Biology Commons^™

A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud

Biology: Faculty Publications and Other Works

Background: While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and expression associated with a high-fat diet in mice. Results: We weaned genetically identical Small (SM/J) mice onto a high-fat or low-fat diet and measured their weights weekly, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. We measured liver gene expression with RNA-seq (using 21 total libraries, each pooled with 2 mice of the same sex and diet) and DNA methylation …

The Impact Of Online Homework, Time On Homework, Gender, And Metacognition In Improving Student Achievement In Undergraduate Biology Courses, Donald Bishop Cook Jr

Doctoral Dissertations and Projects

This study sought to address a gap in the literature to determine whether a relationship exists between use of online homework and student achievement in undergraduate biology courses. Previous studies have examined other STEM courses, but few have considered biology. The purpose of the study was to determine whether homework grades in online homework systems can predict student achievement in introductory undergraduate biology courses. This study utilized a correlational analysis by multiple regression using archival data to determine whether final course grades in undergraduate biology courses can be predicted by grades on online homework, time spent on online homework, gender, …

Modeling The Effect Of Post-Dispersal Seed Predation On Tropical Tree Species In Panama, Justin Tirrell

Fall Student Research Symposium 2018

Palm trees provide a unique opportunity to study what conditions optimize the probability that a seed will grow successfully. The seeds of palm trees, endocarps, are large and easy to locate. When they don't grow, predators leave marks on them that tell the story of their fate. The focus of my experiment is to determine how the current distribution pattern of parent palm trees in Panama Palm trees affects the the future distribution of seedlings. I have programmed a versatile model that takes the assumption that bruchid beetles are the sole predators acting on the seeds, and that these fall …

The Effects Of Feliway On The Stress Of Cats During Veterinary Examination, Colleen Doonan

Honors Theses

The purpose of this study was to examine the effects of Feliway® during veterinary examination. Feliway® contains a synthetic version of the F3 pheromone, secreted from the cheeks of Felis sylvestris catus when rubbing against objects in the environment. It is presumed to allow cats to establish a home range to feel secure. A double-blind study was conducted to address the limitations of another study that concluded Feliway® is useful for reducing stress experienced by cats during veterinary examination. The current study found that Feliway® is not useful by itself for adequate stress reduction during feline examinations. It was concluded …

The Genomic Landscape Of Molecular Responses To Natural Drought Stress In Panicum Hallii., John T. Lovell, Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice Macqueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger

Biological Sciences Faculty Research

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory …

Canvass: A Crowd-Sourced, Natural-Product Screening Library For Exploring Biological Space, Sara E. Kearney, Gergely ZahoráNszky-KőHalmi, Kyle R. Brimacombe, Mark J. Henderson, Caitlin Lynch, Tongan Zhao, Kanny K. Wan, Zina Itkin, Christopher Dillon, Min Shen, Dorian M. Cheff, Tobie D. Lee, Danielle Bougie, Ken Cheng, Nathan P. Coussens, Dorjbal Dorjsuren, Richard T. Eastman, Ruili Huang, Michael J. Iannotti, Surendra Karavadhi, Carleen Klumpp-Thomas, Jacob S. Roth, Srilatha Sakamuru, Wei Sun, Steven A. Titus, Adam Yasgar, Ya-Qin Zhang, Jinghua Zhao, Rodrigo B. Andrade, M. Kevin Brown, Robert B. Grossman

Chemistry Faculty Publications

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The …

Priming Of Grasping Muscles When Viewing A Safety Handle Is Diminished With Age, David A.E. Bolton, Sarah E. Schwartz, Manhoud Mansour, Garrett Rydalch, Douglas W. Mcdannald

