Pathways evolution

Oil and gas field waters have long been used in diagenetic studies, primarily as vehicles for understanding basin fluid flow, oil migration pathways, evolution of water composition, and reservoir com-partmentalization. However, water samples used for these purposes must be original formation water, not mixed with drilling mud or with injected fluids such as fracture fluid, waterflood water, or other fluids used for enhanced oil recovery (EOR),... 

Matus DG, Magie C, Pang K, Martindale MQ, Thomsen GH. The Hedgehog gene family of the cnidarians, Nematostella vectensis, and implications ftn understanding metazoan Hedgehog pathway evolution. Dev Biol. 2008 313 501-18. 

Thermoanaerobacter saccharolyticum Ethanol Using EMA to design, construct, characterize, and validate an engineered T. saccharolyticum for efficient ethanol production and predict the metabolic pathway evolution of the engineered and evolved mutant. Yes Unrean and Srienc, (2011) and Unrean and Srienc (2012) ... 

It should be pointed out that a similar approach to the MMF technique, FBA-based technique such as OPTKNOCK also seeks to design engineered strains to couple growth and product formation and employ the metabolic pathway evolution strategy to improve the strain performance, e.g. development of an engineered and evolved E. coli strains for improved production of lactate (Fong et al. 2005), 1,4-butanediol (Yim et al. 2011), and various flavonoids (Fowler et al. 2009). 

CathaCyc presents a variety of tools for the visualization and analysis of metabolic networks and omics data [61] and will certainly help in discovering missing enzymes, studying metabolic pathway evolution, and, ultimately, improving... 

Whatever hypothesis may be stated, thermodynamic or kinetic control of the formation of the tertiary structure, it seems realistic to admit a limitation of the number of possible pathways. Evolution (with thermodynamics dictating the folding), has selected the amino acid sequence to form a biologically active molecule with presumably a limited number of pathways from the unfolded form to a unique native structure of the lowest free energy (Anfinsen and Scheraga 1975). 

Aquatic organisms, such as fish and invertebrates, can excrete compounds via passive diffusion across membranes into the surrounding medium and so have a much reduced need for specialised pathways for steroid excretion. It may be that this lack of selective pressure, together with prey-predator co-evolution, has resulted in restricted biotransformation ability within these animals and their associated predators. The resultant limitations in metabolic and excretory competence makes it more likely that they will bioacciimiilate EDs, and hence they may be at greater risk of adverse effects following exposure to such chemicals. 

Fothergill-Gilmore, L., 1986. The evolution of die glycolytic pathway. Trends in Biochemical Sciences 11 47—51. 

Wachtershanser has also suggested that early metabolic processes first occurred on the surface of pyrite and other related mineral materials. The iron-sulfur chemistry that prevailed on these mineral surfaces may have influenced the evolution of the iron-sulfur proteins that control and catalyze many reactions in modern pathways (including the succinate dehydrogenase and aconitase reactions of the TCA cycle). 

Careful observations of the course of iodo-de-diazoniation demonstrate that the detailed pathway of such reactions is still relatively complex. For instance, after adding a solution of KI to a solution of an arenediazonium salt, normally molecular iodine appears to be formed first, followed by a precipitate and evolution of N2. Carey and Millar (1960) isolated the salt ArNJIj- on adding iodide to the diazo-nium salt. Ion pairs (ArNjHlg-), suggested as primary products by Meyer et al. (1979), were identified for diazonium halides (Cl- and Br-) by Israel et al. (1983) as 1 1 complexes on the basis of JOB analyses of visible spectra (Benesi-Hildebrand method). Iodides were, however, not included in that investigation. 

Still more confusion plagued early researches, when it was not realized that the biosynthetic routes to thiamine in prokaryotes and eukaryotes are quite different, a fact not expected at the outset. Thus, evidence collected from the study of yeast could not be transposed to bacteria, and vice-versa. For instance, formate is a most efficient precursor of one of the carbon atoms of the pyrimidine part of thiamine (pyramine), both in yeasts and enterobacteria, but incorporates at C-2 in bacteria and at C-4 in yeast. However, as is briefly covered in Section VIII, this dichotomy of pathways might have a deep significance in the perspective of biochemical evolution during primitive life on Earth. 

Fig. 11. The metal sites in D. gigas hydrogenase (Hase) (A) and aldehyde oxidore-ductase (AOR) (B). The figure emphasizes the relative positioning of the metal sites Emd their proximity, suggesting an attractive electron transfer pathway. The arrows indicate electron trsmsfer for hydrogen evolution requiring an electron donor (A) Emd aldehyde conversion to carboxylic acid, the electrons being transferred to Em electron acceptor (B).

Fothergill-Gilmore LA The evolution of the glycolytic pathway. Trends Biochem Sci 1986 11 47. 

Algal blooms in fresh water ponds occasionally poison livestock and waterfowl. Axenic cultures of Anabaena flos-aquae NRC 44-1 were shown to produce the toxic principle (5) which can be present in the algae and in the water of mature cultures (6). The discovery of the toxin was fortuitous in the sense that AChR agonists do not have a (known) constructive function in the algae evolution of the synthetic pathway was likely a by-product of metabolic pathways in the algae. The compound became evident only through its toxic effects on other organisms. 

The proposed mechanism of H2 evolution by a model of [FeFeJ-hydrogenases based upon DFT calculations [204-206] and a hybrid quanmm mechanical and molecular mechanical (QM/MM) investigation is summarized in Scheme 63 [207]. Complex I is converted into II by both protonation and reduction. Migration of the proton on the N atom to the Fe center in II produces the hydride complex III, and then protonation affords IV. In the next step, two pathways are conceivable. One is that the molecular hydrogen complex VI is synthesized by proton transfer and subsequent reduction (Path a). The other proposed by De Gioia, Ryde, and coworkers [207] is that the reduction of IV affords VI via the terminal hydride complex V (Path b). Dehydrogenation from VI regenerates I. 

Before the application of a pulse, only equilibrium magnetization exists, directed toward the z-axis corresponding to the zero coherence level for all coherence pathways. When the pulse is applied, two coherence levels, + 1 and —1, are created during the evolution period that evolve into M and respectively, where [Pg.74]

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