Life Sciences Commons^™

Characterizing The Evolutionary Path(S) To Early Homo, Lauren Schroeder, Charles C. Roseman, James M. Cheverud, Rebecca R. Ackermann

Biology: Faculty Publications and Other Works

Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must …

Acute Effects Of Tio2 Nanomaterials On The Viability And Taxonomic Composition Of Aquatic Bacterial Communities Assessed Via High-Throughput Screening And Next Generation Sequencing, Binh Chu, Tiezheng Tong, Jean-François Gaillard, Kimberley A. Gray, John J. Kelly

Biology: Faculty Publications and Other Works

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of …

Effects Of Contaminated St. Lucie River Saltwater Sediments On An Amphipod (Ampelisca Abdita) And A Hard-Shell Clam (Mercenaria Mercenaria), Tham C. Hoang, Gary M. Rand

School of Environmental Sustainability: Faculty Publications and Other Works

The St. Lucie estuary (SLE) ecosystem in South Florida has been shown to be contaminated with metals and pesticides. Our earlier studies also showed that aquatic organisms, especially benthic species in the SLE ecosystem, might be potentially at high risk from copper (Cu) exposure. The objectives of this study were to conduct studies with separate groups of organisms exposed to seven field-collected sediment samples from the St. Lucie River according to standard procedures to evaluate toxicity and tissue concentrations of Cu and zinc (Zn). Short term and longer term whole sediment acute toxicity studies were performed with Ampelisca abdita and …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Temporal Variations In The Abundance And Composition Of Biofilm Communities Colonizing Drinking Water Distribution Pipes, John J. Kelly, Nicole Minalt, Alessandro Culotti, Marsha Pryor, Aaron Packman

Biology: Faculty Publications and Other Works

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities …

The Effect Of Dietary Fat Intake On Hepatic Gene Expression In Lg/J And Sm/J Mice, Charlyn G. Partridge, Gloria L. Fawcett, Bing Wang, Clay F. Semenkovich, James M. Cheverud

Biology: Faculty Publications and Other Works

Background

The liver plays a major role in regulating metabolic homeostasis and is vital for nutrient metabolism. Identifying the genetic factors regulating these processes could lead to a greater understanding of how liver function responds to a high-fat diet and how that response may influence susceptibilities to obesity and metabolic syndrome. In this study we examine differences in hepatic gene expression between the LG/J and SM/J inbred mouse strains and how gene expression in these strains is affected by high-fat diet. LG/J and SM/J are known to differ in their responses to a high-fat diet for a variety of obesity- …

Investigating The Role Of The Pgf2 Alpha/Calcineurin-Signaling Pathway In The Regulation Of Adipogenesis, Damodaran Annamalai

Dissertations

Prostaglandin F2α (PGF2α) is a potent physiological inhibitor of adipocyte differentiation. In previous studies, we demonstrated that PGF2α inhibits adipogenesis via activation of the calcium-regulated protein phosphatase, calcineurin. In this current study, we have now extended these findings to identify the IL-11 cytokine and the Nurr1 orphan nuclear hormone receptor as functionally important downstream transcriptional targets of the PGF2α/calcineurin-pathway involved in the inhibition of adipocyte differentiation. In the case of IL-11, we show that this cytokine acts in an autocrine fashion to inhibit adipogenesis via the essential actions of the gp130 cytokine co-receptor signaling subunit. Further, by using a well-characterized …

Host Entry Factors For Human Coronaviruses, Taylor Heald-Sargent

Dissertations

Coronaviruses infect a diverse range of animals from birds to pigs and cats to humans. Coronaviruses employ RNA-based replicative processes and as such are genetically adaptable to acquire novel host ranges. A coronavirus from one species can jump to another by shifting its entry requirements. As we learned from the Severe Acute Respiratory Syndrome (SARS) pandemic, this shift in species can have detrimental consequences. Thus, it is imperative that we understand the virus-host interaction during the entry process.

