Biology Commons^™

Mutation Identification And Functional Analysis Of Mutant Dax-1 Proteins Found In Thai Patients With X-Linked Adrenal Hypoplasia Congenita, Chanisara Suthiworachai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mutations in the DAX-1 gene result in X-linked adrenal hypoplasia congenita (X-linked AHC), a rare congenital disorder of adrenal insufficiency with defects in adrenal gland development and steroid biosynthesis. Male patients usually develop severe adrenal insufficiency in early infancy or childhood. In some cases, hypogonadotropic hypogonadonism (HH) is presented in puberty. DAX-1 gene product, DAX-1 protein, acts as a transcriptional repressor of genes in the steroidogenic pathway by interacting with, and repressing the steroidogenic factor 1 (SF-1) protein. In contrast, the SF-1 protein transactivates the steroidogenic acute regulatory (StAR) protein that functions in the steroid biosynthetic pathway. The aim of …

Effects Of Habitat Enhancement On Bird Diversity In Kaeng Khoi District, Saraburi Province, Dijan Sunar Rukmi

Chulalongkorn University Theses and Dissertations (Chula ETD)

Various techniques of habitat enhancement have been used to increase the habitat quality, consequently enriching biodiversity and maintaining ecosystem services. This study aims to assess the effects of habitat enhancement on bird diversity, guild composition and bird usage pattern by conducting bird censuses and observations as well as arthropod samplings in the landscape-scale (LS) experiment plots and in the teak reforestation (TR) enhanced with sunflower and sunn hemp species over dry and wet seasons of 2015-2016. Sunflower treatment attracted more bird species (LS: 28, TR: 19) than sunn hemp treatment (LS: 25, TR: 15), but bird occurrence was varied based …

Taxonomy And Systematics Of Earthworm Genus Pontodrilus Perrier, 1874 In Thailand, Teerapong Seesamut

Chulalongkorn University Theses and Dissertations (Chula ETD)

A taxonomic study of the littoral earthworm genus Pontodrilus Perrier, 1874 was critically conducted based on material collected from marine sandy coasts along the east and west sides of the Thai-Malay Peninsula (Thailand and Malaysia) and selected localities in Japan. Comparative material from other parts of Southeast Asia, including Myanmar, Vietnam, Malaysia, Singapore and Indonesia, were also collected. Morphological examination identified almost all of the specimens as Pontodrilus litoralis, but as two morphotypes with some character differences in the diverticulum between them. A combined morphological and molecular phylogenetic analyses supported one of these morphotypes as a new species, P. longissimus. …

Characterization Of Two Cyclic Di-Gmp Phosphodiesterases Hypothesized To Regulate Virulence In Streptomyces Scabies, Madison Flasco

Undergraduate Honors Thesis Projects

Common scab is a devastating disease that affects the marketability of potatoes. The disease results in raised and pitted lesions seen on the surface of the potato and is caused by the soil pathogen, Streptomyces scabies. The S. scabies genome has two cyclic-di-GMP phosphodiesterases, RmdA and RmdB, both regulators of morphology and development. These proteins break down the ubiquitous second messenger molecule cyclic di-GMP, a molecule in charge of cell cycle progression and virulence. Both proteins contain diguanylate cyclase domains and phosphodiesterase domains, GGDEF and EAL, respectively, while RmdA contains an additional PAS_4 domain. Despite similar domain configurations, the two …

Effects Of Nonnative Rainbow Trout On Two Species Of Endemic Mexican Amphibians, A. B. Estrella Zamora, Geoffrey R. Smith, J. A. Lemos-Espinal, G. A. Woolrich-Pina, R. Montoya Ayala

Faculty Publications

No abstract provided.

