Life Sciences Commons^™

Grunt Variation In The Oyster Toadfish Opsanus Tau: Effect Of Size And Sex, Michael L. Fine, Tyler D. Waybright

Biology Publications

As in insects, frogs and birds, vocal activity in fishes tends to be more developed in males than in females, and sonic swimbladder muscles may be sexually dimorphic, i.e., either larger in males or present only in males. Male oyster toadfish Opsanus tau L produce a long duration, tonal boatwhistle advertisement call, and both sexes grunt, a short duration more pulsatile agonistic call. Sonic muscles are present in both sexes but larger in males. We tested the hypothesis that males would call more than females by inducing grunts in toadfish of various sizes held in a net and determined incidence …

Does Upper Extremity Training Influence Body Composition After Spinal Cord Injury?, Justin A. Fisher, Meredith A. Mcnelis, Ashraf S. Gorgey, David S. Dolbow, Lance L. Goetz

Biology Publications

Spinal cord injury (SCI) leads to serious body composition adaptations characterized by increasing whole body fat mass and decreased soft tissue lean mass (LM). These adaptations in body composition may lead to several cardio-metabolic disorders that reduce the quality of life, increase patients’ and caregivers’ burden and eventually leads to mortality. Exercise, an appropriate dietary regimen, and an active lifestyle may alleviate several of the negative effects on body composition after a SCI. Today however, there is no established consensus on the recommended dose, frequency or type of exercise to ameliorate several of the body composition sequelae after an acute …

Metagenomic Analysis Of Planktonic Microbial Consortia From A Non-Tidal Urban-Impacted Segment Of James River, Bonnie L. Brown, Rebecca V. Leprell, Rima B. Franklin, Maria C. Rivera, Francine M. Cabral, Hugh L. Eaves, Vicki Gardiakos, Kevin P. Keegan, Timothy L. King

Biology Publications

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 ⁶ reads revealed >3 × 10 ⁶ genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; …

Consequences Of Life History Switch Point Plasticity For Juvenile Morphology And Locomotion In The Túngara Frog, Julie Charbonnier, James R. Vonesh

Biology Publications

Many animals with complex life cycles can cope with environmental uncertainty by altering the timing of life history switch points through plasticity. Pond hydroperiod has important consequences for the fitness of aquatic organisms and many taxa alter the timing of life history switch points in response to habitat desiccation. For example, larval amphibians can metamorphose early to escape drying ponds. Such plasticity may induce variation in size and morphology of juveniles which can result in carry-over effects on jumping performance. To investigate the carry-over effects of metamorphic plasticity to pond drying, we studied the Túngara frog, Physalaemus pustulosus, a …

Evolutionary History Influences The Salinity Preference Of Bacterial Taxa In Wetland Soils, Ember M. Morrisey, Rima B. Franklin

Biology Publications

Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetland soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences) and activity (CO2 and CH4 production, and extracellular enzyme activity). These changes in community composition and activity rates were …

Identification Of Eastern United States Reticulitermes Termite Species Via Pcr-Rflp, Assessed Using Training And Test Data, Ryan C. Garrick, Benjamin D. Collins, Rachel N. Yi, Rodney J. Dyer, Chaz Hyseni

Biology Publications

Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei) have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR) amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP) assay, with banding patterns resolved via agarose gel electrophoresis. The assay …

Metagenomic Analysis Of Planktonic Microbial Consortia From A Non-Tidal Urban-Impacted Segment Of James River, Bonnie L. Brown, Rebecca V. Leprell, Rima B. Franklin, Maria C. Rivera, Francine M. Cabral, Hugh L. Eaves, Vicki Gardiakos, Kevin P. Keegan, Timothy L. King

Biology Publications

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 106 reads revealed >3 × 106 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), …

Risk Assessment Based On Indirect Predation Cues: Revisiting Fine-Grained Variation, Michael W. Mccoy, Stefan K. Wheat, Karen M. Warkentin, James R. Vonesh

