Biology Commons^™

Elucidation Of The Role Of Auxin-Input Pathways In Auxin Homeostasis., Gretchen Spiess

Dissertations

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the most abundant auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. Sequestration of IAA occurs in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or via a two-carbon elongation forming indole-3-butyric acid (IBA). These forms of auxin have decreased activity and are located in multiple organelles. Using a combination of molecular and genetic tools, I examined how these storage forms are working together to contribute to overall IAA levels and IAA response in both the model …

Leaf Mechanical Strength Corresponds To Tissue Water Relations In Twelve Species Of California Ferns, Breahna M. Gillespie, Stephen D. Davis, Jarmila Pittermann

Biology

The dominant vegetation types in southern California’s coastal foothills are chaparral and costal sage scrub. Chaparral shrubs have mechanically strong evergreen leaves whereas coastal sage scrubs bear mechanical weak, facultative deciduous leaves. What about the ferns that live in the understory of these vegetation types, especially considering their adaptations to a summer dry, Mediterranean-type climate? We tested the hypothesis that some fern leaves are stronger than others and mechanically strong leaves are associated with greater dehydration tolerance. Twelve fern species were examined. Tissue water relations were assessed via pressure volume curves using Scholander-Hammel pressure chambers. We estimated osmotic potential at …

Response Of Beta Diversity To Pulses Of Ordovician-Silurian Mass Extinction, Simon A.F. Darroch, Peter J. Wagner

School of Biological Sciences: Faculty Publications

Ecologists are increasingly using the fossil record of mass extinction to build predictive models for the ongoing biodiversity crisis. During mass extinctions, major depletions in global (i.e., gamma) diversity may reflect decrease in alpha diversity (i.e., local assemblages support fewer taxa), and/or decrease in beta diversity (such that similar pools of taxa are common to a greater number of local areas). Contrasting the effects of extinction on alpha and beta diversity is therefore central to understanding how global richness becomes depleted over these critical events. Here we investigate the spatial effects of mass extinction by examining changes in alpha, beta, …

Anthocyanin Characterization, Total Phenolic Quantification And Antioxidant Features Of Some Chilean Edible Berry Extracts, Anghel Brito, Carlos Areche, Beatriz Sepúlveda, Edward J. Kennelly, Mario J. Simirgiotis

Publications and Research

The anthocyanin composition and HPLC fingerprints of six small berries endemic of the VIII region of Chile were investigated using high resolution mass analysis for the first time (HR-ToF-ESI-MS). The antioxidant features of the six endemic species were compared, including a variety of blueberries which is one of the most commercially significant berry crops in Chile. The anthocyanin fingerprints obtained for the fruits were compared and correlated with the antioxidant features measured by the bleaching of the DPPH radical, the ferric reducing antioxidant power (FRAP), the superoxide anion scavenging activity assay (SA), and total content of phenolics, flavonoids and anthocyanins …

Relationship Between Dehydration Tolerance Of California Ferns And The Mechanical Strength Of Their Stipes, Helen I. Holmlund, Stephen D. Davis

Biology

In recent years, experts in plant physiology have begun to explore the functional traits of ferns, especially in regards to their tissue-water relations. However, to our knowledge, no scientist had yet examined the relationship between fern biomechanics and physiology. We examined the mechanical properties of fern stipes (stems) and attempted to relate those properties to ecological and physiological traits. Based on our knowledge of fern anatomy, we hypothesized that stipe mechanical strength would not correlate with water-stress resistance as it does in seed-bearing plants.

We assessed mechanical strength using Modulus of Elasticity (MOE) and tissue-water relations using pressure-volume curves. Water-stress …

Water Use And Water Tolerance In The Riparian Species American Sycamore (Plantanus Occidentalis L.) And How Its Physiology Compares To The Coexisting Black Willow (Salix Nigra Marshall), Eric Duncan

Dissertations, Theses and Capstone Projects (Full IR Collection)

This study set out to compare aspects of water use and tolerance to inundation and drought of two riparian tree species, Platanus occidentalis L. and Salix nigra Marshall. The main goal of the study was to better understand the two species and assess the suitability of P. occidentalis for use in riparian restoration. To accomplish this, potted individuals were subjected to treatments of drought, inundation, or control, under greenhouse conditions, and separately, in order to estimate water use in trees, season-long diurnal measurements of sap flux (using Granier type thermal dissipation probes) were determined in situ for trees growing in …

Phenotypic Analysis Of The Regulatory Role Of The Leucine-Responsive Regulatory Protein (Lrppa) In Pseudomonas Aeruginosa, Stephanie D. Larson

Master of Science in Integrative Biology Theses

Nutrient acquisition is critical to survival and infection by the opportunistic bacterium Pseudomonas aeruginosa. This pathogen expresses a number of virulence factors that are a part of the starvation response and are important in host-pathogen interactions. Additionally, P. aeruginosa is resistant to a large number of antibiotics and has become difficult to treat once it has colonized a tissue. New pharmaceutical treatments are sought while the metabolism of this organism must be fully understood to select new targets for therapy. The leucine- responsive regulatory protein (Lrp) could be a promising target for treatment. The ortholog in Escherichia coli is …

Human Common Fragile Site Fra16d Flexibility Peak Is Not A Strong Mitotic: Recombination Hotspot In Saccharomyces Cerevisiae, Katina G. Kapellas

Master's Theses and Doctoral Dissertations

Common fragile sites (CFS) are areas of the genome that tend to break when DNA replication is stressed or partially inhibited. Breaks at CFS can lead to gene deletions and amplifications that can result in the genesis of cancer cells. There is controversy about the mechanism of CFS instability. This study examines whether an AT-rich sequence called a flexibility peak from FRA16D can induce mitotic recombination events that lead to loss of heterozygosity (LOH) on chromosome III in Saccharomyces cerevisiae. Two experimental yeast strains containing flexibility peak Flex1-(AT)15 from FRA16D were compared to a control strain lacking the Flex1 …

Metagenomic Identification Of A Novel Salt Tolerance Gene From The Human Gut Microbiome Which Encodes A Membrane Protein With Homology To A Brp/Blh-Family Beta-Carotene 15,15'-Monooxygenase, Eamonn P. Culligan, Roy D. Sleator, Julian R. Marchesi, Colin Hill

Department of Biological Sciences Publications

The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.

Metagenomic Identification Of A Novel Salt Tolerance Gene From The Human Gut Microbiome Which Encodes A Membrane Protein With Homology To A Brp/Blh-Family Beta-Carotene 15,15'-Monooxygenase, Roy D. Sleator, Et. Al.

Department of Biological Sciences Publications

The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.

Collective Behaviour Without Collective Order In Wild Swarms Of Midges, Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Stefania Melillo, Leonardo Parisi, Oliver Pohl, Bruno Rossaro, Edward Shen, Edmondo Silvestri, Massimilano Viale

Publications and Research

Collective behaviour is a widespread phenomenon in biology, cutting through a huge span of scales, from cell colonies up to bird flocks and fish schools. The most prominent trait of collective behaviour is the emergence of global order: individuals synchronize their states, giving the stunning impression that the group behaves as one. In many biological systems, though, it is unclear whether global order is present. A paradigmatic case is that of insect swarms, whose erratic movements seem to suggest that group formation is a mere epiphenomenon of the independent interaction of each individual with an external landmark. In these cases, …

The Orientation Of The Pyrococcus Furiosus Transcription Factor Tfb2 In The Transcription Initiation Complex, Arati Bhattarai

Dissertations and Theses

The hyperthermophile archaeon, Pyrococcus furiosus encodes two eukaryotic TFIIB family proteins, TFB1 and TFB2. TFB1 is very similar to TFIIB in terms of sequence homology and function, whereas TFB2 is unusual as it is missing highly conserved sequences in its N-terminal domain that are present in TFIIB and TFB1. Despite this, TFB2 is effective in transcription process, albeit with lower efficiency compared to TFB1. Other archaea also contain multiple TFBs, but unlike Pyrococcus furiosus TFB2, these multiple TFBs have higher sequence homology to each other and have similar transcription efficiencies. Photochemical cross-linking experiments have shown that the B-reader of TFB …

Major Alteration In Coxsackievirus B3 Genomic Rna Structure Distinguishes A Virulent Strain From An A Virulent Strain, Jerome Prusa, Johanna Missak, Jeff Kittrell, John J. Evans, William Tapprich

Biology Faculty Publications

Coxsackievirus B3 (CV-B3) is a cardiovirulent enterovirus that utilizes a 5′ untranslated region (5′UTR) to complete critical viral processes. Here, we directly compared the structure of a 5′UTR from a virulent strain with that of a naturally occurring avirulent strain. Using chemical probing analysis, we identified a structural difference between the two 5′UTRs in the highly substituted stem-loop II region (SLII). For the remainder of the 5′UTR, we observed conserved structure. Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation. To investigate independent folding and function, two chimeric CV-B3 strains were created by exchanging …

Oroya Fever And Verruga Peruana: Bartonelloses Unique To South America, Michael F. Minnick, Burt E. Anderson, Amorce Lima, James M. Battisti, Phillip G. Lawyer, Richard J. Birtles

Biological Sciences Faculty Publications

Bartonella bacilliformis is the bacterial agent of Carrión's disease and is presumed to be transmitted between humans by phlebotomine sand flies. Carrión's disease is endemic to high-altitude valleys of the South American Andes, and the first reported outbreak (1871) resulted in over 4,000 casualties. Since then, numerous outbreaks have been documented in endemic regions, and over the last two decades, outbreaks have occurred at atypical elevations, strongly suggesting that the area of endemicity is expanding. Approximately 1.7 million South Americans are estimated to be at risk in an area covering roughly 145,000 km2 of Ecuador, Colombia, and Peru. Although disease …

Transcriptome Analysis Of A Petal Anthocyanin Polymorphism In The Arctic Mustard, Parrya Nudicaulis, Timothy Butler, Cynthia Dick, Matthew L. Carlson, Justen B. Whittall

Biology

Angiosperms are renown for their diversity of flower colors. Often considered adaptations to pollinators, the most common underlying pigments, anthocyanins, are also involved in plants’ stress response. Although the anthocyanin biosynthetic pathway is well characterized across many angiosperms and is composed of a few candidate genes, the consequences of blocking this pathway and producing white flowers has not been investigated at the transcriptome scale. We take a transcriptome-wide approach to compare expression differences between purple and white petal buds in the arctic mustard, Parrya nudicaulis, to determine which genes’ expression are consistently correlated with flower color. Using mRNASeq and de …

The Wonderfully Made Design Of The Skin And Its Microbiome, Alan L. Gillen

Faculty Publications and Presentations

Many microbes live in a mutualistic relationship with the human body, make up the human microbiome, and play a role in our health by modulating the immune system. Man is “covered” inside and outside his body with millions of microbes to maintain normal bodily functions and sustain life in our changing world. The skin is the largest organ in the human body and is colonized by millions of microbes. This external colonization of the integumentary system is termed our skin microbiome. Man cannot see it (except with a microscope), but we need it for normal functioning, certainly in a pathogenic …

Preparation And Biological Properties Of Ring-Substituted Naphthalene-1-Carboxanilides, Eoghan Nevin, Rodeney Govender, Jim O'Mahony, Aidan Coffey, Et. Al.

Department of Biological Sciences Publications

In this study, a series of twenty-two ring-substituted naphthalene-1-carboxanilides were prepared and characterized. Primary in vitro screening of the synthesized carboxanilides was performed against Mycobacterium avium subsp. paratuberculosis. N-(2-Methoxyphenyl)naphthalene-1-carboxamide, N-(3-methoxy-phenyl)naphthalene-1-carboxamide, N-(3-methylphenyl)naphthalene-1-carboxamide, N-(4-methylphenyl)naphthalene-1-carboxamide and N-(3-fluorophenyl)naphthalene-1-carboxamide showed against M. avium subsp. paratuberculosis two-fold higher activity than rifampicin and three-fold higher activity than ciprofloxacin. The most effective antimycobacterial compounds demonstrated insignificant toxicity against the human monocytic leukemia THP-1 cell line. The testing of biological activity of the compounds was completed with the study of photosynthetic electron transport (PET) inhibition in isolated spinach (Spinacia oleracea L.) chloroplasts. The PET-inhibiting activity expressed by IC50 value …

Identification Of Heat Responsive Genes In Brassica Napus Siliques At The Seed-Filling Stage Through Transcriptional Profiling, Xuemin Wang, Erru Yu, Chuchuan Fan, Qingyong Yang, Xiaodong Li, Bingxi Wan, Yanni Dong, Yongming Zhou

Biology Department Faculty Works

High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, global transcription profiles of 20 d-old siliques of B. napus were analyzed after heat stress using a Brassica 95k EST microarray. The up-regulated genes included many HSF/HSP transcripts and other heat-related marker genes, such as ROF2, DREB2a, MBF1c and Hsa32, reflecting the conservation of key heat resistance factors among plants. Other up-regulated genes were preferentially expressed in heat-stressed silique walls or seeds, including some transcription factors and …

Germination Season And Watering Regime, But Not Seed Morph, Affect Life History Traits In A Cold Desert Diaspore-Heteromorphic Annual, Juan J. Lu, Dun Y. Tan, Jerry M. Baskin, Carol C. Baskin

