Many biological experiments require a protein sequence to be translated to the nucleic acid sequence that codes for it or require an investigator to possess a means to “backtranslate” a protein to its amino acid sequence. However, the degenerate nature of the genetic code greatly frustrates this process through ambiguities in the wobble bases. One possible solution to this dilemma is to predict codon usage frequencies for a target organism through use of an Artificial Neural Network. Consequently, a Neural Network was trained on amino and nucleic acid sequences to determine the network’s capacity in accurate predictions for a twenty amino acid window. Moreover, 10 different network architectures were surveyed to ascertain which one yields optimum (least error) results when trained on the same nucleic acid sequences. The winning architecture was examined using two new training sets that have been partitioned into those with high bias and those with low bias for mRNA secondary structure. The more negative the bias, the more secondary structure it will have, whereas less negative bias will display less secondary structure. Testing of these two training sets revealed that the neural network was able to distinguish between the two sets; i.e., the training set with greater secondary structure learned the patterns in less training cycles and produced a lower error when compared to the training set with less secondary structure given the same network architecture. Ultimately, this work might be beneficial as a computation tool for backtranslation in degenerate PCR cloning and in identifying the unknown coding regions in genes.

Affinity chromatography has been successfully employed for the purification of alkaline phosphatase (APase). A potential inhibitor of APase, 3-aminopropyl-phosphonic acid (3-APPA), was.coup1ed to agarose, Affi-Gel 10, to form an affinity adsorbent for APase. Phosphocellulose was used as a second adsorbent. A partially purified extract from C57BL mice was applied to both adsorbents in 0.1 M acetate buffer, pH 5.0, and eluted with 1.0 M KCl in 0.05 M tris buffer, pH 7.4. Both adsorbents were effective in adsorbing the enzyme, and the specific activity of the enzyme recovered from both adsorbents was greatly enhanced. The relative yields of the adsorbents differed greatly. Approximately 57% of the activity which was bound to the 3-aminopropylphosphonic acid-Affi-Gel 10 adsorbent was recovered in a 140-fold enrichment relative to the extract which was applied to the column. Only 13% of the bound activity could be eluted from the phosphocellulose adsorbent in a 125-fold enrichment. Because of the poor yield, the phosphocellulose adsorbent has been evaluated as noneffective for affinity chromatography purification of APase. Conversely, the 3-aminopropylphosphonic acid-Affi-Gel 10 adsorbent provides a rapid, one-step procedure for APase purification.

During the past thirty years, investigators of the renin-angiotensin system have found renin-like substances in a number of non-traditional locations throughout mammalian systems. These renin-like substances have been found in virtually every component of the brain, as well as the salivary glands, adrenal glands, blood vessels, genital tracts of both males and females, tumor cell lines, and even the eyeball and retina. This thesis is a literary review which will focus on extrarenal renin sources located in the uterus and the testis. These two locations are of particular interest because of the probable function in the regulation of the reproductive cycle. In addition, information on submaxillary gland renin and brain renin will also be discussed but to a lesser extent than uterine and Leydig Cell renin. Extrarenal renin sources have been tagged as renin-like enzymes, or more popularly as isorenins, because immunologically they react as true renin does. The immunoreactivity of these isorenins has been detected by a number of methods which include immunohistochemistry, specific staining characteristics of immunolabelling, native gel electrophoresis, sodium dodecyl sulfate gel electrophoresis, isoelectric focusing, double immunodiffusion, and symmetric chromatographic elution patterns. Extensive research in this area is still underway. Numerous modes of detection are being used to evaluate the specific sites of synthesis for these extrarenal renin sources, as well as their release mechanisms and physiological roles. Undoubtedly, the data resulting from these investigations will reveal significant information regarding these non-traditional renin sources and their clinical relevance in the treatment of hypertension.

Levels of activation and transphosphorylation have been studied using crude preparations of alkaline phosphatase (APase). Tris (Hydroxymethyl) aminomethane, Ammediol (2 Amino-2-methy1 1,3 propandiol) and Borate buffers were employed to buffer the reactions. Para-nitrophenyl phosphate was used as the substrate to assay for APase activity. The concentrations of both the hydrolyzed products, para-nitro-phenol and phosphate were measured colorimetrically at appropriate wavelengths. Evidence is presented showing that transphosphorylation is possible at certain concentrations of Tris and Ammediol. An enhanced activation level was also noted with these two nucleophilic buffers. Borate, however, showed no significant activation of APase either at high or low concentrations and little or no transferase activity was detected. Essentially, no significant differences have been shown among the tissue APases of lymphoma, embryo, and placenta with respect to their activation levels.

