Life Sciences Commons^™

Environmental Effects On The Expression Of Life Span And Aging: An Extreme Contrast Between Wild And Captive Cohorts Of Telostylinus Angusticollis (Diptera: Neriidae), Noriyoshi Kawasaki, Chad Brassil, Robert Brooks, Russell Bonduriansky

School of Biological Sciences: Faculty Publications

Most research on life span and aging has been based on captive populations of short-lived animals; however, we know very little about the expression of these traits in wild populations of such organisms. Because life span and aging are major components of fitness, the extent to which the results of many evolutionary studies in the laboratory can be generalized to natural settings depends on the degree to which the expression of life span and aging differ in natural environments versus laboratory environments and whether such environmental effects interact with phenotypic variation. We investigated life span and aging in Telostylinus angusticollis …

Nucleic Acid Sequences Found In Drosophila Melanogaster That Encode Proteins Essential For Viability And Method Of Use: U.S. Patent No. Us 7,384,745 B2, Alan C. Christensen, Douglas R. Dorer

School of Biological Sciences: Faculty Publications

Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of Drosophila pseudoobscura, and homologs have been found in Aedes aegyptii mosquitoes and the honeybee (Apis mellfera), but it is not present in the sequenced genome of any non-insect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of …

The Role Of Pollinator Shifts In The Floral Diversification Of Iochroma (Solanaceae), Stacey Dewitt Smith, Cécile Ané, David A. Baum

School of Biological Sciences: Faculty Publications

Differences in floral traits among plant species have often been attributed to adaptation to pollinators. We explored the importance of pollinator shifts in explaining floral divergence among 15 species of Iochroma. We examined four continuously varying floral traits: corolla length, nectar reward, display size, and flower color. Pollinator associations were characterized with a continuously varying measure of pollinator importance (the product of visitation and pollen deposition) for four groups of pollinators: hummingbirds, Hymenoptera, Lepidoptera, and Diptera. A phylogenetic generalized least squares approach was used to estimate correlations between pollinator groups and floral traits across a sample of Bayesian trees …

A 15-Myr-Old Genetic Bottleneck, Timothy Paape, Boris Igic, Stacey Dewitt Smith, Richard Olmstead, Lynn Bohs, Joshua R. Kohn

School of Biological Sciences: Faculty Publications

Balancing selection preserves variation at the self-incompatibility locus (S-locus) of flowering plants for tens of millions of years, making it possible to detect demographic events that occurred prior to the origin of extant species. In contrast to other Solanaceae examined, SI species in the sister genera Physalis and Witherinigia share restricted variation at the S-locus. This restriction is indicative of an ancient bottleneck that occurred in a common ancestor. We sequenced 14 S-alleles from the subtribe Iochrominae, a group that is sister to the clade containing Physalis and Witherinigia. At least 6 ancient S-allele lineages are represented among these alleles, …

Genetic Variation In Mother-Child Acute Seroconverter Pairs From Zambia, Federico G. Hoffmann, Xiang He, John T. West, Philippe Lemey, Chipepo Kankasa, Charles Wood

School of Biological Sciences: Faculty Publications

Objective: To characterize the envelope (Env) glycoprotein of HIV-1 in mother-infant pairs (MIP) that underwent near simultaneous or acute-phase seroconversion, we examined the Env sequence of the transmitted viruses and compare viral evolution within the pair.

Design: Three MIP from a Zambian cohort that seroconverted at the same sampling time were identified and followed longitudinally.

Methods: The V1-V5 region of the HIV-1 Env gene was sequenced for each sample collected. Phylogenetic and population genetics analyses were carried out to subtype the viruses, estimate relationships among viral genotypes, and compare molecular evolution between the viral populations.

Results: Genetic analyses demonstrated a …

Monte Carlo Analysis Of Parameter Uncertainty In Matrix Models For The Weed Cirsium Vulgare, Brigitte Tenhumberg, Svata M. Louda, James O. Eckberg, Masaru Takahashi

School of Biological Sciences: Faculty Publications

1. Parameter uncertainty challenges the use of matrix models because it violates key assumptions underlying elasticity analyses. We have developed a matrix model to compare Monte Carlo methods with elasticity analyses for estimation of the relative importance of factors in the asymptotic population growth rate, λ, of Cirsium vulgare (spear thistle) in Nebraska, USA.
2. We calculated λ for a base model using 11 parameter estimates available for Nebraska populations plus eight extracted from the literature, causing parameter uncertainty. We then calculated λ for 10 000 alternative models using Monte Carlo parameter estimation; parameters were drawn from the full range …

Review Of Archaea: Molecular And Cellular Biology, Paul H. Blum

School of Biological Sciences: Faculty Publications

Archaea along with bacteria comprise the two groups of prokaryotes. The discovery of the Archaea, now over 30 years ago, has blossomed into fascinating revelations about the origin of life and the discovery of unique mechanisms that penetrate diverse aspects of biology, biochemistry, and genetics. The field of archaeal biology is growing rapidly. For this reason, we can anticipate a continued need for comprehensive coverage on these organisms that promotes dissemination of relevant information.

Arabidopsis Trithorax1 Dynamically Regulates Flowering Locus C Activation Via Histone 3 Lysine 4 Trimethylation, Stephane Pien, Delphine Fleury, Joshua S. Mylne, Pedro Crevillen, Dirk Inze, Zoya Avramova, Caroline Dean, Ueli Grossniklaus

School of Biological Sciences: Faculty Publications

Trithorax function is essential for epigenetic maintenance of gene expression in animals, but little is known about trithorax homologs in plants. ARABIDOPSIS TRITHORAX1 (ATX1) was shown to be required for the expression of homeotic genes involved in flower organogenesis. Here, we report a novel function of ATX1, namely, the epigenetic regulation of the floral repressor FLOWERING LOCUS C (FLC). Downregulation of FLC accelerates the transition from vegetative to reproductive development in Arabidopsis thaliana. In the atx1 mutant, FLC levels are reduced and the FLC chromatin is depleted of trimethylated, but not dimethylated, histone 3 lysine 4, suggesting a specific …

Herbivore-Mediated Ecological Costs Of Reproduction Shape The Life History Of An Iteroparous Plant, Tom E. X. Miller, Brigitte Tenhumberg, Svata M. Louda

School of Biological Sciences: Faculty Publications

Plant reproduction yields immediate fitness benefits but can be costly in terms of survival, growth, and future fecundity. Lifehistory theory posits that reproductive strategies are shaped by tradeoffs between current and future fitness that result from these direct costs of reproduction. Plant reproduction may also incur indirect ecological costs if it increases susceptibility to herbivores. Yet ecological costs of reproduction have received little empirical attention and remain poorly integrated into life-history theory. Here, we provide evidence for herbivore-mediated ecological costs of reproduction, and we develop theory to examine how these costs influence plant life-history strategies. Field experiments with an iteroparous …

Rarity Of Males In Pea Aphids Results In Mutational Decay, Jennifer A. Brisson, Sergey V. Nuzhdin

School of Biological Sciences: Faculty Publications

The pea aphid, Acyrthosiphon pisum, has a complex life cycle that alternates seasonally between asexual and sexual reproduction. During the spring and summer months, A. pisum reproduces parthenogenetically, producing clonal daughters for 10 to 20 generations. Fall temperatures and photoperiods induce the production of sexual females and males, which mate to produce overwintering eggs that hatch into asexual females.

Polygyny And Female Breeding Failure Reduce Effective Population Size In The Lekking Gunnison Sage-Grouse, Julie R. Stiver, Anthony D. Apa, Thomas E. Remington, Robert M. Gibson

School of Biological Sciences: Faculty Publications

Populations with small effective sizes are at risk for inbreeding depression and loss of adaptive potential. Variance in reproductive success is one of several factors reducing effective population size (N_e) below the actual population size (N). Here, we investigate the effects of polygynous (skewed) mating and variation in female breeding success on the effective size of a small population of the Gunnison sage-grouse (Centrocercus minimus), a ground nesting bird with a lek mating system. During a two-year field study, we recorded attendance of marked birds at leks, male mating success, the reproductive success …

The Genome Sequence Of The Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera Sedula Provides Insights Into Bioleaching-Associated Metabolism, Kathryne S. Auernik, Yukari Maezato, Paul H. Blum, Robert M. Kelly

School of Biological Sciences: Faculty Publications

Despite their taxonomic description, not all members of the order Sulfolobales are capable of oxidizing

reduced sulfur species, which, in addition to iron oxidation, is a desirable trait of biomining microorganisms.

However, the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula

DSM 5348 (2.2 Mb, _2,300 open reading frames [ORFs]) provides insights into biologically catalyzed metal

sulfide oxidation. Comparative genomics was used to identify pathways and proteins involved (directly or

indirectly) with bioleaching. As expected, the M. sedula genome contains genes related to autotrophic carbon

fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence …

Management Recommendations Based On Matrix Projection Models: The Importance Of Considering Biological Limits, Joan Lubben, Brigitte Tenhumberg, Andrew J. Tyre, Richard Rebarber

School of Biological Sciences: Faculty Publications

Matrix population models are a common tool for evaluating different management strategies. In general, under deterministic analyses, management strategies are recommended that improve those matrix transitions that are most sensitive or elastic with respect to the asymptotic population growth rate, λ. These recommendations usually ignore the biological limit for these transitions. In this paper we use the endangered Serengeti cheetah (Acinonyx jubatus) as a case study to illustrate that ignoring biological limits leads to a recommendation that will not always achieve the desired goal of an asymptotic population growth rate, λ ≥ 1. We estimate the survivorships of …

Pea Aphid, Jennifer A. Brisson, Gregory K. Davis

School of Biological Sciences: Faculty Publications

Aphids have long been of interest because of their complex life cycles, environmentally induced morphologies, and importance to agriculture. However, only recently has the resulting wealth of ecological and population genetic data begun to be supplemented by genomic and genetic mapping approaches. In 2004, the International Aphid Genomics Consortium, a collaboration of aphid researchers, chose to establish the pea aphid, Acyrthosiphon pisum, as the aphid of choice for the development of genomic resources. Here we introduce the pea aphid and discuss a number of biological questions for which the species is well suited. We then review previous mapping and quantitative …

Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman

School of Biological Sciences: Faculty Publications

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic …

The Spectrum Of Mitochondrial Mutation Differs Across Species, Kristi L. Montooth, David M. Rand

School of Biological Sciences: Faculty Publications

Mutations are ubiquitous, and many arise during the very process of replicating and transmitting genomes. This process is the source of the genetic variation that provides the raw material for both evolutionary novelty and human disease. Mutation rates are known to vary among nucleotides, across genomic regions, and between taxa. It is conventional wisdom that animal mitochondrial DNA (mtDNA) is one genomic region that has a particularly high mutation rate. Until recently, this high rate of mutation has been predominantly inferred from high levels of mitochondrial sequence divergence between species. However, the apparently simple process of mutation and sequence divergence …

Vulnerability Of Rehabilitated Agricultural Production Systems To Invasion By Nontarget Plant Species, Sara G. Baer, David M. Engle, Johannes M.H. Knops, Kenneth A. Langeland, Bruce D. Maxwell, Fabian D. Menalled, Amy J. Symstad

School of Biological Sciences: Faculty Publications

Vast areas of arable land have been retired from crop production and ‘‘rehabilitated’’ to improved system states through landowner incentive programs in the United States (e.g., Conservation and Wetland Reserve Programs), as well as Europe (i.e., Agri-Environment Schemes). Our review of studies conducted on invasion of rehabilitated agricultural production systems by nontarget species elucidates several factors that may increase the vulnerability of these systems to invasion. These systems often exist in highly fragmented and agriculturally dominated landscapes, where propagule sources of target species for colonization may be limited, and are established under conditions where legacies of past disturbance persist and …

Parasite-Mediated Disruptive Selection In A Natural Daphnia Population, Meghan Duffey, Chad Brassil, Spencer Hall, Alan Tessier, Carla Cáceres, Jeffrey Conner

School of Biological Sciences: Faculty Publications

Background: A mismatch has emerged between models and data of host-parasite evolution. Theory readily predicts that parasites can promote host diversity through mechanisms such as disruptive selection. Yet, despite these predictions, empirical evidence for parasite-mediated increases in host diversity remains surprisingly scant.
Results: Here, we document parasite-mediated disruptive selection on a natural Daphnia population during a parasite epidemic. The mean susceptibility of clones collected from the population before and after the epidemic did not differ, but clonal variance and broad-sense heritability of post-epidemic clones were significantly greater, indicating disruptive selection and rapid evolution. A maximum likelihood method that we developed …

Regulation Of Aromatic Alcohol Production In Candida Albicans, Suman Ghosh, Bessie W. Kebaara, Audrey L. Atkin, Kenneth W. Nickerson

School of Biological Sciences: Faculty Publications

Colonization by the fungal pathogen Candida albicans varies significantly, depending upon the pH and availability of oxygen. Because of our interest in extracellular molecules as potential quorum-sensing molecules, we examined the physiological conditions which regulate the production of the aromatic alcohols, i.e., phenethyl alcohol, tyrosol, and tryptophol. The production of these fusel oils has been well studied for Saccharomyces cerevisiae. Our data show that aromatic alcohol yields for C. albicans are determined by growth conditions. These conditions include the availability of aromatic amino acids, the pH, oxygen levels, and the presence of ammonium salts. For example, for wild-type C. …

Comparative Pollination Biology Of Sympatric And Allopatric Andean Iochroma (Solanaceae), Stacey Dewitt Smith, Steven J. Hall, Pablo R. Izquierdo, David A. Baum

School of Biological Sciences: Faculty Publications

Field studies were conducted for 15 species of Iochroma Benth, and the nested genus Acnistus Schott to quantify the diversity of pollination systems and to assess the potential contribution of pollinator behavior to the persistence of closely related species in sympatry. We combined measures of pollinator visitation and pollen deposition to estimate the importance of major groups of pollinators for each species, and we calculated proportional similarity in the pollinator assemblage among species. We found that 12 species of Iochroma, encompassing a range of flower colors and sizes, were principally pollinated by hummingbirds and, in many cases, by the …

Endogenous And Exogenous Control Of Ecosystem Function: N Cycling In Headwater Streams, H. M. Valett, S. A. Thomas, P. J. Mulholland, J. R. Webster, C. N. Dahm, C. S. Fellows, C. L. Crenshaw, C. G. Peterson

School of Biological Sciences: Faculty Publications

Allochthonous inputs act as resource subsidies to many ecosystems, where they exert strong influences on metabolism and material cycling. At the same time, metabolic theory proposes endogenous thermal control independent of resource supply. To address the relative importance of exogenous and endogenous influences, we quantified spatial and temporal variation in ecosystem metabolism and nitrogen (N) uptake using seasonal releases of ¹⁵N as nitrate in six streams differing in riparian–stream interaction and metabolic character. Nitrate removal was quantified using a nutrient spiraling approach based on measurements of downstream decline in ¹⁵N flux. Respiration (R) and gross primary production (GPP) …

A Novel Ecological Role Of The Firmicutes Identified In Thermophilic Microbial Fuel Cells, Kelly C. Wrighton, Peter Agbo, Falk Warnecke, Karrie A. Weber, Eoin L. Brodie, Todd Z. Desantis, Philip Hugenholtz, Gary L. Andersen, John D. Coates

School of Biological Sciences: Faculty Publications

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 °C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37mW m^–2 with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray …

Arabidopsis Drb4, Ago1, Ago7, And Rdr6 Participate In A Dcl4-Initiated Antiviral Rna Silencing Pathway Negatively Regulated By Dcl1, Feng Qu, Xiaohong Ye, Thomas Jack Morris

School of Biological Sciences: Faculty Publications

Plant RNA silencing machinery enlists four primary classes of proteins to achieve sequence-specific regulation of gene expression and mount an antiviral defense. These include Dicer-like ribonucleases (DCLs), Argonaute proteins (AGOs), dsRNA-binding proteins (DRBs), and RNA-dependent RNA polymerases (RDRs). Although at least four distinct endogenous RNA silencing pathways have been thoroughly characterized, a detailed understanding of the antiviral RNA silencing pathway is just emerging. In this report, we have examined the role of four DCLs, two AGOs, one DRB, and one RDR in controlling viral RNA accumulation in infected Arabidopsis plants by using a mutant virus lacking its silencing suppressor. Our …

Analysis Of Wnt Signaling During Caenorhabditis Elegans Postembryonic Development, Samantha Van Hoffelen, Michael A. Herman

School of Biological Sciences: Faculty Publications

Wnts play a central role in the development of many cells and tissue types in all species studied to date. Like many other extracellular signaling pathways, secreted Wnt proteins are involved in many different processes; in C. elegans these include cell proliferation, differentiation, cell migration, control of cell polarity, axon outgrowth, and control of the stem cell niche. Perturbations in Wnt signaling are also key factors in cancer formation, and therefore of interest to oncobiologists. Wnts are secreted glycoproteins, which bind to Frizzled transmembrane receptors and signal either through, or independently of β-catenin. Both β-catenin-dependent (Wnt/β-catenin) and -independent pathways function …

Evolution Of Set-Domain Protein Families In The Unicellular And Multicellular Ascomycota Fungi, Chendhore Veerappan, Zoya Avramova, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular …

Optimal Data Partitioning And A Test Case For Ray-Finned Fishes (Actinopterygii) Based On Ten Nuclear Loci, Chenhong Li, Guoqing Lu, Guillermo Ortí

School of Biological Sciences: Faculty Publications

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative …

Interspecific Demographic Trade-Offs And Soil-Related Habitat Associations Of Tree Species Along Resource Gradients, Sabrina E. Russo, Patrick Brown, Sylvester Tan, Stuart J. Davies

School of Biological Sciences: Faculty Publications

Summary

1. Interspecific relationships between fundamental demographic rates, often called demographic trade-offs, emerge from constraints within individuals related to morphology, physiology and resource allocation. Plant species that grow fast in high light usually have high mortality in shade, and this well-established relationship in part defines a species’ successional niche. More generally, this relationship represents a trade-off between a species’ ability to grow quickly to exploit abundant resources vs. avoiding mortality when resources are less plentiful, but few studies have described this demographic trade-off with respect to environmental factors other than light.

2. Using demographic data from 960 tree species in …