Biology subjects

Green, K.

Publications and source records attributed to Green, K..

At least 19 recordsLinked to original sources

bioRxiv2026

A minimal two-residue C-terminal truncation of AID in adult-onset hyper-IgM syndrome type 2 (HIGM2)

Activation-induced cytidine deaminase (AID), encoded by AICDA, facilitates class-switch recombination (CSR) and somatic hypermutation (SHM) in activated B cells. Loss of AID function causes hyper-IgM syndrome type 2 (HIGM2). While typically autosomal recessive, three C-terminal truncation variants have been reported to act in autosomal dominant manner. We describe a novel heterozygous AICDA nonsense variant, c.589G>T (p.G197*), that truncates the final two C-terminal residues of AID and results in adult-onset HIGM2. Single-cell sequencing of primary patient B cells revealed a complete block in CSR and a [~]10-fold reduction in SHM. AICDA mRNA expression was balanced between wild-type and variant alleles, yet AID protein abundance was reduced to [~]56% with normal subcellular localization. Remarkably, inducible germinal center (iGB) cultures restored CSR in purified naive patient B cells. CRISPR-Cas9 editing of healthy donor B cells confirmed that the iGB platform can rescue B cells harboring heterozygous, but not homozygous, AICDA variants. These results demonstrate that even a two-amino-acid truncation at the AID C-terminus is sufficient to disrupt its function and cause HIGM2.

immunology↗

bioRxiv2026

A massively parallel synthetic gene atlas for learning compact cis-regulatory grammar across cellular contexts

Virtual-cell models increasingly learn from large perturbation atlases, but their view of cis regulation remains limited to endogenous genes embedded in broad native regulatory contexts. Here we introduce Therna Biosciences' Chronos platform and its first public dataset release, comprising two complementary modules of a massively parallel synthetic gene atlas: Penta-47x27K for 5' UTRs/internal-promoter elements and Tria-47x28K for 3' UTR stability elements. Together, these datasets measure ~60,000 compact cis-regulatory elements across approximately 50 cell lines in one pooled experiment. The choice of cell lines here, provided to us courtesy of Tahoe Tx, was rooted in our aim to make this dataset maximally useful for the virtual-cell modeling community. At Therna, we routinely apply Chronos -- part of our RNA-Logix(TM) platform -- beyond cancer cell-line pools, to systems such as primary cells and organoids, via LNP-formulated mRNA delivery. Chronos captures both transcriptional and post-transcriptional gene expression control. Episomal DNA delivery measures DNA-normalized mRNA output, while direct RNA delivery with longitudinal sampling reliably quantifies RNA decay. The RNA-delivery arm uses chemically modified synthetic mRNA incorporating N1-methylpseudouridine, a modification widely used in mRNA therapeutics. To resolve high-complexity libraries of up to 30,000 elements, Chronos pushes the sensitivity limits of single-cell RNA sequencing to quantify individual RNA molecules within single cells. By massively expanding gene regulatory networks with synthetic genes whose variable regulatory code is short and defined, Chronos provides an auxiliary cis-regulatory lens for virtual-cell modeling and enables context-specific cis-trans regulatory interactions to be learned directly.

systems biology↗

bioRxiv2026

Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera

The tribe Spermacoceae (Rubiaceae) comprises a morphologically diverse assemblage of approximately 1,400 species distributed across the Neotropics, Africa, Asia, Australia, and Pacific region. It remains one of the most taxonomically intractable groups in the family, with generic limits repeatedly redefined for more than two centuries. Previous phylogenetic studies based on a limited number of plastid and nuclear markers left numerous relationships unresolved and provided sparse representation of Neotropical lineages. Here, we present the first phylogenomic study of the tribe based on plastome-scale data and expanded sampling of Neotropical taxa. We sampled 121 species representing 55 genera spanning all major clades and generated 123 new plastomes, including 25 species incorporated into a molecular phylogenetic framework for the first time. Maximum-likelihood and Bayesian analyses recovered a highly resolved and strongly supported phylogeny, with uncertainty restricted to a small number of deep backbone nodes. Pollen and seed micromorphology provided additional evidence for evaluating phylogenetic relationships. The resulting phylogenetic framework clarifies generic boundaries across several problematic lineages and supports multiple taxonomic changes. Pervasive homoplasy in seed and floral characters rendered several traditionally recognized genera non-monophyletic, warranting new combinations, including Edrastima oxycoccoides, Stenotis alexanderae, and S. prostrata, and a reassessment of taxa such as Terrellianthus serpyllaceus and Oldenlandia dusenii. We further identify genera requiring additional study and provide an updated key to the 82 recognized genera of Spermacoceae. Together, these results provide the most robust phylogenetic framework yet available for the tribe and establish a foundation for future systematic, biogeographic, and evolutionary research.

plant biology↗

bioRxiv2026

Thymic Treg-derived T follicular regulatory cells prevent catastrophic humoral autoimmunity in response to TLR7-driven inflammation

T follicular regulatory cells (TFR) are a follicle-resident subset of regulatory T cells (TREG) that limit germinal center (GC) responses and enforce humoral tolerance. Although TFR are known to focus antibody responses to foreign antigens, how GC-specific regulation is maintained during inflammation remains unclear. Here, TLR7-driven inflammation unmasked a critical, non-redundant role for TFR in preserving immune tolerance. Selective loss of TFR caused severe autoimmunity and increased mortality, driven by inflammation-induced expansion of autoreactive B and T cell clones and epitope spreading. Autoreactivity resolved upon cessation of inflammation in TFR-sucicient mice but persisted in their absence. Mechanistically, TFR limited the establishment and expansion of spontaneous GCs in response to inflammation, and responding TFR displayed transcriptional, phenotypic, and clonal features of thymic TREG. This suggests that whereas TFH upregulate FoxP3 to shut down end-stage GCs, it is thymic TREG-derived TFR that safeguard GC integrity under inflammatory stress to prevent lethal autoimmunity.

immunology↗

bioRxiv2025

Central carbon metabolism switching in lytic versus temperate coral reef viral communities

Coral reefs are declining globally due in part to bacterial overgrowth, a process known as microbialization. However, the role of bacteriophages that may inhibit microbialization by infecting and killing these bacteria remains poorly understood, especially their metabolic impacts on bacterial proliferation. To address this, we analyzed central carbon metabolism gene frequencies in viral communities from healthy (lytic-dominated) and degraded (temperate-dominated) Central Pacific coral reefs. We found that viral metabolism shifted broadly from being dominated by metabolism that builds up pools of central intermediates on degraded reefs dominated by temperate viral infection ("anaplerotic" reactions) to metabolism that consumes these pools to prioritize production of metabolic precursors for virion construction on healthy reefs dominated by lytic infection ("cataplerotic" reactions). This switch was shown by the over-representation of Entner-Doudoroff (ED) glycolysis genes on degraded, temperate-dominated reefs and of pentose phosphate pathway (PPP) and reductive tricarboxylic acid cycle (TCA) genes on healthy, lytic-dominated reefs. As a result of this metabolic dichotomy, our qualitative compartment modeling revealed two distinct ecosystem states: (i) healthy reefs, where lytic viral metabolism enhances viral production and suppresses bacterial overgrowth, and (ii) degraded reefs, where temperate viral metabolism accelerates bacterial proliferation. Because viral switching between lytic and temperate lifestyles is a known function of host physiological state, these findings position viral metabolism as both a driver of reef decline and a conservation lever, with metabolically mediated "re-viralization" offering a novel strategy to restore reef resilience.

ecology↗

bioRxiv2025

A simplified hybrid capture approach retains high specificity and enables PCR-free workflow

Hybrid capture is a critical technology for selective enrichment of genomic regions of interest, enabling cost-effective focused sequencing in both clinical and research applications. We present a simplified hybrid capture approach that eliminates complexities typically associated with hybridization-based selection methods by directly loading the hybridization product onto the sequencing flow cell. The workflow removes bead-based steps, washes, and post-hybridization PCR, while retaining high capture specificity and library complexity. The approach is enabled by the development of a streptavidin flow cell surface, a method to circularize and amplify captured targets on the flow cell, and a fast hybridization protocol. We demonstrate application across targeted panel sizes and improvements to library complexity and variant calling. We also show how the approach can be used to create an entirely PCR-free targeted sequencing workflow that further improves variant calling and enables the detection of repeat expansions.

genomics↗

bioRxiv2025

Multiparametric optimization of human primary B-cell cultures using Design of Experiments

