Biology Commons^™

Females Are The Brighter Sex: Differences In External Fluorescence Across Sexes And Life Stages Of A Crab Spider, Erin E. Brandt, Susan E. Masta

Biology Faculty Publications and Presentations

Fluorescence is increasingly recognized to be widespread in nature. In particular, some arachnids fluoresce externally, and in spiders the hemolymph fluoresces. In this study, we examined the external fluorescence and the fluorophores of different sexes and life stages of the crab spider Misumena vatia (Clerk 1757), a sit-and-wait predator that feeds on insects as they visit flowers. We designed novel instrumentation to measure external fluorescence in whole specimens. We found that although males and females possess internal fluorophores with similar properties, the external expression of fluorescence varies across sexes and life stages. Spiders fluoresce brightly as immatures. Females maintain their …

Anthropogenic Noise Changes Arthropod Abundances, Jessie P. Bunkley, Christopher J.W. Mcclure, Akito Y. Kawahara, Clinton D. Francis, Jesse R. Barber

Biology Faculty Publications and Presentations

Anthropogenic noise is a widespread and growing form of sensory pollution associated with the expansion of human infrastructure. One specific source of constant and intense noise is that produced by compressors used for the extraction and transportation of natural gas. Terrestrial arthropods play a central role in many ecosystems, and given that numerous species rely upon airborne sounds and substrate-borne vibrations in their life histories, we predicted that increased background sound levels or the presence of compressor noise would influence their distributions. In the second largest natural gas field in the United States (San Juan Basin, New Mexico, USA), we …

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also …

Transcriptomic Analysis Of Maternally Provisioned Cues For Phenotypic Plasticity In The Annual Killifish, Austrofundulus Limnaeus, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifsh Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal …

Improved Supervised Classification Of Accelerometry Data To Distinguish Behaviors Of Soaring Birds, Maitreyi Sur, Srisarguru Sridhar

Biology Faculty Publications and Presentations

Soaring birds can balance the energetic costs of movement by switching between flapping, soaring and gliding flight. Accelerometers can allow quantification of flight behavior and thus a context to interpret these energetic costs. However, models to interpret accelerometry data are still being developed, rarely trained with supervised datasets, and difficult to apply. We collected accelerometry data at 140Hz from a trained golden eagle (Aquila chrysaetos) whose flight we recorded with video that we used to characterize behavior. We applied two forms of supervised classifications, random forest (RF) models and K-nearest neighbor (KNN) models. The KNN model was substantially …

Each To Their Own Cure: Faculty Who Teach Course-Based Undergraduate Research Experiences Report Why You Too Should Teach A Cure, Erin E. Shortlidge, Gita Bangera, Sara Brownell

Biology Faculty Publications and Presentations

Course-based undergraduate research experiences (CUREs) meet national recommendations for integrating research experiences into life science curricula. As such, CUREs have grown in popularity and many research studies have focused on student outcomes from CUREs. Institutional change literature highlights that understanding faculty is also key to new pedagogies succeeding. To begin to understand faculty perspectives on CUREs, we conducted semi-structured interviews with 61 faculty who teach CUREs regarding why they teach CUREs, what the outcomes are, and how they would discuss a CURE with a colleague. Using grounded theory, participant responses were coded and categorized as tangible or intangible, related to …

Editorial: Genetics, Genomics And –Omics Of Thermophiles, Kian Mau Goh, Kok-Gan Chan, Rajesh Kumar Sani, Edgardo Ruben Donati, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

Thermophilic Archaea and Bacteria occupy heated environments. Advancement of next-generation sequencing (NGS), single-cell analyses, and combinations of –omics and microscopic technologies have resulted in the discovery of new thermophiles. This e-book consists of a review, and 10 original articles authored by 94 authors. The main aim of this Research Topic of Frontiers in Microbiology was to provide a platform for researchers to describe recent findings on the ecology of thermophiles using NGS, functional genomics, comparative genomics, gene evolution, and extremozyme discovery.

Rolling Circle Mutagenesis Of Gst-Mcherry To Understand Mutation, Gene Expression, And Regulation, Jessica Cole, Amanda Ferguson, Verónica A. Segarra, Susan Walsh

Biology Faculty Publications and Presentations

Undergraduates are often familiar with textbook examples of human mutations that affect coding regions and the subsequent disorders, but they may struggle with understanding the implications of mutations in the regulatory regions of genes. We have designed a laboratory sequence that will allow students to explore the effect random mutagenesis can have on protein function, expression, and ultimately phenotype. Students design and perform a safe and time-efficient random mutagenesis experiment using error-prone rolling circular amplification of a plasmid expressing the inducible fusion protein glutathione S-transferase (GST)-mCherry. Mutagenized and wild-type control plasmid DNA, respectively, are then purified and transformed into bacteria …

Evaluation Of Micro-Gps Receivers For Tracking Small-Bodied Mammals, Laura A. Mcmahon, Janet L. Rachlow, Lisa A. Shipley, Jennifer S. Forbey, Timothy R. Johnson, Peter J. Olsoy

Biology Faculty Publications and Presentations

GPS telemetry markedly enhances the temporal and spatial resolution of animal location data, and recent advances in micro-GPS receivers permit their deployment on small mammals. One such technological advance, snapshot technology, allows for improved battery life by reducing the time to first fix via postponing recovery of satellite ephemeris (satellite location) data and processing of locations. However, no previous work has employed snapshot technology for small, terrestrial mammals. We evaluated performance of two types of micro-GPS (< 20 g) receivers (traditional and snapshot) on a small, semi-fossorial lagomorph, the pygmy rabbit (Brachylagus idahoensis), to understand how GPS errors might influence fine-scale assessments of space use and habitat selection. During stationary tests, microtopography (i.e., …

Endoplasmic Reticulum Stress And Unfolded Protein Response In Cartilage Pathophysiology; Contributing Factors To Apoptosis And Osteoarthritis, Alexandria Hughes, Alexandra E. Oxford, Ken Tawara, Cheryl L. Jorcyk, Julia Thom Oxford

Biology Faculty Publications and Presentations

Chondrocytes of the growth plate undergo apoptosis during the process of endochondral ossification, as well as during the progression of osteoarthritis. Although the regulation of this process is not completely understood, alterations in the precisely orchestrated programmed cell death during development can have catastrophic results, as exemplified by several chondrodystrophies which are frequently accompanied by early onset osteoarthritis. Understanding the mechanisms that underlie chondrocyte apoptosis during endochondral ossification in the growth plate has the potential to impact the development of therapeutic applications for chondrodystrophies and associated early onset osteoarthritis. In recent years, several chondrodysplasias and collagenopathies have been recognized as …

Effects Of Delayed Nsaid Administration After Experimental Eccentric Contraction Injury – A Cellular And Proteomics Study, Laura Bond

Biology Faculty Publications and Presentations

Background

Acute muscle injuries are exceedingly common and non-steroidal anti-inflammatory drugs (NSAIDs) are widely consumed to reduce the associated inflammation, swelling and pain that peak 1–2 days post-injury. While prophylactic use or early administration of NSAIDs has been shown to delay muscle regeneration and contribute to loss of muscle strength after healing, little is known about the effects of delayed NSAID use. Further, NSAID use following non-penetrating injury has been associated with increased risk and severity of infection, including that due to group A streptococcus, though the mechanisms remain to be elucidated. The present study investigated the effects of delayed …

Cephalopod Biodiversity In The Vicinity Of Bear Seamount, Western North Atlantic Based On Exploratory Trawling From 2000 To 2014, Elizabeth K. Shea, Heather Judkins, Michelle D. Staudinger, Valerie H. Dimkovikj

Biology Faculty Publications and Presentations

Bear Seamount (BSM) is the most inshore seamount in the New England Seamount chain. It is located within the U.S. Exclusive Economic Zone and is contained within the recently established Northeast Canyons and Seamounts Marine National Monument. In 2000, the National Oceanic and Atmospheric Administration’s (NOAA) National Systematics Laboratory began an exploratory trawling program to document nekton diversity at BSM and its vicinity. Here, we summarize eight exploratory sampling cruises conducted between 2000 and 2014, and describe the cephalopod biodiversity and assemblage structure around BSM. Over the course of 174 deep–midwater and 56 bottom tows, 5088 cephalopods were identified, measured, …

Is Biomass A Reliable Estimate Of Plant Fitness?, Brett Steven Younginger, Dagmara Sirova, Mitchell B. Cruzan, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

The measurement of fitness is critical to biological research. Although the determination of fitness for some organisms may be relatively straightforward under controlled conditions, it is often a difficult or nearly impossible task in nature. Plants are no exception. The potential for long-distance pollen dispersal, likelihood of multiple reproductive events per inflorescence, varying degrees of reproductive growth in perennials, and asexual reproduction all confound accurate fitness measurements. For these reasons, biomass is frequently used as a proxy for plant fitness. However, the suitability of indirect fitness measurements such as plant size is rarely evaluated. This review outlines the important associations …

The Effect Of Nullomer-Derived Peptides 9r, 9s1r And 124r On The Nci-60 Panel And Normal Cell Lines, Abdelkrim Alileche, Greg Hampikian

Biology Faculty Publications and Presentations

Background: Nullomer peptides are the smallest sequences absent from databases of natural proteins. We first began compiling a list of absent 5-amino acid strings in 2006 (1). We report here the effects of Nullomer-derived peptides 9R, 9S1R and 124R on the NCI-60 panel, derived from human cancers of 9 organs (kidney, ovary, skin melanoma, lung, brain, lung, colon, prostate and the hematopoietic system), and four normal cell lines (endothelial HUVEC, skin fibroblasts BJ, colon epithelial FHC and normal prostate RWPE-1).

Methods: NCI-60 cancer cell panel and four normal cell lines were cultured in vitro in RPMI1640 supplemented with 10% Hyclone …

Passive Warming Reduces Stress And Shifts Reproductive Effort In The Antarctic Moss, Polytrichastrum Alpinum, Erin E. Shortlidge, Sarah M. Eppley, Hans Kohler, Todd N. Rosenstiel, Gustavo E. Zúñiga, Angélica Casanova-Katny

Biology Faculty Publications and Presentations

Background and Aims: The Western Antarctic Peninsula is one of the most rapidly warming regions on Earth, and many biotic communities inhabiting this dynamic region are responding to these well-documented climatic shifts. Yet some of the most prevalent organisms of terrestrial Antarctica, the mosses, and their responses to warming have been relatively overlooked and understudied. In this research, the impacts of 6 years of passive warming were investigated using open top chambers (OTCs), on moss communities of Fildes Peninsula, King George Island, Antarctica.

Methods: The effects of experimental passive warming on the morphology, sexual reproductive effort and stress physiology of …

Small Noncoding Rna Expression During Extreme Anoxia Tolerance Of Annual Killifish (Austrofundulus Limnaeus) Embryos, Claire L. Riggs, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days …

Embryonic Development Of The Annual Killifish Austrofundulus Limnaeus: An Emerging Model For Ecological And Evolutionary Developmental Biology Research And Instruction, Jason E. Podrabsky, Claire L. Riggs, Amie L. Romney, S. Cody Woll, Josiah T. Wagner, Kristin M. Culpepper, Timothy Grant Cleaver

Biology Faculty Publications and Presentations

Background: Austrofundulus limnaeus is an annual killifish from the Maracaibo basin of Venezuela. Annual killifishes are unique among vertebrates in their ability to enter into a state of dormancy at up to three distinct developmental stages termed diapause I, II, and III. These embryos are tolerant of a wide variety of environmental stresses and develop relatively slowly compared with nonannual fishes.

Results: These traits make them an excellent model for research on interactions between the genome and the environment during development, and an excellent choice for developmental biology laboratories. Furthermore, A. limnaeus is relatively easy to maintain in a laboratory …

Insulin-Like Growth Factor Signaling Regulates Developmental Trajectory Associated With Diapause In Embryos Of The Annual Killifish Austrofundulus Limnaeus, S. Cody Woll, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Annual killifishes exhibit a number of unique life history characters including the occurrence of embryonic diapause, unique cell movements associated with dispersion and subsequent reaggregation of the embryonic blastomeres, and a short postembryonic life span. Insulin-like growth factor (IGF) signaling is known to play a role in the regulation of metabolic dormancy in a number of animals but has not been explored in annual killifishes. The abundance of IGF proteins during development and the developmental effects of blocking IGF signaling by pharmacological inhibition of the insulin-like growth factor I receptor (IGF1R) were explored in embryos of the annual killifish Austrofundulus …

How To Assess Your Cure: A Practical Guide For Instructors Of Course-Based Undergraduate Research Experiences, Erin Shortlidge, Sara Brownell

Biology Faculty Publications and Presentations

Integrating research experiences into undergraduate life sciences curricula in the form of course-based undergraduate research experiences (CUREs) can meet national calls for education reform by giving students the chance to “do science.” In this article, we provide a step-by-step practical guide to help instructors assess their CUREs using best practices in assessment. We recommend that instructors first identify their anticipated CURE learning outcomes, then work to identify an assessment instrument that aligns to those learning outcomes and critically evaluate the results from their course assessment. To aid instructors in becoming aware of what instruments have been developed, we have also …

Nonmotorized Recreation And Motorized Recreation In Shrub-Steppe Habitats Affects Behavior And Reproduction Of Golden Eagles (Aquila Chrysaetos), Robert J. Spaul, Julie A. Heath

Biology Faculty Publications and Presentations

Different forms of outdoor recreation have different spatiotemporal activity patterns that may have interactive or cumulative effects on wildlife through human disturbance, physical habitat change, or both. In western North America, shrub-steppe habitats near urban areas are popular sites for motorized recreation and nonmotorized recreation and can provide important habitat for protected species, including golden eagles. Our objective was to determine whether recreation use (i.e., number of recreationists) or recreation features (e.g., trails or campsites) predicted golden eagle territory occupancy, egg-laying, or the probability a breeding attempt resulted in ≥1 offspring (nest survival). We monitored egg-laying, hatching and fledging success, …

