Digital Commons Network^™

Cftr Deletion In Mouse Epithelial And Immune Cells Differentially Influence The Intestinal Microbiota, Callie E. Scull, Meng Luo, Scott Jennings, Christopher M. Taylor, Guoshun Wang

School of Medicine Faculty Publications

Cystic fibrosis (CF) is a life-threatening genetic disorder, caused by mutations in the CF transmembrane-conductance regulator gene (cftr) that encodes CFTR, a cAMP-activated chloride and bicarbonate channel. Clinically, CF lung disease dominates the adult patient population. However, its gastrointestinal illness claims the early morbidity and mortality, manifesting as intestinal dysbiosis, inflammation and obstruction. As CF is widely accepted as a disease of epithelial dysfunction, it is unknown whether CFTR loss-of-function in immune cells contributes to these clinical outcomes. Using cftr genetic knockout and bone marrow transplantation mouse models, we performed 16S rRNA gene sequencing of the intestinal microbes. Here we …

Integrating Genomic Information With Tumor-Immune Microenvironment In Triple-Negative Breast Cancer, David Otohinoyi, Aditi Kuchi, Jiande Wu, Chindo Hicks

School of Graduate Studies Faculty Publications

Background: the development and progression of triple-negative breast cancer (TNBC) is driven by somatic driver mutations and the tumor-immune microenvironment. To date, data on somatic mutations has not been leveraged and integrated with information on the immune microenvironment to elucidate the possible oncogenic interactions and their potential effects on clinical outcomes. Here, we investigated possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment, and their correlation with patient survival in TNBC. Methods: We performed analysis combining data on 7,875 somatic mutated genes with information on 1,751 immune-modulated genes, using gene-expression data as the intermediate phenotype, and correlated the resulting …

Contrasting Particle Fluxes And Composition In A Submarine Canyon Affected By Natural Sediment Transport Events And Bottom Trawling, Sarah Paradis, Marta Arjona-Camas, Miguel Goñi, Albert Palanques, Pere Masqué, Pere Puig

Research outputs 2022 to 2026

Submarine canyons are important conduits of sediment and organic matter to deep-sea environments, mainly during high-energy natural events such as storms, river floods, or dense shelf water cascading, but also due to human activities such as bottom trawling. The contributions of natural and trawling-induced sediment and organic matter inputs into Palamós Canyon (NW Mediterranean) were assessed from three instrumented moorings deployed in the axis and northern flank of the canyon covering the trawling closure (February) and the trawling season (March-December) of 2017. During the trawling closure, large sediment fluxes with high contents of labile marine organic matter content were registered …

Faculty Senate Minutes, Georgia Southern University, Faculty Senate

Faculty Senate Minutes

No abstract provided.

Undergraduate Perceptions Of Warmth And Competence Across Academic Professions, Porsha Nichole Neal Mcgregor

Student Theses and Dissertations

The Stereotype Content Model (SCM; Fiske et al., 2002) is utilized to make sense of how individuals and groups assess others. The SCM consist of to two basic dimensions: perceived warmth and competence. Little research has been conducted to analyze how people perceive individuals in relation to their professional roles. To better understand potential stereotypes of professions, participants were asked to rate general professions on the two dimensions of warmth and competence. Results from the study supported some patterns found in previous research by Brambillia et al. (2010) in regards to two professions and indicated similarities in newly studied professions.

Viruses In Astrobiology, Ignacio De La Higuera, Ester Lázaro

Biology Faculty Publications and Presentations

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very …

Reproductive Biology Of Gazella Arabica: Predictors Of Offspring Weight And Short- And Long-Term Offspring Survival, Ryan A. Martin

Faculty Scholarship

Reproductive traits are central to organismal fitness, and so the factors influencing patterns of reproduction and offspring survival are at the heart of biology. Making use of breeding data collected over 16 years at the King Khalid Wildlife Research Centre in Saudi Arabia, we investigated the reproductive biology of Arabian gazelles Gazella arabica. Offspring survival was mainly a function of birth weight, with heavier offspring having higher survival rates than lighter offspring. However, while sons were heavier than daughters, daughters had higher survival rates. We could not find evidence that giving birth to sons negatively impacts offspring weight in the …

