Biology Commons^™

The Holliday Junction In An Inverted Repeat Dna Sequence: Sequence Effects On The Structure Of Four-Way Junctions, Brandt F. Eichman, Jeff Vargason, Blaine H.M. Mooers, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. A sequence comparison with previous …

The Extended And Eccentric E-Dna Structure Induced By Cytosine Methylation Or Bromination, Jeff Vargason, Brandt F. Eichman, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3′-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway …

B2-Adrenergic Receptor Activates Extracellular Signal-Regulated Kinases (Erks) Via The Small G Protein Rap1 And The Serine/Threonine Kinase B-Raf, John M. Schmitt, Philip J. S. Stork

Faculty Publications - Department of Biological & Molecular Science

G protein-coupled receptors can induce cellular proliferation by stimulating the mitogen-activated protein (MAP) kinase cascade. Heterotrimeric G proteins are composed of both a and By subunits that can signal independently to diverse intracellular signaling pathways including those that activate MAP kinases. In this study, we examined the ability of isoproterenol, an agonist of the B2-adrenergic receptor (b2AR), to stimulate extracellular signal-regulated kinases (ERKs). Using HEK293 cells, which express endogenous b2AR, we show that isoproterenol stimulates ERKs via b2AR. This action of isoproterenol requires cAMP-dependent protein kinase and is insensitive to pertussis toxin, suggesting that Gas activation of cAMP-dependent protein kinase …

Cd28 And The Tyrosine Kinase Lck Stimulate Mitogen-Activated Protein Kinase Activity In T Cells Via Inhibition Of The Small G Protein Rap1, Kendall D. Carey, Tara J. Dillon, John M. Schmitt, Allison M. Baird, Amy D. Holdorf, David B. Straus, Andrey S. Shaw, Philip J. S. Stork

Faculty Publications - Department of Biological & Molecular Science

Proliferation of T cells via activation of the T-cell receptor (TCR) requires concurrent engagement of accessory costimulatory molecules to achieve full activation. The best-studied costimulatory molecule, CD28, achieves these effects, in part, by augmenting signals from the TCR to the mitogen-activated protein (MAP) kinase cascade. We show here that TCR-mediated stimulation of MAP kinase extracellular-signal-regulated kinases (ERKs) is limited by activation of the Ras antagonist Rap1. CD28 increases ERK signaling by blocking Rap1 action. CD28 inhibits Rap1 activation because it selectively stimulates an extrinsic Rap1 GTPase activity. The ability of CD28 to stimulate Rap1 GTPase activity was dependent on the …

Interface Between Titanium Miniplate/Screw And Human Calvaria, Kun Hwang, John M. Schmitt, Jeffrey O. Hollinger

Faculty Publications - Department of Biological & Molecular Science

This study demonstrates interfacial changes of titanium miniplate/screw with normal calvaria and nonvascularized calvarial bone graft ensued from craniectomy in a 53-year-old female. In 18 months after operation, a right parietal bone containing an L-shaped miniplate with screws, 5mm long and 2mm in external diameter, was harvested, fixed, and embedded in methylmetacrylate. Fifteen micrometer thick sections were made by an EXAKT cutting-grinding system (Exakt Company, Hamburg, Germany), and reviewed under the bright field light microscope. The mean of the bonecontacting surface ratio (BCSR) in six screwed bone was 64.1%; 69.3% in normal bone, and 60.4% in grafted bone. The trabecular …

Does The Aquatic Salamander, Siren Intermedia, Respond To Chemical Cues From Prey?, Aaron M. Sullivan, Paul W. Frese, Alicia Mathis

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Rana Areolata Circulosa (Northern Crawfish Frog) Vocalization, Paul W. Frese, Aaron M. Sullivan

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Plant Quality And Spider Predation Affects Grasshoppers (Acrididae): Food-Quality-Dependent Compensatory Mortality, Mark A. Oedekoven, Anthony Joern

School of Biological Sciences: Faculty Publications

For insect herbivores, population responses reflect interactions among multiple factors, including abiotic conditions, food plant availability, and biotic interactions guided by food limitation and natural enemies. In this set of field experiments, we evaluated the interactive, dynamic effects of limited food supply and predation from wolf spiders (Lycosidae) on mortality in Ageneotettix deorum, a common grasshopper (Acrididae) from North American sandhills grasslands. We attempted to determine whether the combined effects of food availability and spider predation on mortality were (1) noncompensatory, with the effects of each factor summing to determine ultimate population size, or (2) compensatory, where the effect …

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Genes Classical And Genes Developmental: The Different Uses Of The Gene In Evolutionary Synthesis, Scott F. Gilbert

Biology Faculty Works

Dobzhansky (1964) stated that “Nothing in biology makes sense except in the light of evolution,” and the function of the gene is no exception. The use of genes in population genetics and developmental genetics differs significantly. This is reflected in the roles that genes are postulated to play in evolution. In the Modern Synthesis of population genetics and evolution, genes become manifest by differences in alleles that are active in conferring differential reproductive success in adult individuals. The gene is thought to act as a particulate, atomic unit. In current syntheses of evolution and developmental genetics, important genes are manifest …

A Determination Of Parentage, Mating System, And Genetic Diversity In A Captive Population Of The Straw-Colored Fruit Bat (Eidolon Helvum), Jan Zinck

Dissertations and Theses

Small populations tend to lose genetic variability. The magnitude of this loss is influenced by the number of founding individuals, the genetic diversity of the founders, and the species mating system. Genetic variability is the basis of adaptive evolution, and the loss of genetic variability may have harmful effects on development, growth, and survival. Therefore, a primary management goal for small, captive populations is the retention of genetic variability. Of considerable importance to conservation biology is the determination of parentage, from which mating, genetic, and demographic information can be derived. Microsatellites provide a robust molecular evolutionary tool for the study …

Profiles Of The Highly Invasive Plants In Oregon Including Lists Of Oregon’S Invasive And Naturalized Plants, Rebekah Jane Harper

Dissertations and Theses

The study and control of invasive species are important issues in restoration ecology and land management. Invasive species are among the top contributors to habitat degradation worldwide. Unfortunately, information concerning invasive species and methods for their control is limited and widely scattered throughout the literature.

A comprehensive list of the naturalized and invasive species found in Oregon is important for monitoring invasive and potentially invasive species. It also provides a base of information for people interested in investigating invasive species; however, no such state-wide list existed for Oregon before this work.

Profiles for highly invasive species should provide information concerning …

Dimensionless Invariants For The Optimal Size (Age) Of Sex Change, Eric Charnov, Unnur Skúladóttir

Biology Faculty & Staff Publications

Optimization models have been widely and successfully used in evolutionary ecology to predict the attributes of organisms; perhaps the greatest quantitative success is in the area of sex allocation (sex ratio, sperm versus eggs for hermaphrodites, time as a male [female] for a sex changer), where the fact of having only one mother and one father makes Darwinian fitness a simple product of gain-via-male times gain-via-female. Previous work on sex change used the maximization of this male—female product to successfully predict the direction and age (size) for sex change, and that age has been shown to imply a breeding sex …

Direct And Indirect Effects Of Herbivores On Nitrogen Dynamics: Voles In Riparian Areas, J M. Sirotnak, Nancy J. Huntly

Biology Faculty Publications

Herbivores can directly increase nitrogen mobility by increasing the quality of organic matter entering the decomposition cycle, but they also may decrease nitrogen mobility by decreasing the biomass of high-nitrogen species in the plant community. We assessed effects of voles (Microtus) on nitrogen dynamics using exclosures in two riparian meadows (Crystal Bench and Blacktail Deer Creek) in Yellowstone National Park (USA). At both sites, the quantity of plant litter was decreased by herbivory following a vole population peak in 1992. At Crystal Bench, removal of voles caused a decrease in the nitrogen concentration and an increase in the C:N ratio …

Detection Of Dna Of Nocturnally Periodic Brugia Malayi In Night And Day Blood Samples By A Polymerase Chain Reaction-Elisa-Based Method Using An Internal Control Dna, Peter U. Fischer, Tanianwati Supali, Heri Wibowo, Insa Bonow, Steven A. Williams

Biological Sciences: Faculty Publications

An internal control was used in a polymerase chain reaction (PCR)–ELISA–based technique to detect the Hha I repeat of the filarial parasite Brugia malayi. A single microfilaria added to 200 �l of blood was reliably detected. The assay was evaluated on field samples from persons living in an area endemic for Anopheles-transmitted, nocturnally periodic B. malayi in central Sulawesi, Indonesia. Examination of night blood of 138 individuals for the presence of microfilariae by filtration revealed 44 microfilaria carriers. All microfilaria carriers were also positive in the PCR-ELISA and, in addition, 14 more samples were proven to contain parasite DNA. The …

Multiplex Pcr Detection Of Aac(3)Via And Aac(3)Iia Gentamicin Resistance Genes In Bacteria Isolated From Turtle Farms, Hilary Haines

Honors Capstones

No abstract provided.

Egg-Derived Proteases As A Block To Polyspermy In The Eggs Of The Freshwater Mussel, Dreissena Polymorpha, Alicia Kay Smith Wysong

Honors Capstones

No abstract provided.

Theories Of The Origin And Early Evolution Of Life, David A. Dewitt

Faculty Publications and Presentations

After the theory of spontaneous generation was discredited, only religious explanations were offered to explain the origin of life. Alexander Oparin (1894-1980), an atheist, suggested that natural chemical reactions produced biological molecules that came together to form the first living thing. Later, Stanley Miller tested this hypothesis and produced chemical "building blocks" but not life itself. In spite of much progress, there is still no clear consensus on how life originated on Earth. Some scientists are even looking to outer space for the origin of life.

Relationship Between Pea Crab (Pinnotheres Maculatus) Parasitism And Gonad Mass Of The Bay Scallop (Argopecten Irradians), Paul A.X. Bologna, Kenneth L. Heck

Department of Biology Faculty Scholarship and Creative Works

We investigated the prevalence of pea crabs (Pinnotheres maculatus) in bay scallops (Argopecten irradians) from 1994 through 1996 in a scallop population from St. Joseph Bay, Florida. We also assessed their impacts on scallop reproductive potential. Our results showed that prevalence in bay scallops varied between 0 and 20% and were extremely low during 1996 (< 2%). Comparing Gonadal-Somatic Indices (GSI) between infested and non-infested bay scallops in samples assessed the impact of pinnotherid parasitism. Results showed that GSI was significantly reduced in infested individuals compared to non-infested individuals of the same size range (t₁₂ = 2.3, P < 0.04). These results suggest that P. maculatus infestation may lower the reproductive potential of individual scallops, but the low rates of parasitism may only minimally impact the host population.

A Rapid, Simple & Inexpensive Experiment In Gel Filtration Chromatography, Roger Sauterer, Jody Jones

Research, Publications & Creative Work

We have developed a simple and inexpensive experiment using gel filtration chromatography that can be performed in less than 90 minutes. This procedure not only provides students with hands-on experience in both the preparation and use of chromatography columns, but also uses colored molecules to provide dramatic visual confirmation of the process of size-exclusion chromatography. Additionally, the column can be calibrated using molecules of known molecular weights and can then be used to estimate the molecular weights of unknown samples. Our gel filtration experiment costs only a fraction of that of commercially marketed laboratory exercises. A basic understanding of methods …

Scientific Investigation Of The Plant Pathogen Agrobacterium Tumefaciens, Casey M. Flanagan, Christopher B. Crowell Ii, Bryan P. Markelz

Honors Theses

A. tumefaciensis a plant pathogen and causative agent of Crown Gall Disease, an ailment that results in the development of tumors in plants. It is a unique organism in that it is the only known non-viral pathogen that transfers its DNA into the host cell. Consequently, the majority of the research conducted on A. tumefaciensinvestigates its mechanism of infection. However, A. tumefaciensis also rare to the bacterial world in that its genome is comprised of two chromosomes: one circular and one linear. Most other bacteria only have one circular chromosome. This area of research has been grossly overlooked and therefore …

Phenotypic Effects Of Leptin In An Ectotherm: A New Tool To Study The Evolution Of Life Histories And Endothermy?, Peter H. Niewiarowski

Biology Faculty Research

Leptin is a hormone that regulates energy expenditure and body mass in mammals, and it has attracted considerable attention because of its potential in treating human obesity. Comprehensive data from both pathological and non-pathological systems strongly support a role for leptin in regulating energy metabolism, in thermoregulation and in regulating the onset of puberty. We report here that daily injections of recombinant murine leptin in fence lizards (Sceloporus undulatus) produce phenotypic effects similar to those observed when leptin injections are given to mice, Lizards injected with leptin had body temperatures 0.6 degrees C higher, ate 30 % less food and …

Effect Of Spaceflight On The Maximal Shortening Velocity, Morphology, And Enzyme Profile Of Fast- And Slow-Twitch Skeletal Muscle Fibers In Rhesus Monkeys, Robert H. Fitts, Janell Romatowski, Lourdes De La Cruz, Jeffrey J. Widrick, Dominique Desplanches

Biological Sciences Faculty Research and Publications

No abstract provided.

Prevention Of Hydrogen Peroxide And Cisplatininduced Apoptosis By Intracellular Catalaseoverexpression, H. Barbaros Oral, Andrew J.T. George, Dorian O. Haskard

Turkish Journal of Biology

Apoptosis induced by hydrogen peroxide (H_2O_2 ) was investigated in Chinese hamster ovarian (CHO) cells, and compared to apoptosis induced by cisplatin (25 µM), a well-established apoptosis-inducing agent. In preliminary experiments, CHO cells were treated with low concentrations of H_2O_2 (250-500 µM) continuously or for 3 hours, followed by washing and further incubation in complete growth medium for 1-10 days. Fluorescence microscopy of acridine orange-stained cells indicated morphological changes of apoptosis. Similar changes were observed in cisplatin-treated cells. DNA-laddering also revealed that DNA fragmentation occurred in both adherent and non-adherent cells by day 2. To prevent H_2O_2 -mediated apoptosis, the …

Nonspecific Esterase Patterns Of Rattus Norvegicus(Berkenhout, 1769) In Western Turkey, Reyhan Çolak, Nuri̇ Yi̇ği̇t, Ercüment Çolak, Mustafa Sözen, Şaki̇r Özkurt

Turkish Journal of Biology

Nonspecific esterases in the muscle, heart, kidney and liver tissues of wild rats (Rattus norvegicus) were examined by horizontal starch gel electrophoresis. Zymogram bands corresponding to Es-10 and Es-4 in the muscle, heart, kidney and liver homogenates, Es-3 and Es-17 in the kidney and liver, Es-18 in the liver tissue, Es-15 in kidney and liver, Es-2 in the muscle and heart, Es-16 in the heart tissue were detected. These findings showed that nonspecific esterases are very polymorphic and tissue-specific, and are not of taxonomic importance for the populations of Rattus norvegicus.

Cultural Characteristics Of Morchella Esculentamycelium On Some Nutrients, Peri̇han Güler, Oğuz Arkan

Turkish Journal of Biology

The cultural characteristics of Morchella esculenta mycelium were investigated in potato dextrose agar, malt extract agar and complete medium yeast plates prepared with casein (cas), Casamino Acids (caa), peptone (p) and sodium nitrate (NaNO 3 ). Aerial and vegetative mycelium types were determined in the agar media with cas, caa and p. The third colonial characteristic was observed in the agar media with NaNO 3 . In this media, a colonization increase in circular forms spreading from the centre to the edges was determined. Mycelium colonization periods were 20-24 days in agar media with NaNO 3 .

Isolation, Identification And Toxigenic Tests Of Aeromonas Hydrophila From Several Sources In Izmir, Ataç Uzel, Füsun Uçar

Turkish Journal of Biology

A total of 43 samples (4 sea water, 5 water, 4 river water, 10 oyster and 10 fish samples) from Izmir were examined for the presence of Aeromonas hydrophila. Alkaline peptone Water (APW) for the environmental samples and Trypticase Soy Broth with Ampicillin and Toluidine Blue (TSBA) for the food samples were used for enrichment of the samples. In isolation, 5 different selective media were used: DNase Agar with Toluidine blue and Ampicillin (DNTA), Aeromonas Agar (AA), Rimler Shotts Agar (RSA), mA Agar and Aeromonas Mediums Base (AMB). Identification of the isolates was performed according to Bergey's Manual of Determinative …

Characterizing The Role Of Mapk Phosphates In Plants, Laura Asakura

Honors Theses

Mitogen Activated Protein Kinase (MAPK) pathways e ubiquitous ongst eukaryotes, involved in the signal transduction of various external stimuli to the nucleus. In plants, only MAPK pathways related to pathogen- and stress-related responses have been identified. It has been proposed that another MAPK pathway exists in plants, one that is similar to animal MAPK pathways and postulated to connect the regulation of cell growth and the actions of hormones auxin, cytokinin, and gibberellin. In order to establish whether a link exists between the MAPK pathway and hormone signaling in plants, the role of MAPK phosphatases (MKP) on hormone signaling was …

Temporal And Spatial Variations In Macrofouling Of Silicone Fouling-Release Coatings, Christina Darkangelo Wood, Kathryn Truby, Judith Stein, Deborah Wiebe, Eric Holm, Dean Wendt, Celia Smith, Christopher Kavanagh, Jean Montemarano, Geoff Swain, Anne Meyer

Biological Sciences

Nontoxic, low surface free energy silicone coatings having reduced biofouling adhesion strength have been developed as an alternative to antifouling paints. Silicone coatings permit macrofouling to adhere; however, fouling can be removed easily by water pressure or light scrubbing. One of the current methods used to evaluate the performance of non-toxic silicone fouling-release coatings relies heavily on fouling coverage. The organismal community structure as well as total coverage can affect the ease of fouling removal from these coatings. This paper explores fouling coverage and organismal adhesion over time. Long-term fouling coverage data were collected at four sites (in Massachusetts, Hawaii …

Richard Goldschmidt And The Crossing-Over Controversy, Michael Dietrich, Marsha Richmond

Dartmouth Scholarship

This book, Perspectives on Genetics, collects more than 100 of these essays, which cumulatively are a history of modern genetics research and its continuing evolution.