Biology Commons^™

Detection Of Multi-Drug Resistant Escherichia Coli In The Urban Waterways Of Milwaukee, Wi, Anthony D. Kappell, Maxwell S. Denies, Neha H. Ahuja, Nathan A. Ledeboer, Ryan J. Newton, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of …

Gene Mdpc Plays A Regulatory Role In The Methyl-Tert-Butyl Ether Degradation Pathway Of Methylibium Petroleiphilum Strain Pm1, Geetika Joshi, Radomir Schmidt, Kate M. Scow, Michael S. Denison, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC⁻. We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of …

Comparing Acute Effects Of A Nano-Tio2 Pigment On Cosmopolitan Freshwater Phototrophic Microbes Using High-Throughput Screening, Binh Chu, Christopher G. Peterson, Tiezheng Tong, Kimberly A. Gray, Jean-François Gaillard, John Kelly

Biology: Faculty Publications and Other Works

Production of titanium-dioxide nanomaterials (nano-TiO2) is increasing, leading to potential risks associated with unintended release of these materials into aquatic ecosystems. We investigated the acute effects of nano-TiO2 on metabolic activity and viability of algae and cyanobacteria using high-throughput screening. The responses of three diatoms (Surirella angusta, Cocconeis placentula, Achnanthidium lanceolatum), one green alga (Scenedesmus quadricauda), and three cyanobacteria (Microcystis aeruginosa, Gloeocapsasp., Synechococcus cedrorum) to short-term exposure (15 to 60 min) to a common nano-TiO2 pigment (PW6; average crystallite size 81.5 nm) with simulated solar illumination were assessed. Five concentrations of nano-TiO2 (0.5, 2.5, 5, 10, and 25 mg L-1) …

Organismal Biology, Timothy Henkel, Emily Croteau, Matthew Waters

Biological Sciences Grants Collections

This Grants Collection for Organismal Biology was created under a Round Four ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Evolution And Biodiversity, Timothy Henkel, Emily Croteau, Matthew Waters

Biological Sciences Grants Collections

This Grants Collection for Evolution and Biodiversity was created under a Round Four ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

The Evolutionary Origination And Diversification Of A Dimorphic Gene Regulatory Network Through Parallel Innovations In Cis And Trans, Eric M. Camino, John C. Butts, Alison J. Ordway, Jordan E. Vellky, Mark Rebeiz, Thomas M. Williams

Biology Faculty Publications

The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development. Morphological traits result from gene regulatory networks (GRNs) that form a web of transcription factors, which regulate multiple cis-regulatory element (CRE) sequences to control the coordinated expression of differentiation genes. The formation and modification of GRNs must ultimately be understood at the level of individual regulatory linkages (i.e., transcription factor binding sites within CREs) that constitute the network. Here, we investigate how elements within a network originated and diversified to generate a broad range of abdominal pigmentation phenotypes among Sophophora fruit flies. …

Evolution And Biogeography Of Mesoamerican Small Mammals: With Focus On The Genus Handleyomys And Related Taxa, Ana Villalba Almendra

Theses and Dissertations

Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. For mammals, the patterns of diversification of Mesoamerican taxa still are controversial. Reasons for this include the region's complex geologic history, and the relatively recent timing of such geological events. Previous studies, however, support the view that substantial migration between North (NA) and South America (SA) occurred prior or/and during the Great American Biotic Interchange (GABI) ~3.5 Ma. This was followed by repeated periods of isolation during Pleistocene climatic oscillations, which produced most of the diversification in the region. From a North American origin, …

Biology News, Spring 2015, University Of Northern Iowa. Department Of Biology.

Biology News

Contents:

-- Greetings from the Department of Biology
-- Biology Students and Alumni
-- Faculty awards
-- Department News
-- Biology students travel to University of Kentucky to attend the NCUR Annual Conference
-- Tigers Visit UNI Biology Department
-- Nobel Conference
-- UNI/Iowa Community Colleges STEM Day
-- Carver Grant Purchases SynDavers
-- Steve O'Kane teaches in Korea
-- Biology Living and Learning Community
-- Hallway displays
-- Forensic DNA analysis at Linn-Mar High School
-- Undergraduate Research in Biology
-- New Faculty
-- Reconnect with the Department of Biology
-- You Can Make a Difference!
-- Scholarships and …

Coding Dna Into Music: An Alternate Way Of Analysis, Samuel Fesenmeier

Honors Theses

In the study, we are analyzing the human genome in order to determine patterns that may tell something about how DNA functions. Patterns require an explanation: it is highly improbable that they are random occurrence. These patterns may hint to something about how DNA functions. There are known patterns already discovered in DNA. For example, in the coding portion, three base pairs translate to a specific amino acid. In the non coding portion, however, specific patterns are not as simple.

We will search for patterns by applying a coding system that turns DNA into music. Music may serve as a …

Cell Type-Specific Responses To Wingless, Hedgehog And Decapentaplegic Are Essential For Patterning Early Eye-Antenna Disc In Drosophila, Jong-Hoon Won, Orkhon Tsogtbartarr, Wonseok Son, Amit Singh, Kwang-Wook Choi, Kyung-Ok Cho

Biology Faculty Publications

The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from which most head structures are derived. Secreted morphogens like Wingless (Wg), Hedgehog (Hh), and Decapentaplegic (Dpp) are important for early patterning of ead, but the underlying mechanisms are still largely unknown. To understand how these morphogens function in the ead of early larval stages, we used wg-LacZ and dpp-Gal4 markers for the examination of wild-type and mutant eads. We found that the ead immediately after hatching was crescent-shaped with the Bolwig’s nerve at the ventral edge, suggesting that it consists of dorsal domain. In a subsequent …

Whole Genome Comparison Of A Large Collection Of Mycobacteriophages Reveals A Continuum Of Phage Genetic Diversity, Welkin Pope, Charles Bowman, Daniel Russell, Deborah Jacobs-Sera, David Asai, Steven Cresawn, William Jacobs, Roger Hendrix, Jeffrey Lawrence, Graham Hatfull, Sarah C.R. Elgin

Biology Faculty Research

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows …

Concurrent Coevolution Of Intra-Organismal Cheaters And Resisters, S R. Levin, D A. Brock, David C. Queller, Joan E. Strassmann

Biology Faculty Research

The evolution of multicellularity is a major transition that is not yet fully understood. Specifically, we do not know whether there are any mechanisms by which multicellularity can be maintained without a single-cell bottleneck or other relatedness-enhancing mechanisms. Under low relatedness, cheaters can evolve that benefit from the altruistic behaviour of others without themselves sacrificing. If these are obligate cheaters, incapable of cooperating, their spread can lead to the demise of multicellularity. One possibility, however, is that cooperators can evolve resistance to cheaters. We tested this idea in a facultatively multicellular social amoeba, Dictyostelium discoideum. This amoeba usually exists as …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr.

Biology Faculty Articles

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the …

Human Impacts On Water Systems: Biological Assessment Of Water Quality In The Bosque Protector Río Guajalito (Bprg) Using Aquatic Macroinvertebrates, Harrison Smith

Independent Study Project (ISP) Collection

Benthic macroinvertebrates have been extensively used as bioindicators for water quality due to their varying sensitivity to a diverse range of impacts on hydrographic sources. In this study a sampling of macroinvertebrates was carried out in the Guajalito and Brincador rivers and a small creek that runs through the private reserve Bosque Protector Rio Guajalito in order to analyze if the health of the rivers has changed in relation to previous studies. The sampling stations were located upstream and downstream of potential sources of disturbance in each of the three streams sampled in order to determine what level of impact …

Plasma Activated Air Mediates Gene Transfer, Chelsea M. Edelblute

Biological Sciences Theses & Dissertations

Cold plasma is produced when strong applied electric fields accelerate free electrons, which dissociate, excite, or ionize gaseous molecules [1]. The deposition of ions from the plasma source is dependent on power generation, input gas composition, and gas flow rate. In the presence of reactive species, the membrane of eukaryotic cells is compromised allowing for otherwise impermeant molecules, such as DNA, to enter the inner-cell milieu [2].

