Biology Commons^™

Patterns And Mechanisms Of Heterogeneous Breeding Distribution Shifts Of North American Migratory Birds, Hanna M. Mccaslin, Julie A. Heath

Biology Faculty Publications and Presentations

There is widespread evidence that species distributions are shifting in response to climate change. Warming temperatures and climate niche constraints are hypothesized drivers of northward shifts in temperate migratory bird breeding distributions, but heterogeneity in the direction of distribution shifts suggests that the climate niche hypothesis does not explain all changes in distributions. We propose that: 1) changes in migration costs and benefits related to dampened seasonal differences between breeding and winter areas, 2) sensitivity to supplemental cues that affect duration of migration and onset of reproduction, 3) a latitudinal mismatch-driven fitness gradient, or a combination of these drivers may …

Tolerance Of Novel Toxins Through Generalized Mechanisms: Simulating Gradual Host Shifts Of Butterflieskristin, Kristin L. Sikkink, Reilly Hostager, Megan E. Kobiela, Nathan Fremling, Katherine Johnston, Amod Zambre, Emilie C. Snell-Rood

School of Biological Sciences: Faculty Publications

Organisms encounter a wide range of toxic compounds in their environments, from chemicals that serve anticonsumption or anticompetition functions to pollutants and pesticides. Although we understand many detoxification mechanisms that allow organisms to consume toxins typical of their diet, we know little about why organisms vary in their ability to tolerate entirely novel toxins. We tested whether variation in generalized stress responses, such as antioxidant pathways, may underlie variation in reactions to novel toxins and, if so, their associated costs. We used an artificial diet to present cabbage white butterfly caterpillars (Pieris rapae) with plant material containing toxins not experienced …

Differential Cytotoxicity Induced By Transition Metal Oxide Nanoparticles Is A Function Of Cell Killing And Suppression Of Cell Proliferation, Larry M. Tolliver, Natalie J. Holl, Fang Yao Stephen Hou, Han-Jung Lee, Melissa H. Cambre, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

The application of nanoparticles (NPs) in industry is on the rise, along with the potential for human exposure. While the toxicity of microscale equivalents has been studied, nanoscale materials exhibit different properties and bodily uptake, which limits the prediction ability of microscale models. Here, we examine the cytotoxicity of seven transition metal oxide NPs in the fourth period of the periodic table of the chemical elements. We hypothesized that NP-mediated cytotoxicity is a function of cell killing and suppression of cell proliferation. To test our hypothesis, transition metal oxide NPs were tested in a human lung cancer cell model (A549). …

Life Line March 2020, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

The Department Welcomes Dr. Sinn; Modeling to Help with Global Research; The Paradise of Bombs Revisited; The End of an Era in Conesville Ohio; Reports from two recipients of the Melinda Phinney Award for Pre-Med Travel Experiences; Preparing Skins for Study; Genomics in the Jungle; Zoo Program Gets New T -Shirt and Sweatshirt Designs; Aquarium Track Dives Right In; Dr. Svitana’s Sabbatical Accomplishments;Biology Behind Bars; Grossology: The Science of Icky, Sticky, Disgusting Things.

Thermal Ecology Of The Federally Endangered Blunt-Nosed Leopard Lizard, Kathleen N. Ivey

Master's Theses

Recognizing how climate change will impact populations can aid in making decisions about approaches for conservation of endangered species. The Blunt-nosed Leopard Lizard (Gambelia sila) is a federally endangered species that, despite protection, remains in extremely arid, hot areas and may be at risk of extirpation due to climate change. We collected data on the field-active body temperatures, preferred body temperatures, and upper thermal tolerance of G. sila. We then described available thermal habitat using biophysical models, which allowed us to (1) describe patterns in lizard body temperatures, microhabitat temperatures, and lizard microhabitat use, (2) quantify the …

Testing The Interaction Between The Cystic Fibrosis Transmembrane Regulator And Anoctamin 1 In Amacrine Cells Of Gallus Gallus Retinas, Hailey Danielle Simpson

Honors Capstones

No abstract provided.

Investigating The Origins Of Facultative Heterotrophy In Cyanobacteria, Emily A. Brown

Honors Capstones

No abstract provided.

Gnrh As A Neuromodulator In Midbrain Sensory Regions During The Female Cichlid Reproductive Cycle, Mark Anthony Maier Ii

Honors Capstones

No abstract provided.

Unraveling The Role Of The Enigmatic Matk Maturase In Chloroplast Group Iia Intron Excision, Michelle M. Barthet, Christopher L. Pierpont, Emilie Katherine Tavernier

Biology

Maturases are prokaryotic enzymes that aid self-excision of introns in precursor RNAs and have evolutionary ties to the nuclear spliceosome. Both the mitochondria and chloroplast, due to their prokaryotic origin, encode a single intron maturase, MatR for the mitochondria and MatK for the chloroplast. MatK is proposed to aid excision of seven different chloroplast group IIA introns that reside within precursor RNAs for essential elements of chloroplast function. We have developed an in vitro activity assay to test chloroplast group IIA intron excision. Using this assay, we demonstrate self-excision of the group IIA intron of the second intron of rps12 …

Optimizing Phylogenomics With Rapidly Evolving Long Exons: Comparison With Anchored Hybrid Enrichment And Ultraconserved Elements, Benjamin R. Karin, Tony Gamble, Todd R. Jackman

Biological Sciences Faculty Research and Publications

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), …

Experimental Psychology Meets Behavioral Ecology: What Laboratory Studies Of Learning Polymorphisms Mean For Learning Under Natural Conditions, And Vice Versa, Brian H. Smith, Chelsea N. Cook

Biological Sciences Faculty Research and Publications

Behavior genetics, and specifically the study of learning and memory, has benefitted immensely from the development of powerful forward- and reverse-genetic methods for investigating the relationships between genes and behavior. Application of these methods in controlled laboratory settings has led to insights into gene–behavior relationships. In this perspective article, we argue that the field is now poised to make significant inroads into understanding the adaptive value of heritable variation in behavior in natural populations. Studies of natural variation with several species, in particular, are now in a position to complement laboratory studies of mechanisms, and sometimes this work can lead …

Correction To: High-Coverage Genomes To Elucidate The Evolution Of Penguins, Hailin Pan, Theresa Cole, Xupeng Bi, Miaoquan Fang, Chengran Zhou, Zhengtao Yang, Daniel Ksepka, Tom Hart, Juan Bouzat, Lisa Argilla, Mads Bertelsen, P. Boersma, Charles-Andre Bost, Yves Cherel, Peter Dann, Steven Fiddaman, Pauline Howard, Kim Labuschagne, Thomas Mattern, Gary Miller, Patricia Parker, Richard Phillips, Petra Quillfeldt, Peter Ryan, Helen Taylor, David Thompson, Melanie Young, Martin Ellegaard, M. Thomas Gilbert, Mikkel-Holger Sinding, George Pacheco, Lara Shepherd, Alan Tennyson, Stefanie Grosser, Emily Kay, Lisa Nupen, Ursula Ellenberg, David Houston, Andrew Reeve, Kathryn Johnson, Juan Masello, Thomas Stracke, Bruce Mckinlay, Pablo Garc´Ia Borboroglu, De-Xing Zhang, Guojie Zhang

Biology Department Faculty Works

In the original version of the article “High-coverage genomes to elucidate the evolution of penguins” by Hailin Pan et al. [1], the authors received a request to make some clarifications and changes in the acknowledgements, the following is the modified version:“We thank the following: John Cockrem, Scott Flemming, Helen McConnell, Chris Rickard, Sarah Fraser, Otto Whitehead, Kyle Morrison, and Amy Van Buren for help collecting samples; Jonathan Banks, Kirsten Rodgers, and Jo Hiscock for sample information; Manuel Paredes Oyarzún and Hernán Rivera Meléndez for facilitating permits and sample collection; Lauren Tworkowski, Richard O'Rorke, and Joanna Sumner for facilitating sample collection; …

