Biology subjects

Kirkland, A.

Publications and source records attributed to Kirkland, A..

8 recordsLinked to original sources

bioRxiv2026

Single nucleus RNA sequencing and spatial transcriptomics reveal unique functionalities of gray matter versus white matter oligodendrocytes in aging and Alzheimer's Disease

Oligodendrocyte (OL) dysfunction and white-matter (WM) vulnerability are increasingly recognized as important aspects of aging and Alzheimer's Disease (AD), yet human WM-focused, cellular-resolution transcriptomic data remain limited. Here, we profiled prefrontal WM from 48 brain donors spanning young adulthood and late-life with low versus high AD Neuropathologic Change (ADNC) using single-nucleus RNA sequencing followed by spatial transcriptomics (CosMx) in a subset of matched donors. We integrated aged WM OLs with a reference dorsolateral prefrontal cortex grey-matter (GM) OL dataset (SEA-AD) to define region- and pathology-associated OL programs. Across modalities, GM OLs exhibited a robust synapse/neurotransmitter-associated transcriptional signature relative to WM OLs, whereas this program was reduced with aging and attenuated in high ADNC GM. In contrast, WM OLs showed stronger immune-associated programs with aging and further enhancement in high ADNC, including cytokine/chemokine signaling and antigen presentation-related pathways. High ADNC WM OLs also displayed amplified proteostasis and stress-adaptation signatures, including selective upregulation of chaperone/heat shock genes and ferritin subunits, consistent with increased protein-folding demand and altered iron handling. To resolve OL state organization beyond static differential expression, we annotated OL sub-states using marker panels and inferred pseudotime-guided directional state-to-state flows within each tissue/condition stratum. This analysis identified a conserved newly formed differentiating (NFOL)/differentiating [->] lipid remodeling (APOE/ABCA1/LPL+) [->] Stress/ISR-reactive architecture, with a pronounced expansion of the Stress/ISR-reactive compartment and altered transition-associated pathway enrichment in high ADNC WM. Together, these data define WM-specific OL programs linked to aging and ADNC and nominate a stress/immune-enriched OL state landscape consistent with a putative senescence-like phenotype in diseased WM.

neuroscience↗

bioRxiv2026

Digital Atlases to Unlock the Potential of Brain Biorepository Tissues for Interdisciplinary Research

Human brain tissue preserved in biorepositories is foundational for the structural, cellular, and biomolecular research necessary for a mechanistic understanding of neurological diseases. Realizing the research potential of these valuable resources requires well-characterized research-relevant tissue that can be efficiently identified by investigators and incorporated into the conceptual and computational frameworks of interdisciplinary research. Several large-scale efforts to improve research reliability and reproducibility have sought to characterize and annotate the processes by which these samples are collected, yet limited progress has been made on standardizing spatial information for these samples. Biorepositories systematically collect brain tissue according to a brain sampling protocol (BSP) that differs between institutions, yet explicit spatial information regarding the samples may not be documented in standard operating procedures (SOPs). The amount of anatomical location details available to investigators are inconsistent across biorepositories and typically lack sufficient anatomical precision to ensure correspondence with samples from other biorepositories or research relevant brain regions specified by neuroimaging, functional, or disease-susceptibility criteria. Here, we introduce a pipeline for developing a Spatial Atlas for Mapping Protocol Locations of Ex vivo Samples (SAMPLES), which uses a neuroimaging framework to create a 3D representation of a BSP through a metrically precise digital instantiation of the procedures for brain extraction, segmentation, slicing, and sampling on a modern digital brain template. SAMPLES incorporates modern neuroinformatics conventions to create explicit 3D labels of BSP-defined samples that can be interactively visualized with freely available neuroimaging software. We illustrate the pipeline by developing an atlas for the protocol from the University of Washington BioRepository and Integrated Neuropathology laboratory (UW BRaIN SAMPLES). By providing an explicit, computable reference, SAMPLES atlases can support the efficient identification, referencing, and utilization of postmortem samples for interdisciplinary research. These capabilities enable biorepository workflows, data harmonization across biorepositories, and integration with antemortem neuroimaging.

neuroscience↗

bioRxiv2026

Impacts of vessel noise on red drum (Sciaenops ocellatus) spawning choruses in Saint Andrew Bay, Florida, U.S.A.

Noise pollution is an increasing threat to soniferous fishes, however, research on noise pollution impacts is limited to few species and rarely studied in situ. Red Drum (Sciaenops ocellatus) is an estuarine, fishery species that choruses during spawning. We tested predictions of the hypothesis that Red Drum alter sound production in response to vessel noise. We used passive acoustic monitoring in 2021 and 2022 at an estuarine inlet and Generalized Least Squares (GLS) models to assess vessel sound exposure levels over time (SEL) and other abiotic parameters on Red Drum chorus SELs. GLS models of daily crepuscular choruses indicated a >5% reduction in proportion to crepuscular vessel noise in 2021. GLS models testing influence of abiotic variables and prior vessel noise, predicted reduced chorus SELs proportional to prior noise SEL: ca. 5% and 3% of vessel SEL in 2021 and 2022, respectively. In some instances, SEL during vessel noise was lower than fish chorus SEL immediately prior, indicating instances when fish reduced chorus amplitude during vessel noise or fled the immediate area. In cases when SEL of vessel noise periods exceeded fish calling SEL immediately prior, it is not known if fish modulated calling amplitude because the portion of combined vessel noise and fish chorus amplitude from vessels is unknown. In peak spawning season (September-October) vessel noise was frequent, detected in >31% of recordings in both years and up to 100% of recordings on some dates. Observations of disrupted choruses and high vessel noise prevalence suggest spawning behavior may be impacted by abundant vessel noise.

animal behavior and cognition↗

bioRxiv2025

Age- and alcohol-related differences in adolescent neurometabolite levels

Adolescence is a critical period for neurometabolite maturation as well as the onset of alcohol use, yet remains underexplored despite its significance for long-term neurodevelopmental outcomes. We used 3T proton magnetic resonance spectroscopy (MRS) to examine age- and alcohol-related associations with six neurometabolites in dorsal anterior cingulate cortex (dACC) that are involved in key neural functions: glutamate + glutamine (Glx), GABA plus macromolecules (GABA+), total N-acetylaspartate (tNAA), total choline (tCho), total creatine (tCr), and myo-inositol (mI). Participants were 84 adolescents (ages 17 - 22; 67% female) who completed MRS scans and self-reported past-60-day alcohol use via a modified Timeline Followback survey. Alcohol use variables included total drinking days, total binge drinking days, total number of drinks, and drinks per drinking day. Older adolescents had higher levels of GABA+, tNAA, tCho, and mI, and lower levels of Glx and Glx/GABA+; tCr was not associated with age. More alcohol use - specifically more drinking days, binge drinking days, and number of drinks - was associated with lower tNAA levels. Findings suggest age-related variation in dACC neurometabolites, which potentially reflect ongoing neuronal maturation, myelination, and shifts in excitatory and inhibitory neurotransmission. Lower tNAA among heavier drinkers may reflect associations between alcohol exposure and neuronal damage. Broader neurometabolic effects may emerge only with heavier or prolonged alcohol use.

neuroscience↗

bioRxiv2025

Investigating Cobalt Corrosion Mechanisms in a Phenazine Producing Bacterium

Microbially-induced corrosion (MIC) has been well-studied in the context of damage to iron-bearing infrastructure, where microbes can solubilize solid elemental iron using redox-active metabolites such as phenazines. Whether such pathways can solubilize economically-critical cobalt remains poorly understood. We hypothesized that secondary metabolites produced by the model bacterium Pseudomonas chlororaphis subspecies aureofaciens associated with MIC of iron could corrode cobalt by oxidation (i.e., phenazines) or by acting as a ligand (i.e., cyanide). One-week incubations using live cells supplied with Co(0) wires led to 20-30% cobalt mass losses and [~]2200 {micro}M Co(2+) recovered in solution, which was at least 3-fold higher than filtered cultures and sterile medium controls. Removing the capacity for cells to produce phenazines and cyanide showed similar corrosion compared to wild type cells and phenazine standards did not corrode cobalt, ruling these metabolites out as contributors to MIC. Further experiments testing whether metabolite mixtures devoid of phenazines could corrode Co(0) in the presence and absence of oxygen confirmed that atmospheric oxygen initiates Co(0) oxidation, and that unidentified cell-derived metabolites drive MIC forward by keeping Co(2+) from precipitating as oxides that form a passivation layer on the wire surface. This revised mechanistic explanation underscores the importance of considering how abiotic redox cycling and cellular metabolites that solubilize metals interact in the MIC of non-ferrous metals. Identifying the biosynthetic pathways involved in solubilizing cobalt will be key to reframing MIC as more than an environmental concern and optimizing sustainable cobalt recovery strategies for solid waste that rely on naturally-occurring microbial metabolites. ImportanceCharacterizing microbially-induced corrosion mechanisms for cobalt is important for predicting the fate of critical metals in the environment and optimizing sustainable strategies for cobalt reclamation from electronic waste. This study uses the model bacterium Pseudomonas chlororaphis subspecies aureofaciens to test if redox-active phenazines and the metal-binding metabolite cyanide can corrode elemental cobalt. We repeatedly observed that live cells corroded cobalt, but that corrosion did not rely on phenazines or cyanide. Instead, our results show that oxygen oxidized elemental cobalt and unidentified metabolites keep cobalt ions in solution to limit cobalt oxide precipitation and drive the corrosion reaction forward. Our study reinforces the need to consider connections between abiotic and biotic reactions in the corrosion of metals other than iron. Understanding these mechanisms is critical to reframing microbial corrosion as a sustainable approach for metal recovery and our study makes the case that it is possible for the critical metal cobalt.

microbiology↗

bioRxiv2024

Multi-species genome-wide CRISPR screens identify GPX4 as a conserved suppressor of cold-induced cell death

Cells must adapt to environmental changes to maintain homeostasis. One of the most striking environmental adaptations is entry into hibernation during which core body temperature can decrease from 37C to as low at 4C. How mammalian cells, which evolved to optimally function within a narrow range of temperatures, adapt to this profound decrease in temperature remains poorly understood. In this study, we conducted the first genome-scale CRISPR-Cas9 screen in cells derived from Syrian hamster, a facultative hibernator, as well as human cells to investigate the genetic basis of cold tolerance in a hibernator and a non-hibernator in an unbiased manner. Both screens independently revealed glutathione peroxidase 4 (GPX4), a selenium-containing enzyme, and associated proteins as critical for cold tolerance. We utilized genetic and pharmacological approaches to demonstrate that GPX4 is active in the cold and its catalytic activity is required for cold tolerance. Furthermore, we show that the role of GPX4 as a suppressor of cold-induced cell death extends across hibernating species, including 13-lined ground squirrels and greater horseshoe bats, highlighting the evolutionary conservation of this mechanism of cold tolerance. This study identifies GPX4 as a central modulator of mammalian cold tolerance and advances our understanding of the evolved mechanisms by which cells mitigate cold-associated damage - one of the most common challenges faced by cells and organisms in nature.

cell biology↗

bioRxiv2023

Integrated multimodal cell atlas of Alzheimer's disease

Alzheimers disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms driving AD progression and vulnerable cell populations affected by disease remain coarsely understood. The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types. We used image-based quantitative neuropathology to place 84 donors spanning the spectrum of AD pathology along a continuous disease pseudoprogression score and multiomic technologies to profile single nuclei from each donor, mapping their transcriptomes, epigenomes, and spatial coordinates to a common cell type reference with unprecedented resolution. Pseudo-progression analysis showed two major epochs corresponding with a slow early increase in pathology and a later exponential increase that correlated with cognitive decline. The early phase included inflammatory microglial and reactive astrocyte component, as well as a selective loss of Sst+ inhibitory neuron types in superficial cortical layers, loss of myelinating oligodendrocytes, and up-regulation of a re-myelination program by OPCs. The later phase involved loss of excitatory neurons and Pvalb and Vip neuron subtypes also predominantly in superficial layers. These cell vulnerabilities were also seen in prefrontal cortex and replicated by other independent studies when integrated with the BRAIN Initiative reference. Study data and exploratory tools are freely available to accelerate progress in AD research at SEA-AD.org.

genomics↗

bioRxiv2022

Multi-synaptic boutons are a feature of CA1 hippocampal connections that may underlie network synchrony

Excitatory synapses are typically described as single synaptic boutons (SSBs), where one presynaptic bouton contacts a single postsynaptic spine. Using serial section block face scanning electron microscopy, we found that this textbook definition of the synapse does not fully apply to the CA1 region of the hippocampus. Roughly half of all excitatory synapses in the stratum oriens involved multi-synaptic boutons (MSBs), where a single presynaptic bouton containing multiple active zones contacted many postsynaptic spines (from 2 to 7) on the basal dendrites of different cells. The fraction of MSBs increased during development (from P21 to P100) and decreased with distance from the soma. Curiously, synaptic properties such as active zone (AZ) or postsynaptic density (PSD) size exhibited less within-MSB variation when compared to neighbouring SSBs, features that were confirmed by super-resolution light microscopy. Computer simulations suggest that these properties favour synchronous activity in CA1 networks.

neuroscience↗