4 resultados para 124-770C

em CaltechTHESIS


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Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system’s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

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The sea urchin embryonic skeleton, or spicule, is deposited by mesenchymal progeny of four precursor cells, the micromeres, which are determined to the skeletogenic pathway by a process known as cytoplasmic localization. A gene encoding one of the major products of the skeletogenic mesenchyme, a prominent 50 kD protein of the spicule matrix, has been characterized in detail. cDNA clones were first isolated by antibody screening of a phage expression library, followed by isolation of homologous genomic clones. The gene, known as SM50, is single copy in the sea urchin genome, is divided into two exons of 213 and 1682 bp, and is expressed only in skeletogenic cells. Transcripts are first detectable at the 120 cell stage, shortly after the segregation of the skeletogenic precursors from the rest of the embryo. The SM50 open reading frame begins within the first exon, is 450 amino acids in length, and contains a loosely repeated 13 amino acid motif rich in acidic residues which accounts for 45% of the protein and which is possibly involved in interaction with the mineral phase of the spicule.

The important cis-acting regions of the SM50 gene necessary for proper regulation of expression were identified by gene transfer experiments. A 562 bp promoter fragment, containing 438 bp of 5' promoter sequence and 124 bp of the SM50 first exon (including the SM50 initiation codon), was both necessary and sufficient to direct high levels of expression of the bacterial chloramphenicol acetyltransferase (CAT) reporter gene specifically in the skeletogenic cells. Removal of promoter sequences between positions -2200 and -438, and of transcribed regions downstream of +124 (including the SM50 intron), had no effect on the spatial or transcriptional activity of the transgenes.

Regulatory proteins that interact with the SM50 promoter were identified by the gel retardation assay, using bulk embryo mesenchyme blastula stage nuclear proteins. Five protein binding sites were identified and mapped to various degrees of resolution. Two sites are homologous, may be enhancer elements, and at least one is required for expression. Two additional sites are also present in the promoter of the aboral ectoderm specific cytoskeletal actin gene CyIIIa; one of these is a CCAA T element, the other a putative repressor element. The fifth site overlaps the binding site of the putative repressor and may function as a positive regulator by interfering with binding of the repressor. All of the proteins are detectable in nuclear extracts prepared from 64 cell stage embryos, a stage just before expression of SM50 is initiated, as well as from blastula and gastrula stage; the putative enhancer binding protein may be maternal as well.

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A series of terl-butylperoxide complexes of hafnium, Cp*2Hf(R)(OOCMe3) (Cp* = ((η5-C5Me5); R = Cl, H, CH3, CH2CH3, CH2CH2CH3, CH2CH2CH2CH3, CH2CHMe2, CH=CHCMe3, C6H5, meta-C6H3(CH2)2) and Cp*(η5-C5(CH3)4CH2CH2CH2)Hf(OOCMe3), has been synthesized. One example has been structurally characterized, Cp*2Hf(OOCMe3)CH2CH3 crystallizes in space group P21/c, with a = 19.890(7)Å, b = 8.746(4)Å, c = 17.532(6)Å, β = 124.987(24)°, V = 2498(2)Å3, Z = 4 and RF = 0.054 (2222 reflections, I > 0). Despite the coordinative unsaturation of the hafnium center, the terl-butylperoxide ligand is coordinated in a mono-dentate ligand. The mode of decomposition of these species is highly dependent on the substituent R. For R = H, CH2CH3, CH2CH2CH3, CH2CH2CH2CH3, CH2CHMe2 a clean first order conversion to Cp*2Hf(OCMe3)(OR) is observed (for R CH2CH3, ΔHǂ = 19.6 kcal•mol-1, ΔSǂ = -13 e.u.). These results are discussed in terms of a two step mechanism involving η2-coordination of the terl-butylperoxide ligand. Homolytic O-O bond cleavage is observed upon heating of Cp*2Hf(OOCMe3) R (R = C6H6, meta-C6H3(CH3)2). In the presence of excess 9,10-dihydroanthracene thermolysis of Cp*2Hf(OOCMe3)C6H6 cleanly affords Cp*2Hf(C6H6)OH and HOCMe3 (ΔHǂ = 22.6 kcal•mol-1, ΔSǂ = -9 e.u.). The O-O bond strength in these complexes is thus estimated to be 22 kcal•mol-1.

Cp*2Ta(CH2)H, Cp*2Ta(CHC6H5)H, Cp*2Ta(C6H4)H, Cp*2Ta(CH2=CH2)H and Cp*2Ta(CH2=CHMe)H react, presumably through Cp*2Ta-R intermediates, with H2O to give Cp*2Ta(O)H and alkane. Cp*2Ta(O)H was structurally characterized: space group P21/n, a= 13.073(3)Å, b = 19.337(4)Å, c = 16.002(3)Å, β = 108.66(2)°, V = 3832(1)Å3, Z = 8 and RF = 0.0672 (6730 reflections). Reaction of terlbutylhydroperoxide with these same starting materials ultimately yields Cp*2Ta(O)R and HOCMe3. Cp*2Ta(CH2=CHR)OH species are proposed as intermediates in the olefin hydride reactions. Cp*2Ta(O2)R species can be generated from the reaction of the same starting materials and O2. Lewis acids have been shown to promote oxygen insertion in these complexes.

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Electronic Kαl x-ray isotope shifts have been measured for Sn 116-124, Sm 148-154, W 182-184, W 184-186, and W 182-186 using a curved crystal Cauchois spectrometer. The analysis of the measurements has included the electrostatic volume effect, screening by the transition electron as well as the non-transition electrons, normal and specific mass shifts, dynamical nuclear qudrupole polarization, and a radiative correction effect of the electron magnetic moment in the nuclear charge radii are obtained. Where other experimental data are available, the agreement with the present measurements is satisfactory. Comparisons with several nuclear model predictions yield only partial agreement.