Systems Biology Commons^™

Pathogen Emergence As Complex Biological Invasion: Lessons From Dynamical Systems Modeling, Sudam Surasinghe, Marisabel Rodriguez, Victor Meszaros, Jane Molofksy, Salvador Almagro-Moreno, Brandon Ogbunugafor

Northeast Journal of Complex Systems (NEJCS)

Infectious disease emergence has become the target of cross-disciplinary efforts
that aim to understand and predict the shape of outbreaks. The many challenges
involved with the prediction of disease emergence events is a characteristic that in-
fectious diseases share with biological invasions in many subfields of ecology (e.g.,
how certain plants are able to successfully invade a new niche). Like infectious
diseases, biological invasions by plants and animals involve interactions between
agents (pathogens and plants in their respective cases) and a recipient niche. In
this study, we examine the problem of pathogen emergence through the lens of a
framework first …

City As Cemetery, Siqiao Zhao

Masters Theses

The traditional funeral service industry has enormous environmental and financial costs. In contrast, green burial, and Natural Organic Reduction (NOR), accelerate the human body’s degradation and reduce toxic substances in the land, assuming responsibility for our burden on the earth. They provide a gateway between us and the processes of nature and ask us to set aside self-consciousness to accept our oneness with the universe. By gifting our bodies back to the earth, where decomposition enriches soils and nurtures the growth of other life forms, we honor those who have transitioned to another state by continuing the cycle of renewal. …

The Influence Of Microorganisms On Human Health, Tiffany Bui

University Honors Theses

The purpose of this thesis is to explore the interplay between the environment, lifestyle, and composition of human microbiomes across different communities, with a specific focus on immune and digestive health. This literature review investigates three distinct types of communities: isolated/traditional, transitional, and urban/industrialized communities, each characterized by unique environments, societal structures, and interactions. These factors contribute to the distinct microbial populations and compositions within each community. It is impossible to avoid contact with microorganisms as they are present in every aspect of our lives, from the air we breathe, the water we drink, the soil we walk on, the …

Novel Natural Compounds Derived From Tcm In The Treatment Of Food Induced Anaphylaxis, Ibrahim Musa

NYMC Student Theses and Dissertations

Food allergy is a highly prevalent disease affecting about 30 million people in the U.S. It is managed primarily by food avoidance due to lack of promising treatment options. ASHMI (anti-asthma herbal intervention) which consists of three components, Sophorae flavescentis, Ganoderma lucidum, Glycyrrhiza uralensis has been shown to inhibit allergic lung inflammation in antigen sensitized and challenged mice. In this study we isolate and identify the active compound in Sophorae flavescentis, characterized the mechanism of IgE inhibitory effect, biomarkers and potential to prevent food anaphylaxis.

To separate and identify the compounds we used column chromatography, high-performance liquid chromatography, mass …

Ethical Considerations Of Clinical Research In Emergency Care Settings: A Review, Adith Velavan

Honors Scholar Theses

Emergency and acute care settings are some of the most volatile and high intensity areas of any healthcare operation. Better understanding of systems and treatments in these spaces are critical to improving outcomes for the high risk patients that are treated there. Clinical research serves as a cornerstone of modern medical research, and is critical to the further improvement of clinical care in these settings. This thesis serves to explore the ethicality of such research given the constraints of emergency medicine settings. Not only does this thesis provide a strong foundation regarding the history and current practices of clinical research, …

Do Plants Have The Cognitive Complexity For Sentience?, Ricard V. Solé

Animal Sentience

Are plants sentient? Like other aspects of the cognitive potential of plants, this is a controversial issue, often driven by analogies and seldom supported on solid theoretical grounds. Sentience is understood in cognitive sciences as the capacity to feel. I suggest that because of plants’ evolved adaptations to morphological plasticity, sessile nature and ecological constraints, they are unlikely to have the requisite cognitive complexity for sentience.

Phylogenetics And Integrative Taxonomy Of African Water Snakes (Squamata: Colubridae: Grayia), Teslin Chaney

Open Access Theses & Dissertations

Grayia is a genus of relatively large (1.5 - 2.5 m) aquatic Afrotropical snakes. Recent molecular phylogenies recovered Grayia in its own distinct subfamily (Grayiinae), which was strongly supported as the sister group to Colubrinae. Because tropical African snakes are generally understudied, the relationships within Grayia are poorly known. Due to high degrees of intra- and interspecies variation, identification is often difficult and previous studies involving Grayia included misidentified specimens in other genera. The goal of this study is to create a phylogenetic tree that can be used to understand the relationships and taxonomy of Grayia via an integrative taxonomic …

Cell-Free Metabolic Engineering Strategies For Accelerated Biomanufacturing, Jaime Lorenzo N. Dinglasan

Doctoral Dissertations

Biomanufacturing propels the bioeconomy. Accelerating bioeconomic growth thus requires the expedited development of biomanufacturing processes that can expand the current bioproduct portfolio. Lysate-based cell-free systems provide unique advantages for simplified metabolic pathway construction. Their central metabolic pathways and transcriptional-translational (TX-TL) machineries are free from genome regulation and are amenable to direct manipulation, enabling the streamlined construction of biomanufacturing processes. While their utility as prototyping platforms for accelerating cellular metabolic engineering has been demonstrated, the potential to rapidly build commercial “cell-free factories” capable of sophisticated bioconversion has not been fully realized. Lysates with high-yield pathways are projected to enable commercialized cell-free …

Fecal Pellet Production By North Atlantic Zooplankton, Michael Gibson

Undergraduate Honors Theses

Fecal pellet carbon (FPC) production by zooplankton is a significant component of the ocean’s biological carbon pump: the suite of biological processes that mediate export of carbon to the deep ocean, ultimately leading to the sequestration of atmospheric carbon dioxide in the ocean. In this study, mesozooplankton (zooplankton 0.2 mm to ~2 cm) were collected from the epipelagic zone in the temperate North Atlantic Ocean during day and night in May 2021. Zooplankton were live separated into five size fractions and incubated on board ship in natural surface seawater to measure fecal pellet production rate of the mixed mesozooplankton community. …

The Bellarmine Bee Bed: Organizing A Native Plant Garden Using Feedback From The Local Community, Kate Moran

Undergraduate Theses

Animal pollinators are the cornerstone of healthy ecosystems. Their survival is essential for the persistence of entire food chains: from the flowers they cross-pollinate directly, to the animals who depend on those plants for nutrition. The establishment of pollinator gardens—particularly ones that consist of native plants—is an effective way to enhance their biodiversity, abundance, and well-being.

The main goal of this thesis is to construct a pollinator garden that maximizes the benefits for animal pollinators using feedback from local gardeners. A survey was used to gather information about the popularity and preferences of 40 flowering plants, and after analyzing the …

Linking Science And Literacy Through Multimodal Text Sets: Student Perspectives, Heba Abdelnaby, William L. Romine, Delinda Van Garderen, Tracey Milarsky, Ankita Agarwal, Qingli Lei, Cassandra Smith, Amy Lannin, William Folk, Rachel Juergensen

Biological Sciences Faculty Publications

We present findings of a mixed methods study examining the perceptions of students’ (with and without disabilities) understanding and engagement with multimodal STEM text sets. Exit slip and survey data were used to identify areas for improvement in the development of the multimodal STEM text sets for middle school students. Data were collected from 434 middle school students, 86 of whom had a disability, from six teachers’ classrooms in Spring 2021. Significant differences in perceptions of understanding of argumentation were reported between students with and without disabilities. However, ratings of the lessons and the quality of learning, as well as …

The Impact Of Study Strategies On Knowledge Growth And Summative Exam Performance In The First Year Of Medical School, Markia Black, William L. Romine, Molly Simonis, Jeffrey L. Peters, Volker Bahn, Amber Todd

Biological Sciences Faculty Publications

Although the distinction between deep and surface processing strategies, their potential to differentially impact learning, and data supporting the superiority of deep processing strategies on summative exam scores are well supported by the literature, more work is needed to understand: (1) how medical students combine study strategies into learning practices, and (2) the effectiveness of these learning practices in facilitating knowledge gains as measured by standardized test scores.

Measuring Claim-Evidence-Reasoning Using Scenario-Based Assessments Grounded In Real-World Issues, William L. Romine, Amy Lannin, Ankita Agarwal, Maha Kareem, Emily Burwell

Biological Sciences Faculty Publications

Improving students’ use of argumentation is front and center in the increasing emphasis on scientific practice in K-12 Science and STEM programs. We explore the construct validity of scenario-based assessments of claim-evidence-reasoning (CER) and the structure of the CER construct with respect to a learning progression framework. We also seek to understand how middle school students progress. Establishing the purpose of an argument is a competency that a majority of middle school students meet, whereas quantitative reasoning is the most difficult, and the Rasch model indicates that the competencies form a unidimensional hierarchy of skills. We also find no evidence …

Analysis Of Germany’S Experience On Development Of Biosphere Reserves And Suggestions To China, Yijie Xian, Ning Liu, Na Qiao, Qiang Fang, Qunli Han, Ding Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Germany has integrated biosphere reserves into the national strategy of sustainable development, and has built an outstanding biosphere reserve system nationwide, which has played a key role in maintaining the stability of ecosystem, exploring sustainable use of natural resources, innovating social development models, prospering local economies and providing an important platform to carry out comprehensive research on human and nature relationship. The experience of Germany includes:long and solid accumulation in the development of protected areas; deep understanding from authorities and the folk of the concept of Man and the Biosphere Programme (MAB) and the value of biosphere reserves, and more …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Role Of Parp1 And Nad+ Bioavailability In Base Excision And Single-Strand Break Repair, Kate M. Saville

Theses and Dissertations

High-grade gliomas (HGGs) are malignant, highly metabolically active brain tumors. HGGs are associated with poor patient outcome, attributed to resistance to current therapies, with a survival rate between 12 to 15 months. Gliomas are highly complex tumors, making targeted therapy difficult, highlighting the need for novel approaches and new treatment options. In addition, a large percentage of HGGs are comprised of glioma stem cells (GSCs) that further contribute to therapeutic resistance. Notable characteristics of GSCs are a heightened DNA damage response (DDR) and elevated replication stress that could provide opportunities for therapeutic targeting. A notable feature of many glioma tumors …

Combining Network Modeling And Experimental Approaches To Predict Drug Combination Responses, Deepraj Sarmah

All Dissertations

Cancer is a lethal disease and complex at multiple levels of cell biology. Despite many advances in treatments, many patients do not respond to therapy. This is owing to the complexity of cancer-genetic variability due to mutations, the multi-variate biochemical networks within which drug targets reside and existence and plasticity of multiple cell states. It is generally understood that a combination of drugs is a way to address the multi-faceted drivers of cancer and drug resistance. However, the sheer number of testable combinations and challenges in matching patients to appropriate combination treatments are major issues.

Here, we first present a …

Systematic Evaluation Of Database Builds In Metaproteomics For The Advancement Of Microbiome Research, Katherine E. Ostrouchov

Masters Theses

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host …

Taxonomic Revision And Morphometric Analysis Of Selected Anthurium (Araceae) Species From Bolivia And Peru, Daniel M. Tarazona Ocana

Theses

The genus Anthurium (Araceae) consists of around 1,200 species distributed in the Neotropics, particularly in Central and South America. The montane forests in the eastern flank of the Andes, ranging from northern Ecuador to central Bolivia; hereafter, the East Andes Gradient region, are particularly rich in terms of species diversity, and include an understudied group of Anthurium species endemic to the region. Within this group of species, some taxa are difficult to distinguish from each other mainly due to the lack of identification keys, incomplete species descriptions and unknown synonyms. In this study, a combination of traditional taxonomic techniques and …

Modularity And Boolean Network Decomposition, Matthew Wheeler

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.