Life Sciences Commons^™

Volume 2, Chapter 4-7c: Invertebrates: Rotifer Taxa - Monogononta, Janice M. Glime

Bryophyte Ecology Subchapters

No abstract provided.

Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe

Bioinformatics Faculty Publications

A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N₅₀ of 109,831 bp.

Assessment Of Olfactory Function In Maptassociated Neurodegenerative Disease Reveals Odor-Identification Irreproducibility As A Non-Disease-Specific, General Characteristic Of Olfactory Dysfunction, Katerina Markopoulou, Bruce A. Chase, Piotr Robowski, Audrey Strongosky, Ewa Narożańska, Emilia J. Sitek, Mariusz Berdynski, Maria Barcikowska, Matt C. Baker, Jarosøaw Søawek, Christine Klein, Katja Hückelheim, Meike Kasten, Zbigniew K. Wszolek

Biology Faculty Publications

Olfactory dysfunction is associated with normal aging, multiple neurodegenerative disorders, including Parkinson’s disease, Lewy body disease and Alzheimer’s disease, and other diseases such as diabetes, sleep apnea and the autoimmune disease myasthenia gravis. The wide spectrum of neurodegenerative disorders associated with olfactory dysfunction suggests different, potentially overlapping, underlying pathophysiologies. Studying olfactory dysfunction in presymptomatic carriers of mutations known to cause familial parkinsonism provides unique opportunities to understand the role of genetic factors, delineate the salient characteristics of the onset of olfactory dysfunction, and understand when it starts relative to motor and cognitive symptoms. We evaluated olfactory dysfunction in 28 carriers …

Genome Sequence Of Mycobacterium Phage Waterfoul, Paige N. Jackson, Ella K. Embry, Christa O. Johnson, Jessica R. Douglas, J. Michael Sellers, William A. D'Angelo, Dmitri V. Mavrodi

Faculty Publications

Waterfoul is a new isolated temperate siphovirus of Mycobacterium smegmatis mc²155. It was identified as a member of the K5 cluster of Mycobacterium phages and has a 61,248-bp genome with 95 predicted genes."

Quantitative Proteomic Investigation Of Disease Models Of Type 2 Diabetes, Mark Gabriel Athanason

USF Tampa Graduate Theses and Dissertations

PANcreatic DERived factor (PANDER, FAM3B) is a member of a superfamily of FAM3 proteins that are uniquely structured and strongly expressed from the endocrine pancreas and co-secreted with insulin. Unique animal models available to our lab have indicated that PANDER can induce a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased. The complexity of the biological networks involved with this process warranted the logical approach of employing quantitative mass spectrometry based proteomic analysis using stable isotope labeling of amino acids in cell culture (SILAC) to identify the global proteome differences between the PANDER …

Gene Expression Profiling And The Role Of Hsf1 In Ovarian Cancer In 3d Spheroid Models, Trillitye Paullin

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. These poor statistics are related to a lack of early symptoms and inadequate screening techniques. This results in the cancer going undetected until later stages when the tumor has metastasized through a process that requires the epithelial to mesenchymal transition (EMT). In lieu of traditional monolayer cell culture, EMT and cancer progression in general is best characterized through the use of 3D spheroid models. In this study, we examine gene expression changes through microarray analysis in …

Fluctuating Temperatures Alter Environmental Pathogen Transmission In A Daphnia–Pathogen System, Tad Dallas, John M. Drake

Faculty Publications

Environmental conditions are rarely constant, but instead vary spatially and temporally. This variation influences ecological interactions and epidemiological dynamics, yet most experimental studies examine interactions under constant conditions. We examined the effects of variability in temperature on the host–pathogen relationship between an aquatic zooplankton host (Daphnia laevis) and an environmentally transmitted fungal pathogen (Metschnikowia bicuspidata). We manipulated temperature variability by exposing all populations to mean temperatures of 20°C for the length of the experiments, but introducing periods of 1, 2, and 4 hr each day where the populations were exposed to 28°C followed by periods of …

