Biology subjects

Arnold, S. E.

Publications and source records attributed to Arnold, S. E..

11 recordsLinked to original sources

bioRxiv2026

Achieving near single-molecule sensitivity in separation-free protein detection using engineered kinetic proofreading

Unlike nucleic acids, proteins cannot be directly amplified. Ultrasensitive detection must therefore couple efficient analyte-to-signal conversion with strong suppression of target-independent background. Consistently detecting ~100 molecules (below which Poisson sampling noise alone causes CV to exceed 10%) across protein targets in a format as scalable and accessible as PCR remains unsolved. Separation-based ultrasensitive immunoassays require target binding stable enough to survive stringent washing and are therefore constrained by wash-induced signal loss and, more fundamentally, the relative scarcity of exceptionally tight binders. Performance consequently varies across targets; detection limits below 1,000 molecules remain rare. Conventional separation-free proximity assays avoid washing but incur background from random probe collisions, with reported detection limits frequently exceeding 100,000 molecules. Here we introduce Successive Proximity Extension Amplification Reaction (SPEAR), a separation-free architecture in which autonomous engineered DNA nanodevices emulate biological kinetic proofreading. Two successive irreversible proximity-extension steps compound discrimination between analyte-dependent and background reactions, suppressing spurious signals while preserving efficient analyte-to-signal conversion. This design reduces reliance on high-affinity binders and enables sub-fM detection from 1 uL samples through simple 3-step mixing followed by standard qPCR readout. Across 11 biomarkers tested, SPEAR consistently achieved sub-100-molecule detection limits. Where compared, it outperformed ultrasensitive separation-based platforms, analytically and clinically, including for low-abundance Alzheimer's disease biomarkers. SPEAR also precisely quantified SARS-CoV-2 neutralizing antibody titers from finger-prick dried blood spots, concordant with the cell-based reference assay on venous blood. It detected a distinct mixed phosphorylation state of Tau, and targeting this state resolved previously observed capillary-venous discordance and improved amyloid-status discrimination. These results establish engineered autonomous successive molecular discrimination as a practical strategy for near-single-molecule protein detection, extending the sensitivity, scalability and accessibility of PCR-based testing to non-amplifiable analytes.

bioengineering↗

bioRxiv2026

Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution

Understanding how cells specialize is essential for reconstructing the diversification of life on earth. Cnidocytes (stinging cells) have a single origin in the stem cnidarian ([~]800mya) and have since specialized into extremes in morphology and function. Using single-cell RNA sequencing and transcriptional lineage reconstruction in a coral and a sea anemone, we show that a single gene (FoxL2) controls a critical switch point in the evolution of cnidocyte diversity: the decision to be a piercing cell (nematocyte) or an ensnaring cell (spirocyte). Nematocytes are lowly conserved between species and express younger genes, reflecting the continued diversification of this cell lineage. Surprisingly, ensnaring cells are one of the most highly conserved differentiated cell types and express older genes than nematocytes. This suggests spirocytes reached an adaptive peak early and have changed little during the 600 million years since corals and sea anemones last shared a common ancestor, making them living fossil cells.

evolutionary biology↗

bioRxiv2026

Novel cell and tissue dynamics drive the unusual biology of the catch tentacle, an inducible organ of aggression found in the sea anemone Metridium senile

Metridium senile is a clonal anemone that engages in fighting interactions to defend its territory from non-clonemates utilizing an inducible fighting organ, the catch tentacle. Upon contact with a non-clonemate, the catch tentacle tip detaches onto the non-clonal individual, resulting in necrosis where the tip attaches to the non-clone. The incapacitating function of the catch tentacle is driven by a unique type of cnidocyte, the holotrich, which is not found elsewhere in M. senile, including the feeding tentacles from which catch tentacles develop. Metridium farcimen, the sister species to M. senile, never develops catch tentacles despite their close phylogenetic relationship, as exemplified by their ability to hybridize. Here, we compare the feeding tentacles of both species to the catch tentacles in M. senile to determine how catch tentacles achieve their unusual function. We found that the feeding tentacles of M. senile and M. farcimen house similar types of cnidocytes that develop from proliferative cells distributed throughout the tentacle. By contrast, catch tentacles house distinct cnidocyte types from feeding tentacles and restrict proliferative cells to the base of the tentacle. This suggests immature cnidocytes migrate from base to tip to replace lost cells after an aggressive interaction in the catch tentacle. Additionally, we observed two morphologically and chemically distinct types of holotrichs in the catch tentacles that appear to use different cues to induce firing. Together, our data suggests that the novelty of catch tentacle aggression is mediated by distinct cell and tissue dynamics.

