Biology Commons^™

The Complete Mitochondrial Genome Of The Silver Chub, Macrhybopsis Storeriana, Sarah Gaughan, Robin Johnson, Jun Wang, Michael Wachholtz, Kirk Steffensen, Timothy King, Guoqing Lu

Biology Faculty Publications

The complete mitochondrial genome of the silver chub M. storeriana was determined to be 16,709 bp and contained 22 tRNA genes, 2 rRNA genes and one control region. The whole genome base composition was 30.3% A, 28% T, 25.5% C and 16.2 G. This complete mitochondrial genome provides essential molecular markers for resolving phylogeny and aiding future conservation efforts.

Winter Conditions Influence Biological Responses Of Migrating Hummingbirds, Catherine H. Graham, Sarah R. Supp, Donald R. Powers, Pieter Beck, Marisa C. W. Lim, Anusha Shankar, Scott Goetz, Susan M. Wethington

Faculty Publications - Department of Biological & Molecular Science

Conserving biological diversity given ongoing environmental changes requires the knowledge of how organisms respond biologically to these changes; however, we rarely have this information. This data deficiency can be addressed with coordinated monitoring programs that provide field data across temporal and spatial scales and with process-based models, which provide a method for predicting how species, in particular migrating species that face different conditions across their range, will respond to climate change. We evaluate whether environmental conditions in the wintering grounds of broad-tailed hummingbirds influence physiological and behavioral attributes of their migration. To quantify winter ground conditions, we used operative temperature …

Do Community-Level Models Account For The Effects Of Biotic Interactions? A Comparison Of Community-Level And Species Distribution Modeling Of Rocky Mountain Conifers, Paige E. Copenhaver-Parry, Shannon Albeke, Daniel B. Tinker

Faculty Publications - Department of Biological & Molecular Science

Community-level models (CLMs) aim to improve species distribution modeling (SDM) methods by attempting to explicitly incorporate the influences of interacting species. However, the ability of CLMs to appropriately account for biotic interactions is unclear. We applied CLM and SDM methods to predict the distributions of three dominant conifer tree species in the U.S. Rocky Mountains and compared CLM and SDM predictive accuracy as well as the ability of each approach to accurately reproduce species co-occurrence patterns. We specifically evaluated the performance of two statistical algorithms, MARS and CForest, within both CLM and SDM frameworks. Across all species, differences in SDM …

Flight Mechanics And Control Of Escape Manoeuvres In Hummingbirds. I. Flight Kinematics, Bo Cheng, Bret W. Tobalske, Donald R. Powers, Tyson L. Hedrick, Susan M. Wethington, George T.C. Chiu, Xinyan Deng

Faculty Publications - Department of Biological & Molecular Science

Hummingbirds are nature’s masters of aerobatic manoeuvres. Previous research shows that hummingbirds and insects converged evolutionarily upon similar aerodynamic mechanisms and kinematics in hovering. Herein, we use three-dimensional kinematic data to begin to test for similar convergence of kinematics used for escape flight and to explore the effects of body size upon manoeuvring. We studied four hummingbird species in North America including two large species (magnificent hummingbird, Eugenes fulgens, 7.8 g, and blue-throated hummingbird, Lampornis clemenciae, 8.0 g) and two smaller species (broad-billed hummingbird, Cynanthus latirostris, 3.4 g, and black-chinned hummingbirds Archilochus alexandri, 3.1 g). Starting from a steady hover, …

Development Of New Biological Nanopores And Their Application For Biosensing And Disease Detection, Shaoying Wang

Theses and Dissertations--Pharmacy

Nanopore technology has recently emerged as a new real-time single molecule sensing method. The current dominant technologies, such as mass spectrometry and immunoassay, for protein analysis is still slow and complex, which can’t meet the urgent need and fields of use. Development of a highly simple, portable and sensitive detection system for pathogen detection, disease diagnosis, and environmental monitoring is in great need. Membrane embedded Phi29 connector nanopore, the first protein nanopore coming from bacteriophage, was mainly focusing on DNA and RNA translocation in previous studies. Here, Phi29 connector nanopore was first time established for antibody detection by engineering Epithelial …

Synthetic Functionalized Scaffolds For Culture And Maintenance Of Primary Human Hepatocytes, Douglas Macpherson

Dissertations and Theses

There is deficit in the number of human livers that are available for transplantation. Additionally, there is no reliable model for the liver environment available for laboratory research. Tissue engineering provides alternatives for organ transplantation. We have created a supramolecular biomaterial out of simple peptide and saccharide building blocks to act as a hydrogel scaffold to support culture of liver cells. Using a self-­‐assembling peptide fiber decorated with functional molecules, we were able to culture primary human hepatocytes demonstrate their viability and maintenance of phenotype. The hydrogel material was formed by co-assembly in aqueous buffer and characterized using transmission electron …

Trends And Changes Of Precipitation In Costa Rica, Christopher Rojas

CMC Senior Theses

Measuring and using precipitation data in Costa Rica is a necessary subject matter when one carries out an experiment in this area, whether it be directly related to rainfall or the effects of it on ecosystems. Using geographical information systems (GIS), precipitation maps of Costa Rica were used and digitized to acquire data on where and in what regions precipitation was commonly found. With this information, we were able to track the dry and wet seasons throughout Costa Rica and determine where the precipitation is more likely to occur during certain times of the year. Additionally, trends between longitude, latitude, …

The Effects Of Musical Intervals From Consonant To Dissonant On The Neural Activity Of Earthworms, Charley L. Weaver

Theses and Dissertations

Music is generated through vibrations of a medium creating what is perceived as tone. Two frequencies played simultaneously create intervals, and those ratios of frequencies determine what is consonant and dissonant. Studies have shown a greater neural response in human participants to consonant intervals (Bidelman and Heinz 2011, Bidelman and Krishnan 2009). In this study, the ventral nerve cord of Lumbricus terrestris was exposed to six dichotic intervals in the form of vibrations through a bass actuator. Nerve activity was recorded for amplitude (mV), duration (ms), and maximum depolarization (mV) of the action potential. There was no significant difference in …

Phylogenetic Analyses Of Andean And Amazonian Tree Communities In Ecuador, Samantha J. Worthy

Theses and Dissertations

The forests of Ecuador are known for their high levels of diversity and endemism, classifying the country as a biodiversity hotspot. Both the western Amazon and Andean montane forests are richly populated with tropical tree species that have been little studied in a community phylogenetic context. The implementation of elevational transects and trait based analyses having proven useful in gaining a better understanding of how environmental factors are affecting the tree community structure in these habitats. The goal of this research was to evaluate the magnitude ofDNA barcode diversity among Amazonian and Andean tree species. Specifically, the objectives were to …

The Utilization Of Morphological And Genetic Diagnostic Techniques For The Description Of Trematode Species Collected From Waterbirds From Lake Winnibigoshish, Minnesota, Usa, Tyler Joseph Achatz

All Graduate Theses, Dissertations, and Other Capstone Projects

Historically, morphological techniques for species identification were the leading diagnostic methodology, however, the increased usage of genetic techniques has led to a decrease in reports of morphometrics. The decrease in morphological reports increases the chance of missing diagnostic morphometrics. The three studies described herein used morphological and genetic diagnostic methods to identify trematodes from five families in order to improve genetic and morphological information for trematode species identification.

The first study identified ten species of trematodes from intestines of waterbirds previously collected from Lake Winnibigoshish, Minnesota. Nine of the species were sequenced for 28S ribosomal DNA (rDNA). Two species were …

Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer

Publications and Research

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

Evaluation Of Apoptotic Cell Death Mechanisms Induced By Hypericin-Mediated Photodynamic Therapy In Colon Cancer Cells, Aysun Kiliç Süloğlu, Eli̇f Karacaoğlu, Güldeni̇z Selmanoğlu, Hayri̇ye Akel, İbrahi̇m Çağatay Karaaslan

