Genetics and Genomics Commons^™

Phenotypic/Genotypic Profile Of Oxa-10-Like-Harboring, Carbapenem-Resistant Pseudomonas Aeruginosa: Using Validated Pharmacokinetic/Pharmacodynamic In Vivo Models To Further Evaluate Enzyme Functionality And Clinical Implications, Fred C. Tenover, Christian M. Gill, Adrian Brink, Chun Yat Chu, Jennifer Coetzee, George Dimopoulos, Clinton Moodley, Christoffel Johannes Opperman, Spyros Pournaras, Isabella A. Tickler, Hafsah Deepa Tootla, Sophia Vourli, David P. Nicolau

Biology Faculty Publications

In vitro MICs and in vivo pharmacodynamics of ceftazidime and cefepime human-simulated regimens (HSR) against modified carbapenem inactivation method (mCIM)-positive Pseudomonas aeruginosa isolates harboring different OXA-10-like subtypes were described. The murine thigh model assessed ceftazidime (2 g every 8 h [q8h] HSR) and cefepime (2 g and 1 g q8h HSR). Phenotypes were similar despite possessing OXA-10-like subtypes with differing spectra. Ceftazidime produced ≥1-log10 killing in all isolates. Cefepime activity was dose dependent and MIC driven. This approach may be useful in assessing the implications of β-lactamase variants.

Global Population Divergence Of A Cosmopolian Desert Plant, Victor Ryan Alfaro

Biology ETDs

Genetic and phenotypic variation can have different patterns within a species if it has populations with contrasting histories. Populations can have discrete differences that are shaped by different evolutionary scenarios, but within each population, range, or region, traits and association with fitness can also be affected by both edaphic and landscape variation. For my dissertation, I surveyed and experimentally analyzed variation and adaptive potential in Sahara mustard (Brassica tournefortii), a desert annual that has endemic, invasive, and agricultural populations in Africa, Asia, and the Americas. Although my multi-trait analysis generated complex results, my findings can be applied to …

Growth–Defense Trade-Offs Shape Population Genetic Composition In An Iconic Forest Tree Species, Olivia L. Cope, Ken Keefover-Ring, Eric L. Kruger, Richard L. Lindroth

Aspen Bibliography

All organisms experience fundamental conflicts between divergent metabolic processes. In plants, a pivotal conflict occurs between allocation to growth, which accelerates resource acquisition, and to defense, which protects existing tissue against herbivory. Trade-offs between growth and defense traits are not universally observed, and a central prediction of plant evolutionary ecology is that context-dependence of these trade-offs contributes to the maintenance of intraspecific variation in defense [Züst and Agrawal, Annu. Rev. Plant Biol., 68, 513–534 (2017)]. This prediction has rarely been tested, however, and the evolutionary consequences of growth–defense trade-offs in different environments are poorly understood, especially in long-lived species …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent William Bever

Dissertations and Theses

We provide the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. In partial support of a tenet of the mitonuclear sex hypothesis, which predicts that outcrossing will be favored in cases of mitonuclear mismatch, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested--nuclear isp-1, mitochondrial …

Developmental Programming Of Dna Methylation And Gene Expression Patterns Is Associated With Extreme Cardiovascular Tolerance To Anoxia In The Common Snapping Turtle, Ilan Ruhr, Jacob Bierstedt, Turk Rhen, Debojyoti Das, Sunil Kumar Singh, Soleille Miller, Dane A. Crossley Ii, Gina L. J. Galli

Biology Faculty Publications

Background

Environmental fluctuation during embryonic and fetal development can permanently alter an organism’s morphology, physiology, and behaviour. This phenomenon, known as developmental plasticity, is particularly relevant to reptiles that develop in subterranean nests with variable oxygen tensions. Previous work has shown hypoxia permanently alters the cardiovascular system of snapping turtles and may improve cardiac anoxia tolerance later in life. The mechanisms driving this process are unknown but may involve epigenetic regulation of gene expression via DNA methylation. To test this hypothesis, we assessed in situ cardiac performance during 2 h of acute anoxia in juvenile turtles previously exposed to normoxia …

Using Beet Pulp To Adapt Cattle To Finishing Diets Compared To Traditional Grain Adaptation With Alfalfa Hay, C. J. Schneider, Matt K. Luebbe, K. H. Jenkins, Stephanie A. Furman Furman, Galen E. Erickson, Terry J. Klopfenstein

Department of Animal Science: Faculty Publications

A study was conducted to compare grain adaptation programs using beet pulp (BP) to traditional grain adaptation with alfalfa hay (AH). Yearling crossbred steers (n = 232; BW = 326 ± 14.5 kg) were separated into 3 weight blocks, stratified by BW, and assigned randomly, within strata, to 18 feedlot pens, with 12 or 13 steers per pen. Treatments were imposed during grain adaptation (21 d) using 3 grain adaptation programs. Within each grain adaptation program, 4 step rations were fed for 3, 4, 7, and 7 d. Each program increased dry-rolled corn inclusion while roughage inclusion decreased. In the …

Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman

Undergraduate Research Symposium

Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of …

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elaine Lek, Joshua Brown

Fisheries Research Reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Efficacy Study Of Selected Maize (Zea Mays L.) Genotypes Against The Asian Corn Borer, Ostrinia Furnacalis (Guenée), Yoryncita Marfori, Merdelyn Caasi-Lit, Tonette Laude

The Philippine Agricultural Scientist

Laboratory and screen house studies were conducted to assess the efficacy of selected twenty-six maize varieties against Asian corn borer (ACB), Ostrinia furnacalis (Guenée). Hierarchical tree based on resistance parameters clearly revealed that the twenty-six maize varieties are best classified into three groups, viz. resistant, intermediate, and susceptible. In laboratory test, the varieties RCS2, RCS4, RCS5, 'IPB Var13', Bt2, Bt3, and Bt4 were consistently identified as highly resistant. Further examinations in stalk feeding assay showed that the resistant varieties had sharp decline in larval survival (LS) on the 2^nd to the 5^th day of larval feeding in …

Spectral Lights Based Treatment Enhanced Biomass Accumulation And Secondary Metabolites Production In Callus Culture Of Citrus Reticulata, Faiza Anum, Naveed Iqbal Raja, Tahira Sultana, Abeer Kazmi, Amir Ali, Bushra Qayyum, Anza Afzal, Aneela Nijibat, Zia-Ur-Rehman Mashwani, Abeer Kazmi

The Philippine Agricultural Scientist

Citrus reticulata is a common fruit, belongs to the family Rutaceae. It contains terpenes, phenolics, flavonoids, and vitamin C in conjugation with sugars, amino acids, minerals, organic acids and other biologically important compounds. Application of light elicitation strategies in in vitro plant cultures is acquiring more interest for their potential in feasible biomass accumulation and therapeutically important secondary metabolites production. The present study was designed to investigate the effects of different monochromatic lights (white, red, blue, green, and yellow) on the proliferation and secondary metabolites accumulation in callus cultures of Citrus reticulata raised in response to treatment with AgNPs and …

Assesment Of Antibiotic Resistant Gene Expression In Clinical Isolates Of Pseudomonas Aeruginosa, Dustin Esmond

Biology Theses

Increasing prevalence of nosocomial infections by antimicrobial resistant pathogens resulting in higher mortality rates and financial burden is of great concern. Pseudomonas aeruginosa represents one of six highly virulent “ESKAPE” pathogens that exhibit considerable intrinsic drug resistance as well as mechanisms for acquiring further resistance. As many of these mechanisms are regulated through gene expression, we sought to identify regulatory strategies and patterns at play in 23 clinical isolates collected from Baku, Azerbaijan and Tyler, Texas, USA. Real-time quantitative polymerase chain reaction was performed on six gene targets implicated in resistance and contrasted with antibiotic phenotypes. We found AmpC cephalosporinase …

Student Perceptions Of Authoring A Publication Stemming From A Course-Based Undergraduate Research Experience (Cure), Ashley N. Turner, Anil K. Challa, Katelyn M. Cooper

Research, Publications & Creative Work

Course-based undergraduate research experiences (CUREs) engage students in authentic research experiences in a course format and can sometimes result in the publication of that research. However, little is known about student-author perceptions of CURE publications. In this study, we examined how students perceive they benefit from authoring a CURE publication and what they believe is required for authorship of a manuscript in a peer-reviewed journal. All 16 students who were enrolled in a molecular genetics CURE during their first year of college participated in semistructured interviews during their fourth year. At the time of the interviews, students had been authors …

Genetic Diversity And Population Structure Of Sugarcane (Saccharum Officinarum L.) Collected From Seven Philippine Regions For Use As Breeding Stocks For Crop Improvement, Jan Leandro Acedera, Jhun Laurence Rasco, Jemimah Banganan, Antonio Lalusin

The Philippine Agricultural Scientist

Selection of parents for hybridization relies on the information on their genetic relationship and diversity which are essential in any breeding program. This study aimed to estimate the extent of genetic diversity and population structure of 76 sugarcane accessions from seven regions in the Philippines using 57 morphological characters and 50 microsatellite markers. The sugarcane collections exhibited moderate to high diversity with mean of H’ = 0.72 for qualitative and H’ = 0.75 for quantitative morphological characters, respectively. This is corroborated by the analysis of variance (ANOVA) of agronomic parameters, except for stalk length. Unweighted Pair Group Method with Arithmetic …

Effects Of Copper Oxide (Cuo) And Zinc Oxide (Zno) Nano And Bulk Forms To Soil Fungal Community [Research Note], Jonathan Jaime Guerrero, Teresita Dalisay, Nolissa Organo, Ireneo Pangga

The Philippine Agricultural Scientist

The effects of copper oxide (CuO) and zinc oxide (ZnO) in bulk and nano forms on soil fungal community was determined. Lipa clay loam soil collected from the University of the Philippines Los Baños were placed in polypropylene bags and amended with 300 mg/L of CuO or ZnO in either forms. Colony-forming units (CFU) as well as average well color development (AWCD), functional richness and stress index were determined on day 1, 8 and 15 via indirect viable plate count method and community – level physiological profiling (CLPP). Fungal isolates from the same soil samples were likewise identified and tested …

Investigation Of Notch Signaling In Cone Fate Specification In Vertebrate Retina, Xueqing Chen

Dissertations, Theses, and Capstone Projects

In the vertebrate retina, cone photoreceptors are crucial for high acuity color vision. Several retinal diseases lead to loss of cones and there is a need to identify the normal developmental genesis of these cells to inform the development of stem cell-based therapies. Cone genesis has previously been shown to be repressed by Notch signaling, however, the mechanism by which Notch signaling controls cone fate determination is still unclear. It has been identified that cone photoreceptors are formed from multipotent retinal progenitor cells (RPCs) that first generate genetically-defined, restricted RPCs with limited mitotic and fate potential to preferentially form cones …

Exome Sequence Association Study Of Levels And Longitudinal Change Of Cardiovascular Risk Factor Phenotypes In European Americans And African Americans From The Atherosclerosis Risk In Communities Study, Ching-Ti Liu

Faculty, Staff and Student Publications

Cardiovascular disease (CVD) is responsible for 31% of all deaths worldwide. Among CVD risk factors are age, race, increased systolic blood pressure (BP), and dyslipidemia. Both BP and blood lipids levels change with age, with a dose-dependent relationship between the cumulative exposure to hyperlipidemia and the risk of CVD. We performed an exome sequence association study using longitudinal data with up to 7805 European Americans (EAs) and 3171 African Americans (AAs) from the Atherosclerosis Risk in Communities (ARIC) study. We assessed associations of common (minor allele frequency > 5%) nonsynonymous and splice-site variants and gene-based sets of rare variants with levels …

Informed Consent: Foundations And Applications, Joanna Smolenski

Dissertations, Theses, and Capstone Projects

Since its advent in the 20th century, informed consent has become a cornerstone of ethical healthcare, and obtaining it a core obligation in medical contexts. In my dissertation, I aim to examine the theoretical underpinnings of informed consent and identify what values it is taken to protect. I will suggest that the fundamental motivation behind informed consent rests in something I’ll call bodily self-sovereignty, which I argue involves a coupling of two groups of values: autonomy and non-domination on the one hand, and self-ownership and personal integrity on the other. I will then go on to consider two 'case …

The Slit-Binding Ig1 Domain Is Required For Multiple Axon Guidance Activities Of Drosophila Robo2, Lafreda J. Howard, Marie C. Reichert, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. Robo receptors signal midline repulsion in response to Slit ligands, which bind to the N-terminal Ig1 domain in most family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 signal Slit-dependent midline repulsion, while Robo2 also regulates the medial-lateral position of longitudinal axon pathways and acts non-autonomously to promote midline crossing of commissural axons. While Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2's other activities are also Slit-dependent. To determine which of Robo2's axon guidance roles …

Neurological Gene Jus Is Associated With Aging-Related Muscle Loss In The Fly Model Of Sarcopenia., Soobin An

Symposium of Student Scholars

Sarcopenia is a health condition in the elderly that is associated with degradation of muscle size, mass, and function. It can cause physical disability and, in extreme cases, death. The genetic aspect of sarcopenia is still not well understood. To shed light on sarcopenia mechanisms, we investigated muscle loss in aging fruit flies, Drosophila melanogaster. Our hypothesis was that aging-dependent muscle degradation can be affected by suboptimal functioning of the central nervous system (CNS). We used RNA interference and tissue-specific genetic drivers to induce a selective knockdown (KD) of the julius seizure gene (jus), which is associated …

In Silico Identification Of A Streptococcus Phage From An Unpasteurized Dairy Product

Symposium of Student Scholars

This study aimed to identify novel phages from a West African dairy product, nunu, to better understand the uncharacterized virosphere of a food microbiome. Nunu is a yogurt-like product from spontaneous fermentation of unpasteurized cow milk without a standardized starter culture. Phages and their bacterial hosts make up a microbiome, where their collective metagenome can be studied in silico, or computationally, after next generation sequencing (NGS). The targeted dataset for our study can be found in the Sequence Read Archives under the accession number of ERX2041567. This study utilized several bioinformatics software tools with customized settings: Kraken2, MetaVelvet, Edena, NCBI-BLAST, …