Biology Commons^™

Agricultural Management And Labile Carbon Additions Affect Soil Microbial Community Structure And Interact With Carbon And Nitrogen Cycling, Sean T. Berthrong, Daniel H. Buckely, Laurie E. Drinkwater

Scholarship and Professional Work - LAS

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose (¹³C) …

The Role Of Retrotransposons In Gene Family Expansions: Insights From The Mouse Abp Gene Family, Václav Janoušek, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Background: Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes. Results: Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the …

Progress Towards A Phylogeny Of World Tachinidae. Year 1, John O. Stireman Iii, James E. O'Hara, Michael C. Moulton, Pierfilippo Cerretti, Isaac S. Winkler

Biological Sciences Faculty Publications

D eveloping a structural phylogenetic framework for the family Tachinidae has been an interest of mine since I first started working on tachinids as a graduate student. It was then that I developed a new phylogenetic perspective with which to view the world, and many of the questions I wanted to ask of tachinids depended on some level of phylogenetic knowledge of them. I was surprised at the time that no one had attempted a broad quantitative phylogenetic analysis of the family, and a publication from my thesis work on the Exoristinae (Stireman 2002) became the first such study that …

Cam Kk Mediates Mdm2 Activation In Lncap Cells, John M. Schmitt, Philip Graber

Faculty Publications - Department of Biological & Molecular Science

Abstract Agonists and hormones that cause an influx of calcium in LNCaP prostate cancer cells activate the calcium/calmodulin-dependent protein kinase (CaM Kinase) pathway and AKT phosphorylation. CaM KK and AKT are essential for promoting LNCaP cell survival. AKT phosphorylation of MDM2 protein may negatively regulate the tumor suppressor protein, p53. CaM KK and AKT have yet to be demonstrated as upstream regulators of MDM2 and p53 in LNCaP cells. Our goals were to examine the ability of carbachol and testosterone to stimulate MDM2 phosphorylation, its association with p53, and whether CaM KK is upstream of MDM2. Stimulation of LNCaP cells …

Akap7 Regulates Cam Kinase Activation In Mcf-7 Cells, John M. Schmitt, Hannah M. Mcfarland, Kimberly Dodge-Kafka

Faculty Publications - Department of Biological & Molecular Science

Abstract Estrogen (E2) activates calcium/calmodulin-dependent protein kinases (CaM Kinases) in MCF-7 breast cancer cells. In particular E2 activates a CaM KK, CaM KI, and ERK pathway to promote proliferation. CaM Kinase activation of ERK may be blocked by PKA in certain cell types through direct phosphorylation and inhibition of CaM KK. The ability of PKA to phosphorylate its cellular targets may be dictated by protein kinase A anchoring proteins (AKAPs). Hormones that elevate cAMP and activate PKA may utilize AKAPs to regulate signal transduction. Our goal was to evaluate the role of AKAPs in regulating E2 activation of the CaM …

Estrogen Regulation Of Jun And Fos In Mcf-7 Cells, John M. Schmitt, Renee Geck, Jessica N. Magill

Faculty Publications - Department of Biological & Molecular Science

Abstract C-Fos and c-Jun are transcription factors that form the dimer Activator Protein 1 (AP-1) and bind DNA to initiate transcription. C-Fos, c-Jun are targets of the Extracellular Signal-Regulated Kinase (ERK) in multiple cell types, including MCF-7 breast cancer cells. The hormone estrogen (E2) can increase intracellular calcium levels which activates calcium/calmodulin-dependent kinase (CaM Kinase) proteins, which control ERK and gene transcription. Our goal was to evaluate the ability of E2 to activate c-Fos and c-Jun and induce their dimerization, via CaM KK and ERK, in MCF-7 cells. Interestingly, E2 stimulation of MCF-7 cells triggered phosphorylation of c-Jun and c-Fos …

Larval Black Fly (Simulium Vittatum) Responses To Chemical Stimuli From Predators And Injured Conspecifics Under Field Conditions, Aaron M. Sullivan, C. D. Curran, H. M. Gardner, A. G. Hiers, J. S. Hummelman

Faculty Publications - Department of Biological & Molecular Science

We examined chemically-mediated antipredator behaviour in larval Simulium vittatum Zetterstedt 1838 by exposing individuals to one of five stimuli during daytime (1500 hr) and night-time (2300 hr) trials: distilled water, injured earthworm (Lumbricus sp.), injured conspecific (S. vittatum), predator (Corydalus sp.), and a combination of injured conspecific and predator. Larval responses were not homogenous with respect to treatment during daytime and night-time trials and the adjusted residuals show that a higher frequency of larvae curled in response to damaged conspecifics and the combination cue, and drifted when exposed to the combination cue. Additionally, the curling response …

Local And Watershed Influences On The Species Composition And Functional Organization Of Stream Diatom Communities In The Acid-Impacted Adirondack Region Of New York, Katrina Lynn Pound

Biology Dissertations - Archive

For over 40 years, acid deposition has been recognized as a serious international environmental problem, but efforts to restore acidified streams and biota have had limited success. The need to better understand the effects of different sources of acidity on streams has become more pressing with the recent increases in surface water organic acids, or `brownification', associated with climate change and decreased acid deposition. This dissertation is a large scale multi-seasonal investigation of stream diatom communities in the Adirondack region of New York, one of the most acid-impacted regions in the United States. My first objective is to explore the …

Biological Relevance Of Jaz Proteins In The Interaction Between Pseudomonas Syrinage And Arabiopsis Thaliana, Nisita Obulareddy

Biology Dissertations - Archive

Stomata, micro-pores on the leaf surface, are formed by a pair of guard cells. In addition to controlling water loss and gas exchange between the plant and the environment, these cells act as immunity gates to prevent pathogen invasion of the plant apoplast. Some Plant pathogens produce virulence factors that enable them to reopen the stomatal immunity gates to favor bacterial entry. Pseudomonas syringae pv. Tomato strain DC3000 (Pst DC3000) produces a phytotoxin called coronatine that assists pathogen entry via re-opening the closed stomata. Earlier studies report that Pst DC3000 regulates a family of genes called JASMONATE ZIM-DOMAIN (JAZ) genes …

Role Of The Extracytoplasmic Function Sigma Factor Carq In Oxidative Response Of Bradyrhizobium Japonicum, Anchana Thaweethawakorn

Biology Theses - Archive

Bradyrhizobium japonicum is a nitrogen-fixing bacterium that can establish a symbiotic relationship with the soybean plant. To be a successful symbiont, B. japonicum must have an effective mechanism to deal with plant defense responses such as oxidative burst. Our previous transcriptomic study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (108-fold induction) in response to Hâ‚‚Oâ‚‚-mediated oxidative stress. In this study, a carQ knock-out mutant was constructed to identify the role of carQ in the oxidative response of B. japonicum. The mutant exhibited a significant decrease in survival at 10 mM Hâ‚‚Oâ‚‚ for 10 min …

Inge Revsbech Wins The Journal Of Experimental Biology’S Outstanding Paper Prize 2013, Nicola Stead, Inge G. Revsbech, Hideaki Moriyama, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

The Editors of The Journal of Experimental Biology are pleased to announce that Inge Revsbech from Aarhus University, Denmark, is the winner of this year’s JEB Outstanding paper prize. The prize is awarded in memory of Bob Boutillier (JEB Editor-in-Chief 1994–2003) to a junior author who has made the most significant contribution to an outstanding paper. ‘The prize aims to promote and reward the hard work that individual young scientists have put into solving different riddles of any particular species using ingenuity, perseverance and sound technology and methodology’, explains Hans Hoppeler, Editor-In-Chief.

Revsbech was the first author on the paper …

Effects Of Nitrogen Availability On The Fate Of Litter-Carbon And Soil Organic Matter Decomposition, Amy Kochsiek, Johannes Knops

School of Biological Sciences: Faculty Publications

Aims: To determine whether addition of inorganic nitrogen (N) directly to maize litter (stalk and leaf) with differing tissue quality impacts litter and soil organic matter (SOM) decomposition. We tested whether N addition leads to 1) faster litter decomposition, 2) less SOM-C decomposition and 3) increased incorporation of organic-C into soil-C fractions thereby increasing C sequestration potential in maize-based systems.

Methodology: We investigated decomposition of two types of maize litter (stalk and leaf) with differing tissue quality both in the field and in a laboratory incubation experiment. In the field, litter was placed on the soil surface and at …

Tlr-Trif Pathway Enhances The Expression Of Kshv Replication And Transcription Activator, Florencia Meyer, Erica Ehlers, Andrew Steadman, Thomas Waterbury, Mingxia Cao, Luwen Zhang

School of Biological Sciences: Faculty Publications

Background: Host innate immunity is against virus infection and replication.

Results: Toll-like receptor 3 activation leads to enhanced expression of a key Kaposi’s sarcoma-associated herpesvirus (KSHV) protein.

Conclusion: KSHV uses host Toll-like receptor pathway to augment its critical gene expression. Significance: A virus may usurp host innate immunity for its own benefits.

Deer Mouse Hemoglobin Exhibits A Lowered Oxygen Affinity Owing To Mobility Of The E Helix, Noriko Inoguchi, Jake R. Oshlo, Chandrasekhar Natarajan, Roy E. Weber, Angela Fago, Jay F. Storz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hangingdrop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the …

Role Of Merh In Mercury Resistance In The Archaeon Sulfolobus Solfataricus, James Schelert, Deepak Rudrappa, Tyler Johnson, Paul H. Blum

School of Biological Sciences: Faculty Publications

Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal

environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II),

inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously

derepresses transcription of a resistance operon, merHAI, through interaction with the MerR

transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of

MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of

MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant

cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH …

Antelope Mating Strategies Facilitate Invasion Of Grasslands By A Woody Weed, Shivani Jadeja, Soumya Prasad, Suhel Quader, Kavita Isvaran

School of Biological Sciences: Faculty Publications

Intra and interspecific variation in frugivore behaviour can have important consequences for seed dispersal outcomes. However, most information comes from among-species comparisons, and within-species variation is relatively poorly understood. We examined how large intraspecific differences in the behaviour of a native disperser, blackbuck antelope Antilope cervicapra, influence dispersal of a woody invasive, Prosopis juliflora, in a grassland ecosystem. Blackbuck disperse P. juliflora seeds through their dung. In lekking blackbuck populations, males defend clustered or dispersed mating territories. Territorial male movement is restricted, and within their territories males defecate on dung-piles. In contrast, mixed-sex herds range over large areas …

Diversification Under Sexual Selection: The Relative Roles Of Mate Preference Strength And The Degree Of Divergence In Mate Preferences, Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes

Eileen Hebets Publications

The contribution of sexual selection to diversification remains poorly understood after decades of research. This may be in part because studies have focused predominantly on the strength of sexual selection, which offers an incomplete view of selection regimes. By contrast, students of natural selection focus on environmental differences that help compare selection regimes across populations. To ask how this disparity in focus may affect the conclusions of evolutionary research, we relate the amount of diversification in mating displays to quantitative descriptions of the strength and the amount of divergence in mate preferences across a diverse set of case studies of …

An Incompatibility Between A Mitochondrial Trna And Its Nuclear-Encoded Trna Synthetase Compromises Development And Fitness In Drosophila, Colin D. Meiklejohn, Marissa A. Holmbeck, Mohammed A. Siddiq, Dawn N. Abt, David M. Rand, Kristi L. Montooth

School of Biological Sciences: Faculty Publications

Mitochondrial transcription, translation, and respiration require interactions between genes encoded in two distinct genomes, generating the potential for mutations in nuclear and mitochondrial genomes to interact epistatically and cause incompatibilities that decrease fitness. Mitochondrial-nuclear epistasis for fitness has been documented within and between populations and species of diverse taxa, but rarely has the genetic or mechanistic basis of these mitochondrial–nuclear interactions been elucidated, limiting our understanding of which genes harbor variants causing mitochondrial–nuclear disruption and of the pathways and processes that are impacted by mitochondrial–nuclear coevolution. Here we identify an amino acid polymorphism in the Drosophila melanogaster nuclear-encoded mitochondrial tyrosyl–tRNA …

Little Evidence For Demasculinization Of The Drosophila X Chromosome Among Genes Expressed In The Male Germline, Colin D. Meiklejohn, Daven C. Presgraves

School of Biological Sciences: Faculty Publications

Male-biased genes—those expressed at higher levels in males than in females—are underrepresented on the X chromosome of Drosophila melanogaster. Several evolutionary models have been posited to explain this so-called demasculinization of the X. Here, we show that the apparent paucity of male-biased genes on the X chromosome is attributable to global X-autosome differences in expression in Drosophila testes, owing to a lack of sex chromosome dosage compensation in the male germline, but not to any difference in the density of testis-specific or testis-biased genes on the X chromosome. First,using genome-wide gene expression data from 20 tissues,we find no evidence …

Long-Term Nitrogen Amendment Alters The Diversity And Assemblage Of Soil Bacterial Communities In Tallgrass Prairie, Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, John M. Blair, Michael A. Herman

School of Biological Sciences: Faculty Publications

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes …

The Mid-Domain Effect: It’S Not Just About Space, Andrew D. Letten, S. Kathleen Lyons, Angela T. Moles

School of Biological Sciences: Faculty Publications

Ecologists and biogeographers have long sought to understand how and why diversity varies across space. Up until the late 20th century, the dominant role of environmental gradients and historical processes in driving geographical species richness patterns went largely undisputed. However, almost 20 years ago, Colwell & Hurtt (1994) proposed a radical reappraisal of ecological gradient theory that called into question decades of empirical and theoretical research. That controversial idea was later termed the ‘the mid-domain effect’: the simple proposition that in the absence of environmental gradients, the random placement of species ranges within a bounded domain will give rise to …

Nitrogen Uptake Strategies Of Edaphically Specialized Bornean Tree Species, Sabrina E. Russo, Amy Kochsiek, Jocelyn Olney, Lauren Thompson, Amy E. Miller, Sylvester Tan

School of Biological Sciences: Faculty Publications

The association of tree species with particular soil types contributes to high b diversity in forests, but the mechanisms producing such distributions are still debated. Soil nitrogen (N) often limits growth and occurs in differentially available chemical forms. In a Bornean forest where tree species composition changes dramatically along a soil gradient varying in supplies of different N-forms, we investigated whether tree species’ N-uptake and soil specialization strategies covaried. We analyzed foliar ¹⁵N natural abundance for a total of 216 tree species on clay or sandy loam (the soils at the gradient’s extremes) and conducted a ¹⁵N-tracer experiment …

Different Modes Of Evolution In Males And Females Generate Dichromatism In Fairy-Wrens (Maluridae), Allison E. Johnson, J. Jordan Price, Stephen Pruett-Jones

School of Biological Sciences: Faculty Publications

Sexual dichromatism in birds is often attributed to selection for elaboration in males. However, evolutionary changes in either sex can result in plumage differences between them, and such changes can result in either gains or losses of dimorphism. We reconstructed the evolution of plumage colors in both males and females of species in Maluridae, a family comprising the fairy-wrens (Malurus, Clytomias, Sipodotus), emu-wrens (Stipiturus), and grasswrens (Amytornis). Our results show that, across species, males and females differ in their patterns of color evolution. Male plumage has diverged at relatively steady rates, whereas …

Reductive Evolution And The Loss Of Pdc/Pas Domains From The Genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, Greg A. Somerville

School of Biological Sciences: Faculty Publications

Background: The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).

Results: A total of 1,007 PAS domains and 686 …

A Whole-Cell Biosensor For The Detection Of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, Frank Reith

School of Biological Sciences: Faculty Publications

Geochemical exploration for gold (Au) is becoming increasingly important to the mining industry. Current processes for Au analyses require sampling materials to be taken from often remote localities. Samples are then transported to a laboratory equipped with suitable analytical facilities, such as Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) or Instrumental Neutron Activation Analysis (INAA). Determining the concentration of Au in samples may take several weeks, leading to long delays in exploration campaigns. Hence, a method for the on-site analysis of Au, such as a biosensor, will greatly benefit the exploration industry. The golTSB genes from Salmonella enterica serovar typhimurium are selectively …

Cd20 Antibody Primes B Lymphocytes For Type I Interferon Production, Dongsheng Xu, Andrew Staedman, Luwen Zhang

School of Biological Sciences: Faculty Publications

CD20 is a B cell surface marker that is expressed in various stages in B lymphocytes and certain lymphomas. Clinical administration of CD20 antibody, such as rituximab, is used widely to treat human B-cell lymphomas and other diseases. However, CD20 antibody failed to treat systemic lupus erythematosus (SLE or lupus). The reason for the failure is currently unknown. Type I interferons (IFN) are a major component for the host innate immunity, and a key pathogenic factor in lupus. We found that CD20 antibody potentiated human B cells for its production of IFNs in vitro. This function was specific to …

Creating An Interdisciplinary Research Course In Mathematical Ecology, Glenn Ledder, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

An integrated interdisciplinary research course in biology and mathematics is useful for recruiting students to interdisciplinary research careers, but there are difficulties involved in creating and implementing it. We describe the genesis, objectives, design policies, and structure of the Research Skills in Theoretical Ecology course at the University of Nebraska–Lincoln and discuss the difficulties that can arise in designing and implementing interdisciplinary courses.

An Interdisciplinary Research Course In Theoretical Ecology For Young Undergraduates, Glenn Ledder, Brigitte Tenhumberg, G. Travis Adams

School of Biological Sciences: Faculty Publications

As part of an interdepartmental effort to attract promising young students to research at the interface between mathematics and biology, we created a course in which groups of recent high school graduates and first-year college students conducted a research project in insect population dynamics. The students set up experiments, collected data, used the data to develop mathematical models, tested their models against further experiments, and prepared their results for dissemination. The course was self-contained in that the lecture portion developed the mathematical, statistical, and biological background needed for the research. A special writing component helped students learn the principles of …

Prevalence And Correlates Of Kaposi’S Sarcoma-Associated Herpesvirus Infection In A Sample Of Men Who Have Sex With Men In Eastern China, T. Zhang, H. Lin, V. Minhas, W. Zhu, Charles Wood, N. He

School of Biological Sciences: Faculty Publications

This study aimed to determine the seroprevalence of Kaposi’s sarcoma-associated herpesvirus (KSHV) and related factors in men who have sex with men (MSM) in China. A total of 208 subjects were recruited from eastern China from 2008 to 2009. Plasma samples were collected and screened for KSHV, HIV and syphilis. Overall, KSHV seroprevalence was 32.7% in the subjects. About 92.7% of subjects reported having ever had anal sex with a man, of whom 67.8% had receptive anal sex and 77.9% had insertive anal sex. About 93.1% of the study participants reported having had oral sex with a man, of whom …

Large-Scale Spatial Synchrony And Cross-Synchrony In Acorn Production By Two California Oaks, Walter D. Koenig, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Seed production that varies greatly from year to year, known as ‘‘masting’’ or ‘‘mast-fruiting’’ behavior, is a population-level phenomenon known to exhibit geographic synchrony extending, at least in some cases, hundreds of kilometers. The two main nonexclusive hypotheses for the driver of such geographically extensive synchrony are (1) environmental factors (the Moran effect), and (2) the mutual dependence of trees on outcrossed pollen (pollen coupling). We tested 10 predictions relevant to these two hypotheses using 18 years of acorn production data on two species of California oaks. Data were obtained across the entire ranges of the two species at 12 …