Digital Commons Network^™

Environmental Factors Influencing Amphibian Community Assemblage In Dune Wetlands On The Lake Michigan Coast, Alex H. Jouney

Masters Theses

Wetlands in dune landscapes provide important breeding habitat for amphibians along the Lake Michigan Coast. Unfortunately, these unique habitats and the corresponding amphibian metapopulations are understudied and threatened. We assessed amphibian species richness and terrestrial habitat type in 16 permanent and ephemeral wetlands along the coast of Lake Michigan in Grand Haven, MI. Wetland area, terrestrial habitat type, depth, hydroperiod, shade, and degree of isolation were measured from April to September of 2017. Nine species of amphibian were found; Green Frog (Rana clamitans melanota) and Spring Peepers (Pseudacris crucifer crucifer) were most abundant and Fowlers Toad …

The Role Of Rad4 In Dna Repair And Its Interplay With Telomeres In Tetrahymena Thermophila, Emily Nischwitz

Graduate Theses/Dissertations

Telomeres are repetitive parts of the genome that act as a protective end cap to the chromosomes. Telomeres are critical to the integrity and stability of the genome, therefore, ensuring that their sequence is maintained, even after damage, is crucial. Much of the pioneering work responsible for explaining telomeres has been conducted in ciliates, specifically in Tetrahymena thermophila. Telomeres in T. thermophila have a high amount of tandem thymine repeats (GGGGTT) and, thus, are susceptible to ultraviolet light (UV) induced lesions called pyrimidine dimers, which must be repaired by nucleotide excision repair (NER). In humans, Xeroderma Pigmentosum C (XPC) …

Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle

Electronic Theses and Dissertations

Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences …

Development And Characterization Of Reporter-Expressing Zika Viruses, Michael E. Woolley

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In recent years, Zika virus (ZIKV) has garnered worldwide attention due to its epidemic spread throughout the Americas and due to the newly recognized link between ZIKV infection and neurological diseases, including microcephaly and Guillain-Barré syndrome. ZIKV is a mosquito-borne member of the genus Flavivirus, which includes the other prominent human pathogens Japanese encephalitis virus, West Nile virus, dengue virus, and yellow fever virus. Many questions about the biology of ZIKV and how it causes disease remain unanswered. Furthermore, there currently are no vaccines or licensed antiviral drugs available to treat ZIKV infection. The goal of this study was to …

Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow

Publications and Research

We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …

Prototype Of A Fish Inspired Swimming Silk Robot, Cassandra M. Donatelli, Sarah A. Bradner, Juanita Mathews, Erin Sanders, Casey R. Culligan, David Kaplan, Eric D. Tytell

Engineering Faculty Articles and Research

Elongate fishes have evolved hundreds of times throughout the tree of life. They occupy many aquatic environments, from streams and ponds to the deepest parts of the ocean. Due to their long body and numerous vertebrae, they are also highly flexible animals, which makes them useful as bioinspiration for designs in the field of soft robotics. We present a biodegradable soft robot prototype, inspired by elongate fishes. The robot's body is primarily composed of a silk hydrogel with embedded fibers to mimic the structure of natural fish skin. When actuated at the front, the flexible gel prototype mimics the undulatory …

Biodiversity And Conservation Study Of Chambers Island, Wisconsin - 2017 Annual Report, Mackenzie Hennes, Mikaela Nowak, Adam L. Brandt

Student Creative and Scholarly Works

Long term biological studies are rare but incredibly valuable for examining natural phenomena. Data collected over many years or decades allows for analyses of trends that would never be apparent in a single season. The research presented here is for the completion of the first field season in a long term study analyzing biodiversity trends on Chambers Island. Using visual searches, live trapping, and trail cameras, the biodiversity and abundance of species was examined. Special emphasis was placed on small mammals, though other species were observed and documented. The goals of this project were to (1) provide preliminary diversity and …

The Diversity Found Among Carbapenem-Resistant Bacteria, Galen Edward Card

Theses and Dissertations

This work will look at two factors that add to the diversity of carbapenem resistant bacteria. First, it focuses on the diversity of carbapenemase resistance plasmids. 446 plasmids were characterized by size, gene content and replicon groups. We identified that on average, over 30% of the encoded proteins on each plasmid have an unknown function. Plasmid sizes ranged from 1.6kb to 500kb, with an average of around 100kb and median of 80kb. Additionally, six replicon groups account for 80% of all the carbapenemase resistance plasmids. We also highlight the lack of data available for carbapenemase carrying plasmids from bacterial genera …

Gesture: An Online Hand-Drawing Tool For Gene Expression Pattern Search, Chunyan Wang, Yiqing Xu, Xuelin Wang, Li Zhang, Suyun Wei, Qiaolin Ye, Youxiang Zhu, Hengfu Yin, Manoj Nainwal, Luis Tanon-Reyes, Feng Cheng, Tongming Yin, Ning Ye

Molecular Biosciences Faculty Publications

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with …

Bird Abundance At Bird Feeders In Response To Temperature, Wind Speed And Precipitation During The Winter Season, Siddhant Kahal

Master's Theses

The goal of this project is to explore how 23 different bird species respond to 3 climatic attributes. These attributes are lower than average temperatures, wind speed and precipitation level. Information about the bird species and all of the data associated with them is provided by Project FeederWatch (PFW). This is a citizen based survey study that provides key information about bird species abundance through the use of backyard and community feeders. The study volunteers from across the United States and Canada monitor these bird feeders and note important information about the species such as the number of individuals seen. …

Biosemiotics As An Argument For The Recontextualization Of Biological Discoveries: A Critical Analysis Of The Biosemiotic Model Of Marcello Barbieri., Augustus Morrissey Snyder

Senior Honors Projects, 2010-2019

The primary purpose of this project was to investigate and explain the philosophical approach of biosemiotics to understanding living systems in contrast to the current scientific paradigm. Secondary goals were to evaluate the potential merits and relevance of this approach to biology and to introduce such a topic for discussion to biologists in a formal academic setting. My method consisted of critical textual analysis supplemented by analogy and biological examples where appropriate. In general, contemporary biosemiotics argues for a teleologic recontextualization of biological discoveries in practice and education. This is accomplished in a sophisticated fashion through the application and modification …

Species And Cultural Management Of Earthworms On Golf Course Turf In Arkansas And Oklahoma, Paige Elizabeth Boyle

Graduate Theses and Dissertations

As earthworms feed, they can egest soil and nutrient-rich aggregates (casts) on the soil surface. In low-cut turfgrass systems, such as golf course greens, tees, and fairways, surface casting can result in a muddy playing surface, ball roll issues, weed and pest invasion, reduced aesthetics, surface softening, and reduced photosynthesis. Because the use of pesticides for earthworm control is illegal in the U.S., earthworm casting must be managed through cultural practices. Sand topdressing is one method of earthworm control studied for use on golf courses, with the supposition being that the abrasive sand particles will deter the soft-bodied earthworms from …

Small Hive Beetle [Aethina Tumida (Murray)], Lori R. Spears, Ann M.M. Mull

All Current Publications

Small hive beetle (SHB) is an exotic pest of honey and bumble bee colonies that is native to Africa. SHB feeds on pollen and honey, kills bee brood and workers, and causes honey to discolor and ferment. This pest is now found throughout much of the U.S. with highest infestations occurring in the Southeast. It was first detected in Utah in 2016 and is now confirmed in Washington and Davis counties. Infestations can be prevented by early detection, using good husbandry techniques, maintaining a high ratio of bees to comb, and keeping hives in partial to full sun. Chemical control …

The Effects Of Passive Integrated Transponder Tagging On Cortisol Release In The Gulf Killifish, Fundulus Grandis, Ariel Marcelo Hernandez

Senior Honors Theses

Due to its ease of use, low cost, and essentially limitless number of unique codes, PIT tagging has become the favored technique for tagging individuals in biological studies. However, studies employing PIT tagging generally assume that stress due to the implantation and presence of a PIT tag has no influence on the experimental results. This study investigated the effects of PIT tagging on levels of the stress hormone cortisol in the Gulf Killifish, Fundulus grandis, an estuarine fish of the Gulf of Mexico that is prone to daily or seasonal environmental stressors. Cortisol was measured non-invasively by extracting and …

