Biology subjects

Fernandez, K.

Publications and source records attributed to Fernandez, K..

13 recordsLinked to original sources

bioRxiv2026

EMITS: expectation-maximization abundance estimation for fungal ITS communities from long-read sequencing

As long-read amplicon sequencing becomes routine for fungal metabarcoding, species-level abundance estimation from ITS amplicons remains limited by naive best-hit classification, which misattributes reads among closely related species sharing similar ITS sequences and fragments abundance across redundant database entries. Expectation-maximization (EM) approaches developed for full-length 16S rRNA, notably EMU [Curry et al., 2022], have recently been benchmarked for fungal ITS metabarcoding [Graetz et al., 2025], but applying EMU to ITS requires custom reference database construction and uses parameters originally tuned for 16S. Here we present EMITS, a Rust-based tool that applies EM to iteratively resolve ambiguous read-to-reference mappings from minimap2 alignments against the UNITE database, producing probabilistic species-level abundance estimates. EMITS provides UNITE-native header parsing with automatic accession aggregation, empirically tuned platform presets for current Oxford Nanopore (R10.4.1, R9.4.1, Duplex) and PacBio HiFi chemistries, and integration with ITSxRust [OBrien et al., 2026] for upstream ITS region extraction. We validated EMITS using three complementary approaches and benchmarked it against both naive best-hit counting and EMU (with a UNITE-formatted reference database). In controlled simulations, EM reduced L1 error by 80- 92% compared to naive counting under realistic noise conditions. On the ATCC fungal ITS mock community, EMITS provided superior within-genus species resolution in taxonomically challenging genera: it correctly identified Trichophyton mentagrophytes (2.21%) where EMU misattributed substantial abundance to T. tonsurans (1.54%); it suppressed Penicillium rubens false positives (0.002% vs. EMU 0.58%); and it more accurately consolidated Nakaseomyces glabratus abundance across UNITE accessions (12.40% vs. EMU 9.95%). On a 21-species synthetic UNITE community lacking substantial within-genus difficulty, all three methods detected expected species at 100% sensitivity, with aggregate L1 errors of 8.64% (naive), 7.48% (EMITS), and 6.71% (EMU). Together with ITSxRust for upstream ITS extraction, EMITS provides a complete pipeline tuned for long-read fungal amplicon profiling.

bioinformatics↗

bioRxiv2026

ITSxRust: ITS region extraction with partial-chain recovery and structured diagnostics for long-read amplicon sequencing

As long-read amplicon sequencing (e.g., Oxford Nanopore and PacBio HiFi) becomes routine for fungal metabarcoding, identifying and extracting ITS subregions at scale has become a throughput and robustness bottleneck. The nuclear ribosomal internal transcribed spacer (ITS) region is the formal DNA barcode for fungi and is widely used for taxonomic profiling of fungal communities [Schoch et al., 2012]. Standard preprocessing locates conserved ribosomal flanks with hidden Markov profile models (profile-HMMs) to extract ITS1, 5.8S, ITS2, or the full ITS, as implemented in ITSx [Bengtsson-Palme et al., 2013] and ITSxpress [Rivers et al., 2018, Einarsson and Rivers, 2024]. Here we describe ITSxRust, a Rust-based ITS extractor designed for long-read scale. ITSxRust coordinates HMMER searches with efficient Rust-native I/O and sequence processing, optionally reduces redundant searches via dereplication, provides ONT and HiFi parameter presets, and emits structured failure diagnostics and QC summaries. On an Oxford Nanopore ITS dataset (54,659 reads), ITSxRust extracted the full ITS region from 75.3% of reads, exceeding both ITSx (69.9%) and ITSxpress v2 (41.4%), while running 4.6x faster than ITSx. In addition, a partial-chain fallback strategy that extracts subregions using two-anchor pairs when the full four-anchor chain is unavailable recovered an additional 10,725 reads that would otherwise be discarded.

bioinformatics↗

bioRxiv2026

Characterization of effects of a neurotropic murine coronavirus infection on Alzheimer's disease neuropathology of 5xFAD mice

