Biology subjects

McDonald, A.

Publications and source records attributed to McDonald, A..

16 recordsLinked to original sources

bioRxiv2026

Loss of ABCA4 from photoreceptor discs triggers changes in glial cell homeostasis

Loss-of-function mutations in the ABCA4 gene cause Stargardt disease (STGD1), the most common inherited macular dystrophy leading to progressive central vision loss. Here, we generated hiPSC-derived retinal organoids harboring a premature stop codon in exon-24 of ABCA4 to evaluate the impact of this mutation on mRNA and protein levels in a human model. Immunofluorescence analysis revealed the absence of ABCA4 protein in the mutant photoreceptor outer segment discs, while single-cell RNA sequencing detected no major transcriptional alterations in rods and cones. Unexpectedly, differential gene expression and pathway enrichment analyses of Muller glial cells (MGCs) and astrocytes highlighted disruption of neuronal development, microenvironment of glial cells, intercellular communication, and programmed cell death pathways. These findings suggest that ABCA4 might play a role in maintaining the retinal microenvironment homeostasis, and that the early transcriptomic response of MGCs and astrocytes preceding photoreceptor degeneration could contribute to Stargardt disease development. Significance StatementHuman induced pluripotent stem cell (hiPSC)-derived retinal organoids provide a powerful platform to investigate inherited retinal diseases. In this study, we generated ABCA4-mutant hiPSC lines and differentiated them into retinal organoids to model Stargardt disease. Despite complete loss of ABCA4 protein from the photoreceptor outer segment discs, rods and cones exhibited minimal transcriptional alterations. In contrast, the ABCA4 variant triggered changes in the glial cell homeostasis, suggesting that Muller glial cells and astrocytes might exhibit an early response to photoreceptor dysfunction in the absence of ABCA4. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/718110v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1d8dbf6org.highwire.dtl.DTLVardef@51239corg.highwire.dtl.DTLVardef@f8fbdborg.highwire.dtl.DTLVardef@5f0b44_HPS_FORMAT_FIGEXP M_FIG Human induced pluripotent stem cells (hiPSCs) were engineered to generate ABCA4-mutant cell lines, later differentiated into retinal organoids as a model of Stargardt disease. The organoids showed loss of ABCA4 from the outer segment discs of rod and cone photoreceptors, while the mutant Muller glial cells and astrocytes exhibited transcriptional changes in pathways involved in neuronal development, microenvironment, and programmed cell death. C_FIG

neuroscience↗

bioRxiv2025

Access to germinal center IL-4 microniches drives tissue-divergence of IgE memoryresponses

Immunoglobulin E (IgE) drives allergic disease, yet how memory B cells (MBCs) reactivate to produce IgE, and how tissue localization shapes recall responses, remains unclear. Using mouse models of airborne exposure to house dust mites and Alternaria, we found that allergen sensitization generates lymphoid- and lung-resident MBCs. Upon allergen re-exposure, these populations followed distinct differentiation trajectories: lymph node MBCs engaged a germinal center (GC)-dependent pathway that generated both IgG1 and IgE plasma cells (PCs), whereas lung MBCs followed a GC-independent route producing mainly IgG1 PCs. GC re-entry granted MBCs access to an IL-4-rich microniche formed by Tfh cells, which was essential for IgE production. Disrupting GC re-entry, IL-4 signaling, or Tfh-derived IL-4 during recall markedly reduced allergen-specific IgE titers. These findings reveal a spatially and cytokine-restricted mechanism that confines IgE memory to lymphoid organs, positioning GC IL-4 microniches as anatomical safeguards against IgE production at barrier sites frequently exposed to environmental antigens.

immunology↗

bioRxiv2025

Intraspecific Variation in Gulf Killifish (Fundulus grandis) Avoidance of Contaminants

Understanding the behavioral response of estuarine fish populations to environmental contaminants is critical for assessing the ecological consequences of disturbances. Here, we examined population-level variation in avoidance behavior to petroleum-contaminated sediments in the Gulf killifish (Fundulus grandis), a sentinel species in northern Gulf of Mexico marshes. Adult fish were collected from four geographically distinct estuaries--Terrebonne Bay, Louisiana; Mississippi Sound, Alabama; Pensacola Bay, Florida; and Cedar Key, Florida. Choice experiments tested fish preference to either uncontaminated sediments or sediments contaminated with fresh or weathered oil. Results found significant differences among populations with individuals from western Gulf sites (Louisiana and Alabama) exhibiting strong avoidance of fresh oil, while those from eastern sites (Florida) showed limited or no avoidance. No populations avoided weathered oil. These findings suggest that sensitivity to oil contamination varies regionally, potentially reflecting local exposure histories or environmental adaptation. The diminished response to weathered oil across all populations highlights a reduced ability to detect residual contamination and indicates that these fish may use more volatile compounds that precipitate or degrade faster as a cue. This study underscores the importance of incorporating behavioral and population-level variability into impact assessments and emphasizes the need for regionally tailored conservation strategies.

