Life Sciences Commons^™

Mammals Adjust Diel Activity Across Gradients Of Urbanization, Travis Gallo, Mason Fidino, Brian Gerber, Adam A. Ahlers, Julia L. Angstmann, Max Amaya, Amy L. Concilio, David Drake, Danielle Gray, Elizabeth W. Lehrer, Maureen H. Murray, Travis J. Ryan, Colleen Cassady St. Clair, Carmen M. Salsbury, Heather A. Sanders, Theodore Stankowich, Jacque Williamson, J. Amy Belaire, Kelly Simon, Seth B. Mangle

Scholarship and Professional Work - LAS

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator–prey dynamics. Yet, changes in animal behavior within the shorter 24-hr light–dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify …

Androgen-Binding Protein (Abp) Evolutionary History: Has Positive Selection Caused Fixation Of Different Paralogs In Different Taxa Of The Genus Mus?, Robert C. Karn, Golbahar Yazdanifar, Željka Pezer, Pierre Boursot, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Comparison of the androgen-binding protein (Abp) gene regions of six Mus genomes provides insights into the evolutionary history of this large murid rodent gene family. We identified 206 unique Abp sequences and mapped their physical relationships. At least 48 are duplicated and thus present in more than two identical copies. All six taxa have substantially elevated LINE1 densities in Abp regions compared with flanking regions, similar to levels in mouse and rat genomes, although nonallelic homologous recombination seems to have only occurred in Mus musculus domesticus. Phylogenetic and structural relationships support the hypothesis that the extensive Abp …

First Report Of Yellow-Flowered Teasel, Dipsacus Strigosus Willd. Ex Roem. & Schult. (Dipsacaceae) In Indiana, A North American Record, Rebecca W. Dolan

Scholarship and Professional Work - LAS

This paper reports the presence of Dipsacus strigosus Willd. ex Roem. & Schult. in Indiana. The species, native to western Asia, is naturalized in several locations in Europe. This is the first documented occurrence in North America. The new record was collected along a recently constructed bike path in a moist wooded area of the Butler University campus in Indianapolis, Indiana, USA. Like the two other species of the genus known in the Indiana, D. strigosus is likely to be invasive, so efforts will be made to eradicate this population. The plant should be monitored and looked for in other …

Landscape-Scale Differences Among Cities Alter Common Species’ Responses To Urbanization, Mason Fidino, Travis Gallo, Elizabeth W. Lehrer, Maureen H. Murray, Cria Kay, Heather A. Sander, Brandon Macdougall, Carmen M. Salsbury, Travis J. Ryan, Julia L. Angstmann, J. Amy Belaire, Barbara Dugelby, Chris Schell, Theodore Stankowich, Max Amaya, David Drake, Sheryl H. Hursh, Adam A. Ahlers, Jacque Williamson, Laurel M. Hartley, Amanda J. Zellmer, Kelly Simon

Scholarship and Professional Work - LAS

Understanding how biodiversity responds to urbanization is challenging, due in part to the single-city focus of most urban ecological research. Here, we delineate continent-scale patterns in urban species assemblages by leveraging data from a multi-city camera trap survey and quantify how differences in greenspace availability and average housing density among 10 North American cities relate to the distribution of eight widespread North American mammals. To do so, we deployed camera traps at 569 sites across these ten cities between 18 June and 14 August. Most data came from 2017, though some cities contributed 2016 or 2018 data if it was …

Ubc-9 Acts In Gaba Neurons To Control Neuromuscular Signaling In C. Elegans, Victoria A. Kreyden, Elly B. Mawi, Jennifer Kowalski

Scholarship and Professional Work - LAS

Regulation of excitatory to inhibitory signaling balance is essential to nervous system health and is maintained by numerous enzyme systems that modulate the activity, localization, and abundance of synaptic proteins. SUMOylation is a key post-translational regulator of protein function in diverse cells, including neurons. There, its role in regulating synaptic transmission through pre- and postsynaptic effects has been shown primarily at glutamatergic central nervous system synapses, where the sole SUMO-conjugating enzyme Ubc9 is a critical player. However, whether Ubc9 functions globally at other synapses, including inhibitory synapses, has not been explored. Here, we investigated the role of UBC-9 and the …

Comparative Analysis Of The Human Serine Hydrolase Ovca2 To The Model Serine Hydrolase Homolog Fsh1 From S. Cerevisiae, Jessica S. Bun, Michael D. Slack, Daniel E. Schemenauer, R. Jeremy Johnson

Scholarship and Professional Work - LAS

Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis …

Small Herbaria Contribute Unique Biogeographic Records To County, Locality, And Temporal Scales, Travis D. Marsico, Erica R. Krimmel, J. Richard Carter, Emily L. Gillespie, Phillip D. Lowe, Ross Mccauley, Ashley B. Morris, Gil Nelson, Michelle Smith, Diana L. Soteropoulos, Anna K. Monfils

Scholarship and Professional Work - LAS

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

A Contemporary View Of Respiratory Syncytial Virus (Rsv) Biology And Strain-Specific Di Erences, Mansi C. Pandya, Sean Callahan, Kyryll G. Savchenko, Christopher C. Stobart

Scholarship and Professional Work - LAS

Respiratory syncytial virus (RSV) is a human respiratory pathogen which remains a leading viral cause of hospitalizations and mortality among infants in their first year of life. Here, we review the biology of RSV, the primary laboratory isolates or strains which have been used to best characterize the virus since its discovery in 1956, and discuss the implications for genetic and functional variations between the established laboratory strains and the recently identified clinical isolates.

Diet Of Trachemys Scripta (Red-Eared Slider) And Graptemys Geographica (Common Map Turtle) In An Urban Landscape, Travis Ryan

Scholarship and Professional Work - LAS

Urban environments present many challenges for aquatic turtle species. Here, we investigated whether the diets of Trachemys scripta (Red-eared Slider) and Graptemys geographica (Common Map Turtle) may help explain the spatial ecology of these 2 species in a pair of constructed aquatic habitats in Indianapolis, IN, USA. We conducted stomach flushings on 43 turtles from 2 sites (Central Canal, n = 33; IMA Lake, n = 10). Common Map Turtles from the Central Canal (n = 27) consumed mostly mollusks and crayfish, which comprised ~86% of the volume of stomach contents. We captured no adult Common Map Turtles at IMA …

Five-Year Response Of Spontaneous Vegetation To Removal Of Invasive Amur Bush Honeysuckle Along An Urban Creek, Rebecca W. Dolan, Kelly H. Brown

Scholarship and Professional Work - LAS

Non-native invasive species have major impacts on landscapes worldwide, but their effects in urban areas are not well documented. We quantified the response of naturally regenerating vegetation along an urban creek to removal of the invasive shrub Lonicera maackii (Amur Bush Honeysuckle). Over the 5-year study, species richness more than doubled. Most new plants were native, disturbance-adapted, early successional species. Trend analysis of function traits revealed annuals that rely on seed dispersal by wind or externally on animals were significantly overrepresented among new plants in comparison to their proportion in the countywide species pool. Increased species richness did not result …

Fourteen Polymorphic Microsatellite Markers For The Widespread Labrador Tea (Rhododendron Groenlandicum), Matthew L. Sheik, Kitty L. Labounty, Erika Mitchell, Emily L. Gillespie

Scholarship and Professional Work - LAS

No abstract provided.

Microsatellite Markers For The Biogeographically Enigmatic Sandmyrtle (Kalmia Buxifolia, Phyllodoceae: Ericaceae), Emily L. Gillespie, Tesa Madsen‐Mcqueen, Torsten Eriksson, Adam Bailey, Zack E. Murrell

Scholarship and Professional Work - LAS

No abstract provided.