The objective of this dissertation is to develop a new research tool, PROMAP, which will allow the construction of models that satisfy the requirement of spatial distribution and hierarchical interactions within a dynamic framework. An analysis of the form of ecosystems is followed by an examination of current attempts at ecosystem modeling using spatial relationships. An examination of the analytical procedures used in the spatial modeling process, results in a set of criteria that a suitable modeling system should incorporate. These criteria are: the use of real numbers; iterative processing; flexible data retrieval; and neighborhood analytical procedures. The basic configuration of PROMAP is discussed with an emphasis on the mathematical procedures and the capability for designing cellular automata within the system. The representation of biophysical systems into a set of spatial transition functions is described in relation to the development of nested hierarchies called Q-morphisms. Having established the design of PROMAP, a suitable test is devised using the simulation of surface fire spread. A model called FIREMAP is developed and the results are compared to expected fire shapes under Zero State Conditions. These conditions are defined as uniform fuel, zero slope and zero wind with additional factors held constant. Other simulations of fire spread are made by relaxing the conditions to achieve wind driven fires and the response to potential impediments to fire spread. The response of the simulation shows an accurate correspondence between the simulation and the expected fire shape. As a final test of the model, all restrictions are removed and a simulation is made under actual conditions of complex terrain, and non-uniform fuels using data collected on the San Carlos Apache Indian Reservation in southeast Arizona. Deficiencies of PROMAP and FIREMAP are discussed as well as future implications for the FIREMAP model as a management tool.

Volume growth was modeled for even-aged Emory oak stands. Data were collected from 84 temporary plots located in the proximity of the Huachuca Mountains of southeastern Arizona. At each plot, trees were measured for current volume using non-destructive sampling techniques. Variable-density yield tables for Emory oak were developed from sample data collected on temporary plots. Yield tables are a system of equations used to estimate current yield and predict future yield. A system of equations consisting of two components was developed in this study. The first component predicts yield, the second predicts future yield by estimating changes in density. Basal area is the density measure used. By using basal area, current yield is obtained by determining present stand conditions. Future yield is estimated by adjusting basal area for future stand conditions. Estimated changes in basal area are placed back into the yield equation and solved, providing an estimate of future yield. Therefore, yield and future yield of Emory oak can be estimated by using basal area as the density variable. The variable-density equations are used to estimate the volume of unthinned or thinned stands of Emory oak.

Sex-pheromone components released by Manduca sexta females are detected solely by male-specific olfactory receptor neurons that innervate long sensilla trichodea on the male antennae. To facilitate studies of the development and physiology of these receptor cells, I have produced primary in vitro cultures of cells dissociated from pupal male antennae. These cultures comprise several morphological types of cells, two of these cell types could be characterized immunocytochemically with a pair of monoclonal antibodies that were shown previously to recognize certain antigens in olfactory receptor neurons at defined stages of development. The good correlation between in vivo and in vitro expression of these antigens suggest that the immunocytochemically recognized cells are olfactory receptor neurons that follow at least partially their normal course of development in vitro. Patch-clamp studies revealed that the immunocytochemically recognized olfactory receptor neurons express three different kinds of Cs⁺-blockable K⁺ channels and at least one kind of Tetrodotoxin-blockable Na⁺ channel after three weeks in vitro. At least one channel, an unspecific cation channel, responds with higher frequency openings after stimulation with female pheromone-gland extracts in vitro. Thus it could be demonstrated for the first time that identifiable cultured insect olfactory receptor neurons differentiate in morphological and physiological terms and are able to respond to pheromones in vitro, providing an ideal model system for studies of primary sensory transduction in vitro.

