Biology Commons^™

The Drosophila Melanogaster Neprilysin Nepl15 Is Involved In Lipid And Carbohydrate Storage, Surya Jyoti Banerjee, Christine Woods, Micheal Burnett, Scarlet J. Park, William W. Ja, Jennifer Curtiss

Faculty Publications - Biological Sciences

The prototypical M13 peptidase, human Neprilysin, functions as a transmembrane “ectoenzyme” that cleaves neuropeptides that regulate e.g. glucose metabolism, and has been linked to type 2 diabetes. The M13 family has undergone a remarkable, and conserved, expansion in the Drosophila genus. Here, we describe the function of Drosophila melanogaster Neprilysin-like 15 (Nepl15). Nepl15 is likely to be a secreted protein, rather than a transmembrane protein. Nepl15 has changes in critical catalytic residues that are conserved across the Drosophila genus and likely renders the Nepl15 protein catalytically inactive. Nevertheless, a knockout of the Nepl15 gene reveals a reduction in triglyceride and …

Exploration Of Dark Chemical Genomics Space Via Portal Learning: Applied To Targeting The Undruggable Genome And Covid-19 Anti-Infective Polypharmacology, Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip Boume, Lei Xie

Publications and Research

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning , to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) …

Understanding Differences In Underrepresented Minorities And First-Generation Student Perceptions In The Introductory Biology Classroom, Jacob Jantzer, Thomas W. Kirkman, Katherine L. Furniss

Biology Faculty Publications

We used quantitative methods to better understand the perceptions of students in an introductory biology course (Biology 101) at a small, liberal arts college (SLAC) that is also a primarily white institution (PWI). In pre/post surveys, we asked students questions related to their attitudes and beliefs about their professor, classmates, and Biology 101. We were especially interested in the responses and outcomes of underrepresented minorities (URM) and first-generation (FG) students. Our findings suggest URM and FG students have a decreased sense of belonging and increased perceptions of exclusion and differential treatment due to race. These findings can explain, in part, …

Patch Size Drives Colonization By Aquatic Insects, With Minor Priority Effects Of A Cohabitant, Reed C. Scott, Matthew R. Pintar, William J. Resetarits

Faculty and Student Publications

Patch size is one of the most important factors affecting the distribution and abundance of species, and recent research has shown that patch size is an important niche dimension affecting community structure in aquatic insects. Building on this result, we examined the impact of patch size in conjunction with presence of larval anurans on colonization by aquatic insects. Hyla chrysoscelis (Cope's gray treefrog) larvae are abundant and early colonists in fishless lentic habitats, and these larvae can fill multiple ecological roles. By establishing larvae in mesocosms prior to colonization, we were able to assess whether H. chrysoscelis larvae have priority …

Rcb Initiates Arabidopsis Thermomorphogenesis By Stabilizing The Thermoregulator Pif4 In The Daytime, Yongjian Qiu, Elise K. Pasoreck, Chan Yul Yoo, Jiangman He, He Wang, Abhishesh Bajracharya, Meina Li, Haley D. Larsen, Stacey Cheung, Meng Chen

Faculty and Student Publications

Daytime warm temperature elicits thermomorphogenesis in Arabidopsis by stabilizing the central thermoregulator PHYTOCHROME INTERACTING transcription FACTOR 4 (PIF4), whose degradation is otherwise promoted by the photoreceptor and thermosensor phytochrome B. PIF4 stabilization in the light requires a transcriptional activator, HEMERA (HMR), and is abrogated when HMR’s transactivation activity is impaired in hmr-22. Here, we report the identification of a hmr-22 suppressor mutant, rcb-101, which surprisingly carries an A275V mutation in REGULATOR OF CHLOROPLAST BIOGENESIS (RCB). rcb-101/hmr-22 restores thermoresponsive PIF4 accumulation and reverts the defects of hmr-22 in chloroplast biogenesis and photomorphogenesis. Strikingly, similar to hmr, the null rcb-10 mutant impedes …

Insight Into The Evolution Of Anuran Foot Flag Displays: A Comparative Study Of Color And Kinematics, Nigel K. Anderson, K. V. Gururaja, Lisa A. Mangiamele, Erin C. Netoskie, Sarah Smith, Matthew J. Fuxjager, Doris Preininger

Biological Sciences: Faculty Publications

Understanding how complex animal displays evolve is a major goal of evolutionary organismal biology. Here, we study this topic by comparing convergently evolved gestural displays in two unrelated species of frog (Bornean Rock Frog, Staurois parvus, and Kottigehara Dancing Frog, Micrixalus kottigeharensis). This behavior, known as a foot flag, is produced when a male ?waves' his hindlimb at another male during bouts of competition for access to mates. We assess patterns of variation in the color of frog feet and the kinematics of the display itself to help pinpoint similarities and differences of the visual signal elements. We find clear …

