Genetics Commons^™

Detection Of Fecal Contamination Using Molecular Methods, Kristina K. Bowen

Independent Research Projects

This study explores the process of designing a molecular method to detect fecal contamination in the urban watersheds of Rock Island and Moline, Illinois. These urban watersheds are known to contain high ammonia levels and total dissolved solids based on previous studies. Additionally there is concern about the aging combined sewer and storm water system. Therefore, these watersheds are thought to have poor water quality including fecal contamination. Existing molecular methods used for detecting fecal contamination require a considerable amount of resources in the laboratory. Our goal was to design a molecular method that requires fewer resources and can continue …

Building A History Of Horizontal Gene Transfer In E. Coli, Matthew Wilber

HMC Senior Theses

Bacteria's ability to pass entire genes between one another, a process called Horizontal Gene Transfer (HGT), has a major impact on bacterial evolution. In an ongoing project at Harvey Mudd, computational methods have been used to catalogue the HGT events that have impacted a group of closely related bacteria.

This thesis builds on that project, by improving our ability to identify gene families --- groups of genes in different strains that are related. Previously, similarity was measured only by comparing two genes' DNA sequences, ignoring their positions on the organism's DNA. Here, we leverage genes' relative position to make a …

And-1 Is Required For Homologous Recombination Repair By Regulating Dna End Resection, Yongming Li, Zongzhu Li, Zhiyong Han, Wenge Zhu

Biochemistry and Molecular Medicine Faculty Publications

Homologous recombination (HR) is a major mechanism to repair DNA double-strand breaks (DSBs). Although tumor suppressor CtIP is critical for DSB end resection, a key initial event of HR repair, the mechanism regulating the recruitment of CtIP to DSB sites remains largely unknown. Here, we show that acidic nucleoplasmic DNA‐binding protein 1 (And‐1) forms complexes with CtIP as well as other repair proteins, and is essential for HR repair by regulating DSB end resection. Furthermore, And-1 is recruited to DNA DSB sites in a manner dependent on MDC1, BRCA1 and ATM, down-regulation of And-1 impairs end resection by reducing the …

Expression Of Zinc Fingers And Homeoboxes 2 (Zhx2) And Zhx2 Target Genes In Multiple Tissues Of Wild-Type And Zhx2 Knockout Mice, Minen Al-Kafajy

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

The Spear lab has had a long-standing interest in gene regulation in the liver during development and disease. Several years ago, these studies identified a novel transcriptional regulator called Zinc fingers and homeoboxes 2 (Zhx2), which is a member of a small family that includes Zhx1 and Zhx3. All Zhx proteins contain two amino-terminal C2-H2 zinc fingers and four or five carboxy-terminal homeodomains. Previous studies indicate that Zhx proteins can form homodimers and heterodimers with each other.

Zhx2 regulates numerous hepatic genes, including alpha-fetoprotein (AFP) and H19. Genes controlling lipid and cholesterol homeostasis are also regulated by …

Corrigendum: The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

The authors wish to draw the attention to two irregularities in Figures 2a and 4. Both concern errors in duplicating images of "empty" lanes illustrating absence of DNA bands. We regret these omissions and apologize to readers for the inconvenience caused. The results and conclusions remain valid.

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Lewis Honors College Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the …

Size Specific Transfection To Mammalian Cells By Micropillar Array Electroporation, Yingbo Zu

Doctoral Dissertations

Electroporation serves as a promising non-viral gene delivery approach, while its current configurations carry drawbacks associated with high-voltage electrical pulses and heterogeneous treatment on individual cells. Here, we developed a new micropillar array electroporation (MAE) platform to advance the delivery of plasmid DNA and RNA to mammalian cells. By introducing well-patterned micropillar array on the electrode surface, the number of pillars each cell faces varies with its cell membrane surface area, despite their large population and random locations. In this way, cell size specific electroporation is conveniently done and contributed to a 2.5~3 fold increase on plasmid DNA transfection and …

