Molecular Genetics Commons^™

Determining The Primary Dna Substrates Of Shld2'S Ob-Fold Domains, Hari Patchigolla

Holster Scholar Projects

Failure to repair DNA double-stranded breaks leads to cell death. Radiation therapy is commonly used to kill cancer cells by inducing these breaks. However resistance to radiation therapy, due to a hyperactive DNA double-stranded break repair pathway, is a common occurrence that makes cancer patients more prone to relapse. The Shieldin complex is shown to promote DNA-double stranded break repair by binding to DNA at sites of damage. Thus, the objective of this project is to understand the affinity and type of DNA that Shieldin binds to, through gel-shift assays, for the eventual creation of an inhibitor for this protein …

Using Molecular Diagnostics To Develop Therapeutic Strategies For Carbapenem-Resistant Gram-Negative Infections, Fred C. Tenover

Biology Faculty Publications

Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly …

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.

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 …

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 …

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 …

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 …

Foe To Friend: Parallel Domestication Of Ophiocordyceps From Fungal Parasite To Beneficial Symbiont In Cicadas, Jason Vailionis, Eric Rl Gordon, Chris Simon

University Scholar Projects

Nutritional symbioses are integral to the survival and diversity of many insects. The majority of herbivorous insects in the order Hemiptera possess stable, inherited symbionts that produce essential amino acids and vitamins. However, instability has been observed in cicadas, with one bacterial symbiont, Hodgkinia cicadicola, being repeatedly replaced by a new fungal symbiont, Ophiocordyceps. The fungal symbionts are thought to be derived from parasitic Ophiocordyceps species, but little is known about these parasitic ancestors or how the transition from parasite to mutualist occurs. We used a combination of targeted amplified genes and metagenomic sequencing to investigate the evolution …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific Ocean, Sydney P. Harned

All HCAS Student Capstones, Theses, and Dissertations

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form large aggregations of mostly adult females, especially in the heavily-fished Eastern Tropical Pacific (ETP) Ocean. This species forms iconic, visually spectacular, seasonal aggregations in the northern Galápagos Islands, and it is hypothesized based on telemetry studies that pregnant females from these aggregations migrate to mainland coastal nurseries for parturition. This study investigated the population genetic dynamics of the scalloped hammerhead across most of its coastal and offshore distribution (Mexico to Ecuador) in the ETP, focusing on young-of-the-year animals sampled from nursery …

Having A High-Activity Catechol-O-Methyltransferase Allele Is Associated With Elevated Anxiety And Lower Salivary Dehydroepiandrosterone But Also Lower Alpha Amylase In Children With Chromosome 22q11.2 Deletion Syndrome., Jessie Beebe

LSU New Orleans Theses and Dissertations

Chromosome 22q11.2 deletion syndrome (22q11.2DS) results from a hemizygous deletion located on the long arm of chromosome 22. The most common deletion sizes affect between 30 and 90 genes. Individuals with 22q11.2DS may develop serious developmental and psychiatric disorders. The phenotype is highly variable, however, and may be influenced by allelic variation of the retained copies of genes covered by the deletion. I set out to examine the effects of two genes, catechol-O-methyltransferase (COMT) and proline dehydrogenase (PRODH), in relation to anxiety in children and adolescents with 22q11.2DS. Individuals with the major COMT allele (higher activity) have significantly higher anxiety …

Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh

Biology Faculty Publications

Numerous imaging modules are utilized to study changes that occur during cellular processes. Besides qualitative (immunohistochemical) or semiquantitative (Western blot) approaches, direct quantitation method(s) for detecting and analyzing signal intensities for disease(s) biomarkers are lacking. Thus, there is a need to develop method(s) to quantitate specific signals and eliminate noise during live tissue imaging. An increase in reactive oxygen species (ROS) such as superoxide (O2•-) radicals results in oxidative damage of biomolecules, which leads to oxidative stress. This can be detected by dihydroethidium staining in live tissue(s), which does not rely on fixation and helps prevent stress on tissues. However, …

Effects Of Trans-Acting Factors On The Translational Machinery In Yeast, Brandon M. Trainor

