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Open Access
Molecular basis of product recognition during PIP5K-mediated production of PI(4,5)P2 with positive feedback
(Journal of Biological Chemistry, 2024-08-03) Duewell, Benjamin R.; Faris, Katherine A.; Hansen, Scott D.
The ability for cells to localize and activate peripheral membrane-binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyzes the phosphorylation of PI(4)P to generate most of the PI(4,5)P2 lipids found in eukaryotic plasma membranes. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. Here, we examine how two motifs contribute to PI(4,5)P2 recognition to control membrane association and catalysis of PIP5K. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PI(4,5)P2 lipids. After correctly orienting on the membrane, PIP5K transitions to binding PI(4,5)P2 lipids near the active site through a motif previously referred to as the substrate or PIP-binding motif (PIPBM). The PIPBM has broad specificity for anionic lipids and serves a role in regulating membrane association in vitro and in vivo. Overall, our data supports a two-step membrane-binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2 production.
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
The numeric understanding measures: Developing and validating adaptive and nonadaptive numeracy scales
(Cambridge University Press, 2023-06-28) Silverstein, Michael C.; Bjälkebring, Pär; Shoots-Reinhard, Brittany; Peters, Ellen
Numeracy—the ability to understand and use numeric information—is linked to good decision-making. Several problems exist with current numeracy measures, however. Depending on the participant sample, some existing measures are too easy or too hard; also, established measures often contain items well-known to participants. The current article aimed to develop new numeric understanding measures (NUMs) including a 1-item (1-NUM), 4-item (4-NUM), and 4-item adaptive measure (A-NUM). In a calibration study, 2 participant samples (n = 226 and 264 from Amazon’s Mechanical Turk [MTurk]) each responded to half of 84 novel numeracy items.We calibrated items using 2-parameter logistic item response theory (IRT) models. Based on item parameters, we developed the 3 new numeracy measures. In a subsequent validation study, 600 MTurk participants completed the new numeracy measures, the adaptive Berlin Numeracy Test, and the Weller Rasch-Based Numeracy Test, in randomized order. To establish predictive and convergent validities, participants also completed judgment and decision tasks, Raven’s progressive matrices, a vocabulary test, and demographics. Confirmatory factor analyses suggested that the 1-NUM, 4-NUM, and A-NUM load onto the same factor as existing measures. The NUM scales also showed similar association patterns to subjective numeracy and cognitive ability measures as established measures. Finally, they effectively predicted classic numeracy effects. In fact, based on power analyses, the A-NUM and 4-NUM appeared to confer more power to detect effects than existing measures. Thus, using IRT, we developed 3 brief numeracy measures, using novel items and without sacrificing construct scope. The measures can be downloaded as Qualtrics files (https://osf.io/pcegz/).
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
Selecting the Number and Labels of Topics in Topic Modeling: A Tutorial
(Sage Journals, 2023-05-25) Weston, Sara J.; Shryock, Ian; Light, Ryan; Fisher, Phillip A.
Topic modeling is a type of text analysis that identifies clusters of co-occurring words, or latent topics. A challenging step of topic modeling is determining the number of topics to extract. This tutorial describes tools researchers can use to identify the number and labels of topics in topic modeling. First, we outline the procedure for narrowing down a large range of models to a select number of candidate models. This procedure involves comparing the large set on fit metrics, including exclusivity, residuals, variational lower bound, and semantic coherence. Next, we describe the comparison of a small number of models using project goals as a guide and information about topic representative and solution congruence. Finally, we describe tools for labeling topics, including frequent and exclusive words, key examples, and correlations among topics.
Open Access
Measuring Hispanics/Latinxs: Racial Heterogeneity and Its Consequences for Modeling Social Outcomes in U.S. Population Samples
(Sage Journals, 2023-05-23) Shiao, Jiannbin Lee
Quantitative sociologists have recognized the challenges of studying Latinx Americans, given their unique racial heterogeneity and unique measurement in surveys through dedicated Latinx-ethnicity questions. Using the National Longitudinal Study of Adolescent to Adult Health, the author examines who identifies as Hispanic/Latinx when the option is a permitted response on a combined race/ethnicity question. The study reveals that national origin, connection to Latinx communities, racial appearance, and consistency in prior ethnic identification as Latinx affect the likelihood of racial identification as Latinx. These associations have heterogeneous consequences for modeling social outcomes in samples with both Latinx and non-Latinx respondents. Latinx Americans divide on skin tone in models of education and health, but they divide on national origin in models of interracial dating. This suggests that researchers should operationalize Latinxs using measures recognizing a modal group of Latinx-only identifiers while capturing heterogeneity by skin tone and national origin across the broader ever-Latinx population.
Open Access
Inequalities of ice loss: a framework for addressing sociocryospheric change
(Cambridge University Press, 2023-05-12) Carey, Mark; Moulton, Holly
Cryospheric change occurs in unequal spaces. Societies living near ice are divided by race, class, gender, geography, politics and other factors. Consequently, impacts of ice loss are not shared equally, and everyone experiences cryospheric changes differently. Responsibility for recent ice loss is also driven by a relatively small portion of humanity: those who emit the most greenhouse gases. Additionally, people who study the cryosphere come from institutions and societies where inequality is often systemic, making research on ice and snow a symptom of and contributor to social inequality. To better understand unequal effects of cryospheric change within and across diverse communities, including research communities, this paper focuses on three areas, drawing primarily from glacier-related work: (1) the social context of cryospheric changes; (2) attribution and responsibility for cryospheric changes and (3) imbalances in knowledge about the cryosphere. Addressing these dimensions of ice loss requires transdisciplinary approaches that connect research to societies and link glaciology and other cryospheric sciences with social sciences and humanities. These concepts, cases and suggestions to help address inequalities also reveal that no singular conceptualization of sustainability exists. Different societies, residents and researchers possess distinct understandings of and goals for ‘ice in a sustainable society’.
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
Molecular dissection of PI3Kβ synergistic activation by receptor tyrosine kinases, GβGγ, and Rho-family GTPases
(bioRxiv, 2023-05-01) Duewell, Benjamin R.; Wilson, Naomi E.; Bailey, Gabriela M.; Peabody, Sarah E.; Hansen, Scott D.
The class 1A phosphoinositide 3-kinase (PI3K) beta (PI3Kβ) is functionally unique in the ability to integrate signals derived from receptor tyrosine kinases (RTKs), heterotrimeric guanine nucleotidebinding protein (G-protein)-coupled receptors (GPCRs), and Rho-family GTPases. The mechanism by which PI3Kβ prioritizes interactions with various membrane tethered signaling inputs, however, remains unclear. Previous experiments have not been able to elucidate whether interactions with membranetethered proteins primarily control PI3Kβ localization versus directly modulate lipid kinase activity. To address this gap in our understanding of PI3Kβ regulation, we established an assay to directly visualize and decipher how three binding interactions regulate PI3Kβ when presented to the kinase in a biologically relevant configuration on supported lipid bilayers. Using single molecule Total Internal Reflection Fluorescence (TIRF) Microscopy, we determined the mechanism controlling membrane localization of PI3Kβ, prioritization of signaling inputs, and lipid kinase activation. We find that auto-inhibited PI3Kβ must first cooperatively engage a single RTK-derived tyrosine phosphorylated (pY) peptide before it can engage either GβGγ or Rac1(GTP). Although pY peptides strongly localize PI3Kβ to membranes, they only modestly stimulate lipid kinase activity. In the presence of either pY/GβGγ or pY/Rac1(GTP), PI3Kβ activity is dramatically enhanced beyond what can be explained by the increase in membrane avidity for these complexes. Instead, PI3Kβ is synergistically activated by pY/GβGγ and pY/Rac1(GTP) through a mechanism of allosteric regulation.
Open Access
Non-singular and singular flat bands in tunable phononic metamaterials
(APS, 2023-04-18) Karki, Pragalv; Paulose, Jayson
Dispersionless flat bands can be classified into two types: (1) non-singular flat bands whose eigenmodes are completely characterized by compact localized states, and (2) singular flat bands that have a discontinuity in their Bloch eigenfunctions at a band touching point with an adjacent dispersive band, thereby requiring additional extended states to span their eigenmode space. In this study, we design and numerically demonstrate two-dimensional thin-plate phononic metamaterials in which tunable flat bands of both kinds can be achieved. Non-singular flat bands are achieved by fine tuning the ratio of the global tension and the bending stiffness in triangular and honeycomb lattices of plate resonators. A singular flat band arises in a kagome lattice due to the underlying lattice geometry, which can be made degenerate with two additional flat bands by tuning the plate tension. A discrete model of the continuum thin-plate system reveals the interplay of geometric and mechanical factors in determining the existence of flat bands of both types. The singular nature of the kagome lattice flat band is established via a metric called the Hilbert-Schmidt distance calculated between a pair of eigenstates infinitesimally close to the quadratic band touching point.We also simulate a phononic manifestation of a robust boundary mode arising from the singular flat band and protected by real-space topology in a finite system. Our theoretical and computational study establishes a framework for exploring flat-band physics in a tunable classical system, and for designing phononic metamaterials with potentially useful sound manipulation capabilities.
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
Ligand field tuning of d-orbital energies in MOF clusters
(Research Square, 2023-04-12) Diamond, Brian; Payne, Lillian; Hendon, Christopher
Linker functionalization is a common route used to affect the electronic and catalytic properties of metal-organic frameworks. By either pre- or post-synthetically installing linkages with differing linker moieties the band gap, workfunction, and exciton lifetimes have been shown to be affected. One overlooked aspect of linker functionalization, however, has been the impact on the metal dorbital energies to which they are bound. The ligand field differences should result in substantial changes in d-splitting. In this study we use DFT to study the energetics of d-orbital energy tuning as a function of linker chemistry. We offer a general descriptor, linker pKa, as a tool to predict the resultant d-splitting in MOFs. Our calculations reveal that simple functionalizations can affect the d-energies by up to 2 eV and illustrate the significance of this band modularity using four archetypal MOFs: UiO-66, MIL-125, ZIF-8, and MOF-5. Together, we show that linker functionalization dramatically affects d-energies in MOF clusters and highlight that linker functionalization is a useful route for fine-tuning band edges centered on the metals, rather than linkers themselves.
Open Access
Navigating the intersection of 3D printing, software regulation and quality control for point‑of‑care manufacturing of personalized anatomical models
(BMC, 2023-04-07) Paxton, Naomi C.
3D printing technology has become increasingly popular in healthcare settings, with applications of 3D printed anatomical models ranging from diagnostics and surgical planning to patient education. However, as the use of 3D printed anatomical models becomes more widespread, there is a growing need for regulation and quality control to ensure their accuracy and safety. This literature review examines the current state of 3D printing in hospitals and FDA regulation process for software intended for use in producing 3D printed models and provides for the first time a comprehensive list of approved software platforms alongside the 3D printers that have been validated with each for producing 3D printed anatomical models. The process for verification and validation of these 3D printed products, as well as the potential for inaccuracy in these models, is discussed, including methods for testing accuracy, limits, and standards for accuracy testing. This article emphasizes the importance of regulation and quality control in the use of 3D printing technology in healthcare, the need for clear guidelines and standards for both the software and the printed products to ensure the safety and accuracy of 3D printed anatomical models, and the opportunity to expand the library of regulated 3D printers.
Open Access
Maternal opioids age-dependently impair neonatal respiratory control networks
(Frontiers in Physiology, 2023-03-16) Beyeler, Sarah A.; Naidoo, Robyn; Morrison, Nina R.; McDonald, Emilee A.; Albarrán, David; Huxtable, Adrianne G.
Infants exposed to opioids in utero are an increasing clinical population and these infants are often diagnosed with Neonatal Abstinence Syndrome (NAS). Infants with NAS have diverse negative health consequences, including respiratory distress. However, many factors contribute to NAS, confounding the ability to understand how maternal opioids directly impact the neonatal respiratory system. Breathing is controlled centrally by respiratory networks in the brainstem and spinal cord, but the impact of maternal opioids on developing perinatal respiratory networks has not been studied. Using progressively more isolated respiratory network circuitry, we tested the hypothesis that maternal opioids directly impair neonatal central respiratory control networks. Fictive respiratory-related motor activity from isolated central respiratory networks was age-dependently impaired in neonates after maternal opioids within more complete respiratory networks (brainstem and spinal cords), but unaffected in more isolated networks (medullary slices containing the preBötzinger Complex). These deficits were due, in part, to lingering opioids within neonatal respiratory control networks immediately after birth and involved lasting impairments to respiratory pattern. Since opioids are routinely given to infants with NAS to curb withdrawal symptoms and our previous work demonstrated acute blunting of opioid-induced respiratory depression in neonatal breathing, we further tested the responses of isolated networks to exogenous opioids. Isolated respiratory control networks also demonstrated age-dependent blunted responses to exogenous opioids that correlated with changes in opioid receptor expression within a primary respiratory rhythm generating region, the preBötzinger Complex. Thus, maternal opioids agedependently impair neonatal central respiratory control and responses to exogenous opioids, suggesting central respiratory impairments contribute to neonatal breathing destabilization after maternal opioids and likely contribute to respiratory distress in infants with NAS. These studies represent a significant advancement of our understanding of the complex effects of maternal opioids, even late in gestation, contributing to neonatal breathing deficits, necessary first steps in developing novel therapeutics to support breathing in infants with NAS.
Open Access
The influence of explicit local dynamics on range expansions driven by long-range dispersal
(bioRxiv, 2023-02-23) Villiger, Nathan; Paulose, Jayson
Range expansions are common in natural populations. They can take such forms as an invasive species spreading into a new habitat or a virus spreading from host to host during a pandemic. When the expanding species is capable of dispersing offspring over long distances, population growth is driven by rare but consequential long-range dispersal events that seed satellite colonies far from the densely occupied core of the population. These satellites accelerate growth by accessing unoccupied territory, and also act as reservoirs for maintaining neutral genetic variation present in the originating population, which would ordinarily be lost to drift. Prior theoretical studies of dispersal-driven expansions have shown that the sequential establishment of satellites causes initial genetic diversity to be either lost or maintained to a level determined by the breadth of the distribution of dispersal distances. If the tail of the distribution falls off faster than a critical threshold, diversity is steadily eroded over time; by contrast, broader distributions with a slower falloff allow some initial diversity to be maintained for arbitrarily long times. However, these studies used lattice-based models and assumed an instantaneous saturation of the local carrying capacity after the arrival of a founder. Real-world populations expand in continuous space with complex local dynamics, which potentially allow multiple pioneers to arrive and establish within the same local region. Here, we evaluate the impact of local dynamics on the population growth and the evolution of neutral diversity using a computational model of range expansions with long-range dispersal in continuous space, with explicit local dynamics that can be controlled by altering the mix of local and long-range dispersal events. We found that many qualitative features of population growth and neutral genetic diversity observed in lattice-based models are preserved under more complex local dynamics, but quantitative aspects such as the rate of population growth, the level of maintained diversity, and the rate of decay of diversity all depend strongly on the local dynamics. Besides identifying situations in which modeling the explicit local population dynamics becomes necessary to understand the population structure of jump-driven range expansions, our results show that local dynamics affects different features of the population in distinct ways, and can be more or less consequential depending on the degree and form of long-range dispersal as well as the scale at which the population structure is measured.
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
Neuron arbor geometry is sensitive to the limited-range fractal properties of their dendrites
(Frontiers in Network Physiology, 2023-01-25) Rowland, Conor; Smith, Julian H.; Moslehi, Saba; Harland, Bruce; Dalrymple-Alford, John; Taylor, Richard P.
Fractal geometry is a well-known model for capturing the multi-scaled complexity of many natural objects. By analyzing three-dimensional images of pyramidal neurons in the rat hippocampus CA1 region, we examine how the individual dendrites within the neuron arbor relate to the fractal properties of the arbor as a whole. We find that the dendrites reveal unexpectedly mild fractal characteristics quantified by a low fractal dimension. This is confirmed by comparing two fractal methods—a traditional “coastline” method and a novel method that examines the dendrites’ tortuosity across multiple scales. This comparison also allows the dendrites’ fractal geometry to be related to more traditional measures of their complexity. In contrast, the arbor’s fractal characteristics are quantified by a much higher fractal dimension. Employing distorted neuron models that modify the dendritic patterns, deviations from natural dendrite behavior are found to induce large systematic changes in the arbor’s structure and its connectivity within a neural network. We discuss how this sensitivity to dendrite fractality impacts neuron functionality in terms of balancing neuron connectivity with its operating costs. We also consider implications for applications focusing on deviations from natural behavior, including pathological conditions and investigations of neuron interactions with artificial surfaces in human implants.
Open Access
Epitope tag-specific differences in the detection of COSA-1 marked crossover sites in C. elegans spermatocytes
(Caltech Library, 2023-01-06) Cahoon, Cori K.; Uebel, Celja J.; Villeneuve, Anne M.; Libuda, Diana E.
Nascent crossover sites in C. elegans meiocytes can be cytologically detected using epitope-tagged versions of the pro-crossover protein COSA-1. In spermatocytes, differences exist between cytologically-detected and genetically-detected double crossover rates. Here, we examine nascent crossovers using both GFP- and OLLAS-tagged COSA-1. Similar to previous work, we find that most late pachytene spermatocytes display 5 COSA-1 foci, indicating one crossover per autosome bivalent. However, we detected more nuclei with >5 COSA-1 foci using OLLAS::COSA-1, reflecting some bivalents having 2 COSA-1 foci. These results demonstrate tag-specific differences in the detection of COSA-1 marked nascent crossovers in spermatocytes.
Open Access
A generic hierarchical model of organic matter degradation and preservation in aquatic systems
(Nature Communications, 2023-01) Shang, Haitao
Organic matter degradation and preservation are crucial components of Earth’s carbon cycle. Empirical and phenomenological models usually contain parameters determined by site-specific data and focus on different aspects of the decay and accretion characteristics. To investigate more fundamental mechanisms, this study suggests a hierarchical model that links microscopic physical quantities to macroscopic degradation and preservation patterns. This mechanistic model predicts several commonly observed phenomena, including the lognormal distribution of degradation rate constants, the recalcitrance-dependent sensitivity to temperature, the dependence of a heterogeneous organic-matter system’s persistence on its complexity, logarithmic-time decay, and power-law degradation behavior. The theoretical predictions of this model are consistent with the observational data from marine and lake environments. This hierarchical model may provide a step towards a fundamental theory of organic matter degradation and preservation in aquatic and other ecosystems.
Open Access
Trait biases in microbial reference genomes
(Nature Communications, 2023) Albright, Sage; Louca, Stilianos
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.