This dissertation focuses on host entry factors that influence human coronavirus entry. Recently, a new class of proteases, the type II transmembrane …

Adenovirus Vectors As Potent Adjuvants In Vaccine Development, Kathleen Ann Mcguire

Dissertations

Due to their ability to activate the immune system, replication-defective Adenoviruses (Ad) are potential vaccine vectors for several pathogens. The proinflammatory response to Ad contributes to the response to vaccine antigens. We found that reactive oxygen species (ROS) are an important signal in the proinflammatory response to Ad. We identified that serotype 5 adenovirus (Ad5) elicits ROS by inducing mitochondrial membrane damage, a process that is dependent on endosomal membrane rupture and Cathepsin release. This mitochondrial dysfunction contributes to NLRP3 inflammasome- and NFκB-dependent innate immune activation. The ROS-dependent inflammatory response likely contributes to the adaptive immune response by supporting DC …

The Molecular Components Of Estrogen Receptor Beta (Erβ) Signaling In Neuronal Sytems, Natasha Mott

Dissertations

With increasing life expectancy, women are now living upwards of 50 years without circulating estrogens, therefore, it is essential to investigate how the brain is changed by estrogen deprivation and also how aging influences these changes. The Women's Health Initiative (WHI) study spurred rigorous debate regarding estrogen therapy for postmenopausal women due to dichotomous effects of estrogens in menopausal and post-menopausal women. Meta-analyses of the WHI study revealed that after circulating estrogens are depleted for many years re-exposure may cause aberrant, negative health effects, indicating that there is an age-related `switch' in estrogen signaling around menopause. These age-related effects of …

Identifying Novel Factors Involved In Biofilm Formation By Vibrio Fischeri, Valerie Ray

Dissertations

Biofilm formation by bacteria provides them with a means to survive harsh environmental conditions and promote colonization of a particular surface (biotic or abiotic). Due to the resistance properties of biofilms, biofilm-forming bacteria are difficult to treat in the context of host infections. Thus, investigating the processes that control biofilm formation will promote the development of novel therapeutics. To study biofilm formation in the context of a host, I utilized as a model system the marine bacterium Vibrio fischeri, which must be competent to form a biofilm to colonize its squid host Euprymna scolopes. Biofilm formation by V. fischeri requires …

Haploinsufficiency Of Cardiac Myosin Binding Protein-C In The Development Of Hypertrophic Cardiomyopathy, David Barefield

Dissertations

Heart Failure is one of the leading causes of morbidity and mortality in the human population and represents a common endpoint for several diseases including inherited cardiomyopathies. Hypertrophic Cardiomyopathy (HCM) is characterized by left ventricular wall thickening, diastolic dysfunction, and sarcomere disarray. Mutations in sarcomeric protein encoding genes have been established as causative for HCM.

The gene MYBPC3, encoding cardiac myosin binding protein-C (cMyBP-C), is the second most commonly mutated gene in HCM cases. As a majority of these mutations have been determined to result in a null allele which does not produce any protein, it is thought that haploinsufficiency …

Mutations In Phospholamban Alter The Structure And Function Of The Calcium Atpase Regulatory Complex, Neha Abrol

Dissertations

Phospholamban (PLB) is an integral membrane protein that plays an important role in regulation of cardiac calcium handling and contractility. PLB exists as a homopentamer in the membrane, which upon deoligomerization into active monomers reversibly inhibits sarco/endoplasmic reticulum calcium ATPase (SERCA). Mutations in PLB that change the PLB monomer-pentamer equilibrium result in dysregulation of SERCA. To determine the structural and regulatory role of the C-terminal residues of PLB in the membranes of living cells, we fused fluorescent protein tags to PLB and SERCA. We then studied the effect of C-terminal alanine substitutions and truncation mutations on PLB oligomerization and SERCA …

Catalytic Mechanism And Maturation Of The Metalloenzyme Nitrile Hydratase, Natalie I. Gumataotao

Dissertations

Nitrile hydratases are metalloenzymes that catalyze the hydration of nitriles to their corresponding amides in a specific manner at ambient pressures and temperatures at neutral pH. Traditional industrial methods require high temperature and pressure, extreme pH, and heavy metals. NHases are used as biocatalysts in the large scale industrial production of amide precursors to textiles, animal feedstock, and polymers. Notably, NHase is used in the production of ~100,000 tons of acrylamide annually by the Mitsubishi Corporation.

