Biology Commons^™

Use Of Phylogenetic Stains To Determine The Feeding Preferences Of Microbivorous Soil Nematodes, E. Harlan Michelle

Honors Theses

Due to their numerous and diverse roles in soil ecological processes – most notably decomposition and nutrient mineralization – nematodes have long been recognized as important biotic indicators of soil health (Ekschmitt et al., 2001; Ritz and Trudgill, 1999). The predominate means of assessing the information that these organisms might contain has been through nematode community analyses, a methodology that seeks to convert the vast amount of data regarding features such as diversity, maturity and richness into a series of indices which can be used to evaluate soil health and make comparisons across samples. Performance of these analyses typically involves …

Requirement Of A Plasmid-Encoded Catalase For Survival Of Rhizobium Etli Cfn42 In A Polyphenol-Rich Environment, Alejandro García-De Los Santos, Erika López, Ciro A. Cubillas, K. Dale Noel, Susana Brom, David Romero

Biological Sciences Faculty Research and Publications

Nitrogen-fixing bacteria collectively called rhizobia are adapted to live in polyphenol-rich environments. The mechanisms that allow these bacteria to overcome toxic concentrations of plant polyphenols have not been clearly elucidated. We used a crude extract of polyphenols released from the seed coat of the black bean to simulate a polyphenol-rich environment and analyze the response of the bean-nodulating strain Rhizobium etli CFN42. Our results showed that the viability of the wild type as well as that of derivative strains cured of plasmids p42a, p42b, p42c, and p42d or lacking 200 kb of plasmid p42e was not affected in this environment. …

Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi

Dartmouth Scholarship

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of …

All I Really Needed To Know I Learned During Gastrulation, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Supplemental Protocol For Liana Censuses, Stefan A. Schnitzer, Suzanne Rutishauser, Salomón Aguilar

Biological Sciences Faculty Research and Publications

Lianas affect many aspects of tropical forest dynamics and thus the study of their ecology is critical for a comprehensive understanding of tropical forest ecology. Recently, we initiated a complete census of all lianas ≥1 cm diameter in the 50 ha forest dynamics plot on Barro Colorado Island, Panama using the census protocol developed by Gerwing et al. [Gerwing, J.J., Schnitzer, S.A., Burnham, R.J., Bongers, F., Chave, J., DeWalt, S.J., Ewango, C.E.N., Foster, R., Kenfack, D., Martinez-Ramos, M., Parren, M., Parthasarathy, N., Perez-Salicrup, D.R., Putz, F.E., Thomas, D.W., 2006. A standard protocol for liana censuses. Biotropica 38, 256–261]. This protocol …

Lack Of Pathology In A Triple Transgenic Mouse Model Of Alzheimer’S Disease After Overexpression Of The Anti-Apoptotic Protein Bcl-2, Troy T. Rohn, Veera Vyas, Tatiana Hernandez-Estrada, Kathryn E. Nichol, Lori-Ann Christie, Elizabeth Head

Biology Faculty Publications and Presentations

Alzheimer’s disease (AD) is characterized by the accumulation of plaques containing ß-amyloid (Aß) and neurofibrillary tangles (NFTs) consisting of modified tau. Although Aß deposition is thought to precede the formation of NFTs in AD, the molecular steps connecting these two pathologies is not known. Previous studies have suggested that caspase activation plays an important role in promoting the pathology associated with AD. To further understand the contribution of caspases in disease progression, a triple transgenic Alzheimer’s mouse model overexpressing the anti-apoptotic protein Bcl-2 was generated. Here we show that overexpression of Bcl-2 limited caspase-9 activation and reduced the caspase cleavage …

Mapping Of Forest Alliances And Associations Using Fuzzy Systems And Nearest Neighbor Classifiers, F. Jack Triepke, C. Kenneth Brewer, Daniel M. Leavell, Stephen J. Novak

Biology Faculty Publications and Presentations

The study and management of biological communities depends on systems of classification and mapping for the organization and communication of resource information. Recent advances in remote sensing technology may enable the mapping forest plant associations using image classification techniques. But few areas outside Europe have alliances and associations described in detail sufficient to support remote sensing-based modeling. Northwestern Montana has one of the few plant association treatments in the United States compliant with the recently established National Vegetation Classification system. This project examined the feasibility of mapping forest plant associations using Landsat Enhanced Thematic Mapper data and advanced remote sensing …

Dimethylsulfoniopropionate As A Foraging Cue For Reef Fishes, Jennifer L. Debose, Sean C. Lema, Gabrielle A. Nevitt

Biological Sciences

No abstract provided.

Double-Stranded Rna-Activated Protein Kinase Pkr Of Fishes And Amphibians: Varying The Number Of Double-Stranded Rna Binding Domains And Lineage-Specific Duplications, Loubna Tazi, Stefan Rothenburg, Nikolaus Deigendesch, Madhusudan Dey, Thomas E. Dever

Faculty Publications

Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. Results- Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of …

Rotation Of Visual Landmark Cues Influences The Spatial Response Profile Of Hippocampal Neurons In Freely-Moving Homing Pigeons, Gerald E. Hough, Vernon P. Bingman

College of Science & Mathematics Departmental Research

Pigeon hippocampal neurons display two spatial response profiles: location fields frequently at goals, and path fields connecting goals. We recorded from 15 location and six path cells, with color cues positioned near four goal locations. Following color cue rotation, most location cells (12/15) shifted their response fields; path cells (5/6) lost their fields. Therefore, local visual cues can independently define a reference frame for location cells, but path cells may be more broadly tuned to context or alternative reference frames.

Obestatin Inhibits Vasopressin Secretion: Evidence For A Physiological Action In The Control Of Fluid Homeostasis, Willis K. Samson, Gina L.C. Yosten, Jaw Kang Chang, Alastair V. Ferguson, Meghan M. White

Biological Sciences Faculty Research & Creative Works

Obestatin, a product of post-translational processing of the ghrelin prohormone, has been reported to act in the brain to inhibit thirst. We extended our initial studies on water drinking by examining the effects of obestatin on hypovolemia-induced water and saline drinking and vasopressin release in male rats. Intracerebroventricular administration of obestatin significantly inhibited water, but not saline (0-3 M NaCl) drinking in response to a hypovolemic challenge. Obestatin also inhibited, in a dose-related fashion, dehydration-induced vasopressin secretion without affecting plasma oxytocin levels. Vasopressin release induced by central angiotensin II administration was attenuated significantly by prior administration of obestatin. Finally, central …

Phospholipase Dα3 Is Involved In The Hyperosmotic Response In Arabidopsis, Xuemin Wang, Yueyun Hong, Xiangqing Pan, Ruth Welti

Biology Department Faculty Works

Rapid activation of phospholipase D (PLD), which hydrolyzes membrane lipids to generate phosphatidic acid (PA), occurs under various hyperosmotic conditions, including salinity and water deficiency. The Arabidopsis thaliana PLD family has 12 members, and the function of PLD activation in hyperosmotic stress responses has remained elusive. Here, we show that knockout (KO) and overexpression (OE) of previously uncharacterized PLDα3 alter plant response to salinity and water deficit. PLDα3 uses multiple phospholipids as substrates with distinguishable preferences, and alterations of PLDα3 result in changes in PA level and membrane lipid composition. PLDα3-KO plants display increased sensitivities to salinity and water deficiency …

Indirect Effects And Traditional Trophic Cascades: A Test Involving Wolves, Coyotes, And Pronghorn, Kim Murray Berger, Eric M. Gese, Joel Berger

Biological Sciences Faculty Publications

The traditional trophic cascades model is based on consumer - resource interactions at each link in a food chain. However, trophic-level interactions, such as mesocarnivore release resulting from intraguild predation, may also be important mediators of cascades. From September 2001 to August 2004, we used spatial and seasonal heterogeneity in wolf distribution and abundance in the southern Greater Yellowstone Ecosystem to evaluate whether mesopredator release of coyotes ( Canis latrans), resulting from the extirpation of wolves ( Canis lupus), accounts for high rates of coyote predation on pronghorn ( Antilocapra americana) fawns observed in some areas. Results of this ecological …

Riding The Wave: Reconciling The Roles Of Disease And Climate Change In Amphibian Declines, Michael W. Sears, Karen R. Lips, Jay Diffendorfer, Joseph R. Mendelson

Publications

Once introduced, diseases may spread quickly through new areas, infecting naive host populations, such as has been documented in Ebola virus in African primates or rabies in North American mammals. What drives the spread of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, is of particular concern because it has contributed to the global
decline of amphibians. We modeled the spatiotemporal pattern of the loss of upland amphibian populations in Central and South America as a proxy for the arrival of Bd and found that amphibian declines in Central and South America are best explained by Bd spreading through …

Giant African Snail, Achatina Fulica, As A Snail Predator, Wallace Meyer, Kenneth Hayes, Amanda Meyer

Department of Biology Faculty Publications

Individuals of Achatina fulica (Bowdich, 1822) were observed preying on veronicellid slugs at two sites on the island of Oahu, Hawaii. As such, the presence of A. fulica may pose a greater threat to terrestrial mollusc conservation than previously imagined. It is our hope that this note provides some impetus for other researchers to explore the possible predation impacts of introduced populations of A. fulica and to consider the possibility that other introduced snails and slugs may be having as yet unforeseen or unnoticed impacts.

Darwin's Gift To Science And Religion, Michael Dietrich

Dartmouth Scholarship

Review of Darwin's Gift to Science and Religion by Francisco Ayala, 2007.

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 …

Peer Review In An Undergraduate Biology Curriculum: Effects On Students’ Scientific Reasoning, Writing And Attitudes, Briana Eileen Timmerman

Faculty Publications

Scientific reasoning and writing skills are ubiquitous processes in science and therefore common goals of science curricula, particularly in higher education. Providing the individualized feedback necessary for the development of these skills is often costly in terms of faculty time, particularly in large science courses common at research universities. Past educational research literature suggests that the use of peer review may accelerate students’ scientific reasoning skills without a concurrent demand on faculty time per student. Peer review contains many elements of effective pedagogy such as peer-peer collaboration, repeated practice at evaluation and critical thinking, formative feedback, multiple contrasting examples, and …

A Songbird Forebrain Area Potentially Involved In Auditory Discrimination And Memory Formation, Raphael Pinaud, Thomas A. Terleph

Biology Faculty Publications

Songbirds rely on auditory processing of natural communication signals for a number of social behaviors, including mate selection, individual recognition and the rare behavior of vocal learning - the ability to learn vocalizations through imitation of an adult model, rather than by instinct. Like mammals, songbirds possess a set of interconnected ascending and descending auditory brain pathways that process acoustic information and that are presumably involved in the perceptual processing of vocal communication signals. Most auditory areas studied to date are located in the caudomedial forebrain of the songbird and include the thalamo-recipient field L (subfields L1, L2 and L3), …

Geographic Variation In Adult Survival And Reproductive Tactics Of The Mosquito Aedes Albopictus, Paul T. Leisnham, L M. Sala, Steven A. Juliano

Faculty Publications – Biological Sciences

Climate differences across latitude can result in seasonal constraints and selection on life history characters. Since Aedes albopictus (Skuse) invaded North America in the mid-1980s, it has spread across a range of approximate to 14 degrees latitude and populations in the north experience complete adult mortality due to cold winter temperatures that are absent in the south. Life table experiments were conducted to test for differences in the adult survival and reproductive schedules of Ae. albopictus females from two populations from the northern (Bloomington, IN [BL] and Manassas, VA [VA]; approximate to 39 degrees N) and southern (Tampa, FL and …

Broadly Sampled Multigene Trees Of Eukaryotes, Hwan Su Yoon, Jessica Grant, Yonas I. Tekle, Min Wu, Benjamin C. Chaon, Jeffrey C. Cole, John M. Logsdon, David J. Patterson, Debashish Bhattacharya, Laura A. Katz

Biological Sciences: Faculty Publications

Background. Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which …

Variation In Molybdenum Content Across Broadly Distributed Populations Of Arabidopsis Thaliana Is Controlled By A Mitochondrial Molybdenum Transporter (Mot1), Ivan Baxter, Balasubramaniam Muthukumar, Hyeong Cheol Park, Peter Buchner, Brett Lahner, John Danku, Keyan Zhao, Joohyun Lee, Malcolm J. Hawkesford, Mary Lou Guerinot, David E. Salt

Dartmouth Scholarship

Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by variation in a mitochondrially localized transporter (Molybdenum Transporter 1 - MOT1) that belongs to the sulfate transporter superfamily. A deletion in the MOT1 promoter is strongly associated with low shoot Mo, occurring in seven of the accessions with the lowest shoot content of Mo. Consistent with the low Mo phenotype, MOT1 expression in low Mo accessions …

Construction, Alignment And Analysis Of Twelve Framework Physical Maps That Represent The Ten Genome Types Of The Genus Oryza, Hyeran Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip Sanmiguel, James C. Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Luis Goicoechea, Lincoln Stein, Doreen Ware, Scott A. Jackson, Carol Soderlund, Rod A. Wing

Biology Faculty Articles

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

Acid-Sensing Ion Channels Interact With And Inhibit Bk K+ Channels, Elena Petroff, Margaret P. Price, Vladislav Snitsarev, Huiyu Gong, Victoria Korovkina, Francois M. Abboud, Michael J. Welsh

Department of Biology Faculty Scholarship and Creative Works

Acid-sensing ion channels (ASICs) are neuronal non-voltage-gated cation channels that are activated when extracellular pH falls. They contribute to sensory function and nociception in the peripheral nervous system, and in the brain they contribute to synaptic plasticity and fear responses. Some of the physiologic consequences of disrupting ASIC genes in mice suggested that ASIC channels might modulate neuronal function by mechanisms in addition to their H+-evoked opening. Within ASIC channel's large extracellular domain, we identified sequence resembling that in scorpion toxins that inhibit K+ channels. Therefore, we tested the hypothesis that ASIC channels might inhibit K+ channel function by coexpressing …

Nuclear Polyglutamine-Containing Protein Aggregates As Active Proteolytic Centers, Min Chen, Lena Singer, Andrea Scharf, Anna Von Mikecz

Biological Sciences Faculty Research & Creative Works

Protein aggregates and nuclear inclusions (NIs) containing components of the ubiquitin-proteasome system (UPS), expanded polyglutamine (polyQ) proteins, and transcriptional coactivators characterize cellular responses to stress and are hallmarks of neurodegenerative diseases. The biological function of polyQ-containing aggregates is unknown. To analyze proteasomal activity within such aggregates, we present a nanoparticle (NP)-based method that enables controlled induction of sodium dodecyl sulfate-resistant inclusions of endogenous nuclear proteins while normal regulatory mechanisms remain in place. Consistent with the idea that the UPS maintains quality control, inhibition of proteasomal proteolysis promotes extra large protein aggregates (1.4-2 μm), whereas formation of NP-induced NIs is found …

Louis Pasteur’S Views On Creation, Evolution, And The Genesis Of Germs, Alan L. Gillen, Frank Sherwin

Faculty Publications and Presentations

“There is no remembrance of men of old, and even those who are yet to come will not be remembered by those who follow.” Ecclesiastes 1:11 (NIV)

In past years revisionist historians have been rewriting the worldview of Christians who have made some of the major discoveries in biology and medicine. It appears that postmodern revisionists are rewriting history to support their agenda of a more “secular” explanation to science. The Judeo-Christian worldview is not politically correct in most universities. This is true in regard to past scientists such as Louis Pasteur who believed in creation. According to reliable, primary …

Effect Of Thyroid Hormone Concentration On The Transcriptional Response Underlying Induced Metamorphosis In The Mexican Axolotl (Ambystoma), Robert B. Page, Stephen R. Voss, Amy K. Samuels, Jeramiah J. Smith, Srikrishna Putta, Christopher K. Beachy

Biology Faculty Publications

Background

Thyroid hormones (TH) induce gene expression programs that orchestrate amphibian metamorphosis. In contrast to anurans, many salamanders do not undergo metamorphosis in nature. However, they can be induced to undergo metamorphosis via exposure to thyroxine (T₄). We induced metamorphosis in juvenile Mexican axolotls (Ambystoma mexicanum) using 5 and 50 nM T₄, collected epidermal tissue from the head at four time points (Days 0, 2, 12, 28), and used microarray analysis to quantify mRNA abundances.

Results

Individuals reared in the higher T₄ concentration initiated morphological and transcriptional changes earlier and completed metamorphosis by …

A Synaptic Basis For Auditory-Vocal Integration In The Songbird, Eric E. Bauer, Melissa J. Coleman, Todd F. Roberts, Arani Roy, Jonathan F. Prather, Richard Mooney

WM Keck Science Faculty Papers

Songbirds learn to sing by memorizing a tutor song that they then vocally mimic using auditory feedback. This developmental sequence suggests that brain areas that encode auditory memories communicate with brain areas for learned vocal control. In the songbird, the secondary auditory telencephalic region caudal mesopallium (CM) contains neurons that encode aspects of auditory experience. We investigated whether CM is an important source of auditory input to two sensorimotor structures implicated in singing, the telencephalic song nucleus interface (NIf) and HVC. We used reversible inactivation methods to show that activity in CM is necessary for much of the auditory-evoked activity …

Isolation And Characterization Of Vibrio Tubiashii Outer Membrane Proteins And Determination Of A Toxr Homolog, Broderick Eribo

Department of Biology Faculty Publications

Outer membrane proteins (OMPs) expressed by Vibrio tubiashii under different environmental growth conditions were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and PCR analyses. Results showed the presence of a 38- to 40-kDa OmpU-like protein and ompU gene, a maltoporin-like protein, several novel OMPs, and a regulatory toxR homolog.

A New Species Of Giant Sengi Or Elephant-Shrew (Genus Rhynchocyon) Highlights The Exceptional Biodiversity Of The Udzungwa Mountains Of Tanzania, F Rovero, G B. Rathbun, A Perkin, T Jones, David O. Ribble, C Leonard, R R. Mwakisoma, N Doggart

Biology Faculty Research

A new species of sengi, or elephant-shrew, is described. It was discovered in the northern Udzungwa Mountains of Tanzania in 2005. Sengis (Order Macroscelidea, super-cohort Afrotheria) include four genera and 15 species of mammals that are endemic to Africa. This discovery is a significant contribution to the systematics of this small order. Based on 49 camera trap images, 40 sightings and five voucher specimens, the new sengi is diurnal and distinguished from the other three species of Rhynchocyon by a grizzled grey face, pale yellow to cream chest and chin, orange-rufous sides, maroon back and jet-black lower rump and thighs. …