B cells are essential in the immune system, driving antibody production, cytokine secretion, and antigen presentation. Studies in mouse models have illuminated key mechanisms underlying B-cell activation, differentiation, class-switch recombination, and somatic hypermutation. However, the extent to which these findings translate to human biology remains unclear. To address this, we developed a human primary B-cell culture system using feeder cells engineered to express CD40L, supplemented with the cytokines BAFF, IL-4, and IL-21. Using a Design of Experiments (DOE) approach, we optimized critical parameters and dissected the individual contributions of each specific factor. Our results reveal that BAFF plays a negligible role, and IL-21 has more subtle effects, whereas CD40L and IL-4 are critical determinants of cell viability, proliferation and IgE class-switching. Furthermore, we find that engineered feeder cells can serve equally well as a source of cytokines, but providing these in purified form increases the flexibility of the system. This platform enables detailed investigation of human B-cell biology, offering insights into intrinsic and extrinsic regulators of antibody responses and providing a foundation for in vitro production of human primary antibodies.

immunology↗

bioRxiv2024

FLEXIBLE, PRODUCTION-SCALE, HUMAN WHOLE GENOME SEQUENCING ON A BENCHTOP SEQUENCER

Human whole-genome sequencing (hWGS) provides comprehensive genomic information that can potentially help guide research in disease prevention and treatment and ultimately improve human health. Recent advancements in sequencing technology have improved sequencing quality and further reduced sequencing costs on bench-top sized instruments, making whole-genome sequencing an accessible technology for broader use. Here, we demonstrate the feasibility of a large whole genome sequencing project using a benchtop sequencer in a small laboratory setting, on a scale previously reserved for production-scale factory-sized machines. In this project, 807 samples were prepared and sequenced across 313 flow cells, with high sequencing quality at a median %Q30 of 96.6% and a median %Q40 of 89.31%. To screen library quality and maximize sample yield, we utilized 48-plex sample pre-pool QC runs to provide >1x coverage per sample prior to sample pooling and full-depth sequencing. With this strategy, we consistently achieved >30x human whole genome sequencing of three-plex sample trios with standard settings or up to 4 samples per run with a high-throughput run setting. Additionally, this low-pass data provided valuable sample-level insights, allowing for detection of chromosome copy number variations (CNV) prior to full-depth sequencing. With three instruments running concurrently, >2,800 30x human whole genomes could be sequenced per year. To further demonstrate additional flexibility present in the platform, we also explored two different use cases 1) large insert sizes (1kb+) library to achieve superior genome coverage; 2) a proof of concept for rapid WGS sequencing to minimize sample to answer turnaround time for time-critical sequencing applications. Sequencing of a 2x100 >30x human WGS can be achieved in <12 hours and subsequent generation of fastq, bam and vcf in <1 additional hour. This study provides a cost-effective and flexible real-world demonstration of achieving both high quality hWGS sequencing and instrument flexibility without the need for complex batching schemes or factory-sized sequencers.

molecular biology↗

bioRxiv2024

Antigenic determinants of HAstV-VA1 neutralization and their relevance in the human immune response

Astroviruses are highly divergent and infect a wide variety of animal hosts. In 2009, a genetically divergent human astrovirus (HAstV) strain VA1 was first identified in an outbreak of acute gastroenteritis. This strain has also been associated with fatal central nervous system disease. In this work, we report the isolation of three high-affinity neutralizing monoclonal antibodies (Nt-MAbs) targeting the capsid spike domain of HAstV-VA1. These antibodies (7C8, 2A2, 3D8) were used to select individual HAstV-VA1 mutants resistant to their neutralizing activity and also select a HAstV-VA1 triple mutant that escapes neutralization from all three Nt-MAbs. Sequencing of the virus genome capsid region revealed escape mutations that map to the surface of the capsid spike domain, define three potentially independent neutralization epitopes, and help delineate four antigenic sites in rotaviruses. Notably, two of the escape mutations were found to be present in the spike sequence of the HAstV-VA1-PS strain isolated from an immunodeficient patient with encephalitis, suggesting that those mutations arose as a result of the immune pressure generated by the patients immunotherapy. In accordance with this observation, human serum samples exhibiting strong neutralization activity against wild-type HAstV-VA1 had a 2.6-fold reduction in neutralization titer when evaluated against the triple-escape HAstV-VA1 mutant, indicating shared neutralization epitopes between the mouse and human antibody response. The isolated Nt-MAbs reported in this work will help characterize the functional sites of the virus during cell entry and have the potential for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1. ImportanceHuman astroviruses (HAstVs) have been historically associated with acute gastroenteritis. However, the genetically divergent HAstV-VA1 strain has been associated with central nervous system disease. This work isolated high-affinity neutralizing monoclonal antibodies directed to HAstV-VA1. The proposed binding sites for these antibodies, together with previously reported sites for neutralizing antibodies against classical HAstVs, suggest the existence of at least four neutralization sites on the capsid spike of astroviruses. Our data show that natural infection with human astrovirus VA1 elicits a robust humoral immune response that targets the same antigenic sites recognized by the mouse monoclonal antibodies and strongly suggests the emergence of a variant HAstV-VA1 virus in an immunodeficient patient with prolonged astrovirus infection. The isolated Nt-MAb reported in this work will be helpful in defining the functional sites of the virus involved in cell entry and hold promise for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.

