Life Sciences Commons^™

Forest Measurements, Yuhi Weng

Faculty Publications

Forest measurements, one of the cornerstones in the foundation of forestry, is the art and science of providing the quantitative information about trees and forest stands necessary for forest management, planning, and research. The updated edition (sixth edition) of this longstanding classic textbook, Forest Measurements, provides new and complete coverage of conventional and current measurement practices and technological applications that link the role of forest measurements with management of forest resources.

Resin Flow In Loblolly And Shortleaf Pines Used By Red-Cockaded Woodpeckers, David L. Kulhavy, W G. Ross, J H. Sun, Daniel Unger, I-Kuai Hung, Richard N. Conner

Faculty Publications

We measured resin flow in loblolly (Pinus taeda L.) and shortleaf (Pinus echinata Mill.) pines in stands used by red-cockaded woodpecker, Picoides borealis (Vieillot), in the Angelina and Davy Crockett National Forests in eastern Texas. We also measured resin flow in a mature loblolly pine stand not used by the woodpeckers. Resin flow varied by study area, species, and stand position. In woodpecker stands, pines experiencing low levels of competition seemed better able to tolerate the continual resin drainage associated with red-cockaded woodpecker resin well pecking. In the Angelina National Forest, all new cavity trees excavated during the study were …

A New Site Index Model For Intensively Managed Loblolly Pine (Pinus Taeda) Plantations In The West Gulf Coastal Plain, Kynda R. Trim, Dean W. Coble, Yuhi Weng, Jeremy P. Stovall, I-Kuai Hung

Faculty Publications

Site index (SI) estimation for loblolly pine (Pinus taeda L.) plantations is important for the successful management of this important commercial tree species in the West Gulf Coastal Plain of the United States. This study evaluated various SI models for intensively managed loblolly plantations in the West Gulf Coastal Plain using data collected from permanent plots installed in intensively managed loblolly pine plantations across east Texas and western Louisiana. Six commonly used SI models (Cieszewski GADA model, both Chapman-Richards ADA and GADA models, both Schumacher ADA and GADA models, and McDill-Amateis GADA model) were fit to the data and compared. …

Crossed Tracks: Mesolimulus, Archaeopteryx, And The Nature Of Fossils, Leonard Finkelman

Faculty Publications

Organisms leave a variety of traces in the fossil record. Among these traces, vertebrate and invertebrate paleontologists conventionally recognize a distinction between the remains of an organism’s phenotype (body fossils) and the remains of an organism’s life activities (trace fossils). The same convention recognizes body fossils as biological structures and trace fossils as geological objects. This convention explains some curious practices in the classification, as with the distinction between taxa for trace fossils and for tracemakers. I consider the distinction between “parallel taxonomies,” or parataxonomies, which privileges some kinds of fossil taxa as “natural” and others as “artificial.” The motivations …

Betting & Hierarchy In Paleontology, Leonard Finkelman

Faculty Publications

In his Rock, Bone, and Ruin: An Optimist’s Guide to the Historical Sciences, Adrian Currie argues that historical scientists should be optimistic about success in reconstructing the past on the basis of future research. This optimism follows in part from examples of success in paleontology. I argue that paleontologists’ success in these cases is underwritten by the hierarchical nature of biological information: extinct organisms have extant analogues at various levels of taxonomic, ecological, and physiological hierarchies, and paleontologists are adept at exploiting analogies within one informational hierarchy to infer information in another. On this account, fossils serve the role …

Dosage Compensation Of The X Chromosomes In Bovine Germline, Early Embryos, And Somatic Tissues, Zongliang Jiang

Faculty Publications

Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno's hypothesis in bovine preattachment embryos, germline, and somatic …

Vector Tick Transmission Model Of Spotted Fever Rickettsiosis, Tais Berelli Saito, Jeremy Bechelli, Claire Smalley, Shahid Karim, David H. Walker

Faculty Publications

Many aspects of rickettsial infections have been characterized, including pathogenic and immune pathways and mechanisms of rickettsial survival within the vertebrate host and tick vector. However, very few studies are focused on the complex pathogen–vector–host interactions during tick feeding. Therefore, our objective was to develop a tick transmission model of the spotted fever group of rickettsial infections to study the initial events in disease development. The most appropriate strain of mouse was identified for evaluation as a transmission model, and the course of infection, bacterial levels, histopathologic changes, and antibody response during tick transmission in mice infested with Amblyomma maculatum …

Periphytic Algae Decouple Fungal Activity From Leaf Litter Decomposition Via Negative Priming, Halvor M. Halvorson, Jacob R. Barry, Matthew B. Lodato, Robert H. Findlay, Steven N. Francoeur, Kevin A. Kuehn

Faculty Publications

1. Well‐documented in terrestrial settings, priming effects describe stimulated heterotrophic microbial activity and decomposition of recalcitrant carbon by additions of labile carbon. In aquatic settings, algae produce labile exudates which may elicit priming during organic matter decomposition, yet the directions and mechanisms of aquatic priming effects remain poorly tested.

