Life Sciences Commons^™

A Generic Pixel-To-Point Comparison For Simulated Large-Scale Ecosystem Properties And Ground-Based Observations: An Example From The Amazon Region, Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley O. Christoffersen, Philippe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith

Biology Faculty Publications and Presentations

Comparing model output and observed data is an important step for assessing model performance and quality of simulation results. However, such comparisons are often hampered by differences in spatial scales between local point observations and large-scale simulations of grid cells or pixels. In this study, we propose a generic approach for a pixel-to-point comparison and provide statistical measures accounting for the uncertainty resulting from landscape variability and measurement errors in ecosystem variables. The basic concept of our approach is to determine the statistical properties of small-scale (within-pixel) variability and observational errors, and to use this information to correct for their …

Review: Using Physiologically Based Models To Predict Population Responses To Phytochemicals By Wild Vertebrate Herbivores, J. S. Forbey, T. T. Caughlin

Biology Faculty Publications and Presentations

To understand how foraging decisions impact individual fitness of herbivores, nutritional ecologists must consider the complex in vivo dynamics of nutrient–nutrient interactions and nutrient–toxin interactions associated with foraging. Mathematical modeling has long been used to make foraging predictions (e.g. optimal foraging theory) but has largely been restricted to a single currency (e.g. energy) or using simple indices of nutrition (e.g. fecal nitrogen) without full consideration of physiologically based interactions among numerous co-ingested phytochemicals. Here, we describe a physiologically based model (PBM) that provides a mechanistic link between foraging decisions and demographic consequences. Including physiological mechanisms of absorption, digestion and metabolism …

Dynamics Of Prochlorococcus Diversity And Photoacclimation During Short-Term Shifts In Water Column Stratification At Station Aloha, Anne W. Thompson, Ger Van Den Engh, Nathan A. Ahlgren, Kathleen Kouba, Samantha Ward, Samuel T. Wilson, David M. Karl

Biology Faculty Publications and Presentations

The cyanobacterium Prochlorococcus is the dominant phototroph in surface waters of the vast oligotrophic oceans, the foundation of marine food webs, and an important component of global biogeochemical cycles. The prominence of Prochlorococcus across the environmental gradients of the open ocean is attributed to its extensive genetic diversity and flexible chlorophyll physiology, enabling light capture over a wide range of intensities. What remains unknown is the balance between temporal dynamics of genetic diversity and chlorophyll physiology in the ability of Prochlorococcus to respond to a variety of short (approximately 1 day) and longer (months to year) changes in the environment. …

Resolving Authorship Disputes By Mediation And Arbitration, Zen Faulkes

Biology Faculty Publications and Presentations

Background Disputes over authorship are increasing. This paper examines the options that researchers have in resolving authorship disputes. Discussions about authorship disputes often address how to prevent disputes but rarely address how to resolve them. Both individuals and larger research communities are harmed by the limited options for dispute resolution. Main body When authorship disputes arise after publication, most existing guidelines recommend that the authors work out the disputes between themselves. But this is unlikely to occur, because there are often large power differentials between team members, and institutions (e.g., universities, funding agencies) are unlikely to have authority over all …

Modeling How Land Use Legacy Affects The Provision Of Ecosystem Services In Mediterranean Southern Spain, Juan Miguel Requena-Mullor, Cristina Quintas-Soriano, Jodi Brandt, Javier Cabello, Antonio J. Castro

Biology Faculty Publications and Presentations

Land use decisions induce legacies that affect the welfare of future generations. Here, we present a spatial modeling approach for quantifying how past land use decisions influence provision of multiple ecosystem services(ESs) based on different land use trajectories. We modeled the effect of past land use changes on water regulation, soil protection and habitat quality in southern Spain, one of the most transformed areas of the Mediterranean region. We demonstrate a measurable influence of antecedent land use changes on the capacity of a given land use to provide ESs, and that the effect size can vary among different services and …

Prohibiting Pet Crayfish Does Not Consistently Reduce Their Availability Online, Zen Faulkes

Biology Faculty Publications and Presentations

The pet trade is a significant source of introductions of non-indigenous aquatic species, such as crayfish. To test whether legislation that regulates the ownership of ornamental animals for aquariums had the desired effect of reducing the availability of those pets, classified advertising websites were monitored for sales of crayfish in jurisdictions with and without legislation regulating the ownership of crayfish. Advertisements from Canadian provinces with legislation against owning crayfish were compared to provinces without such legislation. The population adjusted number of advertisements for crayfish, and number of distinct sellers of crayfish, was significantly lower in one of two provinces that …