Biology Faculty Publications

Seed morph, abiotic conditions and time of germination can affect plant fitness, but few studies have tested their combined effects on plasticity of plant life history traits. Thus, we tested the hypothesis that seed morph, germination season and watering regime influence phenotypic expression of post-germination life history traits in the diaspore-heteromorphic cold desert winter annual/spring ephemeral Diptychocarpus strictus. The two seed morphs were sown in watered and non-watered plots in late summer, and plants derived from them were watered or not-watered throughout the study. Seed morph did not affect phenology, growth and morphology, survival, dry mass accumulation and allocation or …

Sox11 Is Required To Maintain Proper Levels Of Hedgehog Signaling During Vertebrate Ocular Morphogenesis, Lakshmi Pillai-Kastoori, Wen Wen, Stephen G. Wilson, Erin Strachan, Adriana Lo-Castro, Marco Fichera, Sebastiano A. Musumeci, Ordan J. Lehmann, Ann C. Morris

Biology Faculty Publications

Ocular coloboma is a sight-threatening malformation caused by failure of the choroid fissure to close during morphogenesis of the eye, and is frequently associated with additional anomalies, including microphthalmia and cataracts. Although Hedgehog signaling is known to play a critical role in choroid fissure closure, genetic regulation of this pathway remains poorly understood. Here, we show that the transcription factor Sox11 is required to maintain specific levels of Hedgehog signaling during ocular development. Sox11-deficient zebrafish embryos displayed delayed and abnormal lens formation, coloboma, and a specific reduction in rod photoreceptors, all of which could be rescued by treatment with the …

Development Of An Efficient Human Hepatocyte Culture Platform For Assessing Novel Therapeutic Efficacy Against Plasmodium Liver Parasites, Steven Patrick Maher

USF Tampa Graduate Theses and Dissertations

Malaria is a critical and global public health problem, affecting over 200 million people every year, resulting in over 500,000 deaths. A vaccine is not currently available and only one drug, primaquine, is effective against the dormant stages of Plasmodium vivax. Preclinical assessment of novel therapeutic drugs and vaccines is hampered by the lack of an in vitro liver model for P. falciparum and P. vivax. To provide a stable human hepatocyte-based culture platform for parasite development, we engineered a microfluidic bilayer device capable of both simple and complex culture methods, including perfusion and co-culture, to better understand the requirements …

A Multi-Scale Approach To Study Predator-Prey Interactions And Habitat Use Of Pinfish, Lagodon Rhomboids, Dinorah Helena Chacin

USF Tampa Graduate Theses and Dissertations

Biological processes like species interactions and patterns such as abundance and distribution observed in nature can vary depending on the scale at which the subject of interest is evaluated. Knowing that there is no single natural scale at which systems should be studied, in this thesis, I conducted a series of basic and applied ecological approaches in order to examine the phenomena that can occur at different scales of space, time, and ecological organization.

Species abundances can vary over large spatial and temporal scales. By studying the habitat use of an abundant species, which uses a wide range of habitats, …

Feeding Performance Of King Mackerel, Scomberomorus Cavalla, Amber Rose Ferguson

USF Tampa Graduate Theses and Dissertations

Although bite force is a commonly used metric of feeding performance, other factors such as bite pressure and strike speed are also likely to affect prey capture. Therefore, this study investigated static bite force, dynamic speeds, and predator and prey forces resulting from ram strikes, as well as bite pressure of the king mackerel, Scomberomorus cavalla, in order to examine their relative contributions to overall feeding performance. Theoretical posterior bite force ranged from 14.0-318.7 N. Ram speed, recorded with a rod and reel incorporated with a line counter and video camera, ranged from 3.3-15.8 BL/s. Impact forces on the …

Oswald Biological Sciences First Place: Development Of Three-Dimensional Lung Multicellular Spheroids In Air And Liquid Interface Culture For The Evaluation Of Anti-Cancer Therapeutics, Alexandra Tsoras

Kaleidoscope

The implementation of in vitro results to in vivo applications has limitations due to conventional two-dimensional (2D) in vitro conditions lacking the ability to create a physiologically representative model. This study investigated a three-dimensional (3D) cell culture technique to model lung tumors in vitro. A 3D lung cancer model was created by applying collagen (a semi-non-adhesive material) to a transwell, which allowed for nutrient transfer through the collagen. Two lung cancer cells lines (H358, a bronchioalveolar carcinoma and A549, a lung adenocarcinoma) were seeded on top of the collagen. The non-adhesive collagen allowed the cells to preferentially attach to one …

Oswald Biological Sciences Second Place: Rna Degradation Is Elevated With Age-, But Not Disuse-Associated Skeletal Muscle Atrophy, Aman Shah

Kaleidoscope

Aging and inactivity are both associated with decreased muscle size and protein content. The possible role of RNA degradation in the loss of protein has not yet been investigated. Therefore, we hypothesized that RNA degradation was elevated with muscle atrophy in aging and disuse. Brown Norway/Fisher344 male rats at 6 and 32 months were hindlimb suspended (HS) for 14 days to induce muscle atrophy or remained weight bearing (WB). Cytosolic extracts from gastrocnemius muscles were prepared for Western analysis of DCP-2 protein (marker of p-bodies) and RNA degradation assay. In vitro total RNA decay assay was performed using 30ug of …

Investigation Of Spatial Isotope Ratios In Soil And The Effects Of Fertilizer On Plant Isotope Ratios, Jamie Kim, H. Thomas Goodwin Ph.D.