Rescue Of Deficits By Brwd1 Copy Number Restoration In The Ts65dn Mouse Model Of Down Syndrome, Sasha L. Fulton, Wendy Wenderski, Ashley E. Lepack, Andrew L. Eagle, Tomas Fanutza, Ryan M. Bastle, Aarthi Ramakrishnan, Emma C. Hays, Arianna Neal, Jaroslav Bendl, Lorna A. Farrelly, Amni Al-Kachak, Yang Lyu, Bulent Cetin, Jennifer C. Chan, Tina N. Tran, Rachael L. Neve, Randall J. Roper, Kristen J. Brennand, Panos Roussos, John C. Schimenti, Allyson K. Friedman, Li Shen, Robert D. Blitzer, Alfred J. Robison, Gerald R. Crabtree, Ian Maze

Publications and Research

With an incidence of ~1 in 800 births, Down syndrome (DS) is the most com- mon chromosomal condition linked to intellectual disability worldwide. While the genetic basis of DS has been identified as a triplication of chromosome 21 (HSA21), the genes encoded from HSA 21 that directly contribute to cognitive de fi cits remain incompletely understood. Here, we found that the HSA21- encoded chromatin effector, BRWD1, was upregulated in neurons derived from iPS cells from an individual with Down syndrome and brain of trisomic mice. We showed that selective copy number restoration of Brwd1 in trisomic animals rescued de fi …

Dysfunctional Glymphatic System With Disrupted Aquaporin 4 Expression Pattern On Astrocytes Causes Bacterial Product Accumulation In The Csf During Pneumococcal Meningitis, Jaqueline S Generoso, Sigrun Thorsdottir, Allan Collodel, Diogo Dominguini, Roberta R E Santo, Fabricia Petronilho, Tatiana Barichello, Federico Iovino

Faculty, Staff and Student Publications

Pneumococcal meningitis, inflammation of the meninges due to an infection of the Central Nervous System caused by Streptococcus pneumoniae (the pneumococcus), is the most common form of community-acquired bacterial meningitis globally. Aquaporin 4 (AQP4) water channels on astrocytic end feet regulate the solute transport of the glymphatic system, facilitating the exchange of compounds between the brain parenchyma and the cerebrospinal fluid (CSF), which is important for the clearance of waste away from the brain. Wistar rats, subjected to either pneumococcal meningitis or artificial CSF (sham control), received Evans blue-albumin (EBA) intracisternally. Overall, the meningitis group presented a significant impairment of …

The Hard Work Of Hard Conversations, Benjamin Scott Savard

UNH Today Archive

No abstract provided.

Exploring Parenthood And The Influence Of Lived Experiences On Parenting Behaviors Among Child Welfare-Involved Adults, Veronica Howell

USF Tampa Graduate Theses and Dissertations

The World Health Organization asserts the healthy development of children is essential. Cases of violence and maltreatment impede the development of children worldwide. Six in 10 adults in the general US population have reported at least one adverse childhood experience (ACE), while vulnerable populations, including child welfare-involved adults (i.e., parents and caregivers), often report more. This history is associated with higher morbidity and mortality rates alongside higher economic costs; therefore, preventing ACEs and promoting safe, stable, and nurturing relationships between parents and children is critical. The purpose of this exploratory qualitative study was to understand the meanings and responsibilities associated …

Measurement In Chemistry, Mathematics, And Physics Education: Student Explanations Of Organic Chemistry Reaction Mechanisms And Instructional Practices In Introductory Courses, Brandon J. Yik

USF Tampa Graduate Theses and Dissertations

The work in this dissertation is presented in two parts. The first part (Chapters 3 and 4) details work relating to students’ explanations of reaction mechanisms in organic chemistry. The second part (Chapters 5 and 6) details work relating to the evaluating the uptake of research-based instructional practices in introductory chemistry, mathematics, and physics courses.