My dissertation explores octopod ecoloy, morphology and evolution. Using an artificial shelter trap technique (Voight, 1988a), parameters of a wild population of Octopus digueti are monitored for one year. Octopus movement correlates with sea temperature but is reduced under full moonlight. Enlarged suckers reliably indicate male maturity in this species. This first definition of an age class in octopuses allows field growth rates to be compared to those from laboratory studies. Octopus digueti growth in the wild equals that in the lab; average life span may be only 6 months during which time individuals may grow from a hatching weight of 40 mg to over 40g. Individuals show the uniparous life history documented in lab studies. Cohorts appear not due to reproductive synchrony, but to seasonal temperature fluctuations. Genetic differences probably control individual growth rate and life span. To test the reliability of morphology of preserved octopus specimens, ln-transformed measurements are plotted versus ln mantle length. Body measurements are strongly correlated with size; preservation does not therefore eliminate information contained in specimens. Principal component analysis reveals shallow water tropical octopuses vary primarily in arm length, mantle length and sucker diameter. Trans-Atlantic conspecific populations are morphologically indistinguishable. Hypothesized species relationships (Voight, 1988b) are supported, despite considerable overlap among species. No secondary sexual dimorphism except enlarged suckers is present in these species. Octopuses from rocky habitats have longer arms and smaller mantles than do those from sandy habitats. In the Octopodidae, arm length, head width and sucker diameter contribute most size-free morphological variation. Sucker size correlates inversely with depth due to hydrostatic pressure. Arm length and head width variation correlate inversely with latitudinal distribution, and are associated with the number of sucker rows. Subfamilies defined by the number of sucker rows (Voss, 1988a), may represent overtly similar, paraphyletic groups. Cladistic analysis of the suborder Incirrata show that Voss' subfamilies are paraphyletic groups; Robson's (1932) subfamilies are supported. The Argonautida are the most primitive incirrate group, the Ctenoglossa and Octopodidae are sister taxa. The incirrate octopods may have evolved from a deep sea, rather than a shallow-water, ancestor.

Animals are decision-makers. While we cannot examine directly their decision-making process, we can observe the results of such decisions: their behavior. Behavioral ecologists, attempt to understand and predict the behavior of animals. To do so, clearly requires an understanding of the kinds of information individuals possess about their environment. Here, I explore how foragers exploit resource patches. When resource items are discrete and hidden, individuals must estimate the quality of encountered patches. Solitary foragers can use two sources of information. First, they can obtain information by sampling a patch. This is called patch-sample information. Second, foragers may use their prior experience and learn the distribution of resources in the environment. Individuals that combine these two sources of information are called Bayesian foragers. Foragers that cannot distinguish patch differences must rely on patch-sample information. Those that can, should employ Bayesian estimation because this generates better patch estimates. I examined the patch assessment ability of a wide variety of species. When patch variation is small, Arizona pocket mice (Perognathus amplus), and round-tail ground squirrels (Spermophilus tereticaudus) use patch-sample information; when patch variation is great, they both are Bayesian foragers. Gambel's quail (Callipepla gambelii) and mourning doves use patch sample information regardless of patch variation, while Merriam's kangaroo rat appears to always employ Bayesian foraging. If patches are spatially predictable and quality is temporally predictable, foragers can use this information to generate patch estimates prior to exploitation. Inca doves (Columbina inca) do just this. Black-chinned hummingbirds (Archilochus alexandri) are Bayesian foragers in predictable environments but rely much more on patch-sample information in unpredictable environments. Group foragers can use one additional source of patch information: they can observe the foraging success of other group members. I call this public information. In a series of Monte Carlo simulations, I show that Public information allows groups to estimate patch quality faster than solitary foragers and may prevent the underutilization of patches. Individuals in groups that cannot obtain public information can be faced with a dilemma because each group member will generate a different patch estimate. These individuals should abandon the patch when the first individual does so.

Experiments with bluegill (Lepomis macrochirus) were conducted using the open system proposed by Matter et al. (1989) to examine factors that influence animal residency in these systems. Tests of the exits from the system suggested that they accurately identified resident and emigrant animals. The food and cover provided were shown to be appropriate and sufficient resources for bluegill. Shade covers and initial closure of exit used by Bianchi (1984) were unnecessary to achieve animal residency. The number of resident fish at a fixed level of resources fluctuated widely due to some undetermined and uncontrolled environmental conditions. These results indicate that falsification tests of hypothesized mechanisms of population regulation in open systems, may not be conclusive unless all possible confounding variables can be excluded.