Life Sciences Commons^™

Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis

Dissertations, Theses, and Capstone Projects

Uncovering how species respond to environmental change is a central question in biology (Ehrlén & Morris 2015; Habibullah et al. 2022). It is the key to elucidating the past, understanding the present and predicting the future of species’ population dynamics. This dissertation investigates the influence of environmental change on intertidal species’ distributions and genomics at several timescales, with implications for conservation.

Environmental changes have occurred throughout history, on a geological scale, and have shaped the global patterns of species’ distributions and population sizes. Biologists have long studied how geological history has shaped species distributions (Sanmartín 2012) in both terrestrial (Liu …

Characterization Of Pathological Tau Mutants, Charles J. Mcdonald

Dissertations, Theses, and Capstone Projects

Tau is a protein expressed exclusively in glia and neurons in the central nervous system and implicated in several neurogenerative diseases called “tauopathies”. Among all the tauopathies, one third is characterized by the presence of genetic mutations leading to the synthesis of tau proteins with single amino acid substitutions at specific locations and affecting protein function. While most of the initial studies have emphasize the functional role of tau as modulator of the axonal cytoskeleton, it has recently been well accepted that tau is also an intrinsically disordered protein that tends to form membraneless organelles called coacervates, due to a …

You Hurt My Feelings: Autonomic And Behavioral Responses To Social Exclusion And The Moderating Effect Of Psychopathic Traits, Liat Kofler

Dissertations, Theses, and Capstone Projects

Humans have a fundamental need to form and maintain social connections, and thus experiencing social exclusion is extremely distressing as it threatens this basic human need. Individuals who are socially excluded often respond aggressively, not only towards their ostracizers but also towards innocent bystanders, with ostracism being implicated in extreme acts of violence such as school shootings. However, individual differences in behavior exist within the context of social exclusion as not everyone responds aggressively after being ostracized. Identifying risk factors for retaliatory aggressive behavior following experiences of social exclusion may facilitate the development of targeted interventions aimed at mitigating such …

Examining Metacognitive Access To Low-Level Ensemble Representations, Vladimir Mudragel

Dissertations, Theses, and Capstone Projects

Ensemble perception is a process that allows our sensory systems to rapidly extract summary information about the stimuli in the environment. For example, we are able to get a sense of the average number of items in a group of similar items (Burr & Ross, 2008; Halberda, Sires, & Feigenson, 2006) or the average size of a group of similar shapes of different sizes (Ariely, 2001). It is theorized that the qualitative result of ensemble perception is that it provides a gist impression of the current environment, which then enables attentional processes in the brain to determine which parts of …

Out-Of-Distribution Generalization Of Deep Learning To Illuminate Dark Protein Functional Space, Tian Cai

Dissertations, Theses, and Capstone Projects

Dark protein illumination is a fundamental challenge in drug discovery where majority human proteins are understudied, i.e. with only known protein sequence but no known small molecule binder. It's a major road block to enable drug discovery paradigm shift from single-targeted which looks to identify a single target and design drug to regulate the single target to multi-targeted in a Systems Pharmacology perspective. Diseases such as Alzheimer's and Opioid-Use-Disorder plaguing millions of patients call for effective multi-targeted approach involving dark proteins. Using limited protein data to predict dark protein property requires deep learning systems with OOD generalization capacity. Out-of-Distribution (OOD) …

Electrophysiological Signatures Of Stress Adaptability In The Bnst-Vta Pathway, Yuka Miura

Dissertations, Theses, and Capstone Projects

Chronic stress has detrimental effects on psychological and physiological health. Incapability to adapt to chronic stress can lead to depression, anxiety disorders, and addiction. The brain regions critical for reward processing share diverse physiological and molecular changes linked to depressive-like behaviors as a result of chronic stress. Cumulative evidence shows that counteraction or prevention of these alterations in neurons, occasionally in a projection-specific manner, can enhance stress adaptation or resilience.

Chronic stress induces various changes in the brain, including in the bed nucleus of the stria terminalis (BNST) and the ventral tegmental area (VTA). The neural projections from the BNST …

Optimization And Application Of Graph Neural Networks, Shuo Zhang

Dissertations, Theses, and Capstone Projects

Graph Neural Networks (GNNs) are widely recognized for their potential in learning from graph-structured data and solving complex problems. However, optimal performance and applicability of GNNs have been an open-ended challenge. This dissertation presents a series of substantial advances addressing this problem. First, we investigate attention-based GNNs, revealing a critical shortcoming: their ignorance of cardinality information that impacts their discriminative power. To rectify this, we propose Cardinality Preserved Attention (CPA) models that can be applied to any attention-based GNNs, which exhibit a marked improvement in performance. Next, we introduce the Directional Node Pair (DNP) descriptor and the Robust Molecular Graph …

Drug Repurposing Using Gene Expression Data Mining, Yue Qiu

Dissertations, Theses, and Capstone Projects

The conventional drug discovery process that employs the "one disease, one target, one drug'' paradigm is expensive, time-consuming, and has a high rate of failure for multi-genic complex diseases. An alternative approach to drug discovery is to repurpose an existing drug that has been used to treat some medical conditions. Drug repurposing is considered a promising method due to its accelerated the process of drug discovery and lower overall cost and risk.

Drug-perturbed gene expression profiles are powerful phenotype readouts of biological systems, and they have been widely used in drug repurposing studies. However, the existing drug-perturbed gene expression datasets …

Characterization Of The Conformational Binding Of N-Methyl Mesoporphyrin Ix With Dna Model Telomeric G-Quadruplex Forming Sequences, Jessica Desamero

Dissertations, Theses, and Capstone Projects

DNA G-quadruplexes are alternative secondary structures formed from guanine rich DNA sequences. G-quadruplexes are found most abundantly at the ends of chromosomes called telomeres, where they can ultimately prevent further tumor growth and progression. Thus, quadruplex interactive agents, or ligands that can bind to and stabilize DNA G-quadruplex structures, are of high interest for their potential chemotherapeutic abilities. One quadruplex interactive agent is the porphyrin N-methyl mesoporphyrin IX (NMM), which has high binding selectivity for quadruplex structures. While the NMM-quadruplex complex in crystallized form has been greatly studied, this complex in solution form is not as well studied. Through circular …

Magnetically-Driven Therapeutic Agents Delivery System Using Iron Oxide Nanocages And Enhancement Of Exosome Secretion, A Potential Biological Drug Delivery Carrier, Min A Kang

Dissertations, Theses, and Capstone Projects

Nano-scale particles have attracted research attention due to their differences in properties such as penetration, circulation, and toxicity compared to bulk materials. This thesis mainly focused on using 20 nm iron oxide nanoparticles as siRNA delivery carriers under the alternating magnetic field and the development of a method to amplify the secretion of 150 nm exosomes from the cells, which could potentially use as a biological drug carrier.

Chapter 2 discusses a magnetically driven nanoparticle therapeutic agent delivery system, which efficiently modified the gene expression post-transcriptionally. In this work, we examined whether the caged-shaped 20nm iron oxide nanoparticles (IO-nanocages) can …

Brainwaves, Memory, And Reward, Rebecca Mccune

Dissertations, Theses, and Capstone Projects

The development of effective educational curricula for enhancing learning involves the crucial consideration of effort and rewards. In the realm of education, teachers commonly employ rewards as motivational tools. Traditionally, these rewards are given to students as a recognition of their successful performance. However, a thought-provoking idea emerges: What if we were to extend rewards to students not solely based on accurate answers, but also on the effort they invest, even in cases where their actual response might be incorrect? Our study explores the potential impact of this approach on the way information is absorbed and subsequently retained, specifically focusing …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Automatic Analysis Of The Frequency, Vigor, And Complexity Of Spontaneous Locomotion Bouts Of Mice With Loss And Gain Of Function Of The G Protein-Coupled Receptor Smoothened In Cholinergic Neurons, Aleksandra Feshchenko

Dissertations, Theses, and Capstone Projects

Locomotion, a fundamental behavior, is classically assessed using simple metrics of velocity and total distance moved in an open field. This behavior however offers rich data about the organization and breadth of actions an animal can take while only facing limitations due to the bio-mechanical constraints of the organism. Importantly, these actions are not biased towards a particular task-solution space imposed by many behavioral paradigms. Here, to analyze motor complexity in freely ambulating mice, we developed a method for the automatic and unbiased identification of locomotor bouts which we call Bout Finder (BF). This analysis utilizes Open Feld data to …

Body Movement Syllabus - The City College Of New York - Department Of Theatre - Prof Timothy Allen, Timothy J. Allen

Open Educational Resources

This course will explore three modules of learning.

1. Anatomy and Psycho-Physical Centering, will explore two foundations: (1) the start of our research and practical application of the human anatomy in regards to how our body moves; and (2) your ability to tune into movement centers within the body by utilizing Chakra as a guiding study. Please note: Anatomy will be a continuous study throughout the entire semester.

2. THE SECOND MODULE, Partnered Connection, will focus on partnering with lifts, counter-balances, falls, and rolls that will build to a partnering sequence of the tools presented.

3. THE LAST MODULE, Global Archetypes, …

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Hair And Drugs: The Impact Of Dry Shampoo And Gel On Cocaine-Contaminated Hair, Marialejandra Faure Betancourt

Student Theses

Hair is a biological sample used in forensic toxicology to identify and quantify drug exposure. However, when interpreting analytical results, hair can be challenging due to the presence of external contamination. Previous studies have shown that cosmetic treatments remove drugs within the hair shaft decreasing their concentration. Nevertheless, not enough information is available to explain this phenomenon. This study focused to determine whether cosmetic products such as dry shampoo and gel influence the concentration of externally deposited cocaine (COC) and benzoylecgonine (BE) in different hair types/colors. Hair samples from fifteen COC-free volunteers of various hair colors/types were collected and divided …

Bio 013: Writing In The Sciences - Human Origins, Esther Muehlbauer

Open Educational Resources

Bio. 013: Writing in the Sciences - Human Origins is an OER syllabus for a College Writing 2 course that develops student writing for different audiences, following the trajectory of how scientists work: Scientists Writing for themselves (a field journal); Scientists writing for other scientists (a review article); Scientists writing for society (an essay for Natural History Magazine).

Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata

Dissertations, Theses, and Capstone Projects

Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …

The Development Of Novel Radioimmunoconjugates For The Pet Imaging And Radioimmunotherapy Of Cancer, Samantha M. Sarrett

Dissertations, Theses, and Capstone Projects

Antibodies have long played a vital role in nuclear medicine for both the diagnosis and therapy of various malignancies. The role and development of antibodies in nuclear medicine can be broadly separated into three different categories: 1) bioconjugation strategies, 2) immunoPET imaging, and 3) radioimmunotherapy. This dissertation will attempt to comprehensively cover each of these categories through a series of studies, protocols, and reviews. For the bioconjugation strategies, we will describe the development of a novel site-selective bioconjugation strategy using an innovative lysine-targeting reagent, PFP-bisN₃, to prepare [⁸⁹Zr]Zr-^SSKDFO-pertuzumab for visualizing HER2+ breast cancer. Further, …

Modulatory Effects Of Schreckstoff On The Startle Escape Response Of Goldfish (Carassius Auratus), Denis Shor

Dissertations, Theses, and Capstone Projects

Fish face a variety of stressors in nature, a prominent one being a predatory threat to which they respond with an adaptive behavioral response thus maximizing their chances of survival. A primary anti-predatory behavior is a startle response or C-start. This behavior is controlled by two large reticulospinal neurons, the Mauthner cells (M-cells) which integrate multimodal sensory inputs. Detecting a predator involves various sensory information such as visual and mechanosensory cues but also olfaction. Indeed, following an attack, an injured fish will release an alarm pheromone (Schreckstoff) and thus acutely alert close by conspecifics. However, whether the alarm pheromone in …

A Review Of Theropithecus Oswaldi With The Proposal Of A New Subspecies, Dagmawit Abebe Getahun, Eric Delson, Chalachew Mesfin Seyoum

Publications and Research

Theropithecus oswaldi darti, as currently understood, is the oldest Theropithecus taxon in the fossil record and the earliest subspecies in the Theropithecus oswaldi lineage. Theropithecus oswaldi darti is typified at the site of Makapansgat in South Africa, and a similar form (T. o. cf. darti) is usually recognized at Hadar, Dikika, some Middle Awash localities, and Woranso-Mille in Ethiopia. This taxon is also tentatively believed to occur in Kenya at Kanam and Koobi Fora and in Member C of the Shungura Formation in Ethiopia. While there is a general consensus that the East African ‘darti’ specimens are …

Leveraging Local Perturbations To Map Allosteric Networks Of Phosphatases, Tamar (Skaist) Mehlman

Dissertations, Theses, and Capstone Projects

Allostery is central to regulation of protein function, but our mechanistic understanding remains incomplete. A deeper understanding of how redistributions of conformational states drive allostery in proteins could allow us to better grasp natural regulatory principles in cells and open new doors to therapeutic development. Conformationally dynamic human Protein Tyrosine Phosphatases (PTPs) exemplify the challenges and opportunities associated with allostery. The archetypal PTP, PTP1B, has been highly validated as a therapeutic target but no allosteric inhibitors have been approved for clinical use. This is largely because our understanding of the mechanisms underlying allostery in PTP1B remains limited, despite the discovery …

The Effects Of Music Therapy On Elderly Adults With Dementia, Jeante J. Jackson

Dissertations, Theses, and Capstone Projects

As people age, the brain is more susceptible to changes that diminish cognitive function. In recent years neuroscience has found convergent evidence between music therapy and brain architecture, as it has shown the generation of new connections in the brain or a reorganization and possible strengthening of existing connections already in the brain. However, the literature regarding music training’s effects on executive control, selective attention, and speech processing is lacking particularly when it comes to older populations.

This study investigated Verbal Working Memory, Visuospatial Attention and Task Initiation, and Auditory Selective Attention in a 91-year-old adult (B.P.) diagnosed with dementia. …

Statistical And Biological Analyses Of Acoustic Signals In Estrildid Finches, Moises Rivera

Dissertations, Theses, and Capstone Projects

Acoustic communication is a process that involves auditory perception and signal processing. Discrimination and recognition further require cognitive processes and supporting mechanisms in order to successfully identify and appropriately respond to signal senders. Although acoustic communication is common across birds, classical research has largely disregarded the perceptual abilities of perinatal altricial taxa. Chapter 1 reviews the literature of perinatal acoustic stimulation in birds, highlighting the disproportionate focus on precocial birds (e.g., chickens, ducks, quails). The long-held belief that altricial birds were incapable of acoustic perception in ovo was only recently overturned, as researchers began to find behavioral and physiological evidence …

Transcranial Direct Current Stimulation Studies Investigating The Role Of The Dlpfc In Memory And Metamemory, Casey M. Imperio

Dissertations, Theses, and Capstone Projects

Metamemory, broadly defined as knowledge about one’s own memory, is thought to consist of two separate processes, monitoring, the ability to assess the contents of your own memory, and control, altering behavior in service of memory, that work together to aide in encoding and retrieval processes. Prior work has shown that metamemory monitoring accuracy can be improved in a semantic memory task via high-definition transcranial direct current stimulation (HD-tDCS), a form of non-invasive brain stimulation, over the left dorsolateral prefrontal cortex (DLPFC). Over three experiments, the current dissertation sought to replicate and extend this work by: 1) testing the effects …

Metabolic Reprogramming In Kras-Driven Cancer Cells, Ahmet Hatipoglu

Dissertations, Theses, and Capstone Projects

Cancer cells require nutrient uptake for anabolic reactions needed for cellular growth and proliferation. The mammalian target of rapamycin (mTOR) is a key regulator of cellular growth that links nutrient availability and growth factor signals. mTOR mediated signaling pathways are often dysregulated in a wide range of cancers. We previously reported that KRas-driven cancer cells sense exogenous lipids via de novo production of phosphatidic acid, which ultimately activates both mTOR complexes – mTORC1 and mTORC2. Activated mTORC2 phosphorylates the survival kinase Akt at Ser 473 which is required for full Akt activation. A direct substrate of Akt and a major …

Into The Unknown: Exploring The Role Of Uncertainty In Threat-Safety Discrimination, Maia Kinney-Petrucha

Dissertations, Theses, and Capstone Projects

Learning to predict the arrival of threat is crucial to survival. Key to this learning process is the ability to discriminate between which stimuli signify safety and which signify threat. The extent to which a threat is uncertain impacts this ability, but which factors of uncertainty are primarily responsible remains unresolved. Uncertainty at the level of the stimulus can be examined in threat learning paradigms by adjusting threat reinforcement rate, referring to the frequency at which a cue is reinforced with an aversive stimulus. Previous research has shown that a continuous (more certain) threat reinforcement is associated with enhanced threat …

Characterization Of Boreal-Arctic Vegetation Growth Phases And Active Soil Layer Dynamics In The High-Latitudes Of North America: A Study Combining Multi-Year In Situ And Satellite-Based Observations, Michael G. Brown

Dissertations, Theses, and Capstone Projects

This dissertation examined the seasonal freeze/thaw activity in boreal-Arctic soils and vegetation physiology in Alaska, USA and Alberta, Canada, using in situ environmental measurements and passive microwave satellite observations. The boreal-Arctic high-latitudes have been experiencing ecosystem changes more rapidly in comparison to the rest of Earth due to the presently warming climatic conditions having a magnified effect over Polar Regions. Currently, the boreal-Arctic is a carbon sink; however, recent studies indicate a shift over the next century to become a carbon source. High-latitude vegetation and cold soil dynamics are influenced by climatic shifts and are largely responsible for the regions …

Multi-Target Ligand-Guided Selection (Ligs) Against B-Cell Specific Antigens Expressed In A Single Lymphoma Cell Population, Nicole B. Williams

Dissertations, Theses, and Capstone Projects

Nucleic acid ligands called aptamers are single-stranded DNA or RNA molecules which fold into functional three-dimensional structures to facilitate their target binding with high affinity and specificity. The method used to generate aptamers is an in vitro process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). A variant of SELEX, cell-SELEX has been used to select aptamers against cell-surface proteins in their native state. We recently introduced a novel method called Ligand-Guided Selection (LIGS) to identify aptamers against cell-surface markers. Herein, we expanded LIGS method into a multiplexing platform to partition multiple aptamers against B-cell-specific antigens, CD19 and CD20, …

Extraction Of Challenging Forensic Samples Using The Microgem Dna Extraction Kit, Falyn R. Vega

Student Theses

In forensic science, DNA extraction can be a tedious and resource-intensive process. Extraction with Proteinase K is an industry standard but has its drawbacks, such as requiring multiple ionic detergents and washing steps. MicroGEM has developed a new enzyme called forensicGEM that is temperature-dependent and compatible with mesophilic enzymes, offering complete DNA extraction in about 20 minutes in a single tube, limiting contamination, loss of sample, and working time. ForensicGEM can extract DNA from highly degraded samples, potentially leading to more complete STR profiles. Highly degraded tissue and bone samples were collected and extracted with the forensicGEM …

Effects Of Climate Change On Human Health, Sara El Houzaly, Richa Gupta

Publications and Research

The effects of climate change are evident worldwide as average global land and air temperatures have been rising, glaciers and ice sheets are shrinking with the concomitant rise in sea levels, extreme weather events have become more frequent, and oceans are warming and acidifying. Humanity is facing a big environmental challenge which not only impacts our habitat but will also have ramifications on our health. The present review describes a detailed examination of the scientific evidence proving the relationship between climate change and various fatal human diseases in different geographical regions. Our findings indicate that variations in the patterns of …