Digital Commons Network^™

Locke On Individuation And Kinds, Joseph Stenberg

Faculty Publications

Locke has been accused of endorsing a theory of kinds that is inconsistent with his theory of individuation. This purported inconsistency comes to the fore in Locke’s treatment of cases involving organisms and the masses of matter that constitute them, for example, the case of a mass constituting an oak tree. In this essay, I argue that this purported problem, known as ‘The Kinds Problem’, can be solved. The Kinds Problem depends on the faulty assumption that nominal essences include only features observable at a time t. Once this assumption is rejected, new candidates open up for the relevant difference …

Atonement In The Book Of Mormon And In The New Testament, Noel B. Reynolds

Faculty Publications

New Testament writers consistently and vigorously testify that Jesus Christ has atoned for the sins of all mankind and has provided for their resurrection from the dead. In so doing they point to historical facts, the things he did to accomplish this—to his sufferings in Gethsemane and to his crucifixion and resurrection. Some of these writers also offer explanations or characterizations of that atonement intended to illuminate how it was possible or how it works. The various explanations offered are not identical or even always consistent with each other as they vary somewhat between writers, or sometimes even within the …

Heart Rate-Defined Sustained Attention In Infants At Risk For Autism, Bridgette L. Tonnsen, J. E. Richards, Jane E. Roberts

Faculty Publications

Background: Although aberrant visual attention has been identified in infants at high familial risk for autism, the developmental emergence of atypical attention remains unclear. Integrating biological measures of attention into prospective high-risk infant studies may inform more nuanced developmental trajectories, clarifying the onset and course of atypical attention and potentially advancing early screening or treatment protocols. Heart rate-defined sustained attention (HRDSA) is a well-validated biological measure of attentional engagement that, in non-clinical infant populations, provides incremental information about attentional engagement beyond looking behaviors alone. The present study aimed to examine the characteristics and clinical correlates of HRDSA in high-risk infants, …

A Novel Mir-375-Hoxb3-Cdca3/Dnmt3b Regulatory Circuitry Contributes To Leukemogenesis In Acute Myeloid Leukemia, Laixi Bi, Bin Zhou, Haiying Li, Licai He, Chunjing Wang, Zhonggai Wang, Liqing Zhu, Mengqian Chen, Shenmeng Gao

Faculty Publications

Background: Acute myeloid leukemia (AML) is a heterogeneous group of hematopoietic malignancies due to sophisticated genetic mutations and epigenetic dysregulation. MicroRNAs (miRNAs), a class of small non-coding RNAs, are important regulators of gene expression in all biological processes, including leukemogenesis. Recently, miR-375 has been reported to be a suppressive miRNA in multiple types of cancers, but its underlying anti-leukemia activity in AML is largely unknown. Methods: Quantitative reverse transcriptase PCR (qRT-PCR) was used to measure the expression of miR-375 and HOXB3 in leukemic cells and normal controls. Targets of miR-375 were confirmed by western blot and luciferase assay. Phenotypic effects …

Recently Integrated Alu Insertions In The Squirrel Monkey (Saimiri) Lineage And Application For Population Analyses, Jasmine N. Baker, Jerilyn A. Walker, Michael W. Denham, Charles D. Loupe, Mark A. Batzer

Faculty Publications

© 2018 The Author(s). Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus …

Dietary Inflammatory Index And Cardiovascular Risk And Mortality—A Meta-Analysis, Nitin Shivappa, Justyna Godos, James R. Hébert, Michael Wirth, Gabriele Piuri, Attilio Speciani, Giuseppe Grosso

Faculty Publications

Diet and chronic inflammation have been suggested to be risk factors in the development of cardiovascular disease (CVD) and related mortality. The possible link between the inflammatory potential of diet measured through the Dietary Inflammatory Index (DII^®) and CVD has been investigated in several populations across the world. The aim of this study was to conduct a meta-analysis on studies exploring this association. Data from 14 studies were eligible, of which two were case-control, eleven were cohort, and one was cross-sectional. Results from the random-effects meta-analysis showed a positive association between increasing DII, indicating a pro-inflammatory diet, and …

Parasite Component Community Of Smalltooth Sawfish Off Florida: Diversity, Conservation Concerns, And Research Applications, Micah D. Bakenhaster, Stephen A. Bullard, Stephen S. Curran, Delane C. Kritsky, Erin H. Leone, Lauren K. Partridge, Carlos F. Ruiz, Rachel M. Scharer, Gregg R. Poulakis

Faculty Publications

Compared with that of other charismatic elasmobranchs, the component community of metazoan parasites infecting endangered smalltooth sawfish Pristis pectinata is exceedingly poorly characterized: adults of Dermophthirioides pristidis and Neoheterocotyle inpristi (ectoparasitic flatworms of skin and gill, respectively) were the only confirmed parasites prior to the description, based on specimens reported herein, of Mycteronastes caalusi. Our opportune and directed parasitological examinations of 290 smalltooth sawfish (277 live inspections; 13 necropsies; 671 to 2640 mm stretch total length) in south Florida coastal waters revealed at least 8 species of Platyhelminthes, 9 of Arthropoda, 4 of Annelida, and 1 of Nematoda. This …

The Absence Of Dhhc3 Affects Primary And Latent Herpes Simplex Virus 1 Infection, Shaohui Wang, Kevin R. Mott, Marianne Cilluffo, Casey L. Kilpatrick, Shoko Murakami, Alexander V. Ljubimov, Konstantin G. Kousoulas, Sita Awasthi, Bernhard Luscher, Homayon Ghiasi

Faculty Publications

© 2018 American Society for Microbiology. UL20, an essential herpes simplex virus 1 (HSV-1) protein, is involved in cytoplasmic envelopment of virions and virus egress. We reported recently that UL20 can bind to a host protein encoded by the zinc finger DHHC-type containing 3 (ZDHHC3) gene (also known as Golgi-specific DHHC zinc finger protein [GODZ]). Here, we show for the first time that HSV-1 replication is compromised in murine embryonic fibroblasts (MEFs) isolated from GODZ-/- mice. The absence of GODZ resulted in blocking palmitoylation of UL20 and altered localization and expression of UL20 and glycoprotein K (gK); the expression of …

Ecological Drivers Of Song Evolution In Birds: Disentangling The Effects Of Habitat And Morphology, Elizabeth Perrault Derryberry, Nathalie Seddon, Graham Earnest Derryberry, Santiago Claramunt, Glenn Fairbanks Seeholzer, Robb Thomas Brumfield, Joseph Andrew Tobias

Faculty Publications

© 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Environmental differences influence the evolutionary divergence of mating signals through selection acting either directly on signal transmission (“sensory drive”) or because morphological adaptation to different foraging niches causes divergence in “magic traits” associated with signal production, thus indirectly driving signal evolution. Sensory drive and magic traits both contribute to variation in signal structure, yet we have limited understanding of the relative role of these direct and indirect processes during signal evolution. Using phylogenetic analyses across 276 species of ovenbirds (Aves: Furnariidae), we compared the extent to …

Hidden Endemism, Deep Polyphyly, And Repeated Dispersal Across The Isthmus Of Tehuantepec: Diversification Of The White-Collared Seedeater Complex (Thraupidae: Sporophila Torqueola), Nicholas A. Mason, Arturo Olvera-Vital, Irby J. Lovette, Adolfo G. Navarro-Sigüenza

Faculty Publications

© 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White-collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements …

Insect Effects On Ecosystem Services—Introduction, T. D. Schowalter, J. A. Noriega, T. Tscharntke

Faculty Publications

Natural ecosystems provide a variety of services on which humans, and other organisms, depend for survival and well-being. These ecosystem services can be categorized as provisioning (production of food, fiber, water and other resources), cultural (non-material benefits, such as recreation, spiritual and other aesthetic values), supporting (primary production, pollination, decomposition and soil formation necessary for resource production) and regulating (biological control and other feedback mechanisms that maintain relatively consistent delivery of services). Ecosystems also have been viewed as producing “disservices” such as pests, litter, biological hazards such as diseases, animal attacks, allergenic and poisonous organisms, and geophysical hazards such as …

Recently Integrated Alu Insertions In The Squirrel Monkey (Saimiri) Lineage And Application For Population Analyses, Mark Batzer, Jasmine N. Baker, Jerilyn A. Walker, Michael W. Denham, Charles D. Loupe

Faculty Publications

Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups. …

A Strategy For Sperm Cryopreservation Of Atlantic Salmon, Salmo Salar, For Remote Commercial-Scale High-Throughput Processing, Huiping Yang, E. Hu, John T. Buchanan, Terrence R. Tiersch

Faculty Publications

Sperm cryopreservation is an essential tool for long-term storage of genetic resources for aquaculture fishes. The goal of this study was to develop an efficient and streamlined protocol for high-throughput processing for sperm cryopreservation in Atlantic salmon, Salmo salar. The objectives were to evaluate: (1) osmolality of blood serum for determining extender osmolality, (2) effects of extenders for fresh sperm dilution and refrigerated storage, (3) effects of methanol and dimethyl sulfoxide (DMSO) on fresh sperm motility, and (4) motility and fertility after thawing. In this study, sperm samples were collected at a hatchery site in Canada and shipped to a …

A Three Year Study Of Metal Levels In Skin Biopsies Of Whales In The Gulf Of Mexico After The Deepwater Horizon Oil Crisis, John Pierce Wise, James T.F. Wise, Catherine F. Wise, Sandra S. Wise, Christy Gianios, Hong Xie, Ron Walter, Mikki Boswell, Cairong Zhu, Tongzhang Zheng, Christopher Perkins, John Pierce Wise

Faculty Publications

In response to the explosion of the Deepwater Horizon and the massive release of oil that followed, we conducted three annual research voyages to investigate how the oil spill would impact the marine offshore environment. Most investigations into the ecological and toxicological impacts of the Deepwater Horizon Oil crisis have mainly focused on the fate of the oil and dispersants, but few have considered the release of metals into the environment. From studies of previous oil spills, other marine oil industries, and analyses of oil compositions, it is evident that metals are frequently encountered. Several metals have been reported in …

News In Lights: The Times Square Zipper And Newspaper Signs In An Age Of Technological Enthusiasm, Dale L. Cressman Phd

Faculty Publications

During the latter half of the nineteenth century, when the telegraph had produced an appetite for breaking news, New York City newspaper publishers used signs on their buildings to report headlines and promote their newspapers. Originally chalkboards were used to post headlines. But, fierce competition led to the use of new technologies, such as magic lantern projections. These and, later, electrically lighted signs, would evoke amazement. In 1928, during an age of invention, The New York Times installed an electric "moving letter" sign on its building in Times Square. Popularly known as "the zipper," the monograph drew significant attention from …

Natural Sensations Evoked In Distal Extremities Using Surface Electrical Stimulation, Julia P. Slopsema, John M. Boss, Lane A. Heyboer, Carson M. Tobias, Brooke P. Draggoo, Kathleen E. Finn, Payton J. Hoff, Katharine H. Polasek

Faculty Publications

Background: Electrical stimulation is increasingly relevant in a variety of medical treatments. In this study, surface electrical stimulation was evaluated as a method to non-invasively target a neural function, specifically natural sensation in the distal limbs.

Method: Electrodes were placed over the median and ulnar nerves at the elbow and the common peroneal and lateral sural cutaneous nerves at the knee. Strength-duration curves for sensation were compared between nerves. The location, modality, and intensity of each sensation were also analyzed. In an effort to evoke natural sensations, several patterned waveforms were evaluated.

Results: Distal sensation was obtained in all but …

Rewired Rnai-Mediated Genome Surveillance In House Dust Mites, Mosharrof H. Mondal, Pavel Klimov, Alex S. Flynt

Faculty Publications

House dust mites are common pests with an unusual evolutionary history, being descendants of a parasitic ancestor. Transition to parasitism is frequently accompanied by genome rearrangements, possibly to accommodate the genetic change needed to access new ecology. Transposable element (TE) activity is a source of genomic instability that can trigger large-scale genomic alterations. Eukaryotes have multiple transposon control mechanisms, one of which is RNA interference (RNAi). Investigation of the dust mite genome failed to identify a major RNAi pathway: the Piwi-associated RNA (piRNA) pathway, which has been replaced by a novel small-interfering RNA (siRNA)-like pathway. Co-opting of piRNA function by …

Rice Nucleosome Patterns Undergo Remodeling Coincident With Stress-Induced Gene Expression, Qi Zhang, Dong Ha Oh, Sandra Feuer Ditusa, Mangu V. Ramanarao, Niranjan Baisakh, Maheshi Dassanayake, Aaron P. Smith

Faculty Publications

© 2018 The Author(s). Background: Formation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated. Results: We mapped nucleosomes along with transcriptional changes after 24-h of Pi starvation in rice (Oryza sativa) by deep sequencing of micrococcal nuclease digested chromatin and ribosome-depleted RNA. We demonstrated that nucleosome patterns at rice genes were affected by both cis- and trans-determinants, including GC content and transcription. Also, categorizing rice genes by nucleosome patterns across the …

Dietary Overlap Between Jellyfish And Forage Fish In The Northern Gulf Of Mexico, Isabella D'Ambra, William M. Graham, Ruth H. Carmichael, Frank J. Hernandez Jr.

Faculty Publications

Despite the speculations that jellyfish (hydromedusae, siphonophores, scyphomedusae and ctenophores) may compete with forage fish for prey, there are few direct comparisons of their diets. To determine the dietary overlap between Aurelia sp. (Cnidaria, Scyphozoa) and Brevoortia patronus (Goode, 1878) (Pisces, Clupeidae) in the northern Gulf of Mexico, we collected monthly samples in Louisiana, Mississippi and Alabama coastal waters (USA) during summer and early fall 2009−2010. We determined carbon and nitrogen stable isotope ratios in predators and their potential prey, including small plankton (<200 µm) and mesozooplankton (200− 2000 µm), and identified prey in the stomachs of adult Aurelia sp. and B. patronus. Trophic niche overlap was defined using the stable isotope Bayesian …

Experimental Evidence Of A Pathogen Invasion Threshold, Tad A. Dallas, Martin Krkošek, John M. Drake

Faculty Publications

© 2018 The Authors. Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and diseasefree states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean …

Experimental Evidence Of A Pathogen Invasion Threshold, Tad Dallas, Martin Krkošek, John M. Drake

Faculty Publications

Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and disease-free states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean zooplankton (Daphnia dentifera …

Preparing The Next Generation Of Instructional Designers: A Cross-Institution Faculty Collaboration, Patricia J. Slagter Van Tryon, Jason K. Mcdonald, Atsusi Hirumi

Faculty Publications

The ability of novice instructional designers to become skilled problem-solvers, who select and apply appropriate instructional design (ID) models in their work environments, are key competencies generally sought after in introductory ID courses. Yet, the proliferation of ID models, coupled with varied philosophies and practices about how ID is taught may pose challenges for ID educators seeking to prepare the next generation of leaders in the field. With little empirical research or documented best practices, ID educators are left to their own judgment about to how to navigate the practical challenges that can arise in the pursuit of their teaching …

Identifying Genome-Wide Immune Gene Variation Underlying Infectious Disease In Wildlife Populations - A Next Generation Sequencing Approach In The Gopher Tortoise, Jean P. Elbers, Mary B. Brown, Sabrina S. Taylor

Faculty Publications

Background: Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i.e., the immunomes) in 16 Florida gopher tortoises, Gopherus polyphemus. All tortoises produced antibodies against Mycoplasma agassizii …

Temporal Migration Patterns Between Natal Locations Of Ruby-Throated Hummingbirds (Archilochus Colubris) And Their Gulf Coast Stopover Site, Theodore J. Zenzal Jr., Andrea J. Contina, Jeffrey F. Kelly, Frank R. Moore

Faculty Publications

Background

Autumn latitudinal migrations generally exhibit one of two different temporal migration patterns: type 1 where southern populations migrate south before northern populations, or type 2 where northern populations overtake southern populations en route. The ruby-throated hummingbird (Archilochus colubris) is a species with an expansive breeding range, which allows opportunities to examine variation in the timing of migration. Our objective was to determine a relationship between natal origin of ruby-throated hummingbirds and arrival at a Gulf coast stopover site; and if so, what factors, such as differences in body size across the range as well as the …

Nextgen Voices: Research Resolutions, Felicia Olmeta-Schult, Lauren Massa Segal, Sam Tyner, Twila Alexandra Moon, Ryan Dz Wei Chow, Prosanta Chakrabarty, Martin Pacesa, Anna Igorevna Podgornaia, Jennifer Chen, Bipin Singh, Bo Cao, Rishi Raj Singh Sidhu, Bryce W.Q. Tan, Prashant Sood, Stuart Parker, Matthew A. Scult, Desiree Van Haute, Nikos Konstantinides, Beat A. Schwendimann, Sudhakar Srivastava, Raffaele Fiorenza, Ken Dutton-Regester, Rachel Hale, Emre Ozan Polat, Edward Lau, Audrey L. Mayer, Easton R. White

Faculty Publications

No abstract provided.

Resistance And Resilience Of Social–Ecological Systems To Recurrent Typhoon Disturbance On A Subtropical Island: Taiwan, Chung-Te Chang, Matthew A. Vadeboncoeur, Teng-Chiu Lin

Faculty Publications

Tropical cyclones (TCs) have major effects on ecological and social systems. However, studies integrating the effects of TCs on both social and ecological systems are rare, especially in the northwest Pacific, where the frequency of TCs (locally named typhoons) is the highest in the world. We synthesized studies of effects of recurrent typhoons on social and ecological systems in Taiwan over the last several decades. Many responses to TCs are comparable between social and ecological systems. High forest ecosystem resistance, evident from tree mortality below 2% even following multiple strong typhoons, is comparable with resistance of social systems, including the …

Metavirome Sequencing Of The Termite Gut Reveals The Presence Of An Unexplored Bacteriophage Community, Chinmay V. Tikhe, Claudia Husseneder

Faculty Publications

The Formosan subterranean termite; Coptotermes formosanus is nutritionally dependent on the complex and diverse community of bacteria and protozoa in their gut. Although, there have been many studies to decipher the taxonomic and functional diversity of bacterial communities in the guts of termites, their bacteriophages remain unstudied. We sequenced the metavirome of the guts of Formosan subterranean termite workers to study the diversity of bacteriophages and other associated viruses. Results showed that the termites harbor a virome in their gut comprised of varied and previously unknown bacteriophages. Between 87-90% of the predicted dsDNA virus genes by Metavir showed similarity to …

Game Spirituality: How Games Tell Us More Than We Might Think, Chad Carlson

Faculty Publications

While we often see games as less serious or at least less transcendental than religion there is reason to believe that games can evoke similarly meaningful narratives that allow us to learn a great deal about ourselves and our world. And games do so often using the same symbolic and metaphorical mechanisms that generate meaning in religious experience. In this paper, I explore some of the ways in which game myths—the myths created from and through games—generate meaning in our lives. People experience myths in games very similarly to how they might in religion. I first explain what myth means …

In Vivo Inhibition Of Tryptophan Catabolism Reorganizes The Tuberculoma And Augments Immune-Mediated Control Of Mycobacterium Tuberculosis, Uma S. Gautam, Taylor W. Foreman, Allison N. Bucsan, Ashley V. Veatch, Xavier Alvarez, Toidi Adekambi, Nadia A. Golden, Kaylee M. Gentry, Lara A. Doyle-Meyers, Kasi E. Russell-Lodrigue, Peter J. Didier, James L. Blanchard, K. Gus Kousoulas, Andrew A. Lackner, Daniel Kalman, Jyothi Rengarajan, Shabaana A. Khader, Deepak Kaushal, Smriti Mehra

Faculty Publications

Mycobacterium tuberculosis continues to cause devastating levels of mortality due to tuberculosis (TB). The failure to control TB stems from an incomplete understanding of the highly specialized strategies that M. tuberculosis utilizes to modulate host immunity and thereby persist in host lungs. Here, we show that M. tuberculosis induced the expression of indoleamine 2,3-dioxygenase (IDO), an enzyme involved in tryptophan catabolism, in macrophages and in the lungs of animals (mice and macaque) with active disease. In a macaque model of inhalation TB, suppression of IDO activity reduced bacterial burden, pathology, and clinical signs of TB disease, leading to increased host …

Looking High And Low For Salvation In Luke, Matthew L. Skinner

Faculty Publications

No abstract provided.