Two Notes on APCol Systems

In this work, we continue our research in the eld of string processing mem- brane systems - APCol systems. We focus on a relation of APCol systems with PM colonies - colonies whose agents can only perform point mutation transformations of the common string, in a vicinity of the agent. The second part is devoted to a connection of APCol systems and logic circuits using AND, OR and NOT gates

Effects of Partial Mortality on Growth, Reproduction and Total Lipid Content in the Elkhorn Coral Acropora palmata

Partial mortality (PM) is increasingly common in the Elkhorn coral Acropora palmata and, depending on the causative agent, is potentially lethal. The effects of PM on growth, reproduction and total lipid content in A. palmata were studied by sampling apparently healthy (AH) colonies in comparison with colonies showing signs of PM. Branch growth rates and lesion regeneration rates were estimated using monthly photographs over a four-month period prior to the summer spawning season. No differences were found in the growth rates of colonies with PM compared to AH colonies. The areas affected by PM did not regenerate during the period of the study. Colonization of the lesions by competing species and sediment cover were documented and did not show major changes. During the spawning season, percent fertilization, egg volume and embryonic development were evaluated for comparison between AH colonies and those with PM. Total lipids were also quantified in tissues from three branches per colony. Percentage fertilization was similar in both AH colonies and those with PM. Embryonic development was normal, regardless of proximity to the lesion borders. However, egg volume was significantly lower in PM colonies than in AH colonies. Lower lipid concentrations were found at the edges of the lesions and similar to those found at the growing edges of the branches. The lack of regeneration may be explained by the low lipid concentration, because the polyps adjacent to the lesion do not have an adequate energy budget as a result of the damage. This would also affect their ability to compete against organisms that colonize the site of the lesion, a distinct situation to the rapid regeneration rates characteristic of lesions due to physical injury of the colony. Therefore, we conclude that partial mortality in A. palmata affects the colony, inducing energetic stress due to both competition and decreased egg quality

Intensive Surveys of Watersheds Contributing to McKinney Falls

This report uses Waller Creek as an example of an urbanized stream with high levels of fecal coliform colonies in dry weather conditions.Waller Creek Working Grou

Taxonomy and pathology of Togninia (Diaporthales) and its Phaeoacremonium anamorphs.

The genus Togninia (Diaporthales, Togniniaceae) is here monographed along with its Phaeoacremonium (Pm.) anamorphs. Ten species of Togninia and 22 species of Phaeoacremonium are treated. Several new species of Togninia (T.) are described, namely T. argentinensis (anamorph Pm. argentinense), T. austroafricana (anamorph Pm. austroafricanum), T. krajdenii, T. parasitica, T. rubrigena and T. viticola. New species of Phaeoacremonium include Pm. novae-zealandiae (teleomorph T. novae-zealandiae), Pm. iranianum, Pm. sphinctrophorum and Pm. theobromatis. Species can be identified based on their cultural and morphological characters, supported by DNA data derived from partial sequences of the actin and ß-tubulin genes. Phylogenies of the SSU and LSU rRNA genes were used to determine whether Togninia has more affinity with the Calosphaeriales or the Diaporthales. The results confirmed that Togninia had a higher affinity to the Diaporthales than the Calosphaeriales. Examination of type specimens revealed that T. cornicola, T. vasculosa, T. rhododendri, T. minima var. timidula and T. villosa, were not members of Togninia. The new combinations Calosphaeria cornicola, Calosphaeria rhododendri, Calosphaeria transversa, Calosphaeria tumidula, Calosphaeria vasculosa and Jattaea villosa are proposed. Species of Phaeoacremonium are known vascular plant pathogens causing wilting and dieback of woody plants. The most prominent diseases in which they are involved are Petri disease and esca, which occur on grapevines and are caused by a complex of fungi, often including multiple species of Phaeoacremonium. Various Phaeoacremonium species are opportunistic fungi on humans and cause phaeohyphomycosis. The correct and rapid identification of Phaeoacremonium species is important to facilitate the understanding of their involvement in plant as well as human disease. A rapid identification method was developed for the 22 species of Phaeacremonium. It involved the use of 23 species-specific primers, including 20 primers targeting the ß-tubulin gene and three targeting the actin gene. These primers can be used in 14 multiplex reactions. Additionally, a multiple-entry electronic key based on morphological, cultural and ß-tubulin sequence data was developed to facilitate phenotypic and sequence-based species identification of the different Phaeoacremonium species. Separate dichotomous keys are provided for the identification of the Togninia and Phaeoacremonium species. Keys for the identification of Phaeoacremonium-like fungi and the genera related to Togninia are also provided. The mating strategy of several Togninia species was investigated with ascospores obtained from fertile perithecia produced in vitro. Togninia argentinensis and T. novae-zealandiae have homothallic mating systems, whereas T. austroafricana, T. krajdenii, T. minima, T. parasitica, T. rubrigena and T. viticola were heterothallic.

Undocumented Migrants as New (and Peaceful) American Revolutionaries

This essay situates undocumented migrants in the history of the American revolutionary period. The lawbreaking of both groups produced constructive legal and social change. For example, the masses of American revolutionaries and many of their leading men fought to rid the colonies of hereditary aristocracy. Colonists had come to cherish the proto-meritocracy that had bloomed on colonial shores and rankled at local evidence of aristocratic privilege, like the Crown’s grant of landed estates to absentee English aristocrats. Today’s equivalent hereditary aristocracy is the citizenry of wealthy democracies like the United States. Hereditary citizens use immigration restrictions to reserve the wealth and privilege of rich-world citizenship for themselves and invited guests. The undocumented peacefully challenge this status quo by migrating and remaining in the United States without permission, securing citizenship for their American-born children, and protesting that “no one is illegal.” In these ways the undocumented seize some of the aristocratic privileges of American citizenship and fight for others. For this and other reasons, the undocumented are contemporary heirs to the revolutionary moment—the true tea partiers of the twenty-first century

A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-Associated Protein Kinase and Blebbistatin

Commercial software is available for performing video bioinformatics analysis on cultured cells. Such software is convenient and can often be used to create suitable protocols for quantitative analysis of video data with relatively little background in image processing. This chapter demonstrates that CL-Quant software, a commercial program produced by DRVision, can be used to automatically analyze cell spreading in time-lapse videos of human embryonic stem cells (hESC). Two cell spreading protocols were developed and tested. One was professionally created by engineers at DRVision and adapted to this project. The other was created by an undergraduate student with 1 month of experience using CL-Quant. Both protocols successfully segmented small spreading colonies of hESC, and, in general, were in good agreement with the ground truth which was measured using ImageJ. Overall the professional protocol performed better segmentation, while the user-generated protocol demonstrated that someone who had relatively little background with CL-Quant can successfully create protocols. The protocols were applied to hESC that had been treated with ROCK inhibitors or blebbistatin, which tend to cause rapid attachment and spreading of hESC colonies. All treatments enabled hESC to attach rapidly. Cells treated with the ROCK inhibitors or blebbistatin spread more than controls and often looked stressed. The use of the spreading analysis protocol can provide a very rapid method to evaluate the cytotoxicity of chemical treatment and reveal effects on the cytoskeleton of the cell. While hESC are presented in this chapter, other cell types could also be used in conjunction with the spreading protocol

Engineering orthogonal dual transcription factors for multi-input synthetic promoters

Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still employ the same core set of TFs (for example LacI, TetR and cI). The TFs mostly function via repression and it is difficult to integrate multiple inputs in promoter logic. Here we present to our knowledge the first set of dual activator-repressor switches for orthogonal logic gates, based on bacteriophage λ cI variants and multi-input promoter architectures. Our toolkit contains 12 TFs, flexibly operating as activators, repressors, dual activator–repressors or dual repressor–repressors, on up to 270 synthetic promoters. To engineer non cross-reacting cI variants, we design a new M13 phagemid-based system for the directed evolution of biomolecules. Because cI is used in so many synthetic biology projects, the new set of variants will easily slot into the existing projects of other groups, greatly expanding current engineering capacities