Browsing by Subject "Biology"
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Item A critical analysis of skull osteology in Australian Agamidae with implications for the fossil record(2016-05) Stilson, Kelsey Tull; Bell, Christopher J., 1966-; Clarke, Julia; Maisano, Jessica; LaDuc, TravisThe Australian agamid radiation was long noted for homogeneity of morphological characters and remains one of the most poorly studied major clades of squamates. Anatomical studies of the various lineages of endemic Australian agamids lag far behind genetic studies and would greatly enhance our knowledge of the current status and evolution of this complicated and dynamic clade. Australian agamids are an ideal group with which to test hypotheses of squamate speciation, diversity, and disparity because of their relatively recent diversification into Australia, about 30 Million Years Ago and geographical constraints. The two chapters of this thesis address two aspects of my research. In Chapter 1, I compile and evaluate morphological characters previously suggested to be useful for identifying Agamidae. I evaluate these characters for intraspecific variation, ontogenetic influence, and sexual dimorphism, for which sample sizes approached 20: Ctenophorus caudicinctus, Ctenophorus isolepis, and Ctenophorus reticulatus. Within the invariant characters, six were invariant only in Ctenophorus caudincinctus, five were invariant only for Ctenophorus isolepis, and two were invariant only in Ctenophorus reticulatus. Morphological characters that varied within taxa (thus, excluding all invariant morphological characters) were statistically tested for covariance with ontogeny (using skull length as a proxy) and sexual dimorphism. Sixteen of the 60 characters measured varied for at least one taxon with ontogeny and nine varied with sex. In Chapter 2, I use X-ray computed tomography (CT) of two specimens to describe the skull of the Australian agamid Cryptagama aurita, a species known only from only four alcohol-preserved specimens. Cryptagama aurita appears to share a great number of skull characters with other desert-dwelling Australian agamids. I conclude that the information currently available for Australian Agamidae is inadequate to interpret the fossil record of Australian Agamidae. Any identifications and phylogenetic analyses are likely to be inaccurate because most of the characters proposed by previous authors are not demonstrably apomorphic. Ontogenetic age is an important source of variation for the three species of Ctenophorous I examined. Morphological variation of extant taxa must be understood in order to compare extant and extinct species to study the recent radiation of Australian Agamidae.Item Analysis of factors influencing the teaching of evolution and creationism in Texas public high school biology classes(Texas Tech University, 1989-12) Shankar, GangaThis research examined the emphasis given by Texas high school biology teachers to evolution and creationism. Selected variables were analyzed to determine their influence on the teaching of evolution and creationism. Data were obtained through a questionnaire administered by mail to a random sample of Texas public high school biology teachers during spring, 1988. Results obtained from 307 teachers, who represented 50 percent of the sample receiving the questionnaire, indicated that the majority of Texas biology teachers taught evolution, but did not give it comprehensive coverage as indicated by total time allocated to evolution and twelve topics concerned with evolution. The majority of the teachers thought evolution should be taught in high school biology because of its role as a unifying and central theme in biology.Item Applications of scanning electrochemical microscopy in biological systems(2011-08) Koley, Dipankar; Bard, Allen J.; Crooks, Richard M.; Stevenson, Keith J.; Mullins, Charles B.; Humphrey, Simon M.The main theme in this dissertation is to develop Scanning Electrochemical Microscopy (SECM) based electroanalytical techniques to study quantitative biology in real time. The multidrug resistance (MDR) phenomenon in live cancer cells was studied using mimic drug molecules such as menadione with the aid of SECM. Real time quantitative detection of thiodione (menadione-conjugate) pumped out of the cells was determined to be 140 μM due to exposure of 500 μM menadione to the cells. Selective blocking of these MDR pumps in live intact cells was also achieved by small molecules such as MK571 as well as by the MDR specific antibody. An approximately 50% drop in thiodione flux was observed in both cases of MDR pumps inhibition. This SECM technique was also extended to measure the permeability of a highly charged hydrophilic molecule passing through the membrane of a single living cell. The permeability was measured to be 6.5 ± 2.0 × 10-6 m/s. Real time monitoring of morphological changes in a live HeLa cell due to addition of varying concentration of surfactant such as Triton X-100 was also demonstrated by SECM. This electroanalytical technique was also expanded to study quantitative microbiology. Real time quantitative detection of pyocyanin produced by Pseudomonas aeruginosa (PA14 strain) biofilm locally was determined to be 2.5 μM after 6 h. Pyocyanin (PYO) was also observed to be reduced by PA14 biofilm, thus maintaining a reduced atmosphere above the biofilm even in presence of oxygen. Spatial mapping of this reduced PYO showed that this reduced zone was only formed up to 500 μm above the biofilm. The cells are also able to modulate the height of the reduced PYO zone in accordance to the availability of Fe(III/II) in the solution to scavenge iron from the surrounding environment. Real time spatial mapping hydrogen peroxide across polymicrobial biofilm (Sg and Aa) was also achieved with the aid of SECM. The local peroxide concentration produced by Sg was measured to be 1 mM, which is significantly higher than the bulk peroxide concentration. This study also showed that the local concentration across the microbial film is more important than the bulk concentration since bacteria communicate locally in real world.Item Beyond books : interactive lessons for the college biology classroom(2011-12) Londeore, Cynthia Fay; Jansen, Robert K., 1954-; Fischer, JaniceCollege level science is frequently taught as a recitation of facts in a lecture hall, and the students are expected to gain understanding and insight with their own study. Interactive learning is more effective than lecture based learning and more memorable for the students. Teaching with hands on models has been shown to specifically be beneficial in a college level molecular biology context. Included here is a guide for the instructor leading her through topic selection, activity development, and presentation to the class, as well as five complete and tested lesson plans with notes on alteration made and the reasons for them.Item The Cell Membrane Science Suitcase: An Educational Module for High School Biology Students(2011-02-01T19:37:22Z) Nelson, Roshni; Coulter, KennethThis thesis documents the production and testing of an educational module, the Cell Membrane Science Briefcase, for high school introductory biology students. The module is part of the Science Teacher Access to Resources at Southwestern series of educational Science Suitcases, made available to teachers within the Dallas Independent School District and neighboring communities. The series is funded by the Howard Hughes Medical Institute, and produced by the Biomedical Communications graduate program at the University of Texas Southwestern, and the Dallas Museum of Nature and Science. The Cell Membrane Science Briefcase is intended to supplement the current curriculum with a comprehensive, three-dimensional animation, models, and student activities related to biological membranes. The goal is to not only provide a useful resource for teachers, but to engage and appeal to students through a variety of media and tools not often found in the science classroom.Item Computational identification and evolutionaty enalysis of metazoan micrornas(2009-05-15) Anzola Lagos, Juan ManuelMicroRNAs are a large family of 21-26 nucleotide non-coding RNAs with a role in the post-transcriptional regulation of gene expression. In recent years, microRNAs have been proposed to play a significant role in the expansion of organism complexity. MicroRNAs are expressed in a cell or tissue-specific manner during embryonic development, suggesting a role in cellular differentiation. For example, Let-7 is a metazoan microRNA that acts as developmental timer between larval stages in C. elegans. We conducted a comparative study that determined the distribution of microRNA families among metazoans, including the identification of new family members for several species. MicroRNA families appear to have evolved in bursts of evolution that correlate with the advent of major metazoan groups such as vertebrates, eutherians, primates and hominids. Most microRNA families identified in these organisms appeared with or after the advent of vertebrates. Only a few of them appear to be shared between vertebrates and invertebrates. The distribution of these microRNA families supports the idea that at least one whole genome duplication event (WGS) predates the advent of vertebrates. Gene ontology analyses of the genes these microRNA families regulate show enrichments for functions related to cell differentiation and morphogenesis. MicroRNA genes appear to be under great selective constraints. Identification of conserved regions by comparative genomics allows for the computational identification of microRNAs. We have identified and characterized ultraconserved regions between the genomes of the honey bee (Apis mellifera) and the parasitic wasp (Nasonia vitripennis), and developed a strategy for the identification of microRNAs based on regions of ultraconservation. Ultraconserved regions preferentially localize within introns and intergenic regions, and are enriched in functions related to neural development. Introns harboring ultraconserved elements appear to be under negative selection and under a level of constraint that is higher than in their exonic counterparts. This level of constraint suggests functional roles yet to be discovered and suggests that introns are major players in the regulation of biological processes. Our computational strategy was able to identify new microRNA genes shared between honey bee and wasp. We recovered 41 of 45 previously validated microRNAs for these organisms, and we identified several new ones. A significant fraction of these microRNA candidates are located in introns and intergenic regions and are organized in genomic clusters. Expression of 13 of these new candidates was verified by 454 sequencing.Item Development of an Interactive Program on the Jacobson's Organ and Defense/Prey Methods of Snakes as a Model for Teaching Complex Biological Concepts to Children in Grades Four - Six(2009-01-08) Cammilleri, Aimee L.; Krumwiede, Kim HoggattThe goal of this thesis was to create a model for an educational interactive animated program that explains complex biological concepts to children in grades four through six. The program uses illustrations, animations, photographs, and interactive games to enhance the teaching of the Jacobson's organ in snakes and snake defense/prey methods. The program serves not only as an educational tool, but also engages the learner through its interactive games which reinforce important concepts.Item Incorporating engineering in high school biology(2014-08) Nusz, Jarred Ross; Ren, PengyuThe purpose of this project was to create a series of lessons that incorporate both Biology and Engineering concepts. The three lessons were intended to increase in complexity as the students progress throughout the year. Using PyMol software allowed students to visually represent complex protein structures while introducing and providing an opportunity to practice programming. Each lesson was followed by a worksheet or activity to aid in students' comprehension and application of practice. These lessons were designed to maximize students' time learning to program and using PyMol software while enhancing the current curriculum. Lesson one introduced students to the PyMol software while building and representing the four main structures of proteins. With increased programming knowledge, lesson two focused on modeling the DNA double helix. The final lesson introduced students to evolutionary relationships based on a protein's amino acid sequence.Item Isolation and sequence analysis of the propanediol dehydratase genes of propionibacterium freudenreichii(2007-08) Dey, Asim Bikash; Jeter, Randall M.In many Gram-negative enteric bacteria, vitamin B12-dependent reactions aid in the metabolism of small molecules and provide ATP for the bacteria. Propanediol dehydratase is such an enzyme that catalyzes the conversion of 1,2-propanediol to propionaldehyde, the initial step of the 1,2- propanediol degradation pathway. The presence of this enzyme has been reported in several species of enteric bacteria, although not in Escherichia coli, and the molecular structure, function and genetic regulation of the enzyme has been characterized extensively in Klebsiella oxytoca and Salmonella enterica. The existence of propanediol dehydratase activity has also been reported in some Gram-positive bacteria, including Propionibacterium freudenreichii, a member of the propionic acid bacteria. In this study, several strategies were taken to clone the genes encoding propanediol dehydratase from P. freudenreichii using the information already known about the large subunit of the enzyme from S. enterica. A genomic library of P. freudenreichii was constructed, but phenotypic screening for a clone harboring the genes was unsuccessful. Polymerase chain reaction with degenerate primers and the genomic DNA of P. freudenreichii as template did not produce any amplified product. Southern hybridization using the gene encoding the large subunit of propanediol dehydratase from S. enterica as the probe gave a positive signal with the genomic DNA of P. freudenreichii. The isolated genomic DNA fragment was cloned and named A63. Analysis of both the nucleotide sequences and deduced amino acid sequences of the open reading frames in A63 did not reveal any identity with known B12-dependent dehydratases. Instead, the best homologies were found with non-B12-dependent dehydratases and pyruvate formate-lyases from other bacteria. In addition to the putative propanediol dehydratase genes, the carbon utilization and antibiotic susceptibility patterns of P. freudenreichii were also characterized in this study.Item Light! Carbon! Action!: A Portable Science Suitcase on Photosynthesis for High School Biology Students(2010-05-14) Wu, Derek Thomas; Krumwiede, Kim HoggattThe goal of this thesis was to create a traveling “science suitcase” teaching aid that could encourage the improvement of 9th and 10th grade students’ understanding of the complex physical, chemical, and biological processes involved in photosynthesis. The suitcase includes a narrated animation, an interactive board game, three laboratory experiments, and a hands-on cell model. The suitcase is a resource to enhance the teacher's curriculum on photosynthesis, possibly help students meet the state of Texas science education requirements, and stimulate student interest to take advances science classes such as Advanced Placement Biology.Item Logos Ex Machina: A reasoned approach toward Cancer(2012-05) Avila, Andrew; Gollahon, Lauren; Strauss, Richard E.; Rice, Sean H.; Butler, Boyd; Watson, RichardLimitations in our current ability to integrate a diverse spectrum of genetic information in an effort to elucidate the underlying causes of cancer has spawned the need for a novel cancer modeling approach. Public repositories of biological pathways and gene expression experiments were combined in order to provide a systems biology approach toward cancer. Furthermore, by unifying these sources of knowledge, the ability to predict expression levels of unmeasured genes was developed. This technique was then applied to a variety of cancer types in order to resolve commonalities between heretofore divergent (or disparate) cancers. The results generated in this manner revealed characteristics that challenge the current prevailing paradigm of cancer. Specifically, the predicted results, according to the Somatic Mutation Theory of Cancer, of a significant upregulation of oncogenes and a significant downregulation of tumor suppressor genes was not found. In contrast, it was found that oncogenes were significantly downregulated and tumor suppressor genes were upregulated among the cancers examined. Furthermore, the results demonstrate the differential expression, in cancer cells, of genes involved in the cellular differentiation and wound healing processes. These results were used as a springboard to develop a novel oncogenesis hypothesis, named Umbracesis. In short, the Umbracesis hypothesis proposes that disruption of the wound healing process via carcinogens, occurs in such a way as to prevent organismic homeostasis from being recovered or prevent full re-differentiation of dedifferentiated cells. The former concept is implicated in inflammatory cancers. Whereas the latter concept, is implicated in cancers that show characteristics associated with embryonic tissues. It was concluded, that the instrumental use of the modeling approach, developed within this study, has implications beyond cancer and may be of use within other areas of biomedical concern.Item Organelle Extravaganza: A Portable Science Suitable for High School Biology Students(2009-01-16) Hulsey, Jennifer Leigh; Calver, Lewis E.The goal of this thesis project was to create a portable Science Suitcase on organelles designed to supplement the current high school biology curriculum in the Dallas Independent School District. The Science Suitcase includes a narrated animation, three laboratory experiments, and an interactive game that can be borrowed by teachers and brought into their classrooms. The Science Suitcase will help enhance students' interest in science, bridge the gap between ninth grade biology and Advanced Placement biology, and help students meet the state of Texas science education requirements based on the National Science Education Standards.Item Oxygen Deficient Metabolism in Organs: A Link to Combustion Science(2014-12-10) Miller, Jason MathewIn an attempt to better understand and model transport of oxygen, O2, from capillaries to living cells in surrounding tissue, the group combustion (O2 deficient) concept from the field of combustion science in engineering is applied to the biological field of microvascular O2 transport from capillaries to cells immersed in interstitial fluid (IF). The conventional Krogh model represents typical biological models, considering tissue cylinder with uniform oxygen source/sink term (US) (m''', g/s/cm^3) and O2 transport from capillary on axis (COA) towards the surface; engineering models consider cylinders with O2 supplied from the surface of cylinder (COS); in addition, they present i) transport (diffusion) and ii) kinetics limited sink rates and profiles for O2. Diffusion limitation causes m''' to be proportional to local O2 concentration. Thus, the present work modifies COS engineering models for COA cases and considers only diffusion limited transport of O2 to metabolic cells from IF. O2 profiles and resulting specific metabolic rates, SMRs (W/g), are generated for four models: I) COA with oxygen dependent consumption source term (O2) (COA-O2), II) COA-US, III) COS-O2, and IV) COS-US. In order to validate the current approach, the model results are verified with the following different types of experimental data: A) If SMRs (mq W/g) are given by the allometric law, kbmk^kq=am for organ k, then COS models under limiting conditions suggest -1/3Item Parallelization Methods for the Distribution of High-Throughput Bioinformatics Algorithms(2011-05) Rees, Eric; Youn, Eunseog; Dowd, Scot E.; San Francisco, MichaelThe development of high-throughput bioinformatics technologies has caused a massive influx of biological data over the course of the past decade. During this same span of time, computational hardware has also been rapidly increasing in speed while decreasing in price, multi-core processors have become standard in home and office environments, and distributed and cloud based computing has become affordable and readily available to researchers with implementations such as Amazon’s S3, Microsoft’s Azure, Google’s App Engine, and the 3Tera Cloud. Bioinformatics software tools such as BLAST, a tool for finding local alignments between a set of unknown genetic sequences versus a set of known genetic sequences, have simple interfaces and few installation requirements often so biologists can use them easily in the laboratory without needing an in-depth knowledge of how computer systems work. This, however, is rarely the case for distributed implementations of bioinformatics tools which often require the user to first set up and configure the underlying program that will handle the distribution, such as the Message Passing Interface (MPI). Once the underlying distribution algorithm is chosen, many of the software tools require the user to then configure the program to work with their chosen method and, in some cases, write the necessary source code to link the program with the underlying service. These are difficult steps for most computer scientists and are near impossible for the average biologist. By constructing a modularized set of methods that can connect to, broadcast to, and read from a multicast created by the methods, future bioinformatics software developers will be able to construct the underlying message passing system without requiring the end-user, often a biologist, to set up and configure one of their own. Using these multicast methods will allow any program the ability to seek out and track any nodes on the network that will be used in the distributed system. This communication method allows the program to easily scale up and down depending on available nodes without direct user intervention to alter the size