Historical interrelations among manufacturing, industrialization, and patents has resulted in a distinct “thingliness” , though business models, construction processes, chemical formulas, cartographic systems, methods of manufacturing, and other “nonthings” also have a long history of patent innovation.Things and non-things alike may be granted the protection of a utility patent, given that the nature of their claims is non-obvious, innovative, and discloses the function and configuration of a specific “art.” The hybridizing of geographical studies with patent innovation studies suggests a scale, scope, and orientation for intellectual property claims that verge of the infrastructural, ecological, and environmental. Landscapes are not things, cities are not things, and coastal zones are not things, yet each is subject to the iterative and often deterministic forces of human ingenuity. In the following texts and images, I investigate site specific patents that function at landscape and regional scales but with drawings and diagrams that are siteless and scaleless. We know of each patent’s site specificity through the inclusion of geographical terminology and reference to specific places and regions within the patent text, but the scale and impact of the proposed intervention remains open to interpretation. In one drawing per patent, I adapt claims and technical specifications to the geographical location described in the text, synthesizing historical research and maps with the “new” innovation disclosed in the patent. The texts and images presented here are, in their simplest form, ruminations on the intersections of place and intellectual property. They provide geographical context to patents that may have radically altered the American landscape,vertical growing systems transcending the object-oriented history of patents to suggest a new hybrid at the intersection of technology and environmental geography of innovation.

Fluoroquinolone antibiotics, an important class of synthetic antibacterial agents, were developed through structural modifications of the nonfluorinated quinolone nalidixic acid to act against both Gramnegative and Gram-positive pathogenic bacteria . Due to this broad-spectrum antibacterial activity, the FQs are widely prescribed in both human and veterinary medicine. However, as a result of incomplete metabolism and the relative ineffectiveness of conventional water treatment technologies in removing them , they are now detected frequently in both receiving and surface waters . Although FQs were developed to have specific mechanisms of action against pathogens through the inhibition of bacterial DNA replication and repair , they can exhibit unintended toxicological effects on indigenous bacteria and other sensitive organisms when released into the environment . Of special interest are some recent aquatic microcosm studies indicating that photosynthetic species are perturbed when exposed to FQs . For instance, ciprofloxacin , the dominant FQ antibiotic in current use, has been shown to affect both the structure and richness of algal communities exposed to environmentally relevant concentrations . The ability of Euglena gracilis, a facultative photosynthetic protozoan, to form green colonies was vitiated as a result of exposure to Naldx , which also was shown to be a specific inhibitor of chloroplast DNA synthesis. In a key study of seedlings of the higher plant Arabidopsis thaliana, grown in media containing Cipro, Wall et al. reported that DNA gyrase is a chloroplast-specific enzyme in addition to being a bacterial enzyme, thus revealing a specific target of FQs in photosynthetic organisms that is similar to their bacterial target. The FQs may have other chloroplast-specific targets. For instance, exposure to Naldx led to an inhibition of photosynthetic electron transport that was an order of magnitude greater than the inhibition of chloroplast DNA synthesis and replication in isolated pea chloroplasts and to a reduction in the production of both ATP and NADPH in carrot cell cultures.

These important findings have motivated the proposal that Naldx may be acting as a significant inhibitor of photosynthesis, interfering with the generation of reduced electron carriers, which then can impede the production of both ATP and NADH . In agreement with the hypothesis of Mills et al. , in vitro exposure of spinach chloroplasts to nonfluorinated quinolone-containing compounds resulted in the inhibition of photosystem II and the cytochrome b6f complexes, which are key enzymes involved in PET. In sum, these disconcerting results suggest that quinolones, the moieties upon which the broad-spectrum antibacterial activity of FQs largely depends , may have a toxicological impact on PET similar to that of herbicides . However, there appear to be no published investigations of the most widely used FQs as to their specific targets in PET.In the present study, we employed a combination of modeling and experimental techniques in an effort to probe how FQs may have secondary toxic effects on photosynthetic organisms by interfering with the functioning of PET. We identified the structural components of FQs that may be responsible for photosynthetic inhibition and the possible targeted enzymes by performing a structure-activity relationship analysis using well-known protein substrates in and inhibitors of PET. This was followed by molecular modeling of the interactions of Naldx and Cipro with the most likely site of PET inhibition as predicted by the SAR analysis. Guided by these modeling outcomes, we used intact thylakoids isolated from spinach chloroplasts to characterize the effects of Cipro on PET following both in vitro and in vivo exposure at Cipro concentrations up to 50 µM, corresponding to the levels that may be found near industrial effluents .Quinones, and in particular proteins containing quinone sites , play an important role in mediating electron transport within the bio-energetic membranes of photosynthetic bacteria, mitochondria, and chloroplasts. To evaluate FQ antibiotics as potential Q site antagonists in PET, 50 known Q site inhibitors which target 8 different proteins involved in photosynthetic and mitochondrial electron transport were subjected to SAR analysis using the Lead Scope software package.

This software package employs a database of molecular structures that are typical in medicinal chemistry to build correlations between important chemical substructures in a selected set of compounds and the biological effects of the compounds. Validation studies of the software to ensure structure-activity correlations specific to each protein target were performed before using it for SAR analysis of the FQs. The principal result of the SAR analysis was that four unique chemical substructures were identified in about 80% of the compounds that target reaction center II , the pheophytin-quinone-type center present in PS-II, wherein photoexcited chlorophyll molecules facilitate the flow of electrons from an electron donor chlorophyll to a pheophytin molecule, which then transfers electrons to a primary quinone site to reduce subsequently mobile quinone molecules at a secondary quinone site . Two of the four chemical substructures, namely, secondary amine and halide aryl, are found in the FQ antibiotics pipemidic acid, norfloxacin, enoxacin, lomefloxaicn, and ciprofloxacin. This structural correlation encouraged us to apply molecular docking simulations to explore in more detail the interactions of Naldx and Cipro with the QB site in RC-II, a common target of PS-II inhibitors. The quinolone antibiotic Naldx was used for comparison because, as previously noted, it exhibits herbicidal activity by inhibiting PET and possesses fragments of two of the substructures targeting RC-II that are not found in the FQs. The software package Autodock4 was used to generate favorable binding configurations of Naldx and Cipro at RC-II in Rheudopseudomonas viridis PDB ID 2prc,outdoor vertical plant stands which is homologous to RC-II systems found in other photosynthetic organisms . The docking procedure employs a grid map of a three-dimensional lattice to store both van der Waals and electrostatic potential energies that would result from the interaction of each atom of the antibiotic with the atoms of the R. viridis RC-II located in a specified region considered to be a possible target site of the antibiotic. Accordingly, the L and M subunits of the R. viridis RC-II , which respectively house the binding sites for the protein bound quinone menaquinone and the soluble quinone ubiquinone , were considered in the docking simulations . A simulation cell having 20 Å sides centered on the QB site served to isolate the atoms of the receptor to be included in the grid map. Docking was optimized by allowing the ligand 6 degrees of freedom within the cell and by taking into account rotatable bonds of the ligand to include torsional degrees of freedom. Thermo dynamically favorable binding conformations were identified by sequentially implementing random changes in each of the degrees of freedom mentioned above, calculating the intermolecular interaction energies, and subjecting each configuration to an annealing step to remove those that are energetically unfavorable.Simulations of the structure of R. viridis RC-II cocrystallized with QB were performed to validate the docking procedure; the conformation of the docked ligand predicted by the simulation was in good agreement with that determined experimentally from crystal structure analysis.

Docking simulations of Naldx and Cipro within the L and M subunits were then performed similarly, with a 20 Å×20 Å cell centered on the QB site; the resulting lowest energy docking realizations were analyzed in detail.n vitro exposure to Cipro was not inhibited , a distinct contrast from previous results obtained with Naldx , further suggesting that Cipro may have a mode of action different from that of Naldx. This finding is consistent with our modeling results that Cipro may not exhibit a strong binding competition with the secondary quinone at its PS-II target site. Since Cipro was shown to be structurally similar to known inhibitors of the oxidizing site of PS-II , which can induce disruption of the redox states required in PS-II for PET, we monitored the redox state of the primary quinone in the presence of Cipro. Moreover, a statistically significant increase in the Fo/Fm values indicates a corresponding increase in the amount of photoexcited Chmolecules that are not translating to photo reduction of the quinone molecules. In accordance with this phenomenon, the kinetics of QA photo reduction were affected significantly as a function of [Cipro] . The calculated time to reach half the maximum value of Fv, i.e., the time to produce half the total amount of photo reduced QA, was 0.081 50 µM, i.e., a major delay in the kinetics of QA photo reduction under our experimental conditions. Taken collectively, these in vitro results led us to propose that Cipro interferes with PET indirectly, by decreasing the rate of energy transfer from antenna Chl molecules to the reaction center in the spinach thylakoids. The above conclusions were strengthened by results obtained following in vivo exposure of spinach leaves to Cipro. After in vivo exposure, the maximal fluorescence yield did not change appreciably, but there were pronounced changes in the relative yields of Fo andFv . Increasing concentrations of Cipro caused an increase in the parameter Fo, representing the amount of excited Chl that is blocked from or otherwise incapable of transferring energy to the PSII reaction center . Conversely, the fluorescence parameter Fv decreased systematically with increasing [Cipro] , reflecting the lower levels of excitation energy reaching the PSII reaction center molecule from the antenna chlorophyll. We should point out that this in vivo biochemical effect was observed after a short 8 day exposure to Cipro in the growth media, wherein the plants still appeared to be healthy, with no observable decrease in the green pigment of the leaves, in the amount of newly synthesized leaves, or in the growth of the plant roots. More adverse effects may result from longer exposures. Following growth of the spinach plants in Cipro-containing nutrient solution for 26 days, we observed stunted growth as evidenced by a significant decrease in the number of newly synthesized leaves and the length of the roots . Similarly, the synthesis of new chloroplasts and mitochondria in both seedlings and cell cultures of A. thaliana was severely impaired as a result of exposure to Cipro-containing growth media, with Cipro shown to target DNA gyrase , just as it does in its antibacterial action. A comparable mechanism may be responsible for the longer term adverse effects of Cipro on the morphology of the spinach plants investigated in the present study; the observable decrease in the amount of both new leaves and the green pigment of the leaves 50 µM is in agreement with this mechanism . Both in vitro and in vivo effects of Cipro on QA photo reduction underscore that the observed Cipro-induced decrease in the fraction of photo reduced QA is not likely due to direct chemical inhibition at the quinone binding site, but instead is a downstream effect of Cipro toxicity in the PS-II units characterized by an increase in inactive antenna Chl molecules.