The efficacy of a novel cold plasma reactor based on shielded sliding discharge for the delivery of plasmid DNA was assessed. The device is entirely non-contact, wherein the plasma never directly touches the …

Functional Screening Of The Cronobacter Sakazakii Baa-894 Genome Reveals A Role For Prop (Esa_02131) In Carnitine Uptake, Audrey Feeney, Roy D. Sleator

Department of Biological Sciences Publications

Cronobacter sakazakii is a neonatal pathogen responsible for up to 80% of fatalities in infected infants. Low birth weight infants and neonates infected with C. sakazakii suffer necrotizing enterocolitis, bacteraemia and meningitis. The mode of transmission most often associated with infection is powdered infant formula (PIF) which, with an aw of ∼0.2, is too low to allow most microorganisms to persist. Survival of C. sakazakii in environments subject to extreme hyperosmotic stress has previously been attributed to the uptake of compatible solutes including proline and betaine. Herein, we report the construction and screening of a C. sakazakii genome bank and …

Dna-Based Authentication Of Botanicals And Plant-Derived Dietary Supplements: Where Have We Been And Where Are We Going?, Denise F. Coutinho Moraes, David W. Still, Michelle R. Lum, Ann M. Hirsch

Biology Faculty Works

Herbal medicines and botanicals have long been used as sole or additional medical aids worldwide. Currently, billions of dollars are spent on botanicals and related products, but minimal regulation exists regarding their purity, integrity, and efficacy. Cases of adulteration and contamination have led to severe illness and even death in some cases. Identifying the plant material in botanicals and phytomedicines using organoleptic means or through microscopic observation of plant parts is not trivial, and plants are often misidentified. Recently, DNA-based methods have been applied to these products because DNA is not changed by growth conditions unlike the chemical constituents of …

Crematogaster Pilosa Ants As Bioindicators Of Ecosystem Marsh Health, Elliott R. Thompson

Honors Capstones

No abstract provided.

Animal Habitat Utilization And The Impacts Of Small-Scale Disturbances On Vegetation Within Larch Forests In Northeastern Siberia, Aaron Phillip White

Theses and Dissertations - UTB/UTPA

Boreal forests support a variety of animals distributed across a matrix of habitat patches including forests of different ages and stand densities. These forests occur at high latitudes where cold and moist conditions favor ground layer dominance by mosses and slow decomposition rates, resulting in a thick soil organic layer (SOL) comprised primarily of decomposing mosses and roots. However, limited information is available on how animal use varies across habitat types in northeastern Siberia. Boreal forests of this region are unique because they are comprised of a single deciduous conifer, Cajander larch (Larix cajanderi). These forests also occur on a …

School Of Biological Sciences News, 2015, School Of Biological Sciences

School of Biological Sciences News

Alumni newsletter of Illinois State University's School of Biological Sciences.

Instructor's Guide To Concepts Of Biology, Chapters 12-21, Molly Smith, Sara Selby

Biological Sciences Open Textbooks

Authors' Description:

This Instructor’s Guide contains the brief outlines of Chapters 12-21 as found in Concepts of Biology, though some underwent revision. Also, instructors will find detailed outlines of the text for use in lecturing, as well as structured outlines that may be used by students to take notes while reading the chapter or during lecture. All outlines are derived from the OpenStax text. Additionally, study guides that contain a variety of questions are provided for students.

The appendices contain Web resources where additional information can be found about the topics covered in the text; these Web resources may or …

Computational Development For Secondary Structure Detection From Three-Dimensional Images Of Cryo-Electron Microscopy, Dong Si

Computer Science Theses & Dissertations

Electron cryo-microscopy (cryo-EM) as a cutting edge technology has carved a niche for itself in the study of large-scale protein complex. Although the protein backbone of complexes cannot be derived directly from the medium resolution (5-10 Å) of amino acids from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for ab initio backbone structure derivation in cryo-EM. So far it is challenging to detect the SSEs automatically and accurately from the density images at these resolutions. This dissertation …

Development Of A Therapeutic Model Of Early Liver Cancer Using Crocin-Coated Magnetite Nanoparticles, Rkia El-Kharrag

Dissertations

Hepatocellular carcinoma is one of the most common health problems that is difficult to treat. As a result of the side effects frequently experienced with conventional cancer treatments, there has been a growing interest to develop controlled drug delivery system that can reduce the mortality rate of liver cancer patients and un-harm healthy tissues. Magnetite nanoparticles are potentially important in hepatocellular carcinoma treatment, since they can be used as delivery system. Pure and coated magnetite nanoparticles were synthesized via modified co-precipitation method in air at low temperature. Various reaction parameters and coating materials have been investigated and characterized. Among these …