microbiology↗

bioRxiv2022

Multi-organ functions of yolk sac during human early development

The yolk sac (YS) represents an evolutionarily-conserved extraembryonic structure that ensures timely delivery of nutritional support and oxygen to the developing embryo. However, the YS remains ill-defined in humans. We therefore assemble a complete single cell 3D map of human YS from 3-8 post conception weeks by integrating multiomic protein and gene expression data. We reveal the YS as a site of primitive and definitive haematopoiesis including a YS-specific accelerated route to macrophage production, a source of nutritional/metabolic support and a regulator of oxygen-carrying capacity. We reconstruct the emergence of primitive haematopoietic stem and progenitor cells from YS hemogenic endothelium and their decline upon stromal support modulation as intraembryonic organs specialise to assume these functions. The YS therefore functions as three organs in one revealing a multifaceted relay of vital organismal functions as pregnancy proceeds. One Sentence SummaryHuman yolk sac is a key staging post in a relay of vital organismal functions during human pregnancy.

developmental biology↗

bioRxiv2022

Camera-based monitoring of Bogong moths in Alpine Australia reveals drivers of migratory behaviour

The Bogong moth Agrotis infusa is well known for its remarkable annual round-trip migration from its breeding grounds across eastern Australia to its aestivation sites in the Australian Alps, to which it provides an important annual influx of nutrients. Over recent years, we have benefited from a growing understanding of the navigational abilities of the Bogong moth. Meanwhile, the population of Bogong moths has been shrinking. Recently, the ecologically and culturally important Bogong moth was listed as endangered by the IUCN Red List, and the establishment of a program for long-term monitoring of its population has been identified as critical for its conservation. Here, we present the results of two years of monitoring of the Bogong moth population in the Australian Alps using a recently developed method for automated monitoring of flying insects, named Camfi. We found that the evening flights of Bogong moths occur throughout summer, and are modulated by daily weather factors. We present a simple heuristic model of the arrival to and departure from aestivation sites by Bogong moths, and confirm results obtained from fox-scat surveys which found that aestivating Bogong moths occupy higher elevations as the summer progresses. We also present the first recorded observations of the impact of bushfire smoke on aestivating Bogong moths. We observed a dramatic reduction in the size of a cluster of aestivating Bogong moths during the fire, and evidence of a large departure from the fire-affected area the day after the fire. Our results highlight the challenges of monitoring Bogong moths in the wild, and support the continued use of automated camera-based methods for that purpose.

ecology↗

bioRxiv2021

Microglia do not restrict SARS-CoV-2 replication following infection of the central nervous system of K18-hACE2 transgenic mice

Unlike SARS-CoV-1 and MERS-CoV, infection with SARS-CoV-2, the viral pathogen responsible for COVID-19, is often associated with neurologic symptoms that range from mild to severe, yet increasing evidence argues the virus does not exhibit extensive neuroinvasive properties. We demonstrate SARS-CoV-2 can infect and replicate in human iPSC-derived neurons and that infection shows limited anti-viral and inflammatory responses but increased activation of EIF2 signaling following infection as determined by RNA sequencing. Intranasal infection of K18 human ACE2 transgenic mice (K18-hACE2) with SARS-CoV-2 resulted in lung pathology associated with viral replication and immune cell infiltration. In addition, [~]50% of infected mice exhibited CNS infection characterized by wide-spread viral replication in neurons accompanied by increased expression of chemokine (Cxcl9, Cxcl10, Ccl2, Ccl5 and Ccl19) and cytokine (Ifn-{lambda} and Tnf-) transcripts associated with microgliosis and a neuroinflammatory response consisting primarily of monocytes/macrophages. Microglia depletion via administration of colony-stimulating factor 1 receptor inhibitor, PLX5622, in SARS-CoV-2 infected mice did not affect survival or viral replication but did result in dampened expression of proinflammatory cytokine/chemokine transcripts and a reduction in monocyte/macrophage infiltration. These results argue that microglia are dispensable in terms of controlling SARS-CoV-2 replication in in the K18-hACE2 model but do contribute to an inflammatory response through expression of pro-inflammatory genes. Collectively, these findings contribute to previous work demonstrating the ability of SARS-CoV-2 to infect neurons as well as emphasizing the potential use of the K18-hACE2 model to study immunological and neuropathological aspects related to SARS-CoV-2-induced neurologic disease. ImportanceUnderstanding the immunological mechanisms contributing to both host defense and disease following viral infection of the CNS is of critical importance given the increasing number of viruses that are capable of infecting and replicating within the nervous system. With this in mind, the present study was undertaken to evaluate the role of microglia in aiding in host defense following experimental infection of the central nervous system (CNS) of K18-hACE2 with SARS-CoV-2, the causative agent of COVID-19. Neurologic symptoms that range in severity are common in COVID-19 patients and understanding immune responses that contribute to restricting neurologic disease can provide important insight into better understanding consequences associated with SARS-CoV-2 infection of the CNS.

microbiology↗

bioRxiv2021

Deep Learning Predicts Patterns of Cardiotoxicity in a High-Content Screen Using Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Drug-induced cardiotoxicity and hepatotoxicity are major causes of drug attrition. To decrease late-stage drug attrition, pharmaceutical and biotechnology industries need to establish biologically relevant models that use phenotypic screening to predict drug-induced toxicity. In this study, we sought to rapidly detect patterns of cardiotoxicity using high-content image analysis with deep learning and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). We screened a library of 1280 bioactive compounds and identified those predicted to have cardiotoxic liabilities using a single-parameter score based on deep learning. Compounds with major predicted cardiotoxicity included DNA intercalators, ion channel blockers, epidermal growth factor receptor, cyclin-dependent kinase, and multi-kinase inhibitors. We also screened a diverse library of molecules with unknown targets and identified chemical frameworks with predicted cardiotoxic liabilities. By using this screening approach during target discovery and lead optimization, we can de-risk early-stage drug discovery. We show that the broad applicability of combining deep learning with iPSC technology is an effective way to interrogate cellular phenotypes and identify drugs that protect against diseased phenotypes and deleterious mutations. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/436666v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@695707org.highwire.dtl.DTLVardef@1d0980forg.highwire.dtl.DTLVardef@1af30e7org.highwire.dtl.DTLVardef@b3a312_HPS_FORMAT_FIGEXP M_FIG C_FIG CONTRIBUTION TO THE FIELDIn this article, Grafton and colleagues use induced pluripotent stem cell technology and deep learning to train a neural network capable of detecting patterns of cardiotoxicity. To identify bioactive and chemical classes that lead to cardiotoxicity, they combine the neural network with high-content screening of 2560 compounds. The methods described in this study can be used to de-risk early-stage drug development, triage hits, and identify drugs that protect against disease. This screening paradigm will serve as a useful resource for drug discovery and phenotypic interrogation of stem cells and stem cell-derived cell types.

cell biology↗

bioRxiv2020

Epichloe festucae in mutualistic association with Lolium perenne suppresses host apoplastic cysteine protease activity

Plants secrete various defence-related proteins into the apoplast, including proteases. Papain-like cysteine proteases (PLCPs) are central components of the plant immune system. To overcome plant immunity and successfully colonise their hosts, several plant pathogens secrete effector proteins inhibiting plant PLCPs. We hypothesized that not only pathogens but also mutualistic microorganisms interfere with PLCP-meditated plant defences to maintain endophytic colonisation with their hosts. Epichloe festucae forms mutualist associations with cool season grasses and produces a range of secondary metabolites that protect the host against herbivores. In this study, we performed a genome wide identification of Lolium perenne PLCPs, analysed their evolutionary relationship and classified them into nine PLCP subfamilies. Using activity-based protein profiling, we identified four active PLCPs in the apoplast of L. perenne leaves that are inhibited during endophyte interactions. We characterized the L. perenne cystatin LpCys1 for its inhibitory capacity against ryegrass PLCPs. LpCys1 inhibits LpCP2, indicating that LpCys1 might play a role in the suppression of PLCP activity during the interaction with E. festucae. However, since the activity of other L. perenne PLCPs is not sensitive to LpCys1 we propose that additional inhibitors are involved in the suppression of apoplastic PLCPs during E. festucae infection.

