Biology subjects

Hall, B.

Publications and source records attributed to Hall, B..

At least 19 recordsLinked to original sources

bioRxiv2026

SpiE is a distinct gut microbial 4-cholesten-3-one 5β-reductase that acts with SpiR to convert cholesterol to coprostanol

Gut microbes convert cholesterol into coprostanol, a poorly absorbed sterol that is largely excreted in feces and is linked to lower serum cholesterol levels. However, the enzymes responsible for this process remain poorly characterized. The second step of the pathway, cholestenone reduction into coprostanone, has long been established, yet the enzyme(s) responsible were unknown. Here, we use comparative genomics to identify SpiE, a cholestenone (4-cholesten-3-one) reductase that is part of the steroid processing (spi) pathway with SpiR. We confirm that SpiE binds to and reduces both cholestenone and progesterone into 5{beta}-reduced forms. SpiR and SpiE together convert cholesterol into coprostanol, indicating that both enzymes are sufficient for coprostanol formation. SpiE belongs to the short-chain dehydrogenase (SDR) family and represents an evolutionarily distinct lineage of SDR ene-reductases. Metagenomic analyses reveal that spiE relative abundance is strongly correlated with stool coprostanol (Spearman's {rho}=0.81, p=5.99e-65). In longitudinal patient cohorts, antibiotic treatment coincided with loss of SpiE and coprostanol production. Post antibiotics, the emergence of distinct SpiE-encoding genera rescued coprostanol production in some individuals. Our findings provide the biochemical basis of the cholesterol to coprostanol pathway and lay the groundwork for future studies linking it to host physiology.

microbiology↗

bioRxiv2026

Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes

Gut bacteria reduce bilirubin to urobilinogen, allowing it to be excreted through feces and urine, but studies have long noted a heterogeneous mixture of partially reduced bilirubin-derived intermediates, suggesting that multiple enzymes are involved. Here we identify bilirubin vinyl reductase (BilV), a novel Old Yellow Enzyme family reductase encoded in the genomic neighborhood of the known bilirubin reductase (bilR). Using heterologous expression and LC-MS/MS, we show that BilR acts on the methine bridges in the bilirubin reduction pathway; co-expression with BilV enables vinyl-group reduction and complete conversion to urobilinogen. In bacterial genomes, bilV co-occurs primarily with the bilR-insertion subtype and is largely absent alongside bilR-short. Analysis of 1,197 gut metagenomes across 14 vertebrate species reveals that this differential co-occurrence shapes pathway availability across hosts: carnivores and omnivores carry balanced bilR and bilV, whereas avian microbiomes, dominated by bilR-short, are depleted for bilV. These findings establish that bilirubin reduction to urobilinogen involves two enzymes with complementary regioselectivity, and that their distribution across vertebrate gut microbiomes varies in concert with host bile pigment chemistry.

microbiology↗

bioRxiv2026

Energy Expenditure During Walking With a Novel Treadmill Controller That Induces Gait Asymmetry

Gait asymmetry is a common manifestation of walking impairment among clinical populations. We recently developed a novel treadmill walking approach called dynamic treadmill walking that can provide asymmetric gait training by changing the treadmill speed between fast and slow speeds within a single stride. Here, we studied the energy expenditure associated with a variety of dynamic treadmill walking conditions. We hypothesized that the metabolic power required for dynamic treadmill walking in all conditions would approximate the metabolic power associated with conventional walking at the mean of the fast and slow speeds employed in the task. Eleven young adults without gait impairment walked on an instrumented treadmill and breathed into a metabolic measurement system. During dynamic treadmill walking, the treadmill fluctuated between 0.75m/s and 1.50m/s, each for 50% of an individual's stride time. We used a metronome to synchronize participants' right heel-strikes with four different timing conditions. Net metabolic power during dynamic treadmill walking was significantly greater than normal walking at the mean speed of the task (1.125m/s) and generally lower than walking at the fast speed (1.5m/s). We did not observe any significant associations between net metabolic power and several measures of gait asymmetry during dynamic treadmill walking. These findings establish dynamic treadmill walking as a promising technique for improving gait symmetry in individuals who cannot tolerate fast treadmill walking, a common gait rehabilitation approach. Future work will assess the feasibility, metabolic demands, and clinical efficacy of using dynamic treadmill walking to improve gait symmetry in clinical populations.

