Biology Commons^™

The Arabidopsis Kinesin-4, Fra1, Requires A High Level Of Processive Motility To Function Correctly, Anindya Ganguly, Logan Demott, Ram Dixit

Biology Faculty Research

Processivity is important for kinesins that mediate intracellular transport. Structure–function analyses of N-terminal kinesins (i.e. kinesins comprising their motor domains at the N-terminus) have identified several non-motor regions that affect processivity in vitro. However, whether these structural elements affect kinesin processivity and function in vivo is not known. Here, we used an Arabidopsis thaliana kinesin-4, called Fragile Fiber 1 (FRA1, also known as KIN4A), which is thought to mediate vesicle transport, to test whether mutations that alter processivity in vitro lead to similar changes in behavior in vivo and whether processivity is important for the function of FRA1. We …

Social Amoebae Mating Types Do Not Invest Unequally In Sexual Offspring, T E. Douglas, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Unequal investment by different sexes in their progeny is common and includes differential investment in the zygote and differential care of the young. The social amoeba Dictyostelium discoideum has a sexual stage in which isogamous cells of any two of the three mating types fuse to form a zygote which then attracts hundreds of other cells to the macrocyst. The latter cells are cannibalized and so make no genetic contribution to reproduction. Previous literature suggests that this sacrifice may be induced in cells of one mating type by cells of another, resulting in a higher than expected production of macrocysts …

Groundcover Community Assembly In High-Diversity Pine Savannas: Seed Arrival And Fire-Generated Environmental Filtering, Kyle E. Harms, Paul R. Gagnon, Heather A. Passmore, Jonathan A. Myers, William J. Platt

Biology Faculty Research

Environmental filtering—abiotic and biotic constraints on the demographic performance of individual organisms—is a widespread mechanism of selection in communities. A given individual is “filtered out” (i.e., selectively removed) when environmental conditions or disturbances like fires preclude its survival and reproduction. Although interactions between these filters and dispersal from the regional species pool are thought to determine much about species composition locally, there have been relatively few studies of dispersal × filtering interactions in species-rich communities and fewer still where fire is also a primary selective agent. We experimentally manipulated dispersal and filtering by fire (pre-fire fuel loads and post-fire ash) …

Draft Genome Sequences Of Three Closely Related Isolates Of The Purple Nonsulfur Bacterium Rhodovulum Sulfidophilum, Michael S. Guzman, Beau Mcginley, Natalia Santiago-Merced, Dinesh Gupta, Arpita Bose

Biology Faculty Research

We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.

Fundamental Theorems Of Evolution, David C. Queller

Biology Faculty Research

Evolutionary biology is undergirded by an extensive and impressive set of mathematical models. Yet only one result, Fisher’s theorem about selection and fitness, is generally accorded the status of a fundamental theorem. I argue that although its fundamental status is justified by its simplicity and scope, there are additional results that seem similarly fundamental. I suggest that the most fundamental theorem of evolution is the Price equation, both because of its simplicity and broad scope and because it can be used to derive four other familiar results that are similarly fundamental: Fisher’s average-excess equation, Robertson’s secondary theorem of natural selection, …

The Gep: Crowd-Sourcing Big Data Analysis With Undergraduates, Sarah C.R. Elgin, Charles Hauser, Teresa Holzen, Christopher Jones, Adam Kleinschmit, Judith Leatherman

Biology Faculty Research

The era of 'big data' is also the era of abundant data, creating new opportunities for student-scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience. Keywords: CURE (course-based undergraduate research experience); bioinformatics; crowd-sourcing science; science education; undergraduate research.

Bioelectrohydrogenesis And Inhibition Of Methanogenic Activity In Microbial Electrolysis Cells - A Review, Rengasamy Karthikeyan, Ka Yu Cheng, Ammaiyappan Selvam, Arpita Bose, Jonathan W.C. Wong

Biology Faculty Research

Microbial electrolysis cells (MECs) are a promising technology for biological hydrogen production. Compared to abiotic water electrolysis, a much lower electrical voltage (~0.2V) is required for hydrogen production in MECs. It is also an attractive waste treatment technology as a variety of biodegradable substances can be used as the process feedstock. Underpinning this technology is a recently discovered bioelectrochemical pathway known as "bioelectrohydrogenesis". However, little is known about the mechanism of this pathway, and numerous hurdles are yet to be addressed to maximize hydrogen yield and purity. Here, we review various aspects including reactor configurations, microorganisms, substrates, electrode materials, and …

The Rna Polymerase-Associated Factor 1 Complex Is Required For Plant Touch Responses, Gregory S. Jensen, Kateryna Fal, Olivier Hamant, Elizabeth S. Haswell

Biology Faculty Research

Thigmomorphogenesis is a stereotypical developmental alteration in the plant body plan that can be induced by repeatedly touching plant organs. To unravel how plants sense and record multiple touch stimuli we performed a novel forward genetic screen based on the development of a shorter stem in response to repetitive touch. The touch insensitive (ths1) mutant identified in this screen is defective in some aspects of shoot and root thigmomorphogenesis. The ths1 mutant is an intermediate loss-of-function allele of VERNALIZATION INDEPENDENCE 3 (VIP3), a previously characterized gene whose product is part of the RNA polymerase II-associated factor 1 …

Process-Based Modelling Shows How Climate And Demography Shape Language Diversity, Michael C. Gavin, Thiago F. Rangel, Claire Bowern, Robert K. Colwell, Kathryn R. Kirby, Carlos A. Botero, Michael Dunn, Robert R. Dunn, Joe Mccarter, Marco Tulio Pacheco Coelho, Russell D. Gray

Biology Faculty Research

Aim

Two fundamental questions about human language demand answers: why are so many languages spoken today and why is their geographical distribution so uneven? Although hypotheses have been proposed for centuries, the processes that determine patterns of linguistic and cultural diversity remain poorly understood. Previous studies, which relied on correlative, curve-fitting approaches, have produced contradictory results. Here we present the first application of process-based simulation modelling, derived from macroecology, to examine the distribution of human groups and their languages.

Location

The Australian continent is used as a case study to demonstrate the power of simulation modelling for identifying processes shaping …

Novel Regulation Of The Nonsense-Mediated Rna Decay Pathway, Andrew Keith Nickless

Arts & Sciences Graduate Student Theses and Dissertations

The nonsense mediated RNA decay (NMD) pathway maintains the integrity of cellular RNAs and controls gene expression. NMD is essential for vertebrate development and defects in NMD are associated with a variety of neurodevelopmental disorders and cancers. NMD activity is tightly regulated and is altered in response to environmental and developmental signals. To better study this dynamic pathway and to identify clinically relevant regulators of its activity, we developed a dual-color bioluminescent NMD reporter that rapidly and accurately quantifies NMD activity in mammalian cells. Using this reporter, we performed a chemical screen for small-molecule modulators of NMD activity and identified …

Regulation Of Mycobacterial Transcription Initiation, Jayan Rammohan

Arts & Sciences Graduate Student Theses and Dissertations

Cellular life relies on gene expression, in which DNA is first transcribed into RNA, which is then translated into protein. Transcription is performed by the protein RNA polymerase (RNAP), which interacts with DNA in three sequential events known as initiation, elongation and termination. Mycobacterium tuberculosis (Mtb) represents a global burden to public health, and the transcription factors CarD and RbpA are both essential to Mtb. I have studied the effect of CarD and RbpA on transcription initiation in vitro at the Mtb rrnAP3 promoter. I have shown that CarD stabilizes unwinding of promoter DNA by RNAP using a two-tiered kinetic …

Discovery And Characterization Of A Novel Class Of Metabolic Regulators In The Malaria Parasite Plasmodium Falciparum, Ann Marie Guggisberg

Arts & Sciences Graduate Student Theses and Dissertations

The malaria parasite, Plasmodium falciparum, infects hundreds of millions of people per year and causes hundreds of thousands of deaths. Within the host red blood cell, the parasite relies on glycolysis for energy and synthesis of essential biomolecules. One such anabolic fate of glucose is the synthesis of isoprenoids, a broad and essential class of compounds that participate in a variety of cellular functions. In the face of ever-evolving drug resistance, new inhibitors and better understanding of parasite metabolism are required. The antibiotic fosmidomycin (FSM) targets the methylerythritol phosphate pathway for isoprenoid synthesis and is a well-validated inhibitor of P. …

Genetic Mechanisms For The Maintenance Of Behavioral Mating Barriers In Drosophila, Kathleen M. Mortland

