Biology Commons^™

Structure, Function, And Dynamics Of The Gα Binding Domain Of Ric-8a, Baisen Zeng, Tung-Chung Mou, Tzanko I. Doukov, Andrea Steiner, Wenxi Yu, Makaia Papasergi-Scott, Gregory G. Tall, Franz Hagn, Stephen Sprang

Biological Sciences Faculty Publications

Ric-8A is a 530-amino acid cytoplasmic molecular chaperone and guanine nucleotide exchange factor (GEF) for i, q, and 12/13 classes of heterortrimeric G protein alpha subunits (Gα). We report the 2.2-Å crystal structure of the Ric-8A Gα-binding domain with GEF activity, residues 1-452, and is phosphorylated at Ser435 and Thr440. Residues 1-429 adopt a superhelical fold comprised of Armadillo (ARM) and HEAT repeats, and the C terminus is disordered. One of the phosphorylated residues potentially binds to a basic cluster in an ARM motif. Amino acid sequence conservation and published hydrogen-deuterium exchange data indicate repeats 3 through 6 to be …

Oomycete Metabarcoding Reveals The Presence Of Lagenidium Spp. In Phytotelmata, Paula Leoro-Garzon, Andrew J. Gonedes, Isabel Olivera, Aurelien Tartar

Biology Faculty Articles

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome, and suggested, mirroring the endophytic abilities demonstrated in entomopathogenic fungi, that L. giganteum may have similarly retained capacities to establish interactions with plant tissues. To test this hypothesis, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two …

Tourism And African Elephant (Loxodonta Africana) Behavior In Zambezi National Park, Zimbabwe, Brigit Rooney

Masters Theses & Specialist Projects

As charismatic megafauna and a flagship species, African elephants (Loxodonta africana) are vital to the African tourist economy. Conversely, high levels of wildlife tourism can induce behavioral shifts that push desired animals into less frequented areas and disrupt natural behaviors. In order to examine this trade-off, tourism levels and African elephant behaviors were studied in Zambezi National Park (ZNP) near Victoria Falls, Zimbabwe. Over the course of 14 weeks, in-person observations and camera traps in ZNP were used to collect geographic, demographic, and behavioral data from elephant sightings. As a proxy for human presence, geo-locational data were collected for each …

Documenting Marine Mammal Behavior And Evaluating The Benefits And Consequences Of Viewing Marine Mammals In Southcentral Alaska, Lauren E. Mccaslin

Masters Theses & Specialist Projects

Marine mammals are in a precarious conservation position because of anthropogenic impacts and historic perceptions that they are a consumable commodity. In light of changing abiotic conditions, further evaluation is needed on the habitat use, behavior, and interactions among marine mammals. Conservation legislation has helped protect species, but the greatest ground swelling may be the advent of the commercial whale watching industry. The feeding grounds in Alaskan waters have made this area a prime tourism location, and these nutrient-rich waters have resulted in a confluence of marine mammal species, including the appealing and abundant humpback whale (Megaptera novaeangliae) that may …

Musineon Glaucescens (Apiaceae), A New Species From Central Montana, U.S.A., Peter Lesica

Biological Sciences Faculty Publications

Musineon glaucesens is described as a new species from two populations in the Big Belt Mountains of Montana, U.S.A. It appears to be most closely allied to the small genus Musineon which is endemic to western North America. It occurs just outside the range of M. vaginatum but differs from that species by its larger fruits, more widely lobed and glaucous leaves, and talus-slope habitat.

Gut Yeasts Do Not Improve Desiccation Survival In Drosophila Melanogaster, Joanne M. Tang, Yanira Jiménez Padilla, Marc-André Lachance, Brent J. Sinclair

Biology Publications

A healthy gut microbiota generally improves the performance of its insect host. Although the effects can be specific to the species composition of the microbial community, the role of gut microbiota in determining water balance has not been well explored. We used axenic and gnotobiotic (reared with a known microbiota) Drosophila melanogaster to test three hypotheses about the effects of gut yeasts on the water balance of adult flies: 1) that gut yeasts would improve desiccation survival in adult flies; 2) that larval yeasts would improve adult desiccation survival; 3) that the effects would be species-specific, such that yeasts closely …

Gene Co-Expression Analysis Of The Human Substantia Nigra Identifies Bmp2 As A Neurotrophic Factor That Can Promote Neurite Growth In Cells Overexpressing Wild-Type Or A53t Α-Synuclein, Susan R. Goulding, Aideen M. Sullivan, Gerard W. O'Keeffe, Louise M. Collins