Evaluation And Adaptation Of Live-Cell Interferometry For Applications In Basic, Translational, And Clinical Research, Kevin A. Leslie

Theses and Dissertations

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug …

The Ability Of Phyllospadix Spp., A Pair Of Intertidal Foundation Species, To Maintain Biodiversity And Ameliorate Co2 Stress In Rocky Shore Tidepools, Tayler M. Tharaldson

Cal Poly Humboldt theses and projects

Ocean acidification (OA) is often demonstrated to have negative effects on marine organisms, but less is known about whether marine organisms can mediate OA effects. I examined relationships between surfgrass (Phyllospadix spp.), a foundation species and tidepool biodiversity, and its ability to mediate fluctuations in pH and dissolved oxygen (OA; DO) which are stressors in tidepools. I surveyed tidepools in northern California, where I quantified biodiversity, pH, and DO, and related those variables to surfgrass abundance. Laboratory and field experiments manipulating CO₂ and surfgrass presence were done to examine surfgrass effects on day/night pH and DO fluctuations …

The Genome Of Austrofundulus Limnaeus Offers Insights Into Extreme Vertebrate Stress Tolerance And Embryonic Development, Josiah Tad Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven Cody Woll, Jake Roush, Wesley C. Warren, Anne Brunet, Jason E. Podrabsky

Center for Life in Extreme Environments Publications

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy …

Evolution Belief Trends, Jamie Jensen

ScholarsArchive Data

This is the essay code frequencies along with the raw survey data for both Cohort 1 and Cohort 2 for the following paper:

Bradshaw, WS, Phillips, AJ, Bybee, SM, Gill, RA, Peck, SL, Jensen, JL. 2018. A longitudinal study of attitudes toward evolution among Mormon undergraduates. PLOSONE.

Noninvasive Collection Of Saliva In Panthera Leo : Creation And Validation Of A Novel Technique For Health Assessment In Captive African Lions (Panthera Leo), Elizabeth Sgambelluri

Antioch University Dissertations & Theses

Very little research exists concerning direct correlations between alterations in stress stimuli and direct effects on carnivore physiology. Many studies have researched and documented what factors correlate to increased stress levels in predator species. Lacking, however, are studies observing the specific physiologic influences of increased glucocorticoid concentrations in those individuals. Furthermore, methods for monitoring and assessing health or immune function in many carnivore species often involve invasive techniques, such as physical restraint, blood sampling, and chemical immobilization. This study aimed to create, evaluate, and describe a new device for noninvasive collection of saliva for health assessment. The device itself was …

Influences Of Forest Edges And Human Activities On The Dry Season Ranging Patterns Of Chimpanzees (Pan Troglodytes Schweinfurthii) In Nyungwe National Park, Rwanda, Enathe Hasabwamariya

Antioch University Dissertations & Theses

Great apes, our closest biological relatives are threatened globally by the increasing anthropogenic pressures on their habitat. The major threats to the eastern chimpanzees (Pan troglodytes schweinfurthii) are hunting for bush meat and illegal trade in chimpanzee infants, habitat loss or fragmentation and disease transmission (IUCN, 2010). Nyungwe National Park (NNP), Rwanda has a population of chimpanzees that face several threats, including hunting for bushmeat, habitat degradation from forest fires and human-wildlife conflicts, and much of these impacts are concentrated at forest edges. The main objectives of this research were to assess the use of forest edges by chimpanzees along …

Molecular Characterization Of The Mummichog (Fundulus Heteroclitus) Ovarian Steroidogenic Pathway And Implications For Exogenous Estrogen Effects During Follicular Development, Thiviya Kanagasabesan

Theses and Dissertations (Comprehensive)

This study investigated ovarian development in Fundulus heteroclitus (mummichog), through molecular characterization of key mediators in the ovarian steroidogenic pathway; these included ovarian StAR (steroidogenic acute regulatory protein), cytochrome P450 enzymes, estrogen receptors (ERα, ERβ1 and ERβ2), and gonadotropin receptors (FSHr and LHr); additionally, hepatic vitellogenin (VTG1) and ERs, and brain P450 aromatase (P450arom; CYP19b) were studied. Fish were staged into cortical alveolus, vitellogenic, early mature, late mature, and ovulating stages of maturation; blood (plasma), ovary (tissue and isolated ovarian follicles per stage), liver, and brains were collected. Testosterone (T), 17β-estradiol (E₂) and maturation inducing steroid (MIS), measured …

Evidence For Extra-Gastric Expression Of The Proton Pump H+/K+ -Atpase In The Gills And Kidney Of The Teleost Oreochromis Niloticus, Ebtesam Barnawi

Theses and Dissertations (Comprehensive)

It is well known that stomach acid secretion by oxynticopeptic cells of the gastric mucosa is accomplished by the H⁺/ K⁺-ATPase (HKA), which is comprised of the HKα1 (gene: atp4a) and HKβ (gene: atp4b) subunits. However, the role of the HKA in extra-gastric organs such as the gill and kidney is less clear especially in fishes. This pump may contribute to active ion and/or acid-base regulation either through direct ion transport or through secondary transport proteins against unfavorable concentration gradients via the energy derived from ATP hydrolysis. In the present work I have demonstrated …

Relationships Between Factors Influencing Biofilm Formation And Pathogen Retention In Complex Rhizosphere Microbial Communities, Aaron Coristine

Theses and Dissertations (Comprehensive)

Riparian wetlands are unique habitats facilitating all forms of life. The riverbanks of these environments provide ideal conditions for bacteria, plants, and higher organisms. Of particular interest to this research was the variation in microbial community structure at high, intermediate and poor water quality impacted areas. Assessing the capabilities of plants to retain microbial pathogens was identified. Root systems and corresponding soil are ideal locations for bacterial deposition, resulting in attachment at these areas. Biofilm production in these regions is important for long-term establishment, leading to persistence and potential naturalization. Opportunistic pathogens originating from mammalian fecal matter are introduced into …

Forensic Markers Of Lampricide Toxicity In Oncorhynchsus Mykiss, Chris White

Theses and Dissertations (Comprehensive)

The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been used for decades to control invasive sea lamprey (Petromyzon marinus) populations in the Great Lakes, normally with little harm to other fish populations. However, due to the nature of lampricide treatments and the chemical properties of TFM, adverse effects to non-target fishes and non-target mortality occasionally occur. However, investigations of non-target mortality can be complex, particularly if fish deaths are not noticed immediately, due to decomposition of the carcasses. The objectives of this thesis were to expose rainbow trout (Oncorhynchsus mykiss) to TFM in order to: (i) identify forensic markers …

Distribution And Stability Of The Lampricide 3-Trifluoromethyl-4-Nitrophenol (Tfm) In Non-Target Rainbow Trout (Oncorhynchus Mykiss) And White Sucker (Catostomus Commersonii), Darren Foubister

Theses and Dissertations (Comprehensive)

The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) is applied to tributaries of the Great Lakes to control invasive sea lampreys (Petromyzon marinus). Although TFM is selectively toxic to larval sea lampreys, non-target mortality can occur during lampricide treatments. It is important to know whether or not TFM played a role in the death of these fishes, and the most direct means to do this is using forensic science principles. The objectives of this study were to: (i) determine the acute toxicity of TFM to the non-target fishes, rainbow trout (Oncorhynchus mykiss) and white sucker (Catostomus commersonii), and how the lampricide is …

Charecterization Of The Innate Immune Response In The Rat Intervertebral Disc At The Tissue And Cellular Level, Matthew Guerreiro

Theses and Dissertations (Comprehensive)

Low back pain (LBP) affects up to 80% of the global population at some point during their life. The costs associated with LBP are estimated at $100 billion per year, putting significant strains on our healthcare system. As intervertebral disc (IVD) herniation is one of the major causes of LBP we decided to focus on herniation facilitated inflammatory responses, where damage caused by herniation triggers an innate immune response which likely results in pain, inflammation, and recruitment of specialized innate immune cells like macrophages to the affected area. Since the role of the inflammatory response is relatively uncharacterized in the …

Gill Structure & Function In Parasitic And Non-Parasitic Lampreys: The Effects Of Metamorphosis And Freshwater-Seawater Transfer, Julia Sunga

Theses and Dissertations (Comprehensive)

Lamprey (Petromyzontiformes) are a phylogenetically ancient group of jawless fishes that begin their lives as filter-feeding larvae (ammocoetes) before undergoing a complex metamorphosis into juvenile lamprey that involves major changes to their internal and external body plan. Some parasitic species, such as the sea lamprey (Petromyzon marinus), migrate to sea following metamorphosis, where they use their oral discs and rasping tongue to attach to and ingest vast quantities of blood from fishes. Thus, sea lamprey have to counter the simultaneous challenges of hyposmoregulation in sea water and the generation of large quantities of ammonia due to the …

An Assessment Of The Plant And Mycorrhizal Community At Steeves Lake Shoreline, Colomac Mine, Nwt, Rebekah Hamp, Dr. Kevin Stevens

Theses and Dissertations (Comprehensive)

This study focused on the environmental impacts of mining and potential techniques to mitigate them. The goals of this study were to (1) Quantify vegetation and fungal colonization at a remediated mine site in northern Canada, and to determine if there were effects from petroleum hydrocarbon contamination, (2) Determine the response of northern plants inoculated with mycorrhizal fungi to diesel contamination. Mycorrhizal colonization was observed in field collected roots and trends in colonization and vegetation cover suggested that these communities were no longer impacted by residual contamination. Mean hyphal colonization of Elymus trachycaulus roots collected over two years was 47.3±3.8% …

Near-Surface Permafrost Ground Ice Characteristics And Ecological And Physical Drivers Of Transient Layer Ice Content In Discontinuous Permafrost, Jason Paul

Theses and Dissertations (Comprehensive)

Accelerated climate warming in northern regions is causing permafrost degradation, leading to the reduction of the areal extent of permafrost. Permafrost is the foundation for many northern ecosystems and communities, so its thaw can have important ecological and societal consequences. Thaw of ice-rich permafrost can cause subsidence of the ground surface proportional to excess ice content. Terrain settlement can cause ponding or damage to infrastructure. Following a surface disturbance that removes much of the vegetation cover, a shift in the ground thermal regime can cause an increase in active layer thickness and rapid thaw of the top portion of permafrost. …

Detection Of “Xisco” Gene For Identification Of Streptococcus Pneumoniae Isolates, Francisco Salvà-Serra, Gwendolyn Connolly, Edward Moore, Lucia Gonzales-Siles

Articles

We describe a PCR-assay differentiating Streptococcus pneumoniae from closely-related species of the Mitis group of the genus Streptococcus and identification of pneumococcus clinical isolates, based on the “Xisco” gene discriminatory marker. The complete “Xisco” gene sequence was observed in all S. pneumoniae genomes analyzed and absent in all non-pneumococcus genomes.

A Physical Biology, The Electron Neutrino Mass, And The Role Of Quantum Mechanics In Nature, Maurice Goodman

Articles

In science we need to remove physics and earth science from the fundamental sciences and treat Biology as a fundamental natural (physical) science. Attempts to keep Biology autonomous because it is holistic, from the physical sciences, are just disguised anthropocentrism. Physical sciences have holistic features also. The autonomy of Biology is at odds with a holistic, integrated, science and is preventing progress in science. For example, every cell needs a 'global' communication system to keep order and stability with rapid information transfer across cellular scales. We have yet to figure out how this is achieved. Over the last 30 years, …

Morphological And Behavioral Traits Associated With Locomotion In Lizards, Chase T. Kinsey

College of Graduate Studies: Theses & Dissertations

Morphology, locomotion, and behavior are co-adapted to optimize performance and ultimately fitness. Successfully navigating a complex environment is dictated by an animal’s locomotor behavior, and for some behaviors, its locomotor performance. The locomotor performance of an organism is directly related to the form and function of the structures involved in locomotion such that movement is efficient – that is, minimal loss of energy. The first chapter of this thesis focuses on the effects of obstacle placement and forelimb position on facultative bipedalism. Placing an obstacle beyond a lizard’s acceleration threshold did not affect the frequency of bipedal posture. Furthermore, the …

Predictors Of Fish Assemblage Structure And Dynamics In Atlantic Coastal Plain Streams, Rebecca Scott

College of Graduate Studies: Theses & Dissertations

Effective management of freshwater fishes requires a mechanistic understanding of the drivers of assemblage composition; in other words, what determines who is where and when. Stream fish assemblages are potentially influenced by environmental factors that act on multiple spatiotemporal scales, but the relative influence of these drivers may vary between geophysically distinct regions. This study sought to determine the patterns and drivers of fish taxonomic and functional assemblage composition in the coastal plain, a region possessing unique hydrologies, faunas, and physiochemical conditions. I addressed this goal using two complementary chapters, both of which utilized environmental and biotic data collected from …

Comparison Of Three Benthic Macroinvertebrate Passive Sampling Devices For Non-Wadeable Streams, Kelsey A. Laymon