A Positive Feedback Loop Of Hippo- And C-Jun-Amino-Terminal Kinase Signaling Pathways Regulates Amyloid-Beta-Mediated Neurodegeneration, Madison Irwin, Meghana Tare, Aditi Singh, Oorvashi Roy Puli, Neha Gogia, Matthew Riccetti, Prajakta Deshpande, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD, OMIM: 104300) is an age-related disorder that affects millions of people. One of the underlying causes of AD is generation of hydrophobic amyloid-beta 42 (Aβ42) peptides that accumulate to form amyloid plaques. These plaques induce oxidative stress and aberrant signaling, which result in the death of neurons and other pathologies linked to neurodegeneration. We have developed a Drosophila eye model of AD by targeted misexpression of human Aβ42 in the differentiating retinal neurons, where an accumulation of Aβ42 triggers a characteristic neurodegenerative phenotype. In a forward deficiency screen to look for genetic modifiers, we identified a molecularly …

Hydrophilic Porphyrins Based Chemosensors For First Transition Series Metal Ions [Chemistry], Sunaina Singh

Open Educational Resources

General Chemistry is a two-semester course (General Chemistry I, SCC 201 and General Chemistry II, SCC 202) required for majors in Biology and Environmental Sciences.

This lab experiment, aligned to LaGuardia Community College’s Inquiry and Problem Solving Core Competency and Written Communication Ability was designed for General Chemistry I (SCC 201 Honors) course. Honors courses in LaGuardia emphasize critical thinking, analytical writing, and introduce students to research. This lab experiment provides an opportunity for students to engage in hands-on laboratory work, to develop laboratory skills, and to conduct research in the classroom by using two water soluble porphyrins to detect …

Identifying Viruses From Metagenomic Data Using Deep Learning, Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, Fengzhu Sun

Biology

Background: The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data. Methods: Here we developed a reference-free and alignment-free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using deep learning. Results: Trained based on sequences from viral RefSeq discovered before May 2015, and evaluated on those discovered after that date, DeepVirFinder outperformed the state-of-the-art method VirFinder at all contig lengths, achieving AUROC 0.93, 0.95, …

Spatial Contrasts In Hepatic And Biliary Pahs In Tilefish (Lopholatilus Chamaeleonticeps) Throughout The Gulf Of Mexico, With Comparison To The Northwest Atlantic, Susan M. Snyder, Jill A. Olin, Erin L. Pulster, Steven A. Murawski

Michigan Tech Publications, Part 1

A multinational demersal longline survey was conducted on the Gulf of Mexico continental shelf over the years 2015 and 2016 to generate a Gulf-wide baseline of polycyclic aromatic hydrocarbon (PAH) concentrations in demersal fishes. Tilefish (Lopholatilus chamaeleonticeps) were sampled in all regions of the Gulf of Mexico for biometrics, bile, and liver. Tilefish liver was also obtained from surveys in the northwest Atlantic Ocean for comparison. Liver tissues (n ¼ 305) were analyzed for PAHs and select alkylated homologs using QuEChERS extractions and gas chromatography tandem mass spectrometry. Bile samples (n ¼ 225) were analyzed for biliary PAH metabolites using …

Gender Differences In Diet-Induced Steatotic Disease In Cyp2b-Null Mice, Melissa M. Heintz, Rebecca Mcree, Ramiya Kumar, William S. Baldwin

Publications

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease; however, progression to nonalcoholic steatohepatitis (NASH) is associated with most adverse outcomes. CYP2B metabolizes multiple xeno- and endobiotics, and male Cyp2b-null mice are diet-induced obese (DIO) with increased NAFLD. However, the DIO study was not performed long enough to assess progression to NASH. Therefore, to assess the role of Cyp2b in fatty liver disease progression from NAFLD to NASH, we treated wildtype (WT) and Cyp2b-null mice with a normal diet (ND) or choline-deficient, L-amino acid-defined high fat diet (CDAHFD) for 8 weeks and determined metabolic and molecular changes. CDAHFD-fed …

Probing The Function Of Long Noncoding Rnas In The Nucleus, Sajal Medha K. Akkipeddi , '20, A. J. Velleca, Dawn M. Carone

Biology Faculty Works

The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which …

Do Foliar Endophytes Matter In Litter Decomposition?, Emily R. Wolfe, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their effects on decomposition rates. From 29 studies and 1 review, we compiled a comprehensive table of 710 leaf-associated fungal taxa, including the type of tissue these taxa were associated with and isolated from, whether they were reported as endo- or epiphytic, and whether they had reported saprophytic abilities. Aquatic (i.e., in-stream) decomposition studies of endophyte-affected litter were …

Honeybees Fail To Discriminate Floral Scents In A Complex Learning Task After Consuming A Neonicotinoid Pesticide, Julie A. Mustard, Annie Gott, Jennifer Scott, Nancy L. Chavarria, Geraldine A. Wright

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Neonicotinoids are pesticides used to protect crops but with known secondary influences at sublethal doses on bees. Honeybees use their sense of smell to identify the queen and nestmates, to signal danger and to distinguish flowers during foraging. Few behavioural studies to date have examined how neonicotinoid pesticides affect the ability of bees to distinguish odours. Here, we use a differential learning task to test how neonicotinoid exposure affects learning, memory, and olfactory perception in foraging-age honeybees. Bees fed with thiamethoxam could not perform differential learning and could not distinguish odours during short and long-term memory tests. Our data indicate …

The Pi3k Pathway Impacts Stem Gene Expression In A Set Of Glioblastoma Cell Lines, Eduardo Martinez, Neftali Vazquez, Alma Lopez, Victor Fanniel, Lilia Sanchez, Rebecca Marks, Leetoria Hinojosa, Victoria Cuello, Marisa Cuevas, Andrea Salinas, Erin Schuenzel, Michael W. Persans, Wendy Innis-Whitehouse, Megan Keniry

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Background: The PI3K pathway controls diverse cellular processes including growth, survival, metabolism, and apoptosis. Nuclear FOXO factors were observed in cancers that harbor constitutively active PI3K pathway output and stem signatures. FOXO1 and FOXO3 were previously published to induce stem genes such as OCT4 in embryonic stem cells. Here, we investigated FOXO-driven stem gene expression in U87MG glioblastoma cells.

Methods: PI3K-activated cancer cell lines were investigated for changes in gene expression, signal transduction, and clonogenicity under conditions with FOXO3 disruption or exogenous expression. The impact of PI3K pathway inhibition on stem gene expression was examined in a set of glioblastoma …

Dna, Rna, & Proteins, Oh My!, Cassandra Wissink Armstrong

Professional Learning Day

A staple topic in any life science classroom, we will take a look at some innovative ways to not only teach these topics, but assess them using the Next Generation Science Standards.

Carbonatites As Rock Fertilizers: A Review, James Mc Jones, Frédérique C. Guinel, Pedro M. Antunes

Biology Faculty Publications

Rock fertilizers are geological resources used in agriculture for their nutrient content, but slow weathering rates hinder their effectiveness. Carbonatites are igneous rocks made mostly of carbonate minerals with a relatively high weathering rate and often containing nutrient-bearing accessory minerals (e.g., apatite and biotite). Despite evidence supporting their potential as rock fertilizers, a comprehensive review of such data is missing in the literature. Furthermore, when studies on agricultural uses of carbonatites exist, they typically center on applied research aspects (i.e., “does it work?”) rather than on basic research aspects (i.e., “how does it work?”). Here we evaluate the applicability of …