No Help On The Hard Problem, Derek Ball

Animal Sentience

The hard problem of consciousness is to explain why certain physical states are conscious: why do they feel the way they do, rather than some other way or no way at all? Arthur Reber (2016) claims to solve the hard problem. But he does not: even if we grant that amoebae are conscious, we can ask why such organisms feel the way they do, and Reber’s theory provides no answer. Still, Reber’s theory may be methodologically useful: we do not yet have a satisfactory theory of consciousness, but perhaps the study of simple minds is a way to go about …

Volume 2, Chapter 4-7b: Invertebrates: Rotifer Taxa - Monogononta, Janice M. Glime

Bryophyte Ecology Subchapters

No abstract provided.

Transcriptome Analysis Revealed The Dynamic Oil Accumulation In Symplocos Paniculata Fruit, Qiang Liu, Youping Sun, Jingzhen Chen, Peiwang Li, Genhua Niu, Lijuan Jiang, Changzhu Li

Plants, Soils, and Climate Faculty Publications

Background Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages. Results The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant …

Pld-Specific Small-Molecule Inhibitors Decrease Tumor-Associated Macrophages And Neutrophils Infiltration In Breast Tumors And Lung And Liver Metastases, Karen M. Henkels, Naveen Reddy Muppani, Julian Gomez-Cambronero

Biochemistry and Molecular Biology Faculty Publications

Phospholipase D-2 (PLD2) has a key role in breast cancer formation and metastasis formation with PLD small inhibitors reducing primary tumor growth. This study aimed to evaluate the importance of targeting PLD on the tumor microenvironment. We provide evidence about the beneficial effect of PLD inhibitors [FIPI (dual PLD1/PLD2) or VU0155072-2 (PLD2 inhibitor)] on avoiding infiltration of tumor-helping macrophages and neutrophils. Tumor growth and metastasis within the primary tumors had low (<20% over controls) PLD enzyme activity. Unexpectedly, we found that the inhibitors also affected PLD2 gene expression and protein albeit at a lesser extent. The later could indicate that targeting both the actual PLD enzyme and its activity could be beneficial for potential cancer treatments in vivo. F4/80 and Ly6G staining of macrophages and neutrophils, respectively, and Arg1 staining data were consistent with M2 and N2 polarization. NOS2 staining increased in xenotransplants …

The Nuts And Bolts Of The Platelet Release Reaction, Smita Joshi, Sidney W. Whiteheart

Molecular and Cellular Biochemistry Faculty Publications

Secretion is essential to many of the roles that platelets play in the vasculature, e.g., thrombosis, angiogenesis, and inflammation, enabling platelets to modulate the microenvironment at sites of vascular lesions with a myriad of bioactive molecules stored in their granules. Past studies demonstrate that granule cargo release is mediated by Soluble NSF Attachment Protein Receptor (SNARE) proteins, which are required for granule-plasma membrane fusion. Several SNARE regulators, which control when, where, and how the SNAREs interact, have been identified in platelets. Additionally, platelet SNAREs are controlled by post-translational modifications, e.g., phosphorylation and acylation. Although there have been many …

Barriers, Motivations, And Preferences For Physical Activity Among Female African American Older Adults, Neha P. Gothe, Bradley J. Kendall

Kinesiology, Health and Sport Studies

According to the Centers for Disease Control and Prevention, less than 11% of adults more than the age of 65 meet the 2008 Physical Activity Guidelines for Americans. Among minority populations, only 5% of non-Hispanic Black older adults met the guidelines. Given our limited understanding of psychosocial and environmental factors that affect physical activity participation in these groups, the purpose of our focus groups was to investigate barriers, motivators, and preferences of physical activity for community-dwelling African American older adults. Three focus groups were conducted with female African American older adults (N = 20). Questions posed to each focus group …

The Forest Biomaterials Initiative At Michigan Tech And Across Michigan, Mark Rudnicki

