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Windows Into Changing Landscapes: Bioarchaeological And Geophysical Analysis Of The Grenada Yellow Fever Cemetery, M. Kathryn Mckenna Aug 2024

Windows Into Changing Landscapes: Bioarchaeological And Geophysical Analysis Of The Grenada Yellow Fever Cemetery, M. Kathryn Mckenna

Theses and Dissertations

This project focuses on the Yellow Fever Cemetery of Grenada, Mississippi through geophysical and biological methods. A ground penetrating radar survey was conducted to investigate the landscape and burial patterns in relation to the use of the cemetery throughout high periods of mortality such as a yellow fever epidemic. Additionally, biological methods were used in the analysis of an individual recovered as part of a salvage archaeology event from the cemetery. The multifaceted approach aims to uncover more about the cemetery, landscape, and community as it has changed over time with the influence of extreme events such as the yellow …

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An Evaluation Of Avian Use Of Marsh Terraces In Gulf Coastal Wetlands Of Louisiana, Madelyn Belle Mcfarland Aug 2024

An Evaluation Of Avian Use Of Marsh Terraces In Gulf Coastal Wetlands Of Louisiana, Madelyn Belle Mcfarland

Theses and Dissertations

Louisiana’s coastal wetlands support millions of resident and migratory birds annually but account for 80% of the nation’s coastal wetland loss. Marsh terracing is a restoration technique that constructs segmented ridges in open water areas to enhance marsh conditions. Despite widespread use, their value as avian habitat has received limited study. Using ground and aerial surveys, we evaluated avian use of marsh terraces across 24 paired sites (marsh terrace and non-terrace sites) in coastal Louisiana. Avian surveys focused on breeding secretive marsh birds (SMB) and wintering waterfowl. Results indicate that presence or absence of marsh terraces influenced numbers of ducks …

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Toward Privacy-Preserving Component Certification For Metal Additive Manufacturing, Mahathir Mohammad Bappy Aug 2024

Toward Privacy-Preserving Component Certification For Metal Additive Manufacturing, Mahathir Mohammad Bappy

Theses and Dissertations

Metal-based additive manufacturing (AM) has emerged as a cutting-edge technology for fabricating complex geometries with high precision. However, the major challenges to the wider adoption of metal AM technologies are process uncertainty-induced quality issues. Consequently, there is an urgent need for fast and reliable certification techniques for AM components, which can be achieved by leveraging Artificial Intelligence (AI)-enabled modeling. Developing a robust AI-enabled model presents a significant challenge because of the costly and time-intensive nature of acquiring diverse and high volume of datasets. In this context, the data-sharing attributes of Manufacturing-as-a-Service (MaaS) platforms can facilitate the development of AI-enabled certification …

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International Student-Athletes' Agency, Authorship, And Voice At U.S. Higher Education Institutions, Malia Nicole Schimminger Aug 2024

International Student-Athletes' Agency, Authorship, And Voice At U.S. Higher Education Institutions, Malia Nicole Schimminger

Theses and Dissertations

The purpose of this qualitative, case study research project is to explore international student-athletes’ experiences at U.S. higher education institutions, probing how well nonimmigrant visa holders are prepared for postgraduate success through their college experiences. Six collaborators engaged in photo elicitation interviews to provide insight into how they have navigated their international student identity and student-athlete identity. Collaborators each shared 10-15 media files representative of their experiences, and then they engaged in 90-minute interviews to talk about what their selections meant to them and why they were significant. The frameworks of agency, self-authorship, and voice were used to gauge how …

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Application Of Existing Statistical Models To Thermal Inactivation Of Escherichia Coli In A Lab-Based Circulating Water Bath And Investigation Of A Salmonella Challenge Model In A 42-Day Broiler Grow-Out In An Updated Facility, Michael Carroll Aug 2024

Application Of Existing Statistical Models To Thermal Inactivation Of Escherichia Coli In A Lab-Based Circulating Water Bath And Investigation Of A Salmonella Challenge Model In A 42-Day Broiler Grow-Out In An Updated Facility, Michael Carroll

Theses and Dissertations

The Food Safety Modernization Act has enforced the importance of research in preventative and control measures for known hazards. Experiment 1 applies existing statistical models, Linear and Weibull, to Escherichia coli thermal inactivation in broiler mash feed in a lab-based circulating water bath to simulate conditioning. Linear and Weibull models were determined to be suitable for modeling the thermal inactivation of E. coli in broiler feed. In Experiment 2, a Salmonella challenge model for broilers raised in floor pens in the updated Animal Biosafety Level-2 facility was evaluated over a 42-day grow-out period. Broiler performance and recovery of Salmonella from …

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Investigating The Effects Of Multiple Concussions On Neuropsychological Performance, Michaela S. Patoilo Aug 2024

Investigating The Effects Of Multiple Concussions On Neuropsychological Performance, Michaela S. Patoilo

Theses and Dissertations

It has been well-established in the literature that a history of concussion makes individuals more susceptible to sustaining subsequent concussions. However, there is little neuropsychological evidence of how sustaining multiple lifetime concussions affects cognitive functioning in the general adult population. It is known from previous traumatic brain injury and single concussion literature that impairments in cognitive performance across domains often follow the initial injury, and exploratory studies have shown that multiple concussions can have a measurable impact on cognition. However, existing research is often limited by its reliance on archival data and abbreviated neuropsychological batteries. Therefore, the current study aimed …

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The Impact Of Eye-Tracking Features On Hazard Identification Skill Assessment: An Approach Based On Machine Learning And Virtual Reality, Mohammad Nafe Assafi Aug 2024

The Impact Of Eye-Tracking Features On Hazard Identification Skill Assessment: An Approach Based On Machine Learning And Virtual Reality, Mohammad Nafe Assafi

Theses and Dissertations

Identifying construction hazards is a safety priority. Eye-tracking features have been used in prevalent research to assess hazard identification skills. However, confusion exists over their effectiveness due to certain features being more common. To address this gap, a machine learning-based approach is suggested to identify the most effective eye-tracking features for assessing hazard identification skills, thereby improving workplace safety. Four hazard types and eleven eye-tracking features were identified; accordingly, eighteen strategies were developed using these features. Support vector machines (SVM) and artificial neural networks (ANN) models were developed to assess these strategies. Virtual reality was used for the data collection. …

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Predictions Of Thermo-Fluid Transport Over A Poultry Incubation Period Using High Performance Computing, Melvy Fernandes Aug 2024

Predictions Of Thermo-Fluid Transport Over A Poultry Incubation Period Using High Performance Computing, Melvy Fernandes

Theses and Dissertations

The quality of hatchery conditions significantly impacts the hatchling health. An insight into the spatiotemporal distribution of environmental factors like temperature, ventilation, humidity, and CO2 within an incubator can be the key to reduce the pathogen spread. The objective of this study is to develop an efficient computational fluid dynamics model to predict thermo-fluid and scalar transport over an incubation period using high performance computing systems. Various modeling approaches for grid generation, inflow conditions, fan and heater modeling, and scalar transport are evaluated to identify cost effective numerical models and allow long time simulations with reliable data. The model is …

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Solution Synthesis Of Colloidal Strontium Zirconium Sulfide Nanomaterials, Naira Arrykova Aug 2024

Solution Synthesis Of Colloidal Strontium Zirconium Sulfide Nanomaterials, Naira Arrykova

Theses and Dissertations

Chalcogenide perovskites with a distorted ABX3 structure (A: Ca, Ba, Sr; B: Zr, Hf; X: S, Se) are a prominent focus in optoelectronic materials. One of these is BaZrS3 which has garnered significant attention in perovskite materials due to its distinctive distorted perovskite structure and valuable optical properties that are viable for a single-junction solar cell and present a compelling option for tandem solar cell configurations. Another promising material is SrZrS3 which exists in two phases: needle-like non-perovskite α-SrZrS3 and distorted perovskite β-SrZrS3. The distorted perovskite phase shows promising luminescence properties in bulk, making it potentially viable for LED applications. …

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Buffering The Strained Relation Between Masculinity And Social Support With Self-Compassion, Nathan Barclay Aug 2024

Buffering The Strained Relation Between Masculinity And Social Support With Self-Compassion, Nathan Barclay

Theses and Dissertations

Men experience high rates of negative health outcomes and often have difficulty identifying and seeking support for their issues. Traditional masculine socialization has been identified as a potential determinant of this effect, as masculine ideals often conflict with prosocial help-seeking behaviors. Men who experience this sort of socialization need better support for their mental health and are less likely to seek it out in a professional setting. Therefore, other models of support, like social support, should be investigated. Additionally, factors that impact the way that men perceive social support should be explored, one of which may be self-compassion. The current …

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Predator-Prey Dynamics Among Large Carnivores And Their Ungulate Prey: From The Great Lakes To The Last Frontier, Nathan James Svoboda Aug 2024

Predator-Prey Dynamics Among Large Carnivores And Their Ungulate Prey: From The Great Lakes To The Last Frontier, Nathan James Svoboda

Theses and Dissertations

Identifying factors that influence spatial and temporal resource use is critical to understanding ecological relationships of sympatric species. Spatial and temporal shifts in resource availability, distribution, and vulnerability can influence animal space use, movements, foraging behavior, and prey selection. Identifying these factors is critical to understanding predator-prey dynamics. In Michigan’s Upper Peninsula, white-tailed deer (Odocoileus virginianus) exist in a multi-predator system that includes black bears (Ursus americanus), wolves (Canis lupus), coyotes (C. latrans), and bobcats (Lynx rufus). On Sitkalidak Island, Alaska, plains bison (Bison bison) were recently introduced into a single-predator island landscape that contains some of the largest brown …

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Incorporating Cover Crops Into Successful Corn Production Systems In The Mid-South, Nolan Mullican Aug 2024

Incorporating Cover Crops Into Successful Corn Production Systems In The Mid-South, Nolan Mullican

Theses and Dissertations

Cover crops are known to produce many conservation benefits. However, grower adoption remains low due to various issues and poor economic returns. This study was conducted to identify factors and management practices needed to integrate cover crops into Midsouth corn production systems. The effects of cover crop species, herbicide termination timing, and mechanical termination methods on the growth, grain yields, and economic returns of corn [Zea Mays (L.)] were investigated in Mississippi. The presence of living cover crops at planting stunted corn growth when they were not terminated by herbicides at least four weeks preplant. A legume cover crop reduced …

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Examining Barriers In Building Multicultural Competency Within School Psychology Faculty, Orlandria D. Beamon Aug 2024

Examining Barriers In Building Multicultural Competency Within School Psychology Faculty, Orlandria D. Beamon

Theses and Dissertations

The need for multicultural competency in school psychology is crucial for creating inclusive and culturally responsive learning environments. While research has often focused on graduate student perspectives, there's a notable gap regarding faculty members in school psychology programs. Ensuring that faculty are multiculturally competent is essential, and examining factors that influence their competency is imperative. This study explores multicultural competency from the perspectives of school psychology faculty, involving 75 participants who reflected on their interactions with diverse individuals and assessed their program climate regarding multicultural issues. Using the SPCMS-R and the MEI-R measures, the study analyzed the impact of program …

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Divergent Selection For Anthesis Of Annual Ryegrass (Lolium Perenne Ssp. Multiflorum), Prakriti Adhikari Aug 2024

Divergent Selection For Anthesis Of Annual Ryegrass (Lolium Perenne Ssp. Multiflorum), Prakriti Adhikari

Theses and Dissertations

Annual ryegrass (Lolium perenne ssp. multiflorum) is an excellent cover crop for winter-fallow fields of the Southeast. However, late senescence and herbicide resistance pose challenges for spring eradication. This study aims to develop a ryegrass variety that naturally senescence early using the recurrent phenotypic selection. A base population with anthesis dates from March 21 to April 2 was collected in 2022. 903 seedlings of this population were grown in Cycle0. For Cycle1, the Cycle0 population upon anthesis was segregated into NV0 (11 non-vernalizing), E0 (earliest 70 to anthesis), and L0 (last 70 to anthesis). Isolated groups were allowed to polycross …

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Living With Mamaw And Pawpaw: Examining The Impact Of Context When Raising One’S Grandchildren, Rachel K. Scott Aug 2024

Living With Mamaw And Pawpaw: Examining The Impact Of Context When Raising One’S Grandchildren, Rachel K. Scott

Theses and Dissertations

The parenting literature has long explored the influence that socioeconomic status has on parenting practices, but more recent theorists have suggested that contextual factors may influence or explain this relation in some capacity. The current study sought to explore the influence of these contextual factors within a nationwide sample of caregiving grandparents. The results indicate that grandparental financial well-being, depressive symptoms, scarcity of resources, and grandparenting practices share significant associations. Further, contextual factors (i.e., grandparental depressive symptoms and access to resources) mediate the relation between financial well-being and both the positive and negative grandparenting practices that are employed. These findings …

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Distribution And Abundance Of Breeding Tidal Marsh Birds Across The Mississippi Gulf Coast, Rachel V. Anderson Aug 2024

Distribution And Abundance Of Breeding Tidal Marsh Birds Across The Mississippi Gulf Coast, Rachel V. Anderson

Theses and Dissertations

Tidal marsh and its bird community across the northern Gulf of Mexico are subject to numerous disturbances such as oil spills, hurricanes, habitat loss from land use change, and high relative sea level rise rates looming in the future. Baseline population data and landscape associations are greatly needed to assess the current distribution and the future impact of perturbations on marsh birds across the Mississippi Gulf Coast. Using a standardized sampling design and point count survey protocol, we determined the abundance and population size of Clapper Rails, Common/Purple Gallinules, Least Bitterns, Marsh Wrens, Seaside Sparrows, Red-winged Blackbirds, and Common Yellowthroats …

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Longitudinal Influences Of Parental Relationships On Positive Adolescent Functioning, Rebekah Buckley Sparks Aug 2024

Longitudinal Influences Of Parental Relationships On Positive Adolescent Functioning, Rebekah Buckley Sparks

Theses and Dissertations

This dissertation examines the longitudinal influences of parental relationships – romantic, co-parenting, and parent-child – on positive adolescent functioning. Utilizing data from the Future of Families and Child Wellbeing Study, this study investigates how various dimensions of parental relationships impact adolescent well-being at age 15, as measured by the EPOCH scale. Grounded in Attachment Theory and the Life Course Perspective, this research highlights the interconnectedness of early parental interactions and their long-term effects on adolescents’ emotional and social development. Key findings indicate that supportive and stable parental relationships significantly enhance adolescents’ engagement, perseverance, optimism, connectedness, and happiness. The study emphasizes …

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A Geant4 Based Simulation Toolkit For Detector Response Evaluations In Operational Health Physics And Nuclear Safety Applications, Ronald James Unz Aug 2024

A Geant4 Based Simulation Toolkit For Detector Response Evaluations In Operational Health Physics And Nuclear Safety Applications, Ronald James Unz

Theses and Dissertations

This work describes the development of a Monte Carlo simulation toolkit built on the Geant4 framework for applied health physics applications. The toolkit is designed to construct complex radiation fields and measure how radiation detectors respond to those fields, specifically radiation fields expected to be encountered in environmental and safety applications. The toolkit, along with its development and validation, is described. The use of the toolkit for performing minimum detectable concentration evaluations is outlined, following methods described in the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) and Nuclear Regulatory Guidance Manual 1507, which detail Minimum Detectable Concentrations for Typical …

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Meta-Analysis Of Consumer’S Willingness To Pay For Broadband In The United States, Sabina Regmi Aug 2024

Meta-Analysis Of Consumer’S Willingness To Pay For Broadband In The United States, Sabina Regmi

Theses and Dissertations

The study aims to summarize and synthesize 236 mean willingness to pay (WTP) estimates from 22 studies on WTP for broadband while exploring factors driving heterogeneity using a meta-regression analysis. Employing weighted least square regression, it identifies factors contributing to heterogeneity, including publication characteristics, study-design characteristics, consumer characteristics, and broadband attributes. Key findings reveal higher WTP in working papers and survey reports compared to peer-reviewed journal articles. WTP for broadband after 2015 is lower compared to pre-2007, potentially reflecting a shift in consumer perception over time. Higher download speeds are associated with increased WTP, and rural areas exhibit a nearly …

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The Impact Of Sexual Violence, Social Reactions To Disclosure, Coping, And Intersecting Identities On Ptsd Risk, Sabrina Dicarlo Aug 2024

The Impact Of Sexual Violence, Social Reactions To Disclosure, Coping, And Intersecting Identities On Ptsd Risk, Sabrina Dicarlo

Theses and Dissertations

Sexual violence (SV) affects millions of people, with an estimated 24.8 – 43.6% of people in the United States reporting at least one form of SV in their lifetime. SV has been associated with the development of negative outcomes such as Post-Traumatic Stress Disorder (PTSD). There is a robust body of evidence which demonstrates the impact that social reactions to SV and coping can have on higher post-traumatic stress (PTS) symptoms. Furthermore, studies have shown that individuals from marginalized communities (e.g., racial/ethnic, gender, sexual orientation) may be disproportionately impacted, with greater exposure to SV, negative social reactions, and PTS. Studies …

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Humblebragging As A Self-Promotional Strategy On Social Media, Sangwon Na Aug 2024

Humblebragging As A Self-Promotional Strategy On Social Media, Sangwon Na

Theses and Dissertations

Humblebragging is a tactic where an individual disguises a boast or brag as a complaint or humility while simultaneously emphasizing their achievements or desired results. According to previous literature, individual athletes' social media postings are seen as branding or self-promotional content to enhance their brand image. However, these posts can also be considered a form of bragging, with sport celebrities trying to hide their true intentions by using humbleness. This strategy is often used by sport celebrities to enhance their brand image. However, this subject remains largely unexplored in sport management literature, primarily due to the lack of a clear …

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Adverse Childhood Experiences, Behavioral Problems, And The Role Of Positive Childhood Experiences, Scout Savoy Aug 2024

Adverse Childhood Experiences, Behavioral Problems, And The Role Of Positive Childhood Experiences, Scout Savoy

Theses and Dissertations

Adverse Childhood Experiences (ACEs) are traumatic events that individuals experience in childhood that have been linked to problems with physical and mental health in adulthood (Felitti et al., 1998). Previous research suggests that ACEs are prevalent in almost two-thirds of youth regardless of location across the world and that when an individual experiences three or more ACEs, their quality-adjusted life expectancy is found to decrease (Carlson et al., 2019; Jia & Lubetkin, 2020). Although ACEs have been associated with negative outcomes, not all individuals who experience trauma exhibit problematic behavior and are considered to have high levels of resilience (Agaiba …

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Efficacy Of Fungicides And Herbicides, Applications To Manage Southern Blight In Mississippi Peanut Fields, Subina Tripathi Aug 2024

Efficacy Of Fungicides And Herbicides, Applications To Manage Southern Blight In Mississippi Peanut Fields, Subina Tripathi

Theses and Dissertations

Peanuts are an important legume crop cultivated in Mississippi with an annual production of 71 million kg per hectare. Southern blight (SB), caused by Athelia rolfsii, is a devastating disease resulting in significant losses to peanut production. Cultural practices may not adequately control diseases; therefore, the application of fungicides is important. Recently, the rapid growth of weed species has emphasized herbicide usage and studied weed interaction with SB. In this study, Athelia rolfsii isolates were collected from different counties to identify their biological characteristics and determine the in vitro efficacy in both 2022 and 2023. In the field trial, seven …

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Customers’ Advocacy For Environmentally Friendly Golf Courses: The Role Of Green Brand Image, Feelings Of Gratitude, And Relationship Quality, Taewoong Kyung Aug 2024

Customers’ Advocacy For Environmentally Friendly Golf Courses: The Role Of Green Brand Image, Feelings Of Gratitude, And Relationship Quality, Taewoong Kyung

Theses and Dissertations

The close relationship between sports and the natural environment has been endangered by climate crisis and global warming (Breitbarth et al., 2023; Cunningham et al., 2020; McCullough, 2023; Orr & Inoue, 2019). For this reason, the development of golf courses has been accused of serious impacts on environmental destruction which causes climate change, despite the popularity of golf (Fouillouze et al, 2023). Golf courses have become quite far from the green image. Hence, golf courses began to voluntarily obtain environmental certification (e.g., Audubon Cooperative Sanctuary Program, GEO certified) to protect nature and keep ecosystems sustainable (Gomis et al., 2018; Lee …

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How Teacher-Student Relationships Affect Child And Adolescent Resilience, Tashina R. Vanderwoude Aug 2024

How Teacher-Student Relationships Affect Child And Adolescent Resilience, Tashina R. Vanderwoude

Theses and Dissertations

The significance of positive relationships, particularly between teachers and students, in fostering resilience among children is well-established. While various studies have delved into the dynamics and impacts of these relationships, there is a notable gap in research that directly assesses how teacher-student bonds influence students’ resilience levels. This study aims to bridge the gap by examining students’ perceptions of their relationships with teachers and how these perceptions correlate with their reported resilience levels. Participants (n = 59) included middle and high school students recruited from a school district in northeastern Mississippi. Participants completed surveys measuring their perception of their relationship …

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The Disposition And Metabolism Of A Novel Brain-Penetrating Oxime Reactivator Of Inhibited Acetylcholinesterase, Thomas Christopher Burke Aug 2024

The Disposition And Metabolism Of A Novel Brain-Penetrating Oxime Reactivator Of Inhibited Acetylcholinesterase, Thomas Christopher Burke

Theses and Dissertations

Organophosphates (OPs) were initially designed as insecticides and later engineered as dangerous nerve agents that threaten our livelihood and safety. One of the treatments for OP exposure is the administration of an oxime to reactivate inhibited acetylcholinesterase (AChE). The currently approved oxime therapy in the US, pralidoxime (2-PAM), is unable to reactivate inhibited AChE in the brain due to its low ability to cross the blood-brain barrier (BBB) which has led our laboratory to develop novel substituted phenoxyalkyl pyridinium oximes (US Patent 9,227,937) that penetrate the BBB more effectively. Our lead oxime candidate, Oxime 20, has proven efficacious in reactivating …

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Hardwood Seedling Establishment And Survival For Restoring And Enriching Bottomland Hardwoods In The Lower Mississippi Alluvial Valley, Timothy Jaycob Gatlin Aug 2024

Hardwood Seedling Establishment And Survival For Restoring And Enriching Bottomland Hardwoods In The Lower Mississippi Alluvial Valley, Timothy Jaycob Gatlin

Theses and Dissertations

Degradation and deforestation have taken their toll on bottomland hardwood forests in the Lower Mississippi Alluvial Valley (LMAV). To combat this, many managers, both public and private, have sought silvicultural techniques to ensure future generations have the benefits bottomland hardwoods provide. In the first study of this thesis, artificial regeneration and chemical thinning were implemented to evaluate the effects of these treatments on restoration and enrichment of bottomland hardwoods. Very high mortality rates were seen across all species and sites likely due to improper handling and planting, drought, and competition. The second study explored the feasibility of transplanting bottomland oaks …

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Neoantigen Landscape Supports Feasibility Of Personalized Cancer Vaccine For Follicular Lymphoma, Cody A Ramirez, Michelle Becker-Hapak, Kartik Singhal, David A Russler-Germain, Erica K Barnell, Ethan D Mcclain, Sweta Desai, Timothy Schappe, Onyinyechi C Onyeador, Susanna Kiwala, Jasreet Hundal, Zachary L Skidmore, Marcus P Watkins, Thomas B Mooney, Jason R Walker, Kilannin Krysiak, Felicia Gomez, Catrina C Fronick, Robert S Fulton, Robert D Schreiber, Neha Mehta-Shah, Amanda F Cashen, Brad S Kahl, Nancy L Bartlett, Malachi Griffith, Obi L Griffith, Todd A Fehniger, Et Al. Aug 2024

Neoantigen Landscape Supports Feasibility Of Personalized Cancer Vaccine For Follicular Lymphoma, Cody A Ramirez, Michelle Becker-Hapak, Kartik Singhal, David A Russler-Germain, Erica K Barnell, Ethan D Mcclain, Sweta Desai, Timothy Schappe, Onyinyechi C Onyeador, Susanna Kiwala, Jasreet Hundal, Zachary L Skidmore, Marcus P Watkins, Thomas B Mooney, Jason R Walker, Kilannin Krysiak, Felicia Gomez, Catrina C Fronick, Robert S Fulton, Robert D Schreiber, Neha Mehta-Shah, Amanda F Cashen, Brad S Kahl, Nancy L Bartlett, Malachi Griffith, Obi L Griffith, Todd A Fehniger, Et Al.

2020-Current year OA Pubs

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR …

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Dominance Analysis To Assess Solute Contributions To Multicomponent Phase Equilibria, Daoyuan Qian, Hannes Ausserwoger, Tomas Sneideris, Mina Farag, Rohit V Pappu, Tuomas P J Knowles Aug 2024

Dominance Analysis To Assess Solute Contributions To Multicomponent Phase Equilibria, Daoyuan Qian, Hannes Ausserwoger, Tomas Sneideris, Mina Farag, Rohit V Pappu, Tuomas P J Knowles

2020-Current year OA Pubs

Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework …

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An Integrated Structural Model Of The Dna Damage-Responsive H3k4me3 Binding Wdr76:Spin1 Complex With The Nucleosome, Xingyu Liu, Yixuan Xie, Benjamin A Garcia, Et Al. Aug 2024

An Integrated Structural Model Of The Dna Damage-Responsive H3k4me3 Binding Wdr76:Spin1 Complex With The Nucleosome, Xingyu Liu, Yixuan Xie, Benjamin A Garcia, Et Al.

2020-Current year OA Pubs

Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in …

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