of the system. This system is then tested by creating a program that connects NCBI’s Basic Local Alignment Search Tool to the multicast system to allow the BLAST algorithm to then be distributed across multiple nodes. This new system will demonstrate how future programs could then connect stand alone tools, such as BLAST, to the multicast system to create programs that will execute on a distributed system and automatically scale depending on the network size without altering the tools source code.Item Re-evaluation of museum voucher specimens in the modern biological research(Texas Tech University, 2003-12) Kageyama, MarikoThe previously published definitions of, and the philosophy behind, the voucher specimen are reviewed. The concept of a voucher specimen is re-evaluated in the modern biological research context, and a revised definition of a voucher is proposed. The "primary voucher" and "secondary voucher" are newly categorized within the comprehensive scheme of the voucher. The new definition and the introduction of primary and secondary vouchers enable us to accommodate a wider scope of museum resources of significant research value including those utilized for molecular studies in the framework of the voucher system. Alternatively, the essential roles of natural history museums in society as public voucher archives are evaluated. It is concluded that the shared acknowledgement of vouchers in society will make a substantial difference in our decision making and problem solving, particularly regarding the deposition of vouchers, their use, and their in perpetuity preservation.Item Spatial pattern and temporal dynamics of northern bobwhite abundance and agricultural landuse, and potential casual factors(Texas A&M University, 2006-04-12) Okay, Atiye ZeynepThere was a long-term decline in northern bobwhite (Colinus virginianus, NBW) abundance since the 1920s, based on the Christmas Bird Count (CBC) data, but with substantial spatial and temporal variations across its range. There were four recognizable periods in the spatial and temporal dynamics of NBW abundance between 1920 and 1990. Severe weather conditions and habitat loss due to land use change appeared to be the most important factors influencing the long-term trends and spatial patterns in NBW abundance. A spatial database of agricultural land use was developed based on the Census of Agriculture to evaluate the spatial patterns of land use variables over NBW range from 1920 to 1997. The results showed dramatic changes in land use over the period and the influence of socio-economic events, natural disasters and federal agricultural policies on the dynamics of land use pattern, and potential implications to NBW abundance were identified. Replacement of less intensive agriculture with intensive monoculture production and mechanization coincided with World War I, and the post-war collapse in agriculture and the economy, partly associated with the Dust Bowl, enhanced this trend. Monoculture production and clean farming practices were further intensified during World War II and the years following the war. These land use changes had overall negative effects on NBW habitat. Analysis of the changes in spatial pattern of NBW abundance in the Great Plains region during the severe drought of the 1950s showed a significant decline in NBW abundance during the drought and a contraction of the NBW range at its western edge. The post-drought recovery exhibited spatial patterns significantly different from the predrought ones. These findings suggested that severe drought caused short-term changes in regional distribution of NBW and range contraction, as well as long-lasting, largescale changes in spatial distribution of NBW abundance. This study provides scientific basis for landscape planning and management. Evaluating the spatial pattern and temporal dynamics of certain wildlife species at large scales over long-term periods, and identifying potential causal factors are key strategies for implementing innovative and sustainable approaches to planning and policy. Such strategies will have a significant impact on future landscape and wildlife species.Item Systematics of the Drosophila virilis species group as assessed by two-dimensional electrophoresis(Texas Tech University, 1985-08) Spicer, Gregory S.A primary problem that often faces an evolutionary biologist trying to determine a phylogeny is finding enough characters to build the tree. Increasingly, molecular biology is solving this problem, but many shortcomings and limitations still exist with the techniques currently in use. For example, allozymic studies are very useful, but they constitute a time consuming task that often does not produce enough characters to fully resolve the branching diagram. Immunological and DNA hybridization techniques can often discern phenetic relationships between taxa, but they cannot be used in a phylogenetic analyses, because they are based on overall similarity (Entingh, 1970). Approaches such as DNA, RNA, and protein sequencing are very powerful techniques for phylogenetic reconstruction, but they are extremely time consuming and effectively cost prohibitive, particularly when one is working on lower taxonomic levels. The development of the mitochondrial DNA technology may solve many of these problems, although recent studies seem to indidcate that it may not be more effective than the current electrophoretic studies at producing phylogenetic trees (Kessler and Avise, 1984). However, this research is still in its infancy, so it is difficult to assess its final impact.