Genetic And Molecular Analysis Of Dec-11 In C. Elegans' Intestinal Pacemaker Activity, Adele Joan Gordon

Master's Theses (2009 -)

Rhythmic behaviors are ubiquitous phenomena in plant and animal phyla. Ultradian rhythmic behaviors occur with a period of less than 24 hours and include such rhythmic behaviors as the beating of the heart and peristalsis in the gut. The nematode C. elegans exhibits three well-characterized ultradian rhythmic behaviors: ovulation, pharyngeal pumping, and the defecation motor program (DMP). The DMP occurs every ~45 seconds in wild-type worms and comprises three distinct muscle contractions: a posterior body contraction (pBoc), an anterior body contraction (aBoc), and an enteric muscle contraction (Emc), which is coupled to expulsion (Exp). The rhythmicity of the DMP is …

Blue Carbon In Coastal Freshwater/Brackish Marshes On The Barrier Islands Of Virginia: Belowground Carbon Dynamics, Nathan M. Sedghi

Biological Sciences Theses & Dissertations

Some coastal ecosystems sequester substantially more carbon (blue carbon) than land locked systems due to high net primary production and deposition associated with oceanic influences. Most blue carbon research has focused on mangroves, seagrass beds, and salt marshes. Studies on blue carbon potential of coastal freshwater marshes are less common. Barrier islands frequently flood, with seawater reaching interior ecosystems. I examined brackish/freshwater marshes on Virginia barrier islands for possible roles as blue carbon systems. I studied four interior marshes on Hog Island, which varied in proximity to a direct overwash path and protection by a trail berm that divides northern …

Blue Carbon In Freshwater / Brackish Marshes On The Barrier Islands Of Virginia Aboveground Net Primary Productivity And Carbon Pools, Emily Caitlin Adams

Biological Sciences Theses & Dissertations

"Blue carbon" is a relatively new concept describing carbon distributed tidally and sequestered via net production within coastal ecosystems, including seagrass beds, mangrove forests, and salt-water marshes. These systems sequester carbon at least 10 times faster than terrestrial systems. Fresh to brackish wetlands that receive irregular tidal influence due to overwash and storm events have not been typically studied as blue carbon systems. My objective was to quantify carbon pools within four interdunal fresh to brackish marshes on Hog Island, Virginia to determine their blue carbon potential. Marshes 1 and 2 were farthest from the ocean, below and above a …

Varying Influences Of Selection And Demography In Host-Adapted Populations Of The Tick-Transmitted Bacterium, Anaplasma Phagocytophilum Speciation And Evolutionary Genetics, Matthew Aardema, Friederike D. Von Loewenich

Department of Biology Faculty Scholarship and Creative Works

Background: The host range of a pathogenic bacterial strain likely influences its effective population size, which in turn affects the efficacy of selection. Transmission between competent hosts may occur more frequently for host generalists than for specialists. This could allow higher bacterial population densities to persist within an ecological community and increase the efficacy of selection in these populations. Conversely, specialist strains may be better adapted to their hosts and consequently achieve greater within-host population densities, with corresponding increases in selection efficacy. To assess these different hypotheses, we examined the effective population sizes of three strains of the bacterium Anaplasma …

An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein

Dartmouth Scholarship

Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.

Traversing Swanton Road, 18th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Single-Walled Carbon Nanotube And Graphene: Nano-Delivery Of Gambogic Acid Increases Its Cytotoxicty In Various Cancer Cells, Lamya A. M Saeed

Theses and Dissertations

Nanomedicine is a new branch of medicine that has been developed due to the critical need to treat challenging diseases, especially cancer since it remains a significant cause of morbidity and mortality worldwide and the second most common cause of death after heart disease in the USA. One of the most important health care applications of nanomedicine concerns the development of drug delivery systems. Graphene (Gn), an atom-thick carbon monolayer of sp2- bonded carbon atoms arranged in a two dimensional (2D) honeycomb crystal lattice, and single-walled carbon nanotubes (SWCNTs) (1D, tubular) are among the most promising nanomaterials with the capability …