Biology Commons^™

Land And Energy, Devan Viani

Biology Student Scholarship

Land use has and will continue to be a complicated topic. We need land to succeed as a country and a species, but it is equally as important to keep the land as pristine as possible to not affect natural ecosystems. As population continues to increase, urbanization and economic growth has inevitably had an impact on climate change.¹ Parallel to an increase in land development is an increase in power generation. As cities grow, technology evolves, and energy use goes up. With this increase in technology, new sources of power generation are emerging. While fossil fuels have always been the …

Precipitation Effects On Butterfly Species Richness, Maggie Ritchie

Biology Student Scholarship

Butterflies are important pollinators that have been impacted due to climate change(1). Studies have looked at how the increasing temperatures and precipitation due to climate change may be playing a role in decreasing populations among some species in Mediterranean climates(2). However, the effects of precipitation have not been considered when looking at changing butterfly populations around the United States. Therefore, increasing precipitation amounts due to climate change may contribute to the decreasing populations of butterflies in Massachusetts.BIO 340 final project

The Impact Of Age And Catch Location On The Mortality Rates Of Striped Bass, Owen Finnegan

Biology Student Scholarship

Striped bass are one of the most popular and sought-after gamefish in the United States for recreation and commercial fishermen. This popularity comes from their size, with many fish reaching 40+ pounds, a prominent dish in seafood restaurants, and their expansive habitat as they inhabit waters from Florida to Canada (1). During the late 1970s/80s, the population began sharply declining due to overfishing, and governments enacted regulations to stabilize the population (1). However, as of 2020, overfishing is still occurring, and regulations are continuously evolving (1). Each state has their own rules and regulations for possessing striped bass for commercial …

Does More Pollen Mean More Sneezing?, Diraliz Cruz

Biology Student Scholarship

Every year millions of people suffer from seasonal allergies, according to the CDC about 25% of adults have to deal with these allergies. Pollen comes from all different things like trees, grasses, and weeds and as climate change increases annually the amount of pollen released into the air also increases. Research has shown that climate change has specifically impacted the amount of birch and oak pollen released annually. Although there is data to show that there has been an increase in pollen release there is little to no information on if the prevalence of allergies has increased or decreased along …

The Influence Of Sampling Frequency On Bee Species Richness, Courtney Caccamo

Biology Student Scholarship

As one of Earth’s most valuable pollinators, bees provide important pollination services to wild plant species and crops alike (Winfree 2010). But, in recent years, bee populations appear to be declining due to a variety of anthropogenic drivers (Potts et al. 2010). Quantifying the extent of bee population decline is difficult because there is currently a lack of a standardized protocol for how best to survey bee populations (Tepedino & Portman 2021). One of the commonly used survey methods is pan trapping, which involves leaving out yellow, white, and blue bowls filled with soapy water to passively sample the species …

Intermittent Synchronization In Gamma-Band Neural Oscillations, Anh Nguyen, Leonid L. Rubchinsky

Biology and Medicine Through Mathematics Conference

No abstract provided.

Cover Crop Application On Dredged Sediments Increases Corn Yield Through Microorganism-Associated Enzyme-Driven Nutrient Mineralization, Ashley N. Julian, Louise M. Stevenson, Megan A. Rúa

Biological Sciences Faculty Publications

Background & Aims

Common strategies to mitigate soil degradation of agricultural soils include cover crop application and soil amendment addition. Applying dredged sediments as a soil amendment is gaining popularity since they often provide benefits other amendments lack; however, their use with cover crops is largely unexplored. To understand how cover crop use changes the restorative properties of dredged sediments, we assessed soil physical and chemical properties, enzymatic activities, and corn yield for plots of dredged sediments with and without a cover crop.

