Research and Informatics Division, University Libraries

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Browsing Research and Informatics Division, University Libraries by Author "Brown, Anne M."

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    DESIGN THINKING for Visualizing Acid-Base Chemistry - Documenting a user-centered approach for designing and developing an ADA compliant online tool for visualizing acid-base chemistry
    Stamper, Michael J.; Briganti, Jonathan; Brown, Anne M.; Dietrich, Andrea M.; Godrej, Adil N.; Schreiber, Madeline E.; Walz, Anita R. (2019-07-17)
    This project created an online tool, that we call “The pkAnalyzer”. It enables the exploration of acid-conjugate base distributions in an easy to use Web interface. This project is also an example of the disciplines of Arts and Design into the STEM sciences, i.e. STEM to STEAM, and University Libraries commitment to faculty, students, and staff throughout the Virginia Tech system, in the areas of data visualization and design services to aid in the research process and communication of results. Beyond the functionality of the tool, this project involved the planning and designing a custom, modifiable, and attractive user interface (UI) and visualization that are "user-friendly", and incorporate the World Wide Web Consortium’s Web Content Accessibility Guidelines (WCAG), and falls with the Federal Governement’s Section 508 guidelines pertaining to creating and maintaining information and communications technology (ICT) that is accessible to people with disabilities relating to vision. Using a "Design Thinking" approach, all aspects of the design of this tool – User Interface (UI), User Experience (UX), Interaction Design (IxD), Graphic – were taken into account, and developed to enhance the user's experience using the tool, and undertanding of a complex chemical concept that is widely used in the basic and applied sciences and engineering.
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    Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications
    Hilu, Khidir W.; Friend, Sheena A.; Vallanadu, Viruthika; Brown, Anne M.; Hollingsworth, Louis R. IV (PLOS, 2019-11-01)
    Food allergies are severe immune responses to plant and animal products mediated by immunoglobulin E (IgE). Peanuts (Arachis hypogaea L.) are among the top 15 crops that feed the world. However, peanuts is among the “big eight food allergens”, and allergies induced by peanuts are a significant public health problem and a life-threatening concern. Targeted mutation studies in peanuts demonstrate that single residue alterations in these allergen proteins could result in substantial reduction in allergenicity. Knowledge of peanut allergen proteins is confined to the allotetraploid crop and its two progenitors. We explored frequencies and positions of natural mutations in the hyperallergenic homologues Ara h 2 and Ara h 6 in newly generated sequences for 24 Arachis wild species and the crop species, assessed potential mutational impact on allergenicity using immunoblots and structural modeling, and evaluated whether these mutations follow evolutionary trends. We uncovered a wealth of natural mutations, both substitutions and gaps, including the elimination of immunodominant epitopes in some species. These molecular alterations appear to be associated with substantial reductions in allergenicity. The study demonstrated that Ara h 2 and Ara h 6 follow contrasting modes of natural selection and opposing mutational patterns, particularly in epitope regions. Phylogenetic analysis revealed a progressive trend towards immunodominant epitope evolution in Ara h 2. The findings provide valuable insight into the interactions among mutations, protein structure and immune system response, thus presenting a valuable platform for future manipulation of allergens to minimize, treat or eliminate allergenicity. The study strongly encourages exploration of genepools of economically important plants in allergenicity research.
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    A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation
    Kang, Lin; He, Guijuan; Sharp, Amanda K.; Wang, Xiaofeng; Brown, Anne M.; Michalak, Pawel; Weger-Lucarelli, James (Virginia Tech, 2021-03-05)
    While SARS-CoV-2 likely has animal origins, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mostly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with an alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutation’s impact on virus replication in human cells was much greater than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission.