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The Effect Of Plant Source Location On Restoration Success: A Reciprocal Transplant Experiment With Winterfat (Krascheninnikovia Lanata), Melanie G. Barnes

Biology ETDs

It is increasingly important that plant propagules used in revegetation projects are from a location that is geographically or ecologically similar to the planting site. To better understand the consequences of using non-local plant materials, I chose to study the population biology of the widespread shrub winterfat (Krascheninnikovia lanata, Chenopodiaceae) among five populations in New Mexico, USA. Winterfat plant morphology among the five populations was compared, and the rate of emergence and floral onset was measured in a greenhouse common garden. A reciprocal transplant experiment was planted in which individuals from different locations were planted in replicate common gardens. Transplant …

Statistical Methods In Microarrays And High-Throughput Flow Cytometry, Osorio Meirelles

Biology ETDs

Abstract-I

Background: Heterogeneous cell populations have previously been described as noisy. However, recent studies have demonstrated that heterogeneity can be biologically significant. We present here an approach for rapid and complete identification of heterogeneous cell populations from high-throughput flow cytometry data. We have developed a novel measure Slope Differentiation Identification (SDI) using flow cytometry-based protein expression, quantifying the rate of change in protein expression between two conditions (exponential and stationary phase) of yeast cells, as a function of cell size or cell granularity.

Results: SDI had superior Gene Ontology enrichment when compared with other approaches such as k-means clustering and …

Proteomic Analysis Of Blastema Formation In Regenerating Axolotl Limbs, Nandini Rao, Deepali Jhamb, Derek J. Milner, Bingbing Li, Fengyu Song, Mu Wang, S. Randal Voss, Mathew Palakal, Michael W. King, Behnaz Saranjami, Holly L.D. Nye, Jo Ann Cameron, David L. Stocum

Biology Faculty Publications

BACKGROUND: Following amputation, urodele salamander limbs reprogram somatic cells to form a blastema that self-organizes into the missing limb parts to restore the structure and function of the limb. To help understand the molecular basis of blastema formation, we used quantitative label-free liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS)-based methods to analyze changes in the proteome that occurred 1, 4 and 7 days post amputation (dpa) through the mid-tibia/fibula of axolotl hind limbs.

RESULTS: We identified 309 unique proteins with significant fold change relative to controls (0 dpa), representing 10 biological process categories: (1) signaling, (2) Ca2+ binding and translocation, (3) transcription, …

Prothonotary Warbler (Protonotaria Citrea) Plumage As An Indicator For Infection: The Relationship Between Haemosporidia Infection And Breast Feather Reflectance In A Neotropical Migrant Passerine, Robert Fithian

Theses and Dissertations

Yellow avian plumage is a direct result of carotenoid pigments obtained in a bird’s diet and may act as an indicator for individual health, parasite resistance, and status. This study describes breast feather reflectance of adult Prothonotary Warblers (Protonotaria citrea) (n=169), insectivorous Neotropical migrant passerines, throughout the Ultraviolet (UV) and human visible light spectra and examines the relationship between Haemosporidia (pathogen causing Avian Malaria) infection and feather reflectance (n=41). Reflectance was characterized using a Principle Component Analysis evaluating Intensity, Brightness, Hue, UV Intensity, UV Brightness, and UV Chroma. UV and visible light reflectance was higher in birds sampled earlier in …

Ceramide Kinase Regulates Phospholipase C And Phosphatidylinositol 4, 5, Bisphosphate In Phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun

Dartmouth Scholarship

Phosphoinositide-specific phospholipase C (PLC) is a central effector for many biological responses regulated by G-protein-coupled receptors including Drosophila phototransduction where light sensitive channels are activated downstream of NORPA, a PLCbeta homolog. Here we show that the sphingolipid biosynthetic enzyme, ceramide kinase, is a novel regulator of PLC signaling and photoreceptor homeostasis. A mutation in ceramide kinase specifically leads to proteolysis of NORPA, consequent loss of PLC activity, and failure in light signal transduction. The mutant photoreceptors also undergo activity-dependent degeneration. Furthermore, we show that a significant increase in ceramide, resulting from lack of ceramide kinase, perturbs the membrane microenvironment of …

Susceptibility Of Caenorhabditis Elegans To Burkholderia Infection Depends On Prior Diet And Secreted Bacterial Attractants, Vaughn S. Cooper, Wendy A. Carlson, John J. Lipuma

Molecular, Cellular & Biomedical Sciences

The nematode Caenorhabditis elegans may be killed by certain pathogenic bacteria and thus is a model organism for studying interactions between bacteria and animal hosts. However, growing nematodes on prey bacteria may influence their susceptibility to potential pathogens. A method of axenic nematode culture was developed to isolate and quantify interactions between C. elegans and potentially pathogenic strains of the Burkholderia cepacia complex. Studying these dynamics in liquid solution rather than on agar surfaces minimized nematode avoidance behavior and resolved more differences among isolates. Most isolates of B. cenocepacia, B. ambifaria and B. cepacia caused 60-80% mortality of nematodes after …

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Quantifying And Resolving Multiple Vector Transformants In S. Cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, Karl E. Griswold

Dartmouth Scholarship

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the …

Monitoring Heart Function In Larval Drosophila Melanogaster For Physiological Studies, Ann S. Cooper, Kylah E. Rymond, Matthew A. Ward, Easter L. Bocook, Robin L. Cooper

Biology Faculty Publications

We present various methods to record cardiac function in the larval Drosophila. The approaches allow heart rate to be measured in unrestrained and restrained whole larvae For direct control of the environment around the heart another approach utilizes the dissected larvae and removal of the internal organs in order to bathe the heart in desired compounds. The exposed heart also allows membrane potentials to be monitored which can give insight of the ionic currents generated by the myocytes and for electrical conduction along the heart tube. These approaches have various advantages and disadvantages for future experiments that are discussed. …

Indications Of Potential Toxic/Mutagenic Effects Of World Trade Center Dust On Human Lung Cell Cultures, Constantino G. Lambroussis, Barbara D. Soares, Sergio Perez, David Gaipa, Anise L. Elie, Caitlin M. Ament, Fahad T. Rouf, Lotfi M. Bassa, Ann Marie Dilorenzo

Department of Biology Faculty Scholarship and Creative Works

Problem statement: Respiratory complications have been linked with exposure to dust particulates after the tragedy of September 11th, 2001 at the World Trade Center (WTC) site. Approach: The purpose of these experiments was to investigate the extent of cellular damage resulting from WTC dust exposure. Results: This research project was conducted with human lung fibroblast cells exposed to WTC dust. To determine if cell proliferation levels were affected, cultured cells were exposed to WTC dust at various concentrations in simulated physiological stress environments via decreased serum levels. Results indicated that cell proliferation levels decreased as WTC dust concentrations increased. This …

Immunisation With A Multivalent, Subunit Vaccine Reduces Patent Infection In A Natural Bovine Model Of Onchocerciasis During Intense Field Exposure, Benjamin L. Makepeace, Siv Aina Jensen, Sandra J. Laney, Charles K. Nfon, Leo M. Njongmeta, Vincent N. Tanya, Steven A. Williams, Albert E. Bianco, Alexander J. Trees

Biological Sciences: Faculty Publications

Human onchocerciasis, caused by the filarial nematode Onchocerca volvulus, is controlled almost exclusively by the drug ivermectin, which prevents pathology by targeting the microfilariae. However, this reliance on a single control tool has led to interest in vaccination as a potentially complementary strategy. Here, we describe the results of a trial in West Africa to evaluate a multivalent, subunit vaccine for onchocerciasis in the naturally evolved host-parasite relationship of Onchocerca ochengi in cattle. Na ̈ıve calves, reared in fly-proof accommodation, were immunised with eight recombinant antigens of O. ochengi, administered separately with either Freund’s adjuvant or alum. The selected antigens …

Intraspecific Phylogeography Of Cycladenia Humilis (Apocynaceae), Mariana P. Last

Theses and Dissertations

Cycladenia humilis (Apocynaceae) is a rare perennial herb native to western North America and has a fragmented distribution in California, Utah, and Arizona. Populations in Utah and Arizona are federally listed as threatened, while there is no conservation status applied to California populations. Using genetic (three chloroplast and two nuclear DNA loci) and morphological characters, intraspecific variation between populations of C. humilis and current taxonomic conventions were assessed. Nested Clade Phylogeographic Analysis and Bayesian phylogenies were used to assess patterns within C. humilis and supported three main population groupings: a northern California, southern California, and Colorado Plateau group. The northern …

Historical View And Physiology Demonstration At The Nmj Of The Crayfish Opener Muscle, Ann S. Cooper, Robin L. Cooper

Biology Faculty Publications

Here we present some of the key important discoveries made with the opener neuromuscular (NMJ) preparation of crustaceans and illustrate that there is still much to learn from this model preparation. In understanding the history one can appreciate why even today this NMJ still offers a rich playground to address questions regarding pre- and post-synaptic function and plasticity. The viability and ease of access to the terminal for intracellular as well as extracellular electrophysiology and imaging are significant advantages. The mechanisms behind the modulation of vesicular kinetics and fusion within the high- and low-output terminals are begging for investigation. The …

The Importance Of Fallback Foods In Primate Ecology And Evolution, Paul J. Constantino, Barth W. Wright

Biological Sciences Faculty Research

The role of fallback foods in shaping primate ranging, socioecology, and morphology has recently become a topic of particular interest to biological anthropologists. Although the use of fallback resources has been noted in the ecological and primatological literature for a number of decades, few attempts have been made to define fallback foods or to explore the utility of this concept for primate evolutionary biologists and ecologists. As a preface to this special issue of the American Journal of Physical Anthropology devoted to the topic of fallback foods in primate ecology and evolution, we discuss the development and use of the …

Effects Of Participation In Inquiry Science Workshops And Follow-Up Activities On Middle School Science Teachers' Content Knowledge, Teacher-Held Misconceptions, And Classroom Practices, Linda F. Cepeda

Electronic Theses and Dissertations

An important aspect of developing science literacy for all students is developing science-literate teachers. With the implementation of the No Child Left Behind Act, many middle school teachers found themselves in a position where they were no longer qualified to teach middle school science. This study was designed to help science teachers increase their science content knowledge, identify and resolve misconceptions/errors they may have, and assist them in their teaching by providing strategies for inquiry-based teaching, science laboratory exercises, and science equipment.

Teachers enrolled in biology courses offered by the Rocky Mountain Middle School Math and Science Partnership participated in …

Exhaustive Exercise Training Enhances Aerobic Capacity In American Alligator (Alligator Mississippiensis), John Eme, Tomasz Owerkowicz, June Gwalthney, Jason M. Blank, Bryan C. Rourke, James W. Hicks

Biological Sciences

The oxygen transport system in mammals is extensively remodelled in response to repeated bouts of activity, but many reptiles appear to be ‘metabolically inflexible’ in response to exercise training. A recent report showed that estuarine crocodiles (Crocodylus porosus) increase their maximum metabolic rate in response to exhaustive treadmill training, and in the present study, we confirm this response in another crocodilian, American alligator (Alligator mississippiensis). We further specify the nature of the crocodilian training response by analysing effects of training on aerobic [citrate synthase (CS)] and anaerobic [lactate dehydrogenase (LDH)] enzyme activities in selected skeletal muscles, …

Surgical Removal Of Right-To-Left Cardiac Shunt In The American Alligator (Alligator Mississippiensis) Causes Ventricular Enlargement But Does Not Alter Apnoea Or Metabolism During Diving, John Eme, June Gwalthney, Jason M. Blank, Tomasz Owerkowicz, Gildardo Barron, James W. Hicks

Biological Sciences

Crocodilians have complete anatomical separation between the ventricles, similar to birds and mammals, but retain the dual aortic arch system found in all non-avian reptiles. This cardiac anatomy allows surgical modification that prevents right-to-left (R–L) cardiac shunt. A R–L shunt is a bypass of the pulmonary circulation and recirculation of oxygen-poor blood back to the systemic circulation and has often been observed during the frequent apnoeic periods of non-avian reptiles, particularly during diving in aquatic species. We eliminated R–L shunt in American alligators (Alligator mississippiensis) by surgically occluding the left aorta (LAo; arising from right ventricle) upstream and …

The Development And Role Of Peripheral Auditory Structures In Otocinclus Affinis, Sri Kiran Kumar Reddy Botta

Masters Theses & Specialist Projects

Loricariidae is a very diverse family of catfishes found primarily in the Amazon River basin. These catfishes have a unique characteristic feature of having fenestrae (holes) in the skull region (compound pterotic bone) adjacent to their bi-lobed swim bladder. Since the swim bladders and the compound pterotic may act as an external ear for hearing in this taxon, I hypothesized that these swim bladders structures have an acoustical functional in the loricariid Otocinclus affinis. In order to understand the development of these structures in O. affinis, I first monitored the ontogeny of the compound pterotic bone by clearing …

E Unibus Plurum: Genomic Analysis Of An Experimentally Evolved Polymorphism In Escherichia Coli, Margie A. Kinnersley, William E. Holben, Frank Rosenzweig

Biological Sciences Faculty Publications

Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of …

Phylogeography Of The Frog Leptodactylus Validus (Amphibia: Anura): Patterns And Timing Of Colonization Events In The Lesser Antilles, Arley Camargo, W. Ronald Heyer, Rafael O. De Sá

Biology Faculty Publications

The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred 1 million …

Molecular And Chromosomal Evidence For Allopolyploidy In Soybean, Navdeep Gill, Seth Findley, Jason G. Walling, Christian Hans, Jianxin Ma, Jeff Doyle, Gary Stacey, Scott A. Jackson

Biology Faculty Articles

Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled …

Novel Lc8 Mutations Have Disparate Effects On The Assembly And Stability Of Flagellar Complexes, Pinfen Yang, Chun Yang, Maureen Wirschell, Stephanie Davis

