Biology Commons^™

Attempting Genetic Inference From Directional Asymmetry During Convergent Hindlimb Reduction In Squamates, Samantha Swank, Ethan Elazegui, Sophia Janidlo, Thomas J. Sanger, Michael A. Bell, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Loss and reduction in paired appendages are common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the threespine stickleback and ninespine stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hindlimb reduction stemming from reduced Pitx1 expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of Pitx1 across vertebrates. Notably, hindlimb reduction based …

Discordant Population Structure Among Rhizobium Divided Genomes And Their Legume Hosts, Alex B. Riley, Michael A. Grillo, Brendan Epstein, Peter Tiffin, Katy D. Heath

Biology: Faculty Publications and Other Works

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms …

Gut Dysbiosis In Cutaneous T-Cell Lymphoma Is Characterized By Shifts In Relative Abundances Of Specific Bacterial Taxa And Decreased Diversity In More Advanced Disease, Madeline J. Hooper, T.M. Lewitt, Y. Pang, F.L. Veon, G.E Chlipala, L. Feferman, S.J. Green, D. Sweeney, K.T. Bagnowski, Michael B. Burns, P.C. Seed, J. Choi, J. Guitart, X.A. Zhou

Biology: Faculty Publications and Other Works

Background Cutaneous T-cell lymphoma (CTCL) patients often suffer from recurrent skin infections and profound immune dysregulation in advanced disease. The gut microbiome has been recognized to influence cancers and cutaneous conditions; however, it has not yet been studied in CTCL.ObjectivesTo investigate the gut microbiome in patients with CTCL and in healthy controls.MethodsA case-control study was conducted between January 2019 and November 2020 at Northwestern’s busy multidisciplinary CTCL clinic (Chicago, Illinois, USA) utilizing 16S ribosomal RNA gene amplicon sequencing and bioinformatics analyses to characterize the microbiota present in fecal samples of CTCL patients (n = 38) and age-matched healthy controls (n …

Elucidating The Function Of An Evolutionarily Conserved Col2Α1 Isoform During Vertebrate Development, Charles Lantz H. Ingersoll

Master's Theses

ABSTRACT

Formation of skeletal structural elements during vertebrate embryogenesis is largely a

conserved evolutionary process that employs numerous conserved genes and pathways. One

critical gene in this process is the highly conserved vertebrate Type II Collagen alpha 1 (col2α1).

It produces multiple splice isoforms that have different functions and expression patterns during

skeletogenesis. Two of the primary isoforms are of great interest; variant 1, the primary

embryonic isoform, and variant 2, a post embryonic isoform. While the more commonly known

post-embryonic isoform has been well studied over the last 30 years, identification of a unique

role for the evolutionarily conserved …

Development And Characterization Of A Tissue-Specific Reporter Line For Monitoring Circadian Clock Transcriptional Activity, Lilyan Mather

Master's Theses

Daily rhythms in physiology and behavior are produced by a circadian system consisting of a central clock located in the brain and peripheral clocks located in various peripheral tissues. Circadian clocks track time of day through the presence of a molecular clock that functions as a transcriptional-translational feedback loop. In the nucleus, the transcription factors CLOCK (CLK) and CYCLE (CYC) activate transcription of clock genes period (per) and timeless (tim). PER and TIM proteins slowly accumulate in the cytoplasm before entering the nucleus, where they inhibit CLK and CYC, and therefore repress their own transcription. Degradation of nuclear PER and …

Comparison Of Feeding Functional Morphology Development In North American Esocids, Cheryl Theile

Master's Theses

Esocidae is a family of freshwater fishes within order Esociformes known for its long, cylindrical bodies, duck-bill snouts, and an impressive number of sharp teeth. There are four species, including two subspecies, in North America with areas of overlap of their geographic distribution. These ambush predators change diets from invertebrate prey to vertebrate prey during their first year of life, and the timing of this shift varies between species. In particular, the sister species Esox lucius (Northern Pike) and Esox masquinongy (Muskellunge) overlap in the upper Midwest, but E. masquinongy transitions to a vertebrate diet sooner in its development than …