Cho Endonuclease Functions During Dna Interstrand Crosslink Repair In Escherichia Coli, Anthonige Vidya Perera, James Brian Mendenhall, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

DNA interstrand crosslinks are complex lesions that covalently link both strands of the duplex DNA. Lesion removal is proposed to initiate via the UvrABC nucleotide excision repair complex, however less is known about the subsequent steps of this complex repair pathway. In this study, we characterized the contribution of nucleotide excision repair mutants to survival in the presence of psoralen-induced damage. Unexpectedly, we observed that the nucleotide excision repair mutants exhibit differential sensitivity to psoralen-induced damage, with uvrC mutants being less sensitive than either uvrA or uvrB. We show that Cho, an alternative endonuclease, acts with UvrAB and is …

Variable Effects Of Snow Conditions Across Boreal Mesocarnivore Species, C. B. Pozzanghera, K. J. Sivy, M. S. Lindberg, L. R. Prugh

Biology Faculty Publications and Presentations

Mesocarnivores are increasingly recognized as key drivers of community dynamics, but the effects of bottom-up and abiotic factors on mesocarnivore populations remain poorly understood. We evaluated the effects of snow conditions, prey abundance, and habitat type on the distribution of five sympatric mesocarnivore species in interior Alaska using repeated snow track surveys and occupancy modelling. Snow depth and snow compaction were the best predictors of mesocarnivore occupancy, with differential effects across species. Coyotes (Canis latrans (Say, 1823)) and red foxes (Vulpes vulpes L., 1758) occurred in areas of shallow, compact snow, Canada lynx (Lynx canadensis (Kerr, 1792)) …

A Francisella-Like Endosymbiont In The Gulf Coast Tick Evolved From A Mammalian Pathogen, Jonathan G. Gerhart, Abraham S. Moses, Rahul Raghavan

Biology Faculty Publications and Presentations

Ticks (order Ixodida) vector pathogenic bacteria that cause diseases in humans and other mammals. They also contain bacteria that are closely related to pathogens but function as endosymbionts that provide nutrients that are missing from mammalian blood—their sole food source. For instance, mammalian pathogens such as Coxiella burnetii and Francisella tularensis, as well as Coxiella-like and Francisella-like endosymbionts (CLEs and FLEs, respectively) occur in ticks worldwide. However, it is not clear whether the pathogens evolved from symbionts or symbionts from pathogens. Recent studies have indicated that C. burnetii likely originated from a tick-associated ancestor, but the origins …

Genotypic Diversity Effects On Biomass Production In Native Perennial Bioenergy Cropping Systems, Geoffrey P. Morris, Zhenbin Hu, Paul P. Grabowski, Justin O. Borevitz, Marie-Anne De Graaff, R. Michael Miller, Julie D. Jastrow

Biology Faculty Publications and Presentations

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008–2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars – under low or high species diversity, with or without nitrogen inputs – and …

A Phylum-Level Phylogenetic Classification Of Zygomycete Fungi Based On Genome-Scale Data, Merlin M. White

Biology Faculty Publications and Presentations

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support themonophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, …

Reproductive Output Of Mosses Under Experimental Warming On Fildes Peninsula, King George Island, Maritime Antarctica, Angélica Casanova-Katny, G. A. Torres-Mellado, Sarah M. Eppley

Biology Faculty Publications and Presentations

Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is …

Paternal Mitochondrial Transmission In Intra-Species Caenorhabditis Briggsae Hybrids, Joseph A. Ross, Dana K. Howe, Anna Luella Coleman-Hulbert, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

To study mitochondrial-nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic-nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study the molecular and evolutionary basis of uniparental mitochondrial inheritance.

Mitochondrial Dna Sequence And Lack Of Response To Anoxia In The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Florisela H. Chavez, Jason E. Podrabsky

Biology Faculty Publications and Presentations

The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, …

Selective Foraging By Pogonomyrmex Salinus (Hymenoptera: Formicidae) In Semiarid Grassland: Implications For A Rare Plant, Matthew S. Schmasow, Ian C. Robertson

Biology Faculty Publications and Presentations

Selective foraging by granivores can have important consequences for the structure and composition of plant communities, and potentially severe consequences for rare plant species. To understand how granivore foraging behavior affects common and rare plant species, diet selection should be viewed relative to the availability of alternative seed options, and with consideration of the individual attributes of those seeds (e.g., morphology, nutrient content). We examined the foraging decisions of Owyhee harvester ants, Pogonomyrmex salinus [Olsen], in semiarid grassland dominated by two species of grass, Poa secunda and Bromus tectorum, and two species of mustard, Sisymbrium altissimum and Lepidium papilliferum …

The Intervening Sequence Of Coxiella Burnetii: Characterization And Evolution, Indu Warrier, Mathias C. Walter, Dimitrios Frangoulidis, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biology Faculty Publications and Presentations

The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon …