Biology subjects

Olson, K.

Publications and source records attributed to Olson, K..

13 recordsLinked to original sources

bioRxiv2025

Identification of a putative RBOHD-FERONIA-CRK10-PIP2;6 plasma membrane complex that interacts with phyB to regulate ROS production in Arabidopsis thaliana

O_LIReactive oxygen species (ROS) regulate plant growth, development, and responses to the environment. ROS production by the RESPIRATORY BURST OXIDASE PROTEIN D (RBOHD) protein was recently shown to be regulated by PHYTOCHROME B (phyB), and phyB was found to be phosphorylated by FERONIA, highlighting the possibility that these three proteins interact to regulate ROS levels during stress. C_LIO_LIImmunoprecipitation and proximity labelling, followed by split-luciferase and functional validation assays, were used to study the interactions between FERONIA, phyB, and RBOHD during excess light (EL) stress in Arabidopsis thaliana. C_LIO_LIWe reveal that phyB and FERONIA interact with RBOHD, that phosphorylation of phyB by FERONIA, as well as the kinase activity of FERONIA, are required for RBOHD-driven ROS production in response to EL stress, and that CYSTEINE-RICH RECEPTOR LIKE KINASE 10 (CRK10) and PLASMA MEMBRANE INTRINSIC PROTEIN 2;6 (PIP2;6) interact with RBOHD and phyB and are also required for EL-driven RBOHD ROS production. C_LIO_LIOur findings uncover the existence of a putative plasma membrane complex between FERONIA, RBOHD, CRK10, and PIP2;6 that interacts with phyB to regulate ROS production in Arabidopsis in response to stress. This complex could play a canonical role in the integration and regulation of multiple signaling pathways in plants. C_LI Plain Language SummaryWe identified a complex between several different proteins at the plasma membrane that interacts with the light and temperature receptor protein phytochrome B to regulate reactive oxygen species formation during stress in plants. This complex could be involved in the regulation and integration of multiple abiotic and biotic signals in plants. tenten

plant biology↗

bioRxiv2025

Proximity proteomics reveals the molecular architecture of phytochrome B photobodies in Arabidopsis thaliana

The red/far-red light photoreceptor phytochrome B (phyB) forms light-induced subnuclear condensates, termed photobodies, that coordinate plant responses to light and temperature. Despite their central role in environmental signaling, the molecular composition of phyB photobodies during their early formation has remained unknown. Here, we established an in planta proximity labeling approach using miniTurbo-based biotinylation in Arabidopsis thaliana to capture proteins associated with phyB photobodies during early de-etiolation. Mass spectrometry identified 42 high-confidence proximal proteins, including 11 known core components and 31 previously unrecognized photobody-associated proteins. Among these, the co-chaperone HOP1 forms light-dependent nuclear condensates that partially co-localize with phyB photobodies. HOP1 condensates are smaller in the wild-type background than in phyB-overexpressing seedlings, and HOP1 overexpression enhanced cotyledon expansion under red light. These findings suggest that HOP1 contributes to photomorphogenesis by stabilizing phyB photobodies and sustaining active phyB signaling. Together, our results reveal that nascent large phyB photobodies function as dynamic hubs integrating chaperone-mediated protein quality control with transcriptional regulation, providing the first in planta proteomic framework for understanding photobody assembly and signaling in plants.

plant biology↗

bioRxiv2024

50 years of antibody numbering schemes: a statistical and structural evaluation reveals key differences and limitations

The complementarity determining region (CDR) of antibodies represents the most diverse region both in terms of sequence and structural characteristics, playing the most critical role in antibody recognition and binding for immune responses. Over the past decades, several numbering schemes have been introduced to define CDRs based on sequence. However, the existence of diverse numbering schemes has led to potential confusion, and a comprehensive evaluation of these schemes is lacking. We employ statistical analyses to quantify the diversity of CDRs compared to the framework regions. Comparative analyses across different numbering schemes demonstrates notable variations in CDR definitions. The Kabat and AbM numbering schemes tend to incorporate more conserved residues into their CDR definitions, whereas CDRs defined by the Chothia and IMGT numbering schemes display greater diversity, sometimes missing certain loop residues. Notably, we identify a critical residue, L29, within the kappa light chain CDR1, which appears to act as a pivotal structural point within the loop. In contrast, most numbering schemes designate the topological equivalent point in the lambda light chain as L30, suggesting the need for further refinement in the current numbering schemes. These findings shed light on regional sequence and structural conservation within antibody sequence databases while also highlighting discrepancies stemming from different numbering schemes. These insights yield valuable guidelines for the precise delineation of antibody CDRs and the strategic design of antibody repertoires, with practical implications in developing innovative antibody-based therapeutics and diagnostics. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/602590v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@2240a7org.highwire.dtl.DTLVardef@c2981dorg.highwire.dtl.DTLVardef@190984eorg.highwire.dtl.DTLVardef@1ff5e00_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIAmino acid distribution analysis conducted on 124,317 sequences archived in the abYsis database showed lower conservation among CDR residues, as defined by Kabat numbering, compared to the framework region. C_LIO_LIBoth LCDR3 and HCDR3 exhibited particularly high levels of diversity compared to the other four CDR loops, highlighting additional functional roles of the CDR3 loops relative to the others. C_LIO_LITwo distinct residues, L29 and H30, displayed highly conserved hydrophobic side chain characteristics and played unique conformational roles within the CDR1 loop, contributing to the formation of an M-shaped structure. This residue divides the C-terminus CDR1 loop, which was observed to be less conserved and have greater length diversity, and the N-terminus CRD1 loop. C_LIO_LIThe Kabat numbering scheme appears to overestimate the LCDR2 and HCDR2 loops and underestimate HCDR1, only encompassing the C-terminal loop of the M-shaped CDR1 loop. C_LIO_LIStructural analysis revealed that a residue within LCDR1 was numbered differently in the two subtypes (kappa and lambda) of the variable light domain. This discrepancy suggests the need for further refinement in the current major numbering schemes. C_LI

molecular biology↗

bioRxiv2024

Cholinergic interneurons in the nucleus accumbens are a site of cellular convergence for corticotropin release factor and estrogen regulation

Cholinergic interneurons (ChIs) act as master regulators of striatal output, finely tuning neurotransmission to control motivated behaviors. ChIs are a cellular target of many peptide and hormonal neuromodulators, including corticotropin releasing factor, opioids, insulin and leptin, which can influence an animals behavior by signaling stress, pleasure, pain and nutritional status. However, little is known about how sex hormones via estrogen receptors influence the function of these other neuromodulators. Here, we performed in situ hybridization on mouse striatal tissue to characterize the effect of sex and sex hormones on choline acetyltransferase (Chat), estrogen receptor alpha (Esr1), and corticotropin releasing factor type 1 receptor (Crhr1) expression. Although we did not detect sex differences in ChAT protein levels in the striatum, we found that female mice have more Chat mRNA-expressing neurons than males. At the population level, we observed a sexually dimorphic distribution of Esr1- and Crhr1-expressing ChIs in the ventral striatum that demonstrates an antagonistic correlational relationship, which is abolished by ovariectomy. Only in the NAc did we find a significant population of ChIs that co-express Crhr1 and Esr1. At the cellular level, Crhr1 and Esr1 transcript levels were negatively correlated only during estrus, indicating that changes in sex hormones levels can modulate the interaction between Crhr1 and Esr1 mRNA levels. Together, these data provide evidence for the unique expression and interaction of Esr1 and Crhr1 in ventral striatal ChIs, warranting further investigation into how these transcriptomic patterns might underlie important functions for ChIs at the intersection of stress and reproductive behaviors.

neuroscience↗

bioRxiv2023

Nomadic ungulate movements under threat: Declining mobility of Mongolian gazelles in the Eastern Steppe.

Increasing habitat fragmentation and disturbance threaten long distance movements of ungulates. While the effects of impermeable barriers on ungulate migrations have been well researched, quantitative evidence for gradual and long-term changes of mobility in response to anthropogenic disturbance remains relatively rare. We investigated changes in movement behavior of Mongolian gazelle Procapra gutturosa, a nomadic ungulate species native to the Mongolian steppe. Using GPS tracking data collected from 62 gazelle individuals between 2007 and 2021, we quantified 16-day displacement distances for each individual as a metric for long-distance movements. We used generalized linear mixed models, generalized additive models and additive quantile mixed models to assess how anthropogenic and environmental factors affected gazelle movement behavior. Long distance 16-day movements decreased significantly by up to 36 %, from 142 km in 2007 to 92 km in 2021. Changes in gazelle mobility were affected by the increasing number of vehicles in Mongolia, but could not be explained by concurrent changes in other environmental factors like temperature, precipitation or vegetation greenness that often drive ungulate migration behavior. Moreover, we found that gazelle movement decreased close to roads, and that gazelles stayed further away from roads during the snow-free season, when vehicular traffic likely is most intense. Conserving landscape permeability is essential for maintaining populations of highly mobile species. Our study provides evidence for a gradual decline in gazelle mobility over fifteen years as a response to increasing anthropogenic impact. To date, the transportation infrastructure permeating the Eastern Steppe does not pose physical barriers, yet our findings suggest that increasing traffic volume may create semipermeable barriers to gazelle movement. As human activity is increasing throughout the Eastern Steppe, interactions between ungulates and vehicle traffic need to be closely monitored in order to identify, localize, and mitigate semipermeable barrier effects before landscape permeability is severely altered.

ecology↗

bioRxiv2022

Clarifying space use concepts in ecology: range vs. occurrence distributions

Quantifying animal movements is necessary for answering a wide array of research questions in ecology and conservation biology. Consequently, ecologists have made considerable efforts to identify the best way to estimate an animals home range, and many methods of estimating home ranges have arisen over the past half century. Most of these methods fall into two distinct categories of estimators that have only recently been described in statistical detail: those that measure range distributions (methods such as Kernel Density Estimation that quantify the long-run behavior of a movement process that features restricted space use) and those that measure occurrence distributions (methods such as Brownian Bridge Movement Models and the Correlated Random Walk Library that quantify uncertainty in an animal movement path during a specific period of observation). In this paper, we use theory, simulations, and empirical analysis to demonstrate the importance of applying these two classes of space use estimators appropriately and distinctly. Conflating range and occurrence distributions can have serious consequences for ecological inference and conservation practice. For example, in most situations, home-range estimates quantified using occurrence estimators are too small, and this problem is exacerbated by ongoing improvements in tracking technology that enable more frequent and more accurate data on animal movements. We encourage researchers to use range estimators to estimate the area of home ranges and occurrence estimators to answer other questions in movement ecology, such as when and where an animal crosses a linear feature, visits a location of interest, or interacts with other animals. Open Research StatementTracking data on Aepyceros melampus, Beatragus hunteri, Bycanistes bucinator, Cerdocyon thous, Eulemur rufifrons, Glyptemys insculpta, Gyps coprotheres, Madoqua guentheri, Ovis canadensis, Propithecus verreauxi, Sus scrofa, and Ursus arctos are publicly archived in the Dryad repository (Noonan et al. 2018; https://doi.org/10.5061/dryad.v5051j2), as are data from Procapra gutturosa (Fleming et al. 2014a; https://doi.org/10.5061/dryad.45157). Data on Panthera onca were taken from (Morato et al. 2018). Additional data are publicly archived in the Movebank repository under the following identifiers: Canis latrans, 8159699; Canis lupus, 8159399; Chrysocyon brachyurus, 18156143; Felis silvestris, 40386102; Gyps africanus, 2919708; Lepus europaeus, 25727477; Martes pennanti, 2964494; Panthera leo, 220229; Papio cynocephalus, 222027; Syncerus caffer, 1764627; Tapirus terrestris, 443607536; Torgos tracheliotus, 2919708; and Ursus americanus, 8170674.

ecology↗

bioRxiv2022

Identification of Salivary Gland Escape Barriers to Western Equine Encephalitis Virus in the Natural Vector, Culex tarsalis

Herein we describe a previously uninvestigated salivary gland escape barrier (SEB) in Culex tarsalis mosquitoes infected with two different strains of Western equine encephalitis virus (WEEV). The WEEV strains were originally isolated either from mosquitoes (IMP181) or a human patient (McMillan). Both IMP181 and McMillan viruses were fully able to infect the salivary glands of Culex tarsalis after intrathoracic injection as determined by expression of mCherry fluorescent protein. IMP181, however, was better adapted to transmission as measured by virus titer in saliva as well as transmission rates in infected mosquitoes. We used chimeric recombinant WEEV strains to show that inclusion of IMP181-derived structural genes partially circumvents the SEB. Author StatementDuring the first half of the previous century, WEEV was responsible for large outbreaks throughout the northern United States and Canada that caused severe disease in horses and people. Over the past 60 years, cases of WEEV have mysteriously faded and the pathogen is rarely encountered in the clinic today. Salivary gland escape barriers (SEB) are a relatively neglected field of study in arbovirology, and this study provides a valuable contribution to the field by describing a SEB found in otherwise vector competent Culex tarsalis mosquitoes. Although midgut barriers are well studied, less is known about barriers to transmission in the salivary glands. Although salivary gland infection occurs at a high rate following direct injection of virus into the hemocoel, we noticed that only [~]20-30% of infected mosquitoes transmit detectable infectious virus in their saliva. Additionally, although the more pathogenic patient-derived McMillan strain of WEEV infected salivary glands at a similar rate, its transmission was more severely restricted than the mosquito-derived but less pathogenic Imperial 181 strain. We were able to trace determinants of viral transmission to the 6K/E1 region of the gene encoding the viral structural polyprotein. WEEV is a valuable research model for the closely related Eastern equine encephalitis virus and Venezuelan equine encephalitis virus we believe that our findings are applicable to other members of Togaviridae.

microbiology↗

bioRxiv2021

Defining the Immune Responses for SARS-CoV-2-Human Macrophage Interactions

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end organ malfunctions. All follow an abortive viral infection. To elucidate SARS-CoV-2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the SARS-CoV-2 receptor, the angiotensin-converting enzyme 2, paralleled monocyte-macrophage differentiation it failed to affect productive viral infection. In contrast, simple macrophage viral exposure led to robust pro-inflammatory cytokine and chemokine expression but attenuated type I interferon (IFN) activity. Both paralleled dysregulation of innate immune signaling pathways specifically those linked to IFN. We conclude that the SARS-CoV-2-infected host mounts a robust innate immune response characterized by a pro-inflammatory storm heralding consequent end-organ tissue damage.

immunology↗

bioRxiv2021

Differences in IgG antibody responses following BNT162b2 and mRNA-1273 Vaccines

Studies examining antibody responses by vaccine brand are lacking and may be informative for optimizing vaccine selection, dosage, and regimens. The purpose of this study is to assess IgG antibody responses following immunization with BNT162b2 (30 g S protein) and mRNA-1273 (100 g S protein) vaccines. A cohort of clinicians at a non-for-profit organization is being assessed clinically and serologically following immunization with BNT162b2 or mRNA-1273. IgG responses were measured at the Remington Laboratory by an IgG against the SARS-CoV-2 spike protein-receptor binding domain. Mixed-effect linear (MEL) regression modeling was used to examine whether the SARS-CoV-2 IgG level differed by vaccine brand, dosage, or days since vaccination. Among 532 SARS-CoV-2 seronegative participants, 530 (99.6%) seroconverted with either vaccine. After adjustments for age and gender MEL regression modeling revealed that the average IgG increased after the second dose compared to the first dose (p<0.001). Overall, titers peaked at week six for both vaccines. Titers were significantly higher for mRNA-1273 vaccine on days 14-20 (p < 0.05), 42-48 (p < 0.01), 70-76 (p < 0.05), 77-83 (p < 0.05), and higher for BNT162b2 vaccine on days 28-34 (p < 0.001). In two participants taking immunosuppressive drugs SARS-CoV-2 IgG remained negative. mRNA-1273 elicited both earlier and higher IgG antibody responses than BNT162b2, possibly due to the higher S-protein delivery. Prospective clinical and serological follow-up of defined cohorts such as this may prove useful in determining antibody protection and whether differences in antibody kinetics between the vaccines have manufacturing relevance and clinical significance.

immunology↗

bioRxiv2020

High-Accuracy Multiplexed SARS-CoV-2 Antibody Assay with Avidity and Saliva Capability on a Nano-Plasmonic Platform

The outbreak and rapid spread of SARS-CoV-2 virus has led to a dire global pandemic with millions of people infected and ~ 400,000 deaths thus far. Highly accurate detection of antibodies for COVID-19 is an indispensable part of the effort to combat the pandemic1,2. Here we developed two-plex antibody detection against SARS-CoV-2 spike proteins3 (the S1 subunit and receptor binding domain RBD) in human serum and saliva on a near-infrared nano-plasmonic gold (pGOLD) platform4-8. By testing nearly 600 serum samples, pGOLD COVID-19 assay achieved ~ 99.78 % specificity for detecting both IgG and IgM with 100 % sensitivity in sera collected > 14 days post disease symptom onset, with zero cross-reactivity to other diseases. Two-plex correlation analysis revealed higher binding of serum IgM to RBD than to S1. IgG antibody avidity toward multiple antigens were measured, shedding light on antibody maturation in COVID-19 patients and affording a powerful tool for differentiating recent from remote infections and identifying re-infection by SARS-CoV-2. Just as important, due to high analytical sensitivity, the pGOLD COVID-19 assay detected minute amounts of antibodies in human saliva, offering the first non-invasive detection of SARS-CoV-2 antibodies.

biochemistry↗

bioRxiv2018

Structural and Practical Identifiability of Dual-input Kinetic Modeling in Dynamic PET of Liver Inflammation

Dynamic 18F-FDG PET with tracer kinetic modeling has the potential to noninvasively evaluate human liver inflammation using the FDG blood-to-tissue transport rate K1. Accurate kinetic modeling of dynamic liver PET data and K1 quantification requires the knowledge of dual-blood input function from the hepatic artery and portal vein. While the arterial input function can be derived from the aortic region on dynamic PET images, it is difficult to extract the portal vein input function accurately from PET. The optimization-derived dual-input kinetic modeling approach has been proposed to overcome this problem by jointly estimating the portal vein input function and FDG tracer kinetics from time activity curve fitting. In this paper, we further characterize the model properties by analyzing the structural identifiability of the model parameters using the Laplace transform and practical identifiability using Monte Carlo simulation based on fourteen patient datasets. The theoretical analysis has indicated that all the kinetic parameters of the dual-input kinetic model are structurally identifiable, though subject to local solutions. The Monte Carlo simulation results have shown that FDG K1 can be estimated reliably in the whole-liver region of interest with reasonable bias, standard deviation, and high correlation between estimated and original values, indicating of practical identifiability of K1. The result has also demonstrated the correlation between K1 and histological liver inflammation scores is reliable. FDG K1 quantification by the optimization-derived dual-input kinetic model is promising for assessing liver inflammation.

bioengineering↗

bioRxiv2017

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency, and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. Furthermore, there are concerns that antibiotic feed additives may expand the antibiotic resistome of feedlot cattle by enriching antimicrobial resistance genes in pathogenic and nonpathogenic bacteria in the gut microbiota. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and untreated animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level however treated cattle had reduced the abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachanospira in the gut of treated steers was reduced. This may impact the ability of these animals to exclude pathogens from the gut. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

microbiology↗

bioRxiv2017

Ubiquitin and ATP-dependent unfoldase activity of P97/VCP·NPLOC4·UFD1L1 is enhanced by a mutation that causes multisystem proteinopathy

p97 is a segregase that plays a key role in numerous ubiquitin-dependent pathways, such as ER-associated degradation (ERAD). It has been hypothesized that p97 extracts proteins from membranes or macromolecular complexes to enable their proteasomal degradation; however, the complex nature of p97 substrates has made it difficult to directly observe the fundamental basis for this activity. To address this issue, we developed a soluble p97 substrate--Ub-GFP modified with K48-linked ubiquitin chains--for in vitro p97 activity assays. We demonstrate for the first time that wild type p97 can unfold proteins and that this activity is dependent on the p97 adaptor NPLOC4-UFD1L, ATP hydrolysis, and substrate ubiquitination, with branched chains providing maximal stimulation. Furthermore, we show that a p97 mutant that causes inclusion body myopathy, Pagets Disease of bone, and frontotemporal dementia (IBMPFD) in humans unfolds substrate faster, suggesting that excess activity may underlie pathogenesis. This work overcomes a significant barrier in the study of p97 and will allow the future dissection of p97 mechanism at a level of detail previously unattainable.

biochemistry↗