Biofilms On Plastic Litter: Community Composition And Activity And The Effects On Ecosystem Processes, Raul F. Lazcano

Master's Theses

The rapid increase of plastic production and disposal has resulted in plastic pollution becoming a global problem. In aquatic ecosystems, plastic litter is a substrate for biofilms, but little research has simultaneously assessed the effects of plastic litter on biofilm activity, community composition, and ecosystem processes. Our objectives were to: (1) measure biofilm activity and community composition on plastic litter relative to a natural surface in an urban river and (2) assess the impact of microplastic pollution on ecosystem metabolism and N2 flux in an oligotrophic lake. For objective (1) we incubated three common plastics with distinct physical and chemical …

(Non)Parallel Developmental Mechanisms In Vertebrate Appendage Reduction And Loss, Samantha Swank, Thomas Sanger, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Transcriptome Prediction Performance Across Machine Learning Models And Diverse Ancestries, Paul Chukwuebuka Okoro, Ryan Schubert, Xiuqing Guo, W. Craig Johnson, Jerome I. Rotter, Ina Hoeschele, Yongmei Liu, Hae Kyung Im, Amy Luke, Lara R. Dugas, Heather Wheeler

Biology: Faculty Publications and Other Works

Transcriptome prediction methods such as PrediXcan and FUSION have become popular in complex trait mapping. Most transcriptome prediction models have been trained in European populations using methods that make parametric linear assumptions like the elastic net (EN). To potentially further optimize imputation performance of gene expression across global populations, we built transcriptome prediction models using both linear and non-linear machine learning (ML) algorithms and evaluated their performance in comparison to EN. We trained models using genotype and blood monocyte transcriptome data from the Multi-Ethnic Study of Atherosclerosis (MESA) comprising individuals of African, Hispanic, and European ancestries and tested them using …

Safety Assessment Of Aconitum-Derived Bulleyaconitine A: A 91-Day Oral Toxicity Study And A Tissue Accumulation Study In Rats, Shi Liang Yin, Feng Xu, Hao Wu, Fei Li, Ge Jin, Zu Qian Wu, Ran Meng, Si Man Ma, Fan Zhou, Peter W. Breslin, Chun Fu Wu, Hong Zhang

Biology: Faculty Publications and Other Works

Background: Bulleyaconitine A (BLA) is a diterpenoid alkaloid from the rhizomes of Aconitum bulleyanum Diels and has been clinically used for chronic pain treatment in China for many years. However, the newly reported adverse events of BLA indicated that BLA still has potential safety issues. Materials and Methods: To assess the safety of BLA, analgesic tests, acute toxicity studies, repeated-dose oral toxicity studies, and tissue distribution studies after single and repeated administration of BLA were carried out. Results: Administration of 0.14 mg/kg BLA showed potent analgesic effects in both analgesic tests. In acute toxicity study, the LD50value of BLA was …

Scientism And Secularism: Learning To Respond To A Dangerous Ideology By J. P. Moreland. Wheaton, Il: Crossway, 2018. 224 Pages. Paperback; $16.99. Isbn: 9781433556906., Michael B. Burns, Joseph Vukov

Biology: Faculty Publications and Other Works

No abstract provided.

Il-27 Signaling In The Maintenance Of Intestinal Barrier Following Ethanol Intoxication And Burn Injury, Marisa Luck

Dissertations

Roughly half of burn patients that are hospitalized in the United States each year have detectable blood alcohol levels. Alcohol intoxication at the time of burn injury leads to worse outcomes, including longer hospital stays, increased rates of infection, and death. One of the severe consequences of intoxication and burn injury is the disruption of the gastrointestinal (GI) tract, which houses the largest reservoir of bacteria in the human body. Leakiness of the gut barrier can contribute to inflammation, infection, or sepsis from gut-derived microbes. Interleukin-27 (IL-27) is a cytokine that has shown some beneficial effects in other models of …

The Evolutionary And Morphological Diversification Of The Subtribe Papionina, Sophie B. Labelle

Master's Theses

Analysis of variation is critical in understanding evolutionary processes. The subtribe Papionina, defined commonly as baboons and their closest relatives, is a highly morphologically diverse group of primates that is useful for the examination of the relationship between variation and evolution. The subtribe is also a valuable behavioral, ecological, and morphological analogy for hominins. This study uses landmark-based cranial geometric morphometric data and multivariate analysis to test whether the pattern of morphological diversification present in Papionina is consistent with genetic drift and/or selection. The study sample consists of six extant genera of Papionin, represented by ~500 individuals collected by Michelle …

A Role For Notch Signaling In Drosophila Spermatogenesis, Adrianna Soriano

Master's Theses

The Notch signaling pathway has diverse functions in male and female gonad development. In Drosophila male embryos, Notch specifies hub cell fate in somatic gonadal precursor cells (SGPs), which are important for maintaining germline stem cells and somatic cyst stem cells throughout the lifetime of adult flies. However, a role for Notch signaling in adult males has only started to emerge recently. Nonetheless, we still don’t understand how the Notch pathway functions to regulate spermatogenesis. Notch has been established to be important for the fertility of multiple systems, including mammals, and must be properly regulated for proper spermatogenesis, but the …

Adding The Third Dimension To Studies Of Parallel Evolution Of Morphology And Function: An Exploration Based On Parapatric Lake-Stream Stickleback, Grant E. Haines, Yoel E. Stuart, Dieta Hanson, Tania Tasneem, Daniel I. Bolnick, Hans Ce Larsson, Andrew P. Hendry

Biology: Faculty Publications and Other Works

Recent methodological advances have led to a rapid expansion of evolutionary studies employing three-dimensional landmark-based geometric morphometrics (GM). GM methods generally enable researchers to capture and compare complex shape phenotypes, and to quantify their relationship to environmental gradients. However, some recent studies have shown that the common, inexpensive, and relatively rapid two-dimensional GM methods can distort important information and produce misleading results because they cannot capture variation in the depth (Z) dimension. We use micro-CT scanned threespine stickleback (Gasterosteus aculeatus Linnaeus, 1758) from six parapatric lake-stream populations on Vancouver Island, British Columbia, to test whether the loss …

Scale‐Dependent Effects Of Host Patch Traits On Species Composition In A Stickleback Parasite Metacommunity, Daniel I. Bolnick, Emlyn J. Resetarits, Kimberly Ballare, Yoel E. Stuart, William E. Stutz

Biology: Faculty Publications and Other Works

A core goal of ecology is to understand the abiotic and biotic variables that regulate species distributions and community composition. A major obstacle is that the rules governing species distributions can change with spatial scale. Here, we illustrate this point using data from a spatially nested metacommunity of parasites infecting a metapopulation of threespine stickleback fish from 34 lakes on Vancouver Island, British Columbia. Like most parasite metacommunities, the composition of stickleback parasites differs among host individuals within each host population, and differs between host populations. The distribution of each parasite taxon depends, to varying degrees, on individual host traits …

Molecular And Cellular Mechanisms Of Aging In Hematopoietic Stem Cells And Their Niches, Lei Zhang, Ryan Mack, Peter W. Breslin, Jiwang Zhang

Biology: Faculty Publications and Other Works

Aging drives the genetic and epigenetic changes that result in a decline in hematopoietic stem cell (HSC) functioning. Such changes lead to aging-related hematopoietic/immune impairments and hematopoietic disorders. Understanding how such changes are initiated and how they progress will help in the development of medications that could improve the quality life for the elderly and to treat and possibly prevent aging-related hematopoietic diseases. Here, we review the most recent advances in research into HSC aging and discuss the role of HSC-intrinsic events, as well as those that relate to the aging bone marrow niche microenvironment in the overall processes of …

Axonal Blockage With Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Numerous neurological dysfunctions are characterized by undesirable nerve activity. By providing reversible nerve blockage, electric stimulation with an implanted electrode holds promise in the treatment of these conditions. However, there are several limitations to its application, including poor bio-compatibility and decreased efficacy during chronic implantation. A magnetic coil of miniature size can mitigate some of these problems, by coating it with biocompatible material for chronic implantation. However, it is unknown if miniature coils could be effective in axonal blockage and, if so, what the underlying mechanisms are. Here we demonstrate that a submillimeter magnetic coil can reversibly block action potentials …

Spatiotemporal Analysis Of Cochlear Nucleus Innervation By Spiral Ganglion Neurons That Serve Distinct Regions Of The Cochlea, Jennifer L. Scheffel, Samiha S. Mohammed, Chloe K. Borcean, Annie J. Parng, Hyun Ju Yoon, Darwin A. Gutierrez, Wei-Ming Yu

Biology: Faculty Publications and Other Works

Cochlear neurons innervate the brainstem cochlear nucleus in a tonotopic fashion according to their sensitivity to different sound frequencies (known as the neuron’s characteristic frequency). It is unclear whether these neurons with distinct characteristic frequencies use different strategies to innervate the cochlear nucleus. Here, we use genetic approaches to differentially label spiral ganglion neurons (SGNs) and their auditory nerve fibers (ANFs) that relay different characteristic frequencies in mice. We found that SGN populations that supply distinct regions of the cochlea employ different cellular strategies to target and innervate neurons in the cochlear nucleus during tonotopic map formation. ANFs that will …

Character Displacement In The Midst Of Substantial Background Evolution In Anolis Lizard Island Populations, Ambika Kamath, Nicholas C. Herrmann, Kiyoko M. Gotanda, Kum C. Shim, Jacob Lafond, Gannon Cottone, Heather Falkner, Todd S. Campbell, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Negative interactions between species can generate divergent selection that causes character displacement. However, other processes cause similar divergence. We use spatial and temporal replication across island populations of Anolis lizards to assess the importance of negative interactions in driving trait shifts. Previous work showed that the establishment of Anolis sagrei on islands drove resident Anolis carolinensis to perch higher and evolve larger toepads. To further test the interaction's causality and predictability, we resurveyed a subset of islands nine years later. Anolis sagrei had established on one island between surveys. We found that A. carolinensis on this island now perch higher …

A Review Of The Preclinical And Clinical Efficacy Of Remdesivir, Hydroxychloroquine, And Lopinavir-Ritonavir Treatments Against Covid-19, Dawid Maciorowski, Samir Z. El Idrissi, Yash Gupta, Brian J. Medernach, Michael B. Burns, Daniel P. Becker Ph.D., Ravi Durvasula, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

In December of 2019, an outbreak of a novel coronavirus flared in Wuhan, the capital city of the Hubei Province, China. The pathogen has been identified as a novel enveloped RNA beta-coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus SARS-CoV-2 is associated with a disease characterized by severe atypical pneumonia known as coronavirus 2019 (COVID-19). Typical symptoms of this disease include cough, fever, malaise, shortness of breath, gastrointestinal symptoms, anosmia, and, in severe cases, pneumonia.¹ The high-risk group of COVID-19 patients includes people over the age of 60 years as well as people with existing cardiovascular …

Inferred Genetic Architecture Underlying Evolution In A Fossil Stickleback Lineage, Yoel E. Stuart, Matthew P. Travis, Michael A. Bell

Biology: Faculty Publications and Other Works

Inferring the genetic architecture of evolution in the fossil record is difficult because genetic crosses are impossible, the acquisition of DNA is usually impossible and phenotype–genotype maps are rarely obvious. However, such inference is valuable because it reveals the genetic basis of microevolutionary change across many more generations than is possible in studies of extant taxa, thereby integrating microevolutionary process and macroevolutionary pattern. Here, we infer the genetic basis of pelvic skeleton reduction in Gasterosteus doryssus, a Miocene stickleback fish from a finely resolved stratigraphic sequence that spans nearly 17,000 years. Reduction in pelvic score, a categorical measure of …

Comparative Genomic Study Of Lactobacillus Jensenii And The Newly Defined Lactobacillus Mulieris Species Identifies Species-Specific Functionality, Catherine Putonti, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibere, Alan J. Wolfe

Bioinformatics Faculty Publications

Lactobacilli are dominant members of the “healthy” female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction …

Esociformes: Esocidae, Pikes, And Umbridae (Mudminnows), Frank H. Mccormick, Terry C. Grande, Cheryl Theile, Melvin L. Warren, J. Andrés López, Mark V. H. Wilson, Roger A. Tabor, Julian D. Olden, Lauren M. Kuehne

Biology: Faculty Publications and Other Works

The order Esociformes (Pikes and Mudminnows) comprises two families, Esocidae (Pikes) and Umbridae (Mudminnows). The Pikes are a small Holarctic (Northern Hemisphere) family, that includes large, elongate predators with duckbill-like snouts full of sharp teeth. Popular with sport fishers, the largest Pikes fight fiercely on hook and line. As piscivorous, voracious, ambush predators, the Pikes play an important functional role in the trophic ecology and fish assemblage structure of many aquatic systems, especially in northern lakes. Other esocids, such as the Olympic Mudminnow, Novumbra hubbsi, and Blackfishes, genus Dallia, are interesting because of their tolerance of low dissolved oxygen and …

Abl1, Overexpressed In Hepatocellular Carcinomas, Regulates Expression Of Notch1 And Promotes Development Of Liver Tumors In Mice, Fang Wang, Wei Hou, Lennox Chitsike, Yingchen Xu, Carlee Bettler, Aldeb Perera, Thomas Bank, Scott J. Cotler, Asha Dhanarajan, Mitchell F. Denning, Xianzhong Ding, Peter W. Breslin, Wenan Qiang, Jun Li, Anthony J. Koleske, Wei Qiu

Biology: Faculty Publications and Other Works

Background & Aims

We investigated whether ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1) is involved in development of hepatocellular carcinoma (HCC).

Methods

We analyzed clinical and gene expression data from The Cancer Genome Atlas. Albumin-Cre (HepWT) mice and mice with hepatocyte-specific disruption of Abl1 (HepAbl–/– mice) were given hydrodynamic injections of plasmids encoding the Sleeping Beauty transposase and transposons with the MET gene and a catenin β1 gene with an N-terminal truncation, which induces development of liver tumors. Some mice were then gavaged with the ABL1 inhibitor nilotinib or vehicle (control) daily for 4 weeks. We knocked …

Introducing Lu-1, A Novel Lactobacillus Jensenii Phage Abundant In The Urogenital Tract, Taylor Miller-Ensminger, Rita Mormando, Laura Maskeri, Jason W. Shapiro, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages (phages) play a key role in shaping microbial communities, including those of the human body. Phages are abundant members of the urogenital tract, most often persisting through the lysogenic life cycle as prophages integrated within the genomes of their bacterial hosts. While numerous studies of the urogenital microbiota have focused on the most abundant bacterial member of this niche–Lactobacillus species–very little is known about Lactobacillus phages. Focusing on Lactobacillus jensenii strains from the urinary tract, we identified numerous prophages related to the previously characterized Lv-1 phage from a vaginal L. jensenii strain. Furthermore, we identified a new L. jensenii …

Draft Genome Sequence Of Escherichia Coli Umb1353, Isolated From The Female Urinary Tract, Tanea Crawford, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Here, we present the draft genome sequence of Escherichia coli UMB1353, isolated from a patient with a urinary tract infection. The sequence of this antibiotic-resistant E. coli strain contains one intact P2-like phage.

Draft Genome Sequence Of Actinomyces Neuii Umb1295, Isolated From The Female Urinary Tract, Tijana Markovic, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Actinomyces neuii is an opportunistic pathogen. Within the urogenital tract, it has been associated with bacterial vaginosis and overactive bladder symptoms. Here, we investigate a draft genome sequence of A. neuii UMB1295, which was isolated from a catheterized urine sample from a woman with a urinary tract infection.

Draft Genome Sequence Of Escherichia Coli Umb9246, Isolated From The Bladder Of A Woman With Recurrent Urinary Tract Infection, Mikalina Belmonte, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Escherichia coli is a Gram-negative, motile, rod-shaped bacterium that causes the majority of uncomplicated urinary tract infections (UTIs). Here, we report the draft genome of E. coli strain UMB9246, an isolate from a woman with recurrent UTI.