Biology subjects

Mitchell, J.

Publications and source records attributed to Mitchell, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Human cytomegalovirus microRNAs target the Wnt signaling protein Dishevelled 3 to promote efficient reactivation in CD34+ hematopoietic progenitor cells

Human cytomegalovirus (HCMV) establishes latency in CD34+ hematopoietic progenitor cells (HPCs), yet differentiation of these cells promotes viral gene expression and replication. HCMV must therefore precisely regulate the signaling networks that govern HPC fate to maintain latency while preserving the capacity for reactivation. Virally encoded microRNAs (miRNAs) represent powerful tools used by HCMV to manipulate cellular pathways that are involved in HPC fate decisions. Wnt (Wingless/Integrated)/b-catenin signaling represents one such pathway that plays a critical role in regulating both hematopoiesis and virus replication. Previous work determined that HCMV stimulates b-catenin activity during reactivation in CD34+ HPCs. In contrast, here we show that HCMV miRNAs miR-US5-2 and miR-US25-2 downregulate the Wnt pathway adaptor protein Dvl3 during latency and that this downregulation is required for subsequent virus reactivation. These findings support a model of temporally distinct regulation of Wnt pathway components during latency and reactivation.

microbiology↗

bioRxiv2026

Novelty-seeking and directed exploration scale with dissociable social network outcomes and brain systems in older adults

Social isolation and loneliness are major determinants of well-being in older adults. Shrinking social networks and age-related shifts in social behavior and decision-making may increase vulnerability to loneliness. These changes in social decision-making strategies can be conceptualized within an exploration-exploitation tradeoff framework, in which social options with known outcomes are prioritized over uncertain ones. Yet, no study has characterized how complementary decision-making strategies, undirected novelty seeking and goal-directed exploration, relate to social network constructs or are supported by distinct neural systems. These strategies capture distinct forms of decision-making: undirected novelty seeking is driven by the intrinsic salience of novel options independent of expected informational gain, whereas goal-directed exploration involves deliberately sampling uncertain options to reduce uncertainty and optimize future choices. Here, we used fMRI and a novel social bandit reinforcement task to identify dissociable social constructs and brain systems linked to undirected novelty seeking and goal-directed exploration in older adults. Undirected novelty seeking was associated with social network size and with activity of temporoparietal and mid-cingulate brain areas. Goal-directed exploration predicted subjective feelings of social connectedness and was associated with activity of anterior cingulate and prefrontal brain areas. Crucially, choice probabilities from a non-social version of the three-arm bandit task were not associated with social decision-making nor with social constructs. Our findings suggest that, in later life, dissociable social decision-making strategies, when faced with unknown options, rely on distinct neural systems supporting social network size as well as subjective feelings of social connectedness.

neuroscience↗

bioRxiv2026

FAIM Inhibits Insulin Amyloidogenesis through a Noncanonical Aggregation Pathway

Insulin can misfold and assemble into amyloid fibrils, a process linked not only to complications of insulin therapy but also to proteotoxic stress in pancreatic {beta}-cells. Despite growing interest in the pathological consequences of insulin aggregation, prevention efforts are limited by an incomplete understanding of the endogenous mechanisms that counteract it. Here, we identify Fas apoptosis inhibitory molecule (FAIM) as an endogenous suppressor of insulin amyloid formation. FAIM reduces {beta}-sheet formation and redirects insulin toward disordered, growth-incompetent assemblies. Further, FAIM attenuates the cytotoxicity of insulin aggregates in vitro. We hypothesize that this effect arises from masking aggregation-prone regions of insulin and show through structural modeling that FAIM interacts with both insulin chains. These findings extend the anti-aggregation function of FAIM to insulin and suggest a mechanism for endogenous suppression of insulin amyloid formation. More broadly, our results provide insight into the regulation of insulin assembly and highlight FAIM as a candidate modulator of proteostasis in metabolic disease. Statement for a broader audienceInsulin can clump together into harmful aggregates, contributing to complications of insulin therapy and potentially damaging the insulin-producing cells of the pancreas. This study identifies the naturally occurring protein FAIM as a protective factor that inhibits the formation of these harmful aggregates and reduces their toxicity. These findings improve our understanding of how cells protect insulin from harmful aggregation and may open new avenues for developing therapies to combat diabetes-related protein aggregation.

biochemistry↗

bioRxiv2026

A Paracrine Dietary Lipid Axis Constrains Antitumor Immunity in Liver Cancer

Overnutrition-related liver dysfunction and cancer are increasingly prevalent and highly resistant to immunotherapy. While metabolic dysregulation is a hallmark of hepatocellular carcinoma (HCC), how nutrient overload impairs antitumor immunity remains unclear. Here, we show that short-term Western diet (WD) exposure drives near-complete loss of CD8 T cell infiltration and antitumor function in HCC. We identify dietary linoleic acid (LA), the most abundant {omega}-6 fatty acid, as the dominant immunosuppressive driver. Cancer cell-restricted FADS2-mediated desaturation of LA to longer-chain {omega}-6 PUFAs drives their accumulation in the tumor interstitial fluid, suppressing infiltrating CD8 T cells via lipid peroxidation. FADS2 inhibition restores CD8 T cell function and sensitizes WD-driven HCC to PD-1-based immunotherapy. Further, the Parkinsons disease-associated deglycase DJ-1 protects LA-handling proteins from methylglyoxal-mediated glycation, sustaining tumoral immunosuppressive PUFA production. Across multiple independent human MASLD-HCC cohorts, LA metabolic activity correlates with CD8 T cell impairment, immune exclusion, and immunotherapy resistance. Overall, these studies identify a dietary lipid axis as a therapeutically actionable vulnerability in WD-associated HCC.

Cancer Biology↗

bioRxiv2026

Hoverfly responses to looming stimuli depend on elevation and speed

An object on immediate collision course generates a rapidly expanding visual stimulus on the retina, which will typically trigger a fast reaction, such as an evasive behavior. In hoverflies, for example, visual looming stimuli may be generated if the insect is about to collide with a stationary object in the surround, by an approaching predator, or by conspecifics during territorial interactions. Supporting these behavioral responses is a diverse range of looming sensitive descending neurons that project information from the optic lobes and central brain to the motor control centers in the thoracic ganglia. We here show that the looming sensitive descending neurons are predominantly sensitive to looming stimuli located in the ventral visual field. To investigate if this is matched by behavior, we recorded how tethered hoverflies responded to looming stimuli presented dorsally or ventrally on a visual monitor, at four different speeds (l/|v| of 10 - 667 ms), covering a naturalistic range. We found that ventral stimuli, especially at intermediate speeds (l/|v| = 50 or 200 ms), triggered much stronger behavioral responses than dorsally displayed stimuli. The behavioral data thus not only match the receptive fields of the neurons likely to support the behavior, but also highlight that behavioral output is not entirely reflexive but is strongly modulated by stimulus speed and elevation. Significance StatementIf someone throws a ball at you, this generates a rapidly expanding object across your visual field, which will make you react before you have even had time to think. You may for example duck, dip or dive to avoid the ball, or bring your hands up to grab it. Similarly, many insects respond to rapidly approaching objects. We here show that hoverfly reactions to such looming stimuli depend on stimulus speed and elevation, with the strongest response to stimuli approaching from below. We further demonstrate that the neurons likely supporting these behaviors show highest sensitivity in the ventral visual field, suggesting a close match between neural tuning and behavioral output.

animal behavior and cognition↗

bioRxiv2026

Targeting an RNA Editor to Impede H3K27M+ Pediatric Gliomas

Diffuse midline glioma (DMG) is a lethal pediatric brain tumor with no curative therapies. Immune checkpoint blockade (ICB) has shown limited efficacy in DMG, largely due to poor T cell infiltration, low immune checkpoint (IC) expression, and a low tumor mutational burden. Here, we identify adenosine deaminase acting on RNA (ADAR), an RNA-editing enzyme that suppresses endogenous dsRNA sensing, as a key mediator of immune evasion in H3K27M-mutant DMG. ADAR is significantly overexpressed in H3K27M tumors relative to wild-type high-grade gliomas, and its depletion selectively suppresses proliferation in patient-derived DMG cells. The H3K27M mutation was found to synergize with ADAR loss to increase retroelement expression, activate type I interferon signaling, and induce immune checkpoint expression. We further identify all-trans retinoic acid (ATRA) as a pharmacologic inducer of ADAR degradation. At clinically relevant doses, ATRA phenocopies ADAR depletion, enhancing antiviral and interferon responses while increasing tumor immunogenicity. In orthotopic immunocompetent DMG models, ATRA enhances CD8+ T cell infiltration and synergizes with ICB and irradiation to improve survival.

