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Biogeographic Variation In Resistance Of The Invasive Plant, Alliaria Petiolata, To A Powdery Mildew Fungus And Effect Of Resistance On Competitive Dynamics, Don Cipollini, Sam Davisd, Deah Lieurance, Kendra Cipollini, Volker Bahn 2020 Wright State University - Main Campus

Biogeographic Variation In Resistance Of The Invasive Plant, Alliaria Petiolata, To A Powdery Mildew Fungus And Effect Of Resistance On Competitive Dynamics, Don Cipollini, Sam Davisd, Deah Lieurance, Kendra Cipollini, Volker Bahn

Biological Sciences Faculty Publications

Garlic mustard is an invasive Eurasian biennial that has spread throughout the eastern United States and southern Canada. Populations of this plant vary in their susceptibility to Erysiphe cruciferarum, a causal agent of powdery mildew disease in Brassicaceous plants. We examined whether there were biogeographic patterns in the distribution of resistance in invasive North American and native European populations of this plant. We grew plants from 78 invasive and 20 native populations and screened them for powdery mildew resistance in the greenhouse. We found that populations were mostly monomorphic for either resistance or susceptibility but that some polymorphic populations were ...


Larval Performance Of A Major Forest Pest On Novel Hosts And The Effect Of Stressors, Donnie Lee Peterson, Don Cipollini 2020 Wright State University - Main Campus

Larval Performance Of A Major Forest Pest On Novel Hosts And The Effect Of Stressors, Donnie Lee Peterson, Don Cipollini

Biological Sciences Faculty Publications

Novel hosts lacking a coevolutionary history with herbivores can often support improved larval performance over historic hosts; e.g., emerald ash borer [Agrilus planipennis (Fairmaire) Coleoptera: Buprestidae] on North American ash (Fraxinus spp.) trees. Whether trees are novel or ancestral, stress on plants increases emerald ash borer preference and performance. White fringetree [Chionanthus virginicus (L.) Lamiales: Oleaceae] and olive [Olea europaea (L.) Lamiales: Oleaceae] are closely related non-ash hosts that support development of emerald ash borer to adulthood, but their relative suitability as hosts and the impact of plant stress on larval success has not been well studied. In a ...


The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio 2020 West Virginia University

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted ...


The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans PhD 2020 West Virginia University

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry ...


Characterizing The Requirements For The Matricellular Protein, Dccn, In Nervous System Function, Elizabeth L. Catudio Garrett 2020 University of Montana

Characterizing The Requirements For The Matricellular Protein, Dccn, In Nervous System Function, Elizabeth L. Catudio Garrett

Graduate Student Theses, Dissertations, & Professional Papers

The brain is organized as a complex network of specialized neurons that communicate via a combination of electrical and chemical signals. Our brains function to generate movement, control organ function, or direct complex behaviors; all of which requires the ability to regulate the flow of communication between circuits and networks. Work in this thesis addresses two areas of neuron communication: first, how does the release of more than one neurotransmitter from a single neuron impact behavior, and second, are matricellular proteins (MCPs) key contributors to synaptic transmission and neuron function? The conserved CCN family of MCPs have a unique mosaic ...


Food Web Effects Of Lake Trout (Salvelinus Namaycush) Invasion In Northwestern Montana, Charles Wainright 2020 University of Montana

Food Web Effects Of Lake Trout (Salvelinus Namaycush) Invasion In Northwestern Montana, Charles Wainright

Graduate Student Theses, Dissertations, & Professional Papers

Around the turn of the 20th century, lake trout (Salvelinus namaycush) were widely introduced in several lakes and reservoirs outside their native range in western North America. Since then, lake trout have become problematic in many lakes where they were introduced, causing significant declines in popular sport fishes and native species, most notably federally protected bull trout (Salvelinus confluentus). Despite evidence that invasive fish can cause cascading trophic effects in aquatic communities, the impacts of lake trout introduction / invasion on aquatic food webs remain poorly understood. Moreover, native fish restoration programs tend to focus on suppression of invasive fish and ...