TechTalks

The first statewide effort for a broad, cradle-to-cradle perspective of forest biomaterials originated at the MTU School of Forest Resources in 2012 and held a statewide meeting in Traverse City in 2013. The biomaterials initiative is currently a MTU university wide initiative, and is proceeding with development of educational and research programs that are envisioned to span most schools and colleges at MTU. Because of the work done in Traverse City and subsequent meetings, the Michigan Forest Biomaterials Institute (MiFBI) has evolved into an independent nonprofit with an expansive mission to enhance quality of life in Michigan by fostering sustainable …

Climate Change Drives Outbreaks Of Emerging Infectious Disease And Phenological Shifts, Jeremy Cohen

USF Tampa Graduate Theses and Dissertations

Climate change is expected to impact species by altering infectious disease outcomes, modifying community composition, and causing species to shift their phenology, body sizes and range distributions. However, the outcomes of these impacts are often controversial; for example, scientists have debated whether climate change will exacerbate emerging infectious disease and which species are at greatest risk to advance their phenology. There reason for these controversies may be that climate change is impacting diverse processes across a wide range of ecological scales, as the interplay between fine-scale processes and broad-scale dynamics can often cause unpredictable changes to the biosphere. Therefore, it …

Hypercapnic Hyperoxia Increases Free Radical Production And Cellular Excitability In Rat Caudal Solitary Complex Brain Slice Neurons, Geoffrey Edward Ciarlone

USF Tampa Graduate Theses and Dissertations

The caudal solitary complex (cSC) is a cardiorespiratory integrative center in the dorsal medulla oblongata that plays a vital role in the central CO₂-chemoreceptive network. Neurons in this area respond to hypercapnic acidosis (HA) by a depolarization of the membrane potential and increase in firing rate, however a definitive mechanism for this response remains unknown. Likewise, CO₂-chemoreceptive neurons in the cSC respond to hyperoxia in a similar fashion, but via a free radical mediated mechanism. It remains unknown if the response to increased pO₂ is merely an increase in redox signaling, or if it’s the …

A Framework For Studying Meshfree Geometry And A Method For Explicit Boundary Determination, Joseph Bradley Alford

USF Tampa Graduate Theses and Dissertations

Patient-specific biomechanical analysis is an important tool used to understand the complex processes that occur in the body due to physical stimulation. Patient-specific models are generated by processing medical images; once an object from the image is identified via segmentation, a point cloud representation of the object is extracted. Generating an analysis suitable representation from the point cloud has traditionally required generating a finite element mesh, which often requires a well defined surface to accomplish. Point clouds lack a well defined geometry, meaning that the surface definition is incomplete at best. Point clouds that have been generated from images have …

Significance Of Pten Phosphorylation And Its Nuclear Function In Lung Cancer, Prerna Malaney

USF Tampa Graduate Theses and Dissertations

Phosphorylation mediated inactivation of PTEN leads to multiple malignancies with increased severity. However, the consequence of such inactivation on downstream functions of PTEN are poorly understood. Therefore, the objective of my thesis is to ascertain the molecular mechanisms by which PTEN phosphorylation drives lung cancer. PTEN phosphorylation at the C-terminal serine/threonine cluster abrogates its tumor suppressor function. Despite the critical role of the PTEN C-tail in regulating its function, the crystal structure of the C-tail remains unknown. Using bioinformatics and structural analysis, I determined that the PTEN C-tail is an intrinsically disordered region and is a hot spot for post-translational …

One Health Interactions Of Chagas Disease Vectors, Canid Hosts, And Human Residents Along The Texas-Mexico Border, Melissa N. Garcia, Sarah O’Day, Susan P. Fisher-Hoch, Rodion Gorchakov, Ramiro Patino, Teresa Patricia Feria-Arroyo, Susan T. Laing, Joe E. Lopez, Alexandra Ingber, Kathryn M. Jones, Kristy O. Murray

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Background

Chagas disease (Trypanosoma cruzi infection) is the leading cause of non-ischemic dilated cardiomyopathy in Latin America. Texas, particularly the southern region, has compounding factors that could contribute to T. cruzi transmission; however, epidemiologic studies are lacking. The aim of this study was to ascertain the prevalence of T. cruzi in three different mammalian species (coyotes, stray domestic dogs, and humans) and vectors (Triatoma species) to understand the burden of Chagas disease among sylvatic, peridomestic, and domestic cycles.

Methodology/Principal Findings

To determine prevalence of infection, we tested sera from coyotes, stray domestic dogs housed in public …

Smokejumper Obituary: Tribe, Charles B. (Missoula 1956), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Unconscious Higher-Order Thoughts (Hots) As Pre-Reflective Self-Awareness?, Rocco J. Gennaro

Animal Sentience

Rowlands argues that many nonhuman animals are “persons,” contrary to the prevailing orthodoxy which rests on a mistaken conception of the kind of self-awareness relevant to personhood. He argues that self-awareness bifurcates into two importantly different forms — reflective self-awareness and pre-reflective self-awareness — and that many animals can have the latter, which is sufficient for personhood. I agree that there is good reason to think that many animals can have pre-reflective self-awareness, but I think Rowlands is mistaken about its nature. His account runs the risk of leading to an infinite regress objection, and his notion of pre-reflective self-awareness …

Epithelial-To-Mesenchymal Transition Leads To Disease-Stage Differences In Circulating Tumor Cell Detection And Metastasis In Pre-Clinical Models Of Prostate Cancer, Lori E. Lowes, David Goodale, Ying Xia, Carl Postenka, Matthew M. Piaseczny, Freeman Paczkowski, Alison L. Allan

Anatomy and Cell Biology Publications

Metastasis is the cause of most prostate cancer (PCa) deaths and has been associated with circulating tumor cells (CTCs). The presence of >= 5 CTCs/7.5mL of blood is a poor prognosis indicator in metastatic PCa when assessed by the CellSearch (R) system, the "gold standard" clinical platform. However, similar to 35% of metastatic PCa patients assessed by CellSearch (R) have undetectable CTCs. We hypothesize that this is due to epithelial-to-mesenchymal transition (EMT) and subsequent loss of necessary CTC detection markers, with important implications for PCa metastasis. Two pre-clinical assays were developed to assess human CTCs in xenograft models; one comparable …

A Dna Methylation Biomarker Of Alcohol Consumption, C. Liu, R. E. Marioni, Å. K. Hedman, L. Pfeiffer, P. -C. Tsai, L. M. Reynolds, A. C. Just, Q. Duan, C. G. Boer, T. Tanaka, C. E. Elks, S. Aslibekyan, J. A. Brody, B. Kühnel, C. Herder, L. M. Almli, D. Zhi, Y. Wang, T. Huan, C. Yao, M. M. Mendelson, R. Joehanes, L. Liang, S. -A. Love, W. Guan, S. Shah, A. F. Mcrae, A. Kretschmer, H. Prokisch, K. Strauch, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (n_total=13 317; 54% women; mean age across cohorts 42–76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. We performed meta-analysis and variable selection in …

Intranasal Oxytocin Enhances Connectivity In The Neural Circuitry Supporting Social Motivation And Social Perception In Children With Autism., Ilanit Gordon, Allison Jack, Charlotte M Pretzsch, Brent Vander Wyk, James F Leckman, Ruth Feldman, Kevin A. Pelphrey

Pharmacology and Physiology Faculty Publications

Oxytocin (OT) has become a focus in investigations of autism spectrum disorder (ASD). The social deficits that characterize ASD may relate to reduced connectivity between brain sites on the mesolimbic reward pathway (nucleus accumbens; amygdala) that receive OT projections and contribute to social motivation, and cortical sites involved in social perception. Using functional magnetic resonance imaging and a randomized, double blind, placebo-controlled crossover design, we show that OT administration in ASD increases activity in brain regions important for perceiving social-emotional information. Further, OT enhances connectivity between nodes of the brain's reward and socioemotional processing systems, and does so preferentially for …

Variability Of Particle Size Distributions In The Bohai Sea And The Yellow Sea, Zhongfeng Qui, Deyong Sun, Chuanmin Hu, Sengquiang Wang, Lufei Zheng, Yu Huang, Tian Peng

Marine Science Faculty Publications

Particle size distribution (PSD) is an important parameter that is relevant to many aspects of marine ecosystems, such as phytoplankton functional types, optical absorption and scattering from particulates, sediment fluxes, and carbon export. However, only a handful of studies have documented the PSD variability in different regions. Here, we investigate the PSD properties and variability in two shallow and semi-enclosed seas (the Bohai Sea (BS) and Yellow Sea (YS)), using in situ laser diffraction measurements (LISST-100X Type C) and other measurements at 79 stations in November 2013. The results show large variability in particle concentrations (in both volume and number …

U.S. Drought Monitor, November 15, 2016, Richard R. Heim Jr.

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for November 15, 2016 (11/15/16) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Quantitative Proteomic Profiling Reveals Hepatic Lipogenesis And Liver X Receptor Activation In The Pander Transgenic Model., Mark G. Athanason, Whitney A. Ratliff, Dale Chaput, Catherine B. Marelia, Melanie N. Kuehl, Stanley M. Stevens Jr., Brant R. Burkhardt

Molecular Biosciences Faculty Publications

PANcreatic-DERived factor (PANDER) is a member of a superfamily of FAM3 proteins modulating glycemic levels by metabolic regulation of the liver and pancreas. The precise PANDER-induced hepatic signaling mechanism is still being elucidated and has been very complex due to the pleiotropic nature of this novel hormone. Our PANDER transgenic (PANTG) mouse displays a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased, a phenomena observed in type 2 diabetes. To examine the complex PANDER-induced mechanism of SHIR, we utilized quantitative mass spectrometry-based proteomic analysis using Stable Isotope Labeling by Amino Acids in Cell …

Co2-Fixing One-Carbon Metabolism In A Cellulose-Degrading Bacterium Clostridium Thermocellum, Wei Xiong, Paul P. Lin, Lisa Warner, James C. Liao, Pin-Ching Maness, Katherine J. Chou

Biomedical Research Institute Publications and Presentations

Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO₂. This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO₂ to formate. However, feeding the bacterium ¹³C-bicarbonate and cellobiose followed by NMR analysis showed the production of ¹³C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO₂ to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO₂ to formate serves as a CO₂ entry point into the reductive one-carbon (C1) metabolism, and internalizes CO_{2 …}

Habitual Coffee Consumption And Risk Of Type 2 Diabetes, Ischemic Heart Disease, Depression And Alzheimer’S Disease: A Mendelian Randomization Study, Man Ki Kwok, Gabriel M. Leung, C. Mary Schooling

Publications and Research

Observationally, coffee is inversely associated with type 2 diabetes mellitus (T2DM), depression and Alzheimer’s disease, but not ischemic heart disease (IHD). Coffee features as possibly protective in the 2015 Dietary Guidelines for Americans. Short-term trials suggest coffee has neutral effect on most glycemic traits, but raises lipids and adiponectin. To clarify we compared T2DM, depression, Alzheimer’s disease, and IHD and its risk factors by genetically predicted coffee consumption using two-sample Mendelian randomization applied to large extensively genotyped case-control and cross-sectional studies. Childhood cognition was used as a negative control outcome. Genetically predicted coffee consumption was not associated with T2DM (odds …

Network Inference Driven Drug Discovery, Gergely Zahoránszky-Kőhalmi, Tudor I. Oprea, Cristian G. Bologa, Subramani Mani, Oleg Ursu

Biomedical Sciences ETDs

The application of rational drug design principles in the era of network-pharmacology requires the investigation of drug-target and target-target interactions in order to design new drugs. The presented research was aimed at developing novel computational methods that enable the efficient analysis of complex biomedical data and to promote the hypothesis generation in the context of translational research. The three chapters of the Dissertation relate to various segments of drug discovery and development process.

The first chapter introduces the integrated predictive drug discovery platform „SmartGraph”. The novel collaborative-filtering based algorithm „Target Based Recommender (TBR)” was developed in the framework of this …