Posters, Presentations, and Papers

A previous Honors study analyzed diet of thirteen-lined ground squirrels at the Andrews University Airpark by studying δ13C and δ15N isotope values of their fecal pellets (Chacko, 2013). Fecal samples collected within 25m of a cornfield had elevated isotope values.

High δ13C values indicate greater consumption of C4 plants, such as corn (Ehleringer et al., 1986); high δ15N values indicate increased consumption of animal matter (DeNiro and Epstein, 1981 ). However, the spatial pattern may be due to variation in the soil, reflecting long-term patterns in the vegetation.

Soil samples were taken throughout the airpark and analyzed for δ13C and …

Aquastella Gen. Nov.: A New Genus Of Saprolegniaceous Oomycete Rotifer Parasites Related To Aphanomyces, With Unique Sporangial Outgrowths, Daniel P. Molloy, Sally L. Glockling, Clifford A. Siegfried, Gordon W. Beakes, Timothy Y. James, Sergey E. Mastitsky, Elizabeth S. Wurdak, Laure Giamberini, Michael J. Gaylo, Michael J. Nemeth

Biology Faculty Publications

The oomycete genus Aquastella is described to accommodate two new species of parasites of rotifers observed in Brooktrout Lake, New York State, USA. Three rotifer species – Keratella taurocephala,Polyarthra vulgaris, and Ploesoma truncatum – were infected, and this is the first report of oomycete infection in these species. Aquastella attenuata was specific to K. taurocephala and Aquastella aciculariswas specific to P. vulgaris and P. truncatum. The occurrence of infections correlated with peak host population densities and rotifers were infected in the upper layers of the water column. Sequencing of 18S rRNA and phylogenetic analysis of …

[Accepted Article Manuscript Version (Postprint)] Auxin Input Pathway Disruptions Are Mitigated By Changes In Auxin Biosynthetic Gene Expression In Arabidopsis, Gretchen Spiess, Amanda Hausman, Peng Yu, Jerry Cohen, Rebekah Rampey, Bethany Zolman

Biology Department Faculty Works

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the primary auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. IAA is sequestered in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or through a two-carbon elongation forming indole-3-butyric acid. These sequestered forms of IAA alter hormone activity. To gain a better understanding of how auxin homeostasis is maintained, we have generated Arabidopsis (Arabidopsis thaliana) mutants that combine disruptions in the pathways, converting IAA conjugates and indole-3-butyric acid to free IAA. These mutants show phenotypes indicative …

Cytosolic Phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenases Affect Arabidopsis Cellular Metabolism And Promote Seed Oil Accumulation, Xuemin Wang, Liang Guo, Fangfang Ma, Fang Wei, Brian Fanella, Doug Allen

Biology Department Faculty Works

The cytosolic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPC) catalyzes a key reaction in glycolysis, but its contribution to plant metabolism and growth are not well defined. Here, we show that two cytosolic GAPCs play important roles in cellular metabolism and seed oil accumulation. Knockout or overexpression of GAPCs caused significant changes in the level of intermediates in the glycolytic pathway and the ratios of ATP/ADP and NAD(P)H/NAD(P). Two double knockout seeds had ∼3% of dry weight decrease in oil content compared with that of the wild type. In transgenic seeds under the constitutive 35S promoter, oil content was increased up to 42% …

Granivory Of Invasive, Naturalized, And Native Plants In Communities Differentially Susceptible To Invasion, B. M. Connolly, Dean Pearson, R. N. Mack

Biological Sciences Faculty Publications

Seed predation is an important biotic filter that can influence abundance and spatial distributions of native species through differential effects on recruitment. This filter may also influence the relative abundance of nonnative plants within habitats and the communities’ susceptibility to invasion via differences in granivore identity, abundance, and food preference. We evaluated the effect of postdispersal seed predators on the establishment of invasive, naturalized, and native species within and between adjacent forest and steppe communities of eastern Washington, USA that differ in severity of plant invasion. Seed removal from trays placed within guild-specific exclosures revealed that small mammals were the …