Developing A Writing Intensive (Wi) Microbiology Lab Course, Jeremy Dodsworth

Q2S Enhancing Pedagogy

Students at CSUSB will be required to take two courses designated as writing intensive (WI) after the quarter-to-semester (Q2S) transition in Fall 2020. Having WI courses in the Biology major will allow Biology students to satisfy the WI requirement and a major requirement/elective with one course, and having WI course in the major will help students develop discipline-specific critical thinking and writing skills. The current upper-division Microbiology course involves a significant amount of writing. Here I present plans for augmentation and modification of the writing activities and assignments in this Microbiology course associated with Q2S to potentially fulfill the WI …

Up To Scratch: An Evidence-Based (And Fun!) Assessment Tool, Breanna Putman

Q2S Enhancing Pedagogy

This poster describes a project using Immediate Feedback Assessment. As part of the ISSUES-X Large Lecture Faculty Learning Community, I implemented a different assessment technique in my class. The technique is called Immediate Feedback Assessment Technique (IF-AT) and it basically consists of a scratch-off scantron form. Students scratch off the oval corresponding to their answer and if it is correct, a star will be revealed. They keep scratching until revealing the correct answer. This technique was beneficial because it corrects students’ misunderstandings by providing immediate feedback, it helps students utilize an “internal dialogue” of learning through evaluation of incorrect responses …

Facilitating Growth Through Frustration: Using Genomics Research In A Course-Based Undergraduate Research Experience, Adam Haberman, Et Al.

Biology: Faculty Scholarship

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable …

The Mangroves Of Costa Rica, Kylie Stewart

Honors Projects

Mangroves are a type of coastal vegetation present in the intertidal zone of tropical and subtropical climates. This paper explores the mangroves of Costa Rica, their significance, and various strategies the country utilizes in order to protect mangrove forests. Several books and articles about mangroves and conservationism are examined to explain why mangrove forests are vital to a coastline’s health and growth. The scholarly topic pertains to mangroves located in the United States and Costa Rica along with methods used to maintain the wildlife that live within them. The concept of ecotourism will be explored and how mangrove forests are …

First Evidence Of Production Of The Lantibiotic Nisin P, Enriqueta Garcia-Gutierrez, Paula M. O'Connor, Gerhard Saalbach, Calum J. Walsh, James W. Hegarty, Caitriona M. Guinane, Melinda J. Mayer, Arjan Narbad, Paul D. Cotter

Department of Biological Sciences Publications

Nisin P is a natural nisin variant, the genetic determinants for which were previously identifed in the genomes of two Streptococcus species, albeit with no confrmed evidence of production. Here we describe Streptococcus agalactiae DPC7040, a human faecal isolate, which exhibits antimicrobial activity against a panel of gut and food isolates by virtue of producing nisin P. Nisin P was purifed, and its predicted structure was confrmed by nanoLC-MS/MS, with both the fully modifed peptide and a variant without rings B and E being identifed. Additionally, we compared its spectrum of inhibition and minimum inhibitory concentration (MIC) with that of …

The First Gynandromorph Of The Neotropical Bee Megalopta Amoena (Spinola, 1853) (Halictidae) With Notes On Its Circadian Rhythm, Erin Krichilsky, Álvaro Vega-Hidalgo, Kate Hunter, Callum Kingwell, Chelsey Ritner, William Wcislo, Adam Smith

All PIRU Publications

Gynandromorphy is an anomaly that results in an organism phenotypically expressing both male and female characteristics. Here we describe the first gynandromorph of the bee species Megalopta amoena (Spinola, 1853) (Halictidae, Augochlorini) and the second record of this anomaly within the genus Megalopta. Additionally, we analyzed the bee’s circadian rhythm, which has never before been quantified for a gynandromorph. The gynandromorph showed a deviant activity pattern; it was intermediate between that of the male and female M. amoena. Our results imply that the brains of bilateral gynandromorphs may have mixed sex-specific signaling. Based on four days of recording, …

Inquiry Into Cell And Molecular Biology Cmb 395, Michael Cerbo

Library Impact Statements

No abstract provided.