Graduate School of Biomedical Sciences Theses and Dissertations

Synthesis of proteins, or translation, is a complex biological process requiring the coordinated effort of numerous protein and RNA factors. Central to translation is the ribosome, a complex macromolecular complex consisting of both ribosomal RNA (rRNA) and ribosomal protein (r-protein). Ribosomes are essential and are one of the oldest and most abundant biomolecules across all forms of life. In addition to the ribosome, translation requires messenger RNA (mRNA), transfer-RNA conjugated to an amino acid (aa-tRNA), translation factors, and energy in the form of ATP and GTP. Translation universally occurs in four major stages, initiation, elongation, termination, and recycling, with initiation …

Pedigree And Molecular Assessment Of Relatedness In A Captive Chimpanzee Population, Francesca Golus

Masters Theses

As a crucial component of biodiversity, genetic diversity contributes to variability among individuals, allowing populations of endangered species to be resilient in the face of changing environmental conditions. Zoological institutions have become a cornerstone of conservation efforts and a refuge for endangered species given threats imposed on wild populations by climate change, habitat fragmentation and degradation, and overexploitation. Chimpanzees (Pan troglodytes) are an endangered species experiencing drastic population decline in the wild, yet are common residents in zoos and wildlife sanctuaries. To sustain long-term, genetically viable populations of species of concern, zoos use studbooks and paternity testing to …

Targeting Plasma Membrane Phosphatidylserine Content To Inhibit Oncogenic Kras Function, Walaa E. Kattan

Dissertations and Theses (Open Access)

The small GTPase KRAS, which is frequently mutated in human cancers, must be localized to the plasma membrane (PM) for biological activity. We recently showed that the KRAS C-terminal membrane anchor exhibits exquisite lipid-binding specificity for select species of phosphatidylserine (PtdSer). We therefore investigated whether reducing PM PtdSer content is sufficient to abrogate KRAS oncogenesis. Oxysterol-related binding proteins ORP5 and ORP8 exchange PtdSer synthesized in the ER for phosphatidylinositol-4-phosphate (PI4P) synthesized in the PM. We show that depletion of ORP5 or ORP8 reduced PM PtdSer levels, resulting in extensive mislocalization of KRAS from the PM. Concordantly, ORP5 or ORP8 depletion …

Epithelial Memory Of Resolved Inflammation Limits Tissue Damage While Promoting Pancreatic Tumorigenesis, I-Lin Ho

Dissertations and Theses (Open Access)

Inflammation is a major risk factor for pancreatic ductal adenocarcinoma. When occurring in the context of pancreatitis, mutations of KRAS accelerate tumor development. We discovered that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, epithelial cells of the pancreas display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the prompt reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thus efficiently limiting tissue damage via rapid decrease of zymogen production. We propose that since activating mutations of KRAS …

Npsd4: A New Player In Sumo-Dependent Dna Repair, Erin Atkinson

Dissertations and Theses (Open Access)

The human genome is under constant threat from sources of damage and stress. Improper resolution of DNA damage lesions can lead to mutations, oncogene activation, and genomic instability. Difficult-to-replicate-loci present barriers to DNA replication that, when not properly resolved, lead to replication fork stalling and collapse and genomic instability.

DNA damage and replication stress trigger signaling cascades potentiated by multiple types of post-translational modifications, including SUMOylation. Through proteomic analysis of proteins involved in SUMOylation following DNA damage, our lab identified an uncharacterized protein that we named New Player in SUMO-dependent DNA damage repair 4 (NPSD4). Through an additional proteomic screen, …

Anatomy And Physiology Preparatory Course Textbook (2nd Edition), Carlos Liachovitzky

Open Educational Resources

The goal of this preparatory textbook is to give students a chance to become familiar with some terms and some basic concepts they will find later on in the Anatomy and Physiology course, especially during the first few weeks of the course.