Advancing Urban Wildlife Research Through A Multi-City Collaboration, Seth B. Magle, Mason Fidino, Elizabeth W. Lehrer, Travis Gallo, Matthew P. Mulligan, María Jazmín Ríos, Adam A. Ahlers, Julia L. Angstmann, Amy Belaire, Barbara Dugelby, Ashley Gramza, Laurel Hartley, Brandon Macdougall, Travis J. Ryan, Carmen M. Salsbury, Heather Sander, Christopher Schell, Kelly Simon, Sarah St. Onge, David Drake

Scholarship and Professional Work - LAS

Research on urban wildlife can help promote coexistence and guide future interactions between humans and wildlife in developed regions, but most such investigations are limited to short-term, single-species studies, typically conducted within a single city. This restricted focus prevents scientists from recognizing global patterns and first principles regarding urban wildlife behavior and ecol- ogy. To overcome these limitations, we have designed a pioneering research network, the Urban Wildlife Information Network (UWIN), whereby partners collaborate across several cities to systematically collect data to populate long-term datasets on multiple species in urban areas. Data collected via UWIN support analyses that will enable …

Repeat Associated Mechanisms Of Genome Evolution And Function Revealed By The Mus Caroli And Mus Pahari Genomes, David Thybert, Maša Roller, Fábio C.P. Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C. Karn, Christina M. Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Stefanie Nachtweide, Michael A. Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David J. Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas M. Keane, Duncan T. Odom, Paul Flicek

Scholarship and Professional Work - LAS

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr …

How Metamorphosis Is Different In Plethodontids: Larval Life History Perspectives On Life-Cycle Evolution, Christopher K. Beachy, Travis Ryan, Ronald M. Bonett

Scholarship and Professional Work - LAS

Plethodontid salamanders exhibit biphasic, larval form paedomorphic, and direct developing life cycles. This diversity of developmental strategies exceeds that of any other family of terrestrial vertebrate. Here we compare patterns of larval development among the three divergent lineages of biphasic plethodontids and other salamanders. We discuss how patterns of life-cycle evolution and larval ecology might have produced a wide array of larval life histories. Compared with many other salamanders, most larval plethodontids have relatively slow growth rates and sometimes exceptionally long larval periods (up to 60 mo). Recent phylogenetic analyses of life-cycle evolution indicate that ancestral plethodontids were likely direct …

Analysis Of Copy Number Variation In The Abp Gene Regions Of Two House Mouse Subspecies Suggests Divergence During The Gene Family Expansions, Željka Pezer, Amanda G. Chung, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

The Androgen-binding protein (Abp) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus (Mmd) and Mus musculus musculus (Mmm), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd, primarily representing the presence/absence of the final …

Floristic Response To Urbanization: Filtering Of The Bioregional Flora In Indianapolis, Indiana, Usa, Rebecca W. Dolan, Myla F.J. Aronson, Andrew L. Hipp

Biological Sciences

PREMISE OF THE STUDY: Globally, urban plant populations are becoming increasingly important, as these plants play a vital role in ameliorating effects of ecosystem disturbance and climate change. Urban environments act as filters to bioregional flora, presenting survival challenges to spontaneous plants. Yet, because of the paucity of inventory data on plants in landscapes both before and after urbanization, few studies have directly investigated this effect of urbanization.

METHODS: We used historical, contemporary, and regional plant species inventories for Indianapolis, Indiana USA to evaluate how urbanization filters the bioregional flora based on species diversity, functional traits, and phylogenetic community structure. …

Influence Of Light Quality And Quantity On Heterophylly In The Aquatic Plant Nymphaea Odorata Subsp. Tuberosa (Nymphaeaceae), Travis Ryan

Scholarship and Professional Work - LAS

Heterophylly, the production of different leaf forms on the same plant, is a widespread phenomenon in terrestrial and aquatic plants and provides an opportunity to study how sessile organisms sense and respond to changes in environmental factors. Nymphaea odorata subsp. tuberosa (American White Water Lily) produces 2 distinct leaf forms: a floating surface leaf and an aerial form in which the lamina is held above the water. Previous research suggests that changes in the light environment may be a critical determinant of heterophylly in Nymphaea. In this study, we tested the hypothesis that changes in light quantity and light quality …

Results Of The 2016 Indianapolis Biodiversity Survey, Marion County, Indiana, Jeffrey D. Holland, Rebecca W. Dolan, Jeremy J. Sheets, Michael S. Finkler, Brant E. Fisher, Roger L. Hedge, Tom Swinford, Nick Harby, Robert P. Jean, Megan K. Martin, Bill Mcknight, Marc Milne, Kirk Roth, Paul Rothrock, Carl Strang

Scholarship and Professional Work - LAS

Surprising biodiversity can be found in cities, but urban habitats are understudied. We report on a bioblitz conducted primarily within a 24-hr period on September 16 and 17, 2016 in Indianapolis, Indiana, USA. The event focused on stretches of three waterways and their associated riparian habitat: Fall Creek (20.6 ha; 51 acres), Pleasant Run (23.5 ha; 58 acres), and Pogue’s Run (27.1 ha; 67 acres). Over 75 scientists, naturalists, students, and citizen volunteers comprised 14 different taxonomic teams. Five hundred ninety taxa were documented despite the rainy conditions. A brief summary of the methods and findings are presented here. Detailed …

Floristic Inventory Of Woollen’S Gardens Nature Preserve, Indianapolis, Marion County, Indiana, Usa, With Quantitative Vegetation Sampling Of Permanent Plots In 2003 And 2016, Rebecca W. Dolan, Marcia E. Moore

Scholarship and Professional Work - LAS

Urban forest fragments face challenges to habitat quality due to small size, isolation from larger natural areas, and close association with anthropogenic disturbance. Monitoring changes in vegetation can inform management practices targeted at preserving biodiversity in the face of these threats. Woollen’s Gardens is a high-quality mesic upland forest preserve in the city of Indianapolis, Indiana, USA, with a beechmaple older-growth forest and a significant display of showy spring wildflowers. The entire preserve was inventoried and quantitative vegetation analysis along seven 100 m transects was conducted in 2003 and again in 2016 to track changes. Data from both years document …

Featured Herbarium: But—The Friesner Herbarium Of Butler University, Rebecca W. Dolan

Scholarship and Professional Work - LAS

Feature written by Rebecca Dolan on the BUT—The Friesner Herbarium of Butler University in the Vasculum.

The Role Of Retrotransposons In Gene Family Expansions In The Human And Mouse Genomes, Václav Janoušek, Christina M. Laukaitis, Alexey Yanchukov, Robert C. Karn

Scholarship and Professional Work - LAS

Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. …

The Unusual Substrate Specificity Of A Virulence Associated Serine Hydrolase From The Highly Toxic Bacterium, Francisella Tularensis, Alexander M. Farberg, Whitney K. Hart, R. Jeremy Johnson

Scholarship and Professional Work - LAS

Francisella tularensis is the causative agent of the highly, infectious disease, tularemia. Amongst the genes identified as essential to the virulence of F. tularensis was the proposed serine hydrolase FTT0941c. Herein, we purified FTT0941c to homogeneity and then characterized the folded stability, enzymatic activity, and substrate specificity of FTT0941c. Based on phylogenetic analysis, FTT0941c was classified within a divergent Francisella subbranch of the bacterial hormone sensitive lipase (HSL) superfamily, but with the conserved sequence motifs of a bacterial serine hydrolase. FTT0941c showed broad hydrolase activity against diverse libraries of ester substrates, including significant hydrolytic activity across alkyl ester substrates from …

Nucleosome Distortion As A Possible Mechanism Of Transcription Activation Domain Function, Tamara Y. Erkina, Alexandre M. Erkine

Scholarship and Professional Work – COPHS

After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and …

Invasive Species In An Urban Flora: History And Current Status In Indianapolis, Indiana, Rebecca W. Dolan

Scholarship and Professional Work - LAS

Invasive plant species are widely appreciated to cause significant ecologic and economic damage in agricultural fields and in natural areas. The presence and impact of invasives in cities is less well documented. This paper characterizes invasive plants in Indianapolis, Indiana. Based on historical records and contemporary accounts, 69 of the 120 species on the official Indiana state list are reported for the city. Most of these plants are native to Asia or Eurasia, with escape from cultivation as the most common mode of introduction. Most have been in the flora of Indianapolis for some time. Eighty percent of Indianapolis’ invasive …

Community Involvement To Address A Long-Standing Invasive Species Problem: Aspects Of Civic Ecology In Practice, Rebecca W. Dolan, Kelly Harris, Mark Adler

Scholarship and Professional Work - LAS

Invasive non-native species (INS) are found in every city around the globe, but their impacts in urban settings as biological agents of visual pollution that block views of natural landscapes and disconnect citizens from nature are not as often addressed as comprehensively as their impacts in natural areas or agricultural settings. The multiple impacts of INS in cities make them ideal candidates for aspects of Civic Ecology Practice, where local environmental stewardship action is taken to enhance green infrastructure and community well-being in urban and other human-dominated systems. We present details of a community driven program focused on removal of …

Two Hundred Years Of Forest Change: Effects Of Urbanization On Tree Species Composition And Structure, Rebecca W. Dolan

Scholarship and Professional Work - LAS

Despite their importance, the dynamics of urban floras are not well understood and quantitative historical data are rare. The current study used three data sets for trees in Indianapolis/Marion County, Indiana, U.S., to document change over 200 years to the original beech-maple forest and to examine future implications of contemporary tree planting efforts in light of these changes. Data on tree composition and size collected before significant settlement in the early 1800s are compared with recent surveys of trees in remnant natural areas and with trees found on city streets and rights-of-way. All the species recorded in historical surveys are …

Changes In Plant Species Composition And Structure In Two Peri-Urban Nature Preserves Over 10 Years, Rebecca W. Dolan, Jessica D. Stepens, Marcia E. Moore

Scholarship and Professional Work - LAS

Peri-urban natural areas, at the boundaries of cities and adjacent agricultural/rural land, are subject to ecological threats endemic to both land use types. We used permanent plots to document changes in habitat quality by monitoring herbaceous-layer plant species presence and cover over a decade (1996/97 and 2007) in two peri-urban nature preserves in central Indiana, U.S.A. The preserves are comprised of different forest community types: wet-mesic depressional forest and mesic upland forest. Habitat characteristics, based on Floristic Quality Assessment parameters, showed only a single change for either preserve between survey years: wetness values were lower in the wet-mesic depressional site …

Comparative Proteomics Of Mouse Tears And Saliva: Evidence From Large Protein Families For Functional Adaptation, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

We produced a tear proteome of the genome mouse, C57BL/6, that contained 139 different protein identifications: 110 from a two-dimensional (2D) gel with subsequent trypsin digestion, 19 from a one-dimensional (1D) gel with subsequent trypsin digestion and ten from a 1D gel with subsequent Asp-N digestion. We compared this tear proteome with a C57BL/6 mouse saliva proteome produced previously. Sixteen of the 139 tear proteins are shared between the two proteomes, including six proteins that combat microbial growth. Among the 123 other tear proteins, were members of four large protein families that have no counterparts in humans: Androgen-binding proteins (ABPs) …

A Global Analysis Of The Impacts Of Urbanization On Bird And Plant Diversity Reveals Key Anthropogenic Drivers, Myla F.J. Aronson, Frank A. La Sorte, Charles H. Nilon, Madhusudan Katti, Mark A. Goddard, Christopher A. Lepczyk, Paige S. Warren, Nicholas S.G. Williams, Sarel Cilliers, Bruce Clarkson, Cynnamon Dobbs, Rebecca W. Dolan, Marcus Hedblom, Stefan Klotz, Jip Louwe Kooijmans, Ingolf Kühn, Ian Macgregor-Fors, Mark Mcdonnell, Ulla Mörtberg, Petr Pyšek, Stefan Siebert, Jessica Sushinsky, Peter Werner, Marten Winter

Scholarship and Professional Work - LAS

Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common beingColumba livia and Poa annua. The density of bird and …