Pharmacological Or Genetic Targeting Of Transient Receptor Potential (Trp) Channels Can Disrupt The Planarian Escape Response, Ziad Sabry , '21, A. Ho, D. Ireland, C. Rabeler, O. Cochet-Escartin, Eva-Maria S. Collins 2019 Swarthmore College

Pharmacological Or Genetic Targeting Of Transient Receptor Potential (Trp) Channels Can Disrupt The Planarian Escape Response, Ziad Sabry , '21, A. Ho, D. Ireland, C. Rabeler, O. Cochet-Escartin, Eva-Maria S. Collins

Biology Faculty Works

In response to noxious stimuli, planarians cease their typical ciliary gliding and exhibit an oscillatory type of locomotion called scrunching. We have previously characterized the biomechanics of scrunching and shown that it is induced by specific stimuli, such as amputation, noxious heat, and extreme pH. Because these specific inducers are known to activate Transient Receptor Potential (TRP) channels in other systems, we hypothesized that TRP channels control scrunching. We found that chemicals known to activate TRPA1 (allyl isothiocyanate (AITC) and hydrogen peroxide) and TRPV (capsaicin and anandamide) in other systems induce scrunching in the planarian species Dugesia japonica and, except ...


Regulatory Asymmetry In The Negative Single-Input Module Network Motif: Role Of Network Size, Growth Rate And Binding Affinity, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster 2019 University of Massachusetts Medical School

Regulatory Asymmetry In The Negative Single-Input Module Network Motif: Role Of Network Size, Growth Rate And Binding Affinity, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster

University of Massachusetts Medical School Faculty Publications

The single-input module (SIM) is a regulatory motif capable of coordinating gene expression across functionally related genes. We explore the relationship between regulation of the central autoregulated TF in a negatively regulated SIM and the target genes using a synthetic biology approach paired with stochastic simulations. Surprisingly, we find a fundamental asymmetry in the level of regulation experienced by the TF gene and its targets, even if they have identical regulatory DNA; the TF gene experiences stronger repression than its targets. This asymmetry is not predicted from deterministic modeling of the system but is revealed from corresponding stochastic simulations. The ...


A Minimal Crispr-Cas3 System For Genome Engineering, Bálint Csörgő, Lina M. León, Ilea J. Chau-Ly, Alejandro Vasquez-Rifo, Joel D. Berry, Caroline Mahendra, Emily D. Crawford, Jennifer D. Lewis, Joseph Bondy-Denomy 2019 University of California, San Francisco

A Minimal Crispr-Cas3 System For Genome Engineering, Bálint Csörgő, Lina M. León, Ilea J. Chau-Ly, Alejandro Vasquez-Rifo, Joel D. Berry, Caroline Mahendra, Emily D. Crawford, Jennifer D. Lewis, Joseph Bondy-Denomy

University of Massachusetts Medical School Faculty Publications

CRISPR-Cas technologies have provided programmable gene editing tools that have revolutionized research. The leading CRISPR-Cas9 and Cas12a enzymes are ideal for programmed genetic manipulation, however, they are limited for genome-scale interventions. Here, we utilized a Cas3-based system featuring a processive nuclease, expressed endogenously or heterologously, for genome engineering purposes. Using an optimized and minimal CRISPR-Cas3 system (Type I-C) programmed with a single crRNA, large deletions ranging from 7 - 424 kb were generated in Pseudomonas aeruginosa with high efficiency and speed. By comparison, Cas9 yielded small deletions and point mutations. Cas3-generated deletion boundaries were variable in the absence of a homology-directed ...


The Mayfly Newsletter, Donna Giberson 2019 The Permanent Committee of the International Conferences on Ephemeroptera

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera


Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold 2019 University of Massachusetts Amherst

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to temperature and ...


Linalool Acts As A Fast And Reversible Anesthetic In Hydra, T. Goel, R. Wang, S Martin, Elizabeth Y. Lanphear , '19, Eva-Maria S. Collins 2019 Swarthmore College

Linalool Acts As A Fast And Reversible Anesthetic In Hydra, T. Goel, R. Wang, S Martin, Elizabeth Y. Lanphear , '19, Eva-Maria S. Collins

Biology Faculty Works

The ability to make transgenic Hydra lines has allowed for quantitative in vivo studies of Hydra regeneration and physiology. These studies commonly include excision, grafting and transplantation experiments along with high-resolution imaging of live animals, which can be challenging due to the animal’s response to touch and light stimuli. While various anesthetics have been used in Hydra studies, they tend to be toxic over the course of a few hours or their long-term effects on animal health are unknown. Here, we show that the monoterpenoid alcohol linalool is a useful anesthetic for Hydra. Linalool is easy to use, non-toxic ...


Mathematics Saves Lives: Models And Signals Enabling Medicine And Biology, Raina Robeva 2019 Randolph-Macon College

Mathematics Saves Lives: Models And Signals Enabling Medicine And Biology, Raina Robeva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley 2019 Illinois State University

Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Petri Nets As A Unifying Tool To Link Physiologically Based Toxicokinetic (Pbtk) Models To Adverse Outcome Pathways (Aops), Ian Edhlund 2019 Illinois State University

Petri Nets As A Unifying Tool To Link Physiologically Based Toxicokinetic (Pbtk) Models To Adverse Outcome Pathways (Aops), Ian Edhlund

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren 2019 WSU

Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Highly Structured Homolog Pairing Reflects Functional Organization Of The Drosophila Genome, Jumana AlHaj Abed, Jelena Erceg, Anton Goloborodko, Son C. Nguyen, Ruth B. McCole, Wren Saylor, Geoffrey Fudenberg, Bryan R. Lajoie, Job Dekker, Leonid A. Mirny, C-Ting Wu 2019 Harvard Medical School

Highly Structured Homolog Pairing Reflects Functional Organization Of The Drosophila Genome, Jumana Alhaj Abed, Jelena Erceg, Anton Goloborodko, Son C. Nguyen, Ruth B. Mccole, Wren Saylor, Geoffrey Fudenberg, Bryan R. Lajoie, Job Dekker, Leonid A. Mirny, C-Ting Wu

Program in Systems Biology Publications

Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single ...


The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu 2019 Harvard Medical School

The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana Alhaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. Mccole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu

Program in Systems Biology Publications

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a ...


Domainrbf: A Bayesian Regression Approach To The Prioritization Of Candidate Domains For Complex Diseases., Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang 2019 Rowan University

Domainrbf: A Bayesian Regression Approach To The Prioritization Of Candidate Domains For Complex Diseases., Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang

Yong Chen

BACKGROUND: Domains are basic units of proteins, and thus exploring associations between protein domains and human inherited diseases will greatly improve our understanding of the pathogenesis of human complex diseases and further benefit the medical prevention, diagnosis and treatment of these diseases. Within a given domain-domain interaction network, we make the assumption that similarities of disease phenotypes can be explained using proximities of domains associated with such diseases. Based on this assumption, we propose a Bayesian regression approach named "domainRBF" (domain Rank with Bayes Factor) to prioritize candidate domains for human complex diseases.

RESULTS: Using a compiled dataset containing 1 ...


Creating A Molecular Map Of The Pediatric Lung, Quinlen F. Marshall 2019 College of Saint Benedict/Saint John's University

Creating A Molecular Map Of The Pediatric Lung, Quinlen F. Marshall

Forum Lectures

The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types that exhibit remarkable heterogeneity. (Whitsett, JA. et al. Physiol. Rev, 2019). Surprisingly, few studies have solely focused on human lung development during this critical period, and many current studies of lung maturation rely on adult, murine, or diseased samples, limiting their insights and applicability to longitudinal pediatric lung development. Understanding the molecular and physiological nuances of pulmonary development has important clinical relevance ...


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