Department of Biological Sciences Publications

Introduction: α-synuclein-induced degeneration of dopaminergic neurons has been proposed to be central to the early progression of Parkinson's disease. This highlights the need to identify factors that are neuroprotective or neuroregenerative against α-synuclein-induced degeneration. Due to their potent neurotrophic effects on nigrostriatal dopaminergic neurons, we hypothesized that members of the bone morphogenetic protein (BMP) family have potential to protect these cells against α-synuclein. Methods: To identify the most relevant BMP ligands, we used unbiased gene co-expression analysis to identify all BMP family members having a significant positive correlation with five markers of dopaminergic neurons in the human substantia nigra (SN). …

Correcting Forensic Dna Errors, Greg Hampikian

Biology Faculty Publications and Presentations

DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National Institutes of Standards and Technology (NIST) study of 109 North American crime laboratories in this journal demonstrates this most clearly. This latest study supports earlier work that shows common methods such as the Combined Probability of Inclusion (CPI) have wrongly included innocent people as contributors to DNA mixtures.The 2016 President’s Council of Advisors on Science and Technology report concluded,“In summary, the interpretation of complex DNA mixtures with the CPI statistic has been an inadequately specified—and thus inappropriately subjective—method. …

Development Of A Prolyl Endopeptidase Expression System In Lactobacillus Reuteri To Reduce The Clinical Manifestation Of Celiac Disease, Kara Lynn Jew

Master's Theses

Celiac Disease (CD) is an autoimmune disorder that emerges due to the ingestion of gluten, a protein found in a variety of common grains such as wheat, rye, and barley. Approximately 1 in 100 individuals in the US suffer from CD, making it the most commonly diagnosed gastrointestinal disorder (Ciclitira et. al., 2005). These proline-rich gluten peptides are resistant to proteolysis and accumulate in the duodenum of the small intestine. Once in the duodenum, these peptides illicit an autoimmune response resulting in villous atrophy. Current treatment for CD requires a rigorous adherence to a gluten-free diet. Nevertheless, gluten-containing grains are …

Temporal And Spatial Dynamics Of Competitive Parapatry In Chewing Lice, David J. Hafner, Mark S. Hafner, Theresa A. Spradling, Jessica E. Light, James W. Demastes

Faculty Work

We synthesize observations from 1979 to 2016 of a contact zone involving two subspecies of pocket gophers (Thomomys bottae connectens and T. b. opulentus) and their respective chewing lice (Geomydoecus aurei and G. centralis) along the Rio Grande Valley in New Mexico, U.S.A., to test predictions about the dynamics of the zone. Historically, the natural flood cycle of the Rio Grande prevented contact between the two subspecies of pocket gophers. Flood control measures completed in the 1930s permitted contact, thus establishing the hybrid zone between the pocket gophers and the contact zone between their lice (without hybridization). Since that time, …

Temporal And Spatial Dynamics Of Competitive Parapatry In Chewing Lice, Mark S. Hafner

Faculty Publications

We synthesize observations from 1979 to 2016 of a contact zone involving two subspecies of pocket gophers (Thomomys bottae connectens and T. b. opulentus) and their respective chewing lice (Geomydoecus aurei and G. centralis) along the Rio Grande Valley in New Mexico, U.S.A., to test predictions about the dynamics of the zone. Historically, the natural flood cycle of the Rio Grande prevented contact between the two subspecies of pocket gophers. Flood control measures completed in the 1930s permitted contact, thus establishing the hybrid zone between the pocket gophers and the contact zone between their lice (without hybridization). Since that time, …

Genetically Distinct Behavioral Modules Underlie Natural Variation In Thermal Performance Curves, Gregory W. Stegeman, Scott E. Baird, William S. Ryu, Asher D. Cutter

Biological Sciences Faculty Publications

Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the …

Tlr9 Agonist Mgn1703 Enhances B Cell Differentiation And Function In Lymph Nodes, Mariane H. Schleimann, Maria-Louise Kobberø, Line K. Vibholm, Katherine Kjær, Leila B. Giron, Kathleen Busman-Sahay, Chi Ngai Chan, Michael Nekorchuk, Manuel Schmidt, Burghardt Wittig, Tine E. Damsgaard, Peter Ahlburg, Michel B. Hellfritzsch, Kaja Zuwala, Frederik H. Rothemejer, Rikke Olesen, Phillipp Schommers, Florian Klein, Harsh Dweep, Andrew Kossenkov, Jens R. Nyengaard, Jacob D. Estes, Mohamed Abdel-Mohsen, Lars Østergaard, Ole S. Søgaard, Paul W. Denton

Biology Faculty Publications

Background

TLR9 agonists are being developed as immunotherapy against malignancies and infections. TLR9 is primarily expressed in B cells and plasmacytoid dendritic cells (pDCs). TLR9 signalling may be critically important for B cell activity in lymph nodes but little is known about the in vivo impact of TLR9 agonism on human lymph node B cells. As a pre-defined sub-study within our clinical trial investigating TLR9 agonist MGN1703 (lefitolimod) treatment in the context of developing HIV cure strategies (NCT02443935), we assessed TLR9 agonist-mediated effects in lymph nodes.

Methods

Participants received MGN1703 for 24 weeks concurrent with antiretroviral therapy. Seven …

Electrostatically Localized Proton Bioenergetics: Better Understanding Membrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In Mitchell's chemiosmotic theory, membrane potential Δψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ([H-⁺_L] + ⁿΣ _i=1 [M⁽ⁱ⁺⁾_L]) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane …

Targeting A Highly Repeated Germline Dna Sequence For Improved Real-Time Pcr-Based Detection Of Ascaris Infection In Human Stool, Nils Pilotte, Jacqueline R.M.A. Maasch, Alice V. Easton, Eric Dahlstrom, Thomas B. Nutman, Steven A. Williams

Biological Sciences: Faculty Publications

Background: With the expansion of soil transmitted helminth (STH) intervention efforts and the corresponding decline in infection prevalence, there is an increased need for sensitive and specific STH diagnostic assays. Previously, through next generation sequencing (NGS)-based identification and targeting of non-coding, high copy-number repetitive DNA sequences, we described the development of a panel of improved quantitative real-time PCR (qPCR)-based assays for the detection of Necator americanus, Ancylostoma duodenale, Ancylostoma ceylanicum, Trichuris trichiura, and Strongyloides stercoralis. However, due to the phenomenon of chromosome diminution, a similar assay based on high copy-number repetitive DNA was not developed for the detection of Ascaris …

Preliminary Investigation Of A Diverse Megafossil Floral Assemblage From The Middle Miocene Of Southern Mississippi, Usa, Daniel M. Mcnair, Debra Z. Stults, Brian Axsmith, Mac H. Alford, James E. Starnes

Faculty Publications

Our understanding of Miocene floras in eastern North America is hampered by the rarity of megafossil sites. An early report from the middle Miocene Hattiesburg Formation in Mississippi included palms and Ulmus. A later report listed Taxodium, Salix, either Morus or Celtis, and monocot fragments. The floral assemblage described here was recently recovered from along the Bouie River in southern Mississippi. Ferns are represented by complete Salvinia specimens including attached sporocarps, Woodwardia, and Osmunda. Conifers are represented by branchlets of Taxodium. Angiosperms include leaves attributable to the Lauraceae. Platanus is known from leaves, stipules, and fruits. …

Scale Dependence Of Sex-Specific Movement In A Small-Bodied Stream Fish, Scott R. Clark, Brian R. Kreiser, Jacob F. Schraefer, Laura K. Stewart

Faculty Publications

1. Animal movement at localised scales is often modulated by competing pressures such as avoiding predators while acquiring resources and mates. The relative magnitude of these trade‐offs may affect males and females differently, often resulting in sex‐specific differences in movement.
2. Sex‐biases in movement have been linked to mating systems (e.g. monogamy or polygamy) in birds and mammals; however, this relationship has received less attention among fishes. Using passive integrated transponder tags and a series of stationary antennas, we evaluated the movement dynamics of a small‐bodied, sexually dimorphic stream fish Fundulus olivaceus over a 30‐day period in a fourth‐order tributary to the …

Bioprinting With Human Stem Cell-Laden Alginate-Gelatin Bioink And Bioactive Glass For Tissue Engineering, Krishna C. R. Kolan, Julie A. Semon, Bradley Bromet, D. E. Day, Ming-Chuan Leu

Biological Sciences Faculty Research & Creative Works

Three-dimensional (3D) bioprinting technologies have shown great potential in the fabrication of 3D models for different human tissues. Stem cells are an attractive cell source in tissue engineering as they can be directed by material and environmental cues to differentiate into multiple cell types for tissue repair and regeneration. In this study, we investigate the viability of human adipose-derived mesenchymal stem cells (ASCs) in alginate-gelatin (Alg-Gel) hydrogel bioprinted with or without bioactive glass. Highly angiogenic borate bioactive glass (13-93B3) in 50 wt% is added to polycaprolactone (PCL) to fabricate scaffolds using a solvent-based extrusion 3D bioprinting technique. The fabricated scaffolds …

Larval Development And Morphology Of North American Burbot (Lota Lota Maculosa), Thornton Ritz

All NMU Master's Theses

Burbot (Lota lota) is a freshwater fish that exhibits a circumpolar distribution and is found throughout northern longitudes of North America. It is considered an indicator species for climate change and has a substantial effect on the trophic system as it consumes fish throughout its life. Adult, spawning burbot were captured from the Sturgeon River, Pelkie, MI. Gametes were artificially fertilized and eggs were incubated until hatch in a laboratory setting. Throughout the first ten weeks of development larvae were sampled and photographed in order to measure various morphological features. Geometric and linear morphometrics were used to quantify …

Schlafen 3 Knockout Mice Display Gender-Specific Differences In Weight Gain, Food Efficiency, And Expression Of Markers Of Intestinal Epithelial Differentiation, Metabolism, And Immune Cell Function, Emilie E. Vomhof-Dekrey, Jun Lee, Jack Lansing, Chris Brown, Diane Darland, Marc D. Basson

Biology Faculty Publications

Self-renewal and differentiation are essential for intestinal epithelium absorptive functioning and adaptation to pathological states such as short gut syndrome, ulcers, and inflammatory bowel disease. The rodent Slfn3 and its human analog Slfn12 are critical in regulating intestinal epithelial differentiation. We sought to characterize intestinal function in Slfn3 knockout (KO) mice. Male and female pair-fed Slfn3KO mice gained less weight with decreased food efficiency than wild type (WT) mice, with more pronounced effects in females. RNA sequencing performed on intestinal mucosa of Slfn3KO and WT mice showed gene ontology decreases in cell adhesion molecule signaling, tumor necrosis factor receptor binding, …

Mechanism Of Positive, Non-Additive Litter Decomposition, Na Yin

Theses and Dissertations

Litter decomposition is a fundamental ecosystem process. It is responsible for nutrient cycling and influences carbon (C) sequestration, and soil physical and chemical properties. In nature, litter is usually heterogeneous and may not decompose the way homogeneous litter does. For example, heterogeneous litter decomposition is frequently non-additive. This makes the rate of nutrient cycling as well as fluxes of C into and out of soil C pools impossible to predict. The most frequently proposed mechanisms for positive, non-additive decomposition include the supply of limiting mineral nutrients, the supply of available C (priming), and the improvement of micro-environmental conditions. However, all …

Evaluation Of Copper-Contaminated Marginal Land For The Cultivation Of Vetiver Grass (Chrysopogon Zizanioides) As A Lignocellulosic Feedstock And Its Impact On Downstream Bioethanol Production, Emily Geiger, Dibyendu Sarkar, Rupali Datta

Michigan Tech Publications, Part 1

Metal-contaminated soil could be sustainably used for biofuel feedstock production if the harvested biomass is amenable to bioethanol production. A 60-day greenhouse experiment was performed to evaluate (1) the potential of vetiver grass to phytostabilize soil contaminated with copper (Cu), and (2) the impact of Cu exposure on its lignocellulosic composition and downstream bioethanol production. Dilute acid pretreatment, enzymatic hydrolysis, and fermentation parameters were optimized sequentially for vetiver grass using response surface methodology (RSM). Results indicate that the lignocellulosic composition of vetiver grown on Cu-rich soil was favorably altered with a significant decrease in lignin and increase in hemicellulose and …

Comparison Of Nickel And Cobalt Induced Hypoxic Cell Models Using Cell Proliferation Assay, Melissa Delcasale

Seton Hall University Dissertations and Theses (ETDs)

Hypoxia is an imbalance in oxygen delivery and oxygen consumption, ultimately affecting cell survival. Low levels of oxygen diminish adenosine triphosphate synthesis resulting from a decline in oxidative phosphorylation in the mitochondria, therefore inducing apoptosis and cell death. To create a hypoxia mimicked environment, we used hypoxia mimetic compounds cobalt and nickel to treat human neuroblastoma (NMB) cells. Using hypoxic mimic human neuronal cell models, we examined and compared the effects of compound-induced hypoxia on NMB cell proliferation. The cells were treated with 100mM and 300mM concentrations of each compound at 24- and 48-hour intervals. To investigate cell proliferation, the …

Lipid Biomarkers Of Bering And Chukchi Sea Euphausiids And Their Application To Diet History, Rachel L. Pleuthner

OES Theses and Dissertations

In the eastern Bering Sea, Thysanoessa raschii are the most abundant krill species and a keystone trophic member that serve as both an important grazer and link to upper level consumers. In this system krill experience large annual variation in food resources, especially during ice advance and retreat; multiple lipid classes are used to temper the effects of those fluctuations, as well as to fuel reproduction and growth. Two shipboard feeding experiments that occurred during late spring and early summer of 2010, respectively, monitored the lipid retention in adult T. raschii and examined the fluctuation of specific lipid biomarkers under …

Sex, Drugs, & Prefrontal Cortex: Influence Of Biological Sex On Cocaine Seeking, Elizabeth M. Doncheck

Dissertations (1934 -)

Clinical observations imply that females diagnosed with substance use disorder experience enhanced relapse vulnerability compared to males, particularly within contexts of stress or peak levels of the primary estrogen 17β-estradiol (E2). We previously demonstrated that stress can potentiate cocaine seeking in male rats. The present studies investigated the influence of biological sex on stress-potentiated cocaine seeking, the ability of E2 to potentiate cocaine seeking in females, mechanisms underlying potentiated reinstatement, and sex and stress hormone effects on PrL-PFC synaptic physiology.Initial investigations revealed that, despite comparable self-administration and extinction, females display a lower threshold for cocaine-primed reinstatement than males. Unlike males, …

Thermal Quality Explains Shift In Habitat Association From Forest To Clearings For Terrestrial-Breeding Frogs Along An Elevation Gradient In Colombia, Zachary Lange

Masters Theses

Tropical ectotherms are considered particularly sensitive to changes in the thermal environment from climate change and habitat alteration. Understanding how such species’ thermal physiology relates to their habitat associations in thermally heterogeneous landscapes may help us predict responses and develop sound conservation strategies for the future. We conducted a mark-recapture study of three terrestrial breeding anuran species (Pristimantis medemi, P. savagei, P. frater) in adjacent forest and anthropogenic clearings at field sites spread across seven elevations (415-1350 m asl) in the Colombian Andes. We also performed thermal preference and critical thermal maximum assays in the lab to investigate the relationship …

Folian-Cv1 Is A Member Of A Highly Acidic Phosphoprotein Class Derived From The Foliated Layer Of The Eastern Oyster (Crassostrea Virginica) Shell And Identified In Hemocytes And Mantle, Mary Beth Johnston, A. P. Wheeler, Elizabeth P. Falwell, Meg E. Staton, Christopher A. Saski, Andrew S. Mount

Publications

The proteins derived from the foliated shell layer of the oyster, Crassostrea virginica, are unusually acidic and highly phosphorylated. Here we report the identification of a gene encoding a member of this class of phosphoproteins that we collectively refer to as folian. Using an in silico approach, a virtual probe was constructed from an N-terminal sequence (DEADAGD) determined for a 48 kDa folian phosphoprotein and used to screen an oyster EST databank. A sequence that matched the N-terminus of the 48 kDa protein was found and used to identify the full-length gene from a C. virginica BAC library. The …

Host Genetics And Geography Influence Microbiome Composition In The Sponge Ircinia Campana, Sarah M. Griffiths, Rachael E. Antwis, Luca Lenzi, Anita Lucaci, Donald C. Behringer, Mark J. Butler, Richard F. Preziosi

Biological Sciences Faculty Publications

1. Marine sponges are host to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored, and may shed light on the evolutionary and ecological relationships between host and microbiome.

2. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome.

3. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterised their …

The Role Of The Gut Microbiome In Tumor Development And Response To 5-Fluorouracil In The Apc^Min/+ Mouse, Kristen Michele Hogan

Theses and Dissertations

Colorectal cancer (CRC) is the third most frequent cancer and the second leading cause of cancer related deaths. While CRC is initiated by mutations in critical tumor suppressor genes, its development and progression to malignancy is aided by host derived cells that are recruited to the tumor microenvironment (TME) and by cancer-associated microbiota that constitute the gut microbiome. Components of the gut microbiota have been shown to alter immune cell infiltration into tumors and influence response to therapy, disease stage, and patient survival. In previous studies, we found that ApcMin/+ mice, a model of early colon carcinogenesis, had reduced tumor …

Proteomic And Genomic Evolution Of Phicbkviruses, Kiesha Wilson

Theses and Dissertations

It is estimated that there are 10³¹ phages in the global population. They continue to maintain their populations by undergoing 10²⁴ infections per second. Every time these phages replicate, there is potential for genetic exchange and mutations. Because of this potential, it has been assumed that phage evolution is heavily influenced by mosaicism. However, it is now clear that phage evolution varies by host type and phage type. Here, we use genomic and proteomic analyses to study the evolution of phages that infect Caulobacter crescentus. The study began by comparing six bacteriophage genomes that were larger than …