Organization and functioning of the human organism are generally presented starting from the simplest building blocks, and then moving into levels of increasing complexity. This textbook follows the same presentation. It begins introducing the concept of homeostasis, then covers the chemical level, and later on a basic introduction to cellular level, organ level, and organ system level. This …

Understanding The Pathogenesis Of Renal Medullary Carcinoma, Melinda Soeung

Dissertations and Theses (Open Access)

Renal medullary carcinoma (RMC) is a lethal cancer that predominantly affects young individuals with sickle cell trait (SCT). It is not currently understood why RMC only affects certain individuals with SCT. We found that patients with RMC more frequently participated in high-intensity exercise than matched controls. Using mouse models of SCT, we demonstrated the significant increase of renal hypoxia in the right kidney following high- but not moderate-intensity exercise. We also demonstrated in cell culture studies that SMARCB1 is ubiquitinated for proteasome-mediated degradation in hypoxia, and the re-expression of SMARCB1 leads to compromised proliferation in renal cells specifically in the …

Understanding The Role Of Arglu1 In Interferon Signaling Activation In Breast Cancer, Phuoc Nguyen

Dissertations and Theses (Open Access)

In the U.S., the highest number of new cancer cases belongs to breast cancer in women, and this cancer also bears the second-highest death rate in women. Despite significant progress in breast cancer treatment that has been made in the past several decades, innovative and efficient therapies are still needed to eradicate this deadly disease. Novel cancer immunotherapy with immune checkpoint blockade (ICB) could induce long-lasting responses and improve survival in hard-to-treat malignancies. Regrettably, only a fraction of breast cancer patients respond to this highly promising strategy. To improving ICB therapy in breast cancer treatment, IFN signaling induction is a …

Marker-Assisted Selection To Determine The Introgression Of Rpv-3 Mediated Downy Mildew Resistance In 'Chambourcin' X 'Caberenet Sauvignon' Grapevine Population, Kavya Sri Tummala

Graduate Theses/Dissertations

Downy mildew caused by the fungus, Plasmopara viticola in the grapes is one of the major diseases affecting crop yield throughout the world. Breeding grapes via conventional methods for the downy mildew resistance will take approximately 25-30 years to fully evaluate and release new cultivars. Because of the long breeding cycle in woody plant species like grape, developing DNA markers linked to genes or quantitative trait loci (QTLs) for horticultural traits can greatly accelerate the breeding process and allow a much more accurate selection of progeny. This study aims to determine the presence of resistance in the 267 F1 genotypes …

Mechanisms Of How Diet And Light Interact To Influence Drosophila Longevity Through The Eye, Charles H. Lau

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Previous studies in Drosophila melanogaster have established that overexposure to light damages photoreceptors and that photoreceptor degeneration contributes to shortened lifespans. However, the role of diet and circadian rhythms in the eye has not yet been elucidated. Many vital processes in the eye are regulated by circadian rhythms, and circadian misalignment has been proven as a driver of aging. In the eye, one of the most enriched circadian functions is phototransduction. Phototransduction plays a major role in the organism’s ability to detect light. Our lab has previously proven that Dietary Restrictions (DR) can play a role in amplifying circadian rhythms …

Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino

Pacific Journal of Health

The yeast Pichia pastoris (also known as Komagataella pastoris) has been used for over 30 years to produce thousands of valuable, heterologous proteins, such as insulin to treat diabetes and antibodies to prevent migraine headaches. Despite its success, there are some common, stubborn problems encountered by research scientists when they try to use the yeast to produce their recombinant proteins. In order to provide those working in this field with strategies to overcome these common obstacles, nine experts in P. pastoris protein expression field were interviewed to create a written review and video (https://www.youtube.com/watch?v=FyC9xXVLyD0). This review describes …

Understanding Potassium Toxicity Stress Responses Of The Extremophyte Schrenkiella Parvula Using Systems Biology Approaches, Pramod Pantha

LSU Doctoral Dissertations

Schrenkiella parvula is an extremophyte model closely related to Arabidopsis thaliana and Brassica crops. Its natural habitat includes shores of saline lakes in the Irano-Turanian region. It has adapted to grow in soils rich in multiple salts including Na⁺ and K⁺. I have investigated the genetic basis for high K⁺ tolerance in plants using S. parvula as a stress tolerant model compared to the premier plant model, Arabidopsis thaliana which is highly sensitive to salt stresses using physiological, ionomic, transcriptomic, and metabolomic approaches. Under high K⁺ stress, root system architecture changes significantly compared to control …