2. We tested algal‐induced priming during decomposition of two leaf species of contrasting recalcitrance, Liriodendron tulipifera and Quercus nigra, in experimental streams under light or dark conditions. We measured litter‐associated algal, bacterial, and fungal biomass and activity, stoichiometry, and litter decomposition rates over 43 days.

3. Light increased algal biomass and …

An Army Of One: Predaceous Diving Beetle Life History Stages Affect Interactions With Shared Mosquito Prey, Carmen E. Bofill, Donald A. Yee

Faculty Publications

Predators with complex life cycles often differ in their morphology, behavior, and trophic position across their ontogeny, and may thus have variable effects on shared prey. We used the predaceous diving beetle Laccophilus fasciatus rufus as our predator, whose larvae and adults often co-occur in freshwater lentic systems. As a shared prey we used early and late instar Culex quinquefasciatus, a common wetland mosquito. We found that single adult predators were more likely to consume late instar prey compared to juvenile predators, who ate early and late instar prey equally. A mixture of juvenile and adult predator stages led …

Food Choice By A Free-Ranging Antillean Manatee (Trichechus Manatus Manatus) In Tabasco, Mexico, Daniel Gonzalez-Socoloske, David Olivera-Gomez

Faculty Publications

Understanding foraging ecology is an important element of effective conservation strategies. While West Indian manatees (Trichechus manatus) have been documented to consume a wide variety of vascular plants and algae, little is known about the diet of the Endangered Antillean subspecies (T. m. manatus) at freshwater sites such as the wetlands of Tabasco, the largest manatee habitat in Mexico. Here we present the results of a study of wild manatee diet in a freshwater site in Mexico. Controlled food choice experiments were conducted on a wild adult manatee during the dry seasons of 2011 and 2012. …

A Novel Sparse Compositional Technique Reveals Microbial Perturbations, Cameron Martino, James T. Morton, Clarisse A. Martoz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler

Faculty Publications

The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison …

Differential Oviposition And Offspring Success Of Gray Treefrogs In The Presence Of An Invasive Fish, Geoffrey R. Smith, Johanna J. Harmon

Faculty Publications

No abstract provided.

The Role Of The Midfoot In Drop Landings, Mark T. Olsen, Dustin A. Bruening, A. Wayne Johnson, Sarah T. Ridge

Faculty Publications

Purpose: The midfoot is instrumental to foot function; however, quantifying its roles in human movement has been difficult. A forceful dynamic activity like landing may help elucidate the midfoot’s contribution to foot energetics and function. The main purpose of this study was to measure midtarsal joint kinematics and kinetics during a barefoot single-leg landing task. A secondary aim of this study was to explore the relationship between static foot posture and dynamic midfoot function.

Methods: In a cross-sectional study design, 48 females (age = 20.4 ± 1.8 yr, body mass index = 21.6 ± 1.7 kg/m) performed drop landings from …

Dynamic Responses And Implications To Coastal Wetlands And The Surrounding Regions Under Sea Level Rise, Karim Alizad, Scott C. Hagen, Stephen C. Medeiros, Matthew V. Bilskie, James T. Morris, Len Balthis, Christine A. Buckel

Faculty Publications

Two distinct microtidal estuarine systems were assessed to advance the understanding of the coastal dynamics of sea level rise in salt marshes. A coupled hydrodynamic-marsh model (Hydro-MEM) was applied to both a marine-dominated (Grand Bay, Mississippi) and a mixed fluvial/marine (Weeks Bay, Alabama) system to compute marsh productivity, marsh migration, and potential tidal inundation from the year 2000 to 2100 under four sea level rise scenarios. Characteristics of the estuaries such as geometry, sediment availability, and topography, were compared to understand their role in the dynamic response to sea level rise. The results show that the low sea level rise …

Differential Expression Of Genes Related To Innate Immune Responses In Ex Vivo Spinal Cord And Cerebellar Slice Cultures Infected With West Nile Virus, Parminder J.S. Vig, Deyin Lu, Amber M. Paul, Ram Kuwar, Maria Lopez, Dobrivoje S. Stokic, A. Arturo Leis, Michael R. Garrett, Fengwei Bai

Faculty Publications

West Nile virus (WNV) infection results in a spectrum of neurological symptoms, ranging from a benign fever to severe WNV neuroinvasive disease with high mortality. Many who recover from WNV neuroinvasive infection present with long-term deficits, including weakness, fatigue, and cognitive problems. While neurons are a main target of WNV, other cell types, especially astrocytes, play an important role in promoting WNV-mediated central nervous system (CNS) damage. Conversely, it has been shown that cultured primary astrocytes secrete high levels of interferons (IFNs) immediately after WNV exposure to protect neighboring astrocytes, as well as neurons. However, how intrinsic responses to WNV …

Resveratrol Attenuates Allergic Asthma And Associated Inflammation In The Lungs Through Regulation Of Mirna-34a That Targets Foxp3 In Mice, Esraah Alharris, Hasan Alghetaa, Ratanesh K. Seth, Saurabh Chatterjee, Narendra P. Singh, Mitzi Nagarkatti, Prakash Nagarkatti

Faculty Publications

Asthma is a chronic inflammatory disease of airways mediated by T-helper 2 (Th2) cells involving complex signaling pathways. Although resveratrol has previously been shown to attenuate allergic asthma, the role of miRNA in this process has not been studied. We investigated the effect of resveratrol on ovalbumin-induced experimental allergic asthma in mice. To that end, BALB/c mice were immunized with ovalbumin (OVA) intraperitoneally followed by oral gavage of vehicle (OVA-veh) or resveratrol (100 mg/kg body) (OVA-res). On day 7, the experimental groups received intranasal challenge of OVA followed by 7 days of additional oral gavage of vehicle or resveratrol. At …

Micrat: A Novel Algorithm For Inferring Gene Regulatory Networks Using Time Series Gene Expression Data, Bei Yang, Yaohui Xu, Andrew Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang

Faculty Publications

Background: Reconstruction of gene regulatory networks (GRNs), also known as reverse engineering of GRNs, aims to infer the potential regulation relationships between genes. With the development of biotechnology, such as gene chip microarray and RNA-sequencing, the high-throughput data generated provide us with more opportunities to infer the gene-gene interaction relationships using gene expression data and hence understand the underlying mechanism of biological processes. Gene regulatory networks are known to exhibit a multiplicity of interaction mechanisms which include functional and non-functional, and linear and non-linear relationships. Meanwhile, the regulatory interactions between genes and gene products are not spontaneous since various …

Rhizosphere Microbial Communities Of Spartina Alternifloa And Juncus Roemerianus From Restored And Natural Tidal Marshes On Deer Island, Mississippi, Olga Mavrodi, Carina M. Jung, Jed O. Eberly, Samuel Hendry, Sanchirmaa Namijilsuren, Patrick D. Biber, Karl J. Indest, Dmitri V. Mavrodi

Faculty Publications

The U. S. Gulf of Mexico is experiencing a dramatic increase in tidal marsh restoration actions, which involves planting coastal areas with smooth cordgrass (Spartina alterniflora) and black needlerush (Juncus roemerianus) for erosion control and to provide habitat for fish and wildlife. It can take decades for sedimentary cycles in restored marshes to approach reference conditions, and the contribution of the sediment microbial communities to these processes is poorly elucidated. In this study, we addressed this gap by comparing rhizosphere microbiomes of S. alterniflora and J. roemerianus from two restored marshes and a natural reference marsh located at Deer Island, …

Macromolecular-Clustered Facial Amphiphilic Antimicrobials, Md Anisur Rahman, Marpe Bam, Edgar Luat, Moumita Sharmin Jui, Mitra S. Ganewatta, Tinom Shokfai, Mitzi Nagarkatti, Alan W. Decho

Faculty Publications

Bacterial infections and antibiotic resistance, particularly by Gram-negative pathogens, have become a global healthcare crisis. We report the design of a class of cationic antimicrobial polymers that cluster local facial amphiphilicity from repeating units to enhance interactions with bacterial membranes without requiring a globally conformational arrangement associated with highly unfavorable entropic loss. This concept of macromolecular architectures is demonstrated with a series of multicyclic natural product-based cationic polymers. We have shown that cholic acid derivatives with three charged head groups are more potent and selective than lithocholic and deoxycholic counterparts, particularly against Gram-negative bacteria. This is ascribed to the formation …

Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative Of Phenotypic Outcomes In Western Fence Lizard, Kurt A. Gust, Vijender Chaitankar, Preetam Ghosh, Mitchell S. Wilbanks, Xianfeng Chen, Natalie D. Barker, Don Pham, Leona D. Scanlan, Arun Rawat, Larry G. Talent, Michael J. Quinn Jr., Christopher D. Vulpe, Mohamed O. Elasri, Mark S. Johnson, Edward J. Perkins, Craig A. Mcfarland

Faculty Publications

Background

The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizards (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays.

