Biology subjects

Underwood, J.

Publications and source records attributed to Underwood, J..

9 recordsLinked to original sources

bioRxiv2026

Mutually Repressive Transcription Factors Drive Intestinal Maturation for Weaning

In mammals, rapid neonatal growth depends on specialized intestinal enterocytes that absorb nutrients from milk. These cells exhibit distinct functions, morphologies, and gene expression programs that support neonatal nutrition before transitioning to an adult state at weaning. However, the transcriptional mechanisms that establish neonatal enterocyte identity and coordinate their maturation remain poorly understood. Here we show that the transcription factors BLIMP1 and CASZ1 form a central switch in the timing of enterocyte maturation. While BLIMP1 marks and promotes neonatal enterocytes, CASZ1 is expressed in adult enterocytes and is required for the proper timing of their emergence. Genetic analysis indicates that these neonatal and adult factors are mutually repressive, forming a genetic switch underlying weaning. This regulatory mechanism also controls glucocorticoid-induced maturation, a process relevant to both normal weaning and the clinical use of corticosteroids to promote epithelial maturation in preterm infants. We show that corticosteroids act directly on the intestinal epithelium and require CASZ1 to induce maturation. Together, these findings reveal a transcriptional mechanism that coordinates intestinal epithelial identity with the changing nutritional demands of early life and mediates the response to maturation-promoting hormones.

developmental biology↗

bioRxiv2026

Age and IFN-β-induced changes in glial morphometry can be captured by in vivo diffusion-weighted magnetic resonance spectroscopy.

IntroductionNeuroinflammation is increasingly implicated in age-related cognitive decline, neurodegeneration and neuropsychiatric disorders. During systemic inflammation, microglia are rapidly activated, simultaneously changing their shape and releasing cytokines that perturb neuronal function. This change in glial morphology alters their intracellular diffusion properties and provides a potentially measurable signature of their activation state. Diffusion-weighted magnetic resonance spectroscopy (dMRS) shows promise in detecting these changes. Here, we combined IFN-{beta} challenge with dMRS to assess changes in metabolite diffusion in healthy young and older adults. We hypothesised that IFN-{beta} would increase diffusion of choline-containing compounds (tCho) but not N-acetylaspartate + N-acetylaspartylglutamate (tNAA), age would be associated with an increase in tCho diffusion and concentration, lower tNAA concentration and increased effects of IFN-{beta}. MethodsWe recruited 15 young (mean 25.2 {+/-} 5.1 years, 6 male) and 15 older (mean 62.6 {+/-} 4.1 years, 5 male) healthy volunteers, each tested twice, once after IFN-{beta} and once after placebo. Physiological and behavioural responses were recorded hourly, and blood samples taken at baseline, 4 and 6.5 hours post-injection. dMRS occurred at [~]4.5 hours at 3T, using a semi-LASER sequence with four diffusion weightings (b = 0 and 3 x 3500 s/mm{superscript 2}), in 4.5 cm3 VOIs in the left thalamus and corona radiata. Apparent Diffusion Coefficients (ADCs) of tCho, tNAA and creatine+phosphocreatine (tCr) were calculated from averaged spectra using custom MATLAB software. ResultsIFN-{beta} administration produced a significant increase in thalamic tCho diffusivity compared with placebo (t(28) = -2.15, p = 0.040), with no change in tNAA or tCr ADC, or tCho concentrations. IFN-{beta}-related increases in tCho ADC positively correlated with increases in circulating IL-6 (R{superscript 2} = 0.14, p = 0.040). Age-related effects were also evident during the placebo condition, with older participants showing lower thalamic tNAA diffusivity (t(27) = 2.86, p = 0.008), lower tNAA/tCr in both grey and white matter (grey: t(27) = 2.49, p = 0.023; white: t(27) = 2.94, p = 0.007), and higher white-matter tCho/tCr (t(27) = -2.23, p = 0.034). ConclusiondMRS detected IFN-{beta}-induced increases in thalamic tCho diffusivity corresponding with peripheral inflammation, supporting its sensitivity to acute inflammation-induced changes in glial morphology. Age-related differences in tNAA diffusion and concentrations further highlight metabolite-specific ageing effects. HighlightsO_LIdMRS detects increased thalamic total choline diffusivity following IFN-{beta}-induced inflammation. C_LIO_LIIFN-{beta}-related changes in total choline diffusivity are associated with peripheral IL-6 responses. C_LIO_LIAgeing is linked to reduced NAA diffusion and higher white-matter tCho/tCr C_LIO_LIdMRS is sensitive to inflammation- and age-related neurochemical changes in vivo. C_LI

immunology↗

bioRxiv2025

Improved long transcript representation in Oxford Nanopore direct RNA sequencing with UltraMarathonRT

While most RNA-seq methods sequence amplified cDNA molecules, the advent of direct RNA sequencing (DRS) empowered the scientific community to read native RNA. This technology unlocked characterization of natural RNA modifications and long RNA isoforms without the inherent biases of PCR amplification. In the library preparation prior to Oxford Nanopore (ONT) sequencing, polyadenylated RNAs are copied by a reverse transcriptase (RT) to generate an RNA-cDNA hybrid. The step aims to eliminate the secondary and tertiary structure inherent to most RNA sequences prior to presentation of the RNA strand to the pore for sequencing. The current recommended protocol for DRS utilizes Induro(R) RT and requires reverse transcription at 60{degrees}C. We demonstrate that these RT conditions promote hydrolysis of the RNA strand. We further show that UltraMarathonRT(R) (uMRT), an ultraprocessive reverse transcriptase with intrinsic helicase activity that works optimally at 30{degrees}C, can be incorporated into a new uMRT-based DRS method that results in longer RNA reads in ONT DRS and longer final isoform predictions. We optimize this reaction along with other molecular biology steps and demonstrate the performance improvements of this new workflow on the benchmark sample, Universal Human Reference RNA, along with human brain RNA. This improved DRS protocol should empower new discoveries by the scientific community.

genomics↗

bioRxiv2025

buzzdetect: an open-source deep learning tool for automated bioacoustic pollinator monitoring

Ecological studies of pollinators often require long-term and extensive monitoring, posing a significant cost and limitation to research. Traditional sampling methods of observation such as sweep netting and pan trapping provide valuable information on pollinator diversity, but scale poorly when conducting large sampling efforts across space and time. We introduce "buzzdetect", our tool to apply deep learning models to audio data for conducting passive acoustic monitoring on pollinators, and test our accompanying audio classification model. The model is capable of distinguishing the buzzing of insect flight from environmental noise with a sensitivity of 27% at a precision (true positive rate) of 95%. Application of buzzdetect to recordings made in pumpkin, watermelon, mustard, and soybean reveals differences in timing and intensity of foraging: foraging occurred the earliest in pumpkins and the latest for soybean while foraging activity was most intensive in mustard.

ecology↗

bioRxiv2025

Developing Interferon-β as a safe in-vivo experimental-medicine model of human inflammation.

BackgroundInflammation is increasingly implicated in a wide range of neuropsychiatric disorders ranging from depression through age- and infection-related cognitive decline to dementia. Arguably, the most important evidence supporting an aetiological role for inflammation in these conditions in humans has come from studies of patients receiving IFN- therapeutically or longitudinal follow-up of patients after naturalistic infections (e.g., hepatitis C). These experimental medicine-type approaches have identified a discrete set of brain regions e.g. amygdala-hippocampus-hypothalamus, insula and anterior cingulate as well as dopamine-rich subcortical structures that are particularly sensitive to systemic inflammation. Coupled with renewed interest in developing novel immune-targeted therapies for neuropsychiatric disorders as diverse as depression and neurodegenerative disorders, this has highlighted the urgent need for a safe, reliable in-vivo experimental medicine model of inflammation that can be used across the age range. To date, this need has been partially addressed by access to short-acting forms of Interferon-alpha or human (GMP) grade lipopolysaccharide (LPS). However, unpegylated IFN- is no longer commercially available and the costs and cardiovascular monitoring requirements of low-dose (i.e. 0.8-1ng/Kg i.v. endotoxin) LPS are prohibitive and particularly challenging to use in older or more vulnerable populations. AimDevelop a new experimental model of human inflammation that elicits robust sickness responses within a few hours but with minimal cardiovascular effects, thus avoiding the need for continuous cardiac monitoring and ensuring applicability across diverse experimental contexts and participant groups from the young to the elderly. MethodsUsing a randomized, placebo-controlled, repeated measures cross-over design, physiological, behavioural, immune and transcriptomic responses were collected from 30 healthy volunteers (15 young [18-34] and 15 old [60-75]) following both IFN-{beta} (EXTAVIA(R) [100 {micro}g]) and saline (placebo) injections. ResultsIFN-{beta} induced a robust systemic immune response, evidenced by significant increases in temperature, heart rate, immune cell activation (lymphocytes, monocytes and neutrophils) and levels of IFN-{beta}, IL-10 and TNF- cytokines. These physiological changes were accompanied by significant increases in negative mood, tiredness, tension and sickness symptoms aa well as by a decrease in vigour. ConclusionsFN-{beta} is a safe and robust new experimental model of mild acute inflammation, This minimally invasive and effective design can induce transient changes in systemic inflammation in healthy individuals from 18-75. A more refined, ecologically valid model similar to the mild inflammation typically reported in psychiatric disorders like depression or cognitive impairment.

immunology↗

bioRxiv2024

NKG2A-mediated immune modulation of natural killer cells by Staphylococcus aureus

Natural killer (NK) cells are specialized lymphocytes that help protect against viruses and cancer. However, in the context of bacterial infections, NK cells can be harmful, rather than protective. Such immune pathogenesis by NK cells has been linked to the over-production of pro-inflammatory cytokines like interferon-{gamma} (IFN-{gamma}). In this context, IFN-{gamma}-deficient mice display increased survival rates in response to Staphylococcus aureus (S. aureus), which causes life-threatening, invasive systemic infections with high mortality rates in humans. However, little is known about how NK cells respond to S. aureus in humans. In this study, we found that the peripheral blood of patients with bloodstream S. aureus infection was enriched for NKG2A+ NK cells with greater cytokine producing capacity, compared to those hospitalized with Escherichia coli bloodstream infections. As a possible mechanistic cause, superantigens from S. aureus promoted the expansion of CD57- NKG2A+ NK cells which produced IFN-{gamma} through an IL-12-independent mechanism and exhibited reduced levels of CD16 compared to unstimulated NK cells. These data suggest that S. aureus bloodstream infection in humans promotes a phenotypic shift towards NKG2A+ NK cells with greater IFN-{gamma} producing capacity, providing a plausible way to promote inflammation-driven disease pathogenesis. AUTHOR SUMMARYNatural Killer (NK) cells are specialized immune cells that provide crucial defence against viruses but can also respond to bacterial infections, especially in humans. During bloodstream infection by Staphylococcus aureus, a Gram-positive bacterial pathogen that causes life-threatening infections in humans, NK cells may actually be harmful, rather than protective, to the host. However, very little is known about the NK cell response to invasive Staphylococcus aureus infections in humans. Here, we show that human patients with bloodstream Staphylococcus aureus, but not Escherichia coli, infections have an increased frequency of NK cells with increased pro-inflammatory capacity. Furthermore, we show that toxins produced by Staphylococcus aureus, which help the bacteria evade the protective effects of T cells the immune system ("superantigens"), promoted the expansion of these pro-inflammatory NK cells, providing a possible mechanistic cause for their increased presence in patients with bloodstream Staphylococcus aureus infections. Collectively, these results suggest that Staphylococcus aureus infection triggers phenotypic and functional changes in NK cells that provide a plausible way to promote inflammation-driven disease pathogenesis

immunology↗

bioRxiv2022

Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut

There are fundamental differences in the way that neonatal and adult intestines absorb nutrients. In adults, macromolecules are efficiently broken down into simpler molecular components in the lumen of the small intestine, then absorbed. In contrast, neonates are thought to rely more on bulk intake of nutrients and subsequent degradation in the lysosome. Here, we identify the Maf family transcription factors, MafB and cMaf, as markers of terminally-differentiated intestinal enterocytes throughout life. The expression of these factors is regulated by HNF4/{gamma}, master regulators of the enterocyte cell fate. Loss of Maf factors results in a neonatal-specific failure to thrive and loss of bulk uptake of nutrients. RNA-Seq and CUT&RUN analyses defined an endo-lysosomal program as being downstream of these transcription factors. We demonstrate major transcriptional changes in metabolic pathways, including fatty acid oxidation and increases in peroxisome number in response to loss of Mafs. Finally, we show that deletion of Blimp1, which represses adult enterocyte genes in the neonatal gut, shows highly overlapping changes in gene expression and similar defects in nutrient uptake. This work defines transcriptional regulators that are necessary for bulk uptake in neonatal enterocytes.

physiology↗

bioRxiv2021

Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia

Understanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of the Symbiodiniaceae ITS2 region revealed all colonies to be associated exclusively with the genus Cladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.

genomics↗

bioRxiv2019

Regulated spindle orientation buffers tissue growth in the epidermis

Tissue homeostasis requires a balance between progenitor cell proliferation and loss. Mechanisms that maintain this robust balance are needed to avoid tissue loss or overgrowth. Here we demonstrate that regulation of spindle orientation/asymmetric cell divisions is one mechanism that is used to buffer changes in proliferation and tissue turnover in mammalian skin. Genetic and pharmacologic experiments demonstrate that asymmetric cell divisions were increased in hyperproliferative conditions and decreased under hypoproliferative conditions. Further, active K-Ras also increased the frequency of asymmetric cell divisions. Disruption of spindle orientation in combination with constitutively active K-Ras resulted in massive tissue overgrowth. Together, these data highlight the essential roles of spindle orientation in buffering tissue homeostasis in response to perturbations.

cell biology↗