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Open Access
Accumulation of radiocarbon in ancient landscapes: A small but significant input of unknown origin
(Nature Communications, 2023-05-08) Broz, Adrian; Aguilar, Jerod; Xu, Xiaomei; Silva, Lucas C. R.
The persistence of organic carbon (C) in soil is most often considered at timescales ranging from tens to thousands of years, but the study of organic C in paleosols (i.e., ancient, buried soils) suggests that paleosols may have the capacity to preserve organic compounds for tens of millions of years. However, a quantitative assessment of C sources and sinks from these ancient terrestrial landscapes is complicated by additions of geologically modern (~ 10 Ka) C, primarily due to the infiltration of dissolved organic carbon. In this study, we quantified total organic C and radiocarbon activity in samples collected from 28- to 33-million-year-old paleosols that are naturally exposed as unvegetated badlands near eastern Oregon’s “Painted Hills”. We also used thermal and evolved gas analysis to examine the thermodynamic stability of different pools of C in bulk samples. The study site is part of a ~ 400-m-thick sequence of Eocene–Oligocene (45–28 Ma) paleosols, and thus we expected to find radiocarbon-free samples preserved in deep layers of the lithified, brick-like exposed outcrops. Total organic C, measured in three individual profiles spanning depth transects from the outcrop surface to a 1-m depth, ranged from 0.01 to 0.2 wt% with no clear C-concentration or age-depth profile. Ten radiocarbon dates from the same profiles reveal radiocarbon ages of ~ 11,000–30,000 years BP that unexpectedly indicate additions of potentially modern organic C. A two-endmember mixing model for radiocarbon activity suggests that modern C may compose ~ 0.5–2.4% of the total organic C pool. Thermal and evolved gas analysis showed the presence of two distinct pools of organic C, but there was no direct evidence that C compounds were associated with clay minerals. These results challenge the assumption that ancient badland landscapes are inert and “frozen in time” and instead suggest they readily interact with the modern C cycle.
Open Access
Addressing US Youth Violence and Central American Migration through Fortifying Children, Families, and Educators in Central America: A Collaborative Approach to the Development and Testing of a Youth Violence Preventive Intervention
(IntechOpen, 2022-10-14) McClure, Heather H.; Eddy, J. Mark; Martinez, Charles R., Jr.; Esmail, Rubeena; Figueroa, Ana Lucila; Batz, Ruby
Youth violence is a pressing problem in the United States (US) with multiple contributors. Some violence involving US youth can be linked to a larger global epidemic of youth violence in Latin America and in Central America, specifically. Hemispheric histories of violence fueled by a century of US resource extraction and intervention, and other factors such as internal economic and political strain, contribute to present-day migration from Central America to the US. Addressing the intricate problems of US youth violence and migration requires multi-systemic prevention programs to address youth violence in families, schools, and communities in Central America. One such example is Miles de Manos (MdM; “Thousands of Hands”). MdM is intended to target risk and protective factors related to migration from Central America to the US. It is a multi-modal, culturally-specified and community- based violence prevention intervention for elementary-school aged children, their families, and children’s teachers and school staff. Data collected during pilot trials indicate promise in terms of MdM increasing positive teacher and parent behaviors that promote prosocial behaviors and reduce problem behaviors in youth. Outcomes due to MdM for youth, parents and other caregivers, and teachers are currently being examined in a randomized controlled trial in Tegucigalpa, Honduras.
Open Access
Aesthetics and Psychological Effects of Fractal Based Design
(Frontiers in Psychology, 2021-08-17) Robles, Kelly E.; Roberts, Michelle; Viengkham, Catherine; Smith, Julian H.; Rowland, Conor; Moslehi, Saba; Stadlober, Sabrina; Lesjak, Anastasija; Lesjak, Martin; Taylor, Richard P.; Spehar, Branka; Sereno, Margaret
Highly prevalent in nature, fractal patterns possess self-similar components that repeat at varying size scales. The perceptual experience of human-made environments can be impacted with inclusion of these natural patterns. Previous work has demonstrated consistent trends in preference for and complexity estimates of fractal patterns. However, limited information has been gathered on the impact of other visual judgments. Here we examine the aesthetic and perceptual experience of fractal ‘global-forest’ designs already installed in humanmade spaces and demonstrate how fractal pattern components are associated with positive psychological experiences that can be utilized to promote occupant wellbeing. These designs are composite fractal patterns consisting of individual fractal ‘tree-seeds’ which combine to create a ‘global fractal forest.’ The local ‘tree-seed’ patterns, global configuration of tree-seed locations, and overall resulting ‘global-forest’ patterns have fractal qualities. These designs span multiple mediums yet are all intended to lower occupant stress without detracting from the function and overall design of the space. In this series of studies, we first establish divergent relationships between various visual attributes, with pattern complexity, preference, and engagement ratings increasing with fractal complexity compared to ratings of refreshment and relaxation which stay the same or decrease with complexity. Subsequently, we determine that the local constituent fractal (‘treeseed’) patterns contribute to the perception of the overall fractal design, and address how to balance aesthetic and psychological effects (such as individual experiences of perceived engagement and relaxation) in fractal design installations. This set of studies demonstrates that fractal preference is driven by a balance between increased arousal (desire for engagement and complexity) and decreased tension (desire for relaxation or refreshment). Installations of these composite mid-high complexity ‘globalforest’ patterns consisting of ‘tree-seed’ components balance these contrasting needs, and can serve as a practical implementation of biophilic patterns in human-made environments to promote occupant wellbeing.
Open Access
Aging and sperm signals alter DNA break formation and repair in the C. elegans germline
(PLOS, 2022-11-07) Toraason, Erik; Adler, Victoria L.; Libuda, Diana E.
Female reproductive aging is associated with decreased oocyte quality and fertility. The nematode Caenorhabditis elegans is a powerful system for understanding the biology of aging and exhibits age-related reproductive defects that are analogous to those observed in many mammals, including dysregulation of DNA repair. C. elegans germline function is influenced simultaneously by both reproductive aging and signals triggered by limited supplies of sperm, which are depleted over chronological time. To delineate the causes of DNA repair defects in aged C. elegans germlines, we assessed both DNA double strand break (DSB) induction and repair during meiotic prophase I progression in aged germlines which were depleted of self-sperm, mated, or never exposed to sperm. We find that germline DSB induction is dramatically reduced only in hermaphrodites which have exhausted their endogenous sperm, suggesting that a signal due specifically to sperm depletion downregulates DSB formation. We also find that DSB repair is delayed in aged germlines regardless of whether hermaphrodites had either a reduction in sperm supply or an inability to endogenously produce sperm. These results demonstrate that in contrast to DSB induction, DSB repair defects are a feature of C. elegans reproductive aging independent of sperm presence. Finally, we demonstrate that the E2 ubiquitin-conjugating enzyme variant UEV-2 is required for efficient DSB repair specifically in young germlines, implicating UEV-2 in the regulation of DNA repair during reproductive aging. In summary, our study demonstrates that DNA repair defects are a feature of C. elegans reproductive aging and uncovers parallel mechanisms regulating efficient DSB formation in the germline.
Open Access
Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation
(Oxford Academic, 2023-06-05) Short, Aidan W.; Streisfeld, Matthew A.
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.
Open Access
Animal House: The Dark Tetrad traits and membership in sororities and fraternities
(Elsevier, 2022) Kay, Cameron S.
Very little is known about the relationship between antagonistic personality traits and membership in Greekletter organizations (GLOs). The present study (N = 2191) examined the association between the Dark Tetrad traits—Machiavellianism, grandiose narcissism, psychopathy, and everyday sadism—and membership in sororities and fraternities. Participants who were high in grandiose narcissism were more likely to be in sororities and fraternities, whereas participants who were high in Machiavellianism and everyday sadism were less likely to be in these organizations. Psychopathy was not significantly associated with membership in GLOs. Taken together, the present results suggest that members of GLOs are not necessarily more manipulative, cold-hearted, or cruel than their non-GLO counterparts, but they may be more entitled, domineering, and status-seeking.
Open Access
Anomalous Dynamics in Macromolecular Liquids
(MDPI, 2022-02-22) Guenza, Marina G.
Macromolecular liquids display short-time anomalous behaviors in disagreement with conventional single-molecule mean-field theories. In this study, we analyze the behavior of the simplest but most realistic macromolecular system that displays anomalous dynamics, i.e., a melt of short homopolymer chains, starting from molecular dynamics simulation trajectories. Our study sheds some light on the microscopic molecular mechanisms responsible for the observed anomalous behavior. The relevance of the correlation hole, a unique property of polymer liquids, in relation to the observed subdiffusive dynamics, naturally emerges from the analysis of the van Hove distribution functions and other properties.
Open Access
Associations Among Food Delay of Gratification, Cognitive Measures, and Environment in a Community Preschool Sample
(Frontiers in Nutrition, 2022-04-11) Giuliani, Nicole R.; Kelly, Nichole R.
Much of the work on the development of appetite self-regulation in early childhood employs tasks assessing Delay of Gratification (DoG). While this skill is thought to rely on “cool” cognitive processes like effortful control, executive functioning, and self-regulation, demonstration of how laboratory measures of food DoG relate to common assessments of those cognitive processes in community samples of children is needed. This study presents secondary data investigating the associations between two laboratory tasks of food DoG, the Snack Delay and Tongue Tasks, and an array of laboratory and parent-report cognitive measures in a sample of 88 children ages 3-6 (M age = 4.05, SD = 0.76), as well as how four measures of the child’s environment were associated with food DoG. Results indicated that both measures of food DoG were positively correlated with performance on the cognitive tasks, with stronger associations observed for the Tongue Task. Family income was positively associatedwith food DoG asmeasured by the Tongue Task, and child negative life events in the past year were negatively correlated with food DoG as measured by the Snack Delay Task. These findings present the pattern of associations between cognitive tasks and food DoG, the development of which may be meaningfully affected by specific aspects of family environment.
Open Access
The Big Five Across Socioeconomic Status: Measurement Invariance, Relationships, and Age Trends
(University of California Press, 2021-06-10) Hughes, Bradley T.; Costello, Cory K.; Pearman, Joshua J.; Razavi, Pooya; Bedford-Petersen, Cianna; Ludwid, Rita M.; Srivastava, Sanjay
Associations between socioeconomic status (SES) and personality traits have important implications for theory and application. Progress in understanding these associations depends on valid measurement, unbiased estimation, and careful assessment of generalizability. In this registered report, we used data from AIID, a large online study, to address three basic questions about personality and SES. First, we evaluated the measurement invariance of a common measure of personality, the Big Five Inventory, across indicators of educational attainment, income, and occupational prestige. Fit indices showed some instances of detectable noninvariance, but with little practical impact on substantive results. Second, we estimated associations between SES and personality. Results showed that personality and SES were largely independent (most rs < .1), in contrast to predictions derived from several previous studies. Third, we tested whether age trends in personality were moderated by SES. Results did not support predictions from social investment theory, but they did suggest that age trends were largely generalizable across SES. We discuss the implications of these findings for developing and validating personality measures for use in diverse samples. We also discuss the implications for theories that propose that the Big Five are responsive to, or partially responsible for, people’s economic and social conditions.
Open Access
BIHARMONIC ALMOST COMPLEX STRUCTURES
(Cornell University, 2020-06-10) He, Weiyong
We introduce the notion of \emph{biharmonic almost complex structure} on a compact almost Hermitian manifold and we study its regularity and existence in dimension four. First we show that there always exist smooth energy-minimizing biharmonic almost complex structures for any almost Hermitian structure on a compact almost complex four manifold, and all energy-minimizers form a compact set. Then we study the existence problem when the homotopy class of an almost complex structure is specified. We obtain existence of energy-minimizing biharmonic almost complex structures which depends on the topology of M4. When M is simply-connected and non-spin, then for each homotopy class which is uniquely determined by its first Chern class, there exists an energy-minimizing biharmonic almost complex structure. When M is simply-connected and spin, for each first Chern class, there are exactly two homotopy classes corresponding to the first Chern class. Given a homotopy class [τ] of an almost complex structure, there exists a canonical operation on the homotopy classes p satisfying p2=id such that p([τ]) and [τ] have the same first Chern class. We prove that there exists an energy-minimizing biharmonic almost complex structure in (at least) one of the two homotopy classes, [τ] and p([τ]). In general if M is not necessarily simply-connected, we prove that there exists an energy-minimizing biharmonic almost complex structure in (at least) one of the two homotopy classes [τ] and p([τ]). The study of biharmonic almost complex structures should have many applications, in particular for the smooth topology of the underlying almost complex four manifold. We briefly discuss an approach by considering the moduli space of biharmonic almost complex structures and propose a conjecture.
Open Access
Breathing-Based Meditation for Improving COPD Burden: A Mixed Single- Case and Qualitative Approach
(LISDEN Publishing Inc., 2023-12-19) Lin, Ting-fen; Linville, Deanna; Nese, Rhonda N. T.; Seeley, John; Shune, Samantha
Chronic obstructive pulmonary disease (COPD) impacts the physiological and psychoemotional aspects of life. COPD-related secondary sequelae also synergistically interact with each other. For example, dyspnea affects the severity of breath, body functions, and the mind (e.g., anxiety, panic, fear). Such negative psycho-emotional states can further negatively impact the breath and the body (e.g., increased dyspnea). Given the breadth of the impact of COPD on multiple facets of health and well-being, it is essential to investigate comprehensive approaches to managing COPD, simultaneously addressing the mind, body, and breath. Sudarshan Kriya Yoga (SKY), a breathwork meditation program, has previously yielded a wide range of physiological and psycho-emotional benefits but has not been explored in individuals with COPD. Using single-case multiple-baseline and qualitative phenomenology methodologies, this study investigated 1) the relation between dyspnea and SKY and 2) the feasibility and general perceived effectiveness of SKY among individuals with COPD. Nine individuals with varying severities of COPD participated. Data collection included ratings of perceived dyspnea (work of breathing, shortness of breath, dyspnea-related distress, dyspnea-related anxiety) and semi-structured in-depth interviews. Results suggest that SKY is feasible and acceptable for individuals with COPD. Additionally, the results demonstrate proof of concept that SKY can help alleviate aspects of the COPD disease burden related to the mind, body, and breath as well as reduce the cyclical effect of the disease sequelae. Larger-scale trials are warranted, but this study is the first to support SKY as a viable complementary and integrative health approach for individuals with COPD.
Open Access
Characterizing the impact of adversity, abuse, and neglect on adolescent amygdala resting-state functional connectivity
(Elsevier, 2020) Cheng, Theresa W.; Mills, Kathryn L.; Miranda Dominguez, Oscar; Zeithamova, Dagmar; Perrone, Anders; Sturgeon, Darrick; Feldstein Ewing, Sarah W.; Fisher, Philip A.; Pfeifer, Jennifer H.; Fair, Damian A.; Mackiewicz Seghete, Kristen L.
Characterizing typologies of childhood adversity may inform the development of risk profiles and corresponding interventions aimed at mitigating its lifelong consequences. A neurobiological grounding of these typologies requires systematic comparisons of neural structure and function among individuals with different exposure histories. Using seed-to-whole brain analyses, this study examined associations between childhood adversity and amygdala resting-state functional connectivity (rs-fc) in adolescents aged 11–19 years across three independent studies (N = 223; 127 adversity group) in both general and dimensional models of adversity (comparing abuse and neglect). In a general model, adversity was associated with altered amygdala rs-fc with clusters within the left anterior lateral prefrontal cortex. In a dimensional model, abuse was associated with altered amygdala rs-fc within the orbitofrontal cortex, dorsal precuneus, posterior cingulate cortex, and dorsal anterior cingulate cortex/anterior mid-cingulate cortex, as well as within the dorsal attention, visual, and somatomotor networks. Neglect was associated with altered amygdala rs-fc with the hippocampus, supplementary motor cortex, temporoparietal junction, and regions within the dorsal attention network. Both general and dimensional models revealed unique regions, potentially reflecting pathways by which distinct histories of adversity may influence adolescent behavior, cognition, and psychopathology.
Open Access
Comparison of fractal and grid electrodes for studying the effects of spatial confinement on dissociated retinal neuronal and glial behavior
(Nature, 2022-10-20) Moslehi, Saba; Rowland, Conor; Smith, Julian H.; Griffiths, Willem; Watterson, William J.; Niell, Cristopher M.; Alemán, Benjamín J.; Perez, Maria-Thereza; Taylor, Richard P.
Understanding the impact of the geometry and material composition of electrodes on the survival and behavior of retinal cells is of importance for both fundamental cell studies and neuromodulation applications. We investigate how dissociated retinal cells from C57BL/6J mice interact with electrodes made of vertically-aligned carbon nanotubes grown on silicon dioxide substrates. We compare electrodes with different degrees of spatial confinement, specifically fractal and grid electrodes featuring connected and disconnected gaps between the electrodes, respectively. For both electrodes, we find that neuron processes predominantly accumulate on the electrode rather than the gap surfaces and that this behavior is strongest for the grid electrodes. However, the ‘closed’ character of the grid electrode gaps inhibits glia from covering the gap surfaces. This lack of glial coverage for the grids is expected to have long-term detrimental effects on neuronal survival and electrical activity. In contrast, the interconnected gaps within the fractal electrodes promote glial coverage. We describe the differing cell responses to the two electrodes and hypothesize that there is an optimal geometry that maximizes the positive response of both neurons and glia when interacting with electrodes.
Open Access
Contextual considerations for deception production and detection in forensic interviews
(Frontiers in Psychology, 2023-02-07) Markowitz, David M.; Hancock, Jeffery T.; Woodworth, Michael T.; Ely, Maxwell
Most deception scholars agree that deception production and deception detection effects often display mixed results across settings. For example, some liars use more emotion than truth-tellers when discussing fake opinions on abortion, but not when communicating fake distress. Similarly, verbal and nonverbal cues are often inconsistent predictors to assist in deception detection, leading to mixed accuracies and detection rates. Why are lie production and detection effects typically inconsistent? In this piece, we argue that aspects of the context are often unconsidered in how lies are produced and detected. Greater theory-building related to contextual constraints of deception are therefore required. We reintroduce and extend the Contextual Organization of Language and Deception (COLD) model, a framework that outlines how psychological dynamics, pragmatic goals, and genre conventions are aspects of the context that moderate the relationship between deception and communication behavior such as language. We extend this foundation by proposing three additional aspects of the context — individual differences, situational opportunities for deception, and interpersonal characteristics — for the COLD model that can specifically inform and potentially improve forensic interviewing. We conclude with a forward-looking perspective for deception researchers and practitioners related to the need for more theoretical explication of deception and its detection related to the context.
Open Access
Creating the Qur’an: A Historical-Critical Study
(University of California Press, 2022) Shoemaker, Stephen J.
Creating the Qur’an presents the first systematic historical-critical study of the Qur’an’s origins, drawing on methods and perspectives commonly used to study other scriptural traditions. Demonstrating in detail that the Islamic tradition relates not a single attested account of the holy text’s formation, Stephen J. Shoemaker shows how the Qur’an preserves a surprisingly diverse array of memories regarding the text’s early history and its canonization. To this he adds perspectives from radiocarbon dating of manuscripts, the linguistic history of Arabic, the social and cultural history of late ancient Arabia, and the limitations of human memory and oral transmission, as well as various peculiarities of the Qur’anic text itself. Considering all the relevant data to present the most comprehensive and convincing examination of the origin and evolution of the Qur’an available, Shoemaker concludes that the canonical text of the Qur’an was most likely produced only around the turn of the eighth century.
Open Access
Degeneracies and symmetry breaking in pseudo-Hermitian matrices
(APS, 2023-04-18) Melkani, Abhijeet
Real eigenvalues of pseudo-Hermitian matrices, such as real matrices and PT −symmetric matrices, frequently split into complex conjugate pairs. This is accompanied by the breaking of certain symmetries of the eigenvectors and, typically, also a drastic change in the behavior of the system. In this paper, we classify the eigenspace of pseudo-Hermitian matrices and show that such symmetry breaking occurs if and only if eigenvalues of opposite kinds collide on the real axis of the complex eigenvalue plane. This enables a classification of the disconnected regions in parameter space where all eigenvalues are real—which correspond, physically, to the stable phases of the system. These disconnected regions are surrounded by exceptional surfaces, which comprise all the real-valued exceptional points of pseudo-Hermitian matrices. The exceptional surfaces, together with the diabolic points created by their intersections, comprise all points of pseudo-Hermiticity breaking. In particular, this clarifies that the degeneracy involved in symmetry breaking is not necessarily an exceptional point. We also discuss how our study relates to conserved quantities and derive the conditions for when degeneracies caused by external symmetries are susceptible to thresholdless pseudo-Hermiticity breaking. We illustrate our results with examples from photonics, condensed matter physics, and mechanics.
Open Access
Delay of Gratification Predicts Eating in the Absence of Hunger in Preschool-Aged Children
(Frontiers Media, 2021-03-19) Giuliani, Nicole R.; Kelly, Nichole R.
Poor ability to regulate one's own food intake based on hunger cues may encourage children to eat beyond satiety, leading to increased risk of diet-related diseases. Self-regulation has multiple forms, yet no one has directly measured the degree to which different domains of self-regulation predict overeating in young children. The present study investigated how three domains of self-regulation (i.e., appetitive self-regulation, inhibitory control, and attentional control) predicted eating in the absence of hunger (EAH) in a community sample of 47 preschool-aged children (M age = 4.93, SD = 0.86). Appetitive self-regulation, as measured using a delay of gratification task, was significantly and negatively associated with EAH 1 year later (p < 0.5). Measures of inhibitory and attentional control did not significantly predict EAH. These results suggest that food-related self-regulation may be a better predictor of overeating behaviors than general measures of self-regulation.
Open Access
Differing effects of four building materials on viable bacterial communities and VOCs
(Elsevier, 2021) Mhuireach, Gwynne A.; Dietz, Leslie; Griffiths, Willem; Horve, Patrick Finn; Laguerre, Aurelie; Northcutt, Dale; Vandegrift, Roo; Gall, Elliott; Van Den Wymelenberg, Kevin
Indoor environmental quality is a paramount concern among architects. Exposure to VOCs and microorganisms impacts occupant health, yet the role of materials on these exposures remains poorly understood. In this study, we placed four material types in individual microcosms to test whether material type influences bacterial community structure and VOC emission. We used culture-independent methods to characterize bacterial communities and TD-GC-MS to measure VOC emission. We found that viable bacterial communities had different patterns of abundance, diversity, and composition, in comparison with total (viable plus dead cells) bacterial communities. Examining viable bacteria only, Earth had the highest abundance and diversity, unique community composition, and overall negative VOC emission. Timber had the lowest bacterial abundance, composition similar to Gypsum and Concrete, and the highest VOC emission rate. Our research provides further evidence that architects’ decisions about building materials can influence chemical and microbial exposures indoors.
Open Access
Diffuse optics for glaciology
(Optical Society of America, 2021-06) Allgaier, Markus; Smith, Brian J.
Optical probing of glaciers has the potential for tremendous impact on environmental science. However, glacier ice is turbid, which prohibits the use of most established optical measurements for determining a glacier’s interior structure. Here, we propose a method for determining the depth, scattering and absorption length based upon diffuse propagation of short optical pulses. Our model allows us to extract several characteristics of the glacier. Performing Monte Carlo simulations implementing Mie scattering and mixed boundary conditions, we show that the proposed approach should be feasible with current technology. The results suggest that the optical properties and geometry of the glacier can be extracted from realistic measurements, which could be implemented with a low cost and small footprint.
Open Access
Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms
(Oxford Academic, 2021-01) Beyerle, Eric R.; Dinpajooh, Mohammadhasan; Ji, Huiying; von Hippel, Peter H.; Marcus, Andrew H.; Guenza, Marina G.
Regulatory protein access to the DNA duplex 'interior' depends on local DNA 'breathing' fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.