To evaluate learning of organic chemistry reactions, instructors must ask students to construct written explanations of reaction mechanisms. Written assessments should focus on what is happening and why it is happening to promote deeper student understanding. However, for instructors to gain insight into students’ understanding, …

Rapid Reconstruction Of Neural Circuits Using Tissue Expansion And Light Sheet Microscopy, Joshua L Lillvis, Hideo Otsuna, Xiaoyu Ding, Igor Pisarev, Takashi Kawase, Jennifer Colonell, Konrad Rokicki, Cristian Goina, Ruixuan Gao, Amy Hu, Kaiyu Wang, John Bogovic, Daniel E Milkie, Linus Meienberg, Brett D Mensh, Edward S Boyden, Stephan Saalfeld, Paul W Tillberg, Barry J Dickson

Faculty, Staff and Student Publications

Brain function is mediated by the physiological coordination of a vast, intricately connected network of molecular and cellular components. The physiological properties of neural network components can be quantified with high throughput. The ability to assess many animals per study has been critical in relating physiological properties to behavior. By contrast, the synaptic structure of neural circuits is presently quantifiable only with low throughput. This low throughput hampers efforts to understand how variations in network structure relate to variations in behavior. For neuroanatomical reconstruction, there is a methodological gulf between electron microscopic (EM) methods, which yield dense connectomes at considerable …

Faculty Senate Agenda, Georgia Southern University, Faculty Senate

Faculty Senate Agendas

No abstract provided.

Neurodevelopment Assessment Of Small For Gestational Age Children In A Community-Based Cohort From Pakistan, Sabahat Naz, Zahra Hoodbhoy, Ali Jaffar, Sidra Kaleem Jafri, Babar Hasan, Devyani Chowdhury, Melissa Gladstone

Department of Paediatrics and Child Health

Background: Children born small for gestational age (SGA) may experience more long-term neurodevelopmental issues than those born appropriate for gestational age (AGA). This study aimed to assess differences in the neurodevelopment of children born SGA or AGA within a periurban community in Pakistan.
Methods: This was a prospective cohort study in which study participants were followed from the pilot Doppler cohort study conducted in 2018. This pilot study aimed to develop a pregnancy risk stratification model using machine learning on fetal Dopplers. This project identified 119 newborns who were born SGA (2.4±0.4 kg) based on International Fetal and Newborn Growth …

Epidemiology Of Plasmid Lineages Mediating The Spread Of Extended-Spectrum Beta-Lactamases Among Clinical Escherichia Coli, Bejan Mahmud, Meghan A Wallace, Kimberly A Reske, Kelly Alvarado, Carol E Muenks, David A Rasmussen, Carey-Ann D Burnham, Cristina Lanzas, Erik R Dubberke, Gautam Dantas

2020-Current year OA Pubs

The prevalence of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Escherichia coli has been increasing, with this spread driven by ESBL-encoding plasmids. However, the epidemiology of ESBL-disseminating plasmids remains understudied, obscuring the roles of individual plasmid lineages in ESBL spread. To address this, we performed an in-depth genomic investigation of 149 clinical ESBL-like E. coli isolates from a tertiary care hospital. We obtained high-quality assemblies for 446 plasmids, revealing an extensive map of plasmid sharing that crosses time, space, and bacterial sequence type boundaries. Through a sequence-based network, we identified specific plasmid lineages that are responsible for the dissemination of …

Emergence Of Compensatory Mutations Reveals The Importance Of Electrostatic Interactions Between Hiv-1 Integrase And Genomic Rna, Christian Shema Mugisha, Tung Dinh, Abhishek Kumar, Kasyap Tenneti, Jenna E Eschbach, Keanu Davis, Robert Gifford, Mamuka Kvaratskhelia, Sebla B Kutluay

2020-Current year OA Pubs

HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by mislocalization of the gRNA between the capsid lattice and the lipid envelope. These viruses are noninfectious due to a block at an early reverse transcription stage in target cells. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA; however, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are …

Marijuana Use And Dna Methylation-Based Biological Age In Young Adults, Drew R Nannini, Yinan Zheng, Brian T Joyce, Tao Gao, Lei Liu, David R Jacobs Jr, Pamela Schreiner, Chunyu Liu, Steve Horvath, Ake T Lu, Kristine Yaffe, Stephen Sidney, Philip Greenland, Donald M Lloyd-Jones, Lifang Hou

2020-Current year OA Pubs

BACKGROUND: Marijuana is the third most commonly used drug in the USA and efforts to legalize it for medical and recreational use are growing. Despite the increase in use, marijuana's effect on aging remains understudied and understanding the effects of marijuana on molecular aging may provide novel insights into the role of marijuana in the aging process. We therefore sought to investigate the association between cumulative and recent use of marijuana with epigenetic age acceleration (EAA) as estimated from blood DNA methylation.