physiology↗

bioRxiv2026

Multisite Evaluation of an Amplification-based Nanopore Sequencing Solution to Analyze Challenging Clinically Relevant Variants in Genes Associated with Hereditary Diseases

PurposeCarrier screening for hereditary conditions is challenged by genes with complex genomic architecture, where short-read sequencing can fail to detect clinically relevant variants. This study evaluated a unified, amplification-based nanopore sequencing workflow across multiple laboratories for comprehensive analysis of such loci. MethodsA modular long-read sequencing assay was evaluated across five laboratories using targeted PCR enrichment, Oxford Nanopore sequencing, and automated variant analysis. The workflow interrogated genes associated with spinal muscular atrophy, thalassemia, cystic fibrosis, fragile X syndrome, congenital adrenal hyperplasia, Gaucher disease, and hemophilia A. Performance was assessed against orthogonal methods for single nucleotide variants (SNVs), indels, copy-number variants, repeat expansions, and structural rearrangements. ResultsAcross 882 unique samples (1,266 tests), overall agreement with comparator methods exceeded 96% for variant-level detection and 97% for genotype status classification. Long-read sequencing enabled phasing of paralogous loci, integrated sizing and interruption analysis for FMR1 repeats, and simultaneous detection of SNVs and structural variants in globin loci and CYP21A2-TNXB region, reducing reliance on multiple workflows. ConclusionThis multisite evaluation suggests that targeted long-read sequencing can consolidate complex variant detection into a single workflow, improving analytical completeness and operational efficiency for carrier screening.

genetics↗

bioRxiv2026

Polyclonal and single clonal patient-derived organoid models of Barrett oesophagus and oesophageal adenocarcinoma establish a platform for the analysis of heterogeneity in disease progression and therapy response

SUMMARY/ABSTRACTOesophageal adenocarcinoma (OAC) is a major cause of morbidity and mortality. OAC and its precursor, Barrett oesophagus (BO), are defined by substantial early heterogeneity, complicating prevention and treatment of OAC and remaining poorly recapitulated by current in vitro and animal model systems. We have generated 116 patient- and healthy donor-derived organoids (PDOs) spanning normal oesophagogastric tissue, BO and OAC. These PDOs capture population diversity and recapitulate phenotypic, genomic and transcriptomic features of their respective disease stages. We develop a single cell-derived clonal organoid approach and show that this enables us to capture the heterogeneity and isolate high-risk, subclonal populations that are difficult to discern and maintain in bulk PDO cultures. Using this platform, we demonstrate functional importance of this biobank across the pre-malignant to invasive disease spectrum, including a role for BO in shaping fibroblast phenotype within assembloids, and diverse responses of OAC to chemotherapy, radiotherapy and targeted CDK4/6 inhibition. HIGHLIGHTSO_LIPatient- and healthy donor-derived organoids (PDOs) provide a functional platform of disease progression and heterogeneity across normal gastric, non-dysplastic and dysplastic Barrett oesophagus (BO) and oesophageal adenocarcinoma (OAC). C_LIO_LIWe provide a quantitative phenotypic and molecular framework to assess the provenance and fidelity of each PDO model given the heterogeneity of this disease. C_LIO_LIPDOs recapitulate key features of non-dysplastic and dysplastic BO, as well as invasive OAC. C_LIO_LISingle cell-derived clonal organoids (sc-organoids) isolate and maintain high-risk subclonal populations. C_LIO_LIOAC PDOs mirror known population level variation in response to systemic anti-cancer therapies. C_LI

cancer biology↗

bioRxiv2026

Codon Deoptimization of Multispecific Biologics Reduces Mispairing During Transient Mammalian Protein Expression

Codon optimization is utilized in biologics design to maximize protein expression. Selecting the host organisms most frequently used codons for each amino acid can significantly enhance recombinant protein expression yields. However, non-optimal codons in mRNA can be critical for functional protein production through inducing pauses in or attenuating protein translation. In our study, we have investigated the effect of deoptimizing serine codons in biologics by shifting them from the five most frequently used codons to the least (TCG). Rare serine codons were strategically inserted into the coding sequences of the constant regions in a trispecific antibody (Protein 1), a bispecific antibody (Protein 2), and multiple non-proprietary bispecific antibodies. We observed that inserting 1-2 rare serine codons within an open reading frame led to expression changes that reduced the formation of mispaired 2x light chain and half-molecule species. Protein purity was drastically increased by incorporating two deoptimized serine codons into a single chain. Notably, we observed a negative correlation between total protein expression yield and final product purity. Taken together, our work demonstrates that incorporation of deoptimized serine codons into a single chain can significantly influence multispecific biologic pairing and enhance final product purity. Our findings align with existing literature showing that rare codon usage modulates translation kinetics and protein folding. Future investigation is warranted to enable a priori identification of the rate-limiting chain in multispecific biologics, thereby guiding strategic codon deoptimization prior to expression.

bioengineering↗

bioRxiv2025

Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements

MYC-driven (MYC+) cancers are aggressive and often fatal. MYC dysregulation is a key event in these cancers, but overexpression of MYC alone is not always enough to cause cancer. Plasmocytoma Variant Translocation 1 (PVT1), a long non-coding RNA (lncRNA) adjacent to MYC on chromosome 8 is a rearrangement hotspot in many MYC+ cancers. In addition to being co-amplified with MYC, the genomic rearrangement at PVT1 involves translocation, which has had obscure functional consequences. We report that translocation at the PVT1 locus cause asymmetric enrichment of 5-PVT1 and loss of 3-PVT1. Despite being classified as a non-coding RNA, the retained 5 region of PVT1 generates a circular RNA (CircPVT1) that codes for the novel peptide we call Firefox (FFX). FFX augments AKT signaling and synergistically activates MYC and mTORC1 in these cells. Further, the 3 end of PVT1, which is lost during the translocation, codes for a tumor-suppressing micropeptide we named as Honeybadger (HNB). We demonstrate that HNB interacts with KRAS and disrupts the activation of KRAS effectors. Loss of HNB leads to activation of RAS/MAPK signaling pathway, and enhances MYC stability by promoting phosphorylation of MYC at Ser62. These findings identify PVT1 as a critical node that synchronizes MYC, AKT, and RAS-MAPK activities in cancer. Our study thus identifies a key mechanism by which rearrangements at the PVT1 locus activate additional oncogenic pathways that synergize with MYC to exacerbate the aggressiveness of MYC+ cancers. This newfound understanding explains the poor prognosis associated with MYC+ cancers and offers potential therapeutic targets that could be leveraged in treatment strategies for these cancers.

cancer biology↗

bioRxiv2025

Differential time-restricted sensitivity of enveloped viruses to Sec61 translocon blockade

The morphogenesis of enveloped viruses relies on the trafficking of transmembrane proteins through the secretory pathway to sites of virus envelopment. The first step in this pathway, their translocation into the endoplasmic reticulum, is therefore an attractive target for broad-spectrum intervention. Here, we tested if blockade of the Sec61 translocon by the Mycobacterium ulcerans exotoxin mycolactone, a potent inhibitor of Sec61, could block the production of virus glycoproteins and subsequent production of infectious virus from a range of human enveloped viruses: the DNA virus herpes simplex virus 1 (HSV1), and the RNA viruses, respiratory syncytial virus (RSV), influenza A virus (IAV), SARS coronavirus 2 (SARS CoV2) and Zika virus (ZIKV). In line with known translocation mechanisms, mycolactone blocked in vitro translocation and ectopic expression of type I transmembrane proteins but not type III, multipass or cytosolic proteins. Translocation of the type II protein RSV G was also blocked and although ectopically expressed G protein was detected, it was not glycosylated. Pretreatment of cells with mycolactone also blocked the synthesis of type I transmembrane proteins in infected cells and either the synthesis or glycosylation of type II transmembrane proteins, and the production of progeny from all viruses tested, while having no effect on virus entry or downstream synthesis of cytosolic proteins. While mycolactone treatment of HSV1 infected cells at various times after infection resulted in the immediate inhibition of virus production at the point of addition, IAV, RSV and ZIKV became resistant to the action of mycolactone surprisingly early in infection, and before virus glycoprotein synthesis was even detectable or virus production had begun. We therefore conclude that although inhibition of the translocation of virus transmembrane proteins through the Sec61 translocon can in principle block virus production, the morphogenesis of many enveloped RNA viruses requires only limited amounts of envelope proteins for successful propagation, providing novel insight into the biology of these viruses. Author SummaryMany circulating human pathogens are enveloped viruses that all use the cellular secretory pathway to target their envelope proteins to cellular sites of virus particle assembly. The potential to target this pathway could therefore offer a novel broad-spectrum therapy for existing, emerging and as yet unknown human pathogens. Here we have targeted the initial step in this pathway using a highly potent Sec61 inhibitor, mycolactone, to carry out the first comprehensive assessment of translocation disruption on a range of enveloped human viruses from different virus families, including herpes simplex virus, influenza A virus and SARS-CoV2. Our results have shown that Sec61 inhibition blocks the onward trafficking of many virus envelope proteins that are essential to produce infectious virus at assembly sites. However, unexpectedly, we found that several of the viruses were resistant to the effects of this toxin when it was added early in infection, indicating that the synthesis of these essential virus proteins occurs earlier in infection than previously recognised. Hence, while this approach may not be suitable as a broad intervention strategy, it has revealed new information on virus biology and provides us with a novel tool for exploring a wide range of enveloped viruses.

microbiology↗

bioRxiv2024

Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

The Southern Ocean is warming more rapidly than other parts of our planet. How this regions endemic biodiversity will respond to such changes can be illuminated by studying past events, through genetic analyses of time-series data sets including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analysed ancient seal samples from Australia (Tasmania), New Zealand, and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures, over surprisingly short evolutionary timeframes for such a large, long-lived mammal. Significance StatementGenetic data, alongside historic, archaeological, and subfossil remains show that Australasian populations of the southern elephant seal have been shaped by range expansions and contractions following the Last Glacial Maximum, with subsequent contractions during the late Holocene. These expansion and contraction events are likely to have been a direct result of climate change-induced habitat expansion and contraction, along with Indigenous and European sealing. Prehistoric climate change and more recent human pressures have substantially altered the geographic distribution and population size of southern elephant seals over short evolutionary timescales.

ecology↗

bioRxiv2024

Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE

D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phopshate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3,079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.

microbiology↗

bioRxiv2024

Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway

Steroid hormone metabolism by the gut microbiome affects host physiology, but the underlying microbial pathways remain incompletely understood. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducensT strain HCS.1 that reduces cortisol and related steroid hormones to 3{beta},5{beta}-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-{Delta}1-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-- a frontline Crohns disease therapy. OsrB is a 3-oxo-{Delta}4-steroid reductase that converts steroid hormones to 5{beta}-dihydrosteroid intermediates, which OsrC subsequently reduces to 3{beta},5{beta}-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in Crohns disease patient metagenomes. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.

microbiology↗

bioRxiv2024

Gut Bacteria Encode Reductases that Biotransform Steroid Hormones

The metabolism of steroids by the gut microbiome affects hormone homeostasis, impacting host development, mental health, and reproductive functions. In this study, we identify the {Delta}4-3-ketosteroid 5{beta}-reductase, 3{beta}-hydroxysteroid dehydrogenase/{Delta}5-4 isomerase, and {Delta}6-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, We show that 5{beta}-reductase and {Delta}6-3-ketosteroid reductase have evolved to specialize in converting diverse 3-keto steroid hormones into their 5{beta}- and {Delta}6-reduced derivatives. We also find that the novel 3{beta}-hydroxysteroid dehydrogenase/{Delta}5-4 isomerase is fused with 5{beta}-reductase in multiple species, streamlining the multi-step conversion of pregnenolone, a steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations, being enriched in females over males. These findings provide the molecular basis for studying microbial steroid metabolism in the gut, offering insights into its potential impact on hormonal health in hosts, especially in the context of womens health.

microbiology↗

bioRxiv2024

A Comparison of the Sexual Expression, Biomass, Cannabinoid Content, and Seed Production in XXX and XXY Triploid Cannabis

Cannabis is a multi-billion dollar industry reliant on unpollinated genetically female (XX) plants, as pollination reduces cannabinoid yields and flower quality. The mechanism behind the sexual expression of C. sativa is unclear. This study examines the sexual characteristics of homo- and hetero-gametic triploid cannabis plants (XX(X/Y)) to understand the role of the Y chromosome in cannabis sex determination. Heterogametic triploids were produced by crossing a male diploid C. sativa cv. Durban Poison (2n = 2x = 18 + XY) with a tetraploid female C. sativa cv. Higher Education (2n = 4x = 36 + XXXX) confirmed by flow cytometry and PCR. Measurements include fresh and dry plant weight, dry flower weight, seed counts, seed weights, and cannabinoids quantified using liquid chromatography. Results showed 44.4% of plants were XXY (n = 8), with 75% presenting a monoecious phenotype (n = 6). Of these, 50% produced predominately male flowers (n = 3), while the rest produced predominately female flowers. Plants with predominately female flowers had higher yields and cannabinoids compared to predominantly male plants. XXX genotypes outperformed XXY in several metrics. This study enhances our understanding of C. sativa sex determination and offers insight into breeding and cultivation strategies utilizing triploid cannabis.

plant biology↗

bioRxiv2023

Large-scale computational modelling of the M1 and M2 synovial macrophages in Rheumatoid Arthritis

Macrophages play an essential role in rheumatoid arthritis (RA). Depending on their phenotype (M1 or M2), they can play a role in the initiation or resolution of inflammation. The M1/M2 ratio in RA is higher than in healthy controls. Despite this, no treatment targeting specifically macrophages is currently used in clinics. Thus, devising strategies to selectively deplete proinflammatory macrophages and promote anti-inflammatory macrophages could be a promising therapeutic approach in RA. State-of-the-art molecular interaction maps of M1 and M2 macrophages in rheumatoid arthritis are available and represent a dense source of knowledge; however, these maps remain limited by their static nature. Discrete dynamic modelling can be employed to study the emergent behaviours of these systems. Nevertheless, handling such large-scale models is challenging. Due to their massive size, it is computationally demanding to identify biologically relevant states in a cell- and disease-specific context. In this work, we developed an efficient computational framework that converts molecular interaction maps into Boolean models using the CaSQ tool. Next, we use a newly developed BMA tool version deployed to a high-performance computing cluster to identify the models steady states. The identified attractors are then validated using gene expression datasets and prior knowledge. We successfully applied our framework to generate and calibrate the first RA M1 and M2 macrophage Boolean models. Using single and double knockout simulations, we identified NFkB, JAK1/JAK2, and ERK1/Notch1 as potential targets that could selectively suppress proinflammatory macrophages, and GSK3B as a promising target that could promote anti-inflammatory macrophages in RA.

systems biology↗

bioRxiv2023

Optimizing Cell Therapy by Sorting Cells with High Extracellular Vesicle Secretion

Critical challenges remain in clinical translation of extracellular vesicle (EV)-based therapeutics due to the absence of methods to enrich cells with high EV secretion. Current cell sorting methods are limited to surface markers that are uncorrelated to EV secretion or therapeutic potential. We developed a nanovial technology for enrichment of millions of single cells based on EV secretion. This approach was applied to select mesenchymal stem cells (MSCs) with high EV secretion as therapeutic cells for improving treatment. The selected MSCs exhibited distinct transcriptional profiles associated with EV biogenesis and vascular regeneration and maintained high levels of EV secretion after sorting and regrowth. In a mouse model of myocardial infarction, treatment with high-secreting MSCs improved heart functions compared to treatment with low-secreting MSCs. These findings highlight the therapeutic importance of EV secretion in regenerative cell therapies and suggest that selecting cells based on EV secretion could enhance therapeutic efficacy.

bioengineering↗

bioRxiv2023

Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen

The degradation of heme and the interplay of its catabolic derivative, bilirubin, between humans and their gut microbiota is an essential facet of human health. However, the hypothesized bacterial enzyme that reduces bilirubin to urobilinogen, a key step that produces the excretable waste products of this pathway, has remained unidentified. In this study, we used a combination of biochemical analyses and comparative genomics to identify a novel enzyme, BilR, that can reduce bilirubin to urobilinogen. We delineated the BilR sequences from other members of the Old Yellow Enzyme family through the identification of key residues in the active site that are critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes in the gut microbiome. Our analysis of human gut metagenomes showed that BilR is a common feature of a healthy adult human microbiome but has a decreased prevalence in neonates and IBD patients. This discovery sheds new light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.

microbiology↗

bioRxiv2023

Cancer relevance of circulating antibodies against LINE-1 antigens in humans

LINE-1 (L1), the most abundant family of autonomous retrotransposons occupying over 17% of human DNA, is epigenetically silenced in normal tissues but frequently derepressed in cancer, suggesting that L1-encoded proteins may act as tumor-associated antigens recognized by the immune system. Here, we established an immunoassay for detecting circulating autoantibodies against L1 proteins in human blood. Using this assay in >3,000 individuals with or without cancer, we observed significantly higher IgG titers against L1-encoded ORF1p and ORF2p in patients with lung, pancreatic, ovarian, esophageal, and liver cancers compared to healthy individuals. Remarkably, elevated levels of anti-ORF1p-reactive IgG were observed in cancer patients with disease stages 1 and 2, indicating that immune response to L1 antigens can occur at early phases of carcinogenesis. We conclude that the antibody response against L1 antigens could contribute to the diagnosis and determination of immunoreactivity of tumors among cancer types that frequently escape early detection.

cancer biology↗

bioRxiv2022

Laser Ablation Tomography (LATscan) as a new tool for anatomical studies of woody plants

O_LITraditionally, botanists study the anatomy of plants by carefully sectioning samples, histological staining to highlight tissues of interests, then imaging slides under light microscopy. This approach generates significant details; however, this traditional workflow is laborious and time consuming, and ultimately yields two-dimensional (2D) images. Laser Ablation Tomography (LATscan) is a high-throughput imaging system that yields hundreds of images per minute. This method has proven useful for studying the structure of delicate plant tissues, however its utility in understanding the structure of tougher woody tissues is underexplored. C_LIO_LIWe report LATscan-derived anatomical data from several woody stems (ca. 20 mm) of eight species and compare these results to those obtained through traditional anatomical techniques. C_LIO_LILATscan successfully allows the description of tissue composition by differentiating cell type, size, and shape, but also permits the recognition of distinct cell wall composition (e.g., lignin, suberin, cellulose) based on differential fluorescent signals on unstained samples. C_LIO_LILATscan generate high-resolution 2D images and 3D reconstructions of woody plant samples, therefore this new technology is useful for both qualitative and quantitative analyses. This high-throughput imaging technology has the potential to bolster phenotyping of vegetative and reproductive anatomy, wood anatomy, and other biological systems such as plant-pathogen and parasitic plant associations. C_LI

plant biology↗