Biology Commons^™

Highly Conserved Molecular Pathways, Including Wnt Signaling, Promote Functional Recovery From Spinal Cord Injury In Lampreys, Paige E. Herman, Angelos Papatheodorou, Stephanie A. Bryant, Courtney K. M. Waterbury, Joseph R. Herdy, Anthony A. Arcese, Joseph D. Buxbaum, Jeramiah J. Smith, Jennifer R. Morgan, Ona Bloom

Biology Faculty Publications

In mammals, spinal cord injury (SCI) leads to dramatic losses in neurons and synaptic connections, and consequently function. Unlike mammals, lampreys are vertebrates that undergo spontaneous regeneration and achieve functional recovery after SCI. Therefore our goal was to determine the complete transcriptional responses that occur after SCI in lampreys and to identify deeply conserved pathways that promote regeneration. We performed RNA-Seq on lamprey spinal cord and brain throughout the course of functional recovery. We describe complex transcriptional responses in the injured spinal cord, and somewhat surprisingly, also in the brain. Transcriptional responses to SCI in lampreys included transcription factor networks …

Gene Turnover And Diversification Of The Α- And Β- Globin Gene Families In Sauropsid Vertebrates, Federico G. Hoffmann, Michael W. Vandewege, Jay F. Storz, Juan C. Opazo

School of Biological Sciences: Faculty Publications

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here,we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve …

Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa

Electronic Theses and Dissertations

Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were …

Treatment Of Hiv-Infected Individuals With The Histone Deacetylase Inhibitor Panobinostat Results In Increased Numbers Of Regulatory T Cells And Limits Ex Vivo Lipopolysaccharide-Induced Inflammatory Responses, Christel Rothe Brinkmann, Jesper Falkesgaard Højen, Thomas Aagaard Rasmussen, Anne Sofie Kjær, Rikke Olesen, Paul W. Denton, Lars Østergaard, Zhengyu Ouyang, Mathias Lichterfeld, Xu Yu, Ole Schmeltz Søgaard, Charles Dinarello, Martin Tolstrup

Biology Faculty Publications

Histone deacetylase inhibitors (HDACi) modulate the transcriptional activity of all cells, including innate and adaptive immune cells. Therefore, we aimed to evaluate immunological effects of treatment with the HDACi panobinostat in HIV-infected patients during a clinical phase IIa latency reversal trial. Using flow cytometry, we investigated changes in T cell activation (CD69, CD38, HLA-DR) and the expression of CD39 and CTLA4 on regulatory T cells (Tregs). Whole-blood stimulations were performed and cytokine responses measured using Luminex. Gene expression in purified peripheral blood mononuclear cells (PBMCs) was evaluated using an Affymetrix HTA 2.0 gene chip. We found that proportions of CD4+ …

Transcriptional Characterization Of Osteogenic And Adipogenic Differentiation Of Human Bone Marrow Derived Mesenchymal Stem Cells In 2d And 3d Peptide Hydrogel Culture System, R. M. Imtiaz Karim Rony

Browse all Theses and Dissertations

Mesenchymal stem cells (MSCs) are adult multipotent stem cell that can differentiate into mesodermal lineages such osteoblast, adipocytes, and chondrocytes, or can be transdifferentiated into clinically relevant lineages such as cardiac or neural cells using in vitro reprogramming techniques. In addition to the multilineage differentiation potential, MSCs from most tissue origins such bone marrow derived mesenchymal stem cells (BM-MSCs) or adipose derived mesenchymal stem cells (AD-MSCs) have immune modulatory functions which indicate their promise in clinical applications for cell-based therapy, tissue engineering, and regenerative medicine. In recent years, three-dimensional (3D) cell culture systems, which utilize 3D scaffolds or hydrogels to …

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 …

Assessment Of Iranian Endemic Artemisia Khorassanica: Karyological, Genome Size,And Gene Expressions Involved In Artemisinin Production, Farokh Hamidi, Ghasem Karimzadeh, Sajad Rashidi Monfared, Maryam Salehi

Turkish Journal of Biology

The species of Artemisia, one of the largest genera of the family Asteraceae, are frequently utilized for the treatment of diseases such as malaria, hepatitis, cancer, inflammation, and infections by fungi, bacteria, and viruses. Karyological studies were performed on 18 Artemisia khorassanica populations: eleven were diploid (2n = 18) and seven were tetraploid (2n = 36). The mean chromosome lengths were 3.61 and 3.84 ?m for diploids and tetraploids, respectively. Two chromosome types ("m", "sm") formed karyotype formulas "18m" for diploids and "36m" and "34m + 2sm" for tetraploids. The mean 2C DNA contents were 5.91 and 11.53 pg in …

Investigating The Role Of Small Noncoding Rnas In Vertebrate Anoxia Tolerance, Claire Louise Riggs

Dissertations and Theses

Very few vertebrates survive extended periods of time without oxygen. Entry into metabolic depression is central to surviving anoxia, which is supported by overall suppression of protein synthesis, yet requires increased expression of specific proteins. Studying the rapid and complex regulation of gene expression associated with survival of anoxia may uncover new mechanisms of cellular biology and transform our understanding of cells, as well as inform prevention and treatment of heart attack and stroke in humans. Small non-coding RNAs (sncRNAs) have emerged as regulators of gene expression that can be rapidly employed, can target individual genes or suites of genes, …

Mechanism Of Gene Regulation By Coding Polya Tracks, Laura Lea Arthur

Arts & Sciences Graduate Student Theses and Dissertations

Regulation of gene expression is essential for cellular development and survival. The great variety and complexity of regulatory mechanisms underscores this fact. Messenger RNA stability and translational efficiency are often key determinants of gene expression. mRNA surveillance pathways, discovered for their role in degradation of aberrant mRNA, are now known to be instrumental in the regulation of physiologically correct mRNA stability. Thus, the study of cis elements in a transcript that can induce mRNA surveillance pathways has become an area of particular interest.Here I report on the mechanism of gene regulation by coding polyA tracks, defined as a sequence of …

Transcriptomic Regulation Of Alternative Phenotypic Trajectories In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Amie L. Romney

Dissertations and Theses

The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype …

Ecological Epigenetics Of Avian Range Expansions, Holly J. Kilvitis

USF Tampa Graduate Theses and Dissertations

In light of human-mediated environmental change, a fundamental goal for biologists is to determine which phenotypic characteristics enable some individuals, populations or species to be more adept at coping with such change, while rendering others more vulnerable. Studying ongoing range expansions provide a unique opportunity to address this question by allowing documentation of how novel environments shape phenotypic variation on ecological timescales. At range-edges, individuals are exposed to strong selective pressures and population genetic challenges (e.g. bottlenecks and/or founder effects), which make genetic adaptation difficult. Nevertheless, certain species, such as the house sparrow (Passer domesticus), seem to thrive in their …

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Growth And Stress Response Mechanisms Underlying Post-Feeding Organ Regenerative Growth In Snakes, Audra Leann Andrew

Biology Dissertations - Archive

Snakes represent an emerging model in biological research and provide a valuable system for studying multiple extreme phenotypes unparallel to those seen in mammals. Recently, snakes have become increasingly used in studies of extreme organ regenerative growth due to the ability of some species to rapidly and reversibly upregulate organ form and function upon feeding. The predominant model used to study this feeding response has been the Burmese python (Python molurus bivittatus) because of the particulalry extreme nature of this post-feeding response in this species. Specifically, the wet masses of major organs increase by 50-100% within just 48 hours post-feeding …

Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta

Biological Sciences Faculty Publications

Anaplasma phagocytophilum, the agent of human granulocytic anaplasmosis infects neutrophils and other cells from hematopoietic origin. Using human megakaryocytic cell line, MEG-01, we show that expression of cell cycle genes in these cells are altered upon A. phagocytophilum infection. Expression of several cell cycle genes in MEG-01 cells was significantly up regulated at early and then down regulated at later stages of A. phagocytophilum infection. Lactate dehydrogenase (LDH) assays revealed reduced cellular cytotoxicity in MEG-01 cells upon A. phagocytophilum infection. The levels of both PI3KCA (p110 alpha, catalytic subunit) and PI3KR1 (p85, regulatory subunit) of Class …

Effect Assessment Of Tio2 Nanoparticles Exposure On Medicago By Monitoring Morphophysiology, Charles Towey

Mahurin Honors College Capstone Experience/Thesis Projects

In recent years titanium dioxide nanoparticles (TiO₂NPs) have been ingredients in everything from paints to cosmetics, and even in some kinds of food. This growth in use has resulted in a substantial increase in the amount of titanium released into the environment, which could have detrimental effects on nearby plant and animal life. Currently, the number of studies conducted on the effects of TiO₂NPs is quite small, especially when it comes to edible crops. Because of this lack of research data, this study has been designed to assess the effect of TiO₂ NPs exposure on …

Transcriptomic Analysis Of Maternally Provisioned Cues For Phenotypic Plasticity In The Annual Killifish, Austrofundulus Limnaeus, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifsh Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal …

Immune Responses In Hibernating Little Brown Myotis (Myotis Lucifugus) With White-Nose Syndrome, Thomas M. Lilley, Jenni M. Prokkola, Elisabeth Jeanine Rogers, Sarah Gronsky, Allen Kurta, Deeann Reeder, Kenneth A. Field

Faculty Journal Articles

White-nose syndrome (WNS) is a fungal disease responsible for decimating many bat populations in North America. Pseudogymnoascus destructans (Pd), the psychrophilic fungus responsible for WNS, prospers in the winter habitat of many hibernating bat species. The immune response that Pd elicits in bats is not yet fully understood; antibodies are produced in response to infection by Pd, but they may not be protective and indeed may be harmful. To understand how bats respond to infection during hibernation, we studied the effect of Pd inoculation on the survival and gene expression of captive hibernating Myotis lucifugus with varying …

Age And Sex-Specific Effect Of Caloric Restriction On Circadian Clock And Longevity-Associated Gene Expression, Arten Andreyevich Astafev

ETD Archive

The rhythms in the expression of circadian clock genes are affected by calorie restriction (CR), a dietary paradigm known to increase lifespan. In our current study, we show that circadian rhythms are influenced by sex and the effects of CR are different between males and females. In particular, we found a group of clock genes which showed a sex-dependent difference in expression, as well as in response to CR (Rev-Erb α, Ror γ and both Cryptochromes: Cry1 and Cry2 genes). Two clock genes showed no difference in expression but their response to CR showed sexual dimorphism (Ror α and Rev-Erb …

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

Small Noncoding Rna Expression During Extreme Anoxia Tolerance Of Annual Killifish (Austrofundulus Limnaeus) Embryos, Claire L. Riggs, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days …

Assessment Of The Function And Expression Pattern Of Auxin Response Factor B3 In The Model Legume Plant Medicago Truncatula, Miglena Revalska, Valya Vassileva, Grigor Zehirov, Sofie Goormachtig, Anelia Iantcheva

Turkish Journal of Biology

The phytohormone auxin is a critical signal molecule, regulating fundamental processes in plant growth and development, such as shaping the root and shoot architecture, organ patterning, and nodulation. Auxin regulates plant gene expression mainly through auxin response factors (ARFs), which bind to auxin response elements in the promoter, upstream of auxin-activated genes. Here we examine and assess the function and expression pattern of a gene described as an auxin response factor, containing a DNA-binding pseudobarrel and B3 DNA-binding domains, from Medicago truncatula (MtARF-B3). For the model legume species M. truncatula, stable transgenic plants with MtARF-B3 overexpression, downregulation, and transcriptional reporters …

Molecular Investigations Of The Somatic Embryogenesis Recalcitrancein The Cherry (Prunus Cerasus L.) Rootstock Cab 6p, Kaouther Ben Mahmoud, Emna Jedidi, Fabienne Delporte, Yordan Muhovski, Ahmed Jemmali, Philippe Druart

Turkish Journal of Biology

Somatic embryogenesis is a powerful tool for clonal propagation and plant breeding in many plant species, but its application is limited by the genotype response based on the interaction between gene expression and culture conditions. In this context, the recalcitrance of the nonembryogenic cherry rootstock Prunus cerasus cultivar CAB 6P was investigated via the analysis of the candidate genes PiABP19, Picdc2, and PiSERK3 in comparison with the embryogenic genotype Prunus incisa cultivar N°131. Semiquantitative RT-PCR was employed to assess the transcript level of these genes in leaf explants and derived calli of the two genotypes cultured on picloram-containing MS medium …

The Transcriptional Repressor Icer Binds To Multiple Loci Throughout The Genome, Carlos A. Molina, Luis C. Muñiz

Department of Biology Faculty Scholarship and Creative Works

The events culminating in ovulation are controlled by the cyclical actions of hormones such as Follical Stimulating Hormone (FSH) and Luteinizing Hormone (LH). The secondary messenger, cyclic AMP (cAMP) conveys the intracellular activity of these hormones. It is well established that a family of transcription factors facilitate cAMP mediated gene expression, yet it remains unknown how these factors directly affect ovulation. One of these factors, Inducible cAMP Early Repressor (ICER) has been implicated in the transcriptional regulation of cAMP inducible genes during folliculogenesis and ovulation. In order to better determine the role of ICER in ovarian function we have identified …

Genetic And Transcriptional Analysis Of Human Host Response To Healthy Gut Microbiota, Michael B. Burns, Allison L. Richards, Adnan Alazizi, Luis B. Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca

Biology: Faculty Publications and Other Works

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with …

Gene Expression Differences In Hybrids At Beginning Of Speciation Continuum, Long A. Nicholas

Biology Theses - Archive

The formation of new species results from reproductive isolation, or the barrier to successful mating between organisms of divergent populations. The degree of reproductive isolation can be measured by the reduction in fitness of hybrid offspring that can result from incompatibilities between the genotypes of each parent. In this study, genetic incompatibilities arising at the earliest stage of speciation are examined between intraspecific hybrids in which an effectively sterile hybrid phenotype termed “still” is observed at ~50% frequency in crosses between divergent populations of Tribolium castaneum. Timing and magnitude of gene expression regulation is examined at four stages of development, …

The Effects Of 4-Nonylphenol On The Immune Response Of The Pacific Oyster, Crassostrea Gigas, Following Bacterial Infection (Vibrio Campbellii), Courtney Hart

Master's Theses

Endocrine disrupting chemicals (EDCs) are compounds that can interfere with hormone signaling pathways and are now recognized as pervasive in estuarine and marine waters. One prevalent EDC in California’s coastal waters is the xenoestrogen 4-nonylphenol (4-NP), which has been shown to impair reproduction, development, growth, and in some cases immune function of marine invertebrates. To further investigate effects of 4-NP on marine invertebrate immune function we measured total hemocyte counts (THC), relative transcript abundance of immune-relevant genes, and lysozyme activity in Pacific oysters (Crassostrea gigas) following bacterial infection. To quantify these effects we exposed oysters to dissolved phase …

Gene Expression Patterns Of Bone Morphogenetic Proteins (Bmps) During Early Embryonic Development In The Annual Killifish Austrofundulus Limnaeus, Eva Y. Chan

PSU McNair Scholars Online Journal

The developmental pattern of the annual killifish Austrofundulus limnaeus is unusual compared to other fish. First, the cell movements associated with gastrulation are separated from formation of the embryonic axis. In addition, embryonic diapause can occur. Diapause II and III are often observed when embryos are incubated at 25^oC. Maternal influences and incubation environment are the factors that determine entrance into embryonic diapause, but the molecular mechanisms that regulate diapause are still unknown. Interestingly, embryonic diapause and the unusual cell movements observed during early development are always found together in species of annual killifish that exhibit diapause. Bone …

Investigating The Effects Of 17Α-Ethynylestradiol On Mitochondrial Genome Stability, Alicia M. Chivers

Dissertations and Theses

Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA …

Genome-Wide Analysis Of Response To Low Sulfur (Lsu) Genes In Grass Species And Expression Profiling Of Model Grass Species Brachypodium Distachyon Under S Deficiency, Hüseyi̇n Tombuloğlu, Abdugaffor Ablazov, Ertuğrul Fi̇li̇z

Turkish Journal of Biology

Sulfur (S) affects the plant life cycle and crop yield and has nutritional importance for human and animal diet. Its deficiency is one of the major problems in agriculture. However, the plant-specific LSU (response to Low Sulfur) gene family has not been extensively analyzed in major plant species such as grasses. In this study, we have performed in silico genome-wide analysis of LSU genes in 6 grass species, including Brachypodium distachyon, Sorghum bicolor, Oryza sativa, Zea mays, Triticum aestivum, and Panicum virgatum. All identified LSU genes contained one exon encoding proteins of acidic character with cytoplasmic localization. In silico analysis …

Calorie Restriction Effect On Circadian Clock Gene Expression, Sonal Arvind Patel

ETD Archive

Calorie Restriction (CR) is a powerful paradigm known to delay aging and thus increase longevity in several organisms, from yeast to non-human primates. Many molecular pathways have been proposed to mediate the beneficial effects of CR, however, the mechanism is still unknown. Circadian clock which is an internal time keeping system is regulated by feeding. Thus our aim was to study the effect of CR on the circadian clock. Here we show that CR significantly affects the expression of circadian clock genes in mice at the mRNA and protein levels, suggesting that CR reprograms the clocks at the transcriptional and …