Light Pollution Levels On Beaches: How Window Tinting Effects Disorientation Of Sea Turtles On Hilton Head Island, Kathryn (Kate) Hettiger

Biology: Student Scholarship & Creative Works

Loggerhead sea turtles, an endangered species, are decreasing at alarming rates worldwide. Artificial light from beachfront hotels on Hilton Head Island are causing disorientation in Loggerhead sea turtle hatchlings affecting their ability to successfully find the ocean. To mitigate this, exterior windows facing the ocean will be tinted using either tinting spray, which will be implemented at the Marriott Grande Ocean, or using tinting film, which will be implemented at the Marriott Westin. During the typical nesting and hatching season (May-October), sea turtle hatchling tracks will be recorded using drones to compare the effects of various levels of light pollution …

Climate And Seasonality Drive The Richness And Composition Of Tropical Fungal Endophytes At A Landscape Scale, Shuzo Oita, Alicia Ibáñez, François Lutzoni, Jolanta Miadlikowska, József Geml, Louise A. Lewis, Erik F. Y. Hom, Ignazio Carbone, Jana M. U’Ren, A. Elizabeth Arnold

Faculty and Student Publications

Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves—fungal endophytes—that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and …

Coevolutionary Methods Enable Robust Design Of Modular Repressors By Reestablishing Intra-Protein Interactions, Xian-Li Jiang, Rey P. Dimas, Clement T.Y. Chan, Faruck Morcos

Biology Faculty Publications and Presentations

enetic sensors with unique combinations of DNA recognition and allosteric response can be created by hybridizing DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from distinct transcriptional repressors. This module swapping approach is limited by incompatibility between DBMs and LBMs from different proteins, due to the loss of critical module-module interactions after hybridization. We determine a design strategy for restoring key interactions between DBMs and LBMs by using a computational model informed by coevolutionary traits in the LacI family. This model predicts the influence of proposed mutations on protein structure and function, quantifying the feasibility of each mutation for rescuing hybrid …

Comparative Riverscape Genomics Of The Rainbow Darter (Etheostoma Caeruleum) In Glaciated And Unglaciated Environments, Jon M. Luiken, Tony Gamble, Peter B. Berendzen

Biological Sciences Faculty Research and Publications

Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region, there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate …

Spatial Distribution Of Conspecific Genotypes Within Chimeras Of The Branching Coral Stylophora Pistillata, Gabriele Guerrini, Dor Shefy, Jacob Douek, Nadav Shashar, Tamar L. Goulet, Baruch Rinkevich

Faculty and Student Publications

Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each …

Automatic Camera Trap Classification Using Wildlife-Specific Deep Learning In Nilgai Management, Matthew Kutugata, Jeremy Baumgardt, John A. Goolsby, Alexis Racelis

Biology Faculty Publications and Presentations

Camera traps provide a low-cost approach to collect data and monitor wildlife across large scales but hand-labeling images at a rate that outpaces accumulation is difficult. Deep learning, a subdiscipline of machine learning and computer science, has been shown to address the issue of automatically classifying camera trap images with a high degree of accuracy. This technique, however, may be less accessible to ecologists, to small scale conservation projects, and has serious limitations. In this study, a simple deep learning model was trained using a dataset of 120,000 images to identify the presence of nilgai Boselaphus tragocamelus, a regionally specific …

[Review Of] What Is A Complex System? By James Ladyman And Karoline Wiesner. New Haven (Connecticut): Yale University Press. $35.00 (Paper). Xi + 169 P.; Ill.; Index. Isbn: 978-0-300-25110-4. 2020., Joseph Robert Burger

Biology Faculty Publications

No abstract provided.

Quantifying Planarian Behavior As An Introduction To Object Tracking And Signal Processing, Nicole C. Stowell, T. Goel, Vir Shetty , '22, Jocelyne Noveral, Eva-Maria S. Collins

Biology Faculty Works

Answers to mechanistic questions about biological phenomena require fluency in a variety of molecular biology techniques and physical concepts. Here, we present an interdisciplinary approach to introducing undergraduate students to an important problem in the areas of animal behavior and neuroscience—the neuronal control of animal behavior. In this lab module, students explore planarian behavior by quantitative image and data analysis with freely available software and low-cost resources. Planarians are ∼1–2-cm-long aquatic free-living flatworms famous for their regeneration abilities. They are inexpensive and easy to maintain, handle, and perturb, and their fairly large size allows for image acquisition with a webcam, …

Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …

Commentary: The Past, Present, And Future Of The Global Raptor Impact Network, James R. Belthoff, Julie A. Heath

