Biology subjects

Johnson, P.

Publications and source records attributed to Johnson, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

Previous studies have shown that there may be more species of Azolla in California than currently recognized, including a recent introduction of the non-native Azolla caroliniana. To better assess the status and species diversity of Azolla in California, we sequenced four historical herbarium specimens, some over 100 years old, and increased our sampling of extant populations across seven counties in California. We found that many specimens from California thought to be Azolla microphylla are actually Azolla filiculoides or members of one of two non-native "Azolla caroliniana" clades. We also found that some specimens collected from California from the 1960s through the 1980s fall within an Azolla microphylla-mexicana clade. However, there is no evidence of this species from any recent collections even from counties where it was previously found, which points to a potential extirpation of this species from California.

ecology↗

bioRxiv2026

An Open Test--Retest Dataset of Rapid Myelin Mapping Acquisitions

Myelin supports rapid and efficient neural communication and is implicated in brain development, learning, aging, and neurological disease. Although numerous magnetic resonance imaging (MRI) approaches have been proposed to characterize myelin in vivo, they have rarely been evaluated together within the same participants and across repeated acquisitions. To address these gaps, we introduce the Myelin Imaging Reliability and ReprOducibility Resource (MIRROR), an openly available multimodal test--retest MRI dataset of diffusion MRI (dMRI), inhomogeneous magnetization transfer imaging (ihMT), quantitative susceptibility mapping (QSM), MP2RAGE, T1w/T2w ratio mapping, and transverse relaxometry in 22 healthy adults. We evaluated gray--white matter differentiation, intermetric correspondence, test--retest reliability, and participant specificity across 27 myelin-sensitive metrics. Gray--white matter differentiation was strong for dMRI derivatives, MP2RAGE-derived R1, T1w/T2w, and ihMT, while being substantially weaker for QSM measures. Intermetric spatial correlations were generally strongest within acquisition or modeling families. Test--retest reliability was generally high, particularly for dMRI-derived metrics, but was more variable among QSM-, ihMT-, and R2*-derived measures. Regional spatial profiles were also highly participant-specific, with discriminability approaching its upper bound for most metrics. All imaging data, derived maps, and processing code are openly released. MIRROR provides a benchmark for characterizing the measurement properties and practical tradeoffs of scalable myelin-sensitive MRI methods, supporting principled acquisition selection and accelerating methodological development and validation.

neuroscience↗

bioRxiv2026

Spatially distributed growth factor environments for evaluating hydrogel-based CD34+ cell culture conditions

Suspension culture is the gold standard for ex vivo hematopoietic stem cell (HSC) expansion; however, high media requirement results in expensive cell therapy products. Hydrogel-based HSC culture represents a more realistic in vitro representation of human in vivo HSC microenvironments and may support a more efficient use of media during ex vivo HSC expansion. However, media conditions used for hydrogel-supported cell culture often simply mimic that which are currently used in suspension culture approaches, potentially resulting in an oversupply of cell growth proteins. In this work, we present a microfluidic culture system capable of supporting hydrogel-based cell culture and generating spatial distributions of independent growth factor combinations. Using this device, we image, in real-time, the behaviour of human umbilical cord blood-derived CD34+ cells, within fibrin-based hydrogels, in response to spatial gradients of the human recombinant growth factors stem cell factor, thrombopoietin, angiopoietin-2 and insulin-like growth factor-II. Using live microscopy and image-based single-cell segmentation and quantification, local changes in cell density over time in relation to spatial concentration of factors were identified. This novel microfluidic device has the potential to screen combinations of growth factors required for hydrogel-supported CD34+ cell expansion and inform culture media formulations of future hydrogel-based cell manufacturing processes.

bioengineering↗

bioRxiv2026

Postnatal Reprogramming Shapes Human Intestinal Epithelial Immune Competency

At birth, the intestine must rapidly adapt to enable nutritional function and immune microbial tolerance. Here, integrating single-cell multi-omics and spatial transcriptomics we define the circuits underpinning this process. We identify asynchronous developmental trajectories with postnatal epithelial reprogramming characterised by coordinated changes in metabolism, junctional structure and innate defence. At birth epithelial stem cells demonstrate dynamic enhancer remodelling, with accessibility often preceding transcription. Fetal stemness elements remain accessible despite reduced transcription across epithelial lineages, retaining plasticity potential. Post-natal epithelia experience sequential homing of myeloid cells followed by innate T cells with peri-epithelial B cells localising later in infancy. Using developmentally staged organoids, we show that epithelial responses to inflammatory stimuli are age-dependent and constrained in early life. We identify BHLHE40 as an early-life regulator that attenuates the impact of interferon- and NF-{kappa}B-driven signalling. Altogether we define the events driving epithelial licensing and barrier adaptation at birth and through infancy.

cell biology↗

bioRxiv2026

A genome-wide CRISPR screen reveals cancer-specific regulators of hyaluronan binding and cellular invasion

Metastatic spread of cancer cells is driven by binding between the cell-surface receptor CD44 and hyaluronan (HA) in the extracellular matrix. The specific oncogenes that drive increased CD44-HA binding in cancer remain poorly defined. Using a fluorescently labeled hyaluronan probe, we performed a genome-wide CRISPR screen to identify genes whose knockdown disrupts HA binding in breast cancer cells. We subsequently developed a bioinformatic analysis pipeline that enabled stratification and prioritization of cancer-specific regulators. This work provides a first-in-class resource for the identification of druggable targets to inhibit HA binding. We further validate RAB4A, a top hit from our screen, as a novel regulator of this process. Mechanistically, RAB4A KO dramatically reduces CD44 expression and inhibits the invasion of breast cancer cells through HA-rich matrices. This study validates a novel strategy for identifying regulators of cancer cell invasion and identifies immediate actionable targets for anti-metastatic therapy.

cancer biology↗

bioRxiv2025

A dynamical systems model of arousal-driven behavioural state transitions

When completing a task, animals switch between being engaged and disengaged. What neural and physiological processes trigger these behavioural state transitions? We estimated the engagement state of mice performing a visual decision-making task using a hidden Markov model of response times and found that intermediate arousal, as measured using baseline pupil size, was associated with more engagement in the task. Additionally, we show that changes in arousal (both mean and variability of the pupil baseline) predict changes in behavioural state. To explain this, we propose a double-well model, in which arousal causes behavioural state transitions by reshaping the attractor landscape of population neural activity. These results highlight a possible mechanism of arousal-related changes in behaviour.

animal behavior and cognition↗

bioRxiv2024

Trichomonas vaginalis extracellular vesicles suppress IFNϵ-mediated protection against host cell cytolysis

Trichomonas vaginalis is a commonly acquired sexually transmitted infection (STI) often found in symbiosis with the intracellular bacterium Mycoplasma hominis, an opportunistic pathogen of the female reproductive tract associated with bacterial vaginosis. How this symbiosis affects infection outcomes, and the host cell innate immune response is still poorly understood. Here we show that T. vaginalis extracellular vesicles down-regulate a non-canonical type I interferon, interferon-epsilon, and suppress type I interferon responses. Transcriptomic analysis reveals that infection with T. vaginalis in symbiosis with M. hominis or M. hominis alone upregulates genes involved in the type I IFN response, but infection with T. vaginalis alone does not. Finally, we show that interferon-epsilon stimulation is protective against T. vaginalis cytoadherence and cytolysis of host cells and increases the ability of neutrophils to kill the parasite. These studies provide insight into the innate immune response induced by a highly prevalent STI and its bacterial symbiont.

microbiology↗

bioRxiv2024

Comparative analysis of protein expression between oesophageal adenocarcinoma and normal adjacent tissue

Oesophageal adenocarcinoma (OAC) is the 7th most common cancer in the United Kingdom and remains a significant health challenge. This study presents a proteomic analysis of seven OAC donors complementing our previous neoantigen identification study of their human leukocyte antigen (HLA) immunopeptidomes. Using label-free mass spectrometry proteomics, we compared OAC tumour tissue to matched normal adjacent tissue (NAT) to identify differentially expressed proteins. We identified differential expression of a number of proteins previously linked to OAC and other cancers. We observed enrichment of processes and pathways relating RNA processing and the immune system. Our findings also offer insight into the role of the protein stability in the generation of the neoantigen we previously identified. These results provide independent corroboration of existing oesophageal adenocarcinoma biomarker studies that may inform future diagnostic and therapeutic research.

cancer biology↗

bioRxiv2024

Comparative analysis of transcriptomic and proteomic expression between two non-small cell lung cancer subtypes

Non-small cell lung cancer (NSCLC) is frequently diagnosed at an advanced stage and has poor survival. NSCLC subtypes require different treatment regimes, hence there are extensive efforts to find more precise and non-invasive differential diagnostics tools. Complementing these efforts, we examined two NSCLC subtypes for differences that may inform treatment options and identify potential novel therapeutic pathways. Here we present a comparative analysis of transcriptomic and proteomic expression in tumours from a cohort of 22 NSCLC patients: 8 squamous cell carcinoma (LUSC), 14 adenocarcinoma (LUAD). We examined differential gene and differential protein expression between LUSC and LUAD, and between NSCLC subtypes and either PBMCs or normal adjacent lung tissue (NAT). We found that both NSCLC subtypes shared common differences in gene expression to PBMC relating to developmental and structural changes, and common protein expression differences to NAT relating to protein translation and RNA related processing and splicing. Between NSCLC subtypes we found differential gene expression relating to cell differentiation for LUSC and cellular structure and immune response regulation for LUAD. Differential protein expression between NSCLC subtypes related to extracellular structure for LUSC and metabolic processes, including glucose metabolism for LUAD. Many of our observations of differentially expressed genes and proteins between NSCLC subtypes support and inform existing observations, aiding both basic and clinical research seeking to identify subtype biomarkers or druggable targets.

cancer biology↗

bioRxiv2024

Proteogenomics guided identification of functional neoantigens in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) has poor survival even with modern checkpoint inhibitor therapies. Personalised vaccines based on short peptide neoantigens containing tumour mutations are an attractive precision medicine strategy, but identifying therapeutically relevant neoantigens remains challenging, with existing methods yielding positive responses in only 6% of candidates tested. We developed an immunopeptidomics approach to improve neoantigen identification in 24 NSCLC patients (15 adenocarcinoma, 9 squamous cell carcinoma). We directly identified one neoantigen and using whole exome sequencing, transcriptomics and mass spectrometry-based immunopeptidomics, we filtered predicted neoantigens based on observed cohort HLA peptide presentation. This approach achieved positive functional responses in 5 of 6 patients tested (83% success rate) with 13% of putative neoantigens (9 out of 70) eliciting strong responses. Bayesian modelling of our initial rules-based neoantigen selection further revealed patient specific peptide presentation patterns and propensities. Our findings demonstrate that incorporating donor specific HLA peptide presentation data substantially improves neoantigen identification success rates and immune response specificity, advancing personalised cancer vaccine development.

immunology↗

bioRxiv2024

Polyphosphate mobilization influences the ability of Cryptococcus neoformans to cause disease in a murine model of cryptococcosis

Cryptococcus neoformans, an invasive basidiomycete fungal pathogen, causes one of the most prevalent, life-threatening diseases in immunocompromised individuals and accounts for [~]15% of AIDS-associated deaths. A dire need for the development of novel antifungal drugs, vaccines, and improved diagnostics has emerged with the increased frequency of fungal infections. Therefore, understanding the pathogenesis of C. neoformans and its interactions with the host immune system is critical for the development of therapeutics against cryptococcosis. Previous research demonstrated that C. neoformans cells lacking polyphosphate (polyP), an immunomodulatory polyanionic storage molecule, display altered cell surface architecture. However, the relevance of surface changes and the role of polyP in the virulence of C. neoformans remain unclear. Here we show that mutants lacking the polyphosphatases (Xpp1 and Epp1) are attenuated for virulence in a murine inhalational model of cryptococcosis, demonstrate reduced proliferation in host tissue, and provoke an altered immune response. An analysis of mutants lacking the polyphosphatases and the Vtc4 protein for polyP synthesis indicated that the Xpp1 and Epp1 contribute to the organization of the cell surface, virulence factor production, the response to stress, and mitochondrial function. Overall, we conclude that polyP mobilization plays a multifaceted role in the pathogenesis of C. neoformans. Author SummaryCryptococcus neoformans causes one of the most prevalent fungal diseases in people with compromised immune systems and accounts for 15-20% of AIDS-associated deaths worldwide. The continual increase in the incidence of fungal infections and limited treatment options necessitate the development of new antifungal drugs and improved diagnostics. Polyphosphate (polyP), an under-explored biopolymer, functions as a storage molecule, modulates the host immune response, and contributes to the ability of many fungal and bacterial pathogens to cause disease. However, the role of polyP in cryptococcal disease remains unclear. In this study, we report that the enzymes that regulate polyP synthesis and turnover contribute to the virulence of C. neoformans in a mouse model of cryptococcosis. The polyphosphatases, Xpp1 and Epp1, influenced the survival of C. neoformans in macrophages and altered the host immune response. The loss of Xpp1 and Epp1 led to changes in cell surface architecture, cell size, impaired growth, and defects in both mitochondrial function and the stress response of C. neoformans. Thus, our work establishes polyP as a key factor in the disease caused by C. neoformans, and identifies polyP mobilization as a novel target to support new therapeutic approaches.

microbiology↗

bioRxiv2024

Differential TLR-ERK1/2 activity promotes viral ssRNA and dsRNA mimic-induced dysregulated immunity in macrophages

RNA virus induced excessive inflammation and impaired antiviral interferon (IFN-I) responses are associated with severe disease. This innate immune response, also referred to as dysregulated immunity, is caused by viral single-stranded RNA (ssRNA) and double-stranded-RNA (dsRNA) mediated exuberant inflammation and viral protein-induced IFN antagonism. However, key host factors and the underlying mechanism driving viral RNA-mediated dysregulated immunity are poorly defined. Here, using viral ssRNA and dsRNA mimics, which activate toll-like receptor 7 (TLR7) and TLR3, respectively, we evaluated the role of viral RNAs in causing dysregulated immunity. We show that murine bone marrow-derived macrophages (BMDMs) stimulated with TLR3 and TLR7 agonists induce differential inflammatory and antiviral cytokine response. TLR7 activation triggered a robust inflammatory cytokine/chemokine induction compared to TLR3 activation, whereas TLR3 stimulation induced significantly increased IFN/IFN stimulated gene (ISG) response relative to TLR7 activation. To define the mechanistic basis for dysregulated immunity, we examined cell-surface and endosomal TLR levels and downstream mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-kB) activation. We identified a significantly higher cell-surface and endosomal TLR7 expression compared to TLR3, which further correlated with early and robust MAPK (pERK1/2 and p-P38) and NF-kB activation in TLR7-stimulated macrophages. Furthermore, blocking EKR1/2, p38, and NF-kB activity reduced TLR3/7-induced inflammatory cytokine/chemokine levels, whereas only ERK1/2 inhibition enhanced viral RNA-mimic-induced IFN/ISG responses. Collectively, our results illustrate that high cell surface and endosomal TLR7 expression and robust ERK1/2 activation drive viral ssRNA mimic-induced excessive inflammatory and reduced IFN/ISG responses, and blocking ERK1/2 activity would mitigate viral-RNA/TLR-induced dysregulated immunity.

immunology↗

bioRxiv2024

Evaluation of the potential food allergy risks of recombinant human lactoferrin expressed in Komagataella phaffii

Prior to the introduction of novel food ingredients into the food supply, safety risk assessments are required, and numerous prediction models have been developed and validated to evaluate safety. The allergenic risk potential of Helaina recombinant human lactoferrin (rhLF, Effera), produced in Komagataella phaffii (K. phaffii) was assessed by literature search, bioinformatics sequence comparisons to known allergens, glycan allergenicity assessment, and a simulated pepsin digestion model. The literature search identified no allergenic risk for Helaina rhLF, K. phaffii, or its glycans. Bioinformatics search strategies showed no significant risk for cross-reactivity or allergenicity between rhLF or the 36 residual host proteins and known human allergens. Helaina rhLF was also rapidly digested in simulated gastric fluid and its digestibility profile was comparable to human milk lactoferrin (hmLF), further demonstrating a low allergenic risk and similarity to the hmLF protein. Collectively, these results demonstrate a low allergenic risk potential of Helaina rhLF and do not indicate the need for further clinical testing or serum IgE binding to evaluate Helaina rhLF for risk of food allergy prior to introduction into the food supply.

immunology↗

bioRxiv2023

Aggressive mimicry lure polymorphisms in the parasitic mussel Lampsilis fasciola model fish or leech host prey and differ in morphology and pigmentation, but not in display behavior.

Unionoid freshwater mussels (Bivalvia: Unionidae) are free-living apart from a brief, obligately parasitic, larval stage that infects fish hosts and gravid female mussels have evolved a spectrum of strategies to infect fish hosts with their larvae. In many North American species, this involves displaying a mantle lure: a pigmented fleshy extension that acts as an aggressive mimic of a host fish prey, thereby eliciting a feeding response that results in host infection. The mantle lure of Lampsilis fasciola is of particular interest because it is apparently polymorphic, with two distinct primary lure phenotypes. One, described as "darter-like", has "eyespots", a mottled body coloration, prominent marginal extensions, and a distinct "tail". The other, described as "worm-like", lacks those features and has an orange and black coloration. We investigated this phenomenon to 1) confirm that it is a true polymorphism; 2) investigate its ecological persistence; 3) identify the range of putative model species targeted by this mimicry system within a river drainage; 4) determine whether the mantle lure polymorphism includes a behavioral component. Detection of within-brood lure variation and within-population phylogenomic (ddRAD-seq) analyses of individuals bearing different lures confirmed that this phenomenon is a true polymorphism. It appears stable over ecological timeframes: the ratio of the two lure phenotypes in a River Raisin (MI) population in 2017 was consistent with that of museum samples collected at the same site 6 decades earlier. Within the River Raisin, four main "darter-like" lure motifs visually approximated four co-occurring darter species (Etheostoma blennioides, E. exile, E. microperca, and Percina maculata) and the "worm-like" lure resembled a widespread common leech, Macrobdella decora. Darters and leeches are typical prey of Micropterus dolomieui (smallmouth bass), the primary fish host of L. fasciola. In situ field recordings were made of the L. fasciola "darter" and "leech" lure display behaviors, in addition to the non-polymorphic lure display of co-occurring L. cardium. Despite having putative models in distinct phyla, both L. fasciola lure morphs have similar display behaviors that differ significantly from that of sympatric L. cardium individuals. We conclude that the L. fasciola mantle lure polymorphism does not include a behavioral component. Discovery of discrete within-brood inheritance of the lure polymorphism implies potential control by a single genetic locus and identifies L. fasciola as a promising study system to identify regulatory genes controlling a key adaptive trait of freshwater mussels.

ecology↗

bioRxiv2023

Decoding Remapped Spatial Information in the Peri-Saccadic Period

It has been suggested that, prior to a saccade, visual neurons predictively respond to stimuli that will fall in their receptive fields after completion of the saccade. This saccadic remapping process is thought to compensate for the shift of the visual world across the retina caused by eye movements. To map the timing of this predictive process in the brain, we recorded neural activity using electroencephalography (EEG) during a saccade task. Participants made saccades between two fixation points while covertly attending to oriented gratings briefly presented at various locations on the screen. Data recorded during trials in which participants maintained fixation were used to train classifiers on stimuli in different positions. Subsequently, data collected during saccade trials were used to test for the presence of remapped stimulus information at the post-saccadic retinotopic location in the peri-saccadic period, providing unique insight into when remapped information becomes available. We found that the stimulus could be decoded at the remapped location [~]180 ms post-stimulus onset, but only when the stimulus was presented 100-200 ms before saccade onset. Within this range, we found that the timing of remapping was dictated by stimulus onset rather than saccade onset. We conclude that presenting the stimulus immediately before the saccade allows for optimal integration of the corollary discharge signal with the incoming peripheral visual information, resulting in a remapping of activation to the relevant post-saccadic retinotopic neurons. Significance StatementEach eye movement leads to a shift of the visual world across the retina, such that the visual input before and after the eye movement do not match. Despite this, we perceive the visual world as stable. A predictive mechanism known as saccadic remapping is thought to contribute to this stability. We use a saccade task with time-resolved EEG decoding to obtain a fine-grained analysis of the temporal dynamics of the saccadic remapping process. Probing different stimulus-saccade latencies and an array of stimulus locations, we identify when remapped information becomes available in the visual cortex. We describe a critical window in which feedforward visual information and the preparatory motor signals interact to allow for predictive remapping of a stimulus.

neuroscience↗

bioRxiv2023

The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis

RNA-binding proteins (RBPs) are emerging as important regulators of pathogenesis, including cancer. Here we reveal that the recently characterised RBPs LARP4A and LARP4B are differentially overexpressed in primary osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B inhibited primary tumour growth and metastatic spread in xenograft studies, as well as inhibiting cell proliferation, motility and migration. Transcriptomic profiling combined with high content multiparametric cell cycle analysis unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cell lines, potentially through modulating the post-transcriptional regulation of RNA targets that include key cell cycle proteins such as Cyclins B1 and E2, Aurora B and E2F1. Our work assigns new functions to LARP4A and LARP4B as pro-tumorigenic proteins in bone and prostate cancer, highlights their similarities while indicating distinct functional aspects, and adds significantly to the rapidly increasing roles of RBPs in different cancer models. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying novel tissue-specific targets and potential druggable intervention.

cancer biology↗

bioRxiv2022

Influence of pump laser fluence on ultrafast structural changes in myoglobin

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump probe experiments for investigating electronic and nuclear changes during light-induced reactions. On time scales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1. However, all ultra-fast TR-SFX studies to date have employed such high pump laser energies that several photons were nominally absorbed per chromophore2-14. As multiphoton absorption may force the protein response into nonphysiological pathways, it is of great concern15 whether this experimental approach16 allows valid inferences to be drawn vis-a-vis biologically relevant single-photon-induced reactions17. Here we describe ultrafast pump-probe SFX experiments on photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics15) are seen to depend strongly on pump laser energy. Our results confirm both the feasibility and necessity of performing TR-SFX pump probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing design and interpretation of ultrafast TR-SFX pump probe experiments16 such that biologically relevant insight emerges.

biophysics↗

bioRxiv2022

Identification of neoantigens in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for immunotherapy are short peptide neoantigens containing tumor mutations, presented to cytotoxic T-cells by human leukocyte antigen molecules (HLA). Despite an association between putative neoantigen abundance and therapeutic response across cancers, immunogenic neoantigens are challenging to identify. Here we characterized the mutational and immunopeptidomic landscapes of tumors from a cohort of seven patients with EAC. We directly identified one HLA-I presented neoantigen from one patient, and report functional T-cell responses from a predicted HLA-II neoantigen in a second patient. The predicted class II neoantigen contains both HLA I and II binding motifs. Our exploratory observations are consistent with previous neoantigen studies in finding that neoantigens are rarely directly observed, and an identification success rate following prediction in the order of 10%. However, our identified putative neoantigen is capable of eliciting strong T-cell responses, emphasizing the need for improved strategies for neoantigen identification.

cancer biology↗