plant biology↗

bioRxiv2020

Poised cell circuits in human skin are activated in disease

The human skin confers biophysical and immunological protection through a complex cellular network that is established early in development. We profiled ~500,000 single cells using RNA-sequencing from healthy adult and developing skin, and skin from patients with atopic dermatitis and psoriasis. Our findings reveal a predominance of innate lymphoid cells and macrophages in developing skin in contrast to T cells and migratory dendritic cells in adult skin. We demonstrate dual keratinocyte differentiation trajectories and activated cellular circuits comprising vascular endothelial cells mediating immune cell trafficking, disease-specific clonally expanded IL13/IL22 and IL17A/F-expressing lymphocytes, epidermal IL23-expressing dendritic cells and inflammatory keratinocytes in disease. Our findings provide key insights into the dynamic cellular landscape of human skin in health and disease. One Sentence SummarySingle cell atlas of human skin reveals cell circuits which are quantitatively and qualitatively reconfigured in inflammatory skin disease.

immunology↗

bioRxiv2020

Host infection by the grass-symbiotic fungus Epichloë festucaerequires catalytically active H3K9 and H3K36 methyl transferases

Recent studies have identified key genes in Epichloe festucae that control the symbiotic interaction of this filamentous fungus with its grass host. Here we report on the identification of specific fungal genes that determine its ability to infect and colonize the host. Deletion of setB, which encodes a homolog of the H3K36 histone methyltransferase Set2/KMT3, specifically reduced histone H3K36 trimethylation and led to severe defects in colony growth and hyphal development. The E. festucae {Delta}clrD mutant, which lacks the gene encoding the homolog of the H3K9 methyltransferase KMT1, displays similar developmental defects. Both mutants are completely defective in their ability to infect the host grass, and mutational studies of key residues in the catalytic SET domains from these proteins show that these phenotypes are dependent on the methyltransferase activities of SetB and ClrD. A comparison of the differences in the host transcriptome between seedlings inoculated with wild-type versus mutants suggests that the inability of these mutants to infect the host was not due to an aberrant host defense response. Co-inoculation of either {Delta}setB or {Delta}clrD with the wild-type strain enables these mutants to colonize the host. However, successful colonization by the mutants resulted in death or stunting of the host plant. Transcriptome analysis at the early infection stage identified four fungal candidate genes, three of which encode small-secreted proteins, that are differentially regulated in these mutants compared to wild-type. Deletion of crbA, which encodes a putative carbohydrate binding protein, resulted in significantly reduced host infection rates by E. festucae. Author SummaryThe filamentous fungus Epichloe festucae is an endophyte that forms highly regulated symbiotic interactions with the perennial ryegrass. Proper maintenance of such interactions is known to involve several signalling pathways, but much less is understood about the infection capability of this fungus in the host. In this study, we uncovered two epigenetic marks and their respective histone methyltransferases that are required for E. festucae to infect perennial ryegrass. Null mutants of the histone H3 lysine 9 and lysine 36 methyltransferases are completely defective in colonizing the host intercellular space, and these defects are dependent on the methyltransferase activities of these enzymes. Importantly, we observed no evidence for increased host defense response to these mutants that can account for their non-infection. Rather, these infection defects can be rescued by the wild-type strain in co-inoculation experiments, suggesting that failure of the mutants to infect is due to altered expression of genes encoding infection factors that are under the control of the above epigenetic marks that can be supplied by the wild-type strain. Among genes differentially expressed in the mutants at the early infection stage is a putative small-secreted protein with a carbohydrate binding function, which deletion in E. festucae severely reduced infection efficiency.

genetics↗

bioRxiv2020

Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut.

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. Unexpectedly, the probiotic bacterium Escherichia coli Nissle 1917 exhibited appreciable growth in zinc-limited media even when these transporters were deleted. By utilizing in vitro and in vivo studies, as well as native spray metal infusion mass spectrometry and ion identity molecular networking, we discovered that Nissle utilizes yersiniabactin as a zincophore. Indeed, yersiniabactin enables Nissle to scavenge zinc in zinc-limited media, to resist calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. Moreover, we discovered that yersiniabactins affinity for iron or zinc changes in a pH-dependent manner, with higher affinity for zinc as the pH increased. Altogether, we demonstrate that siderophore metal affinity can be influenced by the local environment and reveal a mechanism of zinc acquisition available to many commensal and pathogenic Enterobacteriaceae.

microbiology↗

bioRxiv2020

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

microbiology↗