The Biodiversity Of Freshwater Crustaceans Revealed By Taxonomy And Mitochondrial Dna Barcodes, Adrian Amelio Vasquez, Brittany L. Bonnici, Donna R. Kashian, Jorge Trejo-Martinez, Carol J. Miller, Jeffrey L. Ram

Physiology Faculty Research Publications

Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from specimens collected by plankton net in western Lake Erie in 2012 & 2013, along with later specimens collected at various locations and times, including some collected in Belize in 2015. Methods and other details about these sequences are described in a paper by the same authors in a submitted publication (2021: URL to be given here when published). The right columns below contain additional notes on lengths of sequences, GenBank accession ID (when obtained), and annotation as to whether the sequence represents a new barcode for its …

Comparative Genomics Methods And Applications, Emily N. Alden

Biomedical Sciences ETDs

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …

Diversity And Host Specificity Of Nycteribiid Bat Flies (Diptera: Nycteribiidae) In Kenya, Taylor Verrett

Masters Theses & Specialist Projects

Bat flies (Diptera: Nycteribiidae and Streblidae) are hematophagous ectoparasites of bats distributed globally. Members of Nycteribiidae are morphologically constrained relative to streblids, and are united by their lack of wings, dorso-ventrally compressed bodies, and a primary distribution across the Eastern hemisphere. Bats are principal reservoirs of infectious diseases, including viral zoonoses of important consideration to human health, but the overall high host specificity of bat flies has largely been thought to curb their potential as inter-specific vectors of bat-borne pathogens. However, nycteribiid diversity and host associations remain critically understudied in some geographic regions, and rare examples of nycteribiid bat flies …

Sensitive And Specific Detection Of Sars-Cov-2 In Saliva Using Reverse Transcriptase Loop-Mediated Isothermal Amplification, Casey Juntila

All NMU Master's Theses

A novel coronavirus called SARS-CoV-2 has caused the emergency release of the most well-known molecular assay, the CDC N1 RT-PCR assay, causing reports of poor analytical performance resulting in false-negative results (20, 26), and inconsistent testing kits received (23, 32). An immediate and dire need for a rapid and reliable SARS-CoV-2 testing workflow specifically designed for a university setting is the purpose this project is aiming and intended to fulfill. The workflow design uses a less invasive saliva sample for rapid screening using colorimetric RT-LAMP detection of three SARS-CoV-2 gene regions for Orf1ab, envelope, and nucleocapsid. Purified SARS-CoV-2 genomic RNA …

Telomeric And Sub-Telomeric Structure And Implications In Fungal Opportunistic Pathogens, Raffaella Diotti, Michelle Esposito, Chang Hui Shen

Publications and Research

Telomeres are long non-coding regions found at the ends of eukaryotic linear chromosomes. Although they have traditionally been associated with the protection of linear DNA ends to avoid gene losses during each round of DNA replication, recent studies have demonstrated that the role of these sequences and their adjacent regions go beyond just protecting chromosomal ends. Regions nearby to telomeric sequences have now been identified as having increased variability in the form of duplications and rearrangements that result in new functional abilities and biodiversity. Furthermore, unique fungal telomeric and chromatin structures have now extended clinical capabilities and understanding of pathogenicity …

Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed

Honors Scholar Theses

Parkinson's Disease (PD) is a progressive neurodegenerative and movement disorder primarily caused by the degradation of dopaminergic neurons. Known markers of neurodegeneration in PD are Lewy Bodies, which are fibrillar aggregates that are found in the brains of PD patients. Lewy Bodies can accumulate from specific mutations in the SNCA gene that codes for alpha-synuclein, a protein enriched in presynaptic neurons. A mutated SNCA gene can cause conformational aggregates of alpha-synuclein to form toxic species mediating neuronal death. Research into alpha-synuclein has led to the discovery of a binding partner known as synphilin-1 that is also found in protein aggregates …