Life Sciences Commons^™

Understanding Disease Network Associations Using Biological And Molecular Networks, Ravi Teja Mahavrathayajula

Theses and Dissertations

Background The genome project had given us a brief view of what and how an organ is made up of. In 2000’s after the genome project, every year the FDA approved around 100 drugs and was an estimate that these numbers would grow up each year, unlike the numbers only decreased. Hence, it was concluded that these facts would not be necessary, as diseases were treated with respect to the organs effected. With a growing data of molecular interaction in a cell or tissue type, proteomic, genomic, and metabolic data, will the old classification still hold good? These large-scale data …

Demographic Transition And The Dynamics Of Measles In Six Provinces In China: A Modeling Study, Sheng Li, Chao Ma, Lixin Hao, Qiru Su, Zhijie An, Fubao Ma, Shuyun Xie, Aiqiang Xu, Yangyang Zhang, Zhengrong Ding, Hui Li, Lisa Cairns, Huaqing Wang, Huiming Luo, Ning Wang, Li Li, Matthew J. Ferrari

Publications and Research

Background Industrialization and demographic transition generate nonstationary dynamics in human populations that can affect the transmission and persistence of infectious diseases. Decades of increasing vaccination and development have led to dramatic declines in the global burden of measles, but the virus remains persistent in much of the world. Here we show that a combination of demographic transition, as a result of declining birth rates, and reduced measles prevalence, due to improved vaccination, has shifted the age distribution of susceptibility to measles throughout China.

Methods and findings We fit a novel time-varying catalytic model to three decades of age-specific measles case …

Acute Kidney Injury And Chronic Kidney Disease, Jin Wei

USF Tampa Graduate Theses and Dissertations

Ischemia and reperfusion are natural steps during kidney transplantation, and IRI is considered one of the most important nonspecific factors affecting allograft dysfunction. Transplanted organs experience several episodes of ischemia, in which cold ischemia occurs during allograft storage in preservation solutions.

Even though cold ischemia has been studied extensively, all of the studies have been carried out in vitro and ex vivo models. There is no in vivo model available to examine renal IRI induced solely by cold ischemia.

In the present study, we developed an in vivo mouse model to study renal IRI induced exclusively by cold ischemia through …

Construction And Comparison Of The Recombinant Strains Of Synechocystis Sp. Pcc 6803 Able To Grow On Wood Sugars, Saurabh Jayant Ranade

Theses and Dissertations

The wood sugars present in the lignocellulosic biomass can be used to support microbial growth to synthesize a number of value added products. The objective of this research was to metabolically engineer model cyanobacterium Synechocystis to enable it to harvest carbon and energy stored in the wood sugars in addition to the light energy. In the xylose-specific work, we generated five Synechocystis strains that heterologously expressed XylAB enzymes, which mediate xylose catabolism, either in combination with or without one of four xylose transporters, namely XylE, XylFGH, GalP, or Glf. In terms of dry biomass accumulation and xylose consumption, the strains …

Life-History And Energetics Of The Diamond-Backed Watersnake, Jeremy David Chamberlain

Theses and Dissertations

Life-history research explores how environmental variation and physiological constraints shift the energy allocation decisions to competing functions of the body among individuals and populations. Variation in the energy available across the environmental landscape is of particular interest as it dictates the amount energy available for organisms to acquire and allocate to their life-history. Additionally, individuals vary in their ability to capture and assimilate energy from the environment. This dissertation seeks to understand how environmental variation in energy availability and physiological constraints of attaining this energy shape allocation decisions among individuals and populations. I examined diamond-backed watersnakes (Nerodia rhombifer) from five …

Data For Allometric Equations Of Chrysolepis Sempervirens, Cornus Sericea, Corylus Cornuta Ssp. Californica, And Leucothoe Davisiae., J. A. Lutz, J. A. Freund, A. J. Larson, M. E. Swanson, T. J. Furniss, K.M. L. Becker, E. M. Blomdahl, C. A. Cansler, S. J. Germain, S. M. A. Jeronimo

Browse all Datasets

This data set includes measurements of 40 stems of Chrysolepis sempervirens (Kellogg) Hjelmq. (bush chinquapin), 41 stems of Cornus sericea L. (redosier dogwood), 50 stems of Corylus cornuta Marsh. ssp. californica (A. DC.) E. Murray, and 40 stems of Leucothoe davisiae Torrey (Sierra laurel), as reported in Lutz et al. (2014, 2017). Nomenclature follows Flora of North America (1993+).

Adaptive Evolution Under Favorable And Unfavorable Population Genetic Conditions In Caenorhabditis Elegans Nematodes, Stephen Fuller Christy

Dissertations and Theses

Mutation is a fundamental process that drives evolutionary change; however, most new mutations are deleterious for organismal fitness and can readily propagate within populations under a broad range of conditions. Mutational processes able to counteract deleterious mutation accumulation include: 1) reversion mutation back to wildtype, 2) acquisition of generally beneficial mutations, and 3) compensatory mutations that specifically mitigate the effects of previously-acquired deleterious mutations through epistasis. The potential for any of these mutation types alters our expectations for the impact of deleterious mutation in populations, but since the fitness effects of individual mutations are rarely characterized, the relative importance of …

Furman University Lake Restoration Project

Furman Lake Restoration Book Gallery

An overview of the Furman Lake Restoration Project. The overview includes photographs and charts. It provides information on the history of the Furman Lake, it's environmental health decline throughout the years, and the lake's restoration. The overview details the Furman Lake's problems, causes of these problems, and solutions. It describes Furman's progress in the restoration project, as well as it's goals for the future.

Succession Planning And Perceived Obstacles And Attractions For Future Generations Entering Beef Cattle Production, Lee L. Schulz, Georgeanne M. Artz, Patrick J. Gunn

Journal of Applied Farm Economics

This study provides valuable insights into cow-calf producer and feedlot operator succession plans for transferring cattle operations upon exiting the industry. Across both cow-calf producers and feedlot operators, about 50% expect to be raising cattle for 10 more years or less; however, about 39% of these producers do not have a succession plan in place. Cow-calf producers view a rural lifestyle, self-employment, working with livestock, and working with family as the biggest attractions to future generations entering beef cattle production. Cow-calf producers view environmental regulations, land tax policy, and expansion of corn and soybean acres as the biggest obstacles. Feedlot …

Ultramafic Geoecology Of South And Southeast Asia, M.L. Galey, A. Van Der Ent, M.C.M. Iqbal, N. Rajakaruna

Biological Sciences

Globally, ultramafic outcrops are renowned for hosting foras with high levels of endemism, including plants with specialised adaptations such as nickel or manganese hyperaccumulation. Soils derived from ultramafic regoliths are generally nutrient-deficient, have major cation imbalances, and have concomitant high concentrations of potentially phytotoxic trace elements, especially nickel. The South and Southeast Asian region has the largest surface occurrences of ultramafic regoliths in the world, but the geoecology of these outcrops is still poorly studied despite severe conservation threats. Due to the paucity of systematic plant collections in many areas and the lack of georeferenced herbarium records and databased information, …

Collaboration And Trust In The Northern Beef Supply Chain In Western Australia: Draft Framework And Plan, Jan Paul Van Moort, Antonia Hodby, Nicki Mazur, Peter Barnard

Animal production and livestock published reports

The Department of Agriculture and Food, Western Australia (the Department) commissioned ACIL Allen Consulting to conduct a study into collaboration in the northern beef supply chain. The study is part of the Northern Beef Futures (NBF), a four year $15 million project led by the Department and funded by Royalties for Regions.

The aim of the study was to scope a framework for measuring collaboration in the northern beef supply chains; and develop an implementation plan for ways to improve collaboration that will benefit the development of the northern beef industry.

Using Knowledge Of Shark Biology And Behavior To Inform Management And Conservation Efforts For The Globally Distributed And Fishery Exploited Shortfin Mako (Isurus Oxyrinchus), Mark Rubinas

HCNSO Student Capstones

The shortfin mako (Isurus oxyrinchus) is a regionally endothermic lamnid shark with a circumglobal distribution in temperate and tropical waters. This species has special adaptations for a highly migratory, apex predator lifestyle, including specialized anatomical structures, the retia mirabilia, that allows maintenance of a higher than ambient internal body temperature, a higher percentage of red muscle fibers located closer to its body core compared to ectothermic sharks, and specialized dermal denticles to help achieve the remarkable swimming speeds for efficient predation. However, many parts of the life history of the shortfin mako are still unknown, and difficult to …

The Optimization Of The Nuclear Protein In Testis (Nut) Antibody And Its Importance And Impact In The Pathology Lab, Lindsey Martinez

USF Tampa Graduate Theses and Dissertations

Optimization in immunohistochemistry is often a time consuming and complex process. There are a varying array of moving parts to consider all while preserving the sensitivity and specificity of the test. When optimizing an antibody it is important to consider the fixation of the tissue and the type of epitope retrieval that would be best suited for the test. The dilution of the primary antibody is a key marker for the efficiency and effectiveness of the laboratory protocol. The purpose of this study was to produce an optimized antibody for the nuclear protein in testis to detect NUT midline carcinoma …

Catalyzed Synthesis Of Zinc Clays By Prebiotic Central Metabolites, Marcelo I. Guzman, Ruixin Zhou, Kaustuv Basu, Hyman Hartman, Christopher J. Matocha, S. Kelly Sears, Hajatollah Vali

Chemistry Faculty Publications

How primordial metabolic networks such as the reverse tricarboxylic acid (rTCA) cycle and clay mineral catalysts coevolved remains a mystery in the puzzle to understand the origin of life. While prebiotic reactions from the rTCA cycle were accomplished via photochemistry on semiconductor minerals, the synthesis of clays was demonstrated at low temperature and ambient pressure catalyzed by oxalate. Herein, the crystallization of clay minerals is catalyzed by succinate, an example of a photoproduced intermediate from central metabolism. The experiments connect the synthesis of sauconite, a model for clay minerals, to prebiotic photochemistry. We report the temperature, pH, and concentration dependence …

Social Interactions Among Giant Panda Cubs (Ailuropoda Melanoleuca): An Investigation Into The Role Of Kin Recognition, Kelly M. Jackson

Undergraduate Distinction Papers

Although giant pandas (Ailuropoda melanoleuca) are known to be solitary in the wild, cubs engage in frequent bouts of affiliative behavior in captive settings. The goal of the project was to investigate whether kinship or familiarity based on housing influenced the frequency of social interactions within one-year old giant panda cubs. Data were collected from June through mid-July 2016 at the Chengdu Research Base of Giant Panda Breeding, Sichuan, China. Over 113 hours of behavioral observations were recorded on four sets of twins and one singleton, focusing specifically on affiliative behaviors. Time housed together was a significant predictor of the …

Motion-Induced Position Shifts Activate Early Visual Cortex, Peter J. Kohler, Patrick Cavanagh, Peter U. Tse

Dartmouth Scholarship

The ability to correctly determine the position of objects in space is a fundamental task of the visual system. The perceived position of briefly presented static objects can be influenced by nearby moving contours, as demonstrated by various illusions collectively known as motion-induced position shifts. Here we use a stimulus that produces a particularly strong effect of motion on perceived position. We test whether several regions-of-interest (ROIs), at different stages of visual processing, encode the perceived rather than retinotopically veridical position. Specifically, we collect functional MRI data while participants experience motion-induced position shifts and use a multivariate pattern analysis approach …

Molecular Mass Of L-Arginine-Based Potentially Carcinogenic Heterocyclic Amines, Irene S. Hwang

Honors Theses

Investigation of cancer-inducing molecules in cooked foods has led to the discovery of mutagenic heterocyclic amines (HCAs) in meat. The amino acids creatin(in)e and L-phenylalanine form the precursors for these HCAs. Recent research here at Andrews University have found similar mutagenic HCAs produced from plant-based proteins when L-arginine, rather than creatin(in)e, is substituted in high temperature reactions (simulated cooking) with L-phenylalanine. Our research focused on developing HPLC methods to isolate individual candidates that are then screened for mutagenicity via the Ames test. Mass spectroscopy methods were also developed to identfy the molecular structure of these lead mutagenic L-arginine-based HCAs.

Soil Sand Content, But Not Solil Myrosinase Enzyme Activity, Affects Mam Efficacy In Suppressing Weed Growth, Warit Chirachevin

Honors Theses

Mustard seed meal (MSM) has been shown to control weeds and pests in crop fields. Prior work showed that a sandy loam soil was superior to a silt loam soil in supporting velvetleaf growth suppression by MSM. To explore this difference, myrosinase enzyme activity was measured in both soils. Results showed no significant difference between the soils. Sand content in Michigan silt loam soil was manipulated in order to test the role of sand content on MSM efficacy in suppressing short-term velvetleaf growth. Results showed that sand enhanced the effect of MSM in suppressing seedling growth and germination.

Chelerythrine Chloride And Its Effects On Phonotactic Behavior In Female Crickets Acheta Domesticus, Haneul Shin

Honors Theses

Selective phonotaxis by female crickets has been shown to be variable. Mechanisms which underlie such behavioral variability are being studied. Juvenile Hormone III is a neuromodulator that has been shown to increase selectivity in phonotactic behavior of female crickets. In an attempt to further explore its effects on the behavioral responses of femaile crickets, experiments have been performed with chelerythrine cloride that is known to have an opposite effect of Juvenile Hormone III. Chelerythrine chloride, a potent protein kinase C blocker, has been hypothesized to block the effect of Juvenile Hormone III which acts through a protein kinase C pathway, …

Ultramafic Geoecology Of South And Southeast Asia, Nishanta Rajakaruna, M. Galey, Van Der Ent, M. Iqbal

Faculty Publications, Biological Sciences

Globally, ultramafic outcrops are renowned for hosting floras with high levels of endemism, including plants with specialised adaptations such as nickel or manganese hyperaccumulation. Soils derived from ultramafic regoliths are generally nutrient-deficient, have major cation imbalances, and have concomitant high concentrations of potentially phytotoxic trace elements, especially nickel. The South and Southeast Asian region has the largest surface occurrences of ultramafic regoliths in the world, but the geoecology of these outcrops is still poorly studied despite severe conservation threats. Due to the paucity of systematic plant collections in many areas and the lack of georeferenced herbarium records and databased information, …

The Relationship Between Cold Stress Syndrome Mortality And Body Shape In Florida Manatees, Purin Chirachevin

Honors Theses

West Indian manatees (Trichechus manatus latirostris) are tropical and subtropical aquatic mamals that can develop cold stress syndrome (CSS) when subjected to water temperatures below 20'C for prolonge dperiods. This study investigtes the potential impact that cold winter water temperatures in Florida may have on manatee body shape as a selective force to reduce surface-area-to-volume ratio (SA:Vol; i.e. Bergmann's and Allen's Rule). Morphometric measurements collected from state-mandated necropsies (1974-2014) were used to calculate surface area, volume, and mass. We found that manatees that died of CSS on average had significantly greater SA:Vol and less mass compared to those that died …

Synthesis Of A-Cyanostilbenes And Testing Of Their Anticancer Properties, Gabrielle Cook

Honors Theses

This research project involves synthesizing cyanostilbenes and testing their anticancer properties in breast cancer cells. Breast cancer is a global issue, one that great improvement has been found in the last few decades, but also one that remains a large killer. The components of the cyanostilbene hybrids have all been shown to have anticancer properties on their own, and we would like to see if we can increase these properties by combining multiple into a single hybrid. Then these cyanostilbene compounds are tested on Her2+ human breast cancer cells. The goals is to assess whether or not the cyanostilbenes have …

Natural Products In Weed Control: Allyl-Isothiocyanate Effects On In Vitro Velvetleaf Seedling Growth And The Influence Of Mustard Seed Meal On Soil Bacterial Populations, Stanford Shin

Honors Theses

Past research has shown that alyl isothiocyanate (AICT) and its sister ITC compounds are effective alternatives to herbicides in reducing growth in weed seedlings. In this project the effects of mustard seed meal (MSM), a source of AITC, on plant-associated soil bacteria populations was assessed along with the effect of AITC on velvetleaf seed in vitro germination. Results show that MSM reduces bacterial levels in the soil. Velvetleaf seed germination was inbibited by micromolar levels of AITC. These results suggest that MSM has the potential to impact velvetleaf growth in the field as well as becoming a weed management tool.

The Role Of Octopamine In Syllable-Period Selective Phonotaxis In Female Cricket Acheta Domesticus, Darley Magno

Honors Theses

Female crickets respond phonotactically to the calls of conspecific males. Females' phonotaxis has been reported to be variable, ranging from unselective to selectve in response to calls with varying syllable periods (30-90 ms). Octopamine, an intertebrate neurotransmitter, has been reported to increase aggressive behavior in crickets, (Stevanson et al. 2005) but the effects of octopamine on behaviors such as phonotaxis have not been investigated. The goal of this study is to determine the effects of octopamine on the syllable-period selective phonotactic response of females. Results suggest a decrease in phonotactic responsiveness shown by 5-10 day-okds after prothroacic nanoinjection of octopamine.

Fluorescence Analysis Of Pamam Dendrimers, Ansel Nam

Honors Theses

Despite their lack of conjugation, polyamidoamine (PAMAM) dendrimers are intrinsically fluorescent, and this fluorescent is somewhat manipulable through altering the dendrimer's solvent. This level of fluorescence is dependent on a number of the dendrimer's qualities: the pH of the solvent, the mass percent concentration of the dendrimer in solvent, and the generation size of the dendrimer. In past studies, fluorescent intensity increased as generation size increased and pH decreased. Thus, this research project will attempt to replicate those results as well as further analyze the efficiency of fluorescence of PAMAM dendrimer in comparison to fluorescein.

Analysis Of The Anti-Cancer Effects Of Cincau Extract (Premna Oblongifolia Merr) And Other Types Of Non- Digestible Fibre Using Faecal Fermentation Supernatants And Caco-2 Cells As A Model Of The Human Colon, Samsu U. Nurdin, Richard K. Le Leu, Graeme P. Young, James Constantine R. Stangoulis, Claus T. Christophersen, Catherine A. Abbott

Research outputs 2014 to 2021

Green cincau (Premna oblongifolia Merr) is an Indonesian food plant with a high dietary fibre content. Research has shown that dietary fibre mixtures may be more beneficial for colorectal cancer prevention than a single dietary fibre type. The aim of this study was to investigate the effects of green cincau extract on short chain fatty acid (SCFA) production in anaerobic batch cultures inoculated with human faecal slurries and to compare these to results obtained using different dietary fibre types (pectin, inulin, and cellulose), singly and in combination. Furthermore, fermentation supernatants (FSs) were evaluated in Caco-2 cells for their effect on …

A Drosophila Model To Examine Collective Migration During Retinogenesis, Caroline Pena, Stephanie Zhang, Mildred Kamara, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

Retinal dysfunction is often caused by aberrant neural cell migration during development. In this study, we observed the migration of neural cells of the Drosophila melanogaster after marking cells of the 3rd instar larvae with the GAL4-UAS expression system when exposed to a concentration gradient of FGF-8 through the use of a microfluidic device. The glial and neuronal cell ratio in the developing brain was determined through immunofluorescent staining and observation. In future studies, a microfluidic device that mimics the developing Drosophila brain and retina will be designed in order to better understand the biological factors that affect the migration …

Sterol Binding By The Tombusviral Replication Proteins Is Essential For Replication In Yeast And Plants, Kai Xu, Peter D. Nagy

Plant Pathology Faculty Publications

Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication have been gaining full attention only recently. Previous work with Tomato bushy stunt tombusvirus (TBSV) in model host yeast has revealed essential roles for phosphatidylethanolamine and sterols in viral replication. To further our understanding of the role of sterols in tombusvirus replication, in this work we showed that the TBSV p33 and p92 replication proteins could bind to …

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

A Simulation Of Anthropogenic Mammoth Extinction, Matthew Klapman

Undergraduate Honors Papers

There are multiple hypotheses as to why the Columbian Mammoth (Mammuthus columbi) and other megafauna in North America went extinct relatively recently and relatively quickly. The most popular of which are disease, climate change, meteorite strikes, and over hunting by humans [2, 9]. There is evidence to show that a combination of factors contributed to the megafaunal extinction, but ”overkill” explores the idea that early humans migrated onto the continent and then hunted the mammoths and other megafauna to extinction. The overkill hypothesis was first proposed by anthropologist Paul Martin in 1973 [8]. Evidence from radiocarbon dating shows that the …