Biology Commons^™

Neuromodulation With Electromagnetic Stimulation For Seizure Suppression: From Electrode To Magnetic Coil, Hui Ye, Stephanie Kaszuba

Biology: Faculty Publications and Other Works

Non-invasive brain tissue stimulation with a magnetic coil provides several irreplaceable advantages over that with an implanted electrode, in altering neural activities under pathological situations. We reviewed clinical cases that utilized time-varying magnetic fields for the treatment of epilepsy, and the safety issues related to this practice. Animal models have been developed to foster understanding of the cellular/molecular mechanisms underlying magnetic control of epileptic activity. These mechanisms include (but are not limited to) (1) direct membrane polarization by the magnetic field, (2) depolarization blockade by the deactivation of ion channels, (3) alteration in synaptic transmission, and (4) interruption of ephaptic …

Genetic Regulatory Variation In Populations Informs Transcriptome Analysis In Rare Disease, Pejman Mohammadi, Stephane E. Castel, Beryl B. Cummings, Jonah Einson, Christina Sousa, Paul Hoffman, Sandra Donkervoort, Zhuoxun Jiang, Payam Mohassel, A. Reghan Foley, Heather E. Wheeler, Hae Kyung Im, Carsten G. Bonnemann, Daniel G. Macarthur, Tuuli Lappalainen

Biology: Faculty Publications and Other Works

Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential …

Bacteriophages Of The Lower Urinary Tract, Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome …

Microplastic Contamination In Karst Groundwater Systems, Samuel V. Panno, Walton R. Kelly, John Scott, Wei Zheng, Rachel E. Mcneish, Nancy Holm, Timothy Hoellein, Elizabeth L. Baranski

Biology: Faculty Publications and Other Works

Groundwater in karst aquifers constitutes about 25% of drinking water sources globally. Karst aquifers are open systems, susceptible to contamination by surface‐borne pollutants. In this study, springs and wells from two karst aquifers in Illinois, USA, were found to contain microplastics and other anthropogenic contaminants. All microplastics were fibers, with a maximum concentration of 15.2 particles/L. The presence of microplastic was consistent with other parameters, including phosphate, chloride and triclosan, suggesting septic effluent as a source. More studies are needed on microplastic sources, abundance, and impacts on karst ecosystems.

Ribosomal/Nucleolar Stress Induction Regulates Tert-Butyl Hydroperoxide (Tbhp) Mediated Oxidative Stress In Anopheles Gambiae Midguts, Brian B. Tarimo, Bernadette A. Hritzo, Henry Chun Hin Law, Dingyin Tao, Rebecca Pastrana-Mena, Stefan M. Kanzok, Joram J. Buza, Rhoel R. Dinglasan

Biology: Faculty Publications and Other Works

Objective

A fundamental understanding of redox homeostasis in Anopheles gambiae midgut cells under different oxidative conditions is missing. Such knowledge can aid in the development of new malaria transmission-blocking strategies aimed at disrupting natural homeostatic processes in the mosquito during Plasmodium parasite uptake (i.e. blood feeding). The aim of this study was to understand how the An. gambiae midgut regulates oxidative stress to reactive oxygen species (ROS), especially to a potent ROS-inducer such as tert-Butyl hydroperoxide (tBHP).

Results

Initial studies using quantitative immunoblot indicated that the expression of the classical antioxidant protein An. gambiae thioredoxin-1 (AgTrx-1) remained unchanged …

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa …

Phylogenetic Relationships Within The Primitive Acanthomorph Fish Genus Polymixia, With Changes To Species Composition And Geographic Distributions, W. Calvin Borden, Terry C. Grande, Mark Vh Wilson

Biology: Faculty Publications and Other Works

The genus Polymixia is the only survivor of a Late Cretaceous marine fish radiation and is often said to be the most primitive living acanthomorph (i.e., Polymixia possesses the greatest number of primitive character states for Acanthomorpha). Recent studies, including this one, place Polymixia as the sister to all other Paracanthopterygii. Despite its importance, most species of Polymixia are extremely difficult to discriminate on the basis of morphology. As a result, the number of valid species is uncertain. Moreover, there has never been a phylogenetic analysis of the genus. Thus, a molecular phylogenetic study was needed to clarify species boundaries …

Pseudomonas Diversity Within Urban Freshwaters, Mary Batrich, Laura Maskeri, Ryan Schubert, Brian Ho, Melanie Kohout, Malik Abdeljaber, Ahmed Abuhasna, Mutah Kholoki, Penelope Psihogios, Tahir Razzaq, Samrita Sawhney, Salah Siddiqui, Eyad Xoubi, Alexandria Cooper, Thomas Hatzopoulos, Catherine Putonti

Bioinformatics Faculty Publications

Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed …

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa …

Role Of Daxx As A Predictive Biomarker In Breast Cancer, Michelle Lucia Fernandez

Master's Theses

Breast cancer is the most commonly diagnosed form of cancer in women, besides skin cancer, and second only to lung cancer for cause of mortality. It is divided into three subtypes, depending on different molecular or pathologic characteristics, including estrogen or progesterone receptor-positive (ER/PR+), human epidermal growth factor receptor-2-positive (HER2+) and triple negative breast cancer (TNBC). There are several therapies used to target these subtypes, but there is still a chance that the cancer will recur into a more aggressive, resistant form even if the therapies were successful before. This recurrence is believed to be due to the Cancer Stem …

Alcohol Induced Bacterial Changes In The Setting Of Colitis, Paulius Kuprys

Dissertations

Inflammatory bowel diseases (IBD) affect a large number of individuals around the world. This group of diseases is largely composed of two types: Crohn's disease (CD) and ulcerative colitis (UC). Upon development of IBD, patients experience cyclical episodes of inflammation, known as flares. Flare induction appears to arise from multiple factors, which can also vary on a person-to-person basis. Alcohol has been shown to trigger IBD flares and onset, though the underlying mechanism has not been established.Defining factors of the IBD intestinal environment include an altered microbiome, bacterial infiltration of the intestinal epithelium, and increased leakage of proinflammatory bacterial byproducts. …

Daxx As A Restrictor Of Tumor Initiating Cell Survival In Er+ Breast Cancer And Its Therapeutic Implications, Daniel Seamus Peiffer

Dissertations

Breast cancer overall is the second most common cause of cancer related death in women, with one in eight women being diagnosed during their lifetime. Breast cancer itself is divided into subtypes based on the expression levels of the hormone receptors including the estrogen receptor (ER) and the progesterone receptor (PR), as well as expression of the growth factor receptor epidermal growth factor receptor 2 (HER2). ER+ breast cancer is the most common breast cancer diagnosis, and these tumors are defined as being initially dependent on activation of the receptor for growth. Based on this, targeted endocrine therapies (ETs) have …