Life Sciences Commons^™

Updating Molecular Diagnostics For Detecting Methicillin- Susceptible And Methicillin-Resistant Staphylococcus Aureus Isolates In Blood Culture Bottles, Fred C. Tenover, Isabella A. Tickler, Victoria M. Le, Scott Dewell, Rodrigo E. Mendes, Richard V. Goering, Mrsa Consortium

Biology Faculty Publications

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotypephenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette …

Global Imprint Of Mycorrhizal Fungi On Whole-Plant Nutrient Economics, Colin Averill, Jennifer M. Bhatnagar, Michael C. Dietze, William D. Pearse, Stephanie N. Kivlin

Biology Faculty Publications

Mycorrhizal fungi are critical members of the plant microbiome, forming a symbiosis with the roots of most plants on Earth. Most plant species partner with either arbuscular or ectomycorrhizal fungi, and these symbioses are thought to represent plant adaptations to fast and slow soil nutrient cycling rates. This generates a second hypothesis, that arbuscular and ectomycorrhizal plant species traits complement and reinforce these fungal strategies, resulting in nutrient acquisitive vs. conservative plant trait profiles. Here we analyzed 17,764 species level trait observations from 2,940 woody plant species to show that mycorrhizal plants differ systematically in nitrogen and phosphorus economic traits. …

Larger Genomes Linked To Slower Development And Loss Of Late-Developing Traits, Molly C. Womack, Marissa J. Metz, Kim L. Hoke

Biology Faculty Publications

Genome size varies widely among organisms and is known to affect vertebrate development, morphology, and physiology. In amphibians, genome size is hypothesized to contribute to loss of late-forming structures, although this hypothesis has mainly been discussed in salamanders. Here we estimated genome size for 22 anuran species and combined this novel dataset with existing genome size data for an additional 234 anuran species to determine whether larger genome size is associated with loss of a late-forming anuran sensory structure, the tympanic middle ear. We established that genome size is negatively correlated with development rate across 90 anuran species and found …

A Genome-Wide Assessment Of The Ancestral Neural Crest Gene Regulatory Network, Dorit Hockman, Vanessa Chong-Morrison, Stephen A. Green, Daria Gavriouchkina, Ivan Candido-Ferreira, Irving T. C. Ling, Ruth M. Williams, Chris T. Amemiya, Jeramiah J. Smith, Marianne E. Bronner, Tatjana Sauka-Spengler

Biology Faculty Publications

The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, …

Piezoelastic Pvdf/Tpu Nanofibrous Composite Membrane: Fabrication And Characterization, Eman Elnabawy, Ahmed H. Hassanin, Nader Shehata, Anton Popelka, Remya Nair, Saifallah Yousef, Ishac Kandas

Biology Faculty Publications

Poly (vinylidene fluoride) nanofibers (PVDF NFs) have been extensively used in energy harvesting applications due to their promising piezoresponse characteristics. However, the mechanical properties of the generated fibers are still lacking. Therefore, we are presenting in this work a promising improvement in the elasticity properties of PVDF nanofibrous membrane through thermoplastic polyurethane (TPU) additives. Morphological, physical, and mechanical analyses were performed for membranes developed from different blend ratios. Then, the impact of added weight ratio of TPU on the piezoelectric response of the formed nanofibrous composite membranes was studied. The piezoelectric characteristics were studied through impulse loading testing where the …

Helianthus Maximiliani And Species Fine-Scale Spatial Pattern Affect Diversity Interactions In Reconstructed Tallgrass Prairies, Thomas P. Mckenna, Jack Mcdonnell, Kathryn A. Yurkonis, Caroline Brophy

Biology Faculty Publications

1. Biodiversity and Ecosystem Function analyses aim to explain how individual spe‐ cies and their interactions affect ecosystem function. With this study, we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) propor‐ tions a better reference point for characterizing grassland diversity effects?

2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted all species in monocultures and mixtures that varied in their species richness, evenness, and spatial pattern. We recorded species‐specific biomass production over three …

The Saint John's Maple Syrup Operation: Something Sweet For Everyone, Sarah Gainey, Kyle Rauch, Stephen G. Saupe

Biology Faculty Publications

No abstract provided.

Celebrating Nj Tea’S Unspecialized Pollination, W. John Hayden

Biology Faculty Publications

Specialized pollination systems are the source of some of the most compelling stories in natural history. There is something appealing to the human psyche about what seems to be a reciprocal agreement between a given plant and its dedicated pollinator: the plant attracts a pollinator and provides ample nectar and/or pollen as a reward for the pollinator’s service in moving pollen from anthers to stigmas while foraging for food. Of course, these organisms have neither signed agreements nor memos of understanding. Instead, it has merely proven to the benefit of the plant, over time, to form certain floral structures, and …

Scaling Of Swimming Performance In Baleen Whales, William T. Gough, Paolo S. Segre, K. C. Bierlich, David E. Cade, Jean Potvin, Frank E. Fish, Julian Dale, Jacopo Di Clemente, Ari S. Friedlaender, David W. Johnston, Shirel R. Kahane-Rapport, John Kennedy, John H. Long, Machiel Oudejans, Gwenith Penry, Matthew S. Savoca, Malene Simon, Simone K. A. Videsen, Fleur Visser, David N. Wiley, Jeremy O. Goldbogen

Biology Faculty Publications

The scale dependence of locomotor factors has long been studied in comparative biomechanics, but remains poorly understood for animals at the upper extremes of body size. Rorqual baleen whales include the largest animals, but we lack basic kinematic data about their movements and behavior below the ocean surface. Here, we combined morphometrics from aerial drone photogrammetry, whale-borne inertial sensing tag data and hydrodynamic modeling to study the locomotion of five rorqual species. We quantified changes in tail oscillatory frequency and cruising speed for individual whales spanning a threefold variation in body length, corresponding to an order of magnitude variation in …

Connective Tissue Fibroblasts From Highly Regenerative Mammals Are Refractory To Ros-Induced Cellular Senescence, Sandeep Saxena, Hemendra J. Vekaria, Patrick G. Sullivan, Ashley W. Seifert

Biology Faculty Publications

A surveillance system in mammals constantly monitors cell activity to protect against aberrant proliferation in response to damage, injury and oncogenic stress. Here we isolate and culture connective tissue fibroblasts from highly regenerative mammals (Acomys and Oryctolagus) to determine how these cells interpret signals that normally induce cellular senescence in non-regenerating mammals (Mus and Rattus). While H₂O₂ exposure substantially decreases cell proliferation and increases p53, p21, p16, and p19 in cells from mice and rats, cells from spiny mice and rabbits are highly resistant to H₂O₂. Quantifying oxygen consumption …

Fgf-Signaling Is Compartmentalized Within The Mesenchyme And Controls Proliferation During Salamander Limb Development, Sruthi Purushothaman, Ahmed Elewa, Ashley W. Seifert

Biology Faculty Publications

Although decades of studies have produced a generalized model for tetrapod limb development, urodeles deviate from anurans and amniotes in at least two key respects: their limbs exhibit preaxial skeletal differentiation and do not develop an apical ectodermal ridge (AER). Here, we investigated how Sonic hedgehog (Shh) and Fibroblast growth factor (Fgf) signaling regulate limb development in the axolotl. We found that Shh-expressing cells contributed to the most posterior digit, and that inhibiting Shh-signaling inhibited Fgf8 expression, anteroposterior patterning, and distal cell proliferation. In addition to lack of a morphological AER, we found that salamander …

Red Oak Seedlings As Indicators Of Deer Browse Pressure: Gauging The Outcome Of Different White-Tailed Deer Management Approaches, Bernd Blossey, Paul Curtis, Jason Boulanger, Andrea Davalos

Biology Faculty Publications

After decades of high deer populations, North American forests have lost much of their previous biodiversity. Any landscape‐level recovery requires substantial reduc‐ tions in deer herds, but modern societies and wildlife management agencies appear unable to devise appropriate solutions to this chronic ecological and human health crisis. We evaluated the effectiveness of fertility control and hunting in reducing deer impacts at Cornell University. We estimated spring deer populations and planted Quercus rubra seedlings to assess deer browse pressure, rodent attack, and other factors compromising seedling performance. Oak seedlings protected in cages grew well, but deer annually browsed ≥60% of unprotected …

Water Entry Impact Dynamics Of Diving Birds, Saburel I. Sharker, Sean Holekamp, Mohammad M. Mansoor, Tadd T. Truscott

Biology Faculty Publications

Some seabirds (such as northern gannets and brown boobies) can dive from heights as high as 30 m reaching speeds of up to 24 m s−1 as they impact the water surface. The physical geometry of plunge diving birds, particularly of the beak, allows them to limit high impact forces compared to non-diving birds. Numerically simulated data for one species (northern gannet) provides some insight into the impact forces experienced during diving, however, no reliable experimental data with real bird geometries exist for comparison purposes. This study utilizes eleven 3D printed diving bird models of three types of birds: plunge-diving …

Measuring Bird Damage To Three Fruit Crops: A Comparison Of Grower And Field Estimates, Julie L. Elser, Catherine A. Lindell, Karen M. M. Steensma, Paul D. Curtis, Deanna K. Leigh, William F. Siemer, Jason Boulanger, Stephanie A. Shwiff

Biology Faculty Publications

Birds are common pests in fruit orchards. They frequently consume and damage fruit resulting in decreased yields for growers. The true extent of damage is difficult to measure. Producer surveys are often implemented to estimate damage, but the accuracy of these estimates is uncertain. We compared damage estimates obtained through field studies with estimates from a producer survey for three fruit crops: wine grapes, sweet cherries, and ‘Honeycrisp’ apples. We also analyzed relationships between use of various damage management methods and levels of bird damage. We found wine grape and sweet cherry growers accurately assessed bird damage, while ‘Honeycrisp’ apple …

Demographic Assessment Of The Triploid Parthenogenetic Lizard Aspidoscelis Neotesselatus At The Northern Edge Of Its Range, Lise M. Aubry, Douglas Eifler, Kaera Utsumi, Susannah S. French

Biology Faculty Publications

Aspidoscelis neotesselatus (Colorado Checkered Whiptail) is a hybrid-derived triploid parthenogenetic lizard with a natural range overlapping with six counties in southeastern Colorado, USA. It has also become established by anthropogenic causation in Grant County, Washington State, approximately 1,600 km northwest of its range in Colorado. Large parts of its natural range are within military reservations. Reduced genetic variation in all-female species makes them especially susceptible to environmental disturbances, such as military activities. At Fort Carson (FC), we estimated an abundance index via a catch-per-unit estimator, weekly survival using Cormack-Jolly-Seber models, and body condition and clutch size as indicators of population …

Phylogeny Of The Subfamilies Of Ichneumonidae (Hymenoptera), Andrew M.R. Bennett, Sophie Cardinal, Ian D. Gauld, David B. Wahl

Biology Faculty Publications

A combined morphological and molecular phylogenetic analysis was performed to evaluate the subfamily relationships of the parasitoid wasp family Ichneumonidae (Hymenoptera). Data were obtained by coding 135 morphological and 6 biological characters for 131 exemplar species of ichneumonids and 3 species of Braconidae (the latter as outgroups). The species of ichneumonids represent all of the 42 currently recognized subfamilies. In addition, molecular sequence data (cytochrome oxidase I “DNA barcoding” region, the D2 region of 28S rDNA and part of the F2 copy of elongation factor 1-alpha) were obtained from specimens of the same species that were coded for morphology (1309 …

Fipronil And Ivermectin Treatment Of Cattle Reduced The Survival And Ovarian Development Of Field-Collection Anopheles Albimanus In A Pilot Trial Conducted In Northern Belize, Staci M. Dreyer, Donovan Leiva, Marla Magana, Marie Pott, Jonathan Kay, Alvaro Cruz, Nicole L. Achee, John P. Grieco, Jefferson A. Vaughan

Biology Faculty Publications

Background: Most malaria vector control programmes rely on indoor residual spraying of insecticides and insecticide-treated bed nets. This is efective against vector species that feed indoors at night and rest inside the house afterwards. In Central America, malaria vectors have diferent behaviours and are typically exophagic (i.e., bite outdoors), exophilic (i.e., remain outdoors after feeding), and zoophagic (i.e., as likely to feed on non-humans as humans). Thus, malaria elimination in Central America may require additional tactics. This pilot study investigated whether commercially-available products used to treat livestock for ticks could also be used to kill and/or sterilize zoophagic malaria vectors …

Resolving The Genetic Paradox Of Invasions: Preadapted Genomes And Postintroduction Hybridization Of Bigheaded Carps In The Mississippi River Basin, Jun Wang, Sarah Gaughan, James T. Lamer, Cao Deng, Wanting Hu, Michael Wachholtz, Shishang Qin, Hu Nie, Xiaolin Liao, Qufei Ling, Weitao Li, Lifeng Zhu, Louis Bernatchez, Chenghui Wang, Guoqing Lu

Biology Faculty Publications

The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate‐to‐high …

Total Rna Extraction From Transgenic Flies Misexpressing Foreign Genes To Perform Next Generation Rna Sequencing, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Due to absence of transgenic approaches in Notopthalmus Viridescens (newt), and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress unique genes from newt. Novel newt genes cloned, and inserted at attP site in Drosophila were misexpressed ubiquitously using tubulin Gal-4. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM. RNA quality was quantitated by calculating absorbance at 260 nm (A260) and 280 nm (A280) wavelengths using Nanodrop 2000 spectrophotometer. Good quality …

Impacts Of Hiv Cure Interventions On Viral Reservoirs In Tissues, Paul W. Denton, Ole S. Søgaard, Martin Tolstrup

Biology Faculty Publications

HIV reservoirs persist in infected individuals despite combination antiretroviral therapy and can be identified in secondary lymphoid tissues, in intestinal tissues, in the central nervous system as well as in blood. Clinical trials have begun to explore effects of small molecule interventions to perturb the latent viral infection, but only limited information is available regarding the impacts of HIV cure-related clinical interventions on viral reservoirs found in tissues. Of the 14 HIV cure-related clinical trials since 2012 that have evaluated the effects of small molecule interventions in vivo, four trials have examined the impacts of the interventions in peripheral …

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

Loss Of Developmental Diapause As Prerequisite For Social Evolution In Bees, Priscila Karla Ferreira Santos, Maria Cristina Arias, Karen M. Kapheim

Biology Faculty Publications

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs have been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction (ASR) of the ecological and evolutionary factors associated with …

Does A Carbonatite Deposit Influence Its Surrounding Ecosystem?, James M.C. Jones, Elizabeth A. Webb, Michael D.J. Lynch, Trevor C. Charles, Pedro M. Antunes, Frédérique C. Guinel

Biology Faculty Publications

Carbonatites are unusual alkaline rocks with diverse compositions. Although previous work has characterized the effects these rocks have on soils and plants, little is known about their impacts on local ecosystems. Using a deposit within the Great Lakes–St. Lawrence forest in northern Ontario, Canada, we investigated the effect of a carbonatite on soil chemistry and on the structure of plant and soil microbial communities. This was done using a vegetation survey conducted above and around the deposit, with corresponding soil samples collected for determining soil nutrient composition and for assessing microbial community structure using 16S/ITS Illumina Mi-Seq sequencing. In some …

The Effects Of Aging On Sleep Parameters In A Healthy, Melatonin-Competent Mouse Model, Jiffin K. Paulose, Chanung Wang, Bruce F. O'Hara, Vincent M. Cassone

Biology Faculty Publications

Background: Sleep disturbances are common maladies associated with human age. Sleep duration is decreased, sleep fragmentation is increased, and the timing of sleep onset and sleep offset is earlier. These disturbances have been associated with several neurodegenerative diseases. Mouse models for human sleep disturbances can be powerful due to the accessibility to neuroscientific and genetic approaches, but these are hampered by the fact that most mouse models employed in sleep research have spontaneous mutations in the biosynthetic pathway(s) regulating the rhythmic production of the pineal hormone melatonin, which has been implicated in human sleep.

Purpose and method: The present study …

A Comparison Of Drone Imagery And Ground-Based Methods For Estimating The Extent Of Habitat Destruction By Lesser Snow Geese (Anser Caerulescens Caerulescens) In La Pérouse Bay, Andrew Barnas, Brian J. Darby, Gregory S. Vandeberg, Robert F. Rockwell, Susan N. Ellis-Felege

Biology Faculty Publications

Lesser snow goose (Anser caerulescens caerulescens) populations have dramatically altered vegetation communities through increased foraging pressure. In remote regions, regular habitat assessments are logistically challenging and time consuming. Drones are increasingly being used by ecologists to conduct habitat assessments, but reliance on georeferenced data as ground truth may not always be feasible. We estimated goose habitat degradation using photointerpretation of drone imagery and compared estimates to those made with ground-based linear transects. In July 2016, we surveyed five study plots in La Pérouse Bay, Manitoba, to evaluate the effectiveness of a fixed-wing drone with simple Red Green Blue …

A Comparison Of Drone Imagery And Groundbased Methods For Estimating The Extent Of Habitat Destruction By Lesser Snow Geese (Anser Caerulescens Caerulescens) In La Pérouse Bay, Andrew F. Barnas, Brian J. Darby, Gregory S. Vandeberg, Robert F. Rockwell, Susan N. Ellis-Felege

Biology Faculty Publications

Lesser snow goose (Anser caerulescens caerulescens) populations have dramatically altered vegetation communities through increased foraging pressure. In remote regions, regular habitat assessments are logistically challenging and time consuming. Drones are increasingly being used by ecologists to conduct habitat assessments, but reliance on georeferenced data as ground truth may not always be feasible. We estimated goose habitat degradation using photointerpretation of drone imagery and compared estimates to those made with ground-based linear transects. In July 2016, we surveyed five study plots in La Pérouse Bay, Manitoba, to evaluate the effectiveness of a fixed-wing drone with simple Red Green Blue …

The Influence Of Signaling Conspecific And Heterospecific Neighbors On Eavesdropper Pressure, Paula A. Trillo, Christopher S. Benson, Michael S. Caldwell, Tiffany L. Lam, Oliver H. Pickering, David M. Logue

Biology Faculty Publications

The study of tradeoffs between the attraction of mates and the attraction of eavesdropping predators and parasites has generally focused on a single species of prey, signaling in isolation. In nature, however, animals often signal from mixed-species aggregations, where interactions with heterospecific group members may be an important mechanism modulating tradeoffs between sexual and natural selection, and thus driving signal evolution. Although studies have shown that conspecific signalers can influence eavesdropper pressure on mating signals, the effects of signaling heterospecifics on eavesdropper pressure, and on the balance between natural and sexual selection, are likely to be different. Here, we review …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Molecular Phylogeny Provides New Insights On The Taxonomy And Composition Of Lyperosomum Looss, 1899 (Digenea, Dicrocoeliidae) And Related Genera, Joanna Hildebrand, Ewa Pyrka, Jiljí Sitko, Witold Jeżewski, Grzegorz Zaleśny, Vasyl V. Tkach, Zdzisław Laskowski

Biology Faculty Publications

Lyperosomum Looss, 1899 is one of the largest genera of the Dicrocoeliidae and is one of the best examples of the systematic complexity and taxonomic instability within this family. We present the molecular analyses based on novel sequences of nuclear and mitochondrial genes obtained from 56 isolates of adult flukes and larval stages of dicrocoeliids belonging to Lyperosomum, Skrjabinus, Zonorchis as well as previously available sequence data. According to obtained results we propose to return Zonorchis clathratus and Z. petiolatus into Lyperosomum, and to recognize L. alagesi as a synonym of L. petiolatum. Our study shows that L. petiolatum commonly …

Emergence Of Oxacillin Resistance In Stealth Methicillin-Resistant Staphylococcus Aureus Due To Meca Sequence Instability, Richard V. Goering, Erin A. Swartzendriber, Anne E. Obradovich, Isabella A. Tickler, Fred C. Tenover

Biology Faculty Publications

Staphylococcus aureus strains that possess a mecA gene but are phenotypically susceptible to oxacillin and cefoxitin (OS-MRSA) have been recognized for over a decade and are a challenge for diagnostic laboratories. The mechanisms underlying the discrepancy vary from isolate to isolate. We characterized seven OS-MRSA clinical isolates of six different spa types from six different states by whole-genome sequencing to identify the nucleotide sequence changes leading to the OS-MRSA phenotype. The results demonstrated that oxacillin susceptibility was associated with mutations in regions of nucleotide repeats within mecA. Subinhibitory antibiotic exposure selected for secondary mecA mutations that restored oxacillin resistance. …