Genetic And Genomic Basis Of Antibody Response To Porcine Reproductive And Respiratory Syndrome (Prrs) In Gilts And Sows, Nick V. Serão, Robert A. Kemp, Benny Mote, Philip Willson, John C.S. Harding, Stephen C. Bishop, Graham S. Plastow, Jack C.M. Dekkers

Department of Animal Science: Faculty Publications

Background: Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTL_MHC and QTL₁₃₀) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of …

Thermal Assisted In Vivo Gene Electrotransfer, Amy Donate, Anna Bulysheva, Chelsea Edelblute, Derrick Jung, A. Malik, Siqi Quo, Niculina Burcus, Karl Schoenbach, Richard Heller

Bioelectrics Publications

Gene electrotransfer is an effective approach for delivering plasmid DNA to a variety of tissues. Delivery of molecules with electric pulses requires control of the electrical parameters to achieve effective delivery. Since discomfort or tissue damage may occur with high applied voltage, the reduction of the applied voltage while achieving the desired expression may be an important improvement. One possible approach is to combine electrotransfer with exogenously applied heat. Previous work performed in vitro demonstrated that increasing temperature before pulsing can enhance gene expression and made it possible to reduce electric fields while maintaining expression levels. In the study reported …

Genetic Structure And Diversity Of Channel Catfish (Ictalurus Punctatus) In Three Large Midwestern Rivers, Vaclav Alexei Sotola

Masters Theses

Little information is available regarding the genetic structure and diversity of sportfishes in large rivers, which can be vital to continuing the sustainable exploitation of these fisheries. Additionally, impoundments often have vast impacts on riverine systems. These impacts include altering the flow regime, changing the nutrient load, and preventing migratory fish from reaching their spawning grounds. If fishes are prevented from reaching their spawning grounds, their genetic diversity and structuring could begin to change relative to historic measures, potentially decreasing their fitness and ability to survive. I screened microsatellite loci to assess the genetic population structure and diversity of channel …

Vanadium Toxicological Potential Versus Its Pharmacological Activity: New Developments And Research, Agnieszka Ścibior, Juan Llopis, Alvin A. Holder, Mario Altamirano-Lozano

Chemistry & Biochemistry Faculty Publications

Scibior, A., Llopis, J., Holder, A. A., & Altamirano-Lozano, M. (2016). Vanadium toxicological potential versus its pharmacological activity: New developments and research. Oxidative Medicine and Cellular Longevity, 2016, 1-2. doi: 10.1155/2016/7612347

Endohelminth Parasites Of Some Midwater And Benthopelagic Stomiiform Fishes From The Northern Gulf Of Mexico, Michael J. Andres, Mark S. Peterson, Robin M. Overstreet

Gulf and Caribbean Research

: Mesopelagic fishes represent significant ecological links between mesozooplankton and the larger pelagic squids, fishes, and marine mammals. As such, these fishes also play a significant role as intermediate or paratenic hosts for parasites that require a crustacean intermediate host and mature in marine mammals or pelagic fishes. We examined a total of 208 individuals representing 5 species of Sternoptychidae and 88 individuals representing 2 species of Phosichthyidae from 20 locations in the northern Gulf of Mexico (nGOM). Six of the 7 species we examined are mesopelagic and one species was benthopelagic. We found the larval stages of Anisakis brevispiculata …

Isolation And Characterization Of Eight Polymorphic Microsatellites For The Spotted Spiny Lobster, Panulirus Guttatus, Nathan Truelove, Donald C. Behringer, Mark J. Butler Iv, Richard F. Preziosi

Biological Sciences Faculty Publications

Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated …

Phenotypic And Genetic Analyses Of Adaptation To Geothermal Soils In Yellow Monkeyflowers Of Yellowstone National Park, Peter Breigenzer

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Microgeographic adaptation, which occurs on a spatial scale smaller than the dispersal distance of the evolving organisms, provides a fertile context for understanding the genetic processes that shape natural variation and contribute to biological diversity. In plants, mosaics of distinct soil conditions can select for microgeographic divergence in the face of gene flow, leading to major life history transitions and novel trait evolution. Mimulus (monkeyflowers) is an emerging model genus for ecological genomics, due to tremendous diversity, experimental tractability, and a wealth of genomic resources. In Yellowstone National Park, Mimulus guttatus occurs in both geothermal soils and nearby nonthermal bogs …

The Role Of Sox4 In Regulating Choroid Fissure Closure And Retinal Neurogenesis, Wen Wen

Theses and Dissertations--Biology

The development of the vertebrate eye is tightly controlled by precise genetic regulations. From a single ocular primordium to bilateral eyes with complex structures and cell types, it requires intensive proliferation and migration for cells in both the ectoderm and mesoderm to accomplish ocular morphogenesis, and during this process cell differentiation and interaction takes place to establish the complex composition of ocular cell types and cellular connections. Genetic defects can lead to severe abnormalities in eye morphogenesis and cell differentiation during ocular development. A tremendous amount of work has been done to identify both intrinsic and extrinsic factors that regulate …

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 …

Differential Gene Expression Of Minnesota (Mn) Hygienic Honeybees (Apis Mellifera) Performing Hygienic Behavior, Eric Northrup

All Graduate Theses, Dissertations, and Other Capstone Projects

Hygienic behavior is the ability to remove dead and diseased brood from the comb early as to limit the detrimental impact of the parasite or pathogen. Minnesota (MN) Hygienic bees are generalists of hygienic behavior with the ability to remove several brood infected with several pathogens including the Varroa mite. This study explored the mechanisms of MN Hygienic behavior by comparing the transcriptome of MN Hygienic bee brains to non-hygienic bee brains via cDNA microarray. The results suggest that the brains of MN Hygienic bees may have a greater number of dendritic connections or are more sensitive to neurotransmitters. Quantitative …

Analysis Of Fy Promoter And Hepatocystis Load In South African Vervet Monkeys (Chlorocebus Aethiops), Benjamin J. Gombash

All Master's Theses

There are species of Hepatocystis and Plasmodium, related blood parasites, that enter the cell through a chemokine receptor, coded for by the Duffy antigen/receptor for chemokines in humans, and the FY*0 (FY Null) allele in the promoter of this gene results in the absence of this receptor on the exterior of the cell (Miller et al., 1977; Miller et al., 1975; Miller et al., 1976; Barnwell et al., 1989; Perkins and Schall, 2002; Martinsen et al., 2008; Tung et al., 2009). Humans without the receptor show resistance to multiple strains of Plasmodium (Tournamelle, et al., 1995; Zimmerman, et al. …

The Impact Of Oxygen On Bacterial Enteric Pathogens, Nathan Wallace, Ashley N. Zani, Elizabeth A. Abrams, Yvonne Sun

Biology Faculty Publications

Bacterial enteric pathogens are responsible for a tremendous amount of foodborne illnesses every year through the consumption of contaminated food products. During their transit from contaminated food sources to the host gastrointestinal tract, these pathogens are exposed and must adapt to fluctuating oxygen levels to successfully colonize the host and cause diseases. However, the majority of enteric infection research has been conducted under aerobic conditions. To raise awareness of the importance in understanding the impact of oxygen, or lack of oxygen, on enteric pathogenesis, we describe in this review the metabolic and physiological responses of nine bacterial enteric pathogens exposed …

What’S In A Gene: Undergraduates’ Ideas And Misconceptions About Gene Function, Justin M. Levaughn

Theses and Dissertations--Science, Technology, Engineering, and Mathematics (STEM) Education

The purpose of this study was to field test a two-tiered instrument including multiple-choice and short answer tasks to assess college students’ ideas and level of understanding in genetics. The instrument was constructed from previously tested assessment tasks and findings from the current research literature. Ninety-seven freshmen enrolled in a biology lab course were surveyed. Test validity and reliability were measured using Chronbach coefficients. Multiple-choice and short answer responses were analyzed using descriptive statistics to identify frequencies of answer selections. Written responses were independently evaluated using a five-point scoring rubric by three researchers to identify common misconceptions revealed in students’ …