cancer biology↗

bioRxiv2026

Sulcal anatomy of ventral temporal cortex and reading development

Individual differences in cognitive abilities have been linked to variability in cortical folding, a stable neuroanatomical scaffold largely established in utero. In the domain of reading, recent findings in small groups of typical readers suggest that a sulcal interruption (superficial annectant gyrus, gyral gap) in the left posterior occipital temporal sulcus (lhpOTS) predicts better reading skills, posing the lhpOTS as a potential early biomarker of reading difficulties. However, it remains unknown whether this relationship found in typical readers generalizes to the dyslexic population and whether the lhpOTS can serve as a biomarker for dyslexia or predict response to targeted instruction.To fill these gaps, we examine the patterns of the lhpOTS in 209 children, including children with dyslexia, from four independently-collected samples. In typical readers, we find that the relationship between the lhpOTS and reading skills is robust, replicating across binary and continuous quantifications of the sulcal interruption. However, lhpOTS patterns neither distinguish dyslexic children from typical readers nor do they predict response to intervention. Instead, targeted reading intervention drives long-term gains in reading skills that are equivalent irrespective of VOTC anatomy. Together, these findings distinguish neuroanatomical correlates of skilled reading from determinants of reading impairment and learning capacity and emphasize the importance of the educational environment in supporting reading acquisition for children with dyslexia. SIGNIFICANCE STATEMENTEarly predictors of dyslexia are important for understanding the etiology of reading difficulties and informing early intervention. One candidate biomarker for dyslexia is the left posterior occipital temporal sulcus (lhpOTS), a neuroanatomical feature established before birth. In typical readers, the presence of an interruption in the lhpOTS has been linked to better reading skills. Here, we examine this neuroanatomical feature in 209 children with and without dyslexia. While the lhpOTS reliably relates to reading skill in typical readers, it neither differentiates dyslexic from typical readers nor predicts response to intensive reading intervention. These results show that brain anatomy reflects reading proficiency but does not constrain learning and highlights the power of targeted intervention to support reading development.

neuroscience↗

bioRxiv2026

Pharmacologic DPP-4 inhibition promotes CD8⁺ T cell metabolic fitness to enhance anti-tumor activity

Metabolic dysfunction is a hallmark of CD8+ T cell exhaustion in the tumor microenvironment. Thus, there is growing interest in developing strategies that enhance anti-tumor functions of CD8+ T cells via metabolic reprogramming. Here, we identify dipeptidyl peptidase 4 (DPP-4) as a previously unknown regulator of CD8+ T cell function and metabolism. We discovered that DPP-4 is upregulated in exhausted CD8+ T cells. Pharmacological inhibition of DPP-4 with the FDA-approved anti-diabetic drug sitagliptin transcriptionally and metabolically reprogrammed CD8+ T cells, increasing spare mitochondrial respiratory capacity, proliferation, cytotoxic mediator production, and antigen-specific cancer cell killing capability. The functional effects of sitagliptin were dependent on upregulation of glutamate decarboxylase 1 (GAD1), an enzyme that feeds glutamate into the tricarboxylic acid (TCA) cycle, highlighting a new role for GAD1 in CD8+ T cell respiration and proliferation. We found that systemic inhibition of DPP-4 in preclinical mouse glioblastoma (GBM) models prolongs survival in a CD8+ T cell-dependent manner, and retrospective clinical cohort analysis revealed better outcomes in GBM patients using DPP-4 inhibitors. Importantly, preconditioning of Chimeric Antigen Receptor (CAR) T-cells with DPP-4 inhibition enhanced their cytotoxicity, persistence, and therapeutic efficacy in pediatric GBM. Together, our findings provide mechanistic and biological rationale for repurposing readily accessible DPP-4 inhibitors to enhance anti-tumor CD8+ T cell responses.