Dual Gain And Loss Of Cullin 3 Function Mediates Familial Hyperkalemic Hypertension, Ryan J. Cornelius, Chang Zhang, Kayla J. Erspamer, Larry N. Agbor, Curt D. Sigmund, Jeffrey Singer, Chao-Ling Yang, David H. Ellison

Biology Faculty Publications and Presentations

Familial hyperkalemic hypertension is caused by mutations in with-no-lysine kinases (WNKs) or in proteins that mediate their degradation, kelch-like 3 (KLHL3) and cullin 3 (CUL3). Although the mechanisms by which WNK and KLHL3 mutations cause the disease are now clear, the effects of the disease-causing CUL3Δ403-459 mutation remain controversial. Possible mechanisms, including hyperneddylation, altered ubiquitin ligase activity, decreased association with the COP9 signalosome (CSN), and increased association with and degradation of KLHL3 have all been postulated. Here, we systematically evaluated the effects of Cul3Δ403-459 using cultured kidney cells. We first identified that the catalytically active CSN subunit jun activation domain-binding …

Laguna Madre Estuary Program Environmental Strategic Plan - Final Report, Kim D. Jones, Lucy Camacho, T. Sinha, Omar Al-Qudah, Hudson R. Deyoe, Augusto Sanchez Gonzalez, Jungseok Ho, Javier Guerrero

Biology Faculty Publications and Presentations

The goal of this effort is to establish a framework of fundamental information and critical ideas to serve as a basis to assist in supporting legislation to found the 29th National Estuary Program for the Laguna Madre of the Gulf coast of Texas.

The National Estuary Program (NEP) was established by the Clean Water Act Amendments of 1987 (Section 320) to protect nationally significant estuaries threatened by development, pollution and overuse. The U.S. Environmental Protection Agency administers the NEP. The Corpus Christi Bay NEP (now the Coastal Bend Bays and Estuary Program) was among the last estuaries accepted into the …

Random Genetic Drift And Selective Pressures Shaping The Blattabacterium Genome, Austin Alleman, Kate L. Hertweck, Srini Kambhampati

Biology Faculty Publications and Presentations

Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium – providing nutritional augmentation to its host in the form of amino acid synthesis – displays radical genome alterations when compared to its most …

Status Update On The Threat Of Babesiosis Returning To The United States, Jason Tidwell, Christopher Vitek, Donald B. Thomas, John M. Thomas

Biology Faculty Publications and Presentations

Babesiosis is a hemolytic disease caused by protozoan parasites in the genus Babesia, transmitted through the saliva of infected ticks. The most economically important species, Babesia bigemina and B. bovis, infect cattle and are the etiological agents of bovine babesiosis. In the southern United States, eradication efforts directed against the tick vectors, Boophilus spp., began in the early 1900s. A quarantine zone in south Texas along the US/Mexico border was subsequently established following the eradication of the disease in the US. The permanent quarantine zone, spanning approximately 33% of the total shared border between Texas and Mexico, has helped limit …

A Disturbance In The Force: Cellular Stress Sensing By The Mitochondrial Network, Robert Gilkerson

Biology Faculty Publications and Presentations

As a highly dynamic organellar network, mitochondria are maintained as an organellar network by delicately balancing fission and fusion pathways. This homeostatic balance of organellar dynamics is increasingly revealed to play an integral role in sensing cellular stress stimuli. Mitochondrial fission/fusion balance is highly sensitive to perturbations such as loss of bioenergetic function, oxidative stress, and other stimuli, with mechanistic contribution to subsequent cell-wide cascades including inflammation, autophagy, and apoptosis. The overlapping activity with m-AAA protease 1 (OMA1) metallopeptidase, a stress-sensitive modulator of mitochondrial fusion, and dynamin-related protein 1 (DRP1), a regulator of mitochondrial fission, are key factors that shape …

Small Noncoding Rna Profiles Along Alternative Developmental Trajectories In An Annual Killifish, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of …

Laboratory Evaluation Of Efficacy Of Entomopathogenic Nematodes On Texas Leaf-Cutting Ants, Atta Texana, Pushpa Soti, Quentin Van Camp, Alexis Racelis

Biology Faculty Publications and Presentations

Entomopathogenic nematodes, a large group of nematodes specialized for parasitism of insects, have been used as classical biological control agents. The nematodes have potential to be used for insect pest management in organic gardening. We studied the potential impact of two entomopathogenic nematodes Steinerneima carpocapsae Weiser and Heterohabditis bacteriophora Poinar on the Texas leaf-cutting ant, Atta texana Buckley, that is considered a problematic agricultural pest in the southern US. We used a relatively large exposure rate of 250,000 nematodes per 10 ants in Petri dishes and monitored ant activity during a 96-hour time period. Results showed no significant differences among …

Influences Of Egyptian Lotus Symbolism And Ritualistic Practices On Sacral Tree Worship In The Fertile Crescent From 1500 Bce To 200 Ce, J. Andrew Mcdonald

Biology Faculty Publications and Presentations

Many conventional features of world tree motifs in the ancient Near East—including stalked palmettes, aureoles of water lily palmettes connected by pliant stems, floral rosettes, winged disks and bud-and-blossom motifs—trace largely from Egyptian practices in lotus symbolism around 2500 BCE, more than a millennium before they appear, migrate and dominate plant symbolism across the Fertile Crescent from 1500 BCE to 200 CE. Several of these motifs were associated singularly or collectively with the Egyptian sema-taui and ankh signs to symbolize the eternal recurrence and everlasting lives of Nilotic lotus deities and deceased pharaohs. The widespread use of lotus imagery in …

Isolation Of Enteric Glial Cells From The Submucosa And Lamina Propria Of The Adult Mouse, Zhen Wang, Ramon Ocadiz-Ruiz, Sinju Sundaresan, Lin Ding, Michael Hayes, Nirakar Sahoo, Haoxing Xu, Juanita L. Merchant

Biology Faculty Publications and Presentations

The enteric nervous system (ENS) consists of neurons and enteric glial cells (EGCs) that reside within the smooth muscle wall, submucosa and lamina propria. EGCs play important roles in gut homeostasis through the release of various trophic factors and contribute to the integrity of the epithelial barrier. Most studies of primary enteric glial cultures use cells isolated from the myenteric plexus after enzymatic dissociation. Here, a non-enzymatic method to isolate and culture EGCs from the intestinal submucosa and lamina propria is described. After manual removal of the longitudinal muscle layer, EGCs were liberated from the lamina propria and submucosa using …

Genetic Testing: Should I Get Tested For Alzheimer’S Risk?, Troy Rohn

Biology Faculty Publications and Presentations

Genetic testing is available to people who want to know if they carry a variant of a gene that confers susceptibility for Alzheimer’s. But knowing whether to get tested is hard.

Field Data On Plant Growth And Insect Damage On The Noxious Weed Solanum Eleaegnifolium In An Unexplored Native Range, Rupesh R. Kariyat, Jesus Chavana

Biology Faculty Publications and Presentations

In this data article, we provide a novel data set on plant growth, insect damage levels, and herbivore community of the noxious and invasive weed Solanum eleaegnifolium (Solanaceae). The data is collected from disturbed and un-disturbed urban populations of the species from one of its unexplored native range in Southern United States (South Texas). The data include plant height measurements, insect damage levels, GPS coordinates of the populations, and their disturbance status. Additional data includes the number of chewing herbivore (specialist herbivore Texas potato beetle (Leptinotarsa texana; Chrysomelidae), their eggs, and any lepidopteran caterpillars found on the plants.

Displacement Of The Transcription Factor B Reader Domain During Transcription Initiation, Stefan Dexl, Robert Reichelt, Katharina Kraatz, Sarah Schulz, Dina Grohmann, Michael S. Bartlett, Michael Thomm

Biology Faculty Publications and Presentations

Transcription initiation by archaeal RNA polymerase (RNAP) and eukaryotic RNAP II requires the general transcription factor (TF) B/ IIB. Structural analyses of eukaryotic transcription initiation complexes locate the B-reader domain of TFIIB in close proximity to the active site of RNAP II. Here, we present the first crosslinking mapping data that describe the dynamic transitions of an archaeal TFB to provide evidence for structural rearrangements within the transcription complex during transition from initiation to early elongation phase of transcription. Using a highly specific UV-inducible crosslinking system based on the unnatural amino acid para-benzoyl-phenylalanine allowed us to analyze contacts of …

Sputum Detection Of Predisposing Genetic Mutations In Women With Pulmonary Nontuberculous Mycobacterial Disease, Julie V. Philley, Kate L. Hertweck, Anbarasu Kannan, Barbara A. Brown-Elliott, Richard J. Wallace, Anna Kurdowska, Harrison Ndetan, Karan P. Singh, Edmund J. Miller, David E. Griffith, Santanu Dasgupta

Biology Faculty Publications and Presentations

Nontuberculous mycobacterial lung disease (NTM), including Mycobacterium avium complex (MAC), is a growing health problem in North America and worldwide. Little is known about the molecular alterations occurring in the tissue microenvironment during NTM pathogenesis. Utilizing next generation sequencing, we sequenced sputum and matched lymphocyte DNA in 15 MAC patients for a panel of 19 genes known to harbor cancer susceptibility associated mutations. Thirteen of 15 NTM subjects had a diagnosis of breast cancer (BCa) before or after NTM infection. Thirty three percent (4/12) of these NTM-BCa cases exhibited at least 3 somatic mutations in sputa compared to matched lymphocytes. …

Snake Venom Phospholipase A2 And Its Antibacterial Potential, Pablo Olvera, Ying Jia

Biology Faculty Publications and Presentations

No abstract provided.

Resolving The Anomaly Of Lomatium Anomalum: Discovery Of A New Species In Southwestern Idaho (U.S.A.), Lomatium Andrusianum (Apiaceae), Mckayla Stevens, Donald H. Mansfield, James F. Smith, Mary Ann E. Feist

Biology Faculty Publications and Presentations

Apparent polyphyly within the unresolved clade of Lomatium (Apiaceae) containing L. triternatum, L. anomalum, L. thompsonii, and L. packardiae suggests conflict among current taxonomic classification schemes. To recover this clade and more clearly define species boundaries, we examined populations of L. anomalum from three geographic regions in Idaho and adjacent Oregon. Using phylogenetic, morphological, and ecological data, we conclude that the L. anomalum complex currently circumscribes multiple species. Phylogenetic analysis of the nuclear ribosomal ITS and ETS, and cpDNA rpl32-trnLUAG, rps-16 intron, trnD-trnT, ndhA intron, and psbA-trnH recovered populations from the Boise foothills as a distinct, monophyletic clade. Principal …

Follow The Rain? Environmental Drivers Of Tyrannus Migration Across The New World, Maggie P. Macpherson, Alex E. Jahn, Michael T. Murphy, Daniel H. Kim, Victor R. Cueto, Diego T. Tuero, Elliot D. Hill

Biology Faculty Publications and Presentations

Predictable seasonal changes in resources are thought to drive the timing of annual animal migrations; however, we currently understand little about which environmental cues or resources are tracked by different migratory bird species across the planet. Understanding which environmental cues or resources birds track in multiple migratory systems is a prerequisite to developing generalizable conservation plans for migratory birds in a changing global environment. Within the New World, climatic differences experienced by Nearctic–Neotropical migratory (NNM; i.e. breed in North America and spend the nonbreeding period in the Neotropics) and Neotropical austral migratory (NAM; i.e. breed and spend the nonbreeding period …

The Evolution Of Anti-Bat Sensory Illusions In Moths, Juliette J. Rubin, Chris A. Hamilton, Christopher J.W. Mcclure, Brad A. Chadwell, Akito Y. Kawahara, Jesse R. Barber

Biology Faculty Publications and Presentations

Prey transmit sensory illusions to redirect predatory strikes, creating a discrepancy between what a predator perceives and reality. We use the acoustic arms race between bats and moths to investigate the evolution and function of a sensory illusion. The spinning hindwing tails of silk moths (Saturniidae) divert bat attack by reflecting sonar to create a misleading echoic target. We characterized geometric morphometrics of moth hindwings across silk moths, mapped these traits onto a new, robust phylogeny, and found that elaborated hindwing structures have converged on four adaptive shape peaks. To test the mechanism underlying these anti-bat traits, we pit bats …

Modification Of Diet And Foraging Range By Harvester Ants In Response To Altered Seed Availability, Ian C. Robertson, Matthew S. Schmasow

Biology Faculty Publications and Presentations

Food collection is a critical component of an individual’s life, and for eusocial insects, the colony that individual foragers support and maintain. Changes to the distribution and composition of food types in the environment are expected influence diet selection if the economics of foraging are altered. For seed-harvesting ants, the abundance and composition of seed types available on the ground typically shows a high degree of spatial and temporal variability, and not all types of seed are equally valued by foragers. We evaluated the response of Owyhee harvester ants (Pogonomyrmex salinus) to reductions in the availability of Sandberg …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses—which infect members of the order Sulfolobales, growing optimally at 80 C and pH 3—are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. Nonetheless, much remains to be learned about these viruses. In order to investigate fusellovirus evolution, we have isolated and characterized a novel fusellovirus, Sulfolobus spindle-shaped virus 10 (formerly SSV-L1). Comparative genomic analyses highlight significant similarity with both SSV8 and SSV9, as well as conservation of promoter elements within the Fuselloviridae. SSV10 encodes five ORFs with no …

Effects Of Mowing And Tebuthiuron On The Nutritional Quality Of Wyoming Big Sagebrush, Kurt T. Smith, Jennifer S. Forbey, Jeffrey L. Black

Biology Faculty Publications and Presentations

Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis Beetle & Young) is the most abundant and widely distributed subspecies of big sagebrush and has been treated through chemical application, mechanical treatments, and prescribed burning in efforts thought to improve habitat conditions for species such as greater sage-grouse (Centrocercus urophasianus) and mule deer (Odocoileus hemionus). Although the response of structural attributes of sagebrush communities to treatments is well understood, there is a need to identify how treatments influence the quality of sagebrush as winter food for wildlife. Our purpose was to identify how mowing and tebuthiuron …

Oxidative Insults Disrupt Opa1-Mediated Mitochondrial Dynamics In Cultured Mammalian Cells, Iraselia Garcia, Wendy Innis-Whitehouse, Alma Lopez, Megan Keniry, Robert Gilkerson

Biology Faculty Publications and Presentations

Objective: To explore the impact of oxidative insults on mitochondrial dynamics. In mammalian cells, oxidative insults activate stress response pathways including inflammation, cytokine secretion, and apoptosis. Intriguingly, mitochondria are emerging as a sensitive network that may function as an early indicator of subsequent cellular stress responses. Mitochondria form a dynamic network, balancing fusion, mediated by optic atrophy-1 (OPA1), and fission events, mediated by dynamin-related protein-1 (DRP1), to maintain homeostasis.

Methods: Here, we examine the impact of oxidative insults on mitochondrial dynamics in 143B osteosarcoma and H9c2 cardiomyoblast cell lines via confocal microscopy, flow cytometry, and protein-based analyses.

Results: When challenged …

Trade-Offs Between Carbon Stocks And Timber Recovery In Tropical Forests Are Mediated By Logging Intensity, Anand Roopsind, T. Trevor Caughlin, Peter Van Der Hout, Eric Arets, Francis E. Putz

Biology Faculty Publications and Presentations

Forest degradation accounts for ~70% of total carbon losses from tropical forests. Substantial emissions are from selective logging, a land-use activity that decreases forest carbon density. To maintain carbon values in selectively logged forests, climate change mitigation policies and government agencies promote the adoption of reduced-impact logging (RIL) practices. However, whether RIL will maintain both carbon and timber values in managed tropical forests over time remains uncertain. In this study, we quantify the recovery of timber stocks and aboveground carbon at an experimental site where forests were subjected to different intensities of RIL (4, 8, and 16 trees/ha). Our census …

Assembly And Analysis Of Unmapped Genome Sequence Reads Reveal Novel Sequence And Variation In Dogs, Lindsay Adrian Holden, Meharji Arumilli, Marjo K. Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H. Brown, Hannes Lohi

Biology Faculty Publications and Presentations

Dogs are excellent animal models for human disease. They have extensive veterinary histories, pedigrees, and a unique genetic system due to breeding practices. Despite these advantages, one factor limiting their usefulness is the canine genome reference (CGR) which was assembled using a single purebred Boxer. Although a common practice, this results in many high-quality reads remaining unmapped. To address this whole-genome sequence data from three breeds, Border Collie (n = 26), Bearded Collie (n = 7), and Entlebucher Sennenhund (n = 8), were analyzed to identify novel, non- CGR genomic contigs using the previously validated pseudo-de novo assembly pipeline. We …

Small Non-Coding Rna Expression And Vertebrate Anoxia Tolerance, Claire L. Riggs, Amanda Summers, Daniel E. Warren, Göran E. Nilsson, Sjannie Lefevre, W. W. Dowd, Sarah Milton, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxiatolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette …