Biology subjects

Robertson, A.

Publications and source records attributed to Robertson, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Proprietary Processing of Placental Tissue Allografts Influences Wound Healing Trajectories in a Rodent Excisional Skin Wound Model

Introduction: Placental tissue allografts are widely utilized in the management of chronic wounds, including diabetic foot ulcers. In addition to serving as wound coverings, these products may influence wound repair through extracellular matrix architecture and biologically active signaling molecules native to human amniotic tissue. Manufacturing and processing methodologies vary considerably across commercially available products and may substantially impact biologic activity, tissue remodeling, and wound-healing trajectories. In this study, a rodent wound-healing model was utilized to compare a proprietary processed placental tissue allograft with a conventionally processed placental tissue comparator. Methods: Two arms of a five-arm pilot rodent wound-healing study were evaluated to compare a proprietary processed human amniotic tissue allograft against a conventionally processed comparator; the remaining arms evaluated test articles under development and will be reported separately. Male rats (n=8 per arm), matched for weight, age, and diet, each received two full-thickness dorsal excisional wounds approximately 10 mm in diameter and 2 mm deep. Test articles were reapplied upon resorption over a 14-day period. At Day 14, sections were scored semi-quantitatively (0-4 Severity Injury Score) across histologic and immunohistochemical parameters spanning epidermal repair, inflammation, angiogenesis, proliferation, and remodeling. Cranial and caudal wounds were averaged within each animal, retaining the animal as the experimental unit. A Day 14 Histology Resolution Score was derived as a signed composite of pro- and anti-regenerative markers and evaluated alongside percent wound closure. Inferential statistics (Welch ANOVA with Games-Howell post hoc) were derived from the full five-arm cohort (n=40). Results: Animals treated with the proprietary processed allograft showed more advanced progression toward wound resolution than those receiving the conventionally processed comparator, across both surface and tissue-level endpoints. Mean animal-level wound closure at Day 14 was 95.2% with the proprietary processed allograft versus 89.9% with the conventional comparator. The integrated Day 14 Histology Resolution Score, a composite of epidermal repair, inflammation, angiogenesis, proliferation, and remodeling endpoints was 8.94 versus 5.13, corresponding to a shift from the poor-resolution range into the partial-resolution range on the pre-defined interpretive scale. Welch ANOVA across the full five-arm cohort (n=40) detected a significant overall effect of treatment on this composite (p = 0.010). The pairwise contrast between these two arms did not reach significance under Games-Howell correction across ten comparisons (p = 0.337); at n=8 per arm the study was not powered to resolve individual pairwise differences, and the observed standardized difference was large (Hedges' g = 0.93). Injury endpoints were consistently lower in the proprietary processed allograft: 69% lower acute inflammation, 60% lower dermal necrosis, approximately 57% lower epithelial erosion, 46% lower ulceration, and 42% less hemorrhage. Importantly, these reductions in residual tissue injury occurred while maintaining robust granulation tissue formation, angiogenesis, collagen remodeling, cellular proliferation, and macrophage recruitment. Discussion: These findings suggest that processing methodologies can materially influence the biologic performance of placental tissue allografts. The proprietary processed allograft was associated with lower residual tissue injury and greater regenerative and reparative activity relative to a conventionally processed comparator. These observations support the concept that placental tissue allografts should not necessarily be viewed as biologically equivalent and may have important implications for clinical outcomes and product selection in wound care.

bioengineering↗

bioRxiv2026

Inhibition of release of intestinal extracellular vesicles in Ascaris suum and immune modulation by the anthelminthic, ivermectin

Ivermectin is an important broad-spectrum anthelmintic used to treat nematode parasites including gastro-intestinal infections of humans and animals. The mode of action for Ivermectin is understood to involve activation of inhibitory glutamate-gated chloride channels (GluCls). Ivermectin has also been reported to inhibit the release of extracellular vesicles (EVs). We found that EVs are released from the whole intestine of the gastro-intestinal parasite, Ascaris suum. Proteomic analysis identified 1,574 proteins within these intestinal EVs, including 96 nematode proteins with putative immune-associated functions based on homology to proteins involved in host immune processes and 130 proteins with predicted digestive functions. Comparative analysis following ivermectin exposure revealed 38 differentially abundant proteins that included the putative immune-related proteins: transthyretin-like proteins, a small heat-shock antigen, a phospholipase A2, and the NF-{kappa}B subunit p105. Thus, ivermectin modulated the potential immune-related cargo of intestinal EVs. The ivermectin inhibition of intestinal EV release was concentration-dependent with an IC50 of 64 nM. We also identified the expression of GluCl subunit receptor genes in the Ascaris intestine. The potent inhibitory effect of ivermectin on the release of these EVs from the nematode intestine and the expression of GluCl channel subunits sheds further light on the site and mechanisms of action of this important anthelmintic.

pharmacology and toxicology↗

bioRxiv2026

NLRX1 is an essential, druggable regulator of mitochondrial permeability transition

The molecular composition of the mitochondrial permeability transition pore (mPTP) remains contested, and several efficacious mPTP inhibitors act through undefined, cyclophilin D (CypD)-independent targets. Using two structurally distinct chemotypes of optimised, brain-penetrant mPTP inhibitors as chemical probes, we applied affinity-based chemoproteomics to identify the mitochondrial NOD-like receptor NLRX1 as their shared target. Both chemotypes bind NLRX1, and binding potency across a compound series tracks mPTP-inhibitory activity. Using CRISPR-Cas9-edited human cells and Nlrx1-/- mouse tissues, we show that NLRX1 is required for normal calcium-induced mPTP opening: its loss raises the calcium threshold for pore opening and its overexpression lowers it, independently of CypD. NLRX1 associates with postulated mPTP components, including ATP synthase and the adenine nucleotide translocase, in a compound-sensitive manner, and sustains mitochondrial protein homeostasis over longer timescales. The lead compound, GSK900, is orally bioavailable, brain-penetrant, and active in an mPTP-sensitive neurological injury model. These findings, converging with recent genetic studies, establish NLRX1 as an essential, CypD-independent regulator of mitochondrial permeability transition and provide brain-penetrant chemical tools to interrogate this biology.

cell biology↗

bioRxiv2026

Noncoding regulatory mutations contribute to the aberrant gene expression in neuroblastoma

Comprehensive analyses of whole-genome and exome sequencing data from high-risk neuroblastoma tumors have identified relatively few recurrent and clinically actionable protein-coding driver mutations at initial diagnosis. This suggests that noncoding genetic variations that alter regulatory sequences and impact gene expression are important drivers of neuroblastoma tumorigenesis. Allele-specific expression (ASE), which quantifies differences in expression between the two alleles of a gene, is a powerful approach for identifying genes with altered dosage resulting from cis-regulatory variation. In this study, we compared ASE profiles of 156 neuroblastoma patients with 220 adrenal gland tissues from the Genotype-Tissue Expression (GTEx) Project to identify 1,363 neuroblastoma-specific ASE genes. We demonstrated that these genes were enriched for biological processes relevant to neuroblastoma pathogenesis including chromatin remodeling, protein ubiquitination, and sympathetic nervous system development, and were preferentially associated with the adrenergic transcriptional program. To elucidate the genetic mechanism underlying aberrant expression of neuroblastoma-specific ASE genes we integrated our ASE data with somatic copy number alterations (SCNA) and somatic mutation profiles. We observed that although many neuroblastoma specific ASE genes were associated with chromosomal gains and losses, a substantial subset was located within copy-number-neutral genomic regions. These genes showed significant enrichment for noncoding somatic single-nucleotide variants (SNVs) within intronic and distal intergenic neuroblastoma-specific open chromatin regions. Furthermore, functional analyses revealed that many of these SNVs disrupt transcription factor binding sites for GATA3, a core component of the regulatory circuitry that maintains the adrenergic identity of neuroblastoma cells, and neuroblastoma-specific ASE genes harboring such mutations were significantly more likely to belong to the GATA3 regulon than expected by chance. Together, our findings identify novel molecular targets of noncoding regulatory mutations in neuroblastoma and highlight the important yet underappreciated contribution of noncoding genetic variation to neuroblastoma tumorigenesis.

bioinformatics↗

bioRxiv2026

Delineating the posterior bank of the feline auditory cortex based on neurofilament proteins expressing SMI-32

The feline auditory cortex is understood to consist of 13 distinct subregions with unique anatomical and functional properties. Differential patterns of SMI-32 immunoreactivity are commonly used to identify the borders between these subregions; however, the detailed description of areal differences that is commonly cited did not include descriptions of the patterns observed along the posterior ectosylvian gyrus. Thus, the current manuscript aims to provide a more complete data set that can used to delineate the dorsal, intermediate, and ventral divisions of the posterior ectosylvian gyrus (auditory cortical regions dPE, iPE, and vPE, respectively) based on SMI-32 reactivity using the same methods and measures. Taken together, the current data and those published previously allow for a standardized approach to identifying all 13 auditory cortical subregions in this essential model of auditory cortical structure and function.

neuroscience↗

bioRxiv2026

E-Selectin Orchestrates IL-1B-Dependent Neuroinflammation via NLRP3 in Vincristine-Induced Neuropathy

Vincristine-induced peripheral neuropathy (VIPN) is a frequent and dose-limiting complication of cancer therapy, yet the upstream mechanisms coupling vascular activation to neuroinflammation remain poorly defined. Here we identify E-selectin as a critical orchestrator of vincristine-induced neuropathy. Systematic interrogation of endothelial adhesion molecules in a murine model of VIPN revealed that blockade of E-selectin, but not ICAM-1, PECAM-1 or P-selectin, completely prevented mechanical hypersensitivity and markedly reduced F4/80 immune cell accumulation in dorsal root ganglia and peripheral nerves. Genetic deletion of E-selectin conferred equivalent protection, despite the absence of structural loss of intraepidermal or myelinated fibres, indicating a predominantly functional neuroimmune pathology. Spatial transcriptomics demonstrated that vincristine induces a conserved stress and neuroinflammation-associated transcriptional programme in dorsal root ganglia, with immune and stromal populations acting as dominant signalling hubs. Genetic or pharmacological perturbation of E-selectin did not abolish injury-associated pathways but redistributed cell-cell communication networks, reducing immune-cell dominance and reshaping interferon and metabolic signalling states without inducing Sele expression. Mechanistically, E-selectin exerted non-canonical effects beyond endothelial adhesion. Local E-selectin administration was sufficient to induce macrophage-dependent mechanical hypersensitivity that was abolished in Fut4/7-deficient mice and following phagocyte depletion. In macrophages, E-selectin enhanced vincristine-driven NF-{kappa}B activation, NLRP3 inflammasome assembly and IL-1{beta} release. Together, these findings position E-selectin as an upstream regulator of IL-1{beta}-dependent neuroinflammation in VIPN and identify selective targeting of E-selectin-mediated immune-neuron interactions as a therapeutic strategy for chemotherapy-induced neuropathy.

neuroscience↗

bioRxiv2025

Evaluating the effect of badger culling on TB incidence in cattle: a critique of Langton et al. 2022

The European Badger (Meles meles) is a wildlife host for Mycobacterium bovis, the causative agent of bovine tuberculosis (TB) in cattle. In England, large scale badger culling has been implemented since 2013 as part of a licenced Badger Control Policy (BCP). While several studies have shown an association between the BCP and disease benefits in cattle, a study by Langton et al. (2022) failed to identify any evidence of such benefits, raising questions about the effectiveness of badger culling as a tool for disease control. In this study I summarise the primary methodology used in the Langton et al. study and identify two significant issues with the approach used, which compares cattle TB incidence in culled areas of SW England to land without culling. Firstly, their analysis groups data together from cull areas into a combined culled vs unculled treatment, regardless of the time that culling has been applied. Secondly, there is evidence of a clear cull area selection bias, such that land enrolled into culling during the period analysed had a significantly higher baseline TB incidence than areas not culling. I then conducted a Monte Carlo analysis using simulated data under scenarios with differing cull effects, and matching the degree of grouping, selection bias and statistical methods used by Langton et al. (2022). The results indicate that even in scenarios with a relatively rapid and large effect of culling seeded into the simulation there is a significant probability that their analyses will fail to find an effect and may even wrongly conclude that culling is associated with an increase in TB. These results potentially explain the discrepancy between Langton et al. (2022) and other studies evaluating badger culling and highlight the importance of rigorous statistical analysis that accounts for temporal and spatial patterns in disease control data.

microbiology↗

bioRxiv2025

Combinatorial phenotypic landscape enables bacterial resistance to phage infection

AbstractSuccess of phage therapies is limited by bacterial defenses against phages. While a large variety of anti- phage defense mechanisms has been characterized, how expression of these systems is distributed across individual cells and how their combined activities translate into protection from phages has not been studied. Using bacterial single-cell RNA sequencing, we profiled the transcriptomes of [~]50,000 cells from cultures of a human pathobiont, Bacteroides fragilis, infected with a lytic bacteriophage. We quantified the asynchronous progression of phage infection in single bacterial cells and reconstructed the infection timeline, characterizing both host and phage transcriptomic changes as infection unfolded. We discovered a subpopulation of bacteria that remained uninfected and determined the heterogeneously expressed host factors associated with protection. Each cells vulnerability to phage infection was defined by combinatorial phase-variable expression of multiple genetic loci, including capsular polysaccharide (CPS) biosynthesis pathways, restriction-modification systems (RM), and a previously uncharacterized operon likely encoding fimbrial genes. By acting together, these heterogeneously expressed phase-variable systems and anti-phage defense mechanisms create a phenotypic landscape where distinct protective combinations enable the survival and re-growth of bacteria expressing these phenotypes without acquiring additional mutations. The emerging model of complementary action of multiple protective mechanisms heterogeneously expressed across an isogenic bacterial population showcases the potent role of phase variation and stochasticity in bacterial anti-phage defenses. One Sentence SummaryCombinatorial phenotypic states with differential vulnerability to phage infection across a Bacteroides fragilis population enable a small number of super-resistant bacterial cells to evade the phage without the need for acquiring mutations.

systems biology↗

bioRxiv2025

Exploring the Role of Kv1.3 and MAPK14 in Mediating Microglial Oxidative Stress and Neuroinflammation Following Organic Dust Exposure

BackgroundAgricultural contaminants, including inhaled organic dust (OD) and gases, are known to cause inflammation in the lungs and the brain. We investigated the role of the potassium channel Kv1.3 in organic dust (OD)-induced neuroinflammation models. Kv1.3 channels play a multifaceted role in microglial immune modulation, cancer, neurodegenerative diseases, and constitute a potential therapeutic target. MethodsWe used in vivo (C57BL/6 mice), in vitro (microglial cell line, primary microglia), and ex vivo (brain slice culture) models of OD-induced neuroinflammation. A sterile OD extract (ODE) was prepared, and mice were exposed to either normal saline or ODE intra-nasally for 5 weeks (5 days/week) to simulate an occupational exposure scenario. Primary microglia were isolated from neonatal mice for total RNA sequencing (RNA-seq). The ODE-induced expression of Kv1.3 was quantified using in vitro and ex vivo models with and without PAP-1 treatments. Exposure-induced changes in cytokines and reactive species markers were measured. Using western blot, we quantified phosphorylated p38 MAPK14 (p-p38 MAPK) and NOX2. We measured the currents through Kv1.3 channels using a microglial patch-clamp assay. ResultsExposure to ODE increased the expression of Kv1.3 and p-p38 MAPK in mouse microglia without affecting the Kv1.3 currents at the cell surface. Exposure increased the levels of inflammatory cytokines and NOX2. Kv1.3 inhibition with PAP-1 decreased inflammatory markers (TNF- and IL-6), levels of Kv1.3, p-p38 MAPK, NOX2, and nitrites. ConclusionOur study revealed that pharmacological inhibition of Kv1.3 potassium channels reduces ODE-induced neuroinflammation by decreasing inflammatory and oxidative stress markers.

pharmacology and toxicology↗

bioRxiv2023

Quantifying myelin density in the feline auditory cortex

The cerebral cortex comprises many distinct regions that differ in structure, function, and patterns of connectivity. Current approaches to parcellating these regions often take advantage of functional neuroimaging approaches that can identify regions involved in a particular process with reasonable spatial resolution. However neuroanatomical biomarkers are also very useful in identifying distinct cortical regions either in addition to, or in place of functional measures. For example, differences in myelin density are thought to relate to functional differences between regions, are sensitive to individual patterns of experience, and have been shown to vary across functional hierarchies in a predictable manner. Accordingly, the current study provides quantitative stereological estimates of myelin density for each of the 13 regions that make up the feline auditory cortex. We demonstrate that significant differences can be observed between auditory cortical regions, with the highest myelin density observed in the regions that comprise the auditory core (i.e., the primary auditory cortex and anterior auditory field). Moreover, our myeloarchitectonic map suggests that myelin density varies in a hierarchical fashion that conforms to the traditional model of spatial organization in auditory cortex. Taken together, these results establish myelin as a useful biomarker for parcellating auditory cortical regions, and provide detailed estimates against which other, less invasive methods of quantifying cortical myelination may be compared.

neuroscience↗

bioRxiv2023

SPAG7 deletion causes intrauterine growth restriction, resulting in adulthood obesity and metabolic dysfunction

From a forward mutagenetic screen to discover mutations associated with obesity, we identified mutations in the spag7 gene linked to metabolic dysfunction in mice. Here we show that SPAG7 KO mice are born smaller and develop obesity and glucose intolerance in adulthood. This obesity does not stem from hyperphagia, but a decrease in energy expenditure. The KO animals also display reduced exercise tolerance and muscle function due to impaired mitochondrial function. Furthermore, SPAG7-deficiency in developing embryos leads to intrauterine growth restriction, brought on by placental insufficiency, likely due to abnormal development of the placental junctional zone. This insufficiency leads to loss of SPAG7-deficient fetuses in utero and reduced birth weights of those that survive. We hypothesize that a "thrifty phenotype" is ingrained in SPAG7 KO animals during development that leads to adult obesity. Collectively, these results indicate that SPAG7 is essential for embryonic development and energy homeostasis later in life.

molecular biology↗

bioRxiv2023

Diethylcarbamazine elicits Ca2+ signals through TRP-2 channels that are potentiated by emodepside in Brugia malayi muscles

Filarial nematode infections are a major health concern in several countries. Lymphatic filariasis is caused by Wucheria bancrofti and Brugia spp. affecting over 120 million people. Heavy infections can lead to elephantiasis having serious effects on individuals lives. Although current anthelmintics are effective at killing the microfilariae in the bloodstream, they have little to no effect against adult parasites found in the lymphatic system. The anthelmintic diethylcarbamazine is one of the central pillars of lymphatic filariasis control. Recent studies have reported that diethylcarbamazine can open Transient Receptor Potential (TRP) channels on the muscles of adult female Brugia malayi leading to contraction and paralysis. Diethylcarbamazine has synergistic effects in combination with emodepside on Brugia inhibiting motility: emodepside is an anthelmintic that has effects on filarial nematodes and is under trials for treatment of river blindness. Here we have studied the effects of diethylcarbamazine on single Brugia muscle cells by measuring the change in Ca2+ fluorescence in the muscle using Ca2+-imaging techniques. Diethylcarbamazine interacts with the TRPC orthologue receptor TRP-2 to promote Ca2+ entry into the Brugia muscle cells which can activate SLO-1 Ca2+ activated K+ channels, the putative target of emodepside. A combination of diethylcarbamazine and emodepside leads to a bigger Ca2+ signal than when either compound is applied alone. Our study shows that diethylcarbamazine targets TRP channels to promote Ca2+ entry that is increased by emodepside activation of SLO-1 channels.

pharmacology and toxicology↗

bioRxiv2023

Bacterial contact induces polar plug disintegration to mediate whipworm egg hatching

The bacterial microbiota promotes the life cycle of the intestine-dwelling whipworm Trichuris by mediating hatching of parasite eggs ingested by the mammalian host. Despite the enormous disease burden associated with Trichuris colonization, the mechanisms underlying this transkingdom interaction have been obscure. Here, we used a multiscale microscopy approach to define the structural events associated with bacteria-mediated hatching of eggs for the murine model parasite Trichuris muris. Through the combination of scanning electron microscopy (SEM) and serial block face SEM (SBFSEM), we visualized the outer surface morphology of the shell and generated 3D structures of the egg and larva during the hatching process. These images revealed that exposure to hatching-inducing bacteria catalyzed asymmetric degradation of the polar plugs prior to exit by the larva. Although unrelated bacteria induced similar loss of electron density and dissolution of the structural integrity of the plugs, egg hatching was most efficient in the presence of bacteria that bound poles with high density such as Staphylococcus aureus. Consistent with the ability of taxonomically distant bacteria to induce hatching, additional results suggest chitinase released from larva within the eggs degrade the plugs from the inside instead of enzymes produced by bacteria in the external environment. These findings define at ultrastructure resolution the evolutionary adaptation of a parasite for the microbe-rich environment of the mammalian gut.

microbiology↗

bioRxiv2022

Gene regulatory network inference in soybean upon infection by Phytophthora sojae

Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae. Author SummaryGlobal food security is threatened continually by plant pathogens. One approach to circumvent these disease-causing agents entails understanding how hosts balance primary growth and defense upon pathogen perception. Molecular signatures of perception-rendered defense may be leveraged subsequently to develop resistant/tolerant crop plants. Additionally, evidence suggests that the plant immune system is characterized by tuning primary and secondary metabolic activity via transcription factor-mediated transcriptional reprogramming. Therefore, we investigated transcription factor-target gene interactions in soybean upon infection by compatible and incompatible races of Phytophthora sojae. Through transcriptome analysis, we found that the interactions elicited vast, overlapping transcriptional responses and identified overrepresented, defense-related transcription factor families. We then generated/acquired DNA-protein interactome data for the most represented transcription factor families in the transcriptome analysis and trained deep learning-based models to predict novel transcription factor targets. Transcription factor/target gene metrics were used to construct a gene regulatory network with prioritized components. We identified hub transcription factors belonging to WRKY and ERF families, the majority of which function in response to various biotic and abiotic stressors. These findings propose novel regulators in the soybean defense response to Phytophthora sojae and provide an avenue for the investigation of transcription factor-target gene interactions in plants.

plant biology↗

bioRxiv2022

Clostridia isolated from helminth-colonized humans promote hatching of Trichuris muris

Soil transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolated and sequenced the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians revealed higher prevalence and abundance of these isolates compared to individuals in the United States, with Peptostreptococcaceae family members displaying a specific association with helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli displayed superior capacity to induce hatching of eggs from the murine helminth Trichuris muris. These findings support a model in which helminths select for gut colonization of microbes that in turn support their life cycle by promoting egg hatching.

microbiology↗

bioRxiv2021

The Food Additive Xanthan Gum Drives Adaptation of the Human Gut Microbiota

The diets of industrialized countries reflect the increasing use of processed foods, often with the introduction of novel food additives. Xanthan gum is a complex polysaccharide with unique rheological properties that have established its use as a widespread stabilizer and thickening agent1. However, little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other, chemically-distinct dietary fiber polysaccharides. Here, we show that the ability to digest xanthan gum is surprisingly common in industrialized human gut microbiomes and appears to be contingent on the activity of a single bacterium that is a member of an uncultured bacterial genus in the family Ruminococcaceae. We used a combination of enrichment culture, multi-omics, and recombinant enzyme studies to identify and characterize a complete pathway in this uncultured bacterium for the degradation of xanthan gum. Our data reveal that this keystone degrader cleaves the xanthan gum backbone with a novel glycoside hydrolase family 5 (GH5) enzyme before processing the released oligosaccharides using additional enzymes. Surprisingly, some individuals harbor a Bacteroides species that is capable of consuming oligosaccharide products generated by the keystone Ruminococcaceae or a purified form of the GH5 enzyme. This Bacteroides symbiont is equipped with its own distinct enzymatic pathway to cross-feed on xanthan gum breakdown products, which still harbor the native linkage complexity in xanthan gum, but it cannot directly degrade the high molecular weight polymer. Thus, the introduction of a common food additive into the human diet in the past 50 years has promoted the establishment of a food chain involving at least two members of different phyla of gut bacteria.

microbiology↗

bioRxiv2019

P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy

FSHD is caused by the loss of repression at the D4Z4 locus leading to DUX4 expression in skeletal muscle, activation of its early embryonic transcriptional program and muscle fiber death. While progress toward understanding the signals driving DUX4 expression has been made, the factors and pathways involved in the transcriptional activation of this gene remain largely unknown. Here, we describe the identification and characterization of p38 as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent and specific inhibitors of p38/{beta}, we show a robust reduction of DUX4 expression, activity and cell death across FSHD1 and FSHD2 patient-derived lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38/{beta} inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38 in the aberrant activation of DUX4 in FSHD and support the potential of p38/{beta} inhibitors as effective therapeutics to treat FSHD at its root cause. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/700195v2_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@d2d55corg.highwire.dtl.DTLVardef@1b5c8fcorg.highwire.dtl.DTLVardef@19e4667org.highwire.dtl.DTLVardef@202b96_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2018

Impending regeneration failure of the IUCN Vulnerable Borneo ironwood (Eusideroxylon zwageri)

The regeneration of many climax species in tropical forest critically depends on adequate seed dispersal and seedling establishment. Here we report the decreased abundance and increased spatial aggregation of younger trees of the Borneo ironwood (Eusideroxylon zwageri) in a protected forest in Sabah Malaysia. We observed a high level of seedling herbivory with strong density dependence, likely exacerbated by local aggregation and contributing to the progressively shrinking size-distribution. We also note the largely undocumented selective herbivory by sambar deer on E. zwageri seedlings. This study highlights the combined impact of altered megafauna community on a tree population through interlinked ecological processes and the need for targeted conservation intervention for this iconic tropical tree species.

ecology↗