Clinical Applications Of Infrared And Raman Spectroscopy: State Of Play And Future Challenges, Matthew Baker, Hugh Byrne, John Chalmers, Peter Gardner, Royston Goodacre, Alex Henderson, Sergei Kazarian, Francis Martin, Julian Moger, Nick Stone, Josep Sule-Suso

Articles

Vibrational spectroscopies, based on Infrared absorption and/or Raman scattering provide a detailed fingerprint of a material, based on the chemical content. Diagnostic and prognostic tools based on these technologies have the potential to revolutionise our clinical systems leading to improved patient outcome, more efficient public services and significant economic savings. However, despite these strong drivers, there are many fundamental scientific and technological challenges which have limited the implementation of this technology in the clinical arena, although recent years have seen significant progress in addressing these challenges. This review examines (i) the state of the art of clinical applications of infrared …

Study On Pyrolysis Characteristic Of The Heat-Not-Burn Reconstituted Tobacco, Ma Pengfei, Li Qiaoling, Lin Kai, Huang Huizhen, Liu Xiucai, Liu Zechun, Xie Wei, Liu Jing, Li Yuefeng

Food and Machinery

In order to study the pyrolysis characteristic of the heat-not-burn reconstituted tobacco, eight kinds of reconstituted tobacco, three kinds of non-tobacco fiber and tobacco own fiber were tested by TGA (Thermogravimetric Analyzer) technology, and the resulting DTG（Derivative Thermogravimetry）data were analyzed by NRMSE (normalized root mean squared error) to calculate the pyrolysis difference degree. The results showed that the pyrolysis behavior of the reconstituted tobacco used in heat-not-burn cigarettes was much different from that in traditional cigarettes and the pyrolysis difference degree was 37.97%. There was an additional peak in DTG curve of the reconstituted tobacco used in heat-not-burn cigarettes, which …

The Innate Immune Response To Ischemic Injury: A Multiscale Modeling Perspective., Elena Dimitrova, Leslie A Caromile, Reinhard Laubenbacher, Linda H Shapiro

Faculty Research 2018

BACKGROUND: Cell death as a result of ischemic injury triggers powerful mechanisms regulated by germline-encoded Pattern Recognition Receptors (PRRs) with shared specificity that recognize invading pathogens and endogenous ligands released from dying cells, and as such are essential to human health. Alternatively, dysregulation of these mechanisms contributes to extreme inflammation, deleterious tissue damage and impaired healing in various diseases. The Toll-like receptors (TLRs) are a prototypical family of PRRs that may be powerful anti-inflammatory targets if agents can be designed that antagonize their harmful effects while preserving host defense functions. This requires an understanding of the complex interactions and consequences …

3d Bioprinting Systems For The Study Of Mammary Development And Tumorigenesis, John Reid

Electrical & Computer Engineering Theses & Dissertations

Understanding the microenvironmental factors that control cell function, differentiation, and stem cell renewal represent the forefront of developmental and cancer biology. To accurately recreate and model these dynamic interactions in vitro requires both precision-controlled deposition of multiple cell types and well-defined three-dimensional (3D) extracellular matrix (ECM). To achieve this goal, we hypothesized that accessible bioprinting technology would eliminate the experimental inconsistency and random cell-organoid formation associated with manual cell-matrix embedding techniques commonly used for 3D, in vitro cell cultures. The first objective of this study was to adapt a commercially-available, 3D printer into a 3D bioprinter. Goal-based computer simulations were …

Acute Loss Of Iron-Sulfur Clusters Results In Metabolic Reprogramming And Generation Of Lipid Droplets In Mammalian Cells, Daniel R. Crooks, Nunziata Maio, Andrew N. Lane, Michal Jarnik, Richard M. Higashi, Ronald G. Haller, Ye Yang, Teresa Whei-Mei Fan, W. Marston Linehan, Tracey A. Rouault