Despite being used extensively in industry, questions remain about NHase. The catalytic mechanism is not defined. Understanding the way in which the nitrile is …

Identification And Analysis Of Omentum Derived Suppressor Cells In Regards To Th17 Inhibition, Nick Huang

Dissertations

Omentum has been harnessed by surgeons for hundreds of years, providing an ideal environment for graft healing and acceptance. However, little is known about the cellular mechanisms that promote the tolergenic environment of the omentum. We examined the cellular composition and role of activated omentum in regards to T-cell immunomodulation. We then tested activated omentum as a cellular therapy in a mouse allogenic lung transplantation model.

Our findings demonstrated activated omentum is mostly comprised of non-hematopoietic cells resembling mesenchymal stem-like cells (MSCs) and myeloid derived suppressor cells (MDSCs). Activated omentum exhibited anti-inflammatory properties through suppression of Th1 and Th17, while …

Coronavirus Proteases As Therapeutic Targets: Development Of Biosensors To Detect Inhibition Of Protease Activity And Separation Of The Multiple Functions Of Coronavirus Papain-Like Proteases, Andrew Kilianski

Dissertations

Coronaviruses are important human pathogens and have the potential to severely impact public health on an international scale. The emergence of SARS-CoV and MERS-CoV highlight the need for research to identify antivirals and vaccines against coronaviruses. To develop therapeutics against current and potentially emergent coronaviruses, I utilized two approaches targeting the proteases encoded within all coronaviruses. The papain-like protease and 3C-like protease of coronaviruses are responsible for cleaving viral polyproteins early during infection, and this step is required for viral replication. To quantitatively assess the inhibition by small-molecule compounds on MERS-CoV protease activity, I developed a luciferase-based biosensor to monitor …

The Role Of Af9 And Af9-Mediated Protein Interactions In Hematopoiesis And Leukemogenesis, Alyson Anne Lokken

Dissertations

The AF9 protein is one of the most common chromosomal translocation partners of the MLL gene in MLL leukemia. Wild-type AF9 is a member of the pTEFb transcription elongation complex, and interacts with gene regulatory proteins such as AF4/AF5q31, DOT1L, Pc3/CBX8 and BCoR. These interactions are retained in the oncogenic MLL-AF9 fusion protein, and may be required for leukemic transformation.

Using bone marrow progenitor cells isolated from conditional Af9 knockout mice, we examined in vitro differentiation of hematopoietic progenitor cells to the erythroid, myeloid and megakaryocytic lineages in the presence or absence of Af9. Based on previously published studies, we …

Host Proteins Interact With The Hiv-1 Core To Facilitate And Restrict, Zana Lukic

Dissertations

Host cell proteins, termed restriction factors, which inhibit viral replication at various stages of the viral life cycle, determine the species-specific tropism of numerous retroviruses. Many members of the TRIM family of proteins act as viral restriction factors. One well-characterized example is the ability of TRIM5á from rhesus macaques (rhTRIM5á) to inhibit human immunodeficiency virus type-1 (HIV-1) soon after viral entry but prior to reverse transcription (RT). It is well established that the restriction requires an interaction between the viral capsid lattice and the B30.2/SPRY domain of TRIM5á. Following the binding of the viral core, TRIM5á mediates an event or …

Functional Importance Of Oxidative Post-Translational Modifications Of Ryanodine Receptor In Cardiac Sarcoplasmic Reticulum Ca2+ Handling During Oxidative Stress, Stefan R. Mazurek

Dissertations

Free ionic calcium (Ca2+) plays an essential role as a second messenger that initiates muscle contraction in the heart. Ryanodine receptor (RyR2) acts as the primary Sarcoplasmic Reticulum (SR) Ca2+ release channel in the heart. In the event that intracellular SR Ca2+ handling is compromised, both the contractility and electrical excitability of the heart can be altered. As a consequence, heart function may not be able to maintain the necessary cardiac output to meet the metabolic demand of the body.

Increased oxidation of RyR2 has been implicated in abnormal Ca2+ handling that promotes the onset and progression of cardiovascular disease. …

Multifunctional Coronavirus Papain-Like Proteases As Targets For Antiviral Therapeutics And Vaccines, Anna Maria Mielech

Dissertations

Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle Ease Respiratory Syndrome coronavirus (MERS-CoV) pose a severe threat to humans because of high mortality. Despite the risk of coronavirus (CoV) emerging in the human population there are no antiviral drugs or vaccines to combat coronavirus infection. The focus of my dissertation was to study the multifunctionality of papain-like proteases (PLPs) encoded within coronavirus genomes to facilitate the development of antiviral drugs and vaccines. The viral PLPs are critical for processing the amino-terminal end of the replicase during virus replication and are attractive targets for antiviral therapies.

In my research, I analyzed …

The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase (Dape) From Haemophilus Influenzae As A Prospective Target For The Development Of Novel Antibiotics, Anna Starus

Dissertations

The rapid emergence of bacteria that are resistant to todayfs antibiotics makes them more and more ineffective. Consequently, the need for a novel class of antibacterial agents is rapidly increasing. The importance of this project is emphasized by the emergence of several pathogenic bacterial strains that are resistant to all currently available antibiotics on the market today. One way to approach this problem is to develop drugs that target essential bacterial biosynthetic pathways. Based on bacterial genetic information, the meso]diaminopimelate (mDAP)/lysine biosynthetic pathway offers several potential anti]bacterial targets that have not been yet explored. One of these, the dapE-encoded N-succinyl-L,L-diaminopimelic …

Elucidating The Transcriptional Regulation Of Col2a1a In Zebrafish, Sonja Dabizljevic

Master's Theses

Cartilage is an important tissue in vertebrates beginning in the early embryo where it lays down the scaffolding for the skeleton, and continuing through adulthood where it makes up joints and intervertebral disks. The major component of cartilage is a filamentous protein known as Collagen type II, alpha 1 (Col2a1). Mutations in col2a1 in humans can lead to multiple congenital disorders and the early onset of joint and retinal deterioration. Our laboratory is interested in understanding the conserved transcriptional regulation of this critical structural gene utilizing the zebrafish, Danio rerio. Previously, we identified a 310 bp regulatory region (R2) 1.7 …

Functional Characterization Of A Novel Thioredoxin Domain-Containing Protein Of The Malaria Parasite Plasmodium, Rachel Kooistra

Master's Theses

A novel thioredoxin domain-containing protein of the malaria parasite Plasmodium was identified and found to be conserved among eukaryotes. This protein belongs to the phosducin-like family of proteins (PhLPs), and was therefore assigned the name PhLP1, since it is the first phosducin-like protein to be identified in Plasmodium. PhLPs have been found to have various roles in G-protein signaling, cell cycle progression, and protein folding. However, the biochemical mechanism by which PhLPs perform their function is unknown. Here is described the cloning and biochemical characterization of both PhLP1 and its human homolog TXNDC9. Both purified PhLP1 and TXNDC9 showed enzymatic …

Environmental Drivers Of Leaf Breakdown Rate In An Urban Watershed, Ashley Rachelle Cook

Master's Theses

Leaf litter breakdown is a critical ecosystem process in urban streams, but environmental conditions in urban streams may generate confounding effects on breakdown rates. Reduced abundance of macroinvertebrate shredders may slow breakdown, but rates may increase if high nutrient concentrations stimulate microbial decomposers and if flooding enhances leaf fragmentation. We used the litter bag technique to measure the relative importance of multiple environmental drivers on breakdown of eastern cottonwood (Populus deltoides) leaves at 5 sites throughout the North Branch of the Chicago River watershed. Sites spanned a gradient of urbanization, but no specialized macroinvertebrate shredders were present at any sites. …

Role Of The Intestinal Microbiota In Gut Barrier Dysfunction Following Burn Injury, Zachary Earley

Master's Theses

Burn injury represents a major medical problem with half a million cases requiring medical attention and 4,000 deaths reported annually. Sepsis and multiple organ failure remain the leading causes of death following injury, and may be brought on by bacterial infections or toxins. The gastrointestinal tract contains approx. 100 trillion microbes; therefore, the indigenous commensal microbiota may play a role in leading to these complications or infections in burn patients. The overall objective of this project is to identify a potential mechanism whereby changes in gut bacteria may lead to intestinal inflammation or bacterial translocation--key factors which may lead to …

Characterization Of The Female Urinary Microbiota And Their Association With The Female Bladder Uroepithelium, Evann Elizabeth Hilt

Master's Theses

The current clinical dogma assumes that urine is sterile in the absence of clinically relevant infection. However, recent evidence has demonstrated the existence of a female urinary microbiota in women with and without lower urinary tract symptoms. With the knowledge that the lower urinary tract possesses its own unique microbiota, I hypothesize that certain bacterial species of the female microbiota may be the cause or play a role in lower urinary tract syndromes such as overactive bladder syndrome (OAB). About 40-50% of OAB patients do not respond to conventional anti-muscarinic and beta-3 adrenergic agonist drug treatment. One possible explanation for …

Reconsidering The Model Of Trim5Α Assembly: The Role Of The Linker2 (L2) Region In Trim5Α Assembly, Laura Johnsen

Master's Theses

The TRIM5α protein from rhesus macaques (TRIM5αrh) exhibits a remarkable ability to potently inhibit infection by Human Immunodeficiency Virus Type-1 (HIV-1). Extensive studies have shown that TRIM5α is capable of self-associating at many levels, eventually leading to the formation of a hexameric assembly that can superimpose on the hexameric lattice of the HIV-1 capsid. The mechanism underlying the self-association of TRIM5α and the molecular determinants of self-association remain to be completely understood. In this study, we show that the Linker 2 (L2) region of TRIM5rh is important for dimerization and higher order self-association, both of which are independent processes. Additionally, …

Denitrification In Urban Coastal Environments: A Functional Gene Study, Samantha Denise Lindemann

Master's Theses

Eutrophication is a major anthropogenic stressor on aquatic ecosystems worldwide. Jamaica Bay is located in the southeastern portion of New York City, NY (NYC). Like many other estuaries, Jamaica Bay is impacted by anthropogenic N inputs from various sources. Despite eutrophic conditions, improvements in water quality over the last few decades have prompted government agencies to promote oyster restoration to help reduce anthropogenic N in NYC waters. The effect of eastern oysters on sediment bacterial communities responsible for denitrification in Jamaica Bay was previously unknown. Those samples exposed to oysters were predicted to have high denitrification gene abundances, and thus …

Identification Of Clinical Markers That Predict The Outcomes Of Methicillin-Resistant Staphylococcus Aureus Infections And Identification Of Synergistic Antibiotic Combinations For The Treatment Of These Infections, Virginia Long

Master's Theses

Methicillin-resistant Staphylococcus aureus(MRSA) is a prominent nosocomial infection. Vancomycin is the mainstay of treatment, but it has a high rate of failure. Combination therapies can be used, but synergy is often not tested in clinical laboratories. Physicians are at a disadvantage because they cannot predict MRSA outcomes. The first aim of the study was to identify clinical and demographic markers that could predict infection recurrence or prolonged bacteremia. This was accomplished using retrospective chart review and statistical analysis. The second aim of the study was to identify which combinations, of those commonly used for MRSA treatment at Loyola, demonstrate the …

An Investigation Of The Role Of Vibrio Vulnificus Rbda And Vibrio Parahaemolyticus Sypa In Biofilm Formation, Cecilia Thompson

Master's Theses

Vibrio vulnificus and Vibrio parahaemolyticus are both bacteria that cause human infection. V. vulnificus has a polysaccharide locus, rbd, responsible for bacterial aggregation, a form of biofilm. This locus is conserved in V. parahaemolyticus and in the non-pathogen V. fischeri.

In V. fischeri, the polysaccharide locus, syp, has been extensively characterized and shown to be important for biofilm formation. In V. fischeri, the first gene, sypA, is critical for biofilm formation. V. fischeri biofilm-proficient strains form wrinkled colonies. In contrast, sypA mutants form smooth colonies, indicating a lack of biofilm formation.

To understand the function of RbdA and SypAVP, proteins …