Biology Commons^™

Bacterial Endophytes Enhance Competition By Invasive Plants, Marnie E. Rout, Thomas H. Chrzanowski, Tara K. Westlie, Thomas H. Deluca, Ragan M. Callaway, William E. Holben

Biological Sciences Faculty Publications

• Premise of the study: Invasive plants can alter soil microbial communities and profoundly alter ecosystem processes. In the invasive grass Sorghum halepense, these disruptions are consequences of rhizome-associated bacterial endophytes. We describe the effects of N₂-fixing bacterial strains from S. halepense (Rout and Chrzanowski, 2009) on plant growth and show that bacteria interact with the plant to alter soil nutrient cycles, enabling persistence of the invasive.
• Methods: We assessed fluxes in soil nutrients for ~4 yr across a site invaded by S. halepense. We assayed the N₂-fixing bacteria in vitro for phosphate solubilization, …

Review Of Report On The “Status Of Nearshore Finfish Stocks In South-Western Western Australia: Australian Herring And Tailor”, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Serdemetan Antagonizes The Mdm2-Hif1Α Axis Leading To Decreased Levels Of Glycolytic Enzymes, Allan R. Albig

Biology Faculty Publications and Presentations

Serdemetan (JNJ-26854165), an antagonist to Mdm2, was anticipated to promote the activation of p53. While regulation of p53 by Mdm2 is important, Mdm2 also regulates numerous proteins involved in diverse cellular functions. We investigated if Serdemetan would alter the Mdm2-HIF1α axis and affect cell survival in human glioblastoma cells independently of p53. Treatment of cells with Serdemetan under hypoxia resulted in a decrease in HIF1α levels. HIF1α downstream targets, VEGF and the glycolytic enzymes (enolase, phosphoglycerate kinase1/2, and glucose transporter 1), were all decreased in response to Serdemetan. The involvement of Mdm2 in regulating gene expression of glycolytic enzymes raises …

Barrier To Autointegration Factor (Baf) Inhibits Vaccinia Virus Intermediate Transcription In The Absence Of The Viral B1 Kinase, Nouhou Ibrahim, April Wicklund, Augusta Jamin, Matthew S. Wiebe

Nebraska Center for Virology: Faculty Publications

Barrier to autointegration factor (BAF/BANF1) is a cellular DNA-binding protein found in the nucleus and cytoplasm. Cytoplasmic BAF binds to foreign DNA and can act as a defense against vaccinia DNA replication. To evade BAF, vaccinia expresses the B1 kinase, which phosphorylates BAF and blocks its ability to bind DNA. Interestingly, B1 is also needed for viral intermediate gene expression via an unknown mechanism. Therefore, we evaluated the impact of B1-BAF signaling on vaccinia transcription. Strikingly, the decrease in vaccinia transcription caused by loss of B1 can be rescued by depletion of BAF. The repressive action of BAF is greatest …

The Science (And Pseudoscience) Of Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Identification And Characterization Of A Nacl Responsive Genetic Locus Involved In 2 Survival During Desiccation In Sinorhizobium Meliloti, Jan A.C. Vriezen, Frans J. De Bruijn, Klaus R. Nüsslein

Biological Sciences: Faculty Publications

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci …

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

Faculty Work

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

Lost Branches On The Tree Of Life, Bryan T. Drew, Romina Gazis, Patricia Cabezas, Kristen S. Swithers, Jiabin Deng, Roseana Rodriguez, Laura A. Katz, Keith A. Crandall, David S. Hibbett, Douglas E. Soltis

Biological Sciences: Faculty Publications

No abstract provided.

One Step Quick Detection Of Cancer Cell Surface Marker By Integrated Nife-Based Magnetic Biosensing Cell Cultural Chip, Chenchen Bao, Lei Chen, Tao Wang, Chong Le, Furong Tian, Daxiang Cui, Yong Zhou

Articles

RGD peptides has been used to detect cell surface integrin and direct clinical effective therapeutic drug selection. Herein we report that a quick one step detection of cell surface marker that was realized by a specially designed NiFe-based magnetic biosensing cell chip combined with functionalized magnetic nanoparticles. Magnetic nanoparticles with 20-30 nm in diameter were prepared by coprecipitation and modified with RGD-4C, and the resultant RGD-functionalized magnetic nanoparticles were used for targeting cancer cells cultured on the NiFe-based magnetic biosensing chip and distinguish the amount of cell surface receptor-integrin. Cell lines such as Calu3, Hela, A549, CaFbr, HEK293 and HUVEC …

Molecular Characterization Of Tick Salivary Gland Glutaminyl Cyclase, Steven W. Adamson, Rebecca E. Browning, Chien-Chung Chao, Robert C. Bateman Jr., Wei-Mei Ching, Shahid Karim

Faculty Publications

Glutaminyl cyclase (QC) catalyzes the cyclization of N-terminal glutamine residues into pyroglutamate. This post-translational modification extends the half-life of peptides and, in some cases, is essential in binding to their cognate receptor. Due to its potential role in the post-translational modification of tick neuropeptides, we report the molecular, biochemical and physiological characterization of salivary gland QC during the prolonged blood feeding of the black-legged tick (Ixodes scapularis) and the gulf-coast tick (Amblyomma maculatum). QC sequences from I. scapularis and A. maculatum showed a high degree of amino acid identity to each other and other arthropods and …

Effects Of Prolonged Space Flight On Human Skeletal Muscle Enzyme And Substrate Profiles, Robert H. Fitts, Patricia Colloton, Scott Trappe, J. L. Bain, Danny A. Riley

Biological Sciences Faculty Research and Publications

Our primary goal was to determine the effects of 6-mo flight on the International Space Station (ISS) on selected anaerobic and aerobic enzymes, and the content of glycogen and lipids in slow and fast fibers of the soleus and gastrocnemius. Following local anesthesia, biopsies were obtained from nine ISS crew members ∼45 days preflight and on landing day (R+0) postflight. We subdivided the crew into those who ran 200 min/wk or more (high treadmill, HT) in-flight from those who ran /wk (low treadmill, LT). In the LT group, there was a loss of lipid in soleus type I fibers, and …

The Role Of Amp-Activated Protein Kinase In Mouse Oocyte Maturation And Subsequent Egg Activation, Ru Ya

Dissertations (1934 -)

Mammalian oogenesis begins during fetal development. Oocytes enter meiosis and arrest at prophase I before birth. Meiosis resumes after proper hormonal signaling, the oocyte completes meiosis I, and then ovulates in metaphase II, at which stage it arrests until fertilization occurs. Egg activation occurs upon sperm fertilization, which includes various physiological processes including calcium influx, release of cortical granules, and completion of meiosis II. However, egg activation can also occur without fertilization, which compromises the later embryonic development. The developmental period from prophase I to metaphase II is referred as oocyte maturation, and involves crucial dynamic change of the cytoskeleton …

Lost Branches On The Tree Of Life, Bryan T. Drew, Romina Gazis, Patricia Cabezas, Kristen S. Swithers, Jiabin Deng, Roseana Rodriguez, Laura A. Katz, Keith A. Crandall, David S. Hibbett, Douglas E. Soltis

Biology

Until recently, uploading sequences to GenBank (or EMBL) was generally considered sufficient to ensure reproducibility of phylogenetic studies using DNA sequence data. Increasingly, however, the systematics community is realizing that archiving raw DNA sequences is not adequate, and that the underlying alignments of DNA sequences as well as the resulting phylogenetic trees are pivotal for reproducibility, comparative purposes, meta-analyses, and ultimately synthesis. Indeed, there has been a growing clamor for journals to adopt and enforce more rigorous data archiving practices across diverse disciplines [4]–[8]. As a result, about 35 evolutionary journals [5],[9] have adopted policies …

Temporal And Spatial Requirements Of Drop-Dead Expression For Adult Survival In Drosophila Melanogaster, Christine Lynn Sansone

Dissertations (1934 -)

Mutations in the gene drop-dead (drd) cause diverse phenotypes in adult Drosophila melanogaster including early lethality, neurodegeneration, fragile tracheae, gut dysfunction, reduced body mass, and female sterility. The cause of early lethality and the function of the drd protein remain unknown. To elucidate a molecular function of DRD, the temporal and spatial requirements of the drd gene for survival were determined. drd expression was manipulated with the Gal4-UAS system, using UAS-RNAi transgenes and a UAS-drd transgene on a drd mutant background to knock down and rescue expression of drd, respectively.

To investigate the temporal requirements of drd expression for adult …

West Coast Rock Lobster Fishery Ecological Risk Assessment 20 February 2013, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Tonic And Phasic Smooth Muscle Contraction Is Not Regulated By The Pkcα - Cpi-17 Pathway In Swine Stomach Antrum And Fundus, Yu Zhang, Meghan E. Hermanson, Thomas J. Eddinger

Biological Sciences Faculty Research and Publications

Regulation of myosin light chain phosphatase (MLCP) via protein kinase C (PKC) and the 17 kDa PKC-potentiated inhibitor of myosin light chain phosphatase (CPI-17) has been reported as a Ca²⁺ sensitization signaling pathway in smooth muscle (SM), and thus may be involved in tonic vs. phasic contractions. This study examined the protein expression and spatial-temporal distribution of PKCα and CPI-17 in intact SM tissues. KCl or carbachol (CCh) stimulation of tonic stomach fundus SM generates a sustained contraction while the phasic stomach antrum generates a transient contraction. In addition, the tonic fundus generates greater relative force than phasic antrum …

Getting To Evo-Devo: Concepts And Challenges For Students Learning Evolutionary Developmental Biology, Anna Hiatt, Gregory K. Davis, Caleb Trujillo, Mark Terry, Donald P. French, Rebecca M. Price, Kathryn E. Perez, Diane Ebert-May

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

In this study we used surveys of evo-devo experts to identify the core concepts of evo-devo and outline an underlying conceptual framework. We also use interviews and surveys of conceptual difficulties with these concepts.

To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution. Based …

Genomic Investigation Into Strain Heterogeneity And Pathogenic Potential Of The Emerging Gastrointestinal Pathogen Campylobacter Ureolyticus, Susan Bullman, Alan Lucid, Roy D. Sleator, Brigid Lucey, Et. Al.

Department of Biological Sciences Publications

The recent detection and isolation of C. ureolyticus from patients with diarrhoeal illness and inflammatory bowel diseases warrants further investigation into its role as an emerging pathogen of the human gastrointestinal tract. Regarding the pathogenic mechanisms employed by this species we provide the first whole genome analysis of two C. ureolyticus isolates including the type strain. Comparative analysis, subtractive hybridisation and gene ontology searches against other Campylobacter species identifies the high degree of heterogenicity between C. ureolyticus isolates, in addition to the identification of 106 putative virulence associated factors, 52 of which are predicted to be secreted. Such factors encompass …

A Survey Of Reproductive Biology Of Zenarchopterus Dispar In Khanh Hoa Province, Vietnam, Tu Tran, Dr. Mark Belk

Journal of Undergraduate Research

Different selective environments could often predict life-history strategies (sensu Endler 1986). Resource levels of the environments strongly affect fitness and evolutionary stable strategies of species (Patrick and Pierre 1993). Similarly, predators also have a major effect on the life history of fish populations. The fish population from the predator’s area attained maturity at a smaller size, produced more, and smaller offspring relative to populations from predator-free environments (Johnson and Belk 2001).

Assessing The Effects Of Primer Specificity On Eliminating Numt Co-Amplification In Dna Barcoding, Matthew Moulton, Dr. Michael Whiting

Journal of Undergraduate Research

DNA barcoding is a method of species identification based on sequencing a short mitochondrial DNA fragment of Cytochrome Oxidase I (COI). A database of over 500,000 of these COI fragments, known as “barcodes,” has been established for nearly 38,000 species and is currently being used to help rapidly assign individuals to known species and highlight potential new species. However, the ability for DNA barcoding to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be co-amplified with the mitochondrial ortholog when using universal primers, which can lead to incorrect species identification and an overestimation …

Orca Report, Tom Beckstead, Dr. Jack W. Sites Jr.

Journal of Undergraduate Research

Snakes of the Neotropical subfamily Dipsadinae are poorly known from both ecological and phylogenetic perspectives, despite unique feeding adaptations and bizarre diets. Some of these snakes specialize on snails and slugs (ecologists refer to them as “goo eaters”), and they have a unique dentition and jaw structure that permits them to extract gastropod snails from their shells. Others have enlarged rear fangs, are mildly venomous, and prey on ectothermal vertebrates such as frogs, frog eggs, and lizards (Fig. 1).

Estimating Dispersal Of Spring Invertebrates Through Genetic Diversity, Keith Tanner, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The Great Basin contains many closed basins, separated by north-south lying mountain ranges and low east-west lying divides. The Sierra Nevada, on the western edge of the Great Basin, generates a rain shadow, making Nevada the driest state in the nation, with Utah as the second driest. The dryness of the Great Basin makes water a critical resource for life – for both humans and native organisms. As western urban areas have grown, water has become a limiting resource for both urban and rural development

Life Histories Of Brook Trout (Salvelinus Fontinalis) And Their Replacement Of Cutthroat Trout (Oncorhynchus Clarki), Amy Burgess, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The cutthroat trout (Oncorhynchus clarki) is a member of the Salmonid family native to the western North America. Brook trout (Salvelinus fontinalis) is also a member of the salmonid family but a native to eastern North America, but has been introduced into many areas in western North America due to its popularity as a game fish. Observations of the invasion of nonnative brook trout (Salvelinus fontinalis) have often resulted in the replacement of cutthroat trout (Oncorhynchus clarki). While this is the case the underlying reasons for this replacement remain largely unknown (Peterson, 2004). Studies have been conducted looking at ecological …

Whose Legs Are In The Water? Parsing Out Community Composition And Turnover Rates Of Plecoptera, Trichoptera, And Ephemeroptera, Sarah Walker, Dr. C. Riley Nelson

Journal of Undergraduate Research

Many beta diversity indicies, like most analytical tools in ecology, abstract the known relative abundances and species presence into outputs primarily useful for obtaining p-values and little else. Therefore, the purposes of this proposed beta diversity method were to simplify currently used similarity analyses for visualization and quantification of beta diversity, investigate its use in seasonal succession and other gradients in communities, and demonstrate an application of these methods in terms of both taxonomic and functional richness.

Crandall Specimen Collection Database, Mark Valentine, Dr. Keith Crandall

Journal of Undergraduate Research

The goal of this project was to design and implement a database and web-based interface, to store information on the specimens collected for study in the Crandall lab. The creation of a user-friendly centralized database to warehouse the information on all of the specimens studied is anticipated to be of great use to the Crandall Lab.

Stable Isotope Ratios In Leg Hairs A Better Diagnostic Tool For Eating Disorders, Stephanie Lindblad, Beverly Roeder

Journal of Undergraduate Research

Anorexia and bulimia are eating disorders that are extremely harmful and difficult to accurately diagnose. Currently the most frequent methods of diagnosis are subjective interviews and questionnaires. One example of these psychological diagnostic tools is the DSM-IV test, which has some serious problems associated with it. It relies heavily on self-report of patients, which subjects the results to dishonesty. The test is also unable to classify certain patients that do not meet specified characteristics. In addition, the DSM-IV has very limited physiological measures, such as BMI and menstrual status. Thus, the physiological consequences of anorexia and bulimia, including a feedback …

The Influence Of Elevation On The Life History Of Mottled Sculpin, Aaron Fordham, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The Mottled Sculpin Cottus bairdii is found in cool to cold streams, creeks and rivers of northern North America (Page and Burr 1991). Sculpin are a benthic fish, living on the bottoms of the streams and rivers that they occupy. They reach 125 to 200 mm in total length when mature and can grow to 31mm-36mm by autumn of their first year of life (Ludwig and Normen 1969). Very little research has been conducted on the age and growth of C. bairdii and no comparative studies have been done examining the influence of elevation in their growth rates.

Determining And Sharing Knowledge About Phylogenetic Relationships Of Collomia Species (Mountain-Trumpet Flowers), Lisa Busby, Dr. Leigh Johnson

Journal of Undergraduate Research

The plant genus Collomia shows great morphological and genetic diversity, however, its current classification is based on a morphological study done in 1940. This year I was able to assemble a great deal of DNA sequence information and compare the variation in these sequences with previous classifications to begin reevaluating the genus and further define relationships between Collomia species. I have also made a great deal of progress in sharing this data with the general public by helping to construct internet web pages for the Tree of Life Web Project.

Altitudinal And Seasonal Comparison Of Insects In The Riparian Corridor Of The American Fork Canyon, Utah, Elizabeth J. Bankhead, Dr. C. Riley Nelson

Journal of Undergraduate Research

A hot topic in ecology right now is the Mid-Domain Effect (MDE) as presented by Robert K. Colwell (2001). This null model states that the greatest species diversity along an elevation gradient will be found at the incline’s mid-point, if no other environmental gradients interfere. Another hypothesis involving elevation gradients is an abundance null-model created by John Terborgh (1971). The research set forth in this paper seeks to understand abundance and richness along an elevation gradient in a riparian system and help validate MDE.

Does Predator Environment Predict Life History Traits In The Livebearing Fish Poecillia Gillii?, K. Nicole Schoonmaker, Dr. Jerald B. Johnson

Journal of Undergraduate Research

The process of natural selection drives the evolution of species which results in the survival of individuals whose traits are most adaptable to a specific environment and the death of individuals whose traits are less fit. Thus, populations of a single species that reside in habitats with differing environmental pressures can have different physical (phenotypic) or genetic (genotypic) traits. An understanding of the environmental pressures that create variation in traits and observation of that variation is important to understanding the adaptability and evolution of living organisms.