ecology↗

bioRxiv2025

High Density Phenotypic Map of Natural Variation for Intermediate Phenotypes Associated with Stalk Lodging Resistance in Maize

The world has food security needs that are currently not being met. Stalk lodging undermines crop productivity and incurs global yield losses of at least $6 billion in maize (Zea mays L.). Genetic architecture of stalk lodging resistance, a measure of the ability of the stalk to withstand lodging, remains poorly resolved, creating a bottleneck for genetic improvement. Identification of diverse plant traits at multiple length scales of biological organizations that contribute to stalk lodging resistance and characterization of natural variation for these traits is critical for improving stalk lodging resistance. We identified and evaluated 11 intermediate phenotypes, traits associated with stalk lodging resistance, in a maize diversity panel of 566 inbred lines evaluated over four environments. The identity of each of the 31,260 stalks evaluated in the study was preserved throughout the phenotyping pipeline which enabled capturing variation at the individual plant level. This high-density phenotypic dataset provided a foundation for statistical genomics, predictive modeling, and machine learning analyses to identify genes and genetic elements underlying stalk lodging resistance. Additionally, phenotypic characterization of multiple intermediate phenotypes on a diverse set of inbred lines provided excellent opportunities to understand the relative contribution of these traits to stalk lodging resistance. Besides improvement of maize for grain and animal feedstock, the inferences from this data will be valuable for improvement of stalk lodging resistance in other grass species.

plant biology↗

bioRxiv2025

Deconvolution to restore cryo-EM maps with anisotropic resolution

With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single particle cryo-EM is premised on randomly orientated particles embedded in a thin layer of vitreous ice to resolve high-resolution structure in all directions. In practice, preferentially distributed particle orientations and/or other imperfections in imaging and data processing deteriorate quality of obtained cryo-EM map. Here we present a deconvolution approach, named AR-Decon, that computationally improves the quality of cryo-EM maps. We tested and validated the procedure, compared its performance with that of machine learning based density modification method, and benchmarked its performance with a wide range of deposited maps. Our results show that AR-Decon is robust and is a generally applicable post-processing procedure for single particle cryo-EM.

biophysics↗

bioRxiv2024

Enzymatic epimerization of monoterpene indole alkaloids in Kratom

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-{beta}-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contain a non-canonical 3R stereocenter. Herein, we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (Kratom). We discover the presence of the iminium species, 20S-3-dehydrocorynantheidine, which led us to hypothesize that isomerization of 3S to 3R occurs by oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments implicated young leaves and stems as the sites for pathway biosynthesis, facilitating the identification of an oxidase/reductase pair that catalyzes this epimerization. This enzyme pair has broad substrate specificity, suggesting that the oxidase and reductase may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in Kratom. These enzymes allow biocatalytic access to a range of previously inaccessible pharmacologically active compounds.

biochemistry↗

bioRxiv2024

Temperature drives seagrass recovery across the Western North Atlantic

Climate-driven shifts in herbivores, temperature and nutrient runoff threaten coastal ecosystem resilience. However, our understanding of ecological resilience, particularly for foundation species, remains limited due to a rarity of field experiments that are conducted across appropriate spatial and temporal scales and that investigate multiple stressors. This study aimed to evaluate the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and how this is impacted by environmental gradients in (a)biotic factors. We assessed the resilience (i.e. recovery) of turtlegrass to a simulated disturbance (complete above- and belowground biomass removal) over a year. Contrary to temperate studies, higher temperature generally enhanced seagrass recovery. While nutrients and light availability had minimal impact, combined high levels of nutrients and herbivore grazing (meso and megaherbivore) reduced aboveground recovery. Our results suggest that the resilience of some tropical species, especially in cooler subtropical waters, may initially increase with warming.

ecology↗

bioRxiv2024

Helical Coiled Nucleosome Chromosome Architectures during Cell Cycle Progression

Recent studies showed an interphase chromosome architecture, --- a specific coiled nucleosome structure, --- derived from cryo-preserved EM tomograms, and dispersed throughout the nucleus. The images were computationally processed to fill in the missing wedges of data caused by incomplete tomographic tilts. The resulting structures increased z-resolution enabling an extension of the proposed architecture to that of mitotic chromosomes. Here we provide additional insights and details into the coiled nucleosome chromosome architectures. We build on the defined chromosomes time-dependent structures in an effort to probe their dynamics. Variants of the coiled chromosome structures, possibly further defining specific regions, are discussed. We propose, based on generalized specific uncoiling of mitotic chromosomes in telophase, large-scale re-organization of interphase chromosomes. Chromosome territories, organized as micron-sized small patches, are constructed, satisfying complex volume considerations. Finally, we unveiled the structures of replicated coiled chromosomes, still attached to centromeres, as part of chromosome architecture. Significance StatementThis study places all 46 sequenced human chromosomes, --- correctly filled with nucleosomes and in micron sized chromosome territories -- into 10micron (average sized) nuclei. The chromosome architecture used a helical nucleosome coiled structure discerned from cryo-EM tomography, as was recently published (https://doi.org/10.1073/pnas.2119101119). This chromosome architecture was further modeled to dynamic structures, structure variations and chromosome replication centromere complications. Finally, this chromosome architecture was modified to allow seamless transition through the cell cycle.

cell biology↗

bioRxiv2023

Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice

The enteric nervous system (ENS) comprises a complex network of neurons whereby a subset appears to be dopaminergic, although the characteristics, roles, and implications in disease are less understood. Most investigations relating to enteric dopamine (DA) neurons rely on immunoreactivity to tyrosine hydroxylase (TH) - a rate-limiting enzyme in the production of DA. However, TH immunoreactivity is likely to provide an incomplete picture given previous work has showed that some DA neurons contain little if any TH and its levels tend to be decreased in response to cellular stress. This study herein provides a comprehensive characterization of DA neurons in the gut using a well-accepted reporter mouse line, expressing a fluorescent protein (tdTomato) under control of the DA transporter (DAT) promoter. Our findings confirm a unique localization of DA neurons in the gut and unveil the discrete subtypes of DA neurons in this organ, which we characterized using both immunofluorescence and single-cell transcriptomics, as well as validated using in situ hybridization. We observed distinct subtypes of DAT-tdTomato neurons expressing co-transmitters and modulators across both plexuses; some of them likely co-releasing acetylcholine, while others were positive for a slew of canonical DA markers (TH, VMAT2 and GIRK2). Interestingly, we uncovered a seemingly novel population of DA neurons unique to the ENS which were ChAT/DAT-tdTomato-immunoreactive neurons and were characterised by the expression of Grp, Calcb and Sst. Given the clear heterogeneity of DAergic gut neurons, further investigation is warranted to define their functional signatures and discover any inherent vulnerabilities in disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/545271v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1e1830borg.highwire.dtl.DTLVardef@625579org.highwire.dtl.DTLVardef@1d9b59aorg.highwire.dtl.DTLVardef@219cab_HPS_FORMAT_FIGEXP M_FIG C_FIG Using a reporter mouse line, expressing a fluorescent protein under control of the dopamine transporter (DAT) promoter, discrete subtypes of dopaminergic neurons were unveiled across the ganglionated plexuses of the gut. A novel subpopulations of enteric DA neurons, expressing genes previously reported involved in dopamine signaling in the brain, exhibit a cholinergic phenotype.

neuroscience↗

bioRxiv2022

Susceptibility of Pseudomonas aeruginosa and Acinetobacter baumannii biofilms grown on denture acrylic to denture-cleaning agents and sonication

BackgroundDentures can act as reservoirs for microorganisms that cause local and systemic diseases, including opportunistic pathogens Pseudomonas aeruginosa and Acinetobacter spp, leading causes of hospital-acquired pneumonia. ObjectivesTo determine the efficacy of a brief cleaning protocol with four commonly used denture cleaning agents combined with ultra-sonic cleaning on P. aeruginosa and A. baumannii biofilms grown on denture acrylic. The effectiveness of a commercial sonicator on bacterial biofilm reduction was also evaluated. Materials and MethodsP. aeruginosa and A. baumannii 48 h biofilms were grown in artificial saliva on polymethyl methacrylate (PMMA) discs, exposed to four disinfectants, with or without ultra-sonication, for 1 min and the number of viable bacteria post-exposure to the treatment determined. P. aeruginosa biofilms were exposed for one or five mins to two disinfectants plus a commercial sonicator. ResultsUltra-sonication alone reduced total viable biofilm from 67.3% (A. baumannii) to 94.8% (P. aeruginosa). Without ultra-sonication, 0.012% sodium hypochlorite, Steradent(R) Active Plus and Ecolab(R) 0.2% chlorhexidine reduced P. aeruginosa and A. baumannii biofilms viable counts by between 99.3% and >99.99%. Sonication further reduced 99.3% kill to undetectable levels (>99.99% kill). Colgate(R)Total Pro-Gum Health Daily mouthwash reduced P. aeruginosa by 17% and A. baumannii biofilms by 2.1 log. These number were further reduced by >99.99% with sonication (p=<0.001). Domestic sonicators, such as those for cleaning jewellery at home, were effective when used in conjunction with denture cleaning agents. ConclusionRapid reduction of P. aeruginosa and A. baumannii biofilms on denture acrylic is possible with denture-cleaning agents and sonication HighlightsO_LIFour antimicrobial agents tested against P. aeruginosa and A. baumannii biofilms C_LIO_LI0.012% NaOCl and Steradent Active Plus were the most effective agents tested C_LIO_LISonication improved chlorhexidine and cetylpyridinium chloride-based agents C_LI

microbiology↗

bioRxiv2021

A Proposed Unified Mitotic Chromosome Architecture

A molecular architecture is proposed for an example mitotic chromosome, human Chromosome 10. This architecture is built on a previously described interphase chromosome structure based on Cryo-EM cellular tomography (1), thus unifying chromosome structure throughout the complete mitotic cycle. The basic organizational principle, for mitotic chromosomes, is specific coiling of the 11-nm nucleosome fiber into large scale approximately 200 nm structures (a Slinky (2, motif cited in 3) in interphase, and then further modification and subsequent additional coiling for the final structure. The final mitotic chromosome architecture accounts for the dimensional values as well as the well known cytological configurations. In addition, proof is experimentally provided, by digital PCR technology, that G1 T-cell nuclei are diploid, thus one DNA molecule per chromosome. Many nucleosome linker DNA sequences, the promotors and enhancers, are suggestive of optimal exposure on the surfaces of the large-scale coils. Significance StatementThe significance of this proposed mitotic chromosome architecture is that a specific, sequenced chromosome, human Chromosome 10, can be built into a specific architecture that accounts for the dimensional values and cytological descriptions, a first time result. Since this molecular architecture is an extension of the interphase chromosome structure, a coiling of the 11-nm nucleosome fiber with further coiling, a unifying molecular structure motif is present throughout the entire mitotic cycle, interphase through mitosis.

cell biology↗

bioRxiv2021

A Proposed Unified Interphase Nucleus Chromosome Structure: Preliminary Preponderance of Evidence

Cellular cryo-electron tomography (CET) of the cell nucleus using Scanning Transmission Electron Microscopy (STEM) and the use of deconvolution (DC) processing technology has highlighted a large-scale, 100-300 nm interphase chromosome structure (LSS), that is present throughout the nucleus. This chromosome structure appears to coil the nucleosome 11-nm fiber into a defined hollow structure, analogous to a Slinky (S) (1, motif used in 2) helical spring. This S architecture can be used to build chromosome territories, extended to polytene chromosome structure, as well as to the structure of Lampbrush chromosomes. Significance StatementCryo-preservation of the nuclear interior allows a large scale interphase chromosome structure--present throughout the nucleus--to be seen for the first time. This structure can be proposed to be a defined coiled entity, a Slinky. This structure can be further used to explain polytene chromosome structure, an unknown chromosome architecture as well as for lampbrush chromosomes. In addition, this new structure can be further organized as chromosome territories, using all 46 human interphase chromosomes as an example, easily into a 10 micron diameter nucleus. Thus, interphase chromosomes can be unified into a flexible defined structure.

cell biology↗

bioRxiv2021

Density Fluctuations Yield Distinct Growth and Fitness Effects in Single Bacteria

Single-cells grow by increasing their biomass and size. Here, we report that while mass and size accumulation rates of single Escherichia coli cells are exponential, their density fluctuates during growth. As such, the rates of mass and size accumulation of a single-cell are generally not the same, but rather cells differentiate into increasing one rate with respect to the other. This differentiation yields a previously unknown density homeostasis mechanism, which we support mathematically. Further, growth differentiation challenges ongoing efforts to predict single-cell reproduction rates (or fitness-levels), through the accumulation rates of size or mass. In contrast, we observe that density fluctuations can predict fitness, with only high fitness individuals existing in the high density fluctuation regime. We detail our imaging approach and the invisible microfluidic arrays that critically enabled increased precision and throughput. Biochemical production, infections, and natural communities start from few, growing, cells, thus, underscoring the significance of density-fluctuations when considering non-genetic variability.

biophysics↗

bioRxiv2021

Sugar feeding enhances gut immunity and protects against arboviral infection in the mosquito vector Aedes aegypti

As mosquito females require a blood meal to reproduce, they can act as vectors of numerous pathogens, such as arboviruses (e.g. Zika, dengue and chikungunya viruses), which constitute a substantial worldwide public health burden. In addition to blood meals, mosquito females can also take sugar meals to get carbohydrates for their energy reserves. It is now recognised that diet is a key regulator of health and disease outcome through interactions with the immune system. However, it has been mostly studied in humans and model organisms. So far, the impact of sugar feeding on mosquito immunity and in turn, how this could affect vector competence for arboviruses has not been analysed. Here, we show that sugar feeding increases and maintains antiviral immunity in the digestive tract of the main arbovirus vector Aedes aegypti. Our data demonstrate that the gut microbiota does not mediate the sugar-induced immunity but partly inhibits it. Importantly, sugar intake prior to an arbovirus-infected blood meal further protects females against infection with arboviruses from different families, highlighting a broad antiviral action of sugar. Sugar feeding blocks arbovirus initial infection and dissemination from the gut, lowers infection prevalence and intensity, thereby decreasing transmission potential of female mosquitoes. Overall, our findings uncover a crucial role of sugar feeding in mosquito antiviral immunity and vector competence for arboviruses. Since Ae. aegypti almost exclusively feed on blood in some natural settings, our findings suggest that this could increase the spread of mosquito-borne arboviral diseases.

physiology↗

bioRxiv2020

Determinants of Real-Time fMRI Neurofeedback Performance and Improvement: a Machine Learning Mega-Analysis

Real-time fMRI neurofeedback is an increasingly popular neuroimaging technique that allows an individual to gain control over his/her own brain signals, which can lead to improvements in behavior in healthy participants as well as to improvements of clinical symptoms in patient populations. However, a considerably large ratio of participants undergoing neurofeedback training do not learn to control their own brain signals and, consequently, do not benefit from neurofeedback interventions, which limits clinical efficacy of neurofeedback interventions. As neurofeedback success varies between studies and participants, it is important to identify factors that might influence neurofeedback success. Here, for the first time, we employed a big data machine learning approach to investigate the influence of 20 different design-specific (e.g. activity vs. connectivity feedback), region of interest-specific (e.g. cortical vs. subcortical) and subject-specific factors (e.g. age) on neurofeedback performance and improvement in 608 participants from 28 independent experiments. With a classification accuracy of 60% (considerably different from chance level), we identified two factors that significantly influenced neurofeedback performance: Both the inclusion of a pre-training no-feedback run before neurofeedback training and neurofeedback training of patients as compared to healthy participants were associated with better neurofeedback performance. The positive effect of pre-training no-feedback runs on neurofeedback performance might be due to the familiarization of participants with the neurofeedback setup and the mental imagery task before neurofeedback training runs. Better performance of patients as compared to healthy participants might be driven by higher motivation of patients, higher ranges for the regulation of dysfunctional brain signals, or a more extensive piloting of clinical experimental paradigms. Due to the large heterogeneity of our dataset, these findings likely generalize across neurofeedback studies, thus providing guidance for designing more efficient neurofeedback studies specifically for improving clinical neurofeedback-based interventions. To facilitate the development of data-driven recommendations for specific design details and subpopulations the field would benefit from stronger engagement in Open Science and data sharing.

neuroscience↗

bioRxiv2020

Can we predict real-time fMRI neurofeedback learning success from pre-training brain activity?

Neurofeedback training has been shown to influence behavior in healthy participants as well as to alleviate clinical symptoms in neurological, psychosomatic, and psychiatric patient populations. However, many real-time fMRI neurofeedback studies report large interindividual differences in learning success. The factors that cause this vast variability between participants remain unknown and their identification could enhance treatment success. Thus, here we employed a meta-analytic approach including data from 24 different neurofeedback studies with a total of 401 participants, including 140 patients, to determine whether levels of activity in target brain regions during pre-training functional localizer or no-feedback runs (i.e., self-regulation in the absence of neurofeedback) could predict neurofeedback learning success. We observed a slightly positive correlation between pre-training activity levels during a functional localizer run and neurofeedback learning success, but we were not able to identify common brain-based success predictors across our diverse cohort of studies. Therefore, advances need to be made in finding robust models and measures of general neurofeedback learning, and in increasing the current study database to allow for investigating further factors that might influence neurofeedback learning.

neuroscience↗