Kinesiology and Health Science Faculty Publications

Merely viewing objects within reachable space can activate motor cortical networks and potentiate movement. This holds potential value for smooth interaction with objects in our surroundings, and could offer an advantage for quickly generating targeted hand movements (e.g. grasping a support rail to maintain stability). The present study investigated if viewing a wall-mounted safety handle resulted in automatic activation of motor cortical networks, and if this effect changes with age. Twenty-five young adults (18–30 years) and seventeen older adults (65+ years) were included in this study. Single-pulse, transcranial magnetic stimulation was applied over the motor cortical hand representation of young …

Investigating The Impact Of Oxidative Stress On Tetrahymena Thermophila Sirtuin,Thd 18, Emmanuel Dubuisson

Publications and Research

Sirtuins are a family of enzymes that fulfill various important biological functions. Investigators have looked for the implication of Sirtuin genes in cell signaling mechanisms, in the formation and silencing of heterochromatin, in the regulation of ion channels, and in the modulation of the cellular redox reactions[2]. Different model organisms have been previously used to conduct these studies; among them, there are yeasts, nematodes, and fruit flies. Each one has made some valuable contribution into the vast body of knowledge related to this field.

However, gaps in the understanding of Sirtuins functions still remain to be filled. In this optic, …

Community-Scale Water Treatment Systems In The Dominican Republic, Jonathan Racey, Annabelle Papai, Elise Fischer, Becca Johnson

Engagement & Service-Learning Summit

Engagement and Service-Learning Summit: Reciprocal and Sustainable Partnerships

How Soil Salinity Affects The Stomatal Conductance Of Baccharis Salicifolia (Mulefat/Seepwillow), Andrew Kim, Caroline Wilkerson, Mahala Bayless, Peter Du

Featured Research

This is a poster presentation demonstrating the project our group has been working on. We hypothesize that the stomatal conductance of mulefat will decrease as soil salinity increases in both pre-rain and post-rain conditions because the plant tries to absorb salt water. However, the salt water cannot pass through plant tissue and draws water out of the plant. Since plant requires water for photosynthesis, water being drawn out means less water is available for the plant to do photosynthesis. We have tested our hypothesis by collecting soil samples in Legacy park, and recorded stomatal conductance by using a leaf porometer

A Comparison Of Different Methods Of Dehydration On Baccharis Salicifolia, Michael Nicholas, Sinjun Hong

Featured Research

Baccharis salicifolia is a native riparian plant living in many places near to the Santa Monica Mountains. One of these locations is Legacy park, which has had many events effect it that has led to some very unfortunate changes. The park’s soil was tested earlier this year by a group of undergraduate students lead by Dr. Stephen Davis and was found to have a very high salinity level. The plants in the park appeared to be struggling to survive and had signs of dehydration and wilting. This led to us questioning the types of dehydration of the plants. Areas of …

A Comparison Of Photosynthetic Rate, Stomatal Conductance, And 
Electron Transport Rate Between Malosma Laurina And Encelia Californica, Yujin Choi, Isabella Armstrong, Catherina Haas, Micah Kim

Featured Research

In the Santa Monica Mountains, there are two main vegetation types: chaparral, which makes up __% of plants in these mountains, and coastal sagebrush, which makes up __%. Despite California’s acute environmental stress, both of these plants manage to survive, and even thrive in some cases. We were interested in seeing if in spite of these vast anatomical and physiological differences, these plants were able to survive at similar health rates, measured in photosynthetic rate, stomatal conductance, and electron transport rate (ETR). We have decided to choose 2 plants from 2 different leaf types of different vegetation types: Malosma laurina …

How Soil Salinity Affects The Stomatal Conductance Of Baccharis Salicifolia (Mulefat/Seepwillow), Andrew Kim, Caroline Wilkerson, Mahala Bayless, Peter Du

Featured Research

This is a poster presentation demonstrating the project our group has been working on. We hypothesize that the stomatal conductance of mulefat will decrease as soil salinity increases in both pre-rain and post-rain conditions because the plant tries to absorb salt water. However, the salt water cannot pass through plant tissue and draws water out of the plant. Since plant requires water for photosynthesis, water being drawn out means less water is available for the plant to do photosynthesis. We have tested our hypothesis by collecting soil samples in Legacy park, and recorded stomatal conductance by using a leaf porometer

