Biology Commons^™

Mining The Arabidopsis Thaliana Genome For Highly-Divergent Seven Transmembrane Receptors, Etsuko N. Moriyama, Pooja K. Strope, Stephen O. Opiyo, Zhongying Chen, Alan M. Jones

School of Biological Sciences: Faculty Publications

To identify divergent seven-transmembrane receptor (7TMR) candidates from the Arabidopsis thaliana genome, multiple protein classification methods were combined, including both alignmentbased and alignment-free classifiers. This resolved problems in optimally training individual classifiers using limited and divergent samples, and increased stringency for candidate proteins. We identified 394 proteins as 7TMR candidates and highlighted 54 with corresponding expression patterns for further investigation.

Mig-5/Dsh Controls Cell Fate Determination And Cell Migration In C. Elegans, Timothy Walston, Chaobo Guo, Rui Proenca, Mingfu Wu, Michael Herman, Jeff Hardin, Edward Hedgecock

School of Biological Sciences: Faculty Publications

Cell fate determination and cell migration are two essential events in the development of an organism. We identify mig-5, a Dishevelled family member, as a gene that regulates several cell fate decisions and cell migrations that are important during C. elegans embryonic and larval development. In offspring from mig-5 mutants, cell migrations are defective during hypodermal morphogenesis, QL neuroblast migration, and the gonad arm migration led by the distal tip cells (DTCs). In addition to abnormal migration, DTC fate is affected, resulting in either an absent or an extra DTC. The cell fates of the anchor cell in hermaphrodites …

Glucocorticoid Hormone Levels Increase With Group Size And Parasite Load In Cliff Swallows, Samrrah A. Raouf, Linda C. Smith, Mary Bomberger Brown, John C. Wingfield, Charles R. Brown

School of Biological Sciences: Faculty Publications

Animals often cope with adverse events by releasing glucocorticoid hormones, which in turn promote increased energy assimilation. In captive animals, crowding also leads to increased glucocorticoid activity, probably because of increased levels of social competition. We investigated how group size and ectoparasite infestations affected endogenous levels of the glucocorticoid hormone, corticosterone, in colonial cliff swallows, Petrochelidon pyrrhonota, in southwestern Nebraska, USA. Parasites were removed from some colonies by fumigating nests. Baseline levels of corticosterone in breeding adults varied significantly with whether parasites were present, colony size (measured by total number of active nests at a site), and nesting stage. …

Nonparametric Estimation Of Natural Selection On A Quantitative Trait Using Mark-Recapture Data, Olivier Gimenez, Rita Covas, Charles R. Brown, Mark D. Anderson, Mary Bomberger Brown, Thomas Lenormand

School of Biological Sciences: Faculty Publications

Assessing natural selection on a phenotypic trait in wild populations is of primary importance for evolutionary ecologists. To cope with the imperfect detection of individuals inherent to monitoring in the wild, we develop a nonparametric method for evaluating the form of natural selection on a quantitative trait using mark-recapture data. Our approach uses penalized splines to achieve flexibility in exploring the form of natural selection by avoiding the need to specify an a priori parametric function. If needed, it can help in suggesting a new parametric model. We employ Markov chain Monte Carlo sampling in a Bayesian framework to estimate …

Regulation Of Mercury Resistance In The Crenarchaeote Sulfolobus Solfataricus, James Schelert, Melissa Drozda, Vidula Dixit, Amanda Dillman, Paul H. Blum

School of Biological Sciences: Faculty Publications

Mercuric ion, Hg(II), inactivates generalized transcription in the crenarchaeote Sulfolobus solfataricus. Metal

challenge simultaneously derepresses transcription of mercuric reductase (merA) by interacting with the

archaeal transcription factor aMerR. Northern blot and primer extension analyses identified two additional

Hg(II)-inducible S. solfataricus genes, merH and merI (SSO2690), located on either side of merA. Transcription

initiating upstream of merH at promoter merHp was metal inducible and extended through merA and merI,

producing a merHAI transcript. Northern analysis of a merRA double mutant produced by linear DNA

recombination demonstrated merHp promoter activity was dependent on aMerR to overcome Hg(II) …

Fire Does Not Alter Vegetation In Infertile Prairie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

The paradigm in prairie ecology is that fire is one of the key factors deter-mining vegetation composition. fire can impact grassland ecosystems in various ways, including changing plant species composition and inducing nitro-gen loss. I found that 17 years of different burning frequencies in infertile grassland had only a minor impact on the vegetation composition and diversity. The only major impact from increasing the frequency of fires was a decrease of Poa pratensis abundance. However, other plant species did not r-spond to the change in Poa abundance. This result contrasts with previous studies in savannas and more productive grasslands, where …

Can Environmental Variation Generate Positive Indirect Effects In A Model Of Shared Predation?, Chad Brassil

School of Biological Sciences: Faculty Publications

Classic models of apparent competition predict negative indirect effects between prey with a shared enemy. If predator per capita growth rates are nonlinear, then endogenously generated periodic cycles are predicted to generate less negative or even positive indirect effects between prey. Here I determine how exogenous mechanisms such as environmental variation could modify indirect effects. I find that exogenous variation can have a broader range of effects on indirect interactions than endogenously generated cycles. Indirect effects are altered by environmental variation even in simple models for which the per capita growth rate of the predator species is a linear function …

Feather Mites Are Positively Associated With Daily Survival In Cliff Swallows, Charles R. Brown, Kathleen R. Brazeal, Stephanie A. Strickler, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Feather mites (Acari: Astigmata) have been reported to be parasitic, commensal, and even mutualis-tic on the birds that serve as their hosts. We investigated whether there was a relationship between number of feather mites (Pteronyssoides obscurus (Berlese, 1885)) on the wing and daily survival of cliff swallows (Petrochelidon pyrrhonota (Vieillot, 1817)) during the breeding season at 12 nesting colonies in Nebraska in 2005. Survival of birds with known mite loads was monitored by mark–recapture, and survival models with and without a linear effect of mites were compared with the program MARK. For adult swallows, mites were positively associated …

Rapid Senescence In Pacific Salmon, Yolanda E. Morbey, Chad Brassil, Andrew P. Hendry

School of Biological Sciences: Faculty Publications

Any useful evolutionary theory of senescence must be able to explain variation within and among natural populations and species. This requires a careful characterization of age-specific mortality rates in nature as well as the intrinsic and extrinsic factors that influence these rates. We perform this task for two populations of semelparous Pacific salmon. During the breeding season, estimated daily mortality rates increased from 0 to 0.2–0.5 (depending on the year) over the course of several weeks. Early-arriving individuals had a later onset and/or a lower rate of senescence in each breeding season, consistent with adaptive expectations based on temporal variation …

Effects Of Endogenous Steroid Hormone Levels On Annual Survival In Cliff Swallows, Charles R. Brown, Mary Bomberger Brown, Samrrah A. Raouf, Linda C. Smith, John C. Wingfield

School of Biological Sciences: Faculty Publications

The hormone corticosterone is an important part of animals’ response to environmental stress, modulating short-term adaptive changes in behavior and physiology. The hormone testosterone is also critical, especially for males, in regulating the expression of sexual behavior and parental care. These hormones can have costly consequences, however, and within populations individuals show variation in endogenous levels of both corticosterone and testosterone. We studied how annual survival varied as a function of natural levels of these hormones in colonially breeding Cliff swallows (Petrochelidon pyrrhonota) in southwestern Nebraska, USA, in 2000–2003. We sampled hormone levels of birds caught at colonies …

Testosterone And Group Size In Cliff Swallows: Testing The “Challenge Hypothesis” In A Colonial Bird, Linda C. Smith, Samrrah A. Raouf, Mary Bomberger Brown, John C. Wingfield, Charles R. Brown

School of Biological Sciences: Faculty Publications

The “challenge hypothesis” states that increases in testosterone levels of male animals during the breeding season are directly related to the extent of intrasexual competition for resources or mates that they experience. Although often tested in territorial species, the challenge hypothesis has not been evaluated for colonial animals that live in groups of different sizes and that thus experience different intensities of intrasexual competition. We measured circulating testosterone levels of male and female cliff swallows (Petrochelidon pyrrhonota) in southwestern Nebraska, where these birds nest in colonies of widely different sizes. Males had significantly higher testosterone levels than females, …

Between-Group Transmission Dynamics Of The Swallow Bug, Oeciacus Vicarius, Charles R. Brown, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

The parasitic cimicid swallow bug, Oeciacus vicarius, is the principal invertebrate vector for Buggy Creek virus (BCRV) and has also been associated with Venezuelan equine encephalitis virus. To help understand the spread of this vector, we experimentally measured the transmission of O. vicarius between groups (colonies) of its main host, the cliff swallow (Petrochelidon pyrrhonota), in the field. Transmission of bugs between colonies varied significantly with year, size of the colony, and week within the season. Bug immigration into sites tended to peak in mid-summer. Swallow nests in larger colonies had more consistent rates of bug introduction than …

Characterization Of Different Crystal Forms Of The Α-Glucosidase Mala From Sulfolobus Solfataricus, Heidi Asschenfeldt Ernst, Martin Willemoës, Leila Lo Leggio, Gordon Leonard, Paul H. Blum, Sine Larsen

School of Biological Sciences: Faculty Publications

MalA is an _-glucosidase from the hyperthermophilic archaeon Sulfolobus

solfataricus. It belongs to glycoside hydrolase family 31, which includes several

medically interesting α-glucosidases. MalA and its selenomethionine derivative

have been overproduced in Escherichia coli and crystallized in four different

crystal forms. Microseeding was essential for the formation of good-quality

crystals of forms 2 and 4. For three of the crystal forms (2, 3 and 4) full data sets

could be collected. The most suitable crystals for structure determination are the

monoclinic form 4 crystals, belonging to space group P21, from which data sets

extending to 2.5 Å resolution …

Upf1p, A Highly Conserved Protein Required For Nonsense-Mediated Mrna Decay, Interacts With The Nuclear Pore Proteins Nup100p And Nup116p, Tara Nazarenus, Rebecca Cedarberg, Ryan Bell, Joseph Cheatle, Amanda Forch, Alexis Haifley, Ann Hou, Bessie Wanja Kebaara, Christina Shields, Kate Stoysich, Rachel Taylor, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

Saccharomyces cerevisiae Upf1p is a 971-amino-acid protein that is required for the nonsense-mediated mRNA decay (NMD) pathway, a pathway that degrades mRNAs with premature translational termination codons. We have identified a two-hybrid interaction between Upf1p and the nuclear pore (Nup) proteins, Nup100p and Nup116p. Both nucleoporins predominantly localize to the cytoplasmic side of the nuclear pore and participate in mRNA transport. The two-hybrid interaction between Upf1p and the nuclear pore proteins, Nup100p and Nup116p, is dependent on the presence of the C-terminal 158 amino acids of Upf1p. Nup100p and Nup116p can be coimmunoprecipitated from whole-cell extracts with Upf1p, confirming in …

Gene Set Coregulated By The Saccharomyces Cerevisiae Nonsense-Mediated Mrna Decay Pathway, Rachel Taylor, Bessie Wanja Kebaara, Tara Nazarenus, Ashley Jones, Rena Yamanaka, Rachel Uhrenholdt, Jason P. Wendler, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a …

Juvenile And Adult Survival In The Sociable Weaver (Philetairus Socius), A Southern-Temperate Colonial Cooperative Breeder In Africa, Rita Covas, Charles R. Brown, Mark D. Anderson, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

We used capture–recapture analyses to describe juvenile and adult survival from 1993 to 2001 in a population of Sociable Weavers (Philetairus socius), a colonial, cooperatively breeding passerine of southern Africa. We examined temporal variation in survival and the role that the breeding season’s length and environmental factors play in determining survival patterns in the population. Annual survival probability (mean ± SE) was 0.66 ± 0.02. In contrast to most passerines, juveniles and adults had similar survival probabilities; survival rates did not vary significantly between years. We found no relationship among temperature, rainfall, and survival. Relatively high survival rates …

Group Size And Ectoparasitism Affect Daily Survival Probability In A Colonial Bird, Charles R. Brown, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Little is known in general about how group size or ectoparasitism affect survival in colonial animals. We estimated daily within-season survival probabilities for nesting adult and recently fledged juvenile cliff swallows (Petrochelidon pyrrhonota) at 239 colonies from 1983 to 2003 in southwestern Nebraska, USA. Some colonies had been fumigated to remove ectoparasites. We conducted mark-recapture at each colony site to estimate daily survival. There were no systematic differences between males and females in daily survival. Adults and juveniles occupying parasite-free colonies had, on average, 4.4% and 62.2% greater daily survival, respectively, than their counterparts in naturally infested colonies. …

Occurrence And Characterization Of Mercury Resistance In The Hyperthermophilic Archaeon Sulfolobus Solfataricus By Use Of Gene Disruption, James Schelert, Vidula Dixit, Viet Hoang, Jessica Simbahan, Melissa Drozda, Paul H. Blum

School of Biological Sciences: Faculty Publications

Mercury resistance mediated by mercuric reductase (MerA) is widespread among bacteria and operates under the control of MerR. MerR represents a unique class of transcription factors that exert both positive and negative regulation on gene expression. Archaea and bacteria are prokaryotes, yet little is known about the biological role of mercury in archaea or whether a resistance mechanism occurs in these organisms. The archaeon Sulfolobus solfataricus was sensitive to mercuric chloride, and low-level adaptive resistance could be induced by metal preconditioning. Protein phylogenetic analysis of open reading frames SSO2689 and SSO2688 clarified their identity as orthologs of MerA and MerR. …

Culture-Independent Analysis Of Fecal Enterobacteria In Environmental Samples By Single-Cell Mrna Profiling, Han Chen, Gomathinayagam Ponniah, Nancy Salonen, Paul H. Blum

School of Biological Sciences: Faculty Publications

A culture-independent method called mRNA profiling has been developed for the analysis of fecal enterobacteria and their physiological status in environmental samples. This taxon-specific approach determines the single-cell content of selected gene transcripts whose abundance is either directly or inversely proportional to growth state. Fluorescence in situ hybridization using fluorochrome-labeled oligonucleotide probes was used to measure the cellular concentration of fis and dps mRNA. Relative levels of these transcripts provided a measure of cell growth state and the ability to enumerate fecal enterobacterial cell number. Orthologs were cloned by inverse PCR from several major enterobacterial genera, and probes specific for …

Ecological Effects Of Transgenic Crops And The Escape Of Transgenes Into Wild Populations, Diana Pilson, Holly R. Prendeville

School of Biological Sciences: Faculty Publications

Ecological risks associated with the release of transgenic crops include nontarget effects of the crop and the escape of transgenes into wild populations. Nontarget effects can be of two sorts: (a) unintended negative effects on species that do not reduce yield and (b) greater persistence of the crop in feral populations. Conventional agricultural methods, such as herbicide and pesticide application, have large and well- documented nontarget effects. To the extent that transgenes have more specific target effects, transgenic crops may have fewer nontarget effects. The escape of transgenes into wild populations, via hybridization and introgression, could …

Mercury Inactivates Transcription And The Generalized Transcription Factor Tfb In The Archaeon Sulfolobus Solfataricus, Vidula Dixit, Elisabetta Bini, Melissa Drozda, Paul H. Blum

School of Biological Sciences: Faculty Publications

Mercury has a long history as an antimicrobial agent effective against eukaryotic and prokaryotic organisms.