evolutionary biology↗

bioRxiv2026

Structural Brain Indicators of Cognitive Performance in Middle and Late Adulthood: The Human Connectome Project in Aging/Aging Adult Brain Connectome Cohort

IntroductionSignificant effort has been put towards mapping patterns of atrophy in the cerebral cortex that are related to pathological aging, including the characteristic patterns of neurodegeneration in Alzheimers disease (AD). In contrast, brain structural patterns that support preserved or even exceptional cognition throughout the adult age-span and especially in later life are much less known. It is possible that superior cognitive performance in late life is supported by a preservation of brain structures vulnerable to typical aging. Alternatively, elevated performance could be related to preservation of brain regions vulnerable to age-associated pathology. Examination of individuals that exhibit superior cognition throughout the adult lifespan may provide unique insights into neural mechanisms that support cognitive resilience in late life. MethodsWe examined cross-sectional associations between cortical brain structure and cognitive performance across three stages of adulthood: midlife (36-59), young-old (60-79), and older adults (80+) in typically aging individuals enrolled as part of the Human Connectome Project Lifespan-Aging (HCP-A)/Aging Adult Brain Connectome (AABC) studies. Participants were considered generally healthy and excluded for significant and/or atypical health conditions for their demographic category, including a clinical diagnosis of cognitive impairment or dementia. Domain-specific cognitive factor scores representing memory, fluid intelligence, and crystalized intelligence were sex-stratified and residualized relative to age, and participants were classified as high, middle, or low performers based on their unique performance relative to the study sample. ResultsIn the full sample, high performers demonstrated greater cortical thickness in regions of somatomotor, visual, and auditory cortices, as well as cortical areas in the frontal, parietal, and insular cortices (e.g., 5m, LIPv, MBelt). We also found associations between medial temporal and cingulate cortical thickness and cognitive performance, but only for select analyses. Group differences in cortical thickness were greatest when contrasting high and low performers for fluid intelligence compared to the other cognitive factors and were most prominent in the midlife participants compared to the other age strata. These group differences were primarily driven by reduced cortical thickness in the low performing individuals in the younger age bins relative to the typically performing sample. Effects were rather limited when contrasting high and low performers in the 80+ age group. The cortical areas of high statistical significance appeared to show a cross-sectional convergence effect, such that the differences in cortical thickness between high vs. low cognitive performance groups diminished with increasing age. Despite lower statistical power, effect sizes were greatest when contrasting individuals at the extremes of performance (e.g., top 10% vs. bottom 10% performers). These effects were robust to subsample replications using longitudinally defined cognitive classifications. DiscussionElevated cognitive performance was cross-sectionally associated with increased regional cortical thickness and effects were most prominent in mid-life compared to later ages. Notably, contrary to brain regions that may be expected to support such high-order cognitive performance, a significant portion of primary sensory, motor, and insular cortical areas exhibited group differences between the high- and low-performing groups in this relatively younger age group. Group differences were due to lower thickness in these regions in the low performing group relative to the typical performers. In contrast to the younger portion of the sample, regions typically considered vulnerable to Alzheimers disease (i.e., regions in the medial temporal lobe) were only infrequently implicated. These results suggest that specific patterns of cortical brain structural integrity including preserved thickness of primary motor and sensory cortical regions may be a necessary but not sufficient mechanism supporting superior cognitive abilities in earlier adulthood, while alternate neural mechanisms may support cognitive resilience later in life. These results must be interpreted with caution given the cross-sectional nature of this study. Cognitive capacity can only be estimated from a single timepoint, and several factors contribute to inter-individual variation that will not be accounted for in the models applied here. Longitudinal assessment of cognitive resilience in the HCP-A/AABC cohort will be performed in future work.

neuroscience↗

bioRxiv2024

A newly evolved gene is essential for efficient sperm entry into eggs in Drosophila melanogaster

While spermatogenesis has been extensively characterized in the Drosophila melanogaster model system, very little is known about the genes required for fly sperm entry into eggs. We identified a lineage-specific gene, which we named katherine johnson (kj), that is required for efficient fertilization. Males that do not express kj produce and transfer sperm that are stored normally in females, but sperm from these males enter eggs with severely reduced efficiency. Using a tagged transgenic rescue construct, we observed that the KJ protein localizes around the edge of the nucleus at various stages of spermatogenesis but is undetectable in mature sperm. These data suggest that kj exerts an effect on sperm development, the loss of which results in reduced fertilization ability. Interestingly, KJ protein lacks detectable sequence similarity to any other known protein, suggesting that kj could be a lineage-specific orphan gene. While previous bioinformatic analyses indicated that kj was restricted to the melanogaster group of Drosophila, we identified putative orthologs with conserved synteny, male-biased expression, and predicted protein features across the genus, as well as likely instances of gene loss in some lineages. Thus, kj was likely present in the Drosophila common ancestor and subsequently evolved an essential role in fertility in D. melanogaster. Our results demonstrate a new aspect of male reproduction that has been shaped by a lineage-specific gene and provide a molecular foothold for further investigating the mechanism of sperm entry into eggs in Drosophila. Article SummaryHow fruit fly sperm enter eggs is poorly understood. Here, we identify a gene required for efficient fertilization. Sperm from males lacking this genes function cannot enter eggs. The gene appears to act during sperm production, rather than in mature sperm. Interestingly, the gene is undetectable outside of genus Drosophila, and its encoded protein shows no discernable similarity to other proteins. This study provides insights into sperm-egg interactions and illustrates how lineage-specific genes can impact important aspects of reproduction.

genetics↗

bioRxiv2024

Identification of Novel Biomarkers for Alzheimer's Disease and Related Dementias Using Unbiased Plasma Proteomics

Alzheimers disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pathways and disease mechanisms and continue to have a huge societal impact for affected individuals and their families. While emerging blood-based biomarkers, such as plasma p-tau181 and p-tau217, accurately detect Alzheimer neuropthology and are associated with faster cognitive decline, the full extension of plasma proteomic changes in ADRD remains unknown. Earlier detection and better classification of the different subtypes may provide opportunities for earlier, more targeted interventions, and perhaps a higher likelihood of successful therapeutic development. In this study, we aim to leverage unbiased mass spectrometry proteomics to identify novel, blood-based biomarkers associated with cognitive decline. 1,786 plasma samples from 1,005 patients were collected over 12 years from partcipants in the Massachusetts Alzheimers Disease Research Center Longitudinal Cohort Study. Patient metadata includes demographics, final diagnoses, and clinical dementia rating (CDR) scores taken concurrently. The ProteographTM Product Suite (Seer, Inc.) and liquid-chromatography mass-spectrometry (LC-MS) analysis were used to process the plasma samples in this cohort and generate unbiased proteomics data. Data-independent acquisition (DIA) mass spectrometry results yielded 36,259 peptides and 4,007 protein groups. Linear mixed effects models revealed 138 differentially abundant proteins between AD and healthy controls. Machine learning classification models for AD diagnosis identified potential candidate biomarkers including MBP, BGLAP, and APoD. Cox regression models were created to determine the association of proteins with disease progression and suggest CLNS1A, CRISPLD2, and GOLPH3 as targets of further investigation as potential biomarkers. The Proteograph workflow provided deep, unbiased coverage of the plasma proteome at a speed that enabled a cohort study of almost 1,800 samples, which is the largest, deep, unbiased proteomics study of ADRD conducted to date.

neuroscience↗

bioRxiv2023

Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis

Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approaches to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery(C) media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.

neuroscience↗

bioRxiv2023

Identification of State Markers in Anorexia Nervosa: Replication and Extension of Inflammation Associated Biomarkers Using Multiplex Profiling in Anorexia Nervosa and Atypical Anorexia Nervosa

Proteomics provides an opportunity for detection and monitoring of anorexia nervosa (AN) and its related variant, atypical-AN (atyp-AN). However, research to date has been limited by the small number of proteins explored, exclusive focus on adults with AN, and lack of replication across studies. This study performed Olink Proseek Multiplex profiling of 92 proteins involved in inflammation among females with AN and atyp-AN (N = 64), all < 90% of expected body weight, and age-matched healthy controls (HC; N=44). After correction for multiple testing, nine proteins differed significantly in the AN/atyp-AN group relative to HC group (lower levels: CXCL1, HGF, IL-18R1, TNFSF14, TRANCE; higher levels: CCL23, Flt3L, LIF-R, MMP-1). The expression levels of three proteins (lower IL-18R1, TRANCE; higher LIF-R) were uniquely disrupted in females with AN. No unique expression levels emerged for atyp-AN. Across the whole sample, twenty-one proteins correlated positively with BMI (ADA, AXIN1, CD5, CD244, CD40, CD6, CXCL1, FGF-21, HGF, IL-10RB, IL-12B, IL18, IL-18R1, IL6, LAP TGF-beta-1, SIRT2, STAMBP, TNFRSF9, TNFSF14, TRAIL, TRANCE) and six (CCL11, CCL23, FGF-19, IL8, LIF-R, OPG) were negatively correlated with BMI. Overall, our results replicate the prior study demonstrating a dysregulated inflammatory status in AN, and extend these results to atyp-AN (AN/atyp-AN all < 90% of expected body weight). Of the 27 proteins correlated with BMI, 18 were replicated from a prior study using similar methods, highlighting the promise of inflammatory protein expression levels as biomarkers of disease monitoring. Additional studies of individuals across the entire weight spectrum are needed to understand the role of inflammation in atyp-AN.

immunology↗

bioRxiv2021

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last [~]15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis. Author SummaryGenomes are in flux, as genes are constantly added and lost throughout evolution. New genes were once thought to arise almost exclusively via the modification or duplication of existing genes. Recently, however, interest has grown in alternative modes of new gene origination, such as de novo evolution from genetic material that previously did not encode proteins. Many de novo genes are expressed in male reproductive tissues, but their significance for fertility is not well understood. We screened likely de novo genes expressed in the Drosophila testis for reproductive roles and found one gene, atlas, essential for male fertility. We leveraged genetic and cell biological experiments to investigate roles for Atlas protein in reproduction and found that it is required during sperm development for proper packaging of DNA in the sperm nucleus. Evolutionary analyses of this gene revealed a complicated history, including loss in some lineages, movement between chromosomes, and fusion with a non-protein-coding gene. Studying both the functions and evolutionary histories of new proteins illustrates how they might evolve critical roles in biological processes despite their relative novelty. Furthermore, the study of atlas identifies an essential genetic player in the fly testis, an important model system for understanding how gametes are produced.

genetics↗

bioRxiv2020

Multiplexed fractionated proteomics reveals synaptic factors associated with cognitive resilience in Alzheimer's Disease

Alzheimers disease (AD) is a complex neurodegenerative disease defined by the presence of amyloid-{beta} (A{beta}) plaques and tau neurofibrillary tangles, and driven by dysproteostatis, inflammation, metabolic dysfunction, and oxidative injury, eventually leading to synapse loss and cell death. Synapse loss correlates with cognitive impairment and may occur independently of the extent of AD pathology. To understand how synaptic composition is changed in relation to AD neuropathology and cognition, highly sensitive multiplexed liquid chromatography mass-spectrometry was used to quantify biochemically enriched synaptic proteins from the parietal association cortex of 100 subjects with contrasting AD pathology and cognitive performance. Functional analysis showed preservation of synaptic signaling, ion transport, and mitochondrial proteins in normal aged and "resilient" (cognitively unimpaired with AD pathology) individuals. Compared to these individuals, those with cognitive impairment showed significant metabolic differences and increased immune- and inflammatory-related proteins, establishing the synapse as a potential integration point for multiple AD pathophysiologies.

neuroscience↗

bioRxiv2018

Prion protein quantification in cerebrospinal fluid as a tool for prion disease drug development

Reduction of native prion protein (PrP) levels in the brain is an attractive and genetically validated strategy for the treatment or prevention of human prion diseases. However, clinical development of any PrP-reducing therapeutic will require an appropriate pharmacodynamic biomarker: a practical and robust method for quantifying PrP, and reliably demonstrating its reduction, in the central nervous system (CNS) of a living patient. Here we evaluate the potential of enzyme-linked immunosorbent assay (ELISA)-based quantification of human PrP in human cerebrospinal fluid (CSF) to serve as a biomarker for PrP-reducing therapeutics. We show that CSF PrP is highly sensitive to plastic adsorption during handling and storage, but its loss can be minimized by addition of detergent. We find that blood contamination does not affect CSF PrP levels, and that CSF PrP and hemoglobin are uncorrelated, together suggesting that CSF PrP is CNS-derived, supporting its relevance for monitoring the tissue of interest and in keeping with high PrP abundance in brain relative to blood. In a cohort with controlled sample handling, CSF PrP exhibits good within-subject test-retest reliability (mean coefficient of variation 13% in samples collected 8-11 weeks apart), a sufficiently stable baseline to allow therapeutically meaningful reductions in brain PrP to be readily detected in CSF. Together, these findings supply a method for monitoring the effect of a PrP-reducing drug in the CNS, enabling the development of prion disease therapeutics with this mechanism of action.

molecular biology↗