Biology Commons^™

Compositions And Methods For Controlling Plant Parasitic Nematodes, Harold N. Trick, Judith L. Roe, Timothy C. Todd, Michael A. Herman

School of Biological Sciences: Faculty Publications

The present invention relates to compositions and methods for controlling nematode infestation of plants. In particular, the present invention provides vectors comprising sequences designed to control nematodes by RNA interference (RNAi) and transgenic plants transformed with Such vectors.

The Polypeptide Syn67 Interacts Physically With Human Holocarboxylase Synthetase, But Is Not A Target For Biotinylation, Yousef I. Hassan, Hideaki Moriyama, Janos Zempleni

School of Biological Sciences: Faculty Publications

Holocarboxylase synthetase (HCS) catalyzes the binding of biotin to lysines in carboxylases and histones in two steps. First, HCS catalyzes the synthesis of biotinyl-5′-AMP; second, the biotinyl moiety is ligated to lysine residues. It has been proposed that step two is fairly promiscuous, and that protein biotinylation may occur in the absence of HCS as long as sufficient exogenous biotinyl-5′- AMP is provided. Here, we identified a novel polypeptide (Syn67) with a basic patch of lysines and arginines. Yeast-two-hybrid assays and limited proteolysis assays revealed that both N- and C-termini of HCS interact with Syn67. A potential target lysine in …

Molecular Determinants Of Hiv-1 Subtype C Coreceptor Transition From R5 To R5x4, Hong Zhang, Damien C. Tully, Tiejun Zhang, Hideaki Moriyama, Jesse Thompson, Charles Wood

School of Biological Sciences: Faculty Publications

The molecular mechanism(s) underlying transition from CCR5 to CXCR4 usage of subtype C viruses remain largely unknown. We previously identified a subtype C HIV-1 infected child whose virus demonstrated CXCR4 usage along with CCR5 upon longitudinal follow-up. Here we delineated the molecular determinants of Env involved in expanded coreceptor usage. Residue changes in three positions of Env V3 domain are critical for the dual-tropic phenotype. These include: substitution of arginine at position 11, MG or LG insertion between positions 13 and 14, and substitution of threonine at the position immediately downstream of the GPGQ crown. Introducing these mutations into V3 …

Locomotion In Response To Shifting Climate Zones: Not So Fast, Martin E. Feder, Theodore Garland Jr., James H. Marden, Anthony J. Zera

School of Biological Sciences: Faculty Publications

Although a species’ locomotor capacity is suggestive of its ability to escape global climate change, such a suggestion is not necessarily straightforward. Species vary substantially in locomotor capacity, both ontogenetically and within/among populations, and much of this variation has a genetic basis. Accordingly, locomotor capacity can and does evolve rapidly, as selection experiments demonstrate. Importantly, even though this evolution of locomotor capacity may be rapid enough to escape changing climate, genetic correlations among traits (often due to pleiotropy) are such that successful or rapid dispersers are often limited in colonization or reproductive ability, which may be viewed as a trade-off. …

Wnt And Egf Pathways Act Together To Induce C. Elegans Male Hook Development, Hui Yu, Adeline Seah, Michael A. Herman, Edwin L. Ferguson, H. Robert Horvitz, Paul W. Sternberg

School of Biological Sciences: Faculty Publications

Comparative studies of vulva development between Caenorhabditis elegans and other nematode species have provided some insight into the evolution of patterning networks. However, molecular genetic details are available only in C. elegans and Pristionchus pacificus. To extend our knowledge on the evolution of patterning networks, we studied the C. elegans male hook competence group (HCG), an equivalence group that has similar developmental origins to the vulval precursor cells (VPCs), which generate the vulva in the hermaphrodite. Similar to VPC fate specification, each HCG cell adopts one of three fates (1°, 2°, 3°), and 2° HCG fate specification …

Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase, Kohei Homma, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but …

Role Of Vapbc Toxin–Antitoxin Loci In The Thermal Stress Response Of Sulfolobus Solfataricus, Charlotte R. Cooper, Amanda J. Daugherty, Sabrina Tachdjian, Paul H. Blum, Robert M. Kelly

School of Biological Sciences: Faculty Publications

TA (toxin–antitoxin) loci are ubiquitous in prokaryotic microorganisms, including archaea, yet

their physiological function is largely unknown. For example, preliminary reports have suggested

that TA loci are microbial stress-response elements, although it was recently shown that knocking

out all known chromosomally located TA loci in Escherichia coli did not have an impact on

survival under certain types of stress. The hyperthermophilic crenarchaeon Sulfolobus solfataricus

encodes at least 26 vapBC (where vap is virulence-associated protein) family TA loci in its

genome. VapCs are PIN (PilT N-terminus) domain proteins with putative ribonuclease activity,

while VapBs are proteolytically labile proteins, which purportedly function …

Evolution And Pleiotropy Of Trithorax Function In Arabidopsis, Zoya Avramova

School of Biological Sciences: Faculty Publications

The SET domain-containing genes of the TRITHORAX family encode epigenetic factors that maintain the expression of targeted genes. Trithorax homologs have been found in both animals and plants. Since these are thought to have evolved multicellularity independently, common mechanisms of epigenetic regulation must be evolutionarily ancient and derived from a common ancestor. In addition, each lineage has evolved unique mechanisms to expand the original repertoire of epigenetic functions. Phylogenetic analysis of SET domain proteins has outlined some intriguing evolutionary trends. In plants, epigenetic gene silencing mechanisms have been aggressively pursued. In contrast, studies of epigenetic mechanisms maintaining active gene expression …

Interactive Effects Of Time, Co2, N, And Diversity On Total Belowground Carbon Allocation And Ecosystem Carbon Storage In A Grassland Community, E. Carol Adair, Peter B. Reich, Sarah E. Hobbie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Predicting if ecosystems will mitigate or exacerbate rising CO2 requires understanding how elevated CO₂ will interact with coincident changes in diversity and nitrogen (N) availability to affect ecosystem carbon (C) storage. Yet achieving such understanding has been hampered by the difficulty of quantifying belowground C pools and fluxes. Thus, we used mass balance calculations to quantify the effects of diversity, CO₂, and N on both the total amount of C allocated belowground by plants (total belowground C allocation, TBCA) and ecosystem C storage in a periodically burned, 8-year Minnesota grassland biodiversity, CO₂, and N experiment …

Caenorhabditis Elegans Genomic Response To Soil Bacteria Predicts Environment-Specific Genetic Effects On Life History Traits, Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, Bryanua C. Carr, Michael A. Herman

School of Biological Sciences: Faculty Publications

With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential expression is predictive of functional importance has yet to be tested. Here we have addressed this expectation by employing Caenorhabditis elegans as a model for the interaction of native soil nematode taxa and …

The Nuclear Receptor Nhr-25 Cooperates With The Wnt/Β-Catenin Asymmetry Pathway To Control Differentiation Of The T Seam Cell In C. Elegans, Martina Hajduskova, Marek Jindra, Michael A. Herman, Masako Asahina

School of Biological Sciences: Faculty Publications

Asymmetric cell divisions produce new cell types during animal development. Studies in Caenorhabditis elegans have identified major signal-transduction pathways that determine the polarity of cell divisions. How these relatively few conserved pathways interact and what modulates them to ensure the diversity of multiple tissue types is an open question. The Wnt/β-catenin asymmetry pathway governs polarity of the epidermal T seam cell in the C. elegans tail. Here, we show that the asymmetry of T-seam-cell division and morphogenesis of the male sensory rays require NHR-25, an evolutionarily conserved nuclear receptor. NHR-25 ensures the neural fate of the T-seam-cell descendants in cooperation …

Ecological Genomics Of Nematode Community Interactions: Model And Non-Model Approaches, Michael A. Herman, Joseph D. Coolon, Kenneth L. Jones, Timothy Todd

School of Biological Sciences: Faculty Publications

The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to …

Something Old, Something New, Something Borrowed; How The Thermoacidophilic Archaeon Sulfolobus Solfataricus Responds To Oxidative Stress, Walid S. Maaty, Blake Wiedenheft, Pavel Tarlykov, Nathan Schaff, Joshua Heinemann, Jim Robinson-Cox, Jacob Valenzuela, Amanda Dougherty, Paul H. Blum, C. Martin Lawrence, Trevor Douglas, Mark J. Young, Brian Bothner

School of Biological Sciences: Faculty Publications

To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts …

Sex Effects On Life Span And Senescence In The Wild When Dates Of Birth And Death Are Unknown, Felix Zajitschek, Chad Brassil, Russell Bonduriansky, Robert C. Brooks

School of Biological Sciences: Faculty Publications

Males and females allocate and schedule reproductive effort in very different ways. Because the timing and amount of reproductive effort influence survival and thus the optimization of life histories, mortality and senescence are predicted to be sex specific. However, age-specific mortality rates of wild animals are often difficult to quantify in natural populations. Studies that report mortality rates from natural populations are, therefore, almost entirely confined to long-lived, easy-to-track species such as large mammals and birds. Here, we employ a novel approach using capture–mark–recapture data from a wild population of black field crickets (Teleogryllus commodus) to test for …

Blood Sampling Reduces Annual Survival In Cliff Swallows (Petrochelidon Pyrrhonota) -- La Toma De Muestras De Sangre Reduce La Supervivencia Anual En Petrochelidon Pyrrhonota, Charles R. Brown, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Researchers commonly collect blood samples from wild birds, and most workers assume that blood sampling has no adverse effect on the birds’ survival. Few studies, however, have done controlled comparisons among bled and non-bled individuals and estimated survival using modern statistical methodology. We used a data set on Cliff Swallows (Petrochelidon pyrrhonota) that included 2,945 bled and 7,822 non-bled birds captured at the same times and sites in southwestern Nebraska from 1986 to 2006 to estimate annual survival and recapture probabilities of each group. Blood was collected with brachial venipuncture in amounts varying from 0.3% to 1.2% of …

Long 3’-Utrs Target Wild-Type Mrnas For Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, Bessie W. Kebaara, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

The nonsense-mediated mRNA decay (NMD) pathway,

present in most eukaryotic cells, is a specialized

pathway that leads to the recognition and rapid

degradation of mRNAs with premature termination

codons and, importantly, some wild-type

mRNAs. Earlier studies demonstrated that aberrant

mRNAs with artificially extended 3’-untranslated

regions (3’-UTRs) are degraded by NMD. However,

the extent to which wild-type mRNAs with long

3’-UTRs are degraded by NMD is not known.

We used a global approach to identify wild-type

mRNAs in Saccharomyces cerevisiae that have

longer than expected 3’-UTRs, and of these

mRNAs tested, 91% were degraded by NMD. We

demonstrate for the first …

The Impact Of Co-Occurring Tree And Grassland Species On Carbon Sequestration And Potential Biofuel Production, Ramesh Laungani, Johannes Knops

School of Biological Sciences: Faculty Publications

We evaluated how three co-occurring tree and four grassland species influence potentially harvestable biofuel stocks and above- and belowground carbon pools. After 5 years, the tree Pinus strobus had 6.5 times the amount of aboveground harvestable biomass as another tree Quercus ellipsoidalis and 10 times that of the grassland species. P. strobus accrued the largest total plant carbon pool (1375 gCm -2 or 394 gCm -2 yr), while Schizachyrium scoparium accrued the largest total plant carbon pool among the grassland species (421 gCm -2 or 137 gCm -2 yr). Quercus ellipsoidalis accrued 850 gCm -2, Q. macrocarpa 370 gCm -2, …

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 …

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 …

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 …

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) …

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 …

Parasites, Proteomics And Performance: Effects Of Gregarine Gut Parasites On Dragonfly Flight Muscle Composition And Function, Rudolf J. Schilder, James H. Marden

School of Biological Sciences: Faculty Publications

In previous work, we found that dragonflies infected with gregarine gut parasites have reduced muscle power output, loss of lipid oxidation in their flight muscles, and a suite of symptoms similar to mammalian metabolic syndrome. Here, we test the hypothesis that changes in muscle protein composition underlie the observed changes in contractile performance. We found that gregarine infection was associated with a 10-fold average reduction in abundance of a ~155·kDa fragment of muscle myosin heavy chain (MHC; ~206·kDa intact size). Insect MHC gene sequences contain evolutionarily conserved amino acid motifs predicted for calpain cleavage, and we found that calpain digestion …

Plant Mitochondrial Recombination Surveillance Requires Unusual Reca And Muts Homologs, Vikas Shedge, Maria P. Arrieta-Montiel, Alan C. Christensen, Sally Ann Mackenzie

School of Biological Sciences: Faculty Publications

For >20 years, the enigmatic behavior of plant mitochondrial genomes has been well described but not well understood. Chimeric genes appear, and occasionally are differentially replicated or expressed, with significant effects on plant phenotype, most notably on male fertility, yet the mechanisms of DNA replication, chimera formation, and recombination have remained elusive. Using mutations in two important genes of mitochondrial DNA metabolism, we have observed reproducible asymmetric recombination events occurring at specific locations in the mitochondrial genome. Based on these experiments and existing models of double-strand break repair, we propose a model for plant mitochondrial DNA replication, chimeric gene formation, …

Microarray Challenges In Ecology, Jan E. Kammenga, Michael A. Herman, N. Joop Ouborg, Loretta Johnson, Rainer Bretling

School of Biological Sciences: Faculty Publications

Microarrays are used to measure simultaneously the amount of mRNAs transcribed from many genes. They were originally designed for gene expression profiling in relatively simple biological systems, such as cell lines and model systems under constant laboratory conditions. This poses a challenge to ecologists who increasingly want to use microarrays to unravel the genetic mechanisms underlying complex interactions among organisms and between organisms and their environment. Here, we discuss typical experimental and statistical problems that arise when analyzing genome-wide expression profiles in an ecological context. We show that experimental design and environmental confounders greatly influence the identification of candidate genes …

The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

Tightly balanced antagonism between the Polycomb group (PcG) and the Trithorax group (TrxG) complexes maintain Hox expression patterns in Drosophila and murine model systems. Factors belonging to the PcG/TrxG complexes control various processes in plants as well but whether they participate in mechanisms that antagonize, balance or maintain each other’s effects at a particular gene locus is unknown. CURLY LEAF (CLF), an Arabidopsis homolog of enhancer of zeste (EZ) and the ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) control the expression of the flower homeotic gene AGAMOUS (AG). Disrupted ATX1 or CLF function results in misexpression of AG, recognizable …

Flagellar Motility And Structure In The Hyperthermoacidophilic Archaeon Sulfolobus Solfataricus, Zalán Szabó, Musa Sani, Maarten Groeneveld, Benham Zolghadr, James Schelert, Sonja-Verena Albers, Paul H. Blum, Egbert J. Boekema, Arnold J.M. Driessen

School of Biological Sciences: Faculty Publications

Flagellation in archaea is widespread and is involved in swimming motility. Here, we demonstrate that the

structural flagellin gene from the crenarchaeaon Sulfolobus solfataricus is highly expressed in stationary-phasegrown

cells and under unfavorable nutritional conditions. A mutant in a flagellar auxiliary gene, flaJ, was

found to be nonmotile. Electron microscopic imaging of the flagellum indicates that the filaments are composed

of right-handed helices.

Evaluation Of Metals In A Defined Medium For Pichia Pastoris Expressing Recombinant Β-Galactosidase, Bradley A. Plantz, Kenneth W. Nickerson, Stephen D. Kachman, Vicki L. Schlegel

School of Biological Sciences: Faculty Publications

Culture growth and recombinant protein yield of the Pichia pastoris GS115 methanol utilization positive system were studied in response to the types and levels of metals present in the growth medium and the supplemental salts typically used for these fermentations. Magnesium and zinc were both required to support cell growth but at significantly reduced levels compared to the control. However, supplementation with calcium, cobalt, iron, manganese, iodine, boron, and molybdenum were not required to sustain cell mass. When the medium was reformulated with only zinc and magnesium, the cells grew to 12–15 generations, which are expected for high cell density …

Asymmetric Localizations Of Lin-17/Fz And Mig-5/Dsh Are Involved In The Asymmetric B Cell Division In C. Elegans, Mingfu Wu, Michael A. Herman

School of Biological Sciences: Faculty Publications

LIN-44/Wnt and LIN-17/Frizzled (Fz) function in a planar cell polarity (PCP)-like pathway to regulate the asymmetric B cell division in Caenorhabditis elegans. We observed asymmetric localization of LIN-17/Frizzled (Fz) and MIG-5/Disheveled (Dsh) during the B cell division. LIN-17∷GFP was asymmetrically localized within the B cell prior to and after the B cell division and correlated with B cell polarity. Asymmetric localization of LIN-17∷GFP was dependent upon LIN-44/Wnt and MIG-5/Dsh function. The LIN-17 transmembrane domain and a portion of the cysteine-rich domain (CRD) were required for LIN-17 function and asymmetric distribution to the B cell daughters, while the conserved KTXXXW …