Biology Publications

To adaptively express inducible defenses, prey must gauge risk based on indirect cues of predation. However, the information contained in indirect cues that enable prey to fine-tune their phenotypes to variation in risk is still unclear. In aquatic systems, research has focused on cue concentration as the key variable driving threat-sensitive responses to risk. However, while risk is measured as individuals killed per time, cue concentration may vary with either the number or biomass killed. Alternatively, fine-grained variation in cue, that is, frequency of cue pulses irrespective of concentration, may provide a more reliable signal of risk. Here, we present …

Highly Iterated Palindromic Sequences (Hips) And Their Relationship To Dna Methyltransferases, Jeff Elhai

Study of Biological Complexity Publications

The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes. An important clue to its function may be the presence of two orphan DNA methyltransferases that recognize internal sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both free-living and obligate symbionts, showed that there are exceptional cases in which HIP1 is at a low frequency or nearly absent. In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific methyltransferases are generally present …

The Truth About Metagenomics: Quantifying And Counteracting Bias In 16s Rrna Studies, J. Paul Brooks, David J. Edwards, Michael D. Harwich, Maria C. Rivera, Jennifer M. Fettweis, Myrna G. Serrano, Robert Reris, Nihar U. Sheth, Bernice Huang, Phillipe Girerd, Vaginal Microbiome Consortium, Jerome F. Strauss Iii, Kimberly K. Jefferson, Gregory A. Buck

Study of Biological Complexity Publications

Background

Characterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 …

Protein Complexes In Bacteria, J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz

Study of Biological Complexity Publications

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometrycharacterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, …

Protein Complexes In Bacteria, J. Harry Caufield, Marco A. Abreu, Christopher Wimble, Peter Uetz

Study of Biological Complexity Publications

Large-scale analyses of protein complexes have recently become available for Escherichia coliand Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: …

Pectoral Sound Generation In The Blue Catfish Ictalurus Furcatus, Yasha Mohajer, Zachary Ghahramani, Michael L. Fine

Forensic Science Publications

Catfishes produce pectoral stridulatory sounds by “jerk” movements that rub ridges on the dorsal process against the cleithrum. We recorded sound synchronized with high-speed video to investigate the hypothesis that blue catfish Ictalurus furcatus produce sounds by a slip–stick mechanism, previously described only in invertebrates. Blue catfish produce a variably paced series of sound pulses during abduction sweeps (pulsers) although some individuals (sliders) form longer duration sound units (slides) interspersed with pulses. Typical pulser sounds are evoked by short 1–2 ms movements with a rotation of 2°–3°. Jerks excite sounds that increase in amplitude after motion stops, suggesting constructive interference, …

Elucidating The Role Of Injury-Induced Electric Fields (Efs) In Regulating The Astrocytic Response To Injury In The Mammalian Central Nervous System, Matthew L. Baer, Scott C. Henderson, Raymond J. Colello

Anatomy and Neurobiology Publications

Injury to the vertebrate central nervous system (CNS) induces astrocytes to change their morphology, to increase their rate of proliferation, and to display directional migration to the injury site, all to facilitate repair. These astrocytic responses to injury occur in a clear temporal sequence and, by their intensity and duration, can have both beneficial and detrimental effects on the repair of damaged CNS tissue. Studies on highly regenerative tissues in non-mammalian vertebrates have demonstrated that the intensity of direct-current extracellular electric fields (EFs) at the injury site, which are 50–100 fold greater than in uninjured tissue, represent a potent signal …

Developmental Remodeling Of Relay Cells In The Dorsal Lateral Geniculate Nucleus In The Absence Of Retinal Input, Rana N. El-Danaf, Thomas E. Krahe, Emily K. Dilger, Martha E. Bickford, Michael A. Fox, William Guido

Anatomy and Neurobiology Publications

Background

The dorsal lateral geniculate nucleus (dLGN) of the mouse has been an important experimental model for understanding thalamic circuit development. The developmental remodeling of retinal projections has been the primary focus, however much less is known about the maturation of their synaptic targets, the relay cells of the dLGN. Here we examined the growth and maturation of relay cells during the first few weeks of life and addressed whether early retinal innervation affects their development. To accomplish this we utilized themath5 null (math5−/−) mouse, a mutant lacking retinal ganglion cells and central projections.

Results

The …

Microglia Processes Associate With Diffusely Injured Axons Following Mild Traumatic Brain Injury In The Micro Pig, Audrey D. Lafrenaye, Masak Todani, Susan A. Walker, John T. Povlishock

Anatomy and Neurobiology Publications

Background

Mild traumatic brain injury (mTBI) is an all too common occurrence that exacts significant personal and societal costs. The pathophysiology of mTBI is complex, with reports routinely correlating diffuse axonal injury (DAI) with prolonged morbidity. Progressive chronic neuroinflammation has also recently been correlated to morbidity, however, the potential association between neuroinflammatory microglia and DAI is not well understood. The majority of studies exploring neuroinflammatory responses to TBI have focused on more chronic phases of injury involving phagocytosis associated with Wallerian change. Little, however, is known regarding the neuroinflammatory response seen acutely following diffuse mTBI and its potential relationship to …

Acetylcholine Release In Mouse Hippocampal Ca1 Preferentially Activates Inhibitory-Selective Interneurons Via Α4Β2* Nicotinic Receptor Activation, L. Andrew Bell, Karen A. Bell, A. Rory Mcquiston

Anatomy and Neurobiology Publications

Acetylcholine (ACh) release onto nicotinic receptors directly activates subsets of inhibitory interneurons in hippocampal CA1. However, the specific interneurons activated and their effect on the hippocampal network is not completely understood. Therefore, we investigated subsets of hippocampal CA1 interneurons that respond to ACh release through the activation of nicotinic receptors and the potential downstream effects this may have on hippocampal CA1 network function. ACh was optogenetically released in mouse hippocampal slices by expressing the excitatory optogenetic protein oChIEF-tdTomato in medial septum/diagonal band of Broca cholinergic neurons using Cre recombinase-dependent adeno-associated viral mediated transfection. The actions of optogenetically released ACh were …

Proteomics: In Pursuit Of Effective Traumatic Brain Injury Therapeutics, Pavel N. Lizhnyak, Andrew K. Ottens

Anatomy and Neurobiology Publications

Effective traumatic brain injury (TBI) therapeutics remain stubbornly elusive. Efforts in the field have been challenged by the heterogeneity of clinical TBI, with greater complexity among underlying molecular phenotypes than initially conceived. Future research must confront the multitude of factors comprising this heterogeneity, representing a big data challenge befitting the coming informatics age. Proteomics is poised to serve a central role in prescriptive therapeutic development, as it offers an efficient endpoint within which to assess post-TBI biochemistry. We examine rationale for multifactor TBI proteomic studies and the particular importance of temporal profiling in defining biochemical sequences and guiding therapeutic development. …

Acetylcholine Release In Mouse Hippocampal Ca1 Preferentially Activates Inhibitory-Selective Interneurons Via Α4Β2* Nicotinic Receptor Activation, L. Andrew Bell, Karen A. Bell, A. Rory Mcquiston

Anatomy and Neurobiology Publications

Acetylcholine (ACh) release onto nicotinic receptors directly activates subsets of inhibitory interneurons in hippocampal CA1. However, the specific interneurons activated and their effect on the hippocampal network is not completely understood. Therefore, we investigated subsets of hippocampal CA1 interneurons that respond to ACh release through the activation of nicotinic receptors and the potential downstream effects this may have on hippocampal CA1 network function. ACh was optogenetically released in mouse hippocampal slices by expressing the excitatory optogenetic protein oChIEF-tdTomato in medial septum/diagonal band of Broca cholinergic neurons using Cre recombinase-dependent adeno-associated viral mediated transfection. The actions of optogenetically released ACh were …

Gabaergic Regulation Of Cerebellar Ng2-Cell Development Is Altered In Perinatal White Matter Injury, Marzieh Zonouzi, Joseph Scafidi, Peijun Li, Brian Mcellin, Jorge Edwards, Jeffrey L. Dupree, Lloyd Harvey, Dandan Sun, Christian A. Hübner, Stuart G. Cull-Candy, Mark Farrant, Vittorio Gallo

Anatomy and Neurobiology Publications

Diffuse white matter injury (DWMI), a leading cause of neurodevelopmental disabilities in preterm infants, is characterized by reduced oligodendrocyte formation. Oligodendrocyte precursor cells (NG2-cells) are exposed to various extrinsic regulatory signals, including the neurotransmitter GABA. We investigated GABAergic signaling to cerebellar white matter NG2-cells in a mouse model of DWMI (chronic neonatal hypoxia). We found that hypoxia caused a loss of GABAA receptor-mediated synaptic input to NG2-cells, extensive proliferation of these cells and delayed oligodendrocyte maturation, leading to dysmyelination. Treatment of control mice with a GABAA receptor antagonist or deletion of the chloride-accumulating transporter NKCC1 mimicked the effects of hypoxia. …

Does Upper Extremity Training Influence Body Composition After Spinal Cord Injury?, Justin A. Fisher, Meredith A. Mcnelis, Ashraf S. Gorgey, David R. Dolbow, Lance L. Goetz

Kinesiology and Health Sciences Publications

Spinal cord injury (SCI) leads to serious body composition adaptations characterized by increasing whole body fat mass and decreased soft tissue lean mass (LM). These adaptations in body composition may lead to several cardio-metabolic disorders that reduce the quality of life, increase patients’ and caregivers’ burden and eventually leads to mortality. Exercise, an appropriate dietary regimen, and an active lifestyle may alleviate several of the negative effects on body composition after a SCI. Today however, there is no established consensus on the recommended dose, frequency or type of exercise to ameliorate several of the body composition sequelae after an acute …

Obesity-Related Oxidative Stress: The Impact Of Physical Activity And Diet Manipulation, Chun-Jung Huang, Matthew J. Mcallister, Aaron L. Slusher, Heather E. Webb, J. Thomas Mock, Edmund O. Acevedo

Kinesiology and Health Sciences Publications

Obesity-related oxidative stress, the imbalance between pro-oxidants and antioxidants (e.g., nitric oxide), has been linked to metabolic and cardiovascular disease, including endothelial dysfunction and atherosclerosis. Reactive oxygen species (ROS) are essential for physiological functions including gene expression, cellular growth, infection defense, and modulating endothelial function. However, elevated ROS and/or diminished antioxidant capacity leading to oxidative stress can lead to dysfunction. Physical activity also results in an acute state of oxidative stress. However, it is likely that chronic physical activity provides a stimulus for favorable oxidative adaptations and enhanced physiological performance and physical health, although distinct responses between aerobic and anaerobic …

A Baseline Study Of Edaphic Characteristics, Vegetation Structure, And Recruitment Of Native Baldcypress (Taxodium Distichum (L). Rich. Var. Distichum) In The Newly Restored Wetland Of The Vcu Rice Rivers Center, Melissa J. Davis, Matthew S. Schibner

Rice Rivers Center Research Symposium

In theory, the ideal of ecological restoration is to reestablish a completely functioning ecosystem, however restoration success is often elusive (Stanturf et al. 2001). There is a significant gap in the current research on the impacts of restoration management of restored wetlands on ecosystem functions, especially biogeochemical cycling (Bernal & Mitsch 2013). Furthermore, there are many questions about management techniques when it comes to ecological engineering versus self-design (Bernal & Mitsch, 2013). However, we do know that it is critical to understand the species' life history, habitat template, and spatio temporal scope when attempting to re-establish populations (Lake et al. …

Using The Past To Restore The Future: Quantifying Historical Vegetation To Assist In Tidal Freshwater Wetland Restoration Former Lake Charles At The Vcu Rice Rivers Center, Christopher D. Gatens, Edward R. Crawford

Rice Rivers Center Research Symposium

Wetlands have been providing humans with critical natural ecosystem services throughout our time on Earth. Nevertheless, these invaluable ecosystems have been habitually altered as a cost of human progression. Two of the most common alterations to wetlands are hydrologic, in the form of damming, and filling. Both occurred along Kimages Creek in Charles City County, VA during the 19th and 20th centuries. In 2010 the Lake Charles dam was partially removed, restoring the creek's tidal communication with the James River and beginning tidal forested freshwater wetland restoration. Upon the recession of the body of water, numerous woody stumps were revealed.