BackgroundRecent studies revealed key immunological mechanisms within the central nervous system (CNS) that contribute to Alzheimers disease pathology. Additionally, analyses of human AD datasets have also associated viral encephalitis exposure (i.e., viral-induced neuroinflammation) with the development of AD and dementia, highlighting the need to better understand how viral encephalitis and neuroimmune mechanisms within the brain may impact AD pathologies such as A{beta} plaque deposition. Intracranial infection of susceptible mice with the neurotropic JHM strain of murine coronavirus (JHMV) results in acute encephalomyelitis characterized by viral infection of glia and a robust inflammatory response comprised of monocytes/macrophages and T cells that aid in controlling viral replication. MethodsTo determine how coronavirus-induced encephalitis may impact established A{beta} plaque deposition, we intracranially inoculated JHMV into aged 5xFAD model of amyloidosis. We utilize immunohistochemical and biochemical analysis to assess the impact on existing A{beta} pathology. We also utilize spatial transcriptomic imaging to explore how viral encephalitis affects cellular responses to plaque pathology with single-cell resolution. ResultsIn aged 5xFAD mice, JHMV-induced encephalitis at 12 days p.i. resulted in minimal changes to overall A{beta} protein within the brain. However, viral encephalitis induces CD4+ and CD8+ T cell infiltration and more Lgals3/MAC2-expressing macrophages surrounding dense-core A{beta} plaques, which appear more compacted in JHMV-infected 5xFAD brains compared to uninfected 5xFAD controls. We compared gene expression within JHMV-infected 5xFAD mice and uninfected controls to identify distinct cellular responses to A{beta} plaques that differed. Utilizing differential gene expression and pathway analysis, we found that viral encephalitis increased the proportion of myeloid cells in the 5xFAD brain, which also showed down-regulated disease-associated (DAM) pathways involving A{beta} clearance, response to lipids, and macrophage activation within the post-encephalitis 5xFAD brains. ConclusionsTogether, these findings suggest an attenuated myeloid cell response to A{beta} plaque burden in 5xFAD mice following acute viral encephalitis. Future experiments aim to further dissect inflammatory mechanisms between infiltrating myeloid cells, T cells, and the progression of A{beta} and tau pathology. Data derived from these experiments will further elucidate the viral-induced neuroimmune mechanisms that affect AD pathology and offer an opportunity to determine how these neuropathologic changes, such as subsequent neuronal damage, occur.

neuroscience↗

bioRxiv2025

Infection of 5xFAD mice with a mouse-adapted SARS-CoV-2 does not alter Alzheimer's disease neuropathology yet induces wide-spread changes in gene expression across diverse cell types

Alzheimers disease (AD) is a progressive neurodegenerative disorder and the leading cause of dementia. It is characterized by cognitive decline and accumulation of amyloid beta (A{beta}) plaques and neurofibrillary tangles. Accumulating evidence indicates that viral infection may worsen and/or increase development of established AD pathology. The COVID-19 pandemic has brought attention to the link between SARS-CoV-2 infection and neurologic conditions that vary in severity and duration, as well as the worsening of clinical symptoms in elderly people with dementia. To better understand potential mechanisms by which SARS-CoV-2 infection impacts AD neuropathology, aged 5xFAD and wildtype (WT) mice were intranasally infected with mouse-adapted SARS-CoV-2 (MA10). Intranasal infection of aged-matched (10-14 month) 5xFAD or wild type (WT) C57BL/6 mice with MA10 resulted in viral infection of the lungs that correlated with acute viral pneumonia characterized by lymphocyte inflammation and antiviral immune responses. Viral RNA was not detected within the central nervous system (CNS) of either WT or 5xFAD mice at days 7 or 21 post-infection (p.i.), nor were there signs of overt glial activation or neuroinflammation. There were no differences in either A{beta} plaque volume or number within the brains of MA10-infected 5xFAD mice compared to uninfected 5xFAD mice. However, bulk RNA sequencing and spatial transcriptomics revealed evidence of altered expression of genes associated with neuronal and glial dysfunction, as well as reduced expression of genes encoding adhesion molecules in vascular endothelial cells. Collectively, these findings demonstrate that MA10 infection did not affect A{beta} plaque size or numbers in 5xFAD mice, yet in both WT and 5xFAD mice, there were numerous down-stream effects on gene expression associated with resident CNS cell function.

pathology↗

bioRxiv2025

Trump Administration Impacts on Early Career Scientists and How To Fight Back

Scientific research drives national progress and innovation, and must be protected at all costs. Actions from the Trump administration in early 2025 sent shockwaves across academic research. Federal science budgets were slashed, hundreds of research grants were abruptly frozen or terminated, and politically appointed agency heads overrode peer-reviewed grant decisions. We conducted rapid-response surveys to capture quotes, stories, and data to understand how these seismic shifts were being felt by early career researchers. The majority of survey respondents were PhD students, and early career trainees in varying years of training at a variety of institutions, mainly in the life sciences. Their future in research, funded by major science agencies including NIH, was threatened by funding cuts with varying impacts to their professional endeavors. Survey respondents highlighted concerns with long-term research job prospects and broader systemic issues in academia, leading them to consider leaving the field altogether and/or pursue science in another country. Their opinions highlighted concerns at the undergraduate, graduate, and postdoctoral levels. While universities provided some resources, trainees called upon Congress to protect, stabilize, and restore science funding. They also undertook a number of advocacy actions across the nation. The fight is far from over. Continued support for early career researchers and their careers in research is imperative to continue both in the current environment and into the future, in order to develop a strong workforce and ensure U.S. global competitiveness in science and technology fields.

scientific communication and education↗

bioRxiv2025

Effects of Cholesterol Modulation on Cisplatin-Induced Hearing Loss

Cisplatin is a widely used and effective anticancer drug. However, it causes permanent sensorineural hearing loss in over 50% of treated patients. There are no FDA-approved therapies to prevent cisplatin-induced hearing loss (CIHL) in adults, highlighting a critical unmet clinical need. Previous studies suggest that statins, commonly prescribed cholesterol-lowering drugs, are associated with reduced incidence and severity of cisplatin-induced hearing loss. Statins are primarily used to lower cholesterol, but they also exert several pleiotropic effects, making the mechanism(s) underlying this protection unclear. Here we examine whether reduced plasma cholesterol confers protection against CIHL independent of statin treatment. We utilized mice lacking serine protease proprotein convertase subtilisin/kexin type 9 (Pcsk9 knockout (KO) mice) as a genetic model of reduced plasma cholesterol. We find that Pcsk9 KO mice are protected against cisplatin-induced hearing loss, as reflected by significantly lower ABR and DPOAE threshold shifts relative to wild type (WT) mice following treatment. Histological analyses confirmed preservation of cochlear outer hair cells (OHCs) in Pcsk9 KO mice treated with cisplatin, whereas WT mice showed significant OHC loss in the high-frequency cochlear regions. Finally, hearing loss positively correlated with baseline plasma cholesterol levels. Together our data demonstrate that systemic cholesterol reduction provides significant protection against CIHL, and they suggest that the protective effect of statins against CIHL is mediated by cholesterol reduction.

neuroscience↗

bioRxiv2025

Choice history biases evidence accumulation: a cross-species comparison from humans to mice

Mice are increasingly used to study the neural circuit-level basis of behavior, often with the ultimate goal of extrapolating these insights to humans. To generalize insights about neural functioning across species, it is crucial to ensure correspondence in behavioral and cognitive strategy. We previously showed that human observers evidence accumulation is biased by previous choices (Urai et al., 2019). To replicate these findings across species, we fit Diffusion Decision Models (Fengler et al., 2025) to behavioral data from 62 mice performing a standardized perceptual decision-making task (The International Brain Laboratory et al., 2021). We identified the same cognitive strategy of history-dependent evidence accumulation: individual differences in choice repetition were explained by a history-dependent bias in the rate of evidence accumulation rather than its starting point. We argue that history-biased evidence integration reflects a fundamental aspect of perceptual decision-making, that may transcend the specific species.

animal behavior and cognition↗

bioRxiv2023

Macrophage Depletion Protects Against Cisplatin-Induced Ototoxicity and Nephrotoxicity

Cisplatin is a widely used and highly effective anti-cancer drug with significant side effects including ototoxicity and nephrotoxicity. Macrophages, the major resident immune cells in the cochlea and kidney, are important drivers of both inflammatory and tissue repair responses. To investigate the roles of macrophages in cisplatin-induced ototoxicity and nephrotoxicity, we used PLX3397, an FDA-approved inhibitor of the colony-stimulating factor 1 receptor (CSF1R), to eliminate tissue-resident macrophages during the course of cisplatin administration. Mice treated with cisplatin alone (cisplatin/vehicle) had significant hearing loss (ototoxicity) as well as kidney injury (nephrotoxicity). Macrophage ablation using PLX3397 resulted in significantly reduced hearing loss measured by auditory brainstem responses (ABR) and distortion-product otoacoustic emissions (DPOAE). Sensory hair cells in the cochlea were protected against cisplatin-induced death in mice treated with PLX3397. Macrophage ablation also protected against cisplatin-induced nephrotoxicity, as evidenced by markedly reduced tubular injury and fibrosis as well as reduced plasma blood urea nitrogen (BUN) and neutrophil gelatinase-associated lipocalin (NGAL) levels. Mechanistically, our data suggest that the protective effect of macrophage ablation against cisplatin-induced ototoxicity and nephrotoxicity is mediated by reduced platinum accumulation in both the inner ear and the kidney. Together our data indicate that ablation of tissue-resident macrophages represents a novel strategy for mitigating cisplatin-induced ototoxicity and nephrotoxicity. Brief summaryMacrophage ablation using PLX3397 was protective against cisplatin-induced ototoxicity and nephrotoxicity by limiting platinum accumulation in the inner ear and kidney.

immunology↗

bioRxiv2023

Large-scale annotated dataset for cochlear hair cell detection and classification

Our sense of hearing is mediated by cochlear hair cells, localized within the sensory epithelium called the organ of Corti. There are two types of hair cells in the cochlea, which are organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains a few thousands of hair cells, and their survival is essential for our perception of sound because they are terminally differentiated and do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. However, the sheer number of cells along the cochlea makes manual quantification impractical. Machine learning can be used to overcome this challenge by automating the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, human, pig and guinea pig cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 90,000 hair cells, all of which have been manually identified and annotated as one of two cell types: inner hair cells and outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to supply other groups within the hearing research community with the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.

neuroscience↗

bioRxiv2022

Environmental Conditions and Vigilance Behaviour in the Smooth-coated Otter, Lutrogale perspicillata

Vigilance is an ecologically important behaviour that acts as a defence mechanism against threats such as predators, competitors, and environmental pressures. Being vigilant can place energetic constraints on an individual, as conducting other behaviours such as grooming can be limited. The smooth-coated otter is a vulnerable species, and understanding baseline behaviour, such as vigilance, and stressor effects can be a crucial step in implementing any conservation strategies. However, literature on this charismatic species is relatively sparse, with the majority of research covering prey items, habitat use and extent of occurrence. Using camera trap footage along with historical climate datasets, the current study assessed various aspects of vigilance behaviour of the smooth-coated otter. These aspects include how long individuals dedicated to being vigilant, what they prioritised being vigilant over, and how intense their vigilance efforts were Variables that are expected to change with global climate change such as temperature, and to an extent, air pressure, were associated with increases in vigilance duration. Wind speeds, which are also expected to be affected by climate change, along with increasing numbers of conspecifics, were linked to increased intensity possibly highlighting that increasing ambient movement results in more frequent head rotations. When vigilance is ineffectual however, such during periods of higher rainfall, cloud cover or at night, intensity decreases, and gazing towards conspecifics increases - possibly to reaffirm where safety lies when threats cannot be adequately monitored.

animal behavior and cognition↗

bioRxiv2020

Trk Agonist Drugs Rescue Noise-Induced Hidden Hearing Loss

TrkB agonist drugs are shown here to have a significant effect on the regeneration of afferent cochlear synapses after noise-induced synaptopathy. The effects were consistent with regeneration of cochlear synapses that we observed in vitro after synaptic loss due to kainic acid-induced glutamate toxicity and were elicited by administration of TrkB agonists, amitriptyline and 7,8-dihydroxyflavone, directly into the cochlea via the posterior semicircular canal 48 h after exposure to noise. Synaptic counts at the inner hair cell and wave 1 amplitudes in the ABR were partially restored 2 weeks after drug treatment. Effects of amitriptyline on wave 1 amplitude and afferent auditory synapse numbers in noise-exposed ears after systemic (as opposed to local) delivery were profound and long-lasting; synapses in the treated animals remained intact one year after the treatment. However, the effect of systemically delivered amitriptyline on synaptic rescue was dependent on dose and the time window of administration: it was only effective when given before noise exposure at the highest injected dose. The long-lasting effect and the efficacy of post-exposure treatment indicate a potential broad application for the treatment of synaptopathy, which often goes undetected until well after the original damaging exposure(s).

neuroscience↗

bioRxiv2020

Global mapping of Salmonella enterica-host protein-protein interactions during infection

Intracellular bacterial pathogens inject effector proteins into host cells to hijack diverse cellular processes and promote their survival and proliferation. To systematically map effector-host protein-protein interactions (PPIs) during infection, we generated a library of 32 Salmonella enterica serovar Typhimurium (STm) strains expressing chromosomally encoded affinity-tagged effector proteins, and quantified PPIs in macrophages and epithelial cells by Affinity-Purification Quantitative Mass-Spectrometry. Thereby, we identified 25 previously described and 421 novel effector-host PPIs. While effectors converged on the same host cellular processes, most had multiple targets, which often differed between cell types. Using reciprocal co-immunoprecipitations, we validated 13 out of 22 new PPIs. We then used this host-pathogen physical interactome resource to demonstrate that SseJ and SseL collaborate in redirecting cholesterol to the Salmonella Containing Vacuole (SCV) via NPC1, PipB directly recruits the organelle contact site protein PDZD8 to the SCV, and SteC promotes actin bundling by directly phosphorylating formin-like proteins.

microbiology↗

bioRxiv2020

Cyclin E1 protein is stabilized in BRCA1 mutated breast cancers leading to synergy between CDK2 and PARP inhibitors

Basal-like breast cancers (BLBC) are aggressive breast cancers that respond poorly to targeted therapies and chemotherapies. In order to define therapeutically targetable subsets of BLBC we examined two markers: cyclin E1 and BRCA1 loss. In high grade serous ovarian cancer (HGSOC) these markers are mutually exclusive, and define therapeutic subsets. We tested the same hypothesis for BLBC. Using a BLBC cohort enriched for BRCA1 loss, we identified convergence between BRCA1 loss and high cyclin E1 expression, in contrast to HGSOC in which CCNE1 amplification drives increased cyclin E1 gene expression. Instead, BRCA1 loss stabilized cyclin E1 during the cell cycle. Using siRNA we showed that BRCA1 loss leads to stabilization of cyclin E1 by reducing phospho-cyclin E1-T62, and conversely the overexpression of BRCA1 increased phospho-T62. Mutation of cyclin E1-T62 to alanine increased cyclin E1 stability. We showed that tumors with high cyclin E1/BRCA1 mutation in the BLBC cohort had decreased phospho-T62, supporting this hypothesis. Since cyclin E1/CDK2 protects cells from DNA damage and cyclin E1 is elevated in BRCA1 mutant cancers, we hypothesized that CDK2 inhibition would sensitize these cancers to PARP inhibition. CDK2 inhibition induced DNA damage and synergized with PARP inhibitors to reduce cell viability in BRCA1 mutated cell lines. Treatment of BLBC patient-derived xenograft models with combination PARP and CDK2 inhibition led to tumor regression and increased survival. We conclude that BRCA1 status and high cyclin E1 have potential as predictive biomarkers to dictate the therapeutic use of combination CDK inhibitors/PARP inhibitors in BLBC.

cancer biology↗