RESULTS: A random subset of participants from The Coronary Artery Risk Development in Young Adults (CARDIA) Study with …

The Effect Of Arbuscular Mycorrhizae On Milkweed Growth And Its Implications For Western Monarchs, Rylee Mattson, Estrella Silva, Katherine Klassen, Laurie Dizney

RURALS: Review of Undergraduate Research in Agricultural and Life Sciences

Western monarch butterfly (Danaus plexippus plexippus) populations in the Pacific Northwest have decreased by approximately 99% in recent decades due in part to the destruction of milkweed (Asclepias spp.) habitat. Milkweeds are one of the only plant genera upon which monarchs will lay eggs and the larvae will feed, so milkweed habitat restoration is critical for the future survival and rehabilitation of western monarch butterfly populations. This research aimed to investigate the effect of the root symbiont arbuscular mycorrhizal fungus (AMF) on growth for two species of milkweed native to Oregon’s Willamette Valley. In showy milkweed …

Using The Embl-Ebi Clustal Omega Tool To Calculate Diversity Of Heavy Chain Phage-Display Libraries, Michael Bodri, Shane A. Webb

Georgia Journal of Science

Here we show that traditional Sanger sequencing combined with analysis tools available from the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), specifically EMBOSS Transeq and Clustal Omega, is extremely effective in the analysis of naïve phage display antibody libraries for the determination of library size and diversity. The free tools are easy to use and require little manipulation of reads by hand, allowing analysis to be performed on a standard personal computer. Utilization of this technique has applicability to researchers with limited access to deep sequencing. The primary drawback to this analysis methodology is that antibodies with particular molecular or …

A 2d Chaotic Oscillator For Analog Ic, Partha Sarathi Paul, Parker Hardy, Maisha Sadia, Md Sakib Hasan

Faculty and Student Publications

In this paper, we have proposed the design of an analog two-dimensional (2D) discrete-time chaotic oscillator. 2D chaotic systems are studied because of their more complex chaotic behavior compared to one-dimensional (1D) chaotic systems. The already published works on 2D chaotic systems are mainly focused either on the complex analytical combinations of familiar 1D chaotic maps such as Sine map, Logistic map, Tent map, and so on, or off-the-shelf component-based analog circuits. Due to complex hardware requirements, neither of them is feasible for hardware-efficient integrated circuit (IC) implementations. To the best of our knowledge, this proposed work is the first-ever …

Spartan Daily, October 25, 2022, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2022

Volume 159, Issue 27

On Airborne Tire Wear Particles Along Roads With Different Traffic Characteristics Using Passive Sampling And Optical Microscopy, Single Particle Sem/Edx, And Μ-Atr-Ftir Analyses, Zhiqiang Gao, James V. Cizdziel, Kendall Wontor, Carly Clisham, Kaylea Focia, Juanita Rausch, David Jaramillo-Vogel

Faculty and Student Publications

Tire wear particles (TWPs) are a major category of microplastic pollution produced by friction between tires and road surfaces. This non-exhaust particulate matter (PM) is transported through the air and with runoff leading to environmental pollution and health concerns. Here, we collected airborne PM along paved roads with different traffic volumes and speeds using Sigma-2 passive samplers. Particles entering the samplers deposit onto substrates for analysis, or, as we modified it, directly into small (60 ml) separatory funnels, which is particularly useful with high particle loads, where a density separation aids in isolating the microplastics. We quantified putative TWPs (∼10–80 …

Pooled Image-Base Screening Of Mitochondria With Microraft Isolation Distinguishes Pathogenic Mitofusin 2 Mutations, Alex L Yenkin, John C Bramley, Colin L Kremitzki, Jason E Waligorski, Mariel J Liebeskind, Xinyuan E Xu, Vinay D Chandrasekaran, Maria A Vakaki, Graham W Bachman, Robi D Mitra, Jeffrey D Milbrandt, William J Buchser

2020-Current year OA Pubs

Most human genetic variation is classified as variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a method termed "Raft-Seq". We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator Mitofusin 2, even when the cellular phenotype is subtle. We also show …

Risk Factors Of Female-Perpetrated Intimate Partner Violence Among Hispanic Young Adults: Attachment Style, Emotional Dysregulation, And Negative Childhood Experiences, Joahana Segundo, Arturo L. Cantos, Gabriela Ontiveros, K. Daniel O'Leary

Psychological Science Faculty Publications

This paper examined whether risk factors commonly associated with intimate partner violence (IPV) are associated with female-perpetrated physical IPV and female physical IPV victimization among young Hispanic women. It also examined how emotion dysregulation, impulsivity, and attachment style exacerbated these relationships. Furthermore, it investigates how these associations differ by the type of self-reported physical violence against their romantic partner. Based on the participants' self-reported physical violence, they were classified into one of four groups: nonviolent, victim-only, perpetrator-only, and bidirectionally violent. Bidirectional violence was by far the most common form of violence reported. Utilizing self-report data from 360 young Hispanic women, …

Traumatic Brain Injury Biomarkers, Simulations And Kinetics, Celeste Hicks, Akshima Dhiman, Chauntel Barrymore, Tarun Goswami

Biomedical, Industrial & Human Factors Engineering Faculty Publications

This paper reviews the predictive capabilities of blood-based biomarkers to quantify traumatic brain injury (TBI). Biomarkers for concussive conditions also known as mild, to moderate and severe TBI identified along with post-traumatic stress disorder (PTSD) and chronic traumatic encephalopathy (CTE) that occur due to repeated blows to the head during one’s lifetime. Since the pathways of these biomarkers into the blood are not fully understood whether there is disruption in the blood–brain barrier (BBB) and the time it takes after injury for the expression of the biomarkers to be able to predict the injury effectively, there is a need to …

Accelerating Multiparametric Mri For Adaptive Radiotherapy, Shraddha Pandey

USF Tampa Graduate Theses and Dissertations

MR guided Radiotherapy (MRgRT) marks an important paradigm shift in the field of radiotherapy. Superior tissue contrast of MRI offers better visualization of the abnormal lesions, as a result precise radiation dose delivery is possible. In case of online treatment planning, MRgRT offers better control of intratumoral motion and quick adaptation to changes in the gross tumor volume. Nonetheless, the MRgRT process flow does suffer from some challenges that limit its clinical usability. The primary aspects of MRgRT workflow are MRI acquisition, tumor delineation, dose map prediction and administering treatment. It is estimated that the acquisition of MRI takes around …

5-Aminolevulinate Synthase Inhibitors And Methods Of Use Thereof, Roman Manetsch, Gloria C. Ferreira, Bosko M. Stojanovski, Katya Pavlova Nacheva

USF Patents

Disclosed herein, are 5-Aminolevulinate synthase inhibitors and methods for their use in the treatment of porphyria. In at least one specific embodiment, the 5-Aminolevulinate synthase inhibitors can include compounds or salts thereof of Formulas (I-V)

Enhancing Production Of Functional Proteins In Plant Cell Culture Through Cellular Engineering And Rational Protein Design, Uddhab Karki

Student Theses and Dissertations

Plant cell culture is emerging as a promising alternative bioproduction platform for valuable proteins due to its low cost of production, safety (free from animal pathogen contamination) and ease of scale-up. However, there are common challenges for commercialization, including low protein yields, difficulty in cryopreservation, and non-human glycosylation, etc. This research project addresses the overarching research hypothesis that strategically modifying the plant cell genome using CRISPR/Cas9 technology and rationally designing protein molecules by fusing with a functional module enhance the production of protein in plant cell culture and improve protein function. There are two specific aims addressed in this project: …

Synthesis Of Carbon Nanohoops And Macrocycles Via Alkyne Metathesis, Xin Zhou

LSU Doctoral Dissertations

Cycloparaphenyleneacetylene (CPPA) and cycloparaphenylene (CPP) are called carbon nanohoops; they are fully conjugated macrocycles with radially oriented aromatic groups. Though many syntheses of CPPA and CPP were reported, in the macrocyclization step, the yields were usually not satisfying, as the reactions were irreversible. Our group utilizes alkyne metathesis to address this problem. Chapter 1 provides backgrounds and an introduction to the carbon nanohoops and alkyne metathesis.

Chapter 2 details the synthesis of the [3]CPP⁴A and [3]CPP⁵A, with good macrocyclization yields via alkyne metathesis. This study showed the error-correction ability of alkyne metathesis, especially with nonsymmetric substrates. …