Turkish Journal of Biology

Hypericin (HYP)-mediated photodynamic therapy (PDT) is a new alternative treatment strategy for colon cancer inducing various cell-death pathways. Apoptotic cell death is the desired cellular fate in cancer cells. Therefore, we investigated the apoptotic pathways by determining apoptosis-related proteins (survivin, caspase-3, caspase-9, Bcl-2, and Bax) at the mRNA level using real-time polymerase chain reaction (qPCR), and the percentage of survivin was determined by survivin ELISA in HT-29 and Caco-2 colon cancer cell lines. The downregulation of survivin was significant 16 h after PDT for both cells, while caspase-3 upregulation was apparent 24 h after PDT. Caspase-9 and caspase-3 upregulations were …

Draft Genome Sequence Of The White-Rot Fungus Obba Rivulosa 3a-2, Otto Miettinen, Robert Riley, Kerrie Barry, Dan Cullen, Ronald P. De Vries, Matthieu Hainaut, Annele Hatakka, Bernard Henrissat, Kristiina Hildén, Rita Kuo, Kurt Labutti, Anna Lipzen, Miia R. Mäkelä, Laura Sandor, Joseph W. Spatafora, Igor V. Grigoriev, David S. Hibbett

Biology

We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

Analyzing The Safety And Efficacy Of Fecal Microbiota Transplantations For Inflammatory Bowel Disease Using Clostridium Difficile Infection As A Reference, Cassie Chan

Scripps Senior Theses

Fecal microbiota transplantation (FMT) is the process by which fecal suspension from a healthy individual is transferred into the gastrointestinal tract of another individual in an attempt to cure certain diseases. This transplantation process has been accredited as being a potential remedy for a growing number of diseases that have been associated with gut microbial imbalances. Interest in FMT has largely been driven by the science community’s increasing interest in the gut microbiome and its role in potentially regulating a multitude of different functions and processes within the human body. One disease that has been found to respond exceptionally well …

Factors Affecting Injury History And Their Overall Impact On Athletic Performance In Distance Runners, Trevor Norris

Williams Honors College, Honors Research Projects

Distance running is a very precise mechanism of many intricate movements and abilities of the body. The amount of miles that a distance runner must run puts a lot of very intense stresses on one’s body. These stresses often appear at the bone level and lead to many injuries such as stress reactions and stress fractures but also may play important roles in tissue damages such as strains and pulls. In this study, we used division one college distance runners and examined many intricacies between their level of fitness and overall composition. These include looking at imbalances, dominant traits, and …

Effect Of Altered Vegfr2 Expression On Oxidative Stress In A Rodent Model Of Preeclampsia Pathology, Madison Kaser

Williams Honors College, Honors Research Projects

Preeclampsia is a disease that results in pathologies in both the mother and the fetus that lead to oxidative stress. A decrease in vascular endothelial growth factor (VEGF) signaling may be one factor that contributes to this pathology. We hypothesize that by increasing vascular endothelial growth factor receptor 2 (VEGFR2) expression via administration of L-tyrosine phosphate (LTP) nanoparticles, the conditions of both the mother and fetus will be improved. Following treatment with the nanoparticles, we will employ a lucigenin chemiluminescence assay to determine levels of oxidative stress within the placenta. There are three groups that will be compared which are …

Case Study: Observing The Effects Of Length Of Exposure To Mnv On Mice Colonies, Beau Brown

Williams Honors College, Honors Research Projects

Four groups of experimental mice are studied in this experiment following intentional exposure to murine norovirus (MNV). Two groups are exposed to the virus at different points in their lives, and the other two are not infected and studied alongside the other groups as controls.

Past research has indicated that B and T immune cells are not essential to MNV resistance. Additionally, antibody production against MNV has shown to be slow as infection progresses. Thus, the expected results from the experiment are that the mice with longer infections of MNV will have larger quantities of IgG than those more recently …

Silver Nanoparticles Induce Pro-Inflammatory Gene Expression And Inflammasome Activation In Human Monocytes, A. Murphy, A. Casey, G. Byrne, Gordon Chambers, Orla L. Howe

Articles

A complete cytotoxic profile of exposure to silver (AgNP) nanoparticles investigating their biological effects on the innate immune response of circulating white blood cells is required to form a complete understanding of the risk posed. This was explored by measuring AgNP-stimulated gene expression of the pro-inflammatory cytokines interleukin-1 (IL-1), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) in THP-1 monocytes. A further study, on human monocytes extracted from a cohort of blood samples, was carried out to compare with the AgNP immune response in THP-1 cells along with the detection of pro-IL-1β which is a key mediator of the inflammasome complex. …

Insights Into Triterpene Metabolism In Model Monocotyledonous And Oilseed Plants Genetically Engineered With Genes From Botryococcus Braunii, Chase F. Kempinski

Theses and Dissertations--Plant and Soil Sciences

Isoprenoids are one of the most diverse classes of natural products and are all derived from universal five carbon, prenyl precursors. Squalene and botryococcene are linear, hydrocarbon triterpenes (thirty carbon compounds with six prenyl units) that have industrial and medicinal values. Squalene is produced by all eukaryotes as it is the first committed precursor to sterols, while botryococcene is uniquely produced by the green algae, Botryococcus braunii (race B). Natural sources for these compounds exist, but there is a desire for more renewable production platforms. The model plant Arabidopsis thaliana was engineered to accumulate botryococcene and squalene in its oil …

Lifelines Winter 2016, Southern Adventist University

Lifelines - Biology Department Newsletter

The Winter 2016 issue of Lifelines contains articles on research on air pollutants, an alumni feature, student mission in Peru, and a pictorial directory of the 2016 biology and allied health graduates.

Impact Of A Diesel Spill On Macroinvertebrate Communities In Ponds In S.E. Alabama, Usa, Katie E. Winkles

Theses and Dissertations

In this study, macroinvertebrate communities were examined to determine an indication of the water quality in ponds on a wetlands property after a diesel spill. In 2012, a train derailed, and at least 3000 gallons of diesel fuel leached into a small pond of the wetlands. Even after clean-up attempts there remains major concerns that the contamination spread throughout the wetlands. This concern led to the present study. Macroinvertebrates were the chosen focus due to their sensitivity to changes in the environment. Two field trials were conducted in which Hester-Dendy multiplate samplers were placed in ponds to allow macroinvertebrates to …

The Involvement Of Estrogen Receptors In Astrocyte Survival, Lauren M. Johnson

Theses and Dissertations

Estrogens are a class of hormones that are demonstrated to be neuroprotective. The levels of estrogen in the body decline during menopause which can cause a variety of symptoms. Hormone replacement therapy (HRT) is a treatment option for menopause, however, it has been demonstrated to have adverse side effects. Of the treatment options for adverse side effects of HRT, Selective estrogen Down-regulators do not appear to have an agonist effects on estrogen receptors while Selective estrogen receptor Modulators do. The aim of this study was to determine the role that estrogen receptors play in the survival of astrocytes when placed …

Emerging Roles Of Adamts Metalloproteinases In Regenerativemedicine And Restorative Biology, Ferah Armutcu, Kadi̇r Demi̇rcan

Turkish Journal of Biology

ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) proteinases degrade proteoglycans and thereby have the potential to alter tissue architecture and regulate cellular function. Recent studies about the roles of these enzymes have produced new perspectives for the molecular mechanisms behind regenerative biology with clinical potential to generate therapeutic targets to resolve tissue injury. ADAMTS enzymes play an important role in the turnover of extracellular matrix proteins in various tissues and their dysregulation has been implicated in disease-related processes such as inflammation and fibrosis. Increasing evidence indicates that they may be of key significance in the physiological and pathological central …

Controlled Nitric Oxide Release For Tissue Repair And Regeneration, Yan Nie, Zongjin Li

Turkish Journal of Biology

The discovery that nitric oxide (NO) plays crucial roles in mammalian systems has spurred considerable interest in its translational application. However, the major problem with its application in clinical settings is the high reactivity of NO, which makes it difficult to supply NO with spatiotemporal accuracy while maintaining its bioactivity. To deliver NO at a specified rate to a preferred location for a precise period of time is highly demanded. The significant technological advancements in controlled release make it possible to control NO release at the target site with a sustained release rate and an optimum concentration, and then provide …

Spatiotemporal Analysis Of Gene Flow Patterns Among Woodland Salamander Populations Inhabitating Contrasting Landscapes, Alexander C. Cameron

Masters Theses

Dispersal is a fundamental evolutionary process that serves as a mechanism by which local populations remain connected through space. Habitat loss and fragmentation remain widespread threats to biodiversity globally, and therefore it is imperative to understand how dispersal patterns are affected by anthropogenic modifications of the environment. Using a panel of 10 novel microsatellite loci, I estimated gene flow patterns over historical and contemporary timescales among populations of Eastern Red-backed Salamanders (Plethodon cinereus) in a previously unstudied portion of the species range. Four focal populations reside within a highly fragmented urban center whereas the remaining four focal populations persist in …

Evolution Of The Mysrs Element In The Genome Of Rodent Species, Megan M. Scott

Master's Theses and Doctoral Dissertations

Retrotransposons are a type of transposable element in which DNA copies are produced via an RNA intermediate and integrate into new chromosomal sites continually contributing to the dynamics of genomes. While sequencing the mys element among the Cricetidae family of rodents, we identified a previously uncharacterized element in the genome of the Mexican volcano mouse that we refer to as mys-related sequence (mysRS). This investigation provides a unique opportunity to contrast the evolution of the two retrotransposon families apparently restricted to a specific taxonomic group of rodents. By analyzing the genomes of various cricetid rodents, our results provide evidence that …

The Impact Of Urban Centers On American Goldfinches (Spinus Tristis) Overwintering At High Latitudes, Corrie Jean Navis

Master's Theses and Doctoral Dissertations

American Goldfinches (Spinus tristis) are partial migrants that overwinter in northern regions where winters can be extreme. To understand the role of urban development in facilitating use of a harsh climate, I conducted winter point count surveys (n = 297) at urban and rural sites across latitudes in Michigan. The following winter I trapped individuals in urban and rural settings to sample baseline and stress-induced plasma corticosterone (CORT) levels. Analyses revealed no interaction of latitude and urbanization in the winter distribution of American Goldfinches. Similarly, CORT concentrations did not differ between individuals trapped in urban and rural settings. …

Automated Solid-Substrate Cultivation Of The Anaerobic Bacterium Clostridium Thermocellum, Mathew J. Ruwaya

Theses and Dissertations--Biosystems and Agricultural Engineering

The organism Clostridium thermocellum grows on cellulosic substrates and produces ethanol, acetate, lactate, formic acid, and CO₂. The organic acids produced alter the growth environment in which the bacteria grows and ultimately inhibit bacterial growth. One method which has been used successfully to maintain the system at acceptable growth conditions is to intermittently flush out the spent media and metabolic products and replace with new fermentation media. Our goal was to design and build an automated system that will automatically flush the spent media from the growing culture and resupply new media without manual intervention. An automated control …

Species Distribution Modeling Of North American Odonates, Rebecca Beilinson

Library Map Prize

Species distribution modeling, which uses species-environment relationships to predict species’ geographic ranges, is a powerful technique for biogeographical and ecological analysis as well as for conservation planning. However, it has typically been underutilized for invertebrates and for freshwater species, as modeling these groups can pose unique challenges. Here I present methods for modeling odonate distributions and demonstrate these methods for four North American species. I show that incorporating expert-derived range maps as spatial priors can significantly improve model performance as compared to MaxEnt models. I also introduce a new distance to freshwater layer as an environmental variable, and show that …

Consequences Of Elevated Salt Concentrations Expression Profiles In The Rhizobium S. Meliloti 1021 Likely Involved In Heat And Desiccation Stress, Jan A.C. Vriezen, Caroline M. Finn

Biological Sciences: Faculty Publications

No abstract provided.