Despite its prolonged use, the basis for mercury toxicity in prokaryotes is not well understood. Archaea, like

bacteria, are prokaryotes but they use a simplified version of the eukaryotic transcription apparatus. This

study examined the mechanism of mercury toxicity to the archaeal prokaryote Sulfolobus solfataricus. In vivo

challenge with mercuric chloride instantaneously blocked cell division, eliciting a cytostatic response at

submicromolar concentrations and a cytocidal response at micromolar concentrations. The cytostatic response

was accompanied by a 70% reduction in bulk RNA synthesis and elevated …

Landscape Vs. Local Habitat Scale Influences To Insect Communities From Tallgrass Prairie Remnants, Kristal J.L. Stoner, Anthony Joern

School of Biological Sciences: Faculty Publications

Habitat loss and fragmentation currently threaten ecosystems worldwide, yet remain difficult to quantify because within-fragment habitat and landscape-scale influences often interact in unique ways. Although individual species respond to fragmentation differently, large-scale conservation planning must unavoidably target multiple species. Although information on a population’s response to fragmentation is critical, and measurements of species richness provide useful insights, exclusive reliance on these responses may mask important information about the taxonomic composition of assemblages in response to fragmentation. The North American tallgrass prairie ecosystem is one of the most threatened and fragmented ecosystems in the world, and insects are significant contributors to …

Mark–Recapture And Behavioral Ecology: A Case Study Of Cliff Swallows, C. R. Brown, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Mark–recapture and behavioral ecology: a case study of Cliff Swallows.— Mark–recapture and the statistical analysis methods associated with it offer great potential for investigating fitness components associated with particular behavioral traits. However, few behavioral ecologists have used these techniques. We illustrate the insights that have come from a long–term mark–recapture study of social behavior in Cliff Swallows (Petrochelidon pyrrhonota). The number of transient swallows passing through a colony per hour increased with colony size and was responsible in part for increased rates of ectoparasite introduction from outside the group into the larger colonies. Annual survival probabilities of …

Body Mass Of Late Quaternary Mammals (Data Set), Felisa A. Smith, S. Kathleen Lyons, S.K. Morgan Ernest, Kate E. Jones, Kansas State University, Tamar Dayan, Pablo A. Marquet, James H. Brown, John P. Haskell

School of Biological Sciences: Faculty Publications

The purpose of this data set was to compile body mass information for all mammals on Earth so that we could investigate the patterns of body mass seen across geographic and taxonomic space and evolutionary time. We were interested in the heritability of body size across taxonomic groups (How conserved is body mass within a genus, family, and order?), in the overall pattern of body mass across continents (Do the moments and other descriptive statistics remain the same across geographic space?), and over evolutionary time (How quickly did body mass patterns iterate on the patterns seen today? Were the Pleistocene …

Multistate Estimates Of Survival And Movement In Relation To Colony Size In The Sociable Weaver, Charles R. Brown, Rita Covas, Mark D. Anderson, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

We estimated survival and movement probabilities in relation to breeding-colony size in the sociable weaver (Philetairus socius) by using multistate statistical methods, in which survival and movement to time t + 1 is conditional on an individual’s colony size at time t. The sociable weaver is a colonial, cooperatively breeding species that builds a massive communal nest, with colony size ranging from fewer than 20 to more than 500 individuals in some areas. We conducted an 8-year capture/mark/re-capture study of sociable weavers near Kimberley, South Africa. By comparing the fit of different multistate models to our data, we found evidence …

Targeted Disruption Of The Α-Amylase Gene In The Hyperthermophilic Archaeon Sulfolobus Solfataricus, Penny Worthington, Viet Hoang, Francisco Perez-Pomares, Paul H. Blum

School of Biological Sciences: Faculty Publications

Sulfolobus solfataricus secretes an acid-resistant _-amylase (amyA) during growth on starch as the sole

carbon and energy source. Synthesis of this activity is subject to catabolite repression. To better understand

_-amylase function and regulation, the structural gene was identified and disrupted and the resulting mutant

was characterized. Internal _-amylase peptide sequences obtained by tandem mass spectroscopy were used to

identify the amyA coding sequence. Anti-_-amylase antibodies raised against the purified protein immunoprecipitated

secreted _-amylase activity and verified the enzymatic identity of the sequenced protein. A new

gene replacement method was used to disrupt the amyA coding sequence by …

Single-Cell Protein Profiling Of Wastewater Enterobacterial Communities Predicts Disinfection Efficiency, Gomathinayagam Ponniah, Han Chen, Ronda Michielutti, Nancy Salonen, Paul H. Blum

School of Biological Sciences: Faculty Publications

The efficiency of enterobacterial disinfection is dependent largely on enterobacterial community physiology. However, the relationship between enterobacterial community physiology and wastewater processing is unclear. The purpose of this study was to investigate this relationship. The influence of wastewater treatment processes on enterobacterial community physiology was examined at the single-cell level by using cultureindependent methods. Intracellular concentrations of two conserved proteins, the growth-related protein Fis and the stationary-phase protein Dps, were analyzed by epifluoresence microscopy of uncultivated cells by using enterobacterial group-specific polyclonal fluorochrome-coupled antibodies. Enterobacterial single-cell community protein profiles were distinct for different types of biological treatment. The differences were …

Putative Subunits Of The Maize Origin Of Replication Recognition Complex Zmorc1±Zmorc5, Xiaohong Witmer, Raul Alvarez-Venegas, Phillip San-Miguel, Olga Danilevskaya, Zoya Avramova

School of Biological Sciences: Faculty Publications

The finding in animal species of complexes homologous

to the products of six Saccharomyces cerevisiae

genes, origin of replication recognition

complex (ORC), has suggested that ORC-related

mechanisms have been conserved in all eukaryotes.

In plants, however, the only cloned putative homologs

of ORC subunits are the Arabidopsis ORC2 and

the rice ORC1. Homologs of other subunits of plant

origin have not been cloned and characterized. A

striking observation was the absence from the

Arabidopsis genome of an obvious candidate genehomolog

of ORC4. This fact raised compelling

questions of whether plants, in general, and

Arabidopsis, in particular, may have lost the …

Hyperthermophilic Alpha-Glucosidase Gene And Its Use, Paul Blum

School of Biological Sciences: Faculty Publications

Recombinant, thermostable alpha-glucosidases from archaeal micro-organisms and isolated DNA encoding for such alpha-glucosidases are provided. The isolated DNA is obtained by use of DNA or antibody probes prepared from the DNA encoding S. sulfataricus alpha-glucosidase. Also provided are methods for producing recombinant archaeal thermostable alpha-glucosidase and transformants incorporating thermostable alpha-glucosidase. Autoprocessing of plant tissue through the use of transgenic thermostable glycosyl hydrolases is described.

Dynamic Versus Instantaneous Models Of Diet Choice, Brian O. Ma, Peter A. Abrams, Chad Brassil

School of Biological Sciences: Faculty Publications

We investigate the dynamics of a series of two-prey-one predator models in which the predator exhibits adaptive diet choice based on the different energy contents and/or handling times of the two prey species. The predator is efficient at exploiting its prey and has a saturating functional response; these two features combine to produce sustained population cycles over a wide range of parameter values. Two types of models of behavioral change are compared. In one class of models (“instantaneous choice”), the probability of acceptance of the poorer prey by the predator instantaneously approximates the optimal choice, given current prey densities. In …