Analysis Of Standard Dna Procedures On Feathers Of Late 19th To Late 20th Century Osprey (Pandion Haliaetus), Alia A. Hamdan, Catherine B. Viverette, Rodney J. Dyer

Rice Rivers Center Research Symposium

Species with well-documented demographic histories and well known perturbations to gene flow provide good models for understanding how historic events impact contemporary population genetic structure1,2. Osprey (Pandion haliaetus), a marine bird-of-prey, experienced steep declines after widespread organochloride pesticide (e.g. DDT) use in the mid-twentieth century 3, however, population genetic consequences remain unknown. Use of historic specimens can aid population genetic studies4,5, however, these samples can degrade over time impacting quantity and quality of extracted DNA5. We compared the concentrations of extracted DNA of Osprey feathers from museum and research collections to those of contemporary samples collected according to standard field …

Behavioral Observations: Foraging And Aggression Of Neotropical Migrants And Resident Birds In Panama, Jessica M. Johnston, Samuel B. King, Ryan A. Levering

Rice Rivers Center Research Symposium

Lyons suggests that foraging data in songbirds can be an indicator of food abundance, with higher attack rate= higher habitat quality; higher foraging speed= lower habitat quality (2005). Territorial behavior such as interspecific aggression among songbirds may also be related to food availability. Previous studies have documented variation in the extent of territorial and aggressive behaviors among resident and Neotropical migratory species on tropical wintering grounds. This research gathered foraging and aggression data at two coastal angroves sites in central Panama, one on the Caribbean Coast (Galeta) and one on the Pacific Coast (Juan Diaz-East). Foraging data was used an …

Communicating The Overall Experience Of Research Through Various Approaches Using Art: A Case Study Of The Prothonotary Warbler, Hannah Huddle, Lesley P. Bulluck, Sarah E. Faris

Rice Rivers Center Research Symposium

Recommended Citation

In general, scientific research has publication of data as the end goal. The process and experience, which are of great importance in art disciplines, is not necessarily represented or valued. However, science has an inherent element of art to it, which deserves to be shown. I have been studying Prothonotary Warblers with a team from the VCU Biology Department to learn how I can reinterpret the research in a way that bridges the gap between the experience and typical scientific products. The research team measured spatial and temporal variation in warbler prey abundance (caterpillars and mayflies) and assessed …

Emergent Non-Consumptive Predator Effects Alter Habitat Colonization By Mosquitoes, Ethan G. Staats, Salvatore J. Agosta, James R. Vonesh

Rice Rivers Center Research Symposium

Top-down consumptive control (suppression) is an important driver of populations and communities of prey organisms. Diverse predator assemblages often yield non-linear suppression with respect to constituent species' effects (emergence); most often diversity enhances suppression. Predators also affect prey organisms non-consumptively through changes in prey physiological, physical, spatial, temporal, and behavioral responses to predators. Role of predator diversity in non-consumptive response by prey is relatively un-studied. Role of predator diversity in shaping prey populations and communities through habitat colonization is a novel question.

Firing Rate Dynamics In Recurrent Spiking Neural Networks With Intrinsic And Network Heterogeneity, Cheng Ly

Statistical Sciences and Operations Research Publications

Heterogeneity of neural attributes has recently gained a lot of attention and is increasing recognized as a crucial feature in neural processing. Despite its importance, this physiological feature has traditionally been neglected in theoretical studies of cortical neural networks. Thus, there is still a lot unknown about the consequences of cellular and circuit heterogeneity in spiking neural networks. In particular, combining network or synaptic heterogeneity and intrinsic heterogeneity has yet to be considered systematically despite the fact that both are known to exist and likely have significant roles in neural network dynamics. In a canonical recurrent spiking neural network model, …

Understanding Host-Switching By Ecological Fitting, Sabrina B. L. Araujo, Mariana Pires Braga, Daniel R. Brooks, Salvatore J. Agosta, Eric P. Hoberg, Francisco W. Von Hartenthal, Walter A. Boeger

Biology Publications

Despite the fact that parasites are highly specialized with respect to their hosts, empirical evidence demonstrates that host switching rather than co-speciation is the dominant factor influencing the diversification of host-parasite associations. Ecological fitting in sloppy fitness space has been proposed as a mechanism allowing ecological specialists to host-switch readily. That proposal is tested herein using an individual-based model of host switching. The model considers a parasite species exposed to multiple host resources. Through time host range expansion can occur readily without the prior evolution of novel genetic capacities. It also produces non-linear variation in the size of the fitness …