College of Graduate Studies: Theses & Dissertations

Rivers and streams provide essential ecosystem services to the degree that the monitoring and maintenance of these systems becomes imperative. Biomonitoring provides managers and policymakers with the tools to make informed decisions, and macroinvertebrates are often the object of biomonitoring because they are ubiquitous in most systems and are known to be good indicators of water quality. However, methods for sampling macroinvertebrates in non-wadeable streams (i.e., large rivers) have not been standardized across states and regions and an established method for macroinvertebrate biomonitoring in large rivers of Georgia is not currently available. My study compared macroinvertebrates collected with three types …

Biochemical And In Silico Evaluation Of Recombinant E. Coli Aminopeptidase And In Vitro Processed Human Interferon α-2b, Amina Arif, Kaleemuddin Mohammed, Muhammad Shahid Nadeem

Turkish Journal of Biology

Escherichia coli is an extensively used host for the production of recombinant proteins, making its N-terminal methionine aminopeptidase (MAP) an attractive candidate for studies on posttranslational protein processing. The present study describes the recombinant production and properties of MAP from the DH5α strain of E. coli. The soluble and active enzyme was produced in E. coli BL21 (DE3) RIL - codon plus cells under a T7 promoter system and purified by anion-exchange chromatography. It exhibited a molecular weight of 29,200.94 Da by MALDI-TOF analysis. The purified enzyme showed specific activity of 1.64 U/mg with methionylp-nitroanilide and 1.51 U/mg with synthetic …

Exploring Allosteric Communication In Multiple States Of The Bacterial Ribosome Using Residue Network Analysis, Ayşe Özge Kürkçüoğlu Levi̇tas

Turkish Journal of Biology

Antibiotic resistance is one of the most important problems of our era and hence the discovery of new effective therapeutics is urgent. At this point, studying the allosteric communication pathways in the bacterial ribosome and revealing allosteric sites/residues is critical for designing new inhibitors or repurposing readily approved drugs for this enormous machine. To shed light onto molecular details of the allosteric mechanisms, here we construct residue networks of the bacterial ribosomal complex at four different states of translation by using an effective description of the intermolecular interactions. Centrality analysis of these networks highlights the functional roles of structural components …

Crispr Genetic Editing: Paths For Christian Acceptance And Analysis Of In Vivo And In Vitro Efficiency, Mandeep Sandhu

Scripps Senior Theses

With advancements in CRISPR-cas9 broadening the potential paths for clinical usage of genetic editing, conversations about genetic editing have grown to outside simply scientific communities and into mainstream conversations. This study focuses specifically on Christian discourse of genetic editing and locates four major tensions for many Christians when they think about genetic editing: beginning of life, Creator-human relationship, imago Dei, and stewardship. With these major concerns in mind, I identify epigenetics, somatic cell genetic editing, and in vivo genetic editing research as important research paths to pursue as they can potentially produce techniques that more Christian individuals would feel comfortable …

The Mechanism Responsible For Mechanically Enhanced Cancer Cell Invasion, Alexander Nicholas Gasparski

Wayne State University Dissertations

Cell invasion is an important process utilized by cancer cells to progress through the metastatic cascade to form deadly secondary tumors. This process can be influenced by the wide array of biomechanical forces that cancer cells within and around a tumor face in their microenvironment. It is not completely clear how these forces, either alone or simultaneously combined with other forces, can impact the metastatic capacity of cancer cells. To address this, we have utilized an in vitro mechano-invasion assay to mimic a transient tugging force that exists within the tumor microenvironment caused by the remodeling of the extracellular matrix …

Comparative Toxicology Of Nio And Ni(Oh)₂ Nanoparticles, Melissa Hope Cambre

Masters Theses

“Understanding the potential toxicity of nanoparticles (NPs) is important to ensure that these new products do not impose harmful effects to human and environmental health. Paper I is a literature review in which we discuss characteristics of nanomaterials, with an emphasis on transition metal oxide nanoparticles that influence cytotoxicity. Identification of those properties may lead to the design of more efficient and safer nanosized products for various industrial purposes and provide guidance for assessment of human and environmental health risk. We then investigate biochemical and molecular mechanisms of cytotoxicity that include oxidative stress-induced cellular events and alteration of the pathways …