Genetics and Genomics Commons^™

Induction Of Il19 Expression Through Jnk And Cgas-Sting Modulates Dna Damage–Induced Cytokine Production, Sara H. Small, E. Jessica Tang, Ryan L. Ragland, Yaroslava Ruzankina, David W. Schoppy, Rahul S. Mandal, M. Rebecca Glineburg, Zgjim Ustelenca, Daniel J. Powell, Fiona Simpkins, F. Bradley Johnson, Eric J. Brown

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Cytokine production is a critical component of cell-extrinsic responses to DNA damage and cellular senescence. Here, we demonstrated that expression of the gene encoding interleukin-19 (IL-19) was enhanced by DNA damage through pathways mediated by c-Jun amino-terminal kinase (JNK) and cGAS-STING and that IL19 expression was required for the subsequent production of the cytokines IL-1, IL-6, and IL-8. IL19 expression was stimulated by diverse cellular stresses, including inhibition of the DNA replication checkpoint kinase ATR (ataxia telangiectasia and Rad3-related protein), oncogene expression, replicative exhaustion, oxidative stress, and DNA double-strand breaks. Unlike the production of IL-6 and IL-8, IL19 expression was …

Citric Acid/Β-Alanine Carbon Dots As A Novel Tool For Delivery Of Plasmid Dna Into E. Coli Cells, Anju Pandey, Asmita Devkota, Anil Sigdel, Zeinab Yadegari, C. Korsi Dumenyo, Ali Taheri

Agricultural and Environmental Sciences Faculty Research

Successful delivery of plasmid DNA into the microbial cells is fundamental in recombinant DNA technology. Natural bacterial transformation is limited to only certain species due in part to the repulsive forces between negatively charged DNA and bacterial membranes. Most common method of DNA delivery into bacteria is artificial transformation through heat shock and electroporation. These methods require sophisticated instruments and tedious steps in preparation of competent cells. Transformation by conjugation is also not applicable to all plasmids. Nanoparticles have been used successfully in therapeutics for drug delivery into animal cells. They are starting to gain popularity in plant sciences as …

Soil Bacteria In Urban Community Gardens Have The Potential To Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer, Abdullah Ibn Mafiz, Yingshu He, Wei Zhang, Yifan Zhang

Agricultural and Environmental Sciences Faculty Research

Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in …

Editorial For The Genetics Of Alzheimer’S Disease Special Issue: October 2021, Laura Ibanez, Justin B. Miller

Sanders-Brown Center on Aging Faculty Publications

No abstract provided.

Dna Barcoding Enhances Large-Scale Biodiversity Initiatives For Deep-Pelagic Crustaceans Within The Gulf Of Mexico And Adjacent Waters, Carlos Varela

FIU Electronic Theses and Dissertations

In this dissertation I investigate the biodiversity of marine deep-water crustaceans of the Gulf of Mexico and adjacent waters, focusing on pelagic crustaceans. Taxonomic and molecular techniques were utilized to document adult and larval crustacean specimens to better under their taxonomy, life history, evolutionary relationships and cryptic biodiversity. The use of molecular techniques to study organisms from habitats with limited accessibility provides tremendous potential. With prevalent anthropogenic threats and the delicate nature of deep-water habitats, the need to improve our understanding of these systems is clear. Molecular techniques can act as a fundamental tool to complement traditional taxonomy. The application …

Invasion Genetics Of The Non-Native Geckos Phelsuma Grandis Gray 1870 And Gekko Gecko (Linnaeus 1758) In Southern Florida, Usa, Thomas William Fieldsend

FIU Electronic Theses and Dissertations

Biological invasions cause tremendous damage to ecosystems, economies, and human livelihoods worldwide. Florida is home to more established non-native species of reptiles and amphibians than anywhere else on Earth, many of which cause substantial harm to native biodiversity and human well-being. The relatively new discipline of invasion genetics promises to significantly improve the understanding, prediction, prevention, and management of biological invasions. The purpose of this dissertation is to utilize invasion genetics techniques to further understanding of the patterns and processes of biological invasions, especially as they pertain to Florida’s destructive and diverse non-native squamate reptile assemblage. In the first phase …

Vps54 Regulates Lifespan And Locomotor Behavior In Adult Drosophila Melanogaster, Emily C. Wilkinson, Emily L. Starke, Scott A. Barbee

Biological Sciences: Faculty Scholarship

Vps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the …

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.

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, Elain 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 …

Atg8 Is Conserved Between Saccharomyces Cerevisiae And Psychrophilic, Polar-Collected Fungi, B. J. Ivory, H. M. Smith, E. Cabrera, M. R. Robinson, J. T. Sparks, A. Solem, J. I. Ishihara, H. Takahashi, M. Tsuji, V. A. Segarra

Osteopathic Medicine, Jerry M. Wallace School of

No abstract provided.

Role Of A Cryptic Trna Gene Operon In Survival Under Translational Stress, Javier Santamaría-Gómez, Miguel Ángel Rubio, Rocío López-Igual, Ana B. Romero-Losada, Fernando M. Delgado-Chaves, Roque Bru-Martínez, Francisco J. Romero-Campero, Antonio Herrero, Michael Ibba, Jesús A. G. Ochoa De Alda, Ignacio Luque

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that …

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, …

Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike

Department of Biochemistry: Dissertations, Theses, and Student Research

Plant oils are an important source of food, fuel, and feed in our society today. The oil found in the seeds of plants is composed almost entirely of triacylglycerol (TAG) molecules, which consist of three fatty acids esterified to a glycerol backbone. As crude oil supplies decline, vegetable oils are gaining traction as a renewable substitute to petroleum-based materials in fuels, lubricants, and specialty oleochemicals. However, as it currently stands vegetable oils do not possess the properties necessary to fill the void of a petroleum free world.

To address this problem, plant biotechnologists have done extensive work on genetic engineering …

Biallelic Variants In Pcdhgc4 Cause A Novel Neurodevelopmental Syndrome With Progressive Microcephaly, Seizures, And Joint Anomalies, Maria Iqbal, Reza Maroofian, Büşranur Çavdarlı, Florence Riccardi, Michael Field, Siddharth Banka, Dalal K. Bubshait, Yun Li, Jozef Hertecant, Shahid Mahmood Baig

Department of Biological & Biomedical Sciences

Purpose: We aimed to define a novel autosomal recessive neurodevelopmental disorder, characterize its clinical features, and identify the underlying genetic cause for this condition.
Methods: We performed a detailed clinical characterization of 19 individuals from nine unrelated, consanguineous families with a neurodevelopmental disorder. We used genome/exome sequencing approaches, linkage and cosegregation analyses to identify disease-causing variants, and we performed three-dimensional molecular in silico analysis to predict causality of variants where applicable.
Results: In all affected individuals who presented with a neurodevelopmental syndrome with progressive microcephaly, seizures, and intellectual disability we identified biallelic disease-causing variants in Protocadherin-gamma-C4 (PCDHGC4). Five variants were …

Conservation Of South Florida Orchid Mycorrhizal Fungi, Ellen Garcia

FIU Electronic Theses and Dissertations

Starting in the late 1800’s orchids were heavily poached, leaving many species to reach critically low numbers. Coupled with habitat loss and urbanization many orchid populations were extirpated in southern Florida. Due to lack of endosperm, orchid seeds are reliant on specific mycorrhizal fungi to obtain nutrients to enable growth and development resulting in very low germination rates in nature. The obligate relationship on mycorrhizal fungi complicates orchid re-establishment. The research project aims are (1) to evaluate the correlation between phenotypic traits and optimal growing conditions in various micro-climate, and (2) to assess the range of mycorrhizal fungi community in …

Genome Wide Association Mapping Of Root Traits In The Andean Genepool Of Common Bean (Phaseolus Vulgaris L.) Grown With And Without Aluminum Toxicity, Daniel Ambachew, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity …

Human Population History At The Crossroads Of East And Southeast Asia Since 11,000 Years Ago, Tianyi Wang, Wei Wang, Guangmao Xie, Zhen Li, Xuechun Fan, Qingping Yang, Xichao Wu, Ling Qin, Fajun Li, Melinda A. Yang

Biology Faculty Publications

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry …

A Screen For Sleep And Starvation Resistance Identifies A Wake-Promoting Role For The Auxiliary Channel Unc79, Kazuma Murakami, Justin Palermo, Bethany A. Stanhope, Allen G. Gibbs, Alex C. Keene

Life Sciences Faculty Research

The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in …

Successful Atac-Seq From Snap-Frozen Equine Tissues, Sichong Peng, Rebecca Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno

Veterinary Science Faculty Publications

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin …

Patterns Of Recent Natural Selection On Genetic Loci Associated With Sexually Differentiated Human Body Size And Shape Phenotypes, Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno, George H. Perry

Anthropology Faculty Publications

Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (~194,000 females and ~167,000 males) to identify a total of 114,199 single nucleotide polymorphisms (SNPs) significantly associated with at least one of …

Long-Term Gene–Culture Coevolution And The Human Evolutionary Transition, Timothy M. Waring, Zachary T. Wood

School of Economics Faculty Scholarship

It has been suggested that the human species may be undergoing an evolutionary transition in individuality (ETI). But there is disagreement about how to apply the ETI framework to our species, and whether culture is implicated as either cause or consequence. Long-term gene–culture coevolution (GCC) is also poorly understood. Some have argued that culture steers human evolution, while others proposed that genes hold culture on a leash. We review the literature and evidence on long-term GCC in humans and find a set of common themes. First, culture appears to hold greater adaptive potential than genetic inheritance and is probably driving …

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …

Transcriptional Analysis Of The Response Of C. Elegans To Ethanol Exposure, Mark G. Sterken, Marijke H. Van Wijk, Elizabeth C. Quamme, Joost A. G. Riksen, Lucinda Carnell, Laura D. Mathies, Andrew G. Davies, Jan E. Kammenga, Jill C. Bettinger

Biology Faculty Scholarship

Ethanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved …

Identifying The Cell Composition And Clonal Diversity Of Supratentorial Ependymoma Using Single Cell Rna-Sequencing, James He

University Scholar Projects

Ependymoma is a primary solid tumor of the central nervous system. Supratentorial ependymoma (ST-EPN), a subtype of ependymomas, is driven by an oncogenic fusion between the ZFTA and RELA genes in 70% of cases. We introduced this fusion into neural progenitor cells of mice embryos via in utero electroporation of a non-viral binary piggyBac transposon system containing ZFTA-RELA. From preliminary data in the LoTurco lab, inducing the expression of ZFTA-RELA into different neural progenitor cells produces tumors of varying lethality and cellular composition. To define the cellular composition and subclonal diversity of ST-EPN tumors, we used single cell RNA-sequencing to …

Sources Of Resistance To Common Bacterial Blight And Charcoal Rot Disease For The Production Of Mesoamerican Common Beans In The Southern United States, Daniel Ambachew, Jacqueline Joshua, Margaret T. Mmbaga, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

University Scholar Projects

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

Honors Scholar Theses

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

New Emerging Roles Of The Novel Hepatokine Serpinb1 In Type 2 Diabetes Mellitus: Crosstalk With B-Cell Dysfunction And Dyslipidemia, Mohamed M. Kamal, Aya A. Ali, Ghada H. Sayed, Shadia Ragab, Dina H. Kassem

Pharmacy

Diabetes mellitus (DM) is a devastating metabolic disease. Recently, the cross-talk between insulin-secreting-β-cells and various organs has sparked much interest. SerpinB1 emerged as a novel hepatokine inducing β-cell proliferation. However, its role in type-2-DM (T2DM) patients has not been adequately studied. This study was designed to investigate its circulating levels in subjects with/without T2DM, and to study its association with β-cell function, as well as various glycemic-control and lipid-profile parameters. Anthropometric data and biochemical markers including fasting plasma glucose (FPG), HbA1C % and lipid profile parameters were measured in 55 T2DM patients, as well as 30 healthy nondiabetic subjects. Serum …