Comparison Of Photosynthesis, Stomatal Conductance, And Water Potential Between Native Rhus Integrifolia And Invasive Nicotiana Glauca, Tiffany J. Egbo, Emma J. Navarro, Malaun A. Phillips, Cameron I. Zohary

Featured Research

Invasive species, such as Nicotiana glauca, are a prominent part of the Santa Monica Mountains, and could be responsible for displacing native species such as Rhus integrifolia. It was observed in the field that Nicotiana glauca was doing better than Rhus integrifolia, so our group decided to indirectly test this. Because of the invasiveness of its species, it is essential to measure the health of a native species to see if the invasive species is posing as a massive threat. Water potential, stomatal conductance, fluorescence, photosynthetic rates and electron transport rates were compared among the two plants …

Reducing Protected Lands In A Hotspot Of Bee Biodiversity: Bees Of Grand Staircase-Escalante National Monument, Joseph S. Wilson, Matt Kelly, Olivia Messinger Carril

Biology Faculty Publications

Grand Staircase-Escalante National Monument is a federally protected area found in central southern Utah. Designated in 1996 by President William J. Clinton, it was recently reduced in size by President Donald J. Trump in a proclamation that turned the one large monument into three smaller ones. A long-term, standardized study of the bees had been conducted from 2000–2003, revealing 660 species. The bee communities of the area are characterized by being spatially heterogeneous; most of the bees occur in isolated areas, with only a few being both abundant and widespread. Here we examine what affect the recent resizing of the …

Long-Term Experimental Hybridisation Results In The Evolution Of A New Sex Chromosome In Swordtail Fish, Paolo Franchini, Julia C. Jones, Peiwen Xiong, Susanne Kneitz, Zachariah Gompert, Wesley C. Warren, Ronald B. Walter, Axel Meyer, Manfred Schartl

Biology Faculty Publications

The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of …

Polyol-Producing Lactic Acid Bacteria Isolated From Sourdough And Their Application To Reduce Sugar In A Quinoa-Based Milk Substitute, Stephanie Jeske, Emanuele Zannini, Kieran M. Lynch, Aidan Coffey, Elke K. Arendt

Department of Biological Sciences Publications

The interest for plant-based dairy substitutes is expanding rapidly and consumers are opting for nutritious and healthy dairy alternatives. The reduction of sugar using different exogenous enzymes in combination with lactic acid fermentation in a quinoa-based milk substitute was explored in this study. Different amylolytic enzymes were used to release sugar from the raw material, which were further metabolised to mannitol, due to fermentation with two heterofermentative lactic acid bacteria. Using these two biotechnological techniques enables the reduction of sugar, while also preserving some of the sweetness. Leuconostoc citreum TR116, and Lactobacillus brevis TR055 were isolated from sourdough. Both strains …

Stability Of Delayed Virus Infection Model With A General Incidence Rate And Adaptive Immune Response, Zhimin Chen, Xiuxiang Liu, Zhongzhong Xie

Applications and Applied Mathematics: An International Journal (AAM)

We present the dynamical behaviors of a virus infection model with general infection rate, immune responses and two intracellular delays which describe the interactions of the HIV virus, target cells, CTL cells and antibodies within host. Three factors are incorporated in this model: (1) the intrinsic growth rate of uninfected cells, (2) a nonlinear incidence rate function considering both virus-tocell infection and cell-to-cell transmission, and (3) a nonlinear productivity and removal function. By the method of Lyapunov functionals and LaSalle’s invariance principle, we show that the global dynamics of the model is determined by the reproductive numbers for viral infection …

Revised Guidelines To Enhance The Rigor And Reproducibility Of Research Published In American Physiological Society Journals, Gina L.C. Yosten, Josephine C. Adams, Christina N. Bennett, Nigel W. Bunnett, Rita Scheman, Curt D. Sigmund, Bill J. Yates, Irving H. Zucker, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

No abstract provided.

