Life Sciences Commons^™

The Development Of Sleep-Wake Rhythms And The Search For Elemental Circuits In The Infant Brain, Mark S. Blumberg, Andrew J. Gall, William D. Todd

Faculty Publications

Despite the predominance of sleep in early infancy, developmental science has yet to play a major role in shaping concepts and theories about sleep and its associated ultradian and circadian rhythms. Here we argue that developmental analyses help us to elucidate the relative contributions of the brainstem and forebrain to sleep-wake control and to dissect the neural components of sleep-wake rhythms. Developmental analysis also makes it clear that sleep-wake processes in infants are the foundation for those of adults. For example, the infant brainstem alone contains a fundamental sleep-wake circuit that is sufficient to produce transitions among wakefulness, quiet sleep, …

Contribution Of Surface Leaf-Litter Breakdown And Forest Composition To Benthic Oxygen Demand And Ecosystem Respiration In A South Georgia Blackwater River, Andrew S. Mehring, Kevin A. Kuehn, Cynthia J. Tant, Catherine M. Pringle, R. Richard Lowrance, George Vellidis

Faculty Publications

Many North American blackwater rivers exhibit low dissolved O₂ (DO) that may be the result of benthic respiration. We examined how tree species affected O₂ demand via the quantity and quality of litter produced. In addition, we compared areal estimates of surface leaf-litter microbial respiration to sediment O₂ demand (SOD) and ecosystem respiration (ER) in stream and swamp reaches of a blackwater river to quantify contributions of surface litter decomposition to O₂ demand. Litter inputs averaged 917 and 678 g m⁻² y⁻¹ in the swamp and stream, respectively. Tree species differentially affected O_{2 …}

Implications Of The Landauer Limit For Quantum Logic, F. Matthew Mihelic

Faculty Publications

The design of any system of quantum logic must take into account the implications of the Landauer limit for logical bits. Useful computation implies a deterministic outcome, and so any system of quantum computation must produce a final deterministic outcome, which in a quantum computer requires a quantum decision that produces a deterministic qubit. All information is physical, and any bit of information can be considered to exist in a physicality represented as a decision between the two wells of a double well potential in which the energy barrier between the two wells must be greater than kT·ln2. Any proposed …

Male-Male Clasping May Be Part Of An Alternative Reproductive Tactic In Xenopus Laevis, Heather J. Rhodes, Rachel J. Stevenson, Courtney L. Ego

Faculty Publications

No abstract provided.

El Niño-Southern Oscillation Is Linked To Decreased Energetic Condition In Long-Distance Migrants, Kristina Paxton, Emily B. Cohen, Zoltán Németh, Frank R. Moore

Faculty Publications

Predicting how migratory animals respond to changing climatic conditions requires knowledge of how climatic events affect each phase of the annual cycle and how those effects carry-over to subsequent phases. We utilized a 17-year migration dataset to examine how El Niño-Southern Oscillation climatic events in geographically different regions of the Western hemisphere carry-over to impact the stopover biology of several intercontinental migratory bird species. We found that migratory birds that over-wintered in South America experienced significantly drier environments during El Niño years, as reflected by reduced Normalized Difference Vegetation Index (NDVI) values, and arrived at stopover sites in reduced energetic …

Quantifying Natural Resources Using Field-Based Instruction And Hands-On Applications, Daniel Unger, David Kulhavy, I-Kuai Hung, Yanli Zhang

Faculty Publications

Undergraduate students pursuing a Bachelor of Science in Forestry (BSF) degree at Stephen F. Austin State University (SFA) attend an intensive 6-week residential hands-on instruction in applied field methods. For students pursuing the BSF degree knowing the exact location, length, or area of a forestland is crucial to the understanding and proper management of any related natural resource. The intensive 6-week instruction includes teaching how to use the Global Positioning System (GPS) to accurately record the true spatial location of an earth’s surface feature. After receiving hands-on instructions during the summer of 2013, students were taken to the field to …

Smoq: A Tool For Predicting The Absolute Residue-Specific Quality Of A Single Protein Model With Support Vector Machine, Renzhi Cao, Zheng Wang, Yiheng Wang, Jianlin Cheng

Faculty Publications

Background: It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models.

Results: We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to …

Hindcasts Of Potential Harmful Algal Bloom Transport Pathways On The Pacific Northwest Coast, S. Giddings, P. Maccready, B. Hickey, N. Banas, K. Davis, S. Siedlecki, V. Trainer, R. Kudela, N. Pelland, Thomas Connolly

Faculty Publications

Harmful algal blooms (HABs) pose a significant threat to human and marine organism health, and negatively impact coastal economies around the world. An improved understanding of HAB formation and transport is required to improve forecasting skill. A realistic numerical simulation of the US Pacific Northwest region is used to investigate transport pathways from known HAB formation hot spots, specifically for Pseudo-nitzschia (Pn), to the coast. We show that transport pathways are seasonal, with transport to the Washington (WA) coast from a northern source (the Juan de Fuca Eddy) during the summer/fall upwelling season and from a southern source (Heceta Bank) …

Designing And Evaluating The Multicom Protein Local And Global Model Quality Prediction Methods In The Casp10 Experiment, Renzhi Cao, Zheng Wang, Jianlin Cheng

Faculty Publications

Background: Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models.

Results: MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based …

Prior Experience Affects Allocation To Current Reproduction In A Burying Beetle, Eric J. Billman, J. Curtis Creighton, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis predicts that the level of reproductive investment to current reproduction is constrained by an individual’s future reproductive potential or residual reproductive value. Therefore, age, or differences between young and old individuals in residual reproductive value, is expected to influence reproductive investment. However, recent theoretical work suggests that residual reproductive value is also influenced by an individual’s state or condition which may in part be determined by prior reproductive experience. We evaluated the reproductive investment of same-aged female burying beetles (Nicrophorus orbicollis) to determine how prior reproductive experience affects current reproduction. Consistent with previous …

Transcriptional Activation Of Antioxidants May Compensate For Selenoprotein Deficiences In Amblyomma Maculatum (Acari: Ixodidae) Injected With Selk- Or Selm- Dsrna, S. Adamson, R. Browning, P. Singh, S. Nobles, A. Villareal, Shahid Karim

Faculty Publications

The Gulf‐Coast tick, Amblyomma maculatum, possesses an elaborate set of selenoproteins, which prevent the deleterious effects from oxidative stress that would otherwise occur during feeding. In the current work, we examined the role of selenoprotein K (SelK) and selenoprotein M (SelM) in feeding A. maculatum by bioinformatics, transcriptional gene expression, RNA interference and antioxidant assays. The transcriptional expression of SelK did not vary significantly in salivary glands or midguts throughout the bloodmeal. However, there was a 58‐fold increase in transcript levels of SelM in tick midguts. Ticks injected with selK‐dsRNA or selM‐dsRNA did not reveal any observable …

Improvements In Blood Pressure Among Undiagnosed Hypertensive Participants In A Community-Based Lifestyle Intervention, Mississippi, 2010, Jamie M. Zoellner, Jessica L. Thomson, Alicia S. Landry, Charkarra Anderson-Lewis, Carol Connell, Elaine Fontenot Molaison, Kathleen Yadrick

Faculty Publications

Introduction

Effective strategies are needed to reach and treat people who lack awareness of or have uncontrolled hypertension. We used data from a community-based participatory research initiative, Hub City Steps, to quantify the prevalence of undiagnosed hypertension and determine the relationship between hypertension status at baseline and postintervention improvements in blood pressure and health-related quality of life.

Methods

Hub City Steps was a 6-month preintervention–postintervention lifestyle intervention targeting hypertension risk factors. Outcome measures were collected at baseline, 3 months, and 6 months. Generalized linear mixed models were used to test for effects by time and hypertension status.

Results

Of the …

Unpermitted Urban Agriculture: Transgressive Actions, Changing Norms And The Local Food Movement, Sarah B. Schindler

Faculty Publications

Roberta keeps four chickens in her backyard. Bob snuck onto the vacant lot next door, which the bank foreclosed upon and now owns, and planted a vegetable garden. Vien operates an occasional underground restaurant from his friends’ microbrewery after beer-making operations cease for the day. The common thread tying these actions together is that they are unauthorized; they are being undertaken in violation of existing laws and often norms. In this Article, I explore ideas surrounding the overlap between food policy and land use law, specifically the transgressive1 actions that people living in urban and suburban communities are undertaking to …

Using Google Earth For Forest Management, Yanli Zhang, Jeremy P. Stovall

Faculty Publications

No abstract provided.

Health Insurance Status, Psychological Processes, And Older African Americans' Use Of Preventive Care, Catherine Walker O'Neal, Kandauda A.S. Wickrama, Penny A. Ralston, Jasminka Z. Elich, Cynthia M. Harris, Catherine Coccia, Iris Young-Clark, Jennifer Lemacks

Faculty Publications

The current study examined the influence of health insurance, psychological processes (i.e. psychological competency and vulnerability), and the interaction of these two constructs on older African Americans' utilization of five preventive care services (e.g. cholesterol screening and mammogram/prostate examination) using data from 211 older African Americans (median age = 60). In addition to direct effects, the influence of health insurance sometimes varied depending on respondents' psychological competency and/or vulnerability. Policies and interventions to increase older African Americans' use of preventive health services should consider structural (e.g. health insurance) and psychological (e.g. psychological competency and vulnerability) factors along with the interaction …