immunology↗

bioRxiv2026

A Broad-Spectrum Chemokine Inhibitor Prevents Preterm Labor in Mice by Supressing Inflammation Induced by Intra-Amniotic Injection of Interleukin-1 alpha

Preterm birth (PTB) is a leading cause of perinatal and infant mortality worldwide. PTB can be induced by systemic maternal or intra-uterine infection or by sterile intra-amniotic inflammation driven by alarmins such as interleukin-1 (IL-1). We reported earlier that a Broad-Spectrum Chemokine Inhibitor (BSCI) prevented PTB in murine and non-human primate models of infection-mediated preterm labor. Here, we investigated whether BSCI can prevent PTB in pregnant C57BL/6 mice following ultrasound-guided intra-amniotic injection of IL-1 (400 ng per sac) on gestational day (GD)16.5. Half the mice received BSCI (10 mg/kg, intravenous daily) beginning GD15.5 and through to term. The impact of IL-1 alone or IL-1 plus BSCI was assessed on (i) injection-to-delivery interval, fetal survival, placental and neonatal weight; (ii) cytokine and chemokine levels in maternal plasma and amniotic fluid and inflammatory gene expression in maternal and fetal tissues (Real-Time RT-qPCR); (iii) global transcriptomic profiling of myometrial tissues at 2 and 24 hrs (RNA sequencing) together with examination of myometrial chromatin accessibility (Assay for transposase accessible chromatin sequencing) at 24 hrs; (iv) uterine leukocyte infiltration (immunofluorescence). Pretreatment with BSCI i) prevented IL-1-induced PTB; (ii) significantly attenuated cytokine and chemokine signals in maternal plasma, myometrium, decidua, and placenta, and amniotic fluid; (iii) suppressed myometrial contraction-associated genes, including Nfkb1, Ptgs2, Akr1c18, and Gja1; (iv) prevented global IL-1-induced changes in myometrial gene expression and chromatin accessibility (v) reduced uterine macrophage (F4/80+) counts and prevented the increase in pro-inflammatory M1-like macrophages observed with IL-1-treatment. BSCI-treated dams that delivered at term had live pups with normal placental and fetal weight. Taken together, BSCI reduced the incidence of IL-1-mediated PTB and maintained uterine quiescence by suppressing uterine inflammation and genome-wide changes in labor gene expression and chromatin accessibility. BSCI represents a promising therapeutic approach for PTB prevention in high-risk pregnant women.

physiology↗

bioRxiv2026

Substance matters: IL5 and IL33 activation of eosinophils on periostin and fibrinogen induce cytoskeletal reorganization and cell death

Human eosinophils activated in suspension with IL5 or IL33 undergo morphological change prior to adhesion. Refractive granules, which contain major basic protein-1 and other toxic proteins, move to one side of the cell, the granulomere, and the two nuclear lobes move to the other. How these features persist when eosinophils become adherent and migrate is not known. We now compare behavior of activated eosinophils on surfaces coated with ITGAM/ITGB2-integrin ligands fibrinogen or periostin using live cell imaging of reporters of tubulin/actin organization and cell viability. We find that unlike eosinophils activated with IL5, IL33-activated eosinophils undergo two stages of activation; a preliminary pear-like activation in which the cell develops polarity, followed by a flattening of the eosinophil into a thin pancake-like morphology with less discrete polarization. IL5-treated eosinophils migrated persistently for more than an hour with nucleopod in the back. In contrast, IL33-treated eosinophils moved more slowly and within 30 min transitioned to a flattened morphology with nuclear lobes in the center and dispersed motile granules. Loss of cell viability after an hour, although variable, in all comparisons was greater among IL33-treated eosinophils on periostin. We sought to understand how cytoskeletal elements may drive these differences in morphology. Cytoskeletal elements had similar responses when activated with IL5/IL33; vimentin collapsed from a web-like network at the periphery of the cell and condensed adjacent to the nucleopod/nuclear interface, f-actin was found in the granulomere as well as the tip of the nucleopod and forward periphery, and microtubules radiated from the microtubule organizing center (MTOC) spanning both the nucleopod and the granulomere. The dynamic formation of microtubules correlated with cellular locomotion, suggesting mesenchymal migration within these cells. These in vitro findings suggest that adhesion plays an important role in determining functional morphology and demonstrates new insights into IL33-activated eosinophils. This work suggests roles for activators and adhesive substrates in regulating the behavior of activated eosinophils in tissues.