Polyglutamine Repeat Proteins Disrupt Actin Structure In Drosophila Photoreceptors., Annie Vu, Tyler Humphries, Sean Vogel, Adam Haberman

Biology: Faculty Scholarship

Expansions of polygutamine-encoding stretches in several genes cause neurodegenerative disorders including Huntington's Disease and Spinocerebellar Ataxia type 3. Expression of the human disease alleles in Drosophila melanogaster neurons recapitulates cellular features of these disorders, and has therefore been used to model the cell biology of these diseases. Here, we show that polyglutamine disease alleles expressed in Drosophila photoreceptors disrupt actin structure at rhabdomeres, as other groups have shown they do in Drosophila and mammalian dendrites. We show this actin regulatory pathway works through the small G protein Rac and the actin nucleating protein Form3. We also find that Form3 has …

Synergistic Negative Effects Of Thermal Stress And Altered Food Resources On Echinoid Larvae, Colette Feehan, Zoe Ludwig, Suzannah Yu, Diane K. Adams

Department of Biology Faculty Scholarship and Creative Works

Multiple changes to the marine environment under climate change can have additive or interactive (antagonistic or synergistic) effects on marine organisms. Prompted by observations of anomalously warm sea temperatures and low chlorophyll concentrations during the 2013–2016 warm “Blob” event in the Northeast Pacific Ocean, we examined the combined effects of thermal stress and a shift in food resources on the development of a larval echinoid (Strongylocentrotus droebachiensis) in the laboratory. A high concentration of phytoplankton yielded faster echinus rudiment development at warm versus historical temperature, indicating a mitigating effect of abundant food on thermal stress; however, low phytoplankton concentration or …

Blue And Red Light Effects On Stomatal Oscillations, Trevor R. Ballard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Plants absorb CO₂ through pores in their leaves called stomata, which are known to open and close in response to myriad environmental and physiological triggers. We demonstrate that blue light inhibits stomatal aperture oscillations in both the guard cells and surrounding tissue layers, whereas these oscillations continue under the influence of red light. This observation of blue light behavior agrees with recent research and suggests another physiological pathway for oscillations.

The Mayfly Newsletter, Donna J. Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Relationships Between Microbial Indicators And Pathogens In Recreational Water Settings, Asja Korajkic, Brian R. Mcminn, Valerie J. Harwood

Integrative Biology Faculty and Staff Publications

Fecal pollution of recreational waters can cause scenic blight and pose a threat to public health, resulting in beach advisories and closures. Fecal indicator bacteria (total and fecal coliforms, Escherichia coli, and enterococci), and alternative indicators of fecal pollution (Clostridium perfringens and bacteriophages) are routinely used in the assessment of sanitary quality of recreational waters. However, fecal indicator bacteria (FIB), and alternative indicators are found in the gastrointestinal tract of humans, and many other animals and therefore are considered general indicators of fecal pollution. As such, there is room for improvement in terms of their use for informing risk assessment …

Towards A Better Understanding Of The Effects Of Praziquantel On The Interaction Between The Helminth Parasite Schistosoma Mansoni And Its Murine Host, Melissa Catherine Sanchez

Biology ETDs

Schistosomiasis is a neglected tropical disease (NTD) that infects 206 million individuals worldwide. This disease is caused by dioecious trematodes of the genus Schistosoma, and its pathology is associated with the large number of eggs that are released by the female. Entrapped eggs lead to host immune and inflammatory responses resulting in disease progression. Chemotherapy provides the main means of control and praziquantel (PZQ) is the only widely available drug that is used in all mass drug administration (MDA) programs. As the number of individuals receiving PZQ continues to grow, the development of PZQ resistance is a concern and …

Cold Acclimation Response Of Non-Native Italian Wall Lizard (Podarcis Siculus) Populations From New York And California, Daniel Haro

Master's Theses

Understanding how organisms respond to climatic variability and novel conditions is becoming an increasingly important task for ecologists. For ectotherms in the northern hemisphere, the response to cold is of special interest, considering that poleward range expansion events and increasing variability of temperatures during winter are already being observed as consequences of a warming planet. Though direction of change in physiological variables in response to cold is well studied in ectotherms, the extent to which traits can change and the rate at which they can change is not.