Hub City Steps: A 6-Month Lifestyle Intervention Improves Blood Pressure Among A Primarily African-American Community, Jamie M. Zoellner, Carol Connell, Michael B. Modson, Jessica L. Thomson, Alicia S. Landry, Elaine Fontenot Molaison, Vickie Blakely Reed, Kathleen Yadrick

Faculty Publications

The effectiveness of community-based participatory research (CBPR) efforts to address the disproportionate burden of hypertension among African Americans remains largely untested. The objective of this 6-month, noncontrolled, pre-/post-experimental intervention was to examine the effectiveness of a CBPR intervention in achieving improvements in blood pressure, anthropometric measures, biological measures, and diet. Conducted in 2010, this multicomponent lifestyle intervention included motivational enhancement, social support provided by peer coaches, pedometer diary self-monitoring, and monthly nutrition and physical activity education sessions. Of 269 enrolled participants, 94% were African American and 85% were female. Statistical analysis included generalized linear mixed models using maximum likelihood estimation. …

Concentrations And Sources Of Polycyclic Aromatic Hydrocarbons In Surface Coastal Sediments Of The Northern Gulf Of Mexico, Zucheng Wang, Zhanfei Liu, Kehui Xu, Lawrence M. Mayer, Zulin Zhang, Alexander S. Kolker, Wei Wu

Faculty Publications

Background: Coastal sediments in the northern Gulf of Mexico have a high potential of being contaminated by petroleum hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), due to extensive petroleum exploration and transportation activities. In this study we evaluated the spatial distribution and contamination sources of PAHs, as well as the bioavailable fraction in the bulk PAH pool, in surface marsh and shelf sediments (top 5 cm) of the northern Gulf of Mexico. Results: PAH concentrations in this region ranged from 100 to 856 ng g(-1), with the highest concentrations in Mississippi River mouth sediments followed by marsh sediments and then …

Drosophila Snap-29 Is An Essential Snare That Binds Multiple Proteins Involved In Membrane Traffic, Hao Xu, Mahmood Mohtashami, Bryan Stewart, Gabrielle Boulianne, William S. Trimble

Faculty Publications

Each membrane fusion event along the secretory and endocytic pathways requires a specific set of SNAREs to assemble into a 4-helical coiled-coil, the so-called trans-SNARE complex. Although most SNAREs contribute one helix to the trans-SNARE complex, members of the SNAP-25 family contribute two helixes. We report the characterization of the Drosophila homologue of SNAP-29 (dSNAP-29), which is expressed throughout development. Unlike the other SNAP-25 like proteins in fruit fly (i.e., dSNAP-25 and dSNAP-24), which form SDS-resistant SNARE complexes with their cognate SNAREs, dSNAP-29 does not participate in any SDS-resistant complexes, despite its interaction with dsyntaxin1 and dsyntaxin 16 in vitro. …

Correction Of The Caulobacter Crescentus Na1000 Genome Annotation, Bert Ely, Latia Etheredge Scott

Faculty Publications

Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading …

Structural And Functional Analyses Of A Glutaminyl Cyclase From Ixodes Scapularis Reveal Metal-Independent Catalysis And Inhibitor Binding, Kai-Fa Huang, Hui-Ling Hsu, Shahid Karim, Andrew H.-J. Wang

Faculty Publications

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-­sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could …

Priming In The Microbial Landscape: Periphytic Algal Stimulation Of Litter-Associated Microbial Decomposers, Kevin A. Kuehn, Steven N. Francoeur, Robert H. Findlay, Robert K. Neely

Faculty Publications

Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected …

Morphological Divergence Driven By Predation Environment Within And Between Species Of Brachyrhaphis Fishes, Spencer J. Ingley, Eric J. Billman, Mark C. Belk, Jerald B. Johnson

Faculty Publications

Natural selection often results in profound differences in body shape among populations from divergent selective environments. Predation is a well-studied driver of divergence, with predators having a strong effect on the evolution of prey body shape, especially for traits related to escape behavior. Comparative studies, both at the population level and between species, show that the presence or absence of predators can alter prey morphology. Although this pattern is well documented in various species or population pairs, few studies have tested for similar patterns of body shape evolution at multiple stages of divergence within a taxonomic group. Here, we examine …

Regional Impact Of Submarine Canyons During Seasonal Upwelling, Thomas Connolly, Barbara Hickey

Faculty Publications

A numerical model of the northern California Current System along the coasts of Washington and British Columbia is used to quantify the impact of submarine canyons on upwelling from the continental slope onto the shelf. Comparisons with an extensive set of observations show that the model adequately represents the seasonal development of near-bottom density, as well as along-shelf currents that are critical in governing shelf-slope exchange. Additional model runs with simplified coastlines and bathymetry are used to isolate the effects of submarine canyons. Near submarine canyons, equatorward flow over the outer shelf is correlated with dense water at canyon heads …

Characterization Of Particle Emissions And Fate Of Nanomaterials During Incineration, Eric P. Vejerano, Elena C. Leon, Amara L. Holder, Linsey C. Marr

Faculty Publications

As the use of nanotechnology in consumer products continues to grow, it is inevitable that some nanomaterials will end up in the waste stream and will be incinerated. Through laboratory-scale incineration of paper and plastic wastes containing nanomaterials, we assessed their effect on emissions of particulate matter (PM) and the effect of incineration on the nanomaterials themselves. The presence of nanomaterials did not significantly influence the particle number emission factor. The PM size distribution was not affected except at very high mass loadings (10 wt%) of the nanomaterial, in which case the PM shifted toward smaller sizes; such loadings are …

Intraspecific Variation In Carapace Morphology Among Fiddler Crabs (Genus Uca) From The Atlantic Coast Of Brazil, Kelsey R. Hampton, Melanie J. Hopkins, John C. Mcnamara, Carl L. Thurman

Faculty Publications

Isolation due to geographical barriers should promote genetic and morphological divergence among populations. Marine currents flowing in opposing directions along landmasses can constitute barriers that isolate populations dependent upon aquatic dispersal. The distribution of fiddler crabs (genus Uca) is regulated primarily by the oceanic transport of their planktonic larvae and by available adult habitat. Along the Brazilian coast of eastern South America, the flow of 2 major oceanic currents separates northern from southern Uca populations, which may promote intraspecific divergence in ‘trans-Brazilian’ species. Populations of 10 Uca species were sampled at 64 locations north and south of the Ponta …

Changing Microspatial Patterns Of Sulfate-Reducing Microorganisms (Srm) During Cycling Of Marine Stromatolite Mats, Alexandru Petrisor, Sandra Szyjka, Tomohiro Kawaguchi, Pieter Visscher, Sean Norman, Alan Decho

Faculty Publications

Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) and “lithifying” (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and ³⁵SO₄²⁻-silver foil patterns showed that SRM were present in surfaces of …

Changing Microspatial Patterns Of Sulfate-Reducing Microorganisms (Srm) During Cycling Of Marine Stromatolite Mats, Alexandru I. Petrisor, Sandra Szyjka, Tomohiro Kawaguchi, Pieter T. Visscher, Robert Sean Norman, Alan W. Decho

Faculty Publications

Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) and “lithifying” (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and ³⁵SO₄²⁻-silver foil patterns showed that SRM were present in surfaces of …

Streamwise Vortices Destabilize Swimming Bluegill Sunfish, Anabela Maia, Alex P. Sheltzer, Eric D. Tytell

Faculty Publications

In their natural environment, fish must swim stably through unsteady flows and vortices, including vertical vortices, typically shed by posts in a flow, horizontal cross-flow vortices, often produced by a step or a waterfall in a stream, and streamwise vortices, where the axis of rotation is aligned with the direction of the flow. Streamwise vortices are commonly shed by bluff bodies in streams and by ships’ propellers and axial turbines, but we know little about their effects on fish. Here, we describe how bluegill sunfish use more energy and are destabilized more often in flow with strong streamwise vorticity. The …

Egg Cannibalism In A Gull Colony Increases With Sea Surface Temperature, Lynelle M. Weldon, Shandelle M. Henson, James Hayward, Brianna G. Payne, Libby C. Megna, Andre E. Moncrieff

Faculty Publications

Cannibalism occurs regularly across a broad range of taxa with a variety of ecological and evolutionary consequences. Rises in sea surface temperature (SST) have been linked to increased cannibalism in some species, including polar bears (Ursus maritimus), Peruvian anchovy (Engraulis ringens), and Peruvian hake (Merluccius gayi peruanus), and might be expected in birds that depend on marine food webs for sustenance. Increased SSTs are associated with lowered ocean thermoclines and weakened upwellings. These changes, in turn, lead to decreased productivity in surface water and movement of surviving forage fish to deeper water, thereby food-stressing surface feeders such as gulls, diminishing …

Feeding Interactions Between Juvenile And Adult Flightless Cormorants., James Hayward, Libby C. Megna, Brianna G. Payne

Faculty Publications

We report observations on chick feedings by adult Flightless Cormorants Phalacrocorax harrisi, indicating that, contrary to the literature, the sequence of interaction is similar to that of other Pelecaniformes.