cell biology↗

bioRxiv2026

LINE-1 retrotransposition is a recurrent cause of MET exon 14 skipping in cancer

MET exon 14 skipping is a pathogenic event that results in decreased ubiquitin-mediated degradation of the MET receptor, sustained oncogenic signaling, and conferred sensitivity to MET tyrosine kinase inhibitors. While exon 14 skipping is most commonly caused by somatically acquired base substitutions and small indels near the exon 14 splice sites, here we report nine cases in which long interspersed element-1 (LINE-1, L1)-mediated insertions within or adjacent to MET exon 14, including one case of a LINE-1-mediated pseudogene insertion, appear to cause exon 14 skipping. These describe the first recurrent and clinically actionable mutations caused by LINE-1 retrotransposition in cancer.

cancer biology↗

bioRxiv2025

The human cytomegalovirus chemokine binding protein UL22A is necessary for efficient reactivation from latency in CD34+ hematopoietic progenitor cells.

Herpesviruses and Poxviruses encode secreted chemokine binding proteins that prevent the interaction between chemokines and their cognate G protein coupled receptors to alter chemotactic gradients and intracellular signaling pathways. Human cytomegalovirus (HCMV) encodes the secreted protein UL22A (formerly UL21.5), which is described as a CCL5 (RANTES) binding protein and requires sulfation at two tyrosine residues (Y65 and Y69) for efficient RANTES interaction. In this report, we show that the UL22A protein, and the UL22A Y65 and Y69 residues are necessary for efficient HCMV reactivation from latency in CD34+ hematopoietic progenitor cells and that UL22A expression is essential for reactivation in a humanized mouse model of latency. However, RANTES neutralization is not sufficient to complement the in vitro reactivation defect of UL22A mutant viruses. These data suggest that UL22A plays an important role in latency, possibly through interactions with additional chemokines or other types of ligands via its tyrosine residues, in order to mediate efficient HCMV reactivation. IMPORTANCEHCMV is a ubiquitous herpesvirus that infects 60-90% of the population worldwide. In immunocompetent individuals, primary infection is asymptomatic and results in lifelong latent infection in CD34+ hematopoietic progenitor cells (HPCs). Viral reactivation remains a major complication for immunosuppressed individuals, but current therapeutics targeting HCMV replication show significant toxicity. Thus, a better understanding of the mechanisms controlling latency and reactivation is necessary to develop new therapeutics targeting these stages of the HCMV lifecycle. We show that virus lacking the HCMV chemokine binding protein UL22A is incapable of efficient reactivation in CD34+ HPCs and in vivo. UL22A tyrosine residues important for interaction with the chemokine RANTES are necessary for reactivation. However, neutralizing RANTES does not complement the reactivation defect of UL22A mutant viruses, demonstrating that UL22A has functions other than RANTES binding. Together, our results reveal a novel role for UL22A in HPCs and a new understanding of UL22A-chemokine interactions.

microbiology↗

bioRxiv2025

Probing the limited oculomotor range of common marmosets (Callithrix jacchus)

The ability to scan visual scenes to gather information is a critical adaptive skill across primates. The common marmoset, a small-bodied New World monkey and emerging model of social and visual neuroscience, relies heavily on rapid head movements in addition to eye movements to orient (Pandey et al., 2020; Singh et al., 2025). Previous studies have found a relatively restricted oculomotor range extending out about 10 visual degrees from the central position of rest (Mitchell et al., 2014; Singh et al., 2025). However, previous studies have either used empty arenas for exploration (Singh et al., 2025), or in head-fixed animals used exploration of images potentially biased centrally with posed stimuli (Mitchell et al., 2014). This leaves open questions about whether this restricted oculomotor range is due to physical constraints or a lack of attention-drawing stimuli in the periphery. Understanding marmosets oculomotor range is important for applying modern methods that use marker-less pose tracking of the head as a proxy for gaze direction, under the assumption eye gaze is relatively restricted and can be ignored (Meisner et al., 2025). Using high-precision eye tracking and free-viewing of a natural image and video with objects of interest placed in the periphery, we quantified the oculomotor range of head-fixed marmosets. Our results show limited changes in the range reported from previous studies, even with naturalistic stimuli including moving animals that were optimized to encourage peripheral viewing.

animal behavior and cognition↗

bioRxiv2025

Human Cytomegalovirus UL78 is a Nuclear-Localized GPCR Necessary for Efficient Reactivation from Latent Infection in CD34+ Hematopoietic Progenitor Cells

Human cytomegalovirus (HCMV) is a ubiquitous pathogen that persists throughout the lifetime of the host due in part to the establishment of latency in CD34+ hematopoietic progenitor cells (HPCs) and CD14+ monocytes. HCMV encodes four putative G protein-coupled receptors (GPCRs): US27, US28, UL33, and UL78. While the roles of most of these receptors have been investigated, a definitive role for UL78 in HCMV infection has yet to be elucidated. Utilizing an in vitro CD34+ HPC model, we demonstrate that a recombinant virus lacking UL78 protein expression fails to efficiently reactivate from latent infection. Furthermore, we show using a Lumit-based assay that UL78 preferentially couples to the Gi family of G proteins and that a recombinant HCMV containing mutations in the UL78 G protein-coupling DRL motif also fails to reactivate from latent infection. Together our findings indicate that Gi coupling is important for UL78 function during reactivation in latently infected CD34+ HPCs, however the protein is not required to establish or maintain latency. To better understand the role of UL78, we conducted proximity-dependent labeling analyses in HCMV-UL78-TurboID infected fibroblasts and CD34+ HPCs undergoing reactivation from latency. Congruent with our coupling data, we found Gi was the only heterotrimeric G protein in proximity to UL78. Pathway analysis of the UL78 interactome revealed proteins associated with membrane trafficking, signaling, and the nuclear pore complex as enriched in both cell types. In addition, the UL78 interactome contained viral proteins with nuclear localization including viral transcription and DNA replication machinery. Nuclear localization of UL78 was validated using cell fractionation, immunofluorescence microscopy, and proximity-dependent labelling of isolated nuclei. Together, our results provide novel insights into the localization and function of UL78, previously unknown to contribute to reactivation from latent infection. Author SummaryHuman cytomegalovirus (HCMV) remains one of the most widespread viral infections globally. Primary HCMV infection is typically asymptomatic and leads to the establishment of latency in myeloid lineage cells, where the virus persists for the hosts lifetime. Reactivation of latent HCMV can cause severe complications, particularly in immunocompromised individuals such as transplant recipients and people living with HIV. Several factors influence the transition from latent to lytic infection, including signal transduction through the viral G protein-coupled receptors: US27, US28, UL33, and UL78. Using an advanced in vitro model, we show that recombinant viruses lacking UL78 fail to efficiently reactivate from latent infection. Moreover, we show that UL78 preferentially couples to the Gi family of G proteins via a conserved DRL motif, and this coupling is required for efficient reactivation. These results were confirmed by proximity-dependent labeling experiments where we identified Gi and several other proteins involved in trafficking, signaling, transcription, and nuclear localization. Nuclear localization of UL78 was confirmed by cell fractionation, immunofluorescence microscopy, and proximity-dependent labeling in isolated nuclei. Collectively, our results uncover a novel role for UL78 in reactivation from latency and shed new light on its localization and function.

microbiology↗

bioRxiv2025

Constructing a consensus serum metabolome

Blood analysis is the most common in biomedical applications and a reference metabolome will be critical for effective annotation and for guiding scientific investigations. However, compiling such a reference is hindered by many technical challenges, despite the availability of large amount of metabolomics data today. Based on a new set of data structures and tools, we have assembled a consensus serum metabolome (CSM) from over 100,000 mass spectrometry acquisitions of more than 200 million spectra. This provides a comprehensive survey of human blood chemistry, revealing the frequency dependent nature of metabolome and exposome. Major gaps are found between CSM and the current databases. The CSM enables community-level data alignment and significantly improves annotation quality of LC-MS metabolomics. HighlightsO_LIA reference of human biochemistry linked to observation frequency C_LIO_LIMajor gaps revealed in current databases and experimental methods C_LIO_LIEnabling cross-laboratory, cross-platform data alignment C_LIO_LIAccelerated and cumulative metabolite annotation C_LI

biochemistry↗

bioRxiv2025

A systematic analysis of in-source fragments in LC-MS metabolomics

There is no consensus on how to interpret the large number of unknown features in untargeted metabolomics, which are sometimes referred as the "dark matter". Are these features real compounds or artifacts? Understanding this problem is critical to the annotation and interpretation of metabolomics data and future development of the field. We propose a "detectable khipu" model here, to show that compounds exhibit ion group patterns that depend on their abundance. We apply this model to a systematic analysis of 61 representative public datasets from blood LC-MS metabolomics, the most common data type in biomedical studies. The results indicate that majority of abundant features have identifiable ion patterns, and in-source fragments contribute to less than 10% of features. Each dataset detects 1[~]2,000 high confidence compounds, over half of which are unknown. The major knowledge gap in LC-MS metabolomics is therefore not the methods of grouping ions or counting fragments, but the identification of unknown compounds.

biochemistry↗

bioRxiv2025

Low Field Magnetic Resonance Imaging to Detect Acute Kidney Injury

Renal oxygenation is essential for maintaining kidney function. Disruptions in oxygen delivery can lead to renal hypoxia, which can exacerbate kidney injury through multiple pathways, including inflammation, oxidative stress, and ischemia-reperfusion injury. Despite the recognized importance of oxygenation in renal pathology, non-invasive and reliable methods for assessing kidney oxygen levels are limited. Current techniques either lack sensitivity or involve invasive procedures, restricting their use in routine monitoring. Therefore, there is a pressing need for innovative approaches to assess renal oxygenation, particularly in kidney injury. This study evaluated Electron Paramagnetic Resonance (EPR)-based oxygen imaging using the paramagnetic tracer Ox071 to assess kidney oxygen levels in mice with cyclophosphamide-induced kidney injury. Urine pO2 was also assessed as a potential surrogate marker. EPR oximetry accurately measured kidney oxygen distribution, revealing a temporary increase in pO2 post-injury. Urine oximetry, however, did not reliably reflect changes in kidney oxygenation. Furthermore, EPR oximetry provided high-resolution spatial mapping of oxygen levels within the kidney, allowing for a detailed understanding of the impact of hypoxia on renal tissue. EPR oximetry is a promising, non-invasive tool for monitoring renal oxygenation, offering high-resolution mapping and longitudinal assessment. Its ability to provide detailed information about oxygen distribution within the kidney makes it a valuable tool for studying the pathophysiology of renal diseases and for developing novel therapeutic strategies. Translational Statement: Quantitative spatially resolved measurement of renal oxygenation has the potential to guide clinical decision making in renal disorders such as acute kidney injury. In this study we demonstrate the utility of electron paramagnetic resonance imaging to provide non-invasive and quantitative high-resolution mapping of kidney oxygen concentrations.

physiology↗

bioRxiv2024

Behavioral and neural correlates of diverse conditioned fear responses in male and female rats

Pavlovian fear conditioning is a widely used tool that models associative learning in rodents. For decades the field has used predominantly male rodents and focused on a sole conditioned fear response: freezing. However, recent work from our lab and others has identified darting as a female-biased conditioned response, characterized by an escape-like movement across a fear conditioning chamber. It is also accompanied by a behavioral phenotype: Darters reliably show decreased freezing compared to Non-darters and males and reach higher velocities in response to the foot shock ("shock response"). However, the relationship between shock response and conditioned darting is not known. This study investigated if this link is due to differences in general processing of aversive stimuli between Darters, Non-darters and males. Across a variety of modalities, including corticosterone measures, the acoustic startle test, and sensitivity to thermal pain, Darters were found not to be more reactive or sensitive to aversive stimuli, and, in some cases, they appear less reactive to Non-darters and males. Analyses of cFos activity in regions involved in pain and fear processing following fear conditioning identified discrete patterns of expression among Darters, Non-darters, and males exposed to low and high intensity foot shocks. The results from these studies further our understanding of the differences between Darters, Non-darters and males and highlight the importance of studying individual differences in fear conditioning as indicators of fear state.

neuroscience↗