Methods

We assessed soil texture, bulk density, water content, pH, nitrogen, phosphorus, cation exchange capacity, calcium, magnesium, …

A Standard Protocol To Report Discrete Stage-Structured Demographic Information, Samuel J. L. Gascoigne, Simon Rolph, Daisy Sankey, Nagalakshmi Nidadavolu, Adrian S. Stell Pičman, Christina M. Hernández, Matthew E. R. Philpott, Aiyla Salam, Connor Bernard, Erola Fenollosa, Young Jun Lee, Jessica Mclean, Shathuki Hetti Achchige Perera, Oliver G. Spacey, Maja Kajin, Anna C. Vinton, C. Ruth Archer, Jean H. Burns, Danielle L. Buss, Hal Caswell, Judy P. Che-Castaldo, Dylan Z. Childs, Pol Capdevila, Aldo Compagnoni, Elizabeth Crone, Thomas H. G. Ezard, Dave Hodgson, Tiffany M. Knight, Owen R. Jones, Eelke Jongejans, Jenni Mcdonald, Brigitte Tenhumberg, Chelsea C. Thomas, Andrew J. Tyre, Satu Ramula, Iain Stott, Raymond L. Tremblay, Phil Wilson, James James Vaupel, Roberto Salguero-Gómez

School of Biological Sciences: Faculty Publications

1. Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported.

2. Here, we summarise current issues related to …

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The Synergistic Response Of Primary Production In Grasslands To Combined Nitrogen And Phosphorus Addition Is Caused By Increased Nutrient Uptake And Retention, Eduardo Vázquez, Elizabeth T. Borer, Miguel N. Bugalho, Maria C. Caldeira, Rebecca L. Mcculley, Anita C. Risch, Eric W. Seabloom, George R. Wheeler, Marie Spohn

School of Biological Sciences: Faculty Publications

Background and aims A synergistic response of aboveground plant biomass production to combined nitrogen (N) and phosphorus (P) addition has been observed in many ecosystems, but the underlying mechanisms and their relative importance are not well known. We aimed at evaluating several mechanisms that could potentially cause the synergistic growth response, such as changes in plant biomass allocation, increased N and P uptake by plants, and enhanced ecosystem nutrient retention.

Methods We studied five grasslands located in Europe and the USA that are subjected to an element addition experiment composed of four treatments: control (no element addition), N addition, …

Ecological Boundaries And Constraints On Viable Eco-Evolutionary Pathways, Kyle E. Coblentz, John P. Delong

School of Biological Sciences: Faculty Publications

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as ‘demographic constraints’, constrain what can occur evolutionarily due to the demographic or dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or the rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and dynamic consequences of evolution also can constrain …

The Effects Of Aluminum Ion Exposure On Planarian Photophobic Response To Different Wavelengths Of Light, Anden J. Velez

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Aluminum exposure has been linked to the development of neurological diseases (Kim et al., 2021). It has increased in quantity in the environment due to industrial activity in producing personal care products and fast food (Tietz et al., 2019). The freshwater invertebrate planarian flatworm Giardia dorotocephala (G. dorotocephala) serves as a model organism. Humans and planarians both express the ion channel transient receptor potential ankyrin 1 (TRPA1), which is responsible for thermotaxis, locomotive response to heat, and pain reception (Arenas et al., 2017). Aluminum exposure can exert ion channel-related toxicity via the TRPA1 protein. It has been found …

Investigating The Role Of Tgf-Beta Signaling In Acoel Regeneration & Fission, Franchesca A. Aziz

Undergraduate Honors Theses

Whole-body regeneration and asexual reproduction are widespread in the Metazoa, yet little is known about the genetic systems that drive the regeneration process outside of a few model organisms. While many animals utilize fission followed by regeneration to accomplish asexual reproduction, Convolutriloba longifissura is unusual in performing a double fission, requiring significant anterior-posterior and medial-lateral regeneration that alters the orthogonal body axes in adult tissues. To better understand the process of axial re-specification during postembryonic development, we studied the genetic mechanisms used by C. longifissura to modify and respecify axial polarity during asexual reproduction and subsequent regeneration. Because conserved signaling …

Secondary Channel Backwaters May Be Superior Nurseries For Native Fishes In The San Juan River Of The American Southwest, But Monsoon-Driven Deteriorations May Lessen Their Quality, Blake Hansen

Electronic Theses & Dissertations

The Razorback Sucker (Xyrauchen texanus) and Colorado Pikeminnow (Ptychocheilus lucius) are federally-endangered species occurring in the San Juan River of NM, CO, and UT, USA. These species have shown little natural recruitment in this system, with a lack of high-quality nursery habitats being one potential explanation for this phenomenon. The young-of-year of both species prefer backwaters, including those that form in secondary channels or in association with islands. However, it is unknown how factors that could limit imperiled fish recruitment, such as hydrologic stability, physicochemical features, resource availability, and nonnative fish densities, differ between secondary channel …

Assessing Paleoenvironmental Change Of A Boca Raton Inlet Through Midden Shell Artifact Analysis, Maria Gabriella Almeida

Graduate Student Dissertations, Theses, Capstones, and Portfolios

In this archeological study of a barrier island shell midden in Boca Raton, FL, we evaluate possible environmental and cultural changes that occurred through time by performing a quantitative analysis of shell artifacts of Giant False Donax (Iphigenia brasiliana) and Common Atlantic Oyster (Crassostrea virginica) collected from the shell midden. Middens are archeological trash sites used by researchers to identify artifacts used by past populations to understand their behaviors. The artifacts collected in shallow portion of the midden are younger (therein representing more recent time periods) and the artifacts collected at the deeper portion are older …

Spike-Timing-Dependent Plasticity Alters Sensory Network Connectivity, Adalee Lube

Arts & Sciences Graduate Student Theses and Dissertations

A fundamental question in neuroscience is: how does a sensory system optimize detection of behaviorally relevant stimuli, when those stimuli and the sensory environment are constantly changing? Spike-timing-dependent plasticity (STDP), in which synapse strength changes based on the relative timing of pre- and post-synaptic spiking, has been implicated in changes in neuronal connectivity thought to underlie learning and memory. Synaptic strength changes caused by STDP have been shown in optic tectum, visual cortex, hippocampus, and other brain regions in vitro across many organisms like fish, frogs, and mice. Although it is possible that STDP mechanisms underlie changes in sensory neuron …

An Evolving View Of Host-Microbiome Co-Development In Healthy And Undernourished Children, Robert Yuzen Chen

Arts & Sciences Graduate Student Theses and Dissertations

Affecting more than 795 million children under the age of 5, childhood undernutrition is one of the greatest impediments to the flourishing of humankind. Current dietary interventions fail to ameliorate many of the long-term sequelae of undernutrition, including immune system dysfunction, impaired vaccine responses, persistent central nervous system (CNS) dysfunction, and early mortality. These shortcomings suggest that our understanding of the biological state of undernutrition is incomplete, and that traditional food therapies fail to target key drivers of undernutrition-dependent pathologies. Recently, work from our lab has provided preclinical evidence demonstrating that impaired development of the distal gut microbiota plays a …

A Mechanistic Study Of Err Α/Γ Agonists For Treatment Of Metabolic Dysfunction In Heart Failure, Mckenna Lael Losby

Arts & Sciences Graduate Student Theses and Dissertations

Heart failure is the leading cause of death in the United States and current therapeutic interventions fail to reverse the disease progression. In the failing heart, pathological cardiac remodeling leads to disease progression: a process characterized by hypertrophy, inflammation, fibrosis, and metabolic remodeling. By pharmacologically targeting the nuclear hormone receptors estrogen receptor-related receptor α and γ (ERRα and γ), it may be possible to reverse the array of metabolic pathways that are pathologically inhibited in the failing heart. Fatty acids are the primary fuel source of the adult heart that generate the ATP required for each contraction; however, in heart …

Histamine Production By Airway Resident Haemophilus Species Induces Rhinitis, Michael Lint

Arts & Sciences Graduate Student Theses and Dissertations

Allergic rhinitis is one of the most common chronic illnesses in America, affecting more than 60 million people each year. Allergies develop when sensitization to an environmental allergen result in the production of antigen-specific IgE. Subsequent exposure to the allergen, detected by IgE, then binds to the surface of mast cells triggering the release of inflammatory mediators particularly histamine, which contribute to characteristic allergic symptoms of nasal itching, sneezing, and wheezing. Although fundamental mechanisms underlying allergy development have been previously characterized, recent research has implicated commensal bacteria residing in the respiratory tract in contributing to the development of allergic inflammation, …

Mechanisms And Consequences Of Microtubule-Based Symmetry Breaking In Plant Roots, Natasha Anriel Bilkey

Arts & Sciences Graduate Student Theses and Dissertations

Directional growth in plants is primarily determined by the axis of cell expansion, which is specified by the net orientation of cortical microtubules. Microtubules guide the deposition of cellulose and other cell wall materials. In rapidly elongating cells, transversely oriented microtubules create material anisotropy in the cell wall that prevents radial cell expansion, channeling cell expansion in the longitudinal direction. Mutations perturbing microtubule organization frequently lead to aberrant cell growth in land plants, with some mutations leading to helical growth patterns (called ‘twisted mutants’), often in roots. This phenotype manifests as right-handed or left-handed twisting of cell files along the …

Understanding The Spectrum Of Dnmt3a Mutations In Neurodevelopmental Disease, Diana Christian Beard

Arts & Sciences Graduate Student Theses and Dissertations

Epigenetic mechanisms are critical for precisely controlling gene expression programs to allow for the development and function of the brain, and disruptions of these processes are highly associated with neurodevelopmental disease. DNA methylation is one mechanism used to regulate gene expression, and neurons employ a unique form of DNA methylation particularly at CA dinucleotides (mCA), that is not widely observed in other somatic cell types. The DNA methyltransferase DNMT3A is required to establish mCA, and mutations in DNMT3A are associated with autism spectrum disorder (ASD) and an overgrowth and intellectual disability disorder called Tatton-Brown Rahman Syndrome (TBRS). However, it remains …

Investigating Disease Progression And Therapeutic Targets In Multiple Myeloma Using Single-Cell Technologies, Lijun Yao

Arts & Sciences Graduate Student Theses and Dissertations

Multiple Myeloma (MM) is a highly heterogeneous disease characterized by uncontrolled clonal expansion of plasma cells. Single-cell techniques are advantageous in providing a more granular understanding of inter- and intratumoral genomics and surrounding microenvironments. The high relapse rate and intrinsic complexity of MM make the application of single-cell technologies particularly beneficial. Understanding the concordance of the measurements across single cell techniques in MM is of great interest. In this dissertation, we first integrated three single-cell technologies, namely scRNA-seq, CyTOF, and CITE-seq, to characterize MM immune microenvironment and assess their concordances of measurement. Overall, cell type abundances were relatively consistent, while …

Single-Molecule Spectroscopy Of The Sars-Cov-2 Nucleocapsid Protein, Jasmine Cubuk

Arts & Sciences Graduate Student Theses and Dissertations

The COVID pandemic has affected over 760,000,000 individuals worldwide since late 2019. Understanding how SARS-CoV-2, the virus responsible for the disease, functions at a mechanistic level is essential to develop therapeutics and vaccines. SARS-CoV-2 utilizes four structural proteins that work together during the viral life cycle to ensure the spread of infections: spike (S), envelope (E), membrane (M) and nucleocapsid (N). Though much work has focused on the S protein for the purpose of vaccines, the N protein plays a key function in the viral life cycle as well. Nucleocapsid is responsible for packaging the viral genome and incorporating the …

Bioinformatic Tools To Alleviate The Annotation Bottleneck Within Precision Oncology, Erica Kay Barnell

Arts & Sciences Graduate Student Theses and Dissertations

In the era of advanced ability to perform complex genomic sequencing, precision oncology has been adopted as the ideal paradigm for optimization of outcomes for patients with cancer. However, despite technological advances in all aspects of the massively parallel sequencing pipeline, the application of precision oncology to every clinical workflow has been unattainable. Suboptimal adoption of custom medicine within oncology is attributable to the annotation bottleneck, which currently demands inordinate manual and computational requirements for completion. Alleviation of the annotation bottleneck requires co-development of bioinformatic strategies and analysis knowledgebanks to automate variant identification and variant annotation for clinical utility. The …

The Influence Of The Gut Microbiota On Asthma In School-Aged Children And Adults, Naomi Grace Wilson

Arts & Sciences Graduate Student Theses and Dissertations

Asthma is a common respiratory disease with a highly heterogeneous pathophysiology. The human gut microbiota, comprising of all the microorganisms that inhabit the gastrointestinal tract, is linked to the development of asthma and can alter airway inflammation in animal models. The idea that the gut microbiota can have bidirectional cross-talk with the lung, such as gut dysbiosis affecting lung disease, is termed the gut-lung axis. While the gut microbiota of early life has been an area of particular interest for asthma pathogenesis research, the effect of its taxonomic and functional composition after asthma diagnosis is less clear. This dissertation employs …

Mechanisms Of Transcription Regulation By Card In Mycobacterium, Dennis Xiaoqian Zhu

Arts & Sciences Graduate Student Theses and Dissertations

Mycobacterium tuberculosis (Mtb) is an important human pathogen that is responsible for over 1 million deaths each year. As a bacterial pathogen, Mtb is highly adapted to survival within the host environment, which imposes numerous environmental stresses on the bacteria. To survive these challenges, Mtb utilizes a network of transcription factors to adapt its gene expression and physiology. CarD is an essential transcription factor in mycobacteria that binds directly to RNA polymerase (RNAP) rather than DNA sequence motifs on the chromosome. Prior mechanistic studies of CarD’s function in mycobacteria have been limited to studies of CarD’s effects on individual kinetic …

Evaluating The Impact Of Temperature And Artificial Light At Night On The Growth, Swimming Performance, And Corticosterone Levels Of Southern Leopard Frog (Lithobates Sphenocephalus) Tadpoles, Skylar Alexander

Honors Theses

Anthropogenic activities caused by urbanization have considerably altered our world’s ecosystems which has led to a global amphibian population decline. Encroaching and unyielding urbanization by humans has contributed to a rise in artificial light at night due to light pollution as well as increased temperature due to climate change. Both rising temperatures and artificial light at night (ALAN) have been shown to individually have negative effects on amphibian physiology such as increased stress and decreased behavior. However, due to the drastic nature of human imposition, amphibians typically encounter these anthropogenic stressors in combination. Therefore, it is important to understand how …

The Role Of The Neurodevelopmental Disorder Gene Myt1l In Mammalian Brain Development, Jiayang Chen

Arts & Sciences Graduate Student Theses and Dissertations

Recent human genetic studies have associated mutations in a gene called Myelin Transcription Factor 1 Like (MYT1L) with neurodevelopmental disorders (NDDs). Patients with MYT1L loss of function (LoF) mutations (MYT1L Syndrome patients) demonstrate shared symptoms such as microcephaly, attention deficit and hyperactivity disorder (ADHD), and obesity. Despite prior studies showing MYT1L overexpression facilitates neuronal differentiation in vitro, its functions in vivo, especially in the mammalian brain, and how its mutation leads to human disease pathology remains poorly understood. Here, I established the first mouse model of MYT1L Syndrome mimicking a patient specific LoF mutation. I found mice with Myt1l heterozygous …

Wide-Field Optical Imaging Of Neurological Disorders And Sleep In Mice, Lindsey M. Brier

Arts & Sciences Graduate Student Theses and Dissertations

Neuroimaging has revolutionized the way in which we understand the hierarchical organization of the amazingly complex, interconnected human brain. Neuroimaging techniques, like functional magnetic resonance imaging (fMRI), have provided high quality structural and functional data, providing multiple in-depth analyses and biomarkers of disease processes. In animal models, mechanistic studies can uncover root pathologies that aren’t explorable in humans. In mice, brain functional connectivity (FC) can be measured via Optical Intrinsic Signal (OIS) imaging – a modality that measures vascular reactivity as a surrogate for neural activity via quantification of fluctuations in oxygenated-hemoglobin (similar to the blood oxygen level dependent (BOLD) …

Improving Neoantigen Prioritization Methods For Personalized Cancer Vaccines, Huiming Xia

Arts & Sciences Graduate Student Theses and Dissertations

Neoantigens are novel peptide sequences resulting from sources such as somatic mutations in tumors. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. Thus, accurate identification and prioritization of neoantigens is critical for conducting neoantigen-based clinical trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of whole exome and RNA sequencing technologies, researchers and clinicians are now able to computationally predict neoantigens based on patient-specific mutation information. However, …

Identification And Characterization Of Targets Of Metastasis In High-Grade Serous Ovarian Cancer, Emilee Nicole Kotnik

Arts & Sciences Graduate Student Theses and Dissertations

High-Grade Serous Ovarian Cancer (HGSC) is a highly metastatic cancer with the majority of patients presenting in advanced stages. Currently there are limited targeted treatment options for patients, especially for women with high metastatic tumor burdens. In order to improve patient outcomes, we have aimed to identify and characterize novel targets of metastasis utilizing sequencing from patient tumors and a functional genomic screen. First, we identified genetic alterations of metastasis and short survival by characterizing the genomic and transcriptomic alterations of primary and metastatic tumors in HGSC patients from 23 short-term survivors (overall survival (OS)5 years). We compared somatic mutations, …