Biology Faculty Publications and Presentations

Most raptor populations are declining and nearly a fifth are threatened with extinction; thus there is a need to increase collaboration to ensure efficient and effective research, management, and conservation. Here, we introduce the Global Raptor Impact Network (GRIN; www.globalraptors.org), a tool to enhance collaboration and conservation impact of the raptor research community. We provide an overview of the history and current state of GRIN, including plans for expansion. Predecessors to GRIN include The African Raptor DataBank, which was launched in 2012 to ascertain the conservation status of raptors across Africa; and the Global Raptor Information Network, which was launched …

Expanding The Conservation Genomics Toolbox: Incorporating Structural Variants To Enhance Genomic Studies For Species Of Conservation Concern, Stephanie J. Galla

Biology Faculty Publications and Presentations

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics …

Open System Metabolism Of The Grand River From Headwaters To Mouth, Colin J. Assenmacher

Honors Projects

The Grand River is the longest river in Michigan and has been greatly impacted by human activities, particularly logging in the mid-1800s, which when coupled with 20th-century urbanization and continued agricultural use, led to historically poor river health. Despite this, actions throughout the past 50 years by federal, state, and local citizen involvement, have resulted in increased river health and broader water quality monitoring within the watershed. During the summer of 2021, rapid bioassessments targeting benthic macroinvertebrates were conducted along the Grand River, with the primary goal of following up on prior state-led surveys conducted at different locations along the …

The Annual Cycle For Whimbrel Populations Using The Western Atlantic Flyway, B. D. Watts, F. Smith, C. Hines, L. Duval, Et Al.

Arts & Sciences Articles

Many long-distance migratory birds use habitats that are scattered across continents and confront hazards throughout the annual cycle that may be population-limiting. Identifying where and when populations spend their time is fundamental to effective management. We tracked 34 adult whimbrels (Numenius phaeopus) from two breeding populations (Mackenzie Delta and Hudson Bay) with satellite transmitters to document the structure of their annual cycles. The two populations differed in their use of migratory pathways and their seasonal schedules. Mackenzie Delta whimbrels made long (22,800 km) loop migrations with different autumn and spring routes. Hudson Bay whimbrels made shorter (17,500 km) …

Local Canopy Disturbance As An Explanation For Long-Term Increases In Liana Abundance, Stefan A. Schnitzer, David M. Defilippis, Marco Visser, Sergio Estrada-Villegas, Rigoberto Rivera-Camaña, Boris Bernal, Salomé Peréz, Abelino Valdéz, Seberino Valdéz, Antonio Aguilar, James W. Dalling, Eben N. Broadbent, Angelica M. Almeyda Zambrano, Stephen P. Hubbell, Maria Garcia-Leon

Biological Sciences Faculty Research and Publications

Canopy disturbance explains liana abundance and distribution within tropical forests and thus may also explain the widespread pattern of increasing liana abundance; however, this hypothesis remains untested. We used a 10-year study (2007–2017) of 117,100 rooted lianas in an old-growth Panamanian forest to test whether local canopy disturbance explains increasing liana abundance. We found that liana density increased 29.2% and basal area 12.5%. The vast majority of these increases were associated with clonal stem proliferation following canopy disturbance, particularly in liana-dense, low-canopy gaps, which had far greater liana increases than did undisturbed forest. Lianas may be ecological niche constructors, arresting …

Phenology Dictates The Impact Of Climate Change On Geographic Distributions Of Six Co-Occurring North American Grasshoppers, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

Throughout the last century, climate change has altered the geographic distributions of many species. Insects, in particular, vary in their ability to track changing climates, and it is likely that phenology is an important determinant of how well insects can either expand or shift their geographic distributions in response to climate change. Grasshoppers are an ideal group to test the hypothesis that phenology correlates with range expansion, given that co-occurring confamilial, and even congeneric, species can differ in phenology. Here, I tested the hypothesis that early- and late-season species should possess different range expansion potentials, as estimated by habitat suitability …

Herbivores Alleviate The Negative Effects Of Extreme Drought On Plant Community By Enhancing Dominant Species, Chong Xu, Yuguang Ke, Honghui Wu, Melinda D. Smith, Nathan P. Lemoine, Weiguo Zhang, Qiang Yu

Biological Sciences Faculty Research and Publications

Aims

Both extreme drought and insect herbivores can suppress plant growth in grassland communities. However, most studies have examined extreme drought and insects in isolation, and there is reason to believe that insects might alter the ability of grasslands to withstand drought. Unfortunately, few studies have tested the interactive effects of extreme drought and insect herbivores in grassland communities.

Methods

Here, we tested the drought–herbivore interactions using a manipulative experiment that factorially crossed extreme drought with the exclusion of insect herbivores in a temperate semiarid grassland in Inner Mongolia.

Important Findings

Our results demonstrated that both extreme drought and insect …

The Philosophy Of Outliers: Reintegrating Rare Events Into Biological Science, Chelsea N. Cook, Angela R. Freeman, James C. Liao, Lisa A. Mangiamele

Biological Sciences Faculty Research and Publications

Individual variation in morphology, physiology, and behavior has been a topic of great interest in the biological sciences. While scientists realize the importance of understanding diversity in individual phenotypes, historically the “minority” results (I.e., outlier observations or rare events) of any given experiment have been dismissed from further analysis. We need to reframe how we view “outliers” to improve our understanding of biology. These rare events are often treated as problematic or spurious, when they can be real rare events or individuals driving evolution in a population. It is our perspective that to understand what outliers can tell us in …

A Global Agenda For Advancing Freshwater Biodiversity Research, Alain Maasri, Sonja C. Jähnig, Hendrik Freitag, 93 Co-Authors

Biology Faculty Publications

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

Ecoacoustic Monitoring Of Lake Sturgeon (Acipenser Fulvescens) Spawning And Its Relation To Anthropogenic Noise, Dennis M. Higgs, Riley K. Beach

Integrative Biology Publications

Lake sturgeon (Acipenser fulvescens) are endangered in the Laurentian Great Lakes with increasing binational efforts to establish spawning grounds to aid restoration. While SCUBA surveys can document spawning activity, these are labour-intensive and may disrupt spawning. We used passive acoustic monitoring to quantify spawning sounds of lake sturgeon as a first step to developing remote sensing of sturgeon spawning grounds. Acipenser sp. are known to make a variety of sounds including, “thunders” (aka drums), which have been documented in A. fulvescens during spawning. We quantified drums from a known spawning bed. We recorded 5 different potential sturgeon sounds but only …

Applying Behavioral And Physiological Measures To Assess The Relative Impact Of The Prolonged Covid-19 Pandemic Closure On Two Mammal Species At The Oregon Zoo: Cheetah (A. Jubatus) And Giraffe (G. C. Reticulata And G. C. Tippelskirchii), Laurel Fink, Candace D. Scarlata, Becca Vanbeek, Todd Bodner, Nadja C. Wielebnowski

Biology Faculty Publications and Presentations

The effect of visitor presence on zoo animals has been explored in numerous studies over the past two decades. However, the opportunities for observations without visitors have been very limited at most institutions. In 2020, the Oregon Zoo was closed, in response to the global SARSCoV-2 (COVID-19) pandemic, from 15 March 2020 to 12 July 2020, resulting in approximately four consecutive months without visitor presence. This study aimed to quantify potential behavioral and hormonal changes expressed during two transition periods in zoo visitor attendance: the initial time period before and after closure in March 2020 and time before and after …

The Philosophy Of Outliers: Reintegrating Rare Events Into Biological Science, Chelsea N. Cook, Angela R. Freeman, James C. Liao, Lisa A. Mangiamele

Biological Sciences: Faculty Publications

Individual variation in morphology, physiology, and behavior has been a topic of great interest in the biological sciences.While scientists realize the importance of understanding diversity in individual phenotypes, historically the minority results (i.e., outlier observations or rare events) of any given experiment have been dismissed from further analysis. We need to reframe how we view outliers to improve our understanding of biology. These rare events are often treated as problematic or spurious, when they can be real rare events or individuals driving evolution in a population. It is our perspective that to understand what outliers can tell us in our …

Development Of Comprehensive Theoretical Morphospaces For Canine Cranial Morphology, Alexa Ortega, Nicholas Hebdon, Lindsay Waldrop

Student Scholar Symposium Abstracts and Posters

Throughout the evolution of the family Canidae, there is a continuous belief that canines have an exceptional olfactory system which allows them to have a heightened sense of smell. Because of this olfactory sophistication, canines have become prevalent as detection animals in the military, homeland security, law enforcement, forensics, and civilian applications. However, while the trait is highly regarded, the exact role of nasal morphology is understudied. We aim to investigate the influences of nasal cavity and internal structure morphology in odor detection. However, nasal structure is a sophisticated morphological target and requires innovative solutions to capture the key variables …

Snook Neurocranium Scan Mello & Glanzmann, Christopher F. Glanzmann, Madison A. Mello

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

This file is a 3D scan of a Snook Neurocranium. Snook head provided by DR. Kerstetter and scan performed by Chris Glanzmann and Madison Mello. Medium detail scan with a simplification ratio of 50.

Tile Fish (Lopholatilus Villarii) Neurocranium, Maeya C. Yeatman, Sebastian K. Chan, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from 12 cm total length (TL) Tile fish (Lopholatilus villarii), collected from Foodtown on 10/22/2021 by Maeya Yeatman and Sebastian Chan