Research Methods in Life Sciences Commons^™

A Deeper Meaning For Shallow-Level Phylogenomic Studies: Nested Anchored Hybrid Enrichment Offers Great Promise For Resolving The Tiger Moth Tree Of Life (Lepidoptera: Erebidae: Arctiinae), Nicolas J. Dowdy, Shannon Keating, Alan R. Lemmon, Emily M. Lemmon, William E. Conner, Clare H. Scott Chialvo, Susan Weller, Rebecca B. Simmons, Melissa S. Sisson, Jennifer M. Zaspel

Department of Entomology: Faculty Publications

Anchored hybrid enrichment (AHE) has emerged as a powerful tool for uncovering the evolutionary relationships within many taxonomic groups. AHE probe sets have been developed for a variety of insect groups, though none have yet been shown to be capable of simultaneously resolving deep and very shallow (e.g., intraspecific) divergences. In this study, we present NOC1, a new AHE probe set (730 loci) for Lepidoptera specialized for tiger moths and assess its ability to deliver phylogenetic utility at all taxonomic levels. We test the NOC1 probe set with 142 individuals from 116 species sampled from all the major lineages of …

Patterns Of Avian Net Avoidance, Kate Noah

Georgia College Student Research Events

Mist netting is the most popular field technique used to estimate avian species abundance. It can, however, provide a biased estimate of species abundance as not all birds are equally likely to be captured. This is partially due to net avoidance, the purposeful evasion of mist nets by birds. Net avoidance depends on several factors, including species, net conditions such as light exposure, and environmental conditions such as cloud cover. The purpose of this research is to explore which factors contribute to net avoidance at the bird banding station located at Panola Mountain State Park in Stockbridge, Georgia. I placed …

Nearshore Vertical Distribution Of Barnacle Cyprids: Temporal Patterns And Hydrographic Variability, Gabriela Yamhure

Theses

Most benthic organisms living in the intertidal zone have planktonic larvae that reside temporarily in the water column before settling in their adult habitats. Larvae aggregate in offshore larval pools, and transport horizontally and vertically in the water to remain in the nearshore and during their pelagic life. While some horizontal transport of larvae can be attributed to advection, behavioral responses, like vertical swimming and buoyancy control, allow larvae to position themselves at depths where flow direction can be exploited. Thus, knowledge on how vertical larval distribution relates to physical processes can be fundamental to better understand larval transport. These …

Using Stable Isotopes And Diet Analysis To Assess The Potential For Competition And Coexistence Among Coyotes (Canis Latransl, Red Foxes (Vulpes Vulpes), And Gray Foxes (Urocyon Cinereoargenteus) In Maine, Henry M. Masters

Student Scholarship

When two species compete for food, one species typically outcompetes the other. Subordinate species can alleviate costs of competition by reducing diet overlap, promoting coexistence. Non-native coyotes (Canis latrans) and historically native gray foxes (Urocyon cineroargenteus) have expanded their range in Maine and may compete with native red foxes (Vulpes vulpes). To investigate competition, I analyzed stable isotopes and stomach contents to determine if coyotes, red foxes, and gray foxes differed in use of anthropogenic foods and trophic position. I predicted that coyotes utilize anthropogenic foods the least (lowest δ13C), and red foxes utilize …

The Impact Of Nicotine Accumulation Exposure On Lithobates Catebeianus Larvae Mortality, Luke Micek

UCARE: Research Products

Cigarette butts are the most littered item in the world and contain over 4,000 chemicals, including the organic compound nicotine (Slaughter et al. 2011). Billions of cigarette butts are littered each year which may wash into bodies of water, impacting the local wildlife. To determine how introduced chemicals impact the environment, it is important to study its effects on indicator species. Amphibians, such as Lithobates catebeianus, act as indicator species due to their extreme sensitivity to chemical changes in its environment. The purpose of this research project was to obtain data to help determine the impact nicotine accumulation has …

It’S Not Cuul To Juul: Nicotine Addiction, The Rise Of E-Cigarette Usage, And How Zebrafish Can Help, Anna Pearson 20

Honor Scholar Theses

No abstract provided.

Macroinvertebrate Community And Temperature Changes In A Michigan Stream, Nyika Campbell

Independent Study Project (ISP) Collection

As the climate warms, global biodiversity is plummeting and extinction rates are rising (Jenkins, 2003). Freshwater ecosystems specifically are experiencing huge losses in diversity (Jenkins, 2003; Ormerod et al., 2010; Collier et al., 2016). Conservation of invertebrates is particularly urgent because they are foundational to the trophic systems in streams and lakes, comprising 95% of all species on earth (Titley et al., 2017), and over 60% of biodiversity in freshwater ecosystems (Collier et al., 2016). Through analysis of both my own field measurements and historical data I seek to gain a preliminary understanding of temperature and macroinvertebrate community changes that …

Parásitos Gastrointestinales De Tierra Del Fuego, Argentina, Sarah Martínez

Independent Study Project (ISP) Collection

Este trabajo intentó encontrar helmintos comunes, especialmente compartidos, en cuatro carnívoros patagónicos del sur con distribuciones geográficas superpuestas y dos carnívoros patagónicos del norte, y esbozar el análisis fecal y los métodos de identificación morfológica para futuros investigadores. El estudiante encontró solo un parásito helminto compartido entre cualquier otra especie y la nutria nativa del sur del río, a pesar de una superposición en el hábitat con el visón americano invasivo, pero esto puede deberse a un bajo recuento de estudios regionales previos de helmintos en cualquiera de las especies. Se encontraron múltiples parásitos en las cuatro especies hospederas de …

Surviving Under The Reign Of El Niño Southern Oscillation: An Analysis Of The Effects Of Extreme El Niño Events On The Oceanographic And Biological Environment Of The Galápagos Islands, Ava Mcilvaine

Independent Study Project (ISP) Collection

El Niño Southern Oscillation (ENSO) is commonly known as the atmospheric and oceanographic powerhouse of the Southern Pacific Ocean. From phytoplankton to apex predators, ENSO controls the stability of species’ populations within this biodiverse ocean environment. El Niño’s 9-15 month alteration of the heat storage in the tropical Pacific drastically shifts the temperature, nutrient, and circulation gradient its marine life is accustomed to. A single degree change in the ocean’s surface layer temperature can have large consequences for marine species, and El Niño is commonly associated with Sea Surface Temperature Anomalies (SSTAs) between 2°- 6° Celsius. The potential danger El …

Climate Change Effects On Volcanoes In The Tropics: A Review Of The Deglaciation Of Antisana And Its Effects On Subsequent Water Streams And Rivers Over 20 Years, Callie C. Rominger

Independent Study Project (ISP) Collection

Located in the Northern end of Ecuador lies the stunning glacier of Antisana which attracts many tourists and whose runoff provides a significant amount of water supply for Quito. Climate change is posing threats to many ecosystems world wide but will have a more substantial impact on the volcanoes in the tropics because they do not have a seasonally altered climate. Small changes in the air temperature can have larger impacts on these areas that are adapted to constant temperatures with seasonal precipitation changes. Climate change, in recent years, had caused an increase in the glacial retreat of the Antisana …

An Apex Predator In Peril In The Western Lowlands Of Ecuador: Mapping The Population Distribution Of Harpy Eagles (Harpia Harpyja) In A Highly Deforested Region, Samuel Zhang

Independent Study Project (ISP) Collection

The Harpy Eagle (Harpia harpyja) is a highly threatened bird of prey in Ecuador. While they are already elusive in the Ecuadorian Amazon, they are even lesser known in the coastal lowlands, and their existence is threatened by rapid deforestation. This study mapped their potential distribution by examining satellite images to find intact humid forest, their ideal habitat. Habitat areas were quantified using ImageJ. The only sites found to be adequate for sustaining Harpy Eagle populations were the primary forests in the vicinities of Reserva Ecológica Mache Chindul and Reserva Ecológica Cotacachi Cayapas. The two reserves are expected to be …

The Current State Of Research On The Global Amphibian Epidemic, Chytridiomycosis: A Systematic Literature Review And View Into The Future Of The Field, Emily Dealto

Independent Study Project (ISP) Collection

Recent years have shown a rapid decline in global frog populations. Among other issues, one main cause of these declines has been linked to chytridiomycosis, a disease caused by the fungus Batrachochytrium dendrobatidis, or Bd. The discovery of this fungus is relatively recent in the field of herpetology, and thus there is much still unknown about the disease such as its distribution and what causes certain areas and species to be more susceptible to it. A systematic literature review was conducted to see where the state of the research is currently, in order to gain a better view of the …

Two (Or More) Viruses In One Bat: A Systematic Quantitative Literature Review Of Viral Coinfection In Bats, Eli J. Kaufman

Independent Study Project (ISP) Collection

Viral coinfection is an important topic in pathogen dynamics, and can increase viral shedding and change disease outcomes. As bats are carriers of important zoonoses, such as the SARS coronaviruses, rabies, and other deadly viruses, knowing more about their coinfection dynamics is important. This quantitative systematic literature review sought to show how many papers reported bat viral coinfections, and created three databases. The first database, the SQLR database was based on searches for coinfections. The second database, the Astrovirus database was to determine how much of the literature was being missed by examining a single viral family more in depth …

Cd44 Receptor Mediates Urate Crystal Phagocytosis By Macrophages And Regulates Inflammation In A Murine Peritoneal Model Of Acute Gout, Emira Bousoik, Marwa Qadri, Khaled A. Elsaid

Pharmacy Faculty Articles and Research

Gout is a chronic arthritis caused by the deposition of poorly soluble monosodium urate monohydrate (MSU) crystals in peripheral joints. Resident macrophages initiate inflammation in response to MSU mediated by NF-κB nuclear translocation and NLRP3 inflammasome activation. We investigated the role of CD44, a transmembrane receptor, in mediating MSU phagocytosis by macrophages. We used an antibody that sheds the extracellular domain (ECD) of CD44 to study the role of the receptor and its associated protein phosphatase 2A (PP2A) in macrophage activation. We also studied the significance of CD44 in mediating MSU inflammation in-vivo. Cd44^−/− BMDMs showed reduced MSU …

The Effects Of Phosphate On The Metamorphosis Of Larval Western Barred Tiger Salamanders (Ambystoma Mavortium), Lexy Polivanov

Honors Program: Senior Projects (Public)

This investigation will collect data to assist in determining if elevated aquatic phosphate levels affects the metamorphosis rate of larval western barred tiger salamanders (Ambystoma mavortium). Monoammonium phosphate fertilizers are being used on crops in Nebraska (NDA, 2017). This area lines up with the area the western barred tiger salamanders are disappearing from (Damme, 2018). Monoammonium phosphate is made up of nitrogen and phosphate. There have been several studies showing how nitrogen is harmful to amphibians such as this salamander (Griffis-Kyle, 2007) (Griffis-Kyle & Richtie, 2007), but there have not been many showing how phosphate affects amphibian’s metamorphosis …

Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex Ms

Transforming Libraries for Graduate Students

As Health Sciences Libraries evolve, the support they offer graduate students has evolved to incorporate many aspects of the research life cycle. At Tompkins-McCaw Library for the Health Sciences, we have partnered with the Wright Center for Clinical and Translational Research to offer training workshops for graduate students who are interested in using bioinformatics to plan, analyze, or execute scientific experiments. We offer two series: 1) an 8-week, 1-hour per week seminar series providing a general overview of available techniques and 2) a week-long intensive, two hours per session, series on utilizing free databases from the National Center for Biotechnology …

A Native Function For Ran Translation And Cgg Repeats In Regulating Fragile X Protein Synthesis, Caitlin M. Rodriguez, Shannon E. Wright, Michael G. Kearse, Jill M. Haenfler, Brittany N. Flores, Yu Liu, Marius F. Ifrim, M. Rebecca Glineburg, Amy Krans, Paymaan Jafar-Nejad, Michael A. Sutton, Gary J. Bassell, Jack M. Parent, Frank Rigo, Sami J. Barmada, Peter K. Todd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Repeat-associated non-AUG-initiated translation of expanded CGG repeats (CGG RAN) from the FMR1 5′-leader produces toxic proteins that contribute to neurodegeneration in fragile X-associated tremor/ataxia syndrome. Here we describe how unexpanded CGG repeats and their translation play conserved roles in regulating fragile X protein (FMRP) synthesis. In neurons, CGG RAN acts as an inhibitory upstream open reading frame to suppress basal FMRP production. Activation of mGluR5 receptors enhances FMRP synthesis. This enhancement requires both the CGG repeat and CGG RAN initiation sites. Using non-cleaving antisense oligonucleotides (ASOs), we selectively blocked CGG RAN. This ASO blockade enhanced endogenous FMRP expression in human …

Activation Of The Sonic Hedgehog Effector Smoothened Counteracts L-Dopa Induced Dyskinesia By Restoring Cholinergic Interneuron Function, Lauren Malave

Dissertations, Theses, and Capstone Projects

Many types of neurons act as multimodal signaling centers. Yet, we have only limited insight into the regulation and functional consequences of neuronal co-transmission. For example, dopamine (DA) neurons, whose degeneration causes motor deficits characteristic of Parkinson’s Diseases (PD), communicate with all their targets by DA but only a selective subset of their targets using GABA, Glutamate, and the secreted cell signaling protein Sonic Hedgehog (Shh). It is unknown whether Levo-dopamine (L-Dopa) induced dyskinesia (LIDs), a severely debilitating side effect of DA supplementation in PD, might appear because DA neuron targets are exposed to high DA- but low Shh- signaling …

A Neural Mechanism For Capnotaxis In The Naked Mole-Rat, Michael Zions

Dissertations, Theses, and Capstone Projects

A Neural Mechanism for Capnotaxis in the Naked Mole-Rat

The Naked Mole-Rat (NM-R) is a small hairless rodent that has thrived underground in the Horn of Africa for the past 40 million years. It was first discovered in 1847, but has only been maintained in captivity and studied as a laboratory animal over the past 40 years. To date, more than 400 scientific papers have been published on this species. This is relatively few compared to established lab animals like rats and mice, but those papers contain a trove of information that has changed our understanding of the constraints of …

Demarcation Of Sepsis-Induced Peripheral And Central Acidosis With Ph (Low) Insertion Cycle Peptide, Kelly E. Henry, Aisling M. Chaney, Veronica L. Nagle, Haley C. Cropper, Saghar Mozaffari, Chip Slaybaugh, Keykavous Parang, Oleg A. Andreev, Yana K. Reshetnyak, Michelle L. James, Jason S. Lewis

Pharmacy Faculty Articles and Research

Acidosis is a key driver for many diseases, including cancer, sepsis, and stroke. The spatiotemporal dynamics of dysregulated pH across disease remain elusive, and current diagnostic strategies do not provide localization of pH alterations. We sought to explore if PET imaging using hydrophobic cyclic peptides that partition into the cellular membrane at low extracellular pH (denoted as pH [low] insertion cycles, or pHLIC) can permit accurate in vivo visualization of acidosis. Methods: Acid-sensitive cyclic peptide c[E₄W₅C] pHLIC was conjugated to bifunctional maleimide-NO2A and radiolabeled with ⁶⁴Cu (half-life, 12.7 h). C57BL/6J mice were administered lipopolysaccharide (15 …