Results

Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms linking transcript expression and toxicological phenotypes. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to …

Taxon-Specific Aerosolization Of Bacteria And Viruses In An Experimental Ocean-Atmosphere Mesocosm, Jennifer M. Michaud, Luke R. Thompson, Drishti Kaul, Josh L. Espinoza, R. Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M. Pham, Charlotte M. Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D. Burkart, Christopher L. Dupont, Kimberly A. Prather

Faculty Publications

Ocean-derived, airborne microbes play important roles in Earth’s climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean–atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa. We observe enhanced transfer into SSA of Actinobacteria, certain Gammaproteobacteria, and lipid-enveloped viruses; conversely, Flavobacteriia, some Alphaproteobacteria, and Caudovirales are generally under-represented in SSA. Viruses do not transfer …

Remote Sensing Of Sargassum Biomass, Nutrients, And Pigments, Mengqiu Wang, Chuanmin Hu, Jennifer Cannizzaro, David English, Xingxing Han, David Naar, Brian Lapointe, Rachel Brewton, Frank J. Hernandez Jr.

Faculty Publications

ield and laboratory experiments are designed to measure Sargassum biomass per area (density), surface reflectance, nutrient contents, and pigment concentrations. An Alternative Floating Algae Index (AFAI)‐biomass density model is established to link the spectral reflectance to Sargassum biomass density, with a relative uncertainty of ~ 12%. Monthly mean integrated Sargassum biomass in the Caribbean Sea and Central West Atlantic reached at least 4.4 million tons in July 2015. The average % C, % N, and % P per dry‐weight are 27.16, 1.06, and 0.10, respectively. The mean chlorophyll‐a (Chl‐a) concentration is ~ 0.05% of the dry‐weight. With these parameters, the …

A Sport-Specific Wearable Jump Monitor For Figure Skating, Dustin A. Bruening, Riley E. Reynolds, Chris W. Adair, Peter Zapalo, Sarah T. Ridge

Faculty Publications

Advancements in wearable technology have facilitated performance monitoring in a number of sports. Figure skating may also benefit from this technology, but the inherent movements present some unique challenges. The purpose of this study was to evaluate the feasibility of using an inertial measurement unit (IMU) to monitor three aspects of figure skating jumping performance: jump count, jump height, and rotation speed. Seven competitive figure skaters, outfitted with a waist-mounted IMU, performed a total of 59 isolated multi-revolution jumps and their competition routines, which consisted of 41 multi-revolution jumps along with spins, footwork, and other skills. The isolated jumps were …

Military-Related Exposures, Social Determinants Of Health, And Dysbiosis: The United States-Veteran Microbiome Project (Us-Vmp), Lisa A. Brenner, Andrew J. Hoisington, Kelly A. Stearns-Yoder, Christopher E. Stamper, Jared A. Heinze, Teodor T. Postolache, Daniel A. Hadidi, Claire A. Hoffmire, Maggie A. Stanislawski

Faculty Publications

Significant effort has been put forth to increase understanding regarding the role of the human microbiome in health- and disease-related processes. In turn, the United States (US) Veteran Microbiome Project (US-VMP) was conceptualized as a means by which to serially collect microbiome and health-related data from those seeking care within the Veterans Health Administration (VHA). In this manuscript, exposures related to military experiences, as well as conditions and health-related factors among patients seen in VHA clinical settings are discussed in relation to common psychological and physical outcomes. Upon enrollment in the study, Veterans complete psychometrically sound (i.e., reliable and valid) …

Carboxypeptidase O Is A Lipid Droplet-Associated Enzyme Able To Cleave Both Acidic And Polar C-Terminal Amino Acids, Linnea C. Burke, Hazel O. Ezeribe, Anna Y. Kwon, Donnell Dockery, Peter J. Lyons

Faculty Publications

Carboxypeptidase O (CPO) is a member of the M14 family of metallocarboxypeptidases with a preference for the cleavage of C-terminal acidic amino acids. CPO is largely expressed in the small intestine, although it has been detected in other tissues such as the brain and ovaries. CPO does not contain a prodomain, nor is it strongly regulated by pH, and hence appears to exist as a constitutively active enzyme. The goal of this study was to investigate the intracellular distribution and activity of CPO in order to predict physiological substrates and function. The distribution of CPO, when expressed in MDCK cells, …

Temporal Dynamics Of Lipid And Fatty Acid Characteristics Of Gulf Menhaden, Brevoortia Patronus In The Northern Gulf Of Mexico, Robert R. Leaf, Jesse Trushenski, Nancy Brown-Peterson, Michael J. Andres

Faculty Publications

Gulf Menhaden, Brevoortia patronus, in the northern Gulf of Mexico support a large commercial fishery and are thought to play an important trophic role in the coastal ecosystem. The temporal dynamics of both fatty acid and oil content have a direct impact on the value of Gulf Menhaden to predators and to the fishery. In this work, we describe how oil content of Gulf Menhaden varies with season, sex, age, condition, and tissue and investigate how fatty acid composition of mature (137.5 mm FL) female tissues varies with season, month, and tissue type. We found pronounced temporal (January to …

The Gut Microbiome And Aquatic Toxicology: An Emerging Concept For Environmental Health, Ondrej Adamovsky, Amanda Buerger, Alexis M. Wormington, Naomi Ector, Robert J. Griffitt, Joseph H. Bisesi Jr., Christopher J. Martyniuk

Faculty Publications

The microbiome plays an essential role in the health and onset of diseases in all animals, including humans. The microbiome has emerged as a central theme in environmental toxicology, as microbes interact with the host immune system in addition to its role in chemical detoxification. Pathophysiological changes in the gastrointestinal tissue caused by ingested chemicals, and metabolites generated from microbial biodegradation, can lead to systemic adverse effects. This critical review dissects what we know about the impacts of environmental contaminants on the microbiome of aquatic species, with special emphasis on the gut microbiome. We highlight some of the known major …

Seascape Connectivity Of Gulf Sturgeon Acipenser Oxyrinchus Desotoi Population Units Across The Northern Gulf Of Mexico, Page E. Vick, Mark S. Peterson, William T. Slack

Faculty Publications

Critical habitat was designated in 2003 for federally threatened anadromous Gulf sturgeon to aid in population recovery. This study examined overwintering Gulf sturgeon spatial use and movement through critical habitat monitored by the Ship Island acoustic array from 2011 to 2015. Previous studies observed western population Gulf sturgeon (Pearl and Pascagoula rivers) overwintering near the ends and within the passes of the barrier islands of the Mississippi Sound, USA. Recent telemetry studies detected eastern population fish (Escambia, Blackwater, Yellow, and Choctawhatchee rivers) overwintering as far west as Mobile Bay, Alabama; however, this study is the first to observe eastern population …

Characterization Of Embyronic Stem Cell-Differentiated Fibroblasts As Mesenchymal Stem Cells With Robust Expansion Capacity And Attenuated Innate Immunity, William D'Angelo, Bohan Chen, Chandan Gurung, Yan-Lin Guo

Faculty Publications

Background: Mesenchymal stem cells (MSCs) isolated from adult tissues (Ad-MSCs) have shown great promise for use in regenerative medicine. However, their poor in vitro expansion capacity and tissue scarcity have been major limitations. In this study, we demonstrate that mouse embryonic stem cells (mESCs) can differentiate into cells with MSC properties.

Methods: Using previously established methods that characterize Ad-MSCs, we analyzed mESC-differentiated fibroblasts (mESC-FBs), including plastic adherence, clonogenic growth, MSC marker expression, tri-lineage differentiation potential, and the capacity to express immunomodulators.

Results: Although previously characterized as mESC-differentiated fibroblasts (mESC-FBs), these cells exhibit major properties of Ad-MSCs. However, …

Genetic And Psychological Factors Interact To Predict Physical Impairment Phenotypes Following Exercise-Induced Shoulder Injury, Paul A. Borsa, Jeffrey J. Parr, Margaret R. Wallace, Samuel S. Wu, Yunfeng Dai, Roger B. Fillingim, Steven Z. George

Faculty Publications

Background: We investigated interactions between genetic and psychological factors in predicting shoulder impairment phenotypes. We hypothesized that pro-inflammatory genes would display stronger relationships compared with pain-related genes when combined with psychological factors for predicting phenotypic changes.
Subjects and methods: Altogether, 190 participants completed a 5-day experimental protocol. An experimental shoulder injury model was used to induce physical impairment, and a priori selected genetic (pain-related, pro-inflammatory) and psychological (anxiety, depressive symptoms, pain catastrophizing, fear of pain, kinesiophobia) factors were included as predictors of interest. Impairment phenotypes were injury-induced deficits in range of motion (ROM) and strength. After controlling for age, sex, …