The Study of Overflow Metabolism and kinetics in a model of metabolism and gene expression of Escherichia coli

Overflow metabolism can be explained by a pathway switch behavior in the cell based on the tradeoffs between metabolic efficiency and proteomic efficiency(enzymatic kinetics). This thesis simulates this behavior on the both small-scale and genome-scale model. By sweeping the enzyme kinetics parameters on multiple pathways or reactions, the simulation could potentially approach the experimental results, however, would converge to some bounds beyond. Therefore, hypotheses of some extra constraints, such as the limitation of oxygen uptake ,electron transport chain, as well as the function of motility protein are presented

Isovists as a Means to Predict Spatial Experience and Behavior

Two experiments are presented studying interrelations between spatial properties of environments and both experience and spatial behavior. In order to systematically study such interrelations, a generic description of space is required that provides comparability between arbitrarily shaped environments and that captures behaviorally relevant properties of space. In this study the suitability of isovist derived measurands for this purpose was explored. Isovist-based descriptions of 16 virtual indoor scenes were correlated with behavioral data from two experimental tasks. For both tasks, an active navigation task and a rating of experiential qualities, strong correlations between subjectsamp;amp;lsquo; behavior and measurands derived from isovist analysis were found. The general outcomes suggest that isovist measurands are indeed a promising means to predict experience of space and spatial behavior for the chosen experimental tasks

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa