Life Sciences Commons^™

Leaf Form Diversification In An Ornamental Heirloom Tomato Results From Alterations In Two Different Homeobox Genes, Hokuto Nakayama, Steven D. Rowland, Zizhang Cheng, Kristina Zumstein, Julie Kang, Yohei Kondo, Neelima R. Sinha

Faculty Publications

Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo …

Mitochondrial Genome Of Geomydoecus Aurei, A Pocket-Gopher Louse, Theresa A. Spradling, Alexandra C. Place, Ashley L. Campbell, James W. Demastes

Faculty Publications

Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average …

Reply To “Programming May Matter Most.” Response To “Metabolic Effects Of Two High-Intensity Circuit Training Protocols: Does Sequence Matter?”, Tony P. Nuñez, Fabiano T. Amorim, Nicholas M. Beltz, Christine M. Mermier, Terence A. Moriarty, Roberto C. Nava, Trisha A. Vandusseldorp, Len Kravitz

Faculty Publications

We appreciate the interest that our study elicited and the comments from a reader. We commend the reader of our paper for critically evaluating the protocol and results of the study. Here, we would like to respond to the statement made in the letter. Indeed, the rest intervals were longer and time at VO2max was lower in our study than recommended by Bucheit and Larsen.1 However, because the reader is interested in the practical implications of our study, we ask that they consider the following:

Evaluating Vegetation Response Subsequent To Crp Mid-Contract Management Across The Western United States: Draft Project Report, Kenneth J. Elgersma

Faculty Publications

It is impossible to explicitly state the degree to which mid-contract management (MCM) impacts the benefits that CRP enrollments provide due to the size of the program and variety of management prescriptions. But it is well documented that all native grasslands evolved with some type of ecological disturbance and the relatively good health of the grassland correlates with its disturbance regime. Concomitantly, all grassland bird communities have habitat requirements that evolved in conjunction with disturbance (primarily grazing).

While natural-disturbance regimes may be desirable from an ecological prospective, dependence on natural disturbances to meet specific conservation objectives is unrealistic. Management policies …

Temporal And Spatial Dynamics Of Competitive Parapatry In Chewing Lice, David J. Hafner, Mark S. Hafner, Theresa A. Spradling, Jessica E. Light, James W. Demastes

Faculty Publications

We synthesize observations from 1979 to 2016 of a contact zone involving two subspecies of pocket gophers (Thomomys bottae connectens and T. b. opulentus) and their respective chewing lice (Geomydoecus aurei and G. centralis) along the Rio Grande Valley in New Mexico, U.S.A., to test predictions about the dynamics of the zone. Historically, the natural flood cycle of the Rio Grande prevented contact between the two subspecies of pocket gophers. Flood control measures completed in the 1930s permitted contact, thus establishing the hybrid zone between the pocket gophers and the contact zone between their lice (without hybridization). Since that time, …

Species Composition Influences Soil Nutrient Depletion And Plantphysiology In Prairie Agroenergy Feedstocks, Mark E. Sherrard, Kenneth Elgersma, Jordan M.A. Koos, Catherine M. Kokemuller, Hannah E. Dietz, Alec J. Glidden, Christina M. Carr, Cynthia A. Cambardella

Faculty Publications

High-diversity mixtures of perennial tallgrass prairie vegetation could be useful biomass feed-stocks for marginal farmland in the Midwestern United States. These agroenergy crops can help meet cel-lulosic agrofuel targets while also enhancing other ecosystem services on the landscape. One proposedadvantage of high-diversity prairie biomass feedstocks is that they should become nutrient limited at aslower rate than monoculture feedstocks. In this study, we examine rates of soil nutrient depletion and thephysiology and performance of a focal species (switchgrass,Panicum virgatumL.) in four prairie agroen-ergy feedstocks with different species composition and diversity. The feedstocks in this study were a1-species switchgrass monoculture, a 5-species …

Oral Glutamine Supplement Reduces Subjective Fatigue Ratings During Repeated Bouts Of Firefighting Simulations, Mary Moore, Terence A. Moriarty, Gavin Connolly, Christine Mermier, Fabiano Amorim, Kevin Miller, Micah Zuhl

Faculty Publications

Wildland firefighting requires repetitive (e.g., consecutive work shifts) physical work in dangerous conditions (e.g., heat and pollution). Workers commonly enter these environments in a nonacclimated state, leading to fatigue and heightened injury risk. Strategies to improve tolerance to these stressors are lacking. Purpose: To determine if glutamine ingestion prior to and after consecutive days of firefighting simulations in the heat attenuates subjective ratings of fatigue, and evaluate if results were supported by glutamine-induced upregulation of biological stress responses. Methods: Participants (5 male, 3 female) ingested glutamine (0.15 g/kg/day) or a placebo before and after two consecutive days (separated by 24 …

Recommendations For Measurement And Management Of An Elite Athlete, William Sands, Marco Cardinale, Jeni Mcneal, Steven Murray, Christopher Sole, Jacob Reed, Nikos Apostolopoulos, Michael Stone

Faculty Publications

Athletes who merit the title elite' are rare and differ both quantitatively and qualitatively from athletes of lower qualifications. Serving and studying elite athletes may demand non-traditional approaches. Research involving elite athletes suffers because of the typical nomothetic requirements for large sample sizes and other statistical assumptions that do not apply to this population. Ideographic research uses single-athlete study designs, trend analyses, and statistical process control. Single-athlete designs seek to measure differences in repeated measurements under prescribed conditions, and trend analyses may permit systematic monitoring and prediction of future outcomes. Statistical process control uses control charting and other methods from …

Host-Parasite Associations Of The Cratogeomys Fumosus Species Group And Their Chewing Lice, Geomydoecus, Alex Popinga, James W. Demastes, Theresa A. Spradling, David J. Hafner, Mark S. Hafner

Faculty Publications

Chewing lice (Phthiraptera: Trichodectidae) and the pocket gophers (Rodentia: Geomyidae) that they inhabit have shared an intimate historical association that has made them a textbook study for cophylogeny. Herein, we examine the chewing lice found on pocket gophers of the Cratogeomys fumosus species group using DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to determine relationships among lice for comparison to published host phylogeny. Although matrix approaches indicate a correlation between host and parasite genetic distances, cophylogenetic reconstruction methods fail to detect a pattern of widespread cophylogeny. In conclusion, this study provides an exception to the …

Sex-Related Differences In Immune Response And Symptomatic Manifestations To Infection With Leishmania Species, Ryan D. Lockard, Mary E. Wilson, Nilda E. Rodriguez

Faculty Publications

Worldwide, an estimated 12 million people are infected with Leishmania spp. and an additional 350 million are at risk of infection. Leishmania are intracellular parasites that cause disease by suppressing macrophage microbicidal responses. Infection can remain asymptomatic or lead to a spectrum of diseases including cutaneous, mucocutaneous, and visceral leishmaniasis. Ultimately, the combination of both pathogen and host factors determines the outcome of infection. Leishmaniasis, as well as numerous other infectious diseases, exhibits sex-related differences that cannot be explained solely in terms of environmental exposure or healthcare access. Furthermore, transcriptomic evidence is revealing that biological sex is a variable impacting …

Transdisciplinary Graduate Training In Predictive Plant Phenomics, Carolyn J. Lawrence-Dill, Theodore J. Heindel, Patrick S. Schnable, Stephanie J. Strong, Jill Wittrock, Mary E. Losch, Julie A. Dickerson

Faculty Publications

Novel methods to increase crop productivity are required to meet anticipated demands for food, feed, fiber, and fuel. It is becoming feasible to use modern sensors and data analysis techniques for predicting plant growth and productivity based on genomic, phenotypic, and environmental data. To design and construct crops that deliver desired traits requires trained personnel with scientific and engineering expertise as well as a variety of “soft” skills. To address these needs at Iowa State University, we developed a graduate specialization called “Predictive Plant Phenomics” (P3). Although some of our experiences may be unique, many of the specialization’s principles are …

Plant Size And Competitive Dynamics Along Nutrient Gradients, Deborah E. Goldberg, Jason P. Martina, Kenneth J. Elgersma, William S. Currie

Faculty Publications

Resource competition theory in plants has focused largely on resource acquisition traits that are independent of size, such as traits of individual leaves or roots or proportional allocation to different functions. However, plants also differ in maximum potential size, which could outweigh differences in module-level traits. We used a community ecosystem model called mondrian to investigate whether larger size inevitably increases competitive ability and how size interacts with nitrogen supply. Contrary to the conventional wisdom that bigger is better, we found that invader success and competitive ability are unimodal functions of maximum potential size, such that plants that are too …

Effectiveness Of Cattail (Typha Spp.) Management Techniques Depends On Exogenous Nitrogen Inputs, Kenneth J. Elgersma, Jason P. Martina, Deborah E. Goldberg, William S. Currie

Faculty Publications

Wetlands occupy a position in the landscape that makes them vulnerable to the effects of current land use and the legacies of past land use. Many wetlands in agricultural regions like the North American Midwest are strongly affected by elevated nutrient inputs as well as high rates of invasion by the hybrid cattail Typha × glauca. These two stressors also exacerbate each other: increased nutrients increase invasion success, and invasions increase nutrient retention and nutrient loads in the wetland. This interaction could create a positive feedback that would inhibit efforts to manage and control invasions, but little is known …

Phylogenetic Patterns And The Adaptive Evolution Of Osmoregulation In Fiddler Crabs (Brachyura, Uca), Samuel Coelho Faria, Diogo Borges Provete, Carl Leo Thurman, John Campbell Mcnamara

Faculty Publications

Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyperosmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher …

Is High Folic Acid Intake A Risk Factor For Autism?—A Review, Darrell Wiens, M. Catherine Desoto

Faculty Publications

Folate is required for metabolic processes and neural development. Insuring its adequate levels for pregnant women through supplementation of grain-based foods with synthetic folic acid (FA) in order to prevent neural tube defects has been an ongoing public health initiative. However, because women are advised to take multivitamins containing FA before and throughout pregnancy, the supplementation together with natural dietary folates has led to a demographic with high and rising serum levels of unmetabolized FA. This raises concerns about the detrimental effects of high serum synthetic FA, including a rise in risk for autism spectrum disorder (ASD). Some recent studies …

Predicting Genome Terminus Sequences Of Bacillus Cereus-Group Bacteriophage Using Next Generation Sequencing Data, Cheng-Han Chung, Michael H. Walter, Luobin Yang, Shu-Chuan (Grace) Chen, Vern Winston, Michael A. Thomas

Faculty Publications

Background: Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends.

Result: We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of …

Nitrogen Loading Leads To Increased Carbon Accretion In Both Invaded And Uninvaded Coastal Wetlands, Jason P. Martina, William S. Currie, Deborah E. Goldberg, Kenneth J. Elgersma

Faculty Publications

Gaining a better understanding of carbon (C) dynamics across the terrestrial and aquatic landscapes has become a major research initiative in ecosystem ecology. Wetlands store a large portion of the global soil C, but are also highly dynamic ecosystems in terms of hydrology and N cycling, and are one of the most invaded habitats worldwide. The interactions between these factors are likely to determine wetland C cycling, and specifically C accretion rates. We investigated these interactions using MONDRIAN, an individual-based model simulating plant growth and competition and linking these processes to N and C cycling. We simulated the effects of …

The Mitochondrial Cytochrome Oxidase Subunit I Gene Occurs On A Minichromosome With Extensive Heteroplasmy In Two Species Of Chewing Lice, Geomydoecus Aurei And Thomomydoecus Minor, Lucas L. Pietan, Theresa A. Spradling, James W. Demastes

Faculty Publications

In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two species of chewing lice found on pocket gophers, Geomydoecus aurei and Thomomydoecus minor, are fragmented with the 1,536 base-pair (bp) cytochrome-oxidase subunit I (cox1) gene occurring as the only protein-coding gene on a 1,916–1,964 bp minicircular chromosome in the two species, respectively. The cox1 gene of T. …

Biochar Amendment Of Grassland Soil May Promote Woody Encroachment By Eastern Red Cedar, Ramesh Laungani, Kenneth Elgersma, Maria Juarez, Kristin Mcelligott, Tyler Kuhfahl

Faculty Publications

Although carbon (C) additions to soil have been used in restoration to combat invasive species through changes in soil nitrogen (N) availability, carbon amendments to soil derived from plant material can impact soil N availability in a species-specific manner. As such, amendment-driven feedbacks on N may impact invasive species success and woody encroachment. Soil amendments like biochar, which is often added to soil to increase C storage in grassland systems, may unintentionally encourage woody encroachment into these grasslands by changing soil N dynamics. Few studies have examined biochar impacts on non-agricultural species, particularly invasive species. Woody encroachment of Eastern Red …

The Fifth Leaf And Spike Organs Of Barley (Hordeum Vulgare L.) Display Different Physiological And Metabolic Responses To Drought Stress, Jordan A. Hein, Mark E. Sherrard, Kirk P. Manfredi, Tilahun Abebe

Faculty Publications

Background: Photosynthetic organs of the cereal spike (ear) provide assimilate for grain filling, but their response to drought is poorly understood. In this study, we characterized the drought response of individual organs of the barley spike (awn, lemma, and palea) and compared them with a vegetative organ (fifth leaf). Understanding differences in physiological and metabolic responses between the leaf and spike organs during drought can help us develop high yielding cultivars for environments where terminal drought is prevalent.

Results: We exposed barley plants to drought by withholding water for 4 days at the grain filling stage and compared …

Self-Reported Race/Ethnicity In The Age Of Genomic Research: Its Potential Impact On Understanding Health Disparities, Tesfaye B. Mersha, Tilahun Abebe

Faculty Publications

This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person’s physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically …

Special Speciation, Lyn L. Countryman, Jill D. Maroo

Faculty Publications

Considerable anecdotal evidence indicates that some of the most difficult concepts that both high school and undergraduate elementary-education students struggle with are those surrounding evolutionary principles, especially speciation. It’s no wonder that entry-level biology students are confused, when biologists have multiple definitions of “species.” We developed this speciation activity to provide clarity and allow students a hands-on experience with a speciation model.

Genetic Dominance & Cellular Processes, Robert D. Seager

Faculty Publications

In learning genetics, many students misunderstand and misinterpret what “dominance” means. Understanding is easier if students realize that dominance is not a mechanism, but rather a consequence of underlying cellular processes. For example, metabolic pathways are often little affected by changes in enzyme concentration. This means that enzyme-producing alleles usually show complete dominance. For genes producing nonenzymatic proteins such as collagen or hemoglobin, the amount of product matters, and dominance relationships are more complicated. Furthermore, with hemoglobin, dominance can change depending on what aspect of the phenotype is being studied and on the environmental conditions. X-linked genes are a special …

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 …

Development And Psychometric Evaluation Of A Post Exercise Exhaustion Scale Utilising The Rasch Measurement Model, Mark D. Hecimovich, Jeremiah J. Peiffer, Allen G. Harbaugh

Faculty Publications

Objectives: The objective of this study to report on the development and psychometric analysis of a scale to measure post exercise exhaustion.

Design: This study utilised the Rasch measurement model for the psychometric analysis of a new scale aimed at measuring acute onset exhaustion in athletes.

Method: An extensive literature review, feedback from athletes and an expert panel from educators in psychology, sports science and exercise physiology provided feedback on the scale, providing evidence of content validity. A final survey, consisting of the 25 items and completed by three hundred and seventynine athletes (Sport: 187 tri-athletes and 192 cyclists; gender: …

Transcriptome Sequences Resolve Deep Relationships Of The Grape Family, Jun Wen, Zhiqiang Xiong, Ze-Long Nie, Likai Mao, Yabing Zhu, Xian-Zhao Kan, Stefanie M. Ickert-Bond, Jean Gerrath, Elizabeth A. Zimmer, Xiao-Dong Fang

Faculty Publications

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic …

Knox1 Genes Regulate Lignin Deposition And Composition In Monocots And Dicots, Brad T. Townsley, Neelima R. Sinha, Julie Kang

Faculty Publications

Plant secondary cell walls are deposited mostly in vascular tissues such as xylem vessels, tracheids, and fibers. These cell walls are composed of a complex matrix of compounds including cellulose, hemicellulose, and lignin. Lignin functions primarily to maintain the structural and mechanical integrity of both the transport vessel and the entire plant itself. Since lignin has been identified as a major source of biomass for biofuels, regulation of secondary cell wall biosynthesis has been a topic of much recent investigation. Biosynthesis and patterning of lignin involves many developmental and environmental cues including evolutionarily conserved transcriptional regulatory modules and hormonal signals. …

Archaeal Assemblages Inhabiting Temperate Mixed Forest Soil Fluctuate In Taxon Composition And Spatial Distribution Over Time, Colby A. Swanson, Marek K. Sliwinski

Faculty Publications

This study explored the persistence and spatial distribution of a diverse Archaeal assemblage inhabiting a temperate mixed forest ecosystem. Persistence under native conditions was measured from 2001 to 2010, 2011, and 2012 by comparison of 16S rRNA gene clone libraries. The Archaeal assemblages at each of these time points were found to be significantly different (AMOVA, P < 0.01), and the nature of this difference was dependent on taxonomic rank. For example, the cosmopolitan genus g_Ca. Nitrososphaera (I.1b) was detected at all time points, but within this taxon the abundance of s_SCA1145, s_SCA1170, and s_Ca. N. gargensis fluctuated over time. In addition, spatial heterogeneity (patchiness) was measured at these time points using 1D TRFLP-SSCP fingerprinting to screen soil samples covering multiple spatial scales. This included soil collected from small volumes of 3 cubic centimeters to larger scales—over a surface area of 50 m², plots located 1.3 km apart, and a separate locality 23 km away. The spatial distribution of Archaea in these samples changed over time, and while g_Ca. Nitrososphaera (I.1b) was dominant over larger scales, patches were found at smaller scales that were …

Expression Of Cadherin-11 During Organogenesis In The Chick Embryo, Kacie D. Flaherty, Alicia F. Paulson, Ashley L. Adamson, Darrell J. Wiens

Faculty Publications

Cadherin-11 (cad-11) is primarily a mesenchymal cadherin that appears in delaminating neural crest cells. Its expression correlates with morphogenetic events and the pattern has been studied in mouse, rat and Xenopus embryos, but not during avian organogenesis. Our purpose was to investigate this pattern in the chick embryo during organogenesis using immunolocalization and in situ hybridization. Cad-11 was expressed in mesenchyme around the pharynx and aortic arches, eyes, auditory vesicles, lung buds, stomach, and nasal placodes. Neural expression included some cranial ganglia and also new neuroepithelium within the tail bud region undergoing secondary neurulation. We also found expression in epithelia …

Gram Stains: A Resource For Retrospective Analysis Of Bacterial Pathogens In Clinical Studies, Usha Srinivasan, Sreelatha Ponnalurl, Lisa Villareal, Brenda Gillespie, Ai Wen, Arianna Miles, Brigette Bucholz, Carl F. Marrs, Ram K. Iyer, Dawn Misra, Betsy Foxman

Faculty Publications

We demonstrate the feasibility of using qPCR on DNA extracted from vaginal Gram stain slides to estimate the presence and relative abundance of specific bacterial pathogens. We first tested Gram stained slides spiked with a mix of 108 cfu/ml of Escherichia coli and 105cfu/ml of Lactobacillus acidophilus. Primers were designed for amplification of total and species-specific bacterial DNA based on 16S ribosomal gene regions. Sample DNA was pre-amplified with nearly full length 16S rDNA ribosomal gene fragment, followed by quantitative PCR with genera and species-specific 16S rDNA primers. Pre-amplification PCR increased the bacterial amounts; relative proportions of Escherichia coli …