We compared the extent and rate of change in cold tolerance (CT …

Indirect Food Web Interactions: Sea Otter Predation Linked To Invasion Success In A Marine Fouling Community, Maggie F. Jenkins

Master's Theses

Humans have caused grave ecological and economic damage worldwide through the introduction of invasive species. Understanding the factors that influence community susceptibility to invasion are important for controlling further spread of invasive species. Predators have been found to provide biotic resistance to invasion in both terrestrial and marine systems. However, predators can also have the opposite effect, and facilitate invasion. Therefore, recovery or expansion of native predators could facilitate the spread of invasive species. Needles et al. (2015) demonstrated that the threatened southern sea otter (Enhydra lutris nereis) facilitated the invasion of an exotic bryozoan, Watersipora subatra. …

The Thermal Ecology Of Sceloporus Occidentalis, Luis Patricio Burgos

Master's Theses

With temperatures rising globally, assessing the possible impacts of the changing climate becomes more and more urgent. Ectotherms are excellent indicators of potential climatic ramifications on biodiversity because of their heavy reliance on the environment for their thermoregulation. Studies have historically looked at thermal tolerance values to establish predictive models for population and species extinctions.

In chapter 1, we looked at recent studies that suggest that thermal tolerance may be a plastic trait and test the effects empirically. Most studies are based on captive lizards acclimated to laboratory conditions that do not necessarily reflect natural environments, and if thermal tolerance …

Lakeshore Modification Reduces Secondary Production Of Macroinvertebrates In Littoral But Not Deeper Zones, Marlene Pätzig, Yvonne Vadeboncoeur, Mario Brauns

Biological Sciences Faculty Publications

Littoral macroinvertebrates are an integral component of lake food webs, but their productivity may be affected by shoreline alteration. We hypothesized that human modification of lake shores simplifies habitat diversity, which, in turn, affects littoral macroinvertebrate production and patterns of depth–production relationships. Furthermore, we expected that lakeshore modification would favor nonnative species, potentially compensating for negative effects of lakeshore modification on production of native taxa. To test these ideas, we estimated benthic macroinvertebrate production in the upper littoral, middle littoral, and profundal zones of a large lowland lake (Lake Scharmützelsee) in Northeast Germany. We collected samples between April and November …

Comprehensive Inventory Of True Flies (Diptera) At A Tropical Site, Brian V. Brown, Art Borkent, Peter H. Adler, Dalton De Souza Amorim, Kevin Barber, Daniel Bickel, Stephanie Boucher, Scott E. Brooks, John Burger, Zelia L. Burington, Renato S. Capellari, Daniel N.R. Costa, Jeffrey M. Cumming, Greg Curler, Carl W. Dick, John H. Epler, Eric Fisher, Stephen D. Gaimari, Jon Gelhaus, David A. Grimaldi, John Hash, Martin Hauser, Heikki Hippa, Sergio Ibáñez-Bernal, Mathias Jaschhof, Elena P. Kameneva, Peter H. Kerr, Valery Korneyev, Cheslavo A. Korytkowski

Biological Sciences Faculty Publications

Estimations of tropical insect diversity generally suffer from lack of known groups or faunas against which extrapolations can be made, and have seriously underestimated the diversity of some taxa. Here we report the intensive inventory of a four-hectare tropical cloud forest in Costa Rica for one year, which yielded 4332 species of Diptera, providing the first verifiable basis for diversity of a major group of insects at a single site in the tropics. In total 73 families were present, all of which were studied to the species level, providing potentially complete coverage of all families of the order likely to …