid spherical systems, namely, spheres, cavities, free bubbles, and bound shells of variable size.

Density modes in spherical 4He shells

We compute the density-fluctuation spectrum of spherical 4HeN shells adsorbed on the outer surface of Cn fullerenes. The excitation spectrum is obtained within the random-phase approximation, with particle-hole elementary excitations and effective interaction extracted from a density-functional description of the shell structure. The presence of one or two solid helium layers adjacent to the adsorbing fullerene is phenomenologically accounted for. We illustrate our results for a selection of numbers of adsorbed atoms on C20, C60, and C120. The hydrodynamical model that has proven successful to describe helium excitations in the bulk and in restricted geometries permits to perform a rather exhaustive analysis of various fluid spherical systems, namely, spheres, cavities, free bubbles, and bound shells of variable size.

Nitrogen fluxes from treefrogs to tank epiphytic bromeliads: an isotopic and physiological approach

Diverse invertebrate and vertebrate species live in association with plants of the large Neotropical family Bromeliaceae. Although previous studies have assumed that debris of associated organisms improves plant nutrition, so far little evidence supports this assumption. In this study we used isotopic ((15)N) and physiological methods to investigate if the treefrog Scinax hayii, which uses the tank epiphytic bromeliad Vriesea bituminosa as a diurnal shelter, contributes to host plant nutrition. In the field, bromeliads with frogs had higher stable N isotopic composition (delta(15)N) values than those without frogs. Similar results were obtained from a controlled greenhouse experiment. Linear mixing models showed that frog feces and dead termites used to simulate insects that eventually fall inside the bromeliad tank contributed, respectively, 27.7% (+/- 0.07 SE) and 49.6% (+/- 0.50 SE) of the total N of V. bituminosa. Net photosynthetic rate was higher in plants that received feces and termites than in controls; however, this effect was only detected in the rainy, but not in the dry season. These results demonstrate for the first time that vertebrates contribute to bromeliad nutrition, and that this benefit is seasonally restricted. Since amphibian-bromeliad associations occur in diverse habitats in South and Central America, this mechanism for deriving nutrients may be important in bromeliad systems throughout the Neotropics.

Aerosol properties, in-canopy gradients, turbulent fluxes and VOC concentrations at a pristine forest site in Amazonia

Aerosol physical and chemical properties were measured in a forest site in central Amazonia (Cuieiras reservation, 2.61S; 60.21W) during the dry season of 2004 (Aug-Oct). Aerosol light scattering and absorption, mass concentration, elemental composition and size distributions were measured at three tower levels (Ground: 2 m; Canopy: 28 m, and Top: 40 m). For the first time, simultaneous eddy covariance fluxes of fine mode particles and volatile organic compounds (VOC) were measured above the Amazonian forest canopy. Aerosol fluxes were measured by eddy covariance using a Condensation Particle Counter (CPC) and a sonic anemometer. VOC fluxes were measured by disjunct eddy covariance using a Proton Transfer Reaction Mass Spectrometer (PTR-MS). At nighttime, a strong vertical gradient of phosphorus and potassium in the aerosol coarse mode was observed, with higher concentrations at Ground level. This suggests a source of primary biogenic particles below the canopy. Equivalent black carbon measurements indicate the presence of light-absorbing aerosols from biogenic origin. Aerosol number size distributions typically consisted of superimposed Aitken (76 nm) and accumulation modes (144 nm), without clear events of new particle formation. Isoprene and monoterpene fluxes reached respectively 7.4 and 0.82 mg m(-2) s(-1) around noon. An average fine particle flux of 0.05 +/- 0.10 10(6) m(-2) s(-1) was calculated, denoting an equilibrium between emission and deposition fluxes of fine mode particles at daytime. No significant correlations were found between VOC and fine mode aerosol concentrations or fluxes. (C) 2009 Elsevier Ltd. All rights reserved.

Modes of sapropel formation in the eastern Mediterranean: some constraints based on pyrite properties

Pyrite formation within and directly below sapropels in the eastern Mediterranean was governed by the relative rates of sulphide production and Fe liberation and supply to the organic-rich layers. At times of relatively high [SO4]2- reduction, sulphide could diffuse downward from the sapropel and formed pyrite in underlying sediments. The sources of Fe for pyrite formation comprised detrital Fe and diagenetically liberated Fe(II) from sapropel-underlying sediments. In organic-rich sapropels, input of Fe from the water column via Fe sulphide formation in the water may have been important as well. Rapid pyrite formation at high saturation levels resulted in the formation of framboidal pyrite within the sapropels, whereas below the sapropels slow euhedral pyrite formation at low saturation levels occurred. d34S values of pyrite are -33 per mil to -50 per mil. Below the sapropels d34S is lower than within the sapropels, as a result of increased sulphide re-oxidation at times of relatively high sulphide production and concentration when sulphide could escape from the sediment. The percentage of initially formed sulphide that was re-oxidized was estimated from organic carbon fluxes and burial efficiencies in the sediment. It ranges from 34% to 80%, varying significantly between sapropels. Increased palaeoproductivity as well as enhanced preservation contributed to magnified accumulation of organic matter in sapropels.

Different coordination modes for disulfoxides towards diorganotin(IV) dichlorides. X-ray crystal structures of 1,2-cis-bis-(phenylsulfinyl)ethene (rac-,cis-cbpse) and adducts [{Ph2SnCl2(meso-bpse)}n] and [{n-Bu2SnCl2(pdtd)}2]

The reactions of meso-1,2-bis(phenylsulfinyl)ethane (meso-bpse) with Ph2SnCl2, 2-phenyl-1,3-dithiane trans-1-trans-3-dioxide (pdtd) with n-Bu2SnCl2 and 1,2-cis-bis-(phenylsulfinyl)ethene (rac-,cis-cbpse) with Ph2SnCl2, in 1:1 molar ratio, yielded [{Ph2SnCl2(meso-bpse)}n], [{n-Bu2SnCl2(pdtd)}2] and [{Ph2SnCl2(rac,cis-cbpse)}x] (x = 2 or n), respectively. All adducts were studied by IR, Mössbauer and 119Sn NMR spectroscopic methods, elemental analysis and single crystal X-ray diffractometry. The X-ray crystal structure of [{Ph2SnCl2(meso-bpse)}n] revealed the occurrence of infinite chains in which the tin(IV) atoms appear in a distorted octahedral geometry with Cl atoms in cis and Ph groups in trans positions. The X-ray crystal structure of [{n-Bu2SnCl2(pdtd)}2] revealed discrete centrosymmetric dimeric species in which the tin(IV) atoms possess a distorted octahedral geometry with bridging disulfoxides in cis and n-butyl moieties in trans positions. The spectroscopic data indicated that the adduct containing the rac,cis-cbpse ligand can be dimeric or polymeric. The X-ray structural analysis of the free rac-,cis-cbpse sulfoxide revealed that the crystals belong to the C2/c space group.

Quantification and source identification of atmospheric particulate polycyclic aromatic hydrocarbons and their dry deposition fluxes at three sites in Salvador Basin, Brazil, impacted by mobile and stationary sources

The present work has aimed to determine the 16 US EPA priority PAH atmospheric particulate matter levels present in three sites around Salvador, Bahia: (i) Lapa bus station, strongly impacted by heavy-duty diesel vehicles; (ii) Aratu harbor, impacted by an intense movement of goods, and (iii) Bananeira village on Maré Island, a non vehicle-influenced site with activities such as handcraft work and fisheries. Results indicated that BbF (0.130-6.85 ng m-3) is the PAH with highest concentration in samples from Aratu harbor and Bananeira and CRY (0.075-6.85 ng m-3) presented higher concentrations at Lapa station. PAH sources from studied sites were mainly of anthropogenic origin such as gasoline-fueled light-duty vehicles and diesel-fueled heavy-duty vehicles, discharges in the port, diesel burning from ships, dust ressuspension, indoor soot from cooking, and coal and wood combustion for energy production.

Quasinormal modes of black holes in anti-de Sitter space: A numerical study of the eikonal limit

Using series solutions and time-domain evolutions, we probe the eikonal limit of the gravitational and scalar-field quasinormal modes of large black holes and black branes in anti-de Sitter backgrounds. These results are particularly relevant for the AdS/CFT correspondence, since the eikonal regime is characterized by the existence of long-lived modes which (presumably) dominate the decay time scale of the perturbations. We confirm all the main qualitative features of these slowly damped modes as predicted by Festuccia and Liu [G. Festuccia and H. Liu, arXiv:0811.1033.] for the scalar-field (tensor-type gravitational) fluctuations. However, quantitatively we find dimensional-dependent correction factors. We also investigate the dependence of the quasinormal mode frequencies on the horizon radius of the black hole (brane) and the angular momentum (wave number) of vector- and scalar-type gravitational perturbations.

Brittle and ductile removal modes observed during diamond turning of carbon nanotube composites

Ultraprecision diamond turning was used to evaluate the surface integrity of a carbon nanotube (CNT) composite as a function of the cutting conditions and the percentage of CNT in the epoxy matrix. The effects of cutting conditions on the chip morphology and surface roughness were analysed. The results showed that an increase in the percentage of CNT may influence the mechanism of material removal and consequently improve the quality of the machined surface. When smaller quantities of CNT (0.02 and 0.07 wt %) are present in the matrix, microcracks form within the cutting grooves (perpendicular to the cutting direction). This indicates that the amount of CNT on the epoxy matrix may have a direct influence on the mechanical properties of these materials. Chips removed from the CNT composite samples were analysed by scanning electron microscopy in order to correlate the material removal mechanism and the surface generation process. The area average surface roughness Sa was influenced by the material removal mechanism (Sa ranging from 0.28 to 1.1 mu m).

A comparison of dry and wet season aerosol number fluxes over the Amazon rain forest

Vertical number fluxes of aerosol particles and vertical fluxes of CO(2) were measured with the eddy covariance method at the top of a 53 m high tower in the Amazon rain forest as part of the LBA (The Large Scale Biosphere Atmosphere Experiment in Amazonia) experiment. The observed aerosol number fluxes included particles with sizes down to 10 nm in diameter. The measurements were carried out during the wet and dry season in 2008. In this study focus is on the dry season aerosol fluxes, with significant influence from biomass burning, and these are compared with aerosol fluxes measured during the wet season. Net particle deposition fluxes dominated in daytime in both seasons and the deposition flux was considerably larger in the dry season due to the much higher dry season particle concentration. The particle transfer velocity increased linearly with increasing friction velocity in both seasons. The difference in transfer velocity between the two seasons was small, indicating that the seasonal change in aerosol number size distribution is not enough for causing any significant change in deposition velocity. In general, particle transfer velocities in this study are low compared to studies over boreal forests. The reasons are probably the high percentage of accumulation mode particles and the low percentage of nucleation mode particles in the Amazon boundary layer, both in the dry and wet season, and low wind speeds in the tropics compared to the midlatitudes. In the dry season, nocturnal particle fluxes behaved very similar to the nocturnal CO(2) fluxes. Throughout the night, the measured particle flux at the top of the tower was close to zero, but early in the morning there was an upward particle flux peak that is not likely a result of entrainment or local pollution. It is possible that these morning upward particle fluxes are associated with emission of primary biogenic particles from the rain forest. Emitted particles may be stored within the canopy during stable conditions at nighttime, similarly to CO(2), and being released from the canopy when conditions become more turbulent in the morning.