Arts & Sciences Graduate Student Theses and Dissertations

One of the most successful and diverse systems involved in the maintenance of behavioral barriers between closely related animal species is pheromonal communication. In the fruit fly, contact chemosensation input is especially important during sexual decision-making as it allows for the sensing of sex and species-specific non-volatile cuticular hydrocarbons (CHCs), which function as insect pheromones. However, how pheromonal systems support the maintenance of mating barriers is puzzling since any change in either pheromone ligands or their cognate receptors would carry a fitness cost, which should be eliminated by stabilizing selection. To resolve this evolutionary conundrum I hypothesized that pleiotropic genes …

A Study On The Role And Regulation Of The Na+-Leak Channel, Non-Selective (Nalcn) In Myometrial Function, Erin Lynn Reinl

Arts & Sciences Graduate Student Theses and Dissertations

Uterine contractions are tightly regulated throughout pregnancy, remaining relatively quiescent for the majority of pregnancy to promote fetal development, while becoming highly activated at term to effectively expel the fetus. Contractions are coordinated through electrical and mechanical coupling of myometrial smooth muscle cells (MSMCs). Ion channel activity, which alters the electrical activity of MSMCs, can directly affect the contraction profile. Thus there is great interest in the field of reproduction to understand which ion channels regulate uterine excitability, and particularly how they may enable the transition from uterine quiescence to uterine activation for labor. The focus thus far has been …

Structure, Dynamics, And Regulation Of Collective Cell Migration, Andrew J. Loza

Arts & Sciences Graduate Student Theses and Dissertations

Collective migration is the process by which cells organize individual motions to productively migrate as a group and plays a fundamental role in organism development, tissue regeneration, and cancer invasion. In development, coordinated migration facilitates the formation of complex organ structures and is required for proper dissemination of neural crest cells throughout an organism. After injury, this process allows breaches in epithelial layers to be repaired while maintaining tissue integrity, and in cancer, collective behavior enhances invasion of tumor cells into the surrounding tissue. Chapter 1 provides an introduction for the role of collective migration across an organism’s lifespan, the …

Epigenomics Of Cell Fate In Development And Disease, Rebecca Faith Lowdon

Arts & Sciences Graduate Student Theses and Dissertations

Epigenetic features at regulatory elements provide instructive cues for transcriptional regulation during development. However, the particular epigenetic alterations necessary for proper cell fate acquisition and differentiation are not well understood. This dissertation explores the epigenetic dynamics of regulatory elements during development and uses epigenome annotations to document inappropriate transcriptional regulation in disease. First, I summarize my contributions to developing a new algorithm for detecting differential DNA methylation, M&M. I report the application of the M&M algorithm to identify distinct classes of DNA methylation dynamics in surface ectoderm (SE) progenitor cells and SE-derived lineages: epigenome alterations, and differential DNA methylation in …

Discovery And Functional Implication Of Genetic Alterations Associated With Clonal Hematopoietic Expansion, Mingchao Xie

Arts & Sciences Graduate Student Theses and Dissertations

Cancers, including hematologic malignancies, arise as a result of the stepwise accumulation of mutations. Some early mutations that potentially initiate clonal expansion might exist in patients many years before they develop obvious disease symptoms. Therefore, identifying and characterizing these early mutations are critical to understanding the genetic basis of tumorigenesis. Here, we analyzed blood-derived DNA sequencing data from 2,728 individuals without apparent hematologic malignancies and identified 77 blood-specific mutations in 31 cancer-associated genes. Importantly, 83% of all mutations occurred in 19 genes that have been previously linked to hematological malignancies, such as DNMT3A, TET2, JAK2, and ASXL1. By investigating these …

The Human Arf Tumor Suppressor Regulates Drosha Nucleolar Localization And Rrna Processing Activity, Sree Chandana Sridhar Yaddanapudi

Arts & Sciences Graduate Student Theses and Dissertations

Ribosomes are vital to the survival of a cell, as they are directly responsible for the synthesis of proteins, which perform critical cellular functions. As such, majority of the energy reserves in a proliferating cell are expended towards synthesis of ribosomes. Cancer cells, with their enhanced proliferation rates, tend to upregulate ribosome biogenesis in order to meet the demand for increased protein synthesis necessary to sustain rapid proliferation. Many of the oncogenes and tumor suppressors known to be deregulated in cancers are capable of positively and negatively regulating ribosome biogenesis, respectively. The ARF tumor suppressor strongly suppresses ribosome biogenesis, particularly …

The Promise And Pitfalls Of Β-Diversity In Ecology And Conservation, Jonathan A. Myers, Joseph A. Lamanna

Biology Faculty Research

A key challenge in ecology and conservation is to determine how processes at different scales create variation in community composition (β-diversity). In this issue, Oldén & Halme show that grazers increase β-diversity through multiple processes at different scales. We discuss how β-diversity can elucidate fundamental processes of community assembly, challenges in linking processes to patterns, and unresolved questions across scales.

Kin Selection And Its Discontents, David C. Queller

Biology Faculty Research

Kin selection is a core aspect of social evolution theory, but a small number of critics have recently challenged it. Here I address these criticisms and show that kin selection remains an important explanation for much (though not all) social evolution. I show how many of the criticisms rest on historical idiosyncrasies of the way the field happened to develop, rather than on the real logic and evidence.

Problems Of Multi-Species Organisms: Endosymbionts To Holobionts, David C. Queller, Joan E. Strassmann

Biology Faculty Research

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that …

Phytochrome B Integrates Light And Temperature Signals In Arabidopsis, Martina Legris, Cornelia Klose, E Sethe Burgie, Cecilia Costigliolo Rojas Rojas, Maximiliano Neme, Andreas Hiltbrunner, Philip A. Wigge, Eberhard Schäfer, Richard D. Vierstra, Jorge J. Casal

Biology Faculty Research

Ambient temperature regulates many aspects of plant growth and development, but its sensors are unknown. Here, we demonstrate that the phytochrome B (phyB) photoreceptor participates in temperature perception through its temperature-dependent reversion from the active Pfr state to the inactive Pr state. Increased rates of thermal reversion upon exposing Arabidopsis seedlings to warm environments reduce both the abundance of the biologically active Pfr-Pfr dimer pool of phyB and the size of the associated nuclear bodies, even in daylight. Mathematical analysis of stem growth for seedlings expressing wild-type phyB or thermally stable variants under various combinations of light and temperature revealed …

Msl1 Is A Mechanosensitive Ion Channel That Dissipates Mitochondrial Membrane Potential And Maintains Redox Homeostasis In Mitochondria During Abiotic Stress, Chun Pong Lee, Grigory Maksaev, Gregory S. Jensen, Monika W. Murcha, Margaret E. Wilson, Mark Fricker, Ruediger Hell, Elizabeth S. Haswell, A Harvey Millar, Lee J. Sweetlove

Biology Faculty Research

Mitochondria must maintain tight control over the electrochemical gradient across their inner membrane to allow ATP synthesis while maintaining a redox-balanced electron transport chain and avoiding excessive reactive oxygen species production. However, there is a scarcity of knowledge about the ion transporters in the inner mitochondrial membrane that contribute to control of membrane potential. We show that loss of MSL1, a member of a family of mechanosensitive ion channels related to the bacterial channel MscS, leads to increased membrane potential of Arabidopsis mitochondria under specific bioenergetic states. We demonstrate that MSL1 localises to the inner mitochondrial membrane. When expressed in …

Purification Of 26s Proteasomes And Their Subcomplexes From Plants, Richard S. Marshall, David C. Gemperline, Richard D. Vierstra

Biology Faculty Research

The 26S proteasome is a highly dynamic, multisubunit, ATP-dependent protease that plays a central role in cellular housekeeping and many aspects of plant growth and development by degrading aberrant polypeptides and key cellular regulators that are first modified by ubiquitin. Although the 26S proteasome was originally enriched from plants over 30 years ago, only recently have significant advances been made in our ability to isolate and study the plant particle. Here, we describe two robust methods for purifying the 26S proteasome and its subcomplexes from Arabidopsis thaliana; one that involves conventional chromatography techniques to isolate the complex from wild-type …

Plastid Osmotic Stress Influences Cell Differentiation At The Plant Shoot Apex, Margaret E. Wilson, Matthew Mixdorf, R Howard Berg, Elizabeth S. Haswell

Biology Faculty Research

The balance between proliferation and differentiation in the plant shoot apical meristem is controlled by regulatory loops involving the phytohormone cytokinin and stem cell identity genes. Concurrently, cellular differentiation in the developing shoot is coordinated with the environmental and developmental status of plastids within those cells. Here, we employ an Arabidopsis thaliana mutant exhibiting constitutive plastid osmotic stress to investigate the molecular and genetic pathways connecting plastid osmotic stress with cell differentiation at the shoot apex. msl2 msl3 mutants exhibit dramatically enlarged and deformed plastids in the shoot apical meristem, and develop a mass of callus tissue at the shoot …

Regulation Of Durable Adaptive Immune Response By The C-Myc-Ap4 Transcriptional Cascade, Chun Chou

Arts & Sciences Graduate Student Theses and Dissertations

The process of amplifying immune responses by expanding a small number of antigen-specific cells, termed clonal expansion, is an important feature of the adaptive immunity. Whereas clonal expansion of cytotoxic T lymphocytes is required for complete eradication of intracellular pathogens, proliferation of B lymphocytes in the germinal centers (GC) is critical for generating a diverse immunoglobulin gene repertoire from which protective antibody carrying multiple mutations can arise. While the proto-oncogene c-MYC is absolutely required for the activation and cell cycle initiation in lymphocytes, its expression is temporally restricted. Activated lymphocytes, however, continue to proliferate after c-MYC levels decay to maximize …

Functions For Murine Norovirus Protein Ns1/2 In Mice And Cells, Broc Taylor Mccune

Arts & Sciences Graduate Student Theses and Dissertations

Noroviruses are a leading cause of epidemic gastroenteritis and a major health burden worldwide. One source for outbreaks is individuals who shed virus asymptomatically and persistently. Viral persistence is a successful strategy for viruses to spread, but the mechanisms and consequences of norovirus persistent infection are unknown. In this dissertation, we sought to determine the norovirus determinant(s) of persistence and explore the functions of the associated viral molecules.To determine the viral determinants of persistent infection and tropism, we used the murine norovirus model system in mice. Using plasmid infectious clones for persistent strain CR6 and non-persistent strain CW3, we mapped …

Molecular Mechanisms Mediating The Effects Of Acute Dietary Vitamin A Deficiency On A Defined Model Human Gut Microbiota, Matthew Charles Hibberd

Arts & Sciences Graduate Student Theses and Dissertations

Micronutrient deficiencies represent a form of "hidden hunger" that afflict two billion people worldwide. To test the hypothesis that dietary micronutrient deficiency has differential effects on members of the human gut microbiota, a consortium containing 92 sequenced phylogenetically diverse bacterial strains was introduced into germ-free mice. Recipient animals were subjected to a diet oscillation that began with highly defined micronutrient-sufficient diet followed by a derivative diet with one of four types of single micronutrient deficiency, or a diet representing combined deficiencies, followed by return to the original sufficient diet. Times-series studies of microbial community structure and transcriptome revealed that acute …

Tau Prion Strains In Cells, Mice, And Patients, David Winland Sanders

Arts & Sciences Graduate Student Theses and Dissertations

Prion-like propagation of tau aggregation may underlie the stereotyped progression of pathology along neuronal networks in neurodegenerative tauopathies such as Alzheimer’s disease. It has become increasingly clear that unique conformations (“strains”) of prion protein (PrP) link aggregate structure to clinical phenotypes in human prion diseases. Intriguingly, vast phenotypic diversity in pathological and clinical presentation is also observed in tauopathies. The mechanisms that account for this phenotypic diversity are completely unknown. During my dissertation work, I put forward and tested the hypothesis that distinct tau amyloid conformations (or “strains”) are responsible for unique tauopathies. First, I found that in experimental models, …

Behavioral And Neurophysiological Mechanisms Of Recovery Post-Stroke, Lenny Eveline Ramsey

Arts & Sciences Graduate Student Theses and Dissertations

Strokes can affect very different behavioral domains causing deficits in language, memory, visual attention and movement. This range of deficits is caused by stroke lesions that occur in different locations, and it reflects both the local structural damage as well as remote and widespread neurophysiological abnormalities of structurally normal regions of the brain. The recovery of behavioral deficits depends both on psychosocial factors like age and education, whose brain substrates are presently poorly defined, structural variables such as lesion size and location, and neurobiological repair mechanisms both locally near the lesion and network-wide.In the current work we hypothesized that behavioral …