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Diffusion limited aggregation and the fractal evolution of gene promoter networks
Preston R. Aldrich
Network Biology , 2011,
Abstract: Gene promoter networks (GPNs) are systems-level representations of the base pair-sharing relationships (graph edges) among promoters (graph nodes). It has been shown in the bacterium E. coli that these networks can contain a fractal nucleus of strong associations suggesting a self-organizing complexity. Here I report results of twenty seven in silico simulations for a diffusion limited aggregation model which accounts for much of the fractal structure previously observed in GPNs. Parameters varied in the model included (a) the frequency of gene duplication events, and the extent of (b) attraction and (c) repulsion presented by the DNAprotein binding chemistry. Both duplication and attraction had significant effects on fractal topology of the GPN nucleus, whereas repulsion due to DNA-protein binding chemistry did not, at least for the levels explored in these simulations. Since repulsion is thought to be a key feature of fractal networks, it is likely that the repulsion in GPNs arises from the sparseness of the promoter space. The generation of a finite random set of promoters leads to sparse occupancy of promoter space which itself presents a considerable repulsion away from the consensus motif, working against the DNA-binding protein's efforts to organize the system of promoters over evolutionary time. This interplay between attractive and repulsive forces in a GPN is sufficient to generate a fractal topology.
The curriculum prerequisite network: a tool for visualizing and analyzing academic curricula
Preston R. Aldrich
Computer Science , 2014,
Abstract: This article advances the prerequisite network as a means to visualize the hidden structure in an academic curriculum. Network technologies have been used for some time now in social analyses and more recently in biology in the areas of genomics and systems biology. Here I treat the curriculum as a complex system with nodes representing courses and links between nodes the course prerequisites as readily obtained from a course catalogue. The resulting curriculum prerequisite network can be rendered as a directed acyclic graph, which has certain desirable analytical features. The curriculum is seen as partitioned into numerous isolated course groupings, the size of the groups varying considerably. Individual courses are seen serving very different roles in the overall organization, such as information sources, hubs, and bridges. This network represents the intrinsic, hard-wired constraints on the flow of information in a curriculum, and is the organizational context within which learning occurs.
Symmetry in the Language of Gene Expression: A Survey of Gene Promoter Networks in Multiple Bacterial Species and Non-σ Regulons
Preston R. Aldrich,Robert K. Horsley,Stefan M. Turcic
Symmetry , 2011, DOI: 10.3390/sym3040750
Abstract: The language of gene expression displays topological symmetry. An important step during gene expression is the binding of transcriptional proteins to DNA promoters adjacent to a gene. Some proteins bind to many promoters in a genome, defining a regulon of genes wherein each promoter might vary in DNA sequence relative to the average consensus. Here we examine the linguistic organization of gene promoter networks, wherein each node in the network represents a promoter and links between nodes represent the extent of base pair-sharing. Prior work revealed a fractal nucleus in several σ-factor regulons from Escherichia coli. We extend these findings to show fractal nuclei in gene promoter networks from three bacterial species, E. coli, Bacillus subtilis, and Pseudomonas aeruginosa. We surveyed several non-σ transcription factors from these species and found that many contain a nucleus that is both visually and numerically fractal. Promoter footprint size scaled as a negative power-law with both information entropy and fractal dimension, while the latter two parameters scaled positively and linearly. The fractal dimension of the diffuse networks (dB = ~1.7) was close to that expected of a diffusion limited aggregation process, confirming prior predictions as to a possible mechanism for development of this structure.
Fractal Topology of Gene Promoter Networks at Phase Transitions
Preston R. Aldrich, Robert K. Horsley, Yousuf A. Ahmed, Joseph J. Williamson and Stefan M. Turcic
Gene Regulation and Systems Biology , 2012, DOI: 10.4137/GRSB.S5389
Abstract: Much is known regarding the structure and logic of genetic regulatory networks. Less understood is the contextual organization of promoter signals used during transcription initiation, the most pivotal stage during gene expression. Here we show that promoter networks organize spontaneously at a dimension between the 1-dimension of the DNA and 3-dimension of the cell. Network methods were used to visualize the global structure of E. coli sigma (σ) recognition footprints using published promoter sequences (RegulonDB). Footprints were rendered as networks with weighted edges representing bp-sharing between promoters (nodes). Serial thresholding revealed phase transitions at positions predicted by percolation theory, and nuclei denoting short steps through promoter space with geometrically constrained linkages. The network nuclei are fractals, a power-law organization not yet described for promoters. Genome-wide promoter abundance also scaled as a power-law. We propose a general model for the development of a fractal nucleus in a transcriptional grammar.
Fractal Topology of Gene Promoter Networks at Phase Transitions
Preston R. Aldrich,Robert K. Horsley,Yousuf A. Ahmed,Joseph J. Williamson
Gene Regulation and Systems Biology , 2010,
Abstract: Much is known regarding the structure and logic of genetic regulatory networks. Less understood is the contextual organization of promoter signals used during transcription initiation, the most pivotal stage during gene expression. Here we show that promoter networks organize spontaneously at a dimension between the 1-dimension of the DNA and 3-dimension of the cell. Network methods were used to visualize the global structure of E. coli sigma (σ) recognition footprints using published promoter sequences (RegulonDB). Footprints were rendered as networks with weighted edges representing bp-sharing between promoters (nodes). Serial thresholding revealed phase transitions at positions predicted by percolation theory, and nuclei denoting short steps through promoter space with geometrically constrained linkages. The network nuclei are fractals, a power-law organization not yet described for promoters. Genome-wide promoter abundance also scaled as a power-law. We propose a general model for the development of a fractal nucleus in a transcriptional grammar.
Genetic Structure of the Invasive Tree Ailanthus altissima in Eastern United States Cities
Preston R. Aldrich,Joseph S. Briguglio,Shyam N. Kapadia,Minesh U. Morker,Ankit Rawal,Preeti Kalra,Cynthia D. Huebner,Gary K. Greer
Journal of Botany , 2010, DOI: 10.1155/2010/795735
Abstract: Ailanthus altissima is an invasive tree from Asia. It now occurs in most US states, and although primarily an urban weed, it has become a problem in forested areas especially in the eastern states. Little is known about its genetic structure. We explore its naturalized gene pool from 28 populations, mostly of the eastern US where infestations are especially severe. Five microsatellite markers were used to examine presumed neutral genetic variation. Results show a gene pool that is moderately diverse and sexually active and has significant but small genetic differences among populations and little correspondence between geographic and genetic distance. These findings are consistent with a model of multiple introductions followed by high rates of gene exchange between cities and regions. We propose movement along road and railway systems as the chief mode of range expansion. 1. Introduction Ailanthus altissima Swingle (stinking ash, Tree-of-Heaven, Chinese sumac) is a widespread member of the tropical tree family Simaroubaceae (Quassia family). Clayton et al. [1] recently clarified phylogenetic relationships within the family. The genus Ailanthus has five recognized extant species. Though four of these are geographically restricted to the Paleotropics, A. altissima is widespread in the New World [2]. Individuals of some of the other species may be present in the United States botanical gardens, but it is thought that naturalized Ailanthus is comprised mostly of the single species A. altissima (hereafter, Ailanthus), though genetic evidence is lacking at present. The first documented introduction of Ailanthus into the U.S. was through England in 1784 by William Hamilton, a Philadelphia gardener. Subsequent introductions have occurred along the east coast, and numerous introductions are thought to have occurred in the west most notably by Chinese immigrant railroad workers who used the plant as a medicinal in the 1800s [3]. The species has since spread to most states in the U.S. [4] following human disturbances [3, 5]. Ailanthus is shade intolerant and an aggressive pioneer, able to grow in the cracks in concrete [6]. It has large pinnate leaves similar to ash (Fraxinus) though the overall growth form is tropical with indeterminate leaf growth producing gently swooping leaves over a meter long. The species is dioecious [7] and pollinated mainly by bees and flies [8]. Juvenile growth is rapid accompanied with early reproduction [9]. Though clonal growth is aggressive, seed production is prolific with a single adult female producing 300,000 seed in a season
Producción de alimentos y energía en un sistema agrícola amigable con el ambiente y con el balance de carbono negativo
Thomas R Preston
Revista Colombiana de Ciencias Pecuarias , 2011,
Abstract:
Four Issues in Auctions and Market Design Four Issues in Auctions and Market Design
R. Preston McAfee
Revista de Análisis Económico (RAE) , 1998,
Abstract: Market designs concerns creation of transaction rules, effectively an automated intermediary. I extend the work of Vives (1998), finding that, for moderately sized auction markets, coordination is more important than strategic behavior in determining efficiency. Second, with Cournot competition, small firm send to win auctions of licences (right to compete) tend to have inefficient outcomes. Finally, I describe on-going work to design selling mechanism for the purpose of extracting surplus when there is only one buyer. Market designs concerns creation of transaction rules, effectively an automated intermediary. I extend the work of Vives (1998), finding that, for moderately sized auction markets, coordination is more important than strategic behavior in determining efficiency. Second, with Cournot competition, small firm send to win auctions of licences (right to compete) tend to have inefficient outcomes. Finally, I describe on-going work to design selling mechanism for the purpose of extracting surplus when there is only one buyer.
Position Auctions with Externalities and Brand Effects
Patrick Hummel,R. Preston McAfee
Computer Science , 2014,
Abstract: This paper presents models for predicted click-through rates in position auctions that take into account two possibilities that are not normally considered---that the identities of ads shown in other positions may affect the probability that an ad in a particular position receives a click (externalities) and that some ads may be less adversely affected by being shown in a lower position than others (brand effects). We present a general axiomatic methodology for how click probabilities are affected by the qualities of the ads in the other positions, and illustrate that using these axioms will increase revenue as long as higher quality ads tend to be ranked ahead of lower quality ads. We also present appropriate algorithms for selecting the optimal allocation of ads when predicted click-through rates are governed by either the models of externalities or brand effects that we consider. Finally, we analyze the performance of a greedy algorithm of ranking the ads by their expected cost-per-1000-impressions bids when the true click-through rates are governed by our model of predicted click-through rates with brand effects and illustrate that such an algorithm will potentially cost as much as half of the total possible social welfare.
Serendipitous, cross familial discovery of the first long-range chemical attractants for antlions (Neuroptera: Myrmeleontidae): (1R,2S,5R,8R)-Iridodial and Z,E-nepetalactol
Qing-He Zhang,Kamlesh R. Chauhan,Jeffrey R. Aldrich
Frontiers in Ecology and Evolution , 2014, DOI: 10.3389/fevo.2014.00080
Abstract: Synthetic (1R,2S,5R,8R)-iridodial, the key pheromone component of many green lacewings in the genus Chrysopa, strongly attracted adult males and females of the North American antlion, Dendroleon speciosus Banks. In addition, one of the common sex pheromone components of many aphids to which Chrysopa spp. are weakly attracted, Z,E-nepetalactol, was also weakly attractive to D. speciosus adults. Iridodial and Z,E-nepetalactol also elicited strong and weak electroantennogram detector (EAD) responses, respectively, in D. speciosus adults. Previously reported semiochemicals from European and Israeli antlion species did not elicit EAD or behavioral responses from D. speciosus adults. The earlier studied antlions release volatile chemicals from male-specific metathoracic glands associated with structures on the hind wings (Eltringham’s organs) that are thought to enhance evaporation of the secretion. Although D. speciosus males have Eltringham’s organs similar to those of other antlion species, we discovered that D. speciosus males have a pair of white tubular glands that extend posteriorly into the abdomen, opening in the resting pits of the Eltringham’s organs. Further gas chromatograph (GC)-EAD analysis of another commercially available antlion species, Myrmeleon crudelis Walker, showed that this species did not respond to the lacewing or aphid related volatile compounds, but strongly responded to the reported antlion semiochemicals, namely, nerol, 10-homonerol and nerol oxide. The male-specific abdominal glands of D. speciosus are presumably pheromone glands; hopefully, positive verification of this supposition will help clarify the semiochemical relationships between antlions, lacewings and aphids.
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