Biological Sciences Faculty Research and Publications

LC8 functions as a dimer crucial for a variety of molecular motors and non-motor complexes. Emerging models, founded on structural studies, suggest that the LC8 dimer promotes the stability and refolding of dimeric target proteins in molecular complexes, and its interactions with selective target proteins, including dynein subunits, is regulated by LC8 phosphorylation, which is proposed to prevent LC8 dimerization. To test these hypotheses in vivo, we determine the impacts of two new LC8 mutations on the assembly and stability of defined LC8-containing complexes in Chlamydomonas flagella. The three types of dyneins and the radial spoke are disparately affected …

Cross-Sectional Dating Of Novel Haplotypes Of Herv-K 113 And Herv-K 115 Indicate These Proviruses Originated In Africa Before Homo Sapiens, Aashish Jha, Satish Pillai, Vanessa York, Elizabeth Sharp, Emily Storm, Douglas Wachter, Jeffrey Martin, Steven Deeks, Michael Rosenberg, Douglas Nixon, Keith Garrison

School of Science Faculty Works

The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in African Americans compared with Caucasians (K113 9% and …

My Confidence In Our Creator God, David Steen

Lake Union Herald

No abstract provided.

Microevolution And Macroevolution Are Governed By The Same Processes, Michael Dietrich

Dartmouth Scholarship

This collection of specially commissioned essays puts top scholars head to head to debate the central issues in the lively and fast growing field of philosophy of biology Brings together original essays on ten of the most hotly debated ...

Mapping Of The Saccharomyces Cerevisiae Oxa1-Mitochondrial Ribosome Interface And Identification Of Mrpl40, A Ribosomal Protein In Close Proximity To Oxa1 And Critical For Oxidative Phosphorylation Complex Assembly, Lixia Jia, Jasvinder Kaur, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The Oxa1 protein plays a central role in facilitating the cotranslational insertion of the nascent polypeptide chains into the mitochondrial inner membrane. Mitochondrially encoded proteins are synthesized on matrix-localized ribosomes which are tethered to the inner membrane and in physical association with the Oxa1 protein. In the present study we used a chemical cross-linking approach to map the Saccharomyces cerevisiae Oxa1-ribosome interface, and we demonstrate here a close association of Oxa1 and the large ribosomal subunit protein, MrpL40. Evidence to indicate that a close physical and functional relationship exists between MrpL40 and another large ribosomal protein, the Mrp20/L23 protein, is …

Influx Of Calcium Through L-Type Calcium Channels In Early Postnatal Regulation Of Chloride Transporters In The Rat Hippocampus, Jennifer Grace Bray, Michelle Mynlieff

Biological Sciences Faculty Research and Publications

During the early postnatal period, GABA_B receptor activation facilitates L-type calcium current in rat hippocampus. One developmental process that L-type current may regulate is the change in expression of the K⁺Cl⁻ co-transporter (KCC2) and N⁺K⁺2Cl⁻ co-transporter (NKCC1), which are involved in the maturation of the GABAergic system. The present study investigated the connection between L-type current, GABA_B receptors, and expression of chloride transporters during development. The facilitation of L-type current by GABA_B receptors is more prominent in the second week of development, with the highest percentage of cells exhibiting …

Camp Pulsing Of Denuded Mouse Oocytes Increases Meiotic Resumption Via Activation Of Amp-Activated Protein Kinase, Jing Chen, Maggie M. Chi, Kelle H. Moley, Stephen M. Downs

Biological Sciences Faculty Research and Publications

cAMP plays a critical role in the control of oocyte maturation, as a high level of cAMP maintains oocyte arrest at the first meiotic prophase. Yet this study shows that pulsing meiotically arrested denuded oocytes (DO) with cAMP induces oocyte maturation through the activation of AMP-activated protein kinase (PRKA). Short-term (3 h) pulsing of meiotically arrested oocytes with forskolin, an adenyl cyclase (AC) activator, increased oocyte cAMP, led to elevated AMP, and induced oocyte meiotic resumption compared to oocytes continuously cultured in the control medium with or without forskolin. Western analysis showed that germinal vesicle (GV)-stage oocytes after forskolin pulsing …

Circadian Timing Of Food Intake Contributes To Weight Gain, Deanna M. Arble, Joseph Bass, Aaron D. Laposky, Martha H. Vitaterna, Fred W. Turek

Biological Sciences Faculty Research and Publications

Studies of body weight regulation have focused almost entirely on caloric intake and energy expenditure. However, a number of recent studies in animals linking energy regulation and the circadian clock at the molecular, physiological, and behavioral levels raise the possibility that the timing of food intake itself may play a significant role in weight gain. The present study focused on the role of the circadian phase of food consumption in weight gain. We provide evidence that nocturnal mice fed a high‐fat diet only during the 12‐h light phase gain significantly more weight than mice fed only during the 12‐h dark …

Genome 10k: A Proposal To Obtain Whole-Genome Sequence For 10 000 Vertebrate Species, Tony Gamble, Genome 10k Community Of Scientists

Biological Sciences Faculty Research and Publications

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G₁₀KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning …