Biology subjects

Swanson, C.

Publications and source records attributed to Swanson, C..

6 recordsLinked to original sources

bioRxiv2025

Small amphiphilic DNA for programmable transmembrane signaling and amplification

Interrogating the sequence-specific DNA/RNA content of a living cell without destroying it, is an elusive goal in biology and diagnostics with transformative potential. A DNA/RNA-based approach, however, must relay the recognition event across the intact lipid bilayer, a step that has long been considered impossible because hydrophilic, massively charged DNA/RNA is incompatible with the hydrophobic membrane interior. Here, we show that DNA branch migration can be driven across a lipid bilayer, converting an intracellular nucleic-acid sequence into an amplified, extracellular optical signal while preserving cell viability and compartmentalization, a synthetic transmembrane signal transduction analogous to natural receptors, such as G-protein-coupled receptors (GPCRs), but operating in reverse. We demonstrate this principle with Hybridization Across Lipid for Oligonucleotide Sensing (HALOS), an amphiphilic DNA hairpin comprising a toehold for recognition, a stem for stability, a loop, and cholesterols for transmembrane anchoring. Upon binding to a sequence-specific nucleic acid target, toehold-mediated strand invasion drives DNA branch migration across the bilayer, switching HALOS from a closed to an open conformation that relays the signal to the opposite face. Molecular dynamics simulations revealed that a cholesterol belt stabilizes the DNA stem within the membrane, preserving the hairpin structure necessary for transmembrane signaling. Notably, this branch migration proceeds despite the kinetic barrier of hybridization through the hydrophobic bilayer interior. By combining HALOS with an isothermal hybridization chain reaction (HCR), we established a platform that enables intracellular nucleic acid target detection and amplified fluorescent reporting from outside synthetic vesicles and live mammalian cells, achieving nanomolar-range sensitivity. These results establish DNA branch migration across lipid membranes as a design principle for programmable lysis-free molecular sensing in intact cells.

biophysics↗

bioRxiv2024

A lack of open data standards for large infrastructure project hampers social-ecological research in the Brazilian Amazon

New infrastructure projects are planned or under construction in several countries, including in the bioculturally diverse Amazon, Mekong, and Congo regions. While infrastructure development can improve human health and living standards, it may also lead to environmental degradation and social change. Accessible, high quality data about infrastructure projects is essential for both monitoring them and studying their social and environmental impacts. We investigated the availability and quality of data on infrastructure projects in the Brazilian Amazon by reviewing the academic literature and surveying researchers from the conservation and development community, then used the results of these surveys to identify critical data attributes for the gathering, organizing, and sharing of infrastructure data by social-ecological researchers and practitioners. Although data on infrastructure in the Brazilian Amazon were generally available, they were often of poor quality and lacked information critical for monitoring and research. Data were often difficult to find and reformat, resulting in loss of time and resources for researchers and other stakeholders. Discrepancies between researchers survey responses on data needs and the types of data used in peer-reviewed articles on infrastructure projects indicate the following information was often missing: geographic extent of the project, construction and operation dates, and project type (e.g., paved vs unpaved road). Including these data in a standardized format, along with making them more readily accessible by hosting them in public repositories and ensuring they are current and comprehensive, would facilitate research and improve planning, decision-making, and monitoring of existing and future infrastructure projects in Brazil and other developing countries. HighlightsO_LIInfrastructure projects across the globe spur economic development but also lead to social- ecological degradation. C_LIO_LIResearchers and practitioners need current and comprehensive data to better mitigate social- ecological changes from infrastructure. C_LIO_LIInfrastructure data are often unavailable, inaccessible, or incomplete. C_LIO_LIFinding and organizing datasets cost researchers hundreds of hours and may lead to abandoned projects. C_LIO_LITo promote better research outcomes, governments and NGOs should ensure datasets on infrastructure are accessible, current, comprehensive, and include such vital information as the projects geographic extent, dates of construction and operation, project type, and essential technical data. C_LI

ecology↗

bioRxiv2024

Effects of point density on interpretability of lidar-derived forest structure metrics in two temperate forests

Three-dimensional forest structure plays an important role in processes such as biomass accumulation and fire spread and provides wildlife with habitat and foraging spaces. Advances in lidar mapping have improved forest structure quantification at local to global scales. However, point cloud density may have effects on estimates of forest structure variables that are not well understood and may vary by forest structural type (e.g. closed vs open canopy). In this study we investigated the effects of lidar point cloud density on forest structure parametrization in an open canopy pine-dominated forest at Assateague Island National Seashore (AINS) and a closed-canopy mixed hardwood temperate forest at the Keweenaw Research Center (KRC) using uncrewed aerial system (UAS)-based lidar. We decimated high point density (> 1000 points m-2) lidar data to between 1 and 175 points m-2 and analyzed 26 forest structure metrics using Tukeys method, reliability ratio, and correlation analyses. Effects of point density on forest structure parameters were often site-dependent, as anticipated. At AINS, maximum (zmax) and mode (zmode) height significantly differed for point densities less than 10 pts m-2 and 25 points m-2, respectively, while at KRC, the thresholds were 75 points m-2 for zmax and 50 points m-2 for zmode. Reliability ratio of zmax, height skewness, height quantiles, and the coefficient of variation of mean leaf area density (LAD) also varied dependent on point density at AINS. At both sites, metrics related LAD varied significantly (p < 0.001) at all but the highest point densities, and the reliability ratio for zmode, kurtosis of height distribution and mean horizontal coefficient of variation of LAD varied across point densities without any clear pattern. Point density mainly affected correlations between LAD-derived structural metrics and other metrics (e.g., as point density increased, Shannon diversity of LAD changed from being positively to negatively correlated to zmax). This study demonstrates how point density differentially affects lidar-derived forest structure parameters in diverse forest types. Scientists must understand these effects to interpret and compare forest structure attributes derived from different lidars.

ecology↗

bioRxiv2021

Regulation of KHNYN antiviral activity by the extended di-KH domain and nucleo-cytoplasmic trafficking

The zinc finger antiviral protein (ZAP) restricts a broad range of viruses by binding CpG dinucleotides in viral RNA to target it for degradation and inhibit its translation. KHNYN was recently identified as an antiviral protein required for ZAP to inhibit retroviral replication, though little is known about its functional determinants. KHNYN contains an N-terminal extended di-KH-like domain, a PIN endoribonuclease domain and a C-terminal CUBAN domain that binds NEDD8 and ubiquitin. We show that deletion of the extended di-KH domain reduces its antiviral activity. However, despite its similarity to RNA binding KH domains, the extended di-KH domain in KHNYN does not appear to bind RNA. Mutation of residues in the CUBAN domain that bind NEDD8 increase KHNYN abundance but do not alter its antiviral activity, suggesting that this interaction regulates KHNYN homeostatic turnover. In contrast, a CRM1-dependent nuclear export signal (NES) at the C-terminus of the CUBAN domain is required for antiviral activity. Deletion of this signal retains KHNYN in the nucleus and inhibits its interaction with ZAP. Interestingly, this NES appeared in the KHNYN lineage at a similar time as when ZAP evolved in tetrapods, indicating that these proteins may have co-evolved to restrict viral replication. AUTHOR SUMMARYAntiviral proteins restrict viral replication in many different ways, including inhibiting viral gene expression. ZAP is an antiviral RNA binding protein that must interact with other cellular proteins to inhibit viral protein synthesis. KHNYN is a ZAP cofactor that is required for it to inhibit retroviral replication. Because little is known about how KHNYN functions in this role, we have analyzed how two of its domains regulate its antiviral activity. We first show that the extended di-KH domain in KHNYN is required for its antiviral activity. While it is related to di-KH domains in RNA binding proteins, it appears to have lost its ability to bind RNA and KHNYN likely acts in the restriction pathway after ZAP binds a target viral RNA. Second, we show that the KHNYN CUBAN domain regulates both its protein abundance and trafficking within the cell. The CUBAN domain contains a nuclear export signal and, when this signal is mutated, KHNYN is sequestered in the nucleus, has substantially reduced antiviral activity and does not interact with ZAP. Overall, we show that the extended di-KH and CUBAN domains in KHNYN are required for it to act as a cofactor for ZAP to restrict viral replication.

microbiology↗

bioRxiv2021

The C-terminal PARP domain of the long ZAP isoform contributes essential effector functions for CpG-directed antiviral activity

The zinc finger antiviral protein (ZAP) is a broad inhibitor of virus replication. Its best-characterized function is to bind CpG dinucleotides present in viral RNA and, through the recruitment of TRIM25, KHNYN and other cellular RNA degradation machinery, target them for degradation or prevent their translation. ZAPs activity requires the N-terminal RNA binding domain that selectively binds CpG-containing RNA. However, much less is known about the functional contribution of the remaining domains. Using ZAP-sensitive and ZAP-insensitive human immunodeficiency virus type I (HIV-1), we show that the catalytically inactive poly-ADP-ribose polymerase (PARP) domain of the long ZAP isoform (ZAP-L) is essential for CpG-specific viral restriction. Mutation of a crucial cysteine in the C-terminal CaaX box that mediates S-farnesylation and, to a lesser extent, the inactive catalytic site triad within the PARP domain, disrupted the activity of ZAP-L. Addition of the CaaX box to ZAP-S partly restored antiviral activity, explaining why ZAP-S lacks CpG-dependent antiviral activity despite conservation of the RNA-binding domain. Confocal microscopy confirmed the CaaX motif mediated localization of ZAP-L to vesicular structures and enhanced physical association with intracellular membranes. Importantly, the PARP domain and CaaX box together modulate the interaction between ZAP-L and its cofactors TRIM25 and KHNYN, implying that its proper subcellular localisation is required to establish an antiviral complex. The essential contribution of the PARP domain and CaaX box to ZAP-Ls CpG-directed antiviral activity was further confirmed by inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Thus, compartmentalization of ZAP-L on intracellular membranes provides an essential effector function in the ZAP-L-mediated antiviral activity. Author summaryCell-intrinsic antiviral factors, such as the zinc-finger antiviral protein (ZAP), provide a first line of defence against viral pathogens. ZAP acts by selectively binding CpG dinucleotide-rich RNAs, which are more common in some viruses than their vertebrate hosts, leading to their degradation. Here, we show that the ability to target these foreign elements is not only dependent on ZAPs N-terminal RNA-binding domain, but additional determinants in the central and C-terminal regions also regulate this process. The PARP domain and its associated CaaX box, are crucial for ZAPs CpG-specific activity and required for optimal binding to cofactors TRIM25 and KHNYN. Furthermore, a CaaX box, known to mediate post-translational modification by a hydrophobic S-farnesyl group, caused re-localization of ZAP from the cytoplasm and increased its association with intracellular membranes. This change in ZAPs distribution was essential for inhibition of both a ZAP-sensitized HIV-1 and SARS-CoV-2. Our work unveils how the determinants outside the CpG RNA-binding domain assist ZAPs antiviral activity and highlights the role of S-farnesylation and membrane association in this process.

microbiology↗

bioRxiv2019

Threat-Induced Anxiety During Goal Pursuit Disrupts Amygdala-Prefrontal Cortex Connectivity in Posttraumatic Stress Disorder

To investigate how unpredictable threat during goal pursuit impacts fronto-limbic activity and functional connectivity in posttraumatic stress disorder (PTSD), we compared military veterans with PTSD (n=25) versus trauma-exposed Control (n=25). Participants underwent functional magnetic resonance imaging (fMRI) while engaged in a computerized chase-and-capture game task that involved optimizing monetary rewards obtained from capturing virtual prey while simultaneously avoiding capture by virtual predators. The game was played under two alternating contexts - one involving exposure to unpredictable, task-irrelevant threat by randomly occurring electrical shocks, and a nonthreat control condition. Activation in and functional connectivity between the amygdala and ventromedial prefrontal cortex (vmPFC) was tested across threat and nonthreat task contexts with generalized psychophysiological interaction (gPPI) analyses. PTSD patients reported higher anxiety than controls across contexts. Better task performance represented by successfully avoiding capture by predators under threat than nonthreat contexts was associated with stronger left amygdala-vmPFC functional connectivity in controls and greater vmPFC activation in PTSD patients. PTSD symptom severity was negatively correlated with vmPFC activation in trauma-exposed controls and with right amygdala-vmPFC functional connectivity across all participants in the threat relative to nonthreat contexts. The findings showed that veterans with PTSD have disrupted amygdala-vmPFC functional connectivity and greater localized vmPFC processing under threat-modulation of goal-directed behavior, specifically related to successful task performance while avoiding loss of monetary rewards. In contrast, trauma survivors without PTSD rely on stronger threat-modulated left amygdala-vmPFC functional connectivity during goal-directed behavior, which may represent a resilience-related functional adaptation.

neuroscience↗