Center for Environmental and Systems Biochemistry Faculty Publications

Iron–sulfur (Fe-S) clusters are ancient cofactors in cells and participate in diverse biochemical functions, including electron transfer and enzymatic catalysis. Although cell lines derived from individuals carrying mutations in the Fe-S cluster biogenesis pathway or siRNA-mediated knockdown of the Fe-S assembly components provide excellent models for investigating Fe-S cluster formation in mammalian cells, these experimental strategies focus on the consequences of prolonged impairment of Fe-S assembly. Here, we constructed and expressed dominant–negative variants of the primary Fe-S biogenesis scaffold protein iron–sulfur cluster assembly enzyme 2 (ISCU2) in human HEK293 cells. This approach enabled us to study the early metabolic reprogramming …

A Review Of The Ambush Bugs (Heteroptera: Reduviidae: Phymatinae) Of Michigan: Identification And Additional Considerations For Two Common Eastern Species, Daniel R. Swanson

The Great Lakes Entomologist

A review of the two species of Phymatinae found in Michigan is presented, along with an identification key, distribution maps, and relevant literature. Also included are brief discussions concerning natural history, variation, distribution, past records, and two additional eastern species.

Pentatomoidea (Hemiptera: Pentatomidae, Scutelleridae) Associated With The Dioecious Shrub Florida Rosemary, Ceratiola Ericoides (Ericaceae), A. G. Wheeler Jr.

The Great Lakes Entomologist

Florida rosemary (Ceratiola ericoides), an ericaceous shrub with needlelike leaves, is characteristic of Florida scrubs and certain other xeric plant communities of well-drained sands. The plant is dioecious, its inconspicuous male and female flowers borne on separate individuals. From 2003 to 2012 (mainly 2007–2012), rosemary was sampled periodically (with all months included at least once during the period) in sand ridges of peninsular Florida and two riverine dunes in southeastern Georgia. Branches of male and female plants were tapped separately into a beating net. Sampling during the final three years was female-plant-biased to facilitate work on fruit- and seed-feeding …

Description Of A New Species Of Atanycolus (Hymenoptera: Braconidae) From Michigan Reared From The Emerald Ash Borer, Agrilus Planipennis (Coleoptera: Buprestidae: Agrilinae), Paul M. Marsh, John S. Strazanac, Stephanie Y. Laurusonis

The Great Lakes Entomologist

A new species of Braconidae, Atanycolus cappaerti Marsh and Strazanac, is described from Michigan where it has been reared from emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), galleries in ash (Fraxi- nus spp.). Molecular evidence (analysis of fragments of the mitochondrial genes COI and 16S and the nuclear genes wingless and elongation factor 1-alpha) is presented to support the distinction of this new species from A. hicoriae Shenefelt that has been documented as a parasitoid of several ash borers.

Demonstration Of Sex Pheromones In Molanna Uniophila (Trichoptera: Molannidae), Platycentropus Radiatus, Pycnopsyche Indiana, And P. Subfasciata (Trichoptera: Limnephilidae), With An Assessment Of Interspecific Attraction Between Four Sympatric Pycnopsyche Species, David C. Houghton, Christine Lux, Megan Spahr

The Great Lakes Entomologist

Evidence for sex pheromones in the caddisflies Molanna uniophila Vorhies, Platycentropus radiatus (Say), Pycnopsyche indiana (Ross), and P. subfasciata (Say) is presented here for the first time based on field studies conducted in southern Michigan. For all species, numbers of males caught in pheromone traps baited with conspecific female extracts were higher than those caught in traps with male extracts, or those without extract. Four sympatric species of Pycnopsyche: P. guttifer (Walker), P. indiana, P. lepida (Hagen), and P. subfasciata exhibited no interspecific pheromonal attraction despite a common mating season and, in the case of P. indiana and P. lepida …

The Alien Hippodamia Variegata (Coleoptera: Coccinellidae) Quickly Establishes Itself Throughout Wisconsin, Andrew H. Williams, Daniel K. Young

The Great Lakes Entomologist

(excerpt)

Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae) is a Palaearctic species that was first reported to be established in the Nearctic near Montreal, Quebec, in 1984 (Gordon 1987). Since then, this small beetle has been expanding its range in North America, a process summarized by Gardiner and Parsons (2005). It was first reported from Michigan in 2005 (Gardiner and Parsons 2005) and from Ohio in 2007 (Pavuk et al. 2007).

Comparative Biology And Life Tables Of Trichogramma Brassicae And Trichogramma Cacoeciae With Ephestia Kuehniella As Host At Three Constant Temperatures, Nihal Ozder

The Great Lakes Entomologist

Egg parasitoids of the genus Trichogramma (Hymenoptera: Trichogrammatidae) have been successfully utilized for biocontrol of several lepidopteran pests world-wide. The age specific fecundity of Trichogramma brassicae Bezdenko and Trichogramma cacoeciae Marchal using Ephestia kuehniell a Zeller (Lepidoptera: Pyralidae) as host were determined at 20, 26, and 30 °C and 60-70 % R.H. in the laboratory. Both T. cacoeciae and T. brassicae demonstrate high parasitism ability and intrinsic rates of increase on E. kuehniella and had a similar response to increasing temperature.

Observations Of First Occurrence And Severity Of Potato Leafhopper, Empoasca Fabae (Harris), (Homoptera: Cicadellidae) In The North Central And Eastern United States., K. M. Maredia, M. E. Whalon, S. H. Gage, M. J. Kaeb

The Great Lakes Entomologist

This paper presents available data on the first occurrence dates and the damage severity of the potato leafhopper in the north central and north eastern United States collected during the past 47 years (1951-1997). The data were collected from a variety of sources including: potato leafhopper literature review; published reports; pest alerts; pest surveys; and delphi surveys. First occurrence and severity data show that the arrival time of potato leafhopper and subsequent damage severity varies substantially from year to year. A correlation analysis between date of first occurrence and severity of damage for Michigan, Minnesota, Wisconsin, the north central region …

Feasibility Of Using Cryostored Colorado Potato Beetle (Coleoptera: Chrysomelidae) Eggs For Rearing Edovum Puttleri (Hymenoptera: Eulophidae), R. F. W. Schroder

The Great Lakes Entomologist

Cryostored eggs of Colorado potato beetle, Leptinotarsa decemlineata (Say) eggs were suitable hosts for Edovum puttleri. Parasitism rates were low, however this study was first to show that rearing the parasite on eggs stored at ultra low temperatures (-70 0 C) is feasible. This method of storage will facilitate mass production of E. puttleri as well as prevent loss of the parasite in the event of a crash in the Colorado potato beetle colony.

Graphene Nanoplatelets-Sericin Surface-Modified Gum Alloy For Improved Biological Response, Valentina Mitran, Valentina Dinca, Raluca Ion, Vasile D. Cojocaru, Patricia Neacsu, Cerasela Zoica Dinu, Laurentiu Rusen, Simona Brajnicov, Anca Bonciu, Maria Dinescu, Doina Raducanu, Ioan Dan

Faculty & Staff Scholarship

In this study a “Gum Metal” titanium-based alloy, Ti-31.7Nb-6.21Zr-1.4Fe-0.16O, was synthesized by melting and characterized in order to evaluate its potential for biomedical applications. The results showed that the newly developed alloy presents a very high strength, high plasticity and a low Young's modulus relative to titanium alloys currently used in medicine. For further bone implant applications, the newly synthesized alloy was surface modified with graphene nanoplatelets (GNP), sericin (SS) and graphene nanoplatelets/sericine (GNP–SS) composite films via Matrix Assisted Pulsed Laser Evaporation (MAPLE) technique. The characterization of each specimen was monitored by scanning electron microscopy (SEM), atomic force microscopy (AFM), …

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen

Senior Honors Projects, 2010-2019

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also …

Methylation-Based Enrichment Facilitates Low-Cost, Noninvasive Genomic Scale Sequencing Of Populations From Feces